Miracle-dz/UniFAR-FTUs huggingface dataset:
A Mixed Methods and Triangulation Model for Increasing the Accuracy of Adherence and Sexual Behaviour Data: The Microbicides Development Programme

Background The collection of accurate data on adherence and sexual behaviour is crucial in microbicide (and other HIV-related) research. In the absence of a “gold standard” the collection of such data relies largely on participant self-reporting. After reviewing available methods, this paper describes a mixed method/triangulation model for generating more accurate data on adherence and sexual behaviour in a multi-centre vaginal microbicide clinical trial. In a companion paper some of the results from this model are presented [1]. Methodology/Principal Findings Data were collected from a random subsample of 725 women (7.7% of the trial population) using structured interviews, coital diaries, in-depth interviews, counting returned gel applicators, focus group discussions, and ethnography. The core of the model was a customised, semi-structured in-depth interview. There were two levels of triangulation: first, discrepancies between data from the questionnaires, diaries, in-depth interviews and applicator returns were identified, discussed with participants and, to a large extent, resolved; second, results from individual participants were related to more general data emerging from the focus group discussions and ethnography. A democratic and equitable collaboration between clinical trialists and qualitative social scientists facilitated the success of the model, as did the preparatory studies preceding the trial. The process revealed some of the underlying assumptions and routinised practices in “clinical trial culture” that are potentially detrimental to the collection of accurate data, as well as some of the shortcomings of large qualitative studies, and pointed to some potential solutions. Conclusions/Significance The integration of qualitative social science and the use of mixed methods and triangulation in clinical trials are feasible, and can reveal (and resolve) inaccuracies in data on adherence and sensitive behaviours, as well as illuminating aspects of “trial culture” that may also affect data accuracy.
Environmentally Relevant Iron Oxide Nanoparticles Produce Limited Acute Pulmonary Effects in Rats at Realistic Exposure Levels

Iron is typically the dominant metal in the ultrafine fraction of airborne particulate matter. Various studies have investigated the toxicity of inhaled nano-sized iron oxide particles (FeOxNPs) but their results have been contradictory, with some indicating no or minor effects and others finding effects including oxidative stress and inflammation. Most studies, however, did not use materials reflecting the characteristics of FeOxNPs present in the environment. We, therefore, analysed the potential toxicity of FeOxNPs of different forms (Fe3O4, α-Fe2O3 and γ-Fe2O3) reflecting the characteristics of high iron content nano-sized particles sampled from the environment, both individually and in a mixture (FeOx-mix). A preliminary in vitro study indicated Fe3O4 and FeOx-mix were more cytotoxic than either form of Fe2O3 in human bronchial epithelial cells (BEAS-2B). Follow-up in vitro (0.003, 0.03, 0.3 µg/mL, 24 h) and in vivo (Sprague–Dawley rats, nose-only exposure, 50 µg/m3 and 500 µg/m3, 3 h/d × 3 d) studies therefore focused on these materials. Experiments in vitro explored responses at the molecular level via multi-omics analyses at concentrations below those at which significant cytotoxicity was evident to avoid detection of responses secondary to toxicity. Inhalation experiments used aerosol concentrations chosen to produce similar levels of particle deposition on the airway surface as were delivered in vitro. These were markedly higher than environmental concentrations. No clinical signs of toxicity were seen nor effects on BALF cell counts or LDH levels. There were also no significant changes in transcriptomic or metabolomic responses in lung or BEAS-2B cells to suggest adverse effects.
The prevalence of infertility and factors associated with infertility in Ethiopia: Analysis of Ethiopian Demographic and Health Survey (EDHS)

Background Despite having a high fertility rate, low-resource countries are also home to couples with infertility problems. Although many couples are suffering from the psychological impacts of infertility, its level and determinants are not adequately known. The main objective of this study is to assess the prevalence and factors associated with infertility among couples in Ethiopia using the 2016 Ethiopian Demographic and Health Survey (EDHS) data. Method The study employed a cross-sectional study design extracting variables from the 2016 EDHS. The study included all married or cohabitating women aged 15 to 49 years in the Couples Recode (CR) file data set. Weighted samples of 6141 respondents were analyzed. We used Stata 14 software for analyzing the data. The association of selected independent variables with primary, secondary, and total infertility was analyzed using a logistic regression model. We presented the results using an adjusted odds ratio (AOR) with a 95% confidence interval (CI) and a p-value <0.05 as a cut-off point for declaring statistical significance. Results The prevalence of infertility in the past 12 months was 24.2% (95% CI: 23.1–25.3%), of which the majority (90.7%) was secondary infertility. Greater than 35 years of age (AOR = 2.45, 95% CI (1.58–3.79)), rural residence (AOR = 1.06, 95% CI (1.01–1.39)), smoking (AOR = 2.29, 95% CI (1.39–3.77)), and <18.5 Body Mass Index (BMI) (AOR = 1.71, 95% CI (1.43–2.04)) were significantly associated with infertility. Conversely, infertility was less likely among women with formal education and better wealth index. Primary infertility was significantly higher among women whose partners drink alcohol (AOR = 1.55; 95% CI 1.06–2.28)) and chew khat (AOR = 1.62; 95% CI (1.12–2.36)). Secondary infertility was significantly higher among women with <18.5 BMI (AOR = 1.59, 95% CI (1.37–1.84)), >30 BMI (AOR = 1.54; 95% CI 1.01–2.35)), and <15 years of age at first birth (AOR = 1.40; 95% CI 1.15–1.69)). Conclusion More than one in five couples in Ethiopia has an infertility problem. Both male and female-related factors are associated with infertility. Primary infertility was significantly higher among women whose partner chews khat and drinks alcohol. Secondary infertility was significantly associated with being underweight, obese, smoking, and young age at first birth. Hence, taking action on preventable factors is the most critical treatment approach and will improve the health status of the couples in other ways.
Lateral variations in attenuation and anisotropy of the upper mantle from seismic waveform tomography

Lateral Variations in Attenuation and Anisotropy of the Upper Mantle from Seismic Waveform Tomography by Yuan-Cheng Gung Doctor of Philosophy in Geophysics University of California at Berkeley Professor Barbara Romanowicz, Chair We present constraints on Earth’s upper mantle structure from seismic tomography. Using the well established waveform inversion technique for seismic velocity, we extend this mode-perturbation-based approach to resolve anelasticity and anisotropy. We develop an inversion procedure for Q tomography involving two steps: (1)3D whole-mantle velocity models are first derived using nonlinear asymptotic coupling theory, which takes into account across-branch coupling effects among Earth’s normal modes; and (2)the surface waveforms thus aligned in phase are inverted to obtain a degree 8 upper mantle Q model, QRLW8. Various stability tests are performed to assess the quality of the model, and in particular to assess possible contamination from focusing effects. We find that the 3D patterns obtained are stable, but the amplitude of the lateral variation in Q is not well constrained. By comparing the Q model to velocity models, we address its implications for thermal upwellings, mantle dynamics and heat flux. We also develop an inversion procedure for transverse anisotropy using three-component surface and body waveform data. The procedure combines non-linear asymptotic theory and appropriate anisotropic kernels for weak transverse anisotropy. The resulting degree 16 model (SAW16AN) shows that significant radial anisotropy with VSH > VSV is present under most cratons in the depth range 250-400 km. This explains the lack of correlation among global tomographic
Biogeochemical processes as drivers of surface fCO2 in contrasting provinces in the subarctic North Pacific Ocean

The effect of temperature, biological processes, air‐sea CO2 exchange and vertical mixing as drivers of the seasonality of the surface water fugacity of CO2 (fCO2sw) were studied for the year 2000 in the subarctic North Pacific Ocean. The regional and seasonal variability of the surface water chemistry was studied using an extensive data set on surface water fCO2 and nutrient concentrations in six contrasting provinces. We observed the largest seasonal amplitude for all parameters in the western provinces (Oyashio and Western Subarctic Gyre, WSG). Our study showed that biological processes and temperature were major controls for the monthly fCO2sw change in all provinces. The magnitude and strength of the processes showed large temporal and spatial variability. The WSG showed larger influence by biological processes and vertical mixing than the Alaska gyre (AG), where the effect caused by temperature was larger, implying different forcing of the fCO2 change in the two gyres. Biological activity, estimated from the monthly nitrate change corrected for addition induced by vertical mixing, resulted in a net annual CO2 loss. The net carbon loss out of the top 50 m driven by biological activity was 3 times higher in the WSG (64 g C m−2 yr−1) than in the AG (23 g C m−2 yr−1). The annual sum of the fCO2sw change based on all processes resulted in a CO2 buildup in the surface waters for all provinces. Although the air‐sea CO2 exchange was of minor importance relative to the other considered processes (4 to 13%), all provinces showed a net annual uptake of atmospheric CO2 from 1 to 23 g C m−2 yr−1 and an average for the whole study area of about 12 (±9) g C m−2 yr−1.
How do adults and teens with self-declared Autism Spectrum Disorder experience eye contact? A qualitative analysis of first-hand accounts

A tendency to avoid eye contact is an early indicator of Autism Spectrum Disorder (ASD), and difficulties with eye contact often persist throughout the lifespan. Eye contact difficulties may underlie social cognitive deficits in ASD, and can create significant social and occupational barriers. Thus, this topic has received substantial research and clinical attention. In this study, we used qualitative methods to analyze self-reported experiences with eye contact as described by teens and adults with self-declared ASD. Results suggest people with a self- declared ASD diagnosis experience adverse emotional and physiological reactions, feelings of being invaded, and sensory overload while making eye contact, in addition to difficulties understanding social nuances, and difficulties receiving and sending nonverbal information. Some data support existing mindblindness frameworks, and hyperarousal or hypoarousal theories of eye contact, but we also present novel findings unaccounted for by existing frameworks. Additionally, we highlight innovative strategies people with self-declared ASD have devised to overcome or cope with their eye contact difficulties.
Thermodynamics, diffusion and structure of NaAlSi2O6 liquid at mantle conditions: A first-principles molecular dynamics investigation

[1] We present results from first-principles molecular dynamics simulations of NaAlSi2O6 liquid at mantle conditions. Liquid state thermodynamics and diffusion are evaluated at temperatures of 3000–6000 K and pressures of 0–144 GPa, and interpreted in the context of the underlying liquid structure and dynamics. Consistent with previous first-principles studies of polymerized liquids, we find that a fourth order finite strain expansion is required to account for the pressure-volume equation of state. Thermodynamic properties for NaAlSi2O6 liquid derived from our results using a self-consistent thermodynamic relation agree well with experimental measurements. Over the pressure range considered, isochoric heat capacity decreases from ∼5.3 NkB to ∼4.2 NkB, while the Gruneisen parameter increases from ∼0.3 to ∼1.1. Liquid structure changes are continuous with compression, showing trends in mean coordination numbers and relative abundances of distinct coordination species consistent with first-principles studies of other silicate liquid compositions. Computed species self-diffusivities generally decrease with pressure, except that those for Si and O increase with pressure below 16 GPa at 3000 K. While self-diffusivities for Na at low pressures are almost an order of magnitude higher than other species, this contrast in species mobility disappears at above 20 GPa. Consequently, alkali-rich silicate liquids associated with low degree melting in Earth's interior are unlikely to have high electrical conductivity and will be difficult to detect by magnetotelluric sounding.
Analysis of Host–Parasite Incongruence in Papillomavirus Evolution Using Importance Sampling

The papillomaviruses (PVs) are a family of viruses infecting several mammalian and nonmammalian species that cause cervical cancer in humans. The evolutionary history of the PVs as it associated with a wide range of host species is not well understood. Incongruities between the phylogenetic trees of various viral genes as well as between these genes and the host phylogenies suggest historical viral recombination as well as violations of strict virus–host cospeciation. The extent of recombination events among PVs is uncertain, however, and there is little evidence to support a theory of PV spread via recent host transfers. We have investigated incongruence between PV genes and hence, the possibility of recombination, using Bayesian phylogenetic methods. We find significant evidence for phylogenetic incongruence among the six PV genes E1, E2, E6, E7, L1, and L2, indicating substantial recombination. Analysis of E1 and L1 phylogenies suggests ancestral recombination events. We also describe a new method for examining alternative host–parasite association mechanisms by applying importance sampling to Bayesian divergence time estimation. This new approach is not restricted by a fixed viral tree topology or knowledge of viral divergence times, multiple parasite taxa per host may be included, and it can distinguish between prior divergence of the virus before host speciation and host transfer of the virus following speciation. Using this method, we find prior divergence of PV lineages associated with the ancestral mammalian host resulting in at least 6 PV lineages prior to speciation of this host. These PV lineages have then followed paths of prior divergence and cospeciation to eventually become associated with the extant host species. Only one significant instance of host transfer is supported, the transfer of the ancestral L1 gene between a Primate and Hystricognathi host based on the divergence times between the υ human type 41 and porcupine PVs.
Substrate Influences on Incised‐Channel Morphology

Surveys of channel geometry and substrate resistance along an incised ephemeral channel in southern India were used to examine the influence of substrate on channel geometry. The surveys indicate that as substrate resistance increases, the channel grows narrower and deeper, with undulating wall and bed topography, more localized erosion in the form of potholes and longitudinal grooves, and a steeper and more variable bed gradient.
Unexpected Genomic Variability in Clinical and Environmental Strains of the Pathogenic Yeast Candida parapsilosis

Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains the main cause, the incidence of emerging Candida species, such as C. parapsilosis is increasing. It has been postulated that C. parapsilosis clinical isolates result from a recent global expansion of a virulent clone. However, the availability of a single genome for this species has so far prevented testing this hypothesis at genomic scales. We present here the sequence of three additional strains from clinical and environmental samples. Our analyses reveal unexpected patterns of genomic variation, shared among distant strains, that argue against the clonal expansion hypothesis. All strains carry independent expansions involving an arsenite transporter homolog, pointing to the existence of directional selection in the environment, and independent origins of the two clinical isolates. Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis.
Reducing Analysis Variability of the Illinois Soil Nitrogen Test with Enclosed Griddles

The Illinois soil N test (ISNT) is a simple laboratory analysis that shows promise as a tool to predict if additional N application for corn (Zea mays L.) will result in a yield increase. Initial testing of the method at Cornell University showed a high degree of day-to-day and within-griddle soil test N variability. At the University of Illinois, similar findings led to modification of the method to include jar rotations 1.5 and 3 h after initiation of the 5-h incubation period used in the test. To determine if variability could be reduced without additional labor by enclosing the griddles using plywood boxes, experiments were designed to compare soil test variability using both the open-bench and enclosed-griddle methods. Enclosing the griddles decreased the coefficient of variance (CV) (p = 0.013) to 2.5% from 3.8% when analyses were done using the open-bench method (using 10 exterior positions of the griddle for each method). Enclosing griddles did not impact recovery of added glucosamine-N but resulted in lower N test values when set at the same temperature as the open-bench griddles. A comparison study of 14 soils analyzed at the University of Illinois using the standard open-bench procedure with jar rotation and at Cornell University using the enclosed-griddle method without rotation showed sample means to be comparable when the enclosed griddles were set at 50.6°C. These results imply that the modified method could be adopted for use beyond well-controlled laboratory environments but that griddle temperature setting is extremely important.
Crustal melting and melt extraction, ascent and emplacement in orogens: mechanisms and consequences

Significant volume of wet melting requires an influx of H2O-rich volatile phase. In hydrate-breakdown melting, initial melt accumulation is diffusion-controlled and melt accumulates around peritectic phases in low-pressure sites. As the melt-bearing rock weakens, it becomes porous at a few volume per cent melt, initiating an advective flow regime; as melt volume reaches the melt connectivity transition, melt may be lost from the system in the first of several melt-build-up–melt-loss events. Using mineral equilibria modelling, major and accessory phase controls on melt chemistry are evaluated. In residual migmatites and granulites, microstructures indicate the former presence of melt whereas leucosome networks record melt extraction pathways. Sites of initial melting nucleate shear instabilities; strain and anisotropy of permeability control the form of millimetre- to centimetre-scale inferred melt channels and strong anisotropy promotes high fluid focusing. Focused melt flow occurs by dilatant shear failure of low melt volume rocks, which leads to the formation of melt flow networks allowing accumulation and storage of melt, and forming the link for melt flow from grain boundaries to ascent conduits. Melt ascent is via ductile fractures, which may propagate from dilation or shear bands. Fractures are characterized by blunt tips; also they may exhibit zigzag geometry close to the tips and petrographic continuity between leucosome in the host and granite in the dyke. Horizontal tabular and wedge-shaped intrusions commonly are associated with the brittle–ductile transition zone. Vertical lozenge-shaped intrusions represent congelation of magma in ascent conduits and blobby plutons record lateral expansion localized by instability; these intrusion types characterize emplacement at deeper levels in the crust.
Artificial small‐scale field‐aligned irregularities in the high latitude F region of the ionosphere induced by an X‐mode HF heater wave

The effects on the high‐latitude F region of the ionosphere by X‐mode powerful HF radio waves injected towards the magnetic zenith (MZ) are analysed. The experiments were conducted using the EISCAT/Heating facility and UHF radar at Tromsø, Norway, the CUTLASS (SuperDARN) radar and the EISCAT ionosonde (dynasonde). The results show that the X‐mode HF pump wave, radiated into the magnetic zenith from the HF heater, can generate very strong small‐scale artificial field aligned irregularities (AFAIs) in the F‐region of the high‐latitude ionosphere. These irregularities, with spatial scales across the geomagnetic field of the order of 8–15 m, are generated when the heater frequency is above the ordinary‐mode critical frequency but comparable with the extraordinary‐mode critical frequency. The generation of the X‐mode AFAIs was accompanied by electron temperature (Te) enhancements up to 50% above the background level and an increase in the electron density (Ne) by up to 30%.
Comparative Visual Performance with ANVIS (Aviator's Night Vision Imaging System) and AN/PVS-5A Night Vision Goggles under Starlight Conditions

Abstract : Experimental testing of 10 subjects wearing the AN/PVS-5A (II GEN) night vision goggles (NVG) and ANVIS (III GEN) NVG was conducted under field conditions of ambient starlight illumination (approx. 10-5 mL). The parameters measured were: 1) binocular visual acuity (BVA), 2) stereopsis (depth perception), and 3) a subjective forced choice test. Results showed that BVA was 20/124 and 20/86 for the II and III GEN NVG, respectively. This difference was statistically as well as clinically significant. The stereopsis test results were inconclusive and variable because of the limited sample size and relative inexperience of the subjects in using NVG. Neither BVA nor stereopsis with the NVG was found to be related to standard baseline measures of these parameters in the clinic. Even though the ANVIS has better gain, resolution and sensitivity, 6 out of 10 subjects preferred the AN/PVS-5A for viewing the subjective test. This seemingly paradoxical finding was surmised to be a result of the presence or lack of scene contrast due to the differential sensitivities in the II and III GEN photocathode tubes.