Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Immunodeficiency Virus Type 1 Vif Protein Is an Integral Component of an mRNP Complex of Viral RNA and Could Be Involved in the Viral RNA Folding and Packaging Process

ABSTRACT Virion infectivity factor (Vif) is a protein encoded by human immunodeficiency virus types 1 and 2 (HIV-1 and -2) and simian immunodeficiency virus, plus other lentiviruses, and is essential for viral replication either in vivo or in culture for nonpermissive cells such as peripheral blood lymphoid cells, macrophages, and H9 T cells. Defects in the vif gene affect virion morphology and reverse transcription but not the expression of viral components. It has been shown that Vif colocalizes with Gag in cells and Vif binds to the NCp7 domain of Gag in vitro. However, it seems that Vif is not specifically packaged into virions. The molecular mechanism(s) for Vif remains unknown. In this report, we demonstrate that HIV-1 Vif is an RNA-binding protein and specifically binds to HIV-1 genomic RNA in vitro. Further, Vif binds to HIV-1 RNA in the cytoplasm of virus-producing cells to form a 40S mRNP complex. Coimmunoprecipitation and in vivo UV cross-linking assays indicated that Vif directly interact with HIV-1 RNA in the virus-producing cells. Vif-RNA binding could be displaced by Gag-RNA binding, suggesting that Vif protein in the mRNP complex may mediate viral RNA interaction with HIV-1 Gag precursors. Furthermore, we have demonstrated that these Vif mutants that lose the RNA binding activity in vitro do not supportvif-deficient HIV-1 replication in H9 T cells, suggesting that the RNA binding capacity of Vif is important for its function. Further studies regarding Vif-RNA interaction in virus-producing cells will be important for studying the function of Vif in the HIV-1 life cycle.
Combined THz and Microwave Dielectric Spectroscopy of Intermolecular Interactions in Homologous Protic Ionic Liquids

We report on a detailed and systematic study of the inter molecular dynamics of a homologous series of protic alkylammonium-formate ionic liquids in a broad spectral window, combining THz time-domain and microwave dielectric methods. The joint experiments yield the complex dielectric function over more than four orders of magnitude in frequency. The dielectric absorption data smoothly join with data from Fourier transform far-infrared (FT-FIR) spectroscopy. All dielectric spectra were fitted to a multimodal relaxation model. The observed processes are assigned to low-frequency re-orientational relaxation of the dipolar ions and to intermolecular vibrations between the cations and anions. The dielectric spectra show a dependence on the length and OH-functionalization of the alkyl residues of the cation.
Performance Improvement of an External-Rotor Split-Phase Induction Motor for Low-Cost Drive Applications Using External Rotor Can

This paper describes the performance of an external-rotor split-phase induction motor for use in such applications as ceiling fans (although the pole number would be much higher than the 2-pole machine studied here). This machine has short axial length with respect to its diameter. The auxiliary winding is only used to start the machine and it is wound orthogonal to the main winding and connected in parallel to it using a centrifugal switch. The paper highlights how an external can, which connects the two end-rings, can be used to improve the motor performance. The paper describes a 2-D finite element analysis (FEA) of the machine to show the performance and also to describe the pulsating torque of the machine
Conserved Features in the Extracellular Domain of Human Toll-like Receptor 8 Are Essential for pH-dependent Signaling*

Toll-like receptor (TLR) 8 has an important role in initiating immune responses to viral single-stranded RNA and the antiviral compound resiquimod. Together with TLR3, -7, and -9, it forms a subgroup of the TLRs that are localized intracellularly and signal in response to pathogen-derived nucleic acids. In this work, we have used site-directed mutagenesis to identify regions of the TLR8 extracellular domain that are required for stimulus-induced signal transduction. We have shown that a cysteinerich sequence predicted to form a loop projecting from the solenoidal ectodomain structure at leucine-rich repeat 8 is essential for signaling in response to both single-stranded RNA and resiquimod. A second region, centered on an aspartic acid residue in leucine-rich repeat 17, is also required for TLR8 function. The corresponding residue in TLR9 is known to be important for pH-dependent binding and signaling in response to unmethylated CpG DNA, suggesting that the TLR7/8/9 subgroups share a common signaling mechanism. We have also shown that TLR8 is localized predominantly in the endoplasmic reticulum but that signaling is completely abolished by an inhibitor of vesicle-type H+ ATPases. This indicates that TLR8 is present at low levels in an acidified compartment and that a lowered pH is required for receptor function. We propose that pH-dependent changes in the ligand facilitate activation of the receptor. The protonated form of resiquimod, a cell-permeable weak base, is likely to concentrate significantly (∼100×) in acidified compartments, and this may potentiate low affinity interactions with either the receptor or a specific binding protein.
How Can Functional Neuroimaging Inform Cognitive Theories?

Work on functional neuroimaging of cognition falls into two categories. The first aims at localizing specific cognitive subsystems in specific brain regions. In this research, the cognitive subsystems in question need to be defined independently of the neuroimaging data because the interpretation of the data requires such definition; so functional neuroimaging is informed by cognitive theories rather than informing them. The second category uses neuroimaging data to test cognitive theories. As cognitive theories are expressed in cognitive terms, such theories have to be embellished by explicit proposals about relationships between cognition and the brain if they are to become capable of generating predictions about the results of experiments that use functional neuroimaging. Whether functional neuroimaging can succeed in informing a cognitive theory depends critically upon the plausibility of such supplementary proposals. It is also critical to avoid the “consistency fallacy. ” When neuroimaging data from an experiment are consistent with predictions from a particular cognitive theory, this cannot be offered as evidence in support of that theory unless it can be shown that there were possible other outcomes of the experiment that are inconsistent with the theory—outcomes that would have falsified predictions from the theory had they been obtained.
Cell shrinkage as a signal to apoptosis in NIH 3T3 fibroblasts

Cell shrinkage is a hallmark of the apoptotic mode of programmed cell death, but it is as yet unclear whether a reduction in cell volume is a primary activation signal of apoptosis. Here we studied the effect of an acute elevation of osmolarity (NaCl or sucrose additions, final osmolarity 687 mosmol l−1) on NIH 3T3 fibroblasts to identify components involved in the signal transduction from shrinkage to apoptosis. After 1.5 h the activity of caspase‐3 started to increase followed after 3 h by the appearance of many apoptotic‐like bodies. The caspase‐3 activity increase was greatly enhanced in cells expressing a constitutively active G protein, Rac (RacV12A3 cell), indicating that Rac acts upstream to caspase‐3 activation. The stress‐activated protein kinase, p38, was significantly activated by phosphorylation within 30 min after induction of osmotic shrinkage, the phosphorylation being accelerated in fibroblasts overexpressing Rac. Conversely, the activation of the extracellular signal‐regulated kinase (Erk1/2) was initially significantly decreased. Subsequent to activation of p38, p53 was activated through serine‐15 phosphorylation, and active p53 was translocated from the cytosol to the nucleus. Inhibition of p38 in Rac cells reduced the activation of both p53 and caspase‐3. After 60 min in hypertonic medium the rate constants for K+ and taurine efflux were increased, particular in Rac cells. We suggest the following sequence of events in the cell shrinkage‐induced apoptotic response: cellular shrinkage activates Rac, with activation of p38, followed by phosphorylation and nuclear translocation of p53, resulting in permeability increases and caspase‐3 activation.
Sustainability in Alternative Food Networks: A Systematic Literature Review

In recent years, increasing attention has been paid to individuals’ organizing themselves and managing food systems in an ‘alternative’ and more sustainable way. Such emerging food initiatives are most commonly known as ‘Alternative Food Networks’ (AFNs). However, there is an ongoing debate concerning the extent to which AFNs facilitate social, economic and environmental change. There are criticisms of the overall sustainability promise of AFNs related to sufficiency of impact, possible counter effects and the relevance of impacts. Because empirical studies often only focus on specific sustainability issues or AFNs, it has been difficult to develop more robust theories about the relations between diverse AFNs arrangements and sustainability. Thus, the aim of this paper is to contribute towards reducing this knowledge gap through a systematic literature review on AFNs in relation to sustainability. We summarize main methodological approaches, the types of AFNs studied and sustainability dimensions addressed in literature to date. Findings serve as reference to propose opportunities for future research regarding sustainability in AFNs.
Histamine H4 Receptor Stimulation Suppresses IL-12p70 Production and Mediates Chemotaxis in Human Monocyte-Derived Dendritic Cells 1

There is increasing evidence that histamine as an important mediator of immediate type allergic reactions also effects professional APCs. Recent reports showed effects of histamine on human monocyte-derived dendritic cells (MoDC) mediated primarily via histamine H1 receptors (H1R) and H2R. We show here that MoDC also express H3R and H4R at the mRNA and protein level. mRNA of the H3R is down-regulated and mRNA of the H4R is up-regulated during the differentiation from monocytes to MoDC. H4R or H2R stimulation suppressed IL-12p70 production in MoDC. Induction of cAMP was necessary for IL-12p70 inhibition mediated via the H2R. In contrast, H4R stimulation did not affect cAMP production but induced the transcription factor AP-1, and U0126, an inhibitor of AP-1 transactivation and MEK, rescued H4R mediated IL-12p70 suppression. Moreover, MoDC responded to a H4R agonist (and also to a H2R agonist) with increased F-actin polymerization and migration in modified Boyden chamber assays, suggesting a chemotactic effect of histamine via the H2R and the H4R. Thus, H4R stimulation on MoDC results in immunomodulatory and chemotactic effects. Histamine induces chemotaxis and IL-12p70 suppression via different receptors using different signaling pathways, which might be important for the pathogenesis of and therapeutic interventions in allergic diseases.
Towards image-based marine habitat classification

It is now fairly routine to quasi-automatically generate acoustic bathymetry and optical mosaics from properly instrumented Autonomous Underwater Vehicles (AUVs). However, further analysis and interpretation of gathered data is needed to address tasks such as habitat characterization and monitoring. This analysis stage is performed by human experts which limits the amount and speed of data processing. While it is unlikely that machines will match humans at fine-scale classification, machines can now perform preliminary, coarser classification to provide timely and relevant feedback to assist human decisions and enable adaptive AUV behavior. This paper presents a preliminary investigation into using a state-of-art object recognition system to classify marine habitat imagery based on labeled examples. We show that performance for such approaches can suffer with typical underwater imagery and present some of the causes for this. We propose modifications that make such a system suitable for automated coarse habitat classification and discuss experiences and results with three applications. The first corresponds to towed imagery from Ningaloo and Scott Reef, Western Australia. The second corresponds to AUV imagery near Hydrographers passage, Queensland. The third application demonstrates adaptive surveying using the output of the modified classification system.
Refractive error and visual impairment in African children in South Africa.

PURPOSE To assess the prevalence of refractive error and visual impairment in school-aged African children in South Africa. METHODS Random selection of geographically defined clusters was used to identify a sample of children 5 to 15 years of age in the Durban area. From January to August 2002, children in 35 clusters were enumerated through a door-to-door survey and examined in temporary facilities. The examination included visual acuity measurements, ocular motility evaluation, retinoscopy and autorefraction under cycloplegia, and examination of the anterior segment, media, and fundus. In nine clusters, children with reduced vision and a sample of those with normal vision underwent independent replicate examinations for quality assurance. RESULTS A total of 5599 children living in 2712 households were enumerated, and 4890 (87.3%) were examined. The prevalence of uncorrected, presenting, and best-corrected visual acuity of 20/40 or worse in the better eye was 1.4%, 1.2%, and 0.32%, respectively. Refractive error was the cause in 63.6% of the 191 eyes with reduced vision, amblyopia in 7.3%, retinal disorders in 9.9%, corneal opacity in 3.7%, other causes in 3.1%, and unexplained causes in the remaining 12.0%. Exterior and anterior segment abnormalities were observed in 528 (10.8%) children, mainly corneal and conjunctival. Myopia (at least -0.50 D) in one or both eyes was present in 2.9% of children when measured with retinoscopy and in 4.0% measured with autorefraction. Beginning with an upward trend at age 14, myopia prevalence with autorefraction reached 9.6% at age 15. Myopia was also associated with increased parental education. Hyperopia (+2.00 D or more) in at least one eye was present in 1.8% of children when measured with retinoscopy and in 2.6% measured with autorefraction, with no significant predictors of hyperopia risk. CONCLUSIONS The prevalence of reduced vision is low in school-age African children, most of it because of uncorrected refractive error. The high prevalence of corneal and other anterior segment abnormalities is a reflection of the inadequacy of primary eye care services in this area.
Bone mineral density changes during the menopause transition in a multiethnic cohort of women.

CONTEXT Rates of bone loss across the menopause transition and factors associated with variation in menopausal bone loss are poorly understood. OBJECTIVE Our objective was to assess rates of bone loss at each stage of the transition and examine major factors that modify those rates. DESIGN, SETTING, AND PARTICIPANTS We conducted a longitudinal cohort study of 1902 African-American, Caucasian, Chinese, or Japanese women participating in The Study of Women's Health Across the Nation. Women were pre- or early perimenopausal at baseline. OUTCOME MEASURE We assessed bone mineral density (BMD) of the lumbar spine and total hip across a maximum of six annual visits. RESULTS There was little change in BMD during the pre- or early perimenopause. BMD declined substantially in the late perimenopause, with an average loss of 0.018 and 0.010 g/cm2.yr from the spine and hip, respectively (P<0.001 for both). In the postmenopause, rates of loss from the spine and hip were 0.022 and 0.013 g/cm2.yr, respectively (P<0.001 for both). During the late peri- and postmenopause, bone loss was approximately 35-55% slower in women in the top vs. the bottom tertile of body weight. Apparent ethnic differences in rates of spine bone loss were largely explained by differences in body weight. CONCLUSIONS Bone loss accelerates substantially in the late perimenopause and continues at a similar pace in the first postmenopausal years. Body weight is a major determinant of the rate of menopausal BMD loss, whereas ethnicity, per se, is not. Healthcare providers should consider this information when deciding when to screen women for osteoporosis.
RADIONUCLIDES IN THE TERRESTRIAL ECOSYSTEM NEAR A CANADIAN URANIUM MILL—PART III: ATMOSPHERIC DEPOSITION RATES (PILOT TEST)

Abstract—Atmospheric deposition rates of uranium series radionuclides were directly measured at three sites near the operating Key Lake uranium mill in northern Saskatchewan. Sites impacted by windblown tailings and mill dusts had elevated rates of uranium deposition near the mill and elevated 226Ra deposition near the tailings compared to a control site. Rainwater collectors, dust jars, and passive vinyl collectors previously used at the Ranger Mine in Australia were pilot-tested. Adhesive vinyl surfaces (1 m2) were oriented horizontally, vertically, and facing the ground as a means of measuring gravitational settling, wind impaction, and soil resuspension, respectively. Although the adhesive glue on the vinyls proved difficult to digest, relative differences in deposition mode were found among radionuclides and among sites. Dry deposition was a more important transport mechanism for uranium, 226Ra, and 210Pb than rainfall, while more 210Po was deposited with rainfall.
Efficient generalized conservative staircase scheme for popular videos

In the advanced generalized conservative staircase (AGCS) method, the video segments are arranged in groups. The first group contains first segment, second group contains next two segments, and pth group (p > 2) contains 3 * 2<sup>p-3</sup> number of segments starting with kth segment S<sub>k</sub>, where k = 3 * 2<sup>p-3</sup> + 1. Each segment of pth group (p > 2) is divided into 3 * 2p<sup>-3</sup> * m<sub>p</sub> + m<sub>p</sub> - 1 subsegments, where m<sub>p</sub> determines the number of subsegments of a segment in pth group that are transmitted in a time slot. The subsegments are arranged in m<sub>p</sub> disjoint sets. The first set consists of subsegments S<sub>q+i,1</sub>, S<sub>q+i,2</sub>, . , S<sub>q+i,q</sub>, where q = 3 * 2p<sup>-3</sup>, 1 les 1 les q, and zth set (1 < z < m<sub>p</sub>) consists of subsegments S<sub>q+i,q*(z-1)+z-1</sub>, S<sub>q+i,q*(z-1)+z</sub>, S<sub>q+i,q*(z-1)+z+1</sub>, . , S<sub>q+i,q*z+z-1</sub>. In the AGCS method, an upper bound on m<sub>p</sub> has been derived to provide continuous data. If larger value of m<sub>p</sub> than its upper bound is taken, then the method will not provide continuous data. But, increasing the value of m<sub>p</sub> decreases the bandwidth requirement, which in turn gives better method. In this paper, we discuss a scheme that removes the bound on m<sub>p</sub> and still provides the continuous video data to users.
C-reactive protein inhibits plasmacytoid dendritic cell interferon responses to autoantibody immune complexes.

OBJECTIVE C-reactive protein (CRP) is a serum pattern recognition molecule that binds to apoptotic cells and nucleoprotein autoantigens and Fcγ receptors (FcγR). In systemic lupus erythematosus (SLE), immune complexes (ICs) containing nucleoprotein autoantigens activate plasmacytoid dendritic cells (PDCs) to produce type I interferon (IFN), which contributes to disease pathogenesis. Autoantibody ICs are taken up by PDCs through FcγR type IIa into endosomes, where the nucleic acid components activate Toll-like receptor 7 (TLR-7) or TLR-9. The objective of this study was to investigate the effect of CRP on PDC and monocyte responses to nucleoprotein autoantigens and ICs. METHODS Peripheral blood mononuclear cells (PBMCs), purified monocytes, and PDCs were isolated from healthy volunteers and stimulated with autoantibody ICs containing apoptotic cells, small nuclear RNPs (snRNPs), or DNA, or directly with TLR-7 and TLR-9 agonists. Supernatants were analyzed for IFNα and cytokine levels by enzyme-linked immunosorbent assay and multiplex assay. Small nuclear RNPs were fluorescence-labeled, and the effect of CRP on binding, uptake, and intracellular localization of autoantibody snRNP complexes was measured by flow cytometry and confocal microscopy. RESULTS CRP bound to autoantigen did not induce IFNα in PBMCs or PDCs, whereas complexes formed with autoantibody did. Significantly, CRP inhibited the IFNα response to both anti-U1 RNP-snRNP complexes and anti-DNA-DNA complexes, but not to other TLR-7 and TLR-9 agonists. CRP directly inhibited PDC IFNα release, promoted PDC differentiation, and increased late endosome localization of autoantigen in PDCs and monocytes. CONCLUSION CRP is a regulator of the type I IFN response to SLE ICs. CRP increased the intracellular processing of ICs in late endosomes, which is associated with decreased synthesis of type I IFN after intracellular TLR activation.
Translating OpenACC program for HAS environment

Heterogeneous System Architecture (HSA) is a newly arising heterogeneous multiprocessor platform which may improve the heavy data transmission between CPU and GPU in traditional heterogeneous multiprocessor platforms through shared virtual memory. However, as other heterogeneous multiprocessor platforms, it is complex and error-prone to write HSA programs. Therefore, we design and implement a translation framework based on LLVM for automatically translating OpenACC programs, directive-based parallel programming programs, into HSA programs. The main components of the framework include an extension version of Clang, a PLIR-annotation parser, and an HAS host/kernel IR generator. The experiment result shows that the translated HSA programs generated by our OpenACC compiler achieve 7.78× speedups in average with respect to the corresponding sequential programs. Moreover, compared with the OpenMP compiler proposed by HSA foundation, our OpenACC compiler achieves 2.91× speedups in average.
A Triple Hurdle Expenditure Analysis of U.S. Saltwater Recreational Fishing

This study used cross-sectional data extracted from the 2011 National Survey of Fishing, Hunting, and WildlifeAssociated Recreation to analyze individual trip-related expenditures associated with saltwater recreational fishing in the United States. Based on the utility maximization framework in the triple hurdle model, all observations can be used to estimate a participant’s final decision for saltwater recreational fishing. Positive observations that are simultaneously passed down the participation and consumption decisions can be used for estimation based on a censored and truncated sample, allowing for richer interpretation of saltwater recreational angler behavior. Empirical results (income, age, gender, ethnicity, urban setting, fishing license, fishing on a boat, fish types) showed significant effects on U.S. saltwater recreational fishing trip-related expenditures. The results of this study can provide insight into the determinants of U.S. saltwater recreational fishing trip-related expenditures, which can be used for saltwater recreational fisheries management and policy.