Miracle-dz/UniFAR-FTUs huggingface dataset:
CHAPTER 16 Fundamentals of Metabolic P Systems

Metabolic P systems, shortly MP systems, are a special class of deterministic P systems, introduced for expressing biological metabolism. Their dynamics are computed by a special type of regulated multiset rewriting. In this chapter the basic results on MP systems are indicated and a procedure is outlined for constructing MP models of biological processes from time series of observed dynamics.
Essential Role of Interferon Regulatory Factor 3 in Direct Activation of RANTES Chemokine Transcription

ABSTRACT Localized and systemic cytokine production in virus-infected cells play an important role in the outcome of viral infection and pathogenicity. Activation of the interferon regulatory factors (IRF) in turn is a critical mediator of cytokine gene transcription. Recent studies have focused on the 55-kDa IRF-3 gene product as a direct transcriptional regulator of type 1 interferon (IFN-α and IFN-β) activation in response to virus infection. Virus infection induces phosphorylation of IRF-3 on specific C-terminal serine residues and permits cytoplasmic-to-nuclear translocation of IRF-3, activation of DNA binding and transactivation potential, and association with the CBP/p300 coactivator. We previously generated constitutively active [IRF-3(5D)] and dominant-negative forms of IRF-3 that control IFN-β and IFN-α gene expression. In an effort to characterize the range of immunoregulatory genes controlled by IRF-3, we now demonstrate that endogenous human RANTES gene transcription is directly induced in tetracycline-inducible IRF-3(5D)-expressing cells or paramyxovirus-infected cells. We also show that a dominant-negative IRF-3 mutant inhibits virus-induced expression of the RANTES promoter. Specific mutagenesis of overlapping ISRE-like sites located between nucleotides −123 and −96 in the RANTES promoter reduces virus-induced and IRF-3-dependent activation. These studies broaden the range of IRF-3 immunoregulatory target genes to include at least one member of the chemokine superfamily.
Asymmetry in the auditory brainstem response following experience of monaural amplification

Hearing aids can induce perceptual changes in some elderly listeners and there is recent evidence that this might be associated with reorganization within the auditory system. We compared the click-evoked auditory brainstem response in adults with and without monaural hearing aid experience. In listeners with monaural hearing aid experience, the mean peak-to-peak amplitude between wave V and SN10 was approximately 100 nV larger in the ear with hearing aid experience and this difference was statistically significant (P<0.01). The response was symmetrical in adults with no hearing aid experience. This suggests that hearing aids can induce physiological changes at the level of the auditory brainstem in elderly monaural hearing aid users.
Proximal Hyperdense Middle Cerebral Artery Sign Predicts Poor Response to Thrombolysis

The aim of our study was to compare the rapid neurological improvement after intravenous recombinant tissue-type plasminogen activator (rtPA) in patients with proximal hyperdense middle cerebral artery sign (p-HMCAS) to those without the sign and those with the distal hyperdense middle cerebral artery sign (d-HMCAS). Admission and 24 hour non-contrast CT scans of 120 patients with middle cerebral artery (MCA) territory stroke who were treated with intravenous rtPA were assessed for the presence of p-HMCAS and d-HMCAS. The sign was classified according to the site of occlusion. Rapid neurological improvement was defined as ≥50% improvement in the NIHSS score at 24 hours after thrombolysis. Rapid neurological recovery after thrombolysis was assessed and compared between the subgroups. Rapid neurological recovery was less common in the pooled group of patients with either p-HMCAS or d-HMCAS than those without the sign (p<0.01). Patients with p-HMCAS were less likely to have rapid neurological recovery than those with d-HMCAS (p<0.01). However, there was no difference in early neurological recovery between patients with d-HMCAS and those without any hyperdense sign. Our study showed that poor neurological recovery post rtPA was confined to p-HMCAS and not to d-HMCAS, indicating that these signs have quite different prognostic significance.
Four-month moxifloxacin-based regimens for drug-sensitive tuberculosis.

BACKGROUND Early-phase and preclinical studies suggest that moxifloxacin-containing regimens could allow for effective 4-month treatment of uncomplicated, smear-positive pulmonary tuberculosis. METHODS We conducted a randomized, double-blind, placebo-controlled, phase 3 trial to test the noninferiority of two moxifloxacin-containing regimens as compared with a control regimen. One group of patients received isoniazid, rifampin, pyrazinamide, and ethambutol for 8 weeks, followed by 18 weeks of isoniazid and rifampin (control group). In the second group, we replaced ethambutol with moxifloxacin for 17 weeks, followed by 9 weeks of placebo (isoniazid group), and in the third group, we replaced isoniazid with moxifloxacin for 17 weeks, followed by 9 weeks of placebo (ethambutol group). The primary end point was treatment failure or relapse within 18 months after randomization. RESULTS Of the 1931 patients who underwent randomization, in the per-protocol analysis, a favorable outcome was reported in fewer patients in the isoniazid group (85%) and the ethambutol group (80%) than in the control group (92%), for a difference favoring the control group of 6.1 percentage points (97.5% confidence interval [CI], 1.7 to 10.5) versus the isoniazid group and 11.4 percentage points (97.5% CI, 6.7 to 16.1) versus the ethambutol group. Results were consistent in the modified intention-to-treat analysis and all sensitivity analyses. The hazard ratios for the time to culture negativity in both solid and liquid mediums for the isoniazid and ethambutol groups, as compared with the control group, ranged from 1.17 to 1.25, indicating a shorter duration, with the lower bounds of the 95% confidence intervals exceeding 1.00 in all cases. There was no significant difference in the incidence of grade 3 or 4 adverse events, with events reported in 127 patients (19%) in the isoniazid group, 111 (17%) in the ethambutol group, and 123 (19%) in the control group. CONCLUSIONS The two moxifloxacin-containing regimens produced a more rapid initial decline in bacterial load, as compared with the control group. However, noninferiority for these regimens was not shown, which indicates that shortening treatment to 4 months was not effective in this setting. (Funded by the Global Alliance for TB Drug Development and others; REMoxTB ClinicalTrials.gov number, NCT00864383.).
Mesoscale Iron Enrichment Experiments 1993-2005: Synthesis and Future Directions

Since the mid-1980s, our understanding of nutrient limitation of oceanic primary production has radically changed. Mesoscale iron addition experiments (FeAXs) have unequivocally shown that iron supply limits production in one-third of the world ocean, where surface macronutrient concentrations are perennially high. The findings of these 12 FeAXs also reveal that iron supply exerts controls on the dynamics of plankton blooms, which in turn affect the biogeochemical cycles of carbon, nitrogen, silicon, and sulfur and ultimately influence the Earth climate system. However, extrapolation of the key results of FeAXs to regional and seasonal scales in some cases is limited because of differing modes of iron supply in FeAXs and in the modern and paleo-oceans. New research directions include quantification of the coupling of oceanic iron and carbon biogeochemistry.
Poor Health and Loneliness in Later Life: The Role of Depressive Symptoms, Social Resources, and Rural Environments

Objectives. We draw on cognitive discrepancy theory to hypothesize and test a pathway from poor health to loneliness in later life. We hypothesize that poor health will have a negative influence on social participation and social resources, and these factors will mediate between health and loneliness. We hypothesize that rural environments will amplify any difficulties associated with social participation or accessing social resources and that depression will moderate how intensely people react to levels of social contact and support. Methods. We conceptualize a mediation model and a moderated-mediation model. Nationally representative data on older people living in the Republic of Ireland are used to validate the hypothesized pathways. Results. In the mediation model, health has a significant indirect effect on loneliness through the mediating variables social resources and social participation. In the moderated-mediation model, rurality moderates the pathway between health and social resources but not social participation. Depressive symptoms moderate the effect of social resources on loneliness but not social participation. Discussion. The results provide further credence to cognitive discrepancy theory, suggesting that depressive symptoms influence cognitive processes, interfering with judgments about the adequacy of social interaction. The theory is extended by demonstrating the impact of the environment on loneliness.
Biological polarized light reflectors in stomatopod crustaceans

Body parts that can reflect highly polarized light have been found in several species of stomatopod crustaceans (mantis shrimps). These polarized light reflectors can be grossly divided into two major types. The first type, usually red or pink in color to the human visual system, is located within an animal's cuticle. Reflectors of the second type, showing iridescent blue, are located beneath the exoskeleton and thus are unaffected by the molt cycle. We used reflection spectropolarimetry and transmission electron microscopy (TEM) to study the reflective properties and the structures that reflect highly polarized light in stomatopods. For the first type of reflector, the degree of polarization usually changes dramatically, from less than 20% to over 70%, with a change in viewing angle. TEM examination indicates that the polarization reflection is generated by multilayer thin-film interference. The second type of reflector, the blue colored ones, reflects highly polarized light to all viewing angles. However, these reflectors show a slight chromatic change with different viewing angles. TEM sections have revealed that streams of oval-shaped vesicles might be responsible for the production of the polarized light reflection. In all the reflectors we have examined so far, the reflected light is always maximally polarized at around 500 nm, which is close to the wavelength best transmitted by sea water. This suggests that the polarized light reflectors found in stomatopods are well adapted to the underwater environment. We also found that most reflectors produce polarized light with a horizontal e-vector. How these polarized light reflectors are used in stomatopod signaling remains unknown.
Flexural Behavior of Innovative Hybrid GFRP-Reinforced Concrete Beams

Fiber-reinforced polymer (FRP) bars are emerging as a competitive option for replacing steel bars as reinforcement in various concrete structures exposed to aggressive environments. However, the low elastic modulus and brittleness of FRP bars significantly reduce the stiffness and the ductility of FRP-reinforced concrete (FRP-RC) members. In order to improve the flexural behavior of FRP-RC members and meanwhile ensure their satisfactory corrosion-resistant performance, an innovative FRP-reinforced concrete encased steel composite (FRP-RCS) member, which consists of ductile structural steel shapes in combination with corrosion-resistant FRP-reinforced concrete, was conceived and studied. An experimental investigation on the flexural behavior of the proposed FRP-RCS beams was conducted by testing a total of five large-scale simply supported beam specimens subjected to four-point bending loads. The test specimens included one FRP-RC beam reinforced with GFRP bars only and four FRP-RCS beams reinforced with both GFRP bars and encased structural steel shapes. The main parameters considered in this study were concrete compressive strength and amounts of GFRP reinforcement. The test results indicated that using encased steel shapes provided a significant enhancement in load carrying capacity, stiffness, ductility and energy absorption capacity of test beams. The tested FRP-RC beam suffered a brittle failure caused by sudden fracture of tensile GFRP bars whereas the proposed FRP-RCS beams behaved in a ductile manner due to the beneficial residual strength of encased steel shapes following concrete crushing. In addition, the experimental results also demonstrated that the concrete compressive strength had little effect on load carrying capacity of FRP-RCS beams whereas the load carrying capacity can be enhanced by increasing the reinforcement ratio. Analytical methods were also constructed using OpenSEES2.2. 2 to simulate the load-deflection response of tested beams.
An Efficient MMSE Equalizer Implementation for 4×4 MIMO-OFDM Systems in Frequency Selective Fast Varying Channels

In this paper a FPGA implementation of a 4 times 4 MIMO MMSE Equalizer based on the QR factorization technique is presented. Considering fast varying channels a new filter is computed at each new channel realization thanks to an efficient architecture of matrix triangularization. The QR decomposition is performed with only 6 unrolled coordinate rotation digital computer (CORDIC) operators, which are efficiently exploited to minimize the latency of computation. Soft LLR obtained in output of the equalizer are validated on an FPGA hardware bench including a 4 times 4 Rayleigh fading channel and turbo- coding.
T Cell Recognition Patterns of Immunodominant Cytomegalovirus Antigens in Primary and Persistent Infection

Replication of human cytomegalovirus is controlled by a vigorous CD8 T cell response. The persistent nature of infection is believed to periodically stimulate T cell responses resulting in considerable expansions of virus-specific CD8 T cells over time. In this study, we describe the magnitude and breadth of CD8 T cell responses against the immunodominant viral Ags, IE-1 and pp65, in acute and long-term infection using the IFN-γ ELISPOT assay. Simultaneously, we have identified several novel MHC class I restricted CD8 T cell epitopes. Acute phase responses in immunocompetent donors appear to be extremely focused as early as 1 week post diagnosis with dominant peptide-specific responses observed against both proteins. These dominant responses remain detectable at all later time points over a 4-year follow-up. Interestingly the IE-1 responses show an increase over time whereas the pp65 responses do not, which contrasts with data showing that responses against both Ags are elevated in elderly individuals. We also observe the rapid emergence of an effector memory phenotype for virus-specific CD8 T cells as observed in persistent infection. Over time the revertant CD45RApos effector cell population is also expanded, and this is more evident in the preferentially expanded IE-1 responses. We postulate that periodic low-level virus reactivation after the acute infection phase preferentially stimulates these responses whereas pp65-specific T cell expansions probably occur during the infrequent episodes of lytic viral replication or secondary infection.
Shot Peening of Ceramics: Damage or Benefit?

Non-transformation toughened ceramics show the typical brittle material behavior of failure before deformation at room temperature. Thus, strengthening of ceramics due to deformation induced compressive residual stresses has been thought to be not possible. Nevertheless, preliminary investigations had shown that, using ceramic-specific parameters, shot peening can introduce high compressive residual stresses into the near-surface of silicon nitride and improve the load capacity. The aim of the presented investigation was to improve the shot peening conditions in order to extend the increase of load capacity while maintaining the surface integrity. The materials investigated where alumina and silicon nitride, the properties determined where residual stresses, load capacity and topography. The results show that high compressive residual stresses in the GPa-range can be introduced in silicon nitride and alumina which may boost the load capacity of the near surface layers by a factor of up to 9. Only little effect on the surface integrity could be obtained.
Successful Aging and Subjective Well-being among Oldest-old Adults ; for the Georgia Centenarian Study 4

Purpose of the Study: This research integrates successful aging and developmental adaptation models to empirically define the direct and indirect effects of 2 distal (i.e., education and past life experiences) and 5 proximal influences (i.e., physical functioning, cognitive functioning, physical health impairment, social resources, and perceived economic status) on subjective well-being. The proximal influences involved predictors outlined in most extant models of successful aging (e. Our model extends such models by including distal impact as well as interactions between distal and proximal impacts. Design and Methods: Data were obtained from 234 centenarians and 72 octogenarians in the Georgia Centenarian Study. Structural equation modeling was conducted with Mplus 6.1. Results: Results showed significant direct effects of physical health impairment and social resources on positive aspects of subjective well-being among oldest-old adults. We also found significant indirect effects of cognitive functioning and education on positive affect among oldest-old adults. Social resources mediated the relationship between cognitive functioning and positive affect; and cognitive functioning and social resources mediated the relationship between education and positive affect. In addition, physical health impairment mediated the relationship between cognitive functioning and positive affect; and cognitive functioning and physical health impairment medicated the relationship between education and positive affect. Implications: Integrating 2 different models (i.e., successful aging and developmental adaptation) provided a comprehensive view of adaptation from a developmental perspective.
Formation of Hexagonal Diamond by Room Temperature Compression of Graphite.

In situ X-ray observation under high pressure was carried out to investigate the phase transformation in graphite induced by room temperature compression. Several diffraction peaks of the high pressure phase were clearly observed and could be indexed as a hexagonal diamond structure. The diffraction profiles from two different directions support the orientation relationship of the martensitic transformation from graphite to hexagonal diamond previously proposed. This hexagonal diamond has a large bulk modulus comparable to the cubic diamond.
Righting the Wrong: Reparative Coping After Going Along With Ostracism

ABSTRACT Most of the focus within the ostracism literature concerns the negative effects on the ostracized and how they cope following ostracism. Research is now beginning to illuminate negative psychological effects for ostracizers, yet no studies to date have examined their coping responses. This study continues this line of inquiry focusing on experiences of going along with ostracism, both by employing a face-to-face interaction and by exploring prosocial versus antisocial coping reactions in ostracizers. Results reveal that compared to those in a neutral condition, compliant ostracizers suffered because ostracizing someone else frustrated their psychological needs for autonomy and relatedness. Further, when given the chance, ostracizers were more inclusive of the person they previously ostracized. Discussion considers important avenues for future research as well as implications of results.
Design of a radiation-hardened curvature compensated bandgap reference circuit

This work presents the design and dimensioning of of a bandgap voltage reference - BGV - generator with second order compensation. The developed circuit provides a steady voltage at the output, stable to noise, temperature and power source drifts, which functions as a reference voltage for other circuit blocks. The main purpose of the work is to obtain a BGV generator with a voltage of 1.25V and performances which can improve a previous proposed circuit. The FOM that primarily characterize the circuit and that will be the focus of improvement are the PSRR, the TC and the current consumption. The achieved results by the proposed circuit are a PSRR of -81.93 dB, a TC of 2 ppm/°C and a current consumption of 2.34 mA.
Infectious Cell Entry Mechanism of Influenza Virus

Interaction between influenza virus WSN strain and MDCK cells was studied by using spin-labeled phospholipids and electron microscopy. Envelope fusion was negligibly small at neutral pH but greatly activated in acidic media in a narrow pH range around 5.0. The half-time was less than 1 min at 37°C at pH 5.0. Virus binding was almost independent of the pH. Endocytosis occurred with a half-time of about 7 min at 37°C at neutral pH, and about 50% of the initially bound virus was internalized after 1 h. Electron micrographs showed binding of virus particles in coated pits in the microvillous surface of plasma membrane and endocytosis into coated vesicles. Chloroquine inhibited virus replication. The inhibition occurred when the drug was added not later than 10 min after inoculation. Chloroquine caused an increase in the lysosomal pH 4.9 to 6.1. The drug did not affect virus binding, endocytosis, or envelope fusion at pH 5.0. Electron micrographs showed many virus particles remaining trapped inside vacuoles even after 30 min at 37°C in the presence of drug, in contrast to only a few particles after 10 min in vacuoles and secondary lysosomes in its absence. Virus replication in an artificial condition, i.e., brief exposure of the inoculum to acidic medium followed by incubation in neutral pH in the presence of chloroquine, was also observed. These results are discussed to provide a strong support for the infection mechanism of influenza virus proposed previously: virus uptake by endocytosis, fusion of the endocytosed vesicles with lysosome, and fusion of the virus envelope with the surrounding vesicle membrane in the secondary lysosome because of the low pH. This allows the viral genome to enter the target cell cytoplasm.
Learning to walk in virtual reality

This article provides longitudinal data for when participants learned to travel with a walking metaphor through virtual reality (VR) worlds, using interfaces that ranged from joystick-only, to linear and omnidirectional treadmills, and actual walking in VR. Three metrics were used: travel time, collisions (a measure of accuracy), and the speed profile. The time that participants required to reach asymptotic performance for traveling, and what that asymptote was, varied considerably between interfaces. In particular, when a world had tight turns (0.75 m corridors), participants who walked were more proficient than those who used a joystick to locomote and turned either physically or with a joystick, even after 10 minutes of training. The speed profile showed that this was caused by participants spending a notable percentage of the time stationary, irrespective of whether or not they frequently played computer games. The study shows how speed profiles can be used to help evaluate participants' proficiency with travel interfaces, highlights the need for training to be structured to addresses specific weaknesses in proficiency (e.g., start-stop movement), and for studies to measure and report that proficiency.