Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistent CCR5 Utilization and Enhanced Macrophage Tropism by Primary Blood Human Immunodeficiency Virus Type 1 Isolates from Advanced Stages of Disease and Comparison to Tissue-Derived Isolates

ABSTRACT Viral phenotype, tropism, coreceptor usage, and envelope gene diversity were examined in blood isolates collected from 27 individuals at different stages of human immunodeficiency virus type 1 (HIV-1) disease and tissue derived isolates from 10 individuals with AIDS. The majority (89%) of blood and all tissue HIV-1 isolates from all stages of infection were non-syncytium inducing and macrophage (M) tropic. Tropism and productive infection by HIV isolates in both monocytes and monocyte-derived macrophages (MDM) increased in advanced disease (HIV tropism for monocytes, 1 of 6 from categories I and II versus 11 of 21 [P = 0.05] from category IV and II [CD4 < 250]; and high-level replication in MDM, 1 of 6 from categories I and II versus 16 of 21 from categories IV and II [P = 0.015]). There was a high level of replication of blood and tissue isolates in T lymphocytes without restriction at any stage. Overall, the level of replication in MDM was 5- to 10-fold greater than in monocytes, with restriction in the latter occurring mainly at entry and later stages of replication. Only three blood isolates were identified as syncytium inducing, and all had a dualtropic phenotype. There was a significant increase of HIV envelope gene diversity, as shown by a heteroduplex mobility assay, in advanced disease; this may partly underlie the increase of HIV replication in MDM. Unlike blood isolates (even those from patients with advanced disease), tissue isolates displayed greater similarities (90%) in productive infection between MDM and monocytes. The majority (87%) of all isolates, including those from patients with advanced disease, used CCR5, and only 5 of 37 isolates showed expanded coreceptor usage. These results indicate that in the late stage of disease with increasing viral load and diversity, CCR5 utilization and M-tropism persist in blood and tissue and the replicative ability in macrophages increases. This suggests that these characteristics are advantageous to HIV and are important to disease progression.
Is there positive in the negative? Understanding the role of guilt and shame in physical activity self-regulation

The high rate of global physical inactivity has led researchers to explore the psychological variables that impact physical activity (PA) behaviours. Drawing from tenets of control theory and literature on self-conscious emotions, the current study investigated the experience of guilt and shame in response to engaged in and missed PA. One hundred and fifty-four adults (Mage = 34.02, SD = 12.27) completed online questionnaires over a three-week period. Paired sample t-tests showed participants experience more guilt and shame after a missed intended PA session than an engaged-in session and, of the two, guilt is felt more strongly (t (150) = 8.31, p < . 001). Following a missed PA session, attribution dimensions were explored; locus of causality was associated with guilt (p = .02) and stability with shame (p =. 01). Logistic regressions showed guilt had a negative relationship with PA intentions, and guilt and shame did not predict future PA. This finding is at odds with control theory and past empirical evidence. This disparity suggests the need for future research to explore these emotions within the PA domain to further inform the nature of their relationship. This research was the first to measure and explore the acute, real-life experience and motivational qualities of guilt and shame relative to PA engagement. Research implications and future directions are discussed.
Interaction of Gentamicin Polycation with Model and Cell Membranes

a r t i c l e i n f o The interaction of positively-charged antibiotic gentamicin with cell membranes was studied to determine if any changes in membrane organization were induced by the drug. Opossum kidney epithelia (OK) cells were used as models of eukaryotic cells. Two methods were used: laurdan fluorescence spectroscopy and fluorescence anisotropy recordings on
Within-Host Speciation of Malaria Parasites

Background Sympatric speciation—the divergence of populations into new species in absence of geographic barriers to hybridization—is the most debated mode of diversification of life forms. Parasitic organisms are prominent models for sympatric speciation, because they may colonise new hosts within the same geographic area and diverge through host specialization. However, it has been argued that this mode of parasite divergence is not strict sympatric speciation, because host shifts likely cause the sudden effective isolation of parasites, particularly if these are transmitted by vectors and therefore cannot select their hosts. Strict sympatric speciation would involve parasite lineages diverging within a single host species, without any population subdivision. Methodology/Principal Findings Here we report a case of extraordinary divergence of sympatric, ecologically distinct, and reproductively isolated malaria parasites within a single avian host species, which apparently occurred without historical or extant subdivision of parasite or host populations. Conclusions/Significance This discovery of within-host speciation changes our current view on the diversification potential of malaria parasites, because neither geographic isolation of host populations nor colonization of new host species are any longer necessary conditions to the formation of new parasite species.
TRMM rainfall correction over the Andean Plateau using wavelet multi-resolution analysis

Quantifying rainfall from remotely sensed data is crucial for regions where meteorological stations are scarce. This might be one of the only options for analysing rainfall patterns at different temporal and spatial scales in data-scarce environments, particularly in developing countries. The Tropical Rainfall Measuring Mission (TRMM) provides rainfall estimation over the tropics. Rainfall estimates from the TRMM satellite exhibit inaccuracies over topographically complex regions, thus warranting suitable corrections. Multi-resolution analysis (MRA) was applied to improve TRMM 3B42 daily rainfall estimation at 19 meteorological stations located over the Andean Plateau. The detailed signal from each meteorological station was added to the trend signal of each TRMM data cell. Comparing raw and corrected TRMM with gauged rainfall revealed that wavelet-based correction of TRMM 3B42 on average improved several metrics: entropy difference (15.45−1.32), determination coefficient (0.07−0.92), bias (0.68−1.01) and relative mean absolute error (RMAE, 0.86−0.59). The entropy difference of corrected TRMM and gauged rainfall was less than 5%, even when TRMM correction was performed with noise from a station located up to 565 km away from the TRMM cell. This entropy difference corresponded to an average bias of less than 10% in the rainfall estimation.
Emotional Valence and Arousal Interact in Attentional Control

A recent study demonstrated that observers' ability to identify targets in a rapid visual sequence was enhanced when they simultaneously listened to happy music. In the study reported here, we examined how the emotion-attention relationship is influenced by changes in both mood valence (negative vs. positive) and arousal (low vs. high). We used a standard induction procedure to generate calm, happy, sad, and anxious moods in participants. Results for an attentional blink task showed no differences in first-target accuracy, but second-target accuracy was highest for participants with low arousal and negative affect (sad), lowest for those with strong arousal and negative affect (anxious), and intermediate for those with positive affect regardless of their arousal (calm, happy). We discuss implications of this valence-arousal interaction for the control of visual attention.
Truth, Communication, and Democracy

This article argues that truth is vital to deliberative democracy and to communication as an academic discipline. Our definition of truth is critical realist in nature—that is, it refers to an ontologically objective reality. We briefly explore the history and concepts of deliberative democracy and its presuppositions of epistemic rationality, doxastic voluntarism, and ontological realism. The article then outlines the breakdown of the concept and practice of truth and deliberative democracy before and during the age of Trump and the treatment of truth by the profession of journalism as well as the academic discipline of journalism studies. Finally, we provide a critical-realist take on the resolution of truth debates and an affirmation of truth as a democratic value.
Anisotropic shear‐wave velocity structure of the Earth's mantle: A global model

[1] We combine a new, large data set of surface wave phase anomalies, long-period waveforms, and body wave travel times to construct a three-dimensional model of the anisotropic shear wave velocity in the Earth's mantle. Our modeling approach is improved and more comprehensive compared to our earlier studies and involves the development and implementation of a new spherically symmetric reference model, simultaneous inversion for velocity and anisotropy, as well as discontinuity topographies, and implementation of nonlinear crustal corrections for waveforms. A comparison of our new three-dimensional model, S362ANI, with two other models derived from comparable data sets but using different techniques reveals persistent features: (1) strong, ∼200-km-thick, high-velocity anomalies beneath cratons, likely representing the continental lithosphere, underlain by weaker, fast anomalies extending below 250 km, which may represent continental roots, (2) weak velocity heterogeneity between 250 and 400 km depths, (3) fast anomalies extending horizontally up to 2000-3000 km in the mantle transition zone beneath subduction zones, (4) lack of strong long-wavelength heterogeneity below 650 km suggesting inhibiting character of the upper mantle-lower mantle boundary, and (5) slow-velocity superplumes beneath the Pacific and Africa. The shear wave radial anisotropy is strongest at 120 km depth, in particular beneath the central Pacific. Lateral anisotropic variations appreciably improve the fit to data that are predominantly sensitive to the uppermost and lowermost mantle but not to the waveforms that control the transition zone and midmantle depths. Tradeoffs between lateral variations in velocity and anisotropy are negligible in the uppermost mantle but noticeable at the bottom of the mantle.
Postsynaptic Complex Spike Bursting Enables the Induction of LTP by Theta Frequency Synaptic Stimulation

Long-term potentiation (LTP), a persistent enhancement of synaptic transmission that may be involved in some forms of learning and memory, is induced at excitatory synapses in the CA1 region of the hippocampus by coincident presynaptic and postsynaptic activity. Although action potentials back-propagating into dendrites of hippocampal pyramidal cells provide sufficient postsynaptic activity to induce LTP under somein vitro conditions, it is not known whether LTP can be induced by patterns of postsynaptic action potential firing that occur in these cells in vivo. Here we report that a characteristic in vivo pattern of action potential generation in CA1 pyramidal cells known as the complex spike burst enables the induction of LTP during theta frequency synaptic stimulation in the CA1 region of hippocampal slices maintainedin vitro. Our results suggest that complex spike bursting may have an important role in synaptic processes involved in learning and memory formation, perhaps by producing a highly sensitive postsynaptic state during which even low frequencies of presynaptic activity can induce LTP.
Evaluation of an intervention program to prevent hospital-acquired catheter-associated urinary tract infections in an ICU in a rural Egypt hospital

Aim: Catheter associated urinary tract infections (CAUTI) are the most common hospital-acquired infection in ICUs. The aim of this study was to estimate the effectiveness of an intervention program by implementing urinary catheter bundle elements to reduce the CAUTI frequency in an ICU. Methods: The intervention study was conducted over a period of 6 months. During a pre-intervention phase, the base line catheter associated CAUTI incidence rates were determined and compared with the incidence rates during the post-intervention phase. The compliance of health care staff with urinary catheter bundle elements was also measured. The implemented CAUTI prevention bundle consisted of hand hygiene, wearing personal protective equipment, use of disposable gloves, cleansing of urethral meatus prior to catheter insertion using sterile saline, assessment of catheter need, aseptic urine sampling technique, and correct draining bag positioning. Results: During the study period, 55 out of 77 patients were diagnosed with a CAUTI. The mean CAUTI incidence rate for the pre-intervention period was 90.12/1,000 catheter days and for the post intervention phase 65.69/1,000 catheter days. The CAUTIs rate was inversely proportional to insertion bundle elements and maintenance bundle elements compliance rate. This negative relationship was statistically significant only with maintenance bundle elements (p=0.042) (rs=–0.828). The compliance rate of the ICU nurses to the bundle elements was raised to 100% during the last 2 months of the post intervention phase. Conclusion: Increased compliance to recommended catheter associated urinary tract infections preventive practices reduced the incidence of CAUTI in an ICU unit. It is simple and effective and is recommended as a part of patient safety culture.
Genetic Structure of Qiangic Populations Residing in the Western Sichuan Corridor

The Qiangic languages in western Sichuan (WSC) are believed to be the oldest branch of the Sino-Tibetan linguistic family, and therefore, all Sino-Tibetan populations might have originated in WSC. However, very few genetic investigations have been done on Qiangic populations and no genetic evidences for the origin of Sino-Tibetan populations have been provided. By using the informative Y chromosome and mitochondrial DNA (mtDNA) markers, we analyzed the genetic structure of Qiangic populations. Our results revealed a predominantly Northern Asian-specific component in Qiangic populations, especially in maternal lineages. The Qiangic populations are an admixture of the northward migrations of East Asian initial settlers with Y chromosome haplogroup D (D1-M15 and the later originated D3a-P47) in the late Paleolithic age, and the southward Di-Qiang people with dominant haplogroup O3a2c1*-M134 and O3a2c1a-M117 in the Neolithic Age.
A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia

Background After the recent successes of genome-wide association studies (GWAS), one key challenge is to identify genetic variants that might have a significant joint effect on complex diseases but have failed to be identified individually due to weak to moderate marginal effect. One popular and effective approach is gene set based analysis, which investigates the joint effect of multiple functionally related genes (eg, pathways). However, a typical gene set analysis method is biased towards long genes, a problem that is especially severe in psychiatric diseases. Methods A novel approach was proposed, namely generalised additive model (GAM) for GWAS (gamGWAS), for gene set enrichment analysis of GWAS data, specifically adjusting the gene length bias or the number of single-nucleotide polymorphisms per gene. GAM is applied to estimate the probability of a gene to be selected as significant given its gene length, followed by weighted resampling and computation of empirical p values for the rank of pathways. We demonstrated gamGWAS in two schizophrenia GWAS datasets from the International Schizophrenia Consortium and the Genetic Association Information Network. Results The gamGWAS results not only confirmed previous findings, but also highlighted several immune related pathways. Comparison with other methods indicated that gamGWAS could effectively reduce the correlation between pathway p values and its median gene length. Conclusion gamGWAS can effectively relieve the long gene bias and generate reliable results for GWAS data analysis. It does not require genotype data or permutation of sample labels in the original GWAS data; thus, it is computationally efficient.
Effects of Multimedia Vocabulary Annotations and Learning Styles on Vocabulary Learning

This first goal of the study described here was to investigate the effectiveness of three types of vocabulary annotations on vocabulary learning for EFL college students in Taiwan: text annotation only, text plus picture, and text plus picture and sound. The second goal of the study was to determine whether learners with certain perceptual learning styles benefited more from a particular type of vocabulary annotations. The perceptual learning styles investigated were auditory, visual-verbal (with text), visual-nonverbal (with pictures), and mixed preferences. The results of the study showed that the version with text plus picture was the most effective type of vocabulary annotation. Perceptual learning styles did not seem to have a significant influence on the effectiveness of vocabulary annotations.
The Role of Infrastructure In Developing New Zealand's Economy

The concept of an ‘infrastructure deficit’ is commonly referred to within New Zealand. A claim that there is a deficit implies that the optimal stock is greater than the existing stock (at least for certain infrastructure types) and hence new investment would yield positive net benefits. Yet little work has been conducted in New Zealand to evaluate impacts of new infrastructure investments or to analyse whether returns to infrastructure investments have been positive. This paper provides an overview of the impacts of some major nineteenth century infrastructure programmes and reports on current work analysing returns to recent infrastructure investments. The paper aims to draw lessons about the role of infrastructure in developing New Zealand’s economy and to understand factors that may currently inhibit the full benefits of these investments from being realised.
Determinants of risk taking behavior : the role of risk attitudes, risk perceptions and beliefs

Our study analyzes the determinants of investors' risk taking behavior. We find that investors' risk taking behavior such as portfolio choices can be predicted using risk attitudes, risk perceptions and belief measures such as optimism and overconfidence. However, the predictive power of these determinants heavily depends on the domain in which they were elicited. More specifically, risk attitudes, risk perceptions and beliefs only allow us to predict investors' risk taking behavior if they are elicited in an investment related context. We believe our results could benefit practitioners who could incorporate some of the determinants we have used in their investment advisory process.
Successful Verbal Encoding into Episodic Memory Engages the Posterior Hippocampus: A Parametrically Analyzed Functional Magnetic Resonance Imaging Study

The medial temporal lobe (MTL) is essential for episodic memory encoding, as evidenced by memory deficits in patients with MTL damage. However, previous functional neuroimaging studies have either failed to show MTL activation during encoding or they did not differentiate between two MTL related processes: novelty assessment and episodic memory encoding. Furthermore, there is evidence that the MTL can be subdivided into subcomponents serving different memory processes, but the extent of this functional subdivision remains unknown. The aim of the present functional magnetic resonance imaging (fMRI) study was to investigate the role of the MTL in episodic encoding and to determine whether this function might be restricted to anatomical subdivisions of the MTL. Thirteen healthy volunteers performed a word list learning paradigm with free recall after distraction. Functional images acquired during encoding were analyzed separately for each participant by a voxel-wise correlation (Kendall’s tau) between the time series of the T2*-signal intensity and the number of subsequently recalled words encoded during each particular scan. Of the 13 participants, 11 showed voxel clusters with statistically significant, positive correlations in the posterior part of the hippocampus. Across participants, an ANOVA on the number of voxels with significant, positive correlations within individually defined volumes of interest confirmed a statistically significant difference in activation for anterior versus posterior regions of the hippocampus. However, no differences between left and right hippocampal activation were revealed. Thus, these findings demonstrate that successful encoding into episodic memory engages neural circuits in the posterior part of the hippocampus.
Foreign Direct Investment, Domestic Investment and Economic Growth: Evidence from ASEAN-5

This study is an empirical analysis of the impact of domestic investment and FDI on the economic growth of ASEAN-5 namely Indonesia, Malaysia, the Philippines, Thailand and Singapore during the last four decades. Also the study focuses on the FDI inflow into ASEAN-5, and the domestic investment accumulation process in the ASEAN-5. This research was conducted following recent events such as the decline in the inflow of foreign capital and growth rates of domestic investment and thereafter the economic growth after the Asian financial crisis, and the search for new policy options that could contribute to sustained economic growth. The growth and FDI models for this study are derived from the endogenous growth model, which can explain the behaviour of ASEAN-5 economies. The theoretical models are based on the previous works of Romer (1991), and developed by Borensztein, e. al. (1998). The domestic investment equation is derived based on the flexible accelerator model, which is an extension of a model established by Fry (1998) and developed by Agrawal (2000a, 2000b). This study utilized the autoregressive distributed lag approach to cointegration (ARDL) developed by Pesaran et al. (1996, 2001). This technique has additional advantages of yielding consistent estimates of the long-run coefficients. It is also free of residual correlation, and can distinguish between dependent and explanatory variables. The major findings of this study can be summarized as follows: (i) domestic investment, FDI, and financial intermediation significantly affect the economic growth of ASEAN-5; (ii) FDI has positive and significant effect on domestic investment and vice-versa. ; (iii) the improvement in the development level of financial intermediation and human capital has a vital role on ASEAN-5’s economic growth through FDI and domestic investment channels; (iv) the growth rate of GDP and domestic investment significantly affect FDI inflows to ASEAN-5; (v) outward-looking together with stable exchange rate policies contribute positively to both FDI and domestic investment and thereafter economic growth; (vi) the results reveal that ASEAN-5 can rely on domestic resources such as investment, saving, human capital, financial intermediation as instruments of economic growth, and FDI alone may not be able to sustain economic growth. Hence, economic growth based on domestic resources should be encouraged.