Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Cerebral Amyloid-&bgr; Aggregation With Cognitive Functioning in Persons Without Dementia

Importance Cerebral amyloid-&bgr; aggregation is an early event in Alzheimer disease (AD). Understanding the association between amyloid aggregation and cognitive manifestation in persons without dementia is important for a better understanding of the course of AD and for the design of prevention trials. Objective To investigate whether amyloid-&bgr; aggregation is associated with cognitive functioning in persons without dementia. Design, Setting, and Participants This cross-sectional study included 2908 participants with normal cognition and 4133 with mild cognitive impairment (MCI) from 53 studies in the multicenter Amyloid Biomarker Study. Normal cognition was defined as having no cognitive concerns for which medical help was sought and scores within the normal range on cognitive tests. Mild cognitive impairment was diagnosed according to published criteria. Study inclusion began in 2013 and is ongoing. Data analysis was performed in January 2017. Main Outcomes and Measures Global cognitive performance as assessed by the Mini-Mental State Examination (MMSE) and episodic memory performance as assessed by a verbal word learning test. Amyloid aggregation was measured with positron emission tomography or cerebrospinal fluid biomarkers and dichotomized as negative (normal) or positive (abnormal) according to study-specific cutoffs. Generalized estimating equations were used to examine the association between amyloid aggregation and low cognitive scores (MMSE score ⩽27 or memory z score⩽−1.28) and to assess whether this association was moderated by age, sex, educational level, or apolipoprotein E genotype. Results Among 2908 persons with normal cognition (mean [SD] age, 67.4 [12.8] years), amyloid positivity was associated with low memory scores after age 70 years (mean difference in amyloid positive vs negative, 4% [95% CI, 0%-7%] at 72 years and 21% [95% CI, 10%-33%] at 90 years) but was not associated with low MMSE scores (mean difference, 3% [95% CI, −1% to 6%], P = .16). Among 4133 patients with MCI (mean [SD] age, 70.2 [8.5] years), amyloid positivity was associated with low memory (mean difference, 16% [95% CI, 12%-20%], P < .001) and low MMSE (mean difference, 14% [95% CI, 12%-17%], P < .001) scores, and this association decreased with age. Low cognitive scores had limited utility for screening of amyloid positivity in persons with normal cognition and those with MCI. In persons with normal cognition, the age-related increase in low memory score paralleled the age-related increase in amyloid positivity with an intervening period of 10 to 15 years. Conclusions and Relevance Although low memory scores are an early marker of amyloid positivity, their value as a screening measure for early AD among persons without dementia is limited.
Capsules for Object Segmentation

Convolutional neural networks (CNNs) have shown remarkable results over the last several years for a wide range of computer vision tasks. A new architecture recently introduced by Sabour et al., referred to as a capsule networks with dynamic routing, has shown great initial results for digit recognition and small image classification. The success of capsule networks lies in their ability to preserve more information about the input by replacing max-pooling layers with convolutional strides and dynamic routing, allowing for preservation of part-whole relationships in the data. This preservation of the input is demonstrated by reconstructing the input from the output capsule vectors. Our work expands the use of capsule networks to the task of object segmentation for the first time in the literature. We extend the idea of convolutional capsules with locally-connected routing and propose the concept of deconvolutional capsules. Further, we extend the masked reconstruction to reconstruct the positive input class. The proposed convolutional-deconvolutional capsule network, called SegCaps, shows strong results for the task of object segmentation with substantial decrease in parameter space. As an example application, we applied the proposed SegCaps to segment pathological lungs from low dose CT scans and compared its accuracy and efficiency with other U-Net-based architectures. SegCaps is able to handle large image sizes (512 x 512) as opposed to baseline capsules (typically less than 32 x 32). The proposed SegCaps reduced the number of parameters of U-Net architecture by 95.4% while still providing a better segmentation accuracy.
Age at antiretroviral therapy initiation and cell-associated HIV-1 DNA levels in HIV-1-infected children

Background The latent viral reservoir is the major obstacle to achieving HIV remission and necessitates life-long antiretroviral therapy (ART) for HIV-infected individuals. Studies in adults and children have found that initiating ART soon after infection is associated with a reduction in the size of the HIV-1 reservoir. Here we quantified cell-associated HIV-1 DNA in early-treated but currently older HIV-infected children suppressed on ART. Methods The study participants comprised of a cohort of 146 early-treated children with HIV-1 RNA <50 copies/ml enrolled as part of a clinical trial in Johannesburg, South Africa. A stored buffy coat sample collected after a median 4.3 years on ART and where HIV-1 RNA was <50 copies/ml was tested for cell-associated HIV-1 DNA levels. An in-house, semi-nested real-time quantitative hydrolysis probe PCR assay to detect total HIV-1 subtype C proviral DNA was used. Children were followed prospectively for up to 3 years after this measurement to investigate subsequent HIV-1 RNA rebound/failure while remaining on ART. Age at ART initiation, HIV-1 RNA decline prior to HIV-1 DNA measurement and other factors were investigated. Results A gradient between age at ART initiation and later HIV-1 DNA levels was observed. When ART was started <2 months of age, the lowest levels of cell-associated HIV-1 DNA (median 1.4 log10copies/106 cells, interquartile range [IQR] 0.95–1.55) were observed compared to ART started at 2–4 months (median 1.68, IQR 1.26–1.97) or 5–14 months of age (median1.98, IQR 1.69–2.25). A low CD4 T-cell count pre-treatment predicted higher levels of HIV-1 DNA on later testing. The probability of HIV-1 RNA rebound >50 copies/ml whilst on ART within 3 years after the DNA measurement was 2.07 (95% CI: 1.352–3.167) times greater if the HIV-1 DNA level was above the median of 55 copies/106 cells. Conclusions Cell-associated HIV-1 DNA levels measured after more than 4 years on ART were lower the younger the age of the child when ART was initiated. This marker of the size of the viral reservoir also predicted subsequent viral rebound/treatment failure while ART was sustained. The results provide additional evidence of the benefits of prompt diagnosis and early ART initiation in newborns and infants.
Population Pharmacokinetic Modeling To Estimate the Contributions of Genetic and Nongenetic Factors to Efavirenz Disposition

ABSTRACT Efavirenz pharmacokinetics is characterized by large between-subject variability, which determines both therapeutic response and adverse effects. Some of the variability in efavirenz pharmacokinetics has been attributed to genetic variability in cytochrome P450 genes that alter efavirenz metabolism, such as CYP2B6 and CYP2A6. While the effects of additional patient factors have been studied, such as sex, weight, and body mass index, the extent to which they contribute to variability in efavirenz exposure is inconsistently reported. The aim of this analysis was to develop a pharmacometric model to quantify the contribution of genetic and nongenetic factors to efavirenz pharmacokinetics. A population-based pharmacokinetic model was developed using 1,132 plasma efavirenz concentrations obtained from 73 HIV-seronegative volunteers administered a single oral dose of 600 mg efavirenz. A two-compartment structural model with absorption occurring by zero- and first-order processes described the data. Allometric scaling adequately described the relationship between fat-free mass and apparent oral clearance, as well as fat mass and apparent peripheral volume of distribution. Inclusion of fat-free mass and fat mass in the model mechanistically accounted for correlation between these disposition parameters and sex, weight, and body mass index. Apparent oral clearance of efavirenz was reduced by 25% and 51% in subjects predicted to have intermediate and slow CYP2B6 metabolizer status, respectively. The final pharmacokinetic model accounting for fat-free mass, fat mass, and CYP2B6 metabolizer status was consistent with known mechanisms of efavirenz disposition, efavirenz physiochemical properties, and pharmacokinetic theory. (This study has been registered at ClinicalTrials.gov under identifier NCT00668395.)
Cement-based sensors for structural health monitoring

The purpose of structural health monitoring is to continuously and accurately assess the performance of structures using a sensory system. Recently introduced, cement-based sensors are piezoresistive and therefore can be used to sense stress/strain, simply by monitoring their electrical resistivity. These sensors, also known as smart (self-monitoring) structural materials can be used as a part or total component of structures and provide both structural capability and response to applied stress and damage. In this study cement-based sensors are developed using two types of carbon fibres, as well as both single-walled and multi-walled carbon nano-tubes. A wide range of experiments were conducted to pinpoint the most efficient fibre content, frequency, electrode type and resistivity measurement technique. The influence of different parameters such as curing, temperature, moisture and chloride were also investigated. The resistivity of the specimens increased with curing time, but became almost constant after a certain amount of time. The resistivity values decreased with increasing temperature and increased with the decrease in temperature at a rate of about 22-35 ohm-cm/°C. It was further found that moisture and chloride have a considerable influence on the electrical resistivity of these sensors. Next, the response of the developed cement-based sensors to compressive, tensile and flexural loading was explored. The resistivity values from the sensors were compared with load and displacement values as well as strain data acquired from conventional strain gauges. The results indicate that electrical resistivity of the sensors increases reversibly upon tension and decreases reversibly under compression provided that substantial cracking does not occur and the sensor remains in the elastic range.
Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

SUMMARY The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
HEAT TREATED WOOD

Heat treated wood is a product which is obtained by intensive treatment of a wood at high temperatures (160-260 oC). Thus, treated wood permanently changes its properties. Changes occur mainly in hemicelluloses degradation. As a consequence, the reduction of equilibrium moisture content, saturation point, shrinkage and swelling is about 50%, which leads to have more stable wood in use. Thermally treated wood shows increase in natural durability and insulating properties and reduction in water permeability. The growth of wood hardness is about 5%. Negative effects of heat treatment may include reduction of some mechanical properties (i.e. bending and tightening). The reduction of the mechanical properties is about 10-30%. Heat-treated wood is an ecologically clean material in the production and use. The most common use is for external cohesion less structure,
Aspen succession and nitrogen loading: a case for epiphytic lichens as bioindicators in the Rocky Mountains, USA

Question: Can lichen communities be used to assess short- and long-term factors affecting seral quaking aspen (Populus tremuloides) communities at the landscape scale? Location: Bear River Range, within the Rocky Mountains, in northern Utah and southern Idaho, USA. Method: Forty-seven randomly selected mid-elevation aspen stands were sampled for lichens and stand conditions. Plots were characterized according to tree species cover, basal area, stand age, bole scarring, tree damage, and presence of lichen species. We also recorded ammonia emissions with passive sensors at 25 urban and agricultural sites throughout an adjacent populated valley upwind of the forest stands. Nonmetric multidimensional scaling (NMS) ordination was used to evaluate an array of 20 variables suspected to influence lichen communities. Results: In NMS, forest succession explained most variance in lichen composition and abundance, although atmospheric nitrogen from local agricultural and urban sources also significantly influenced the lichen communities. Abundance of nitrophilous lichen species decreased with distance from peak ammonia sources and the urban center in all aspen succession classes. One lichen, Phaeophyscia nigricans, was found to be an effective bioindicator of nitrogen loading. Conclusions: Lichen communities in this landscape assessment of aspen forests showed clear responses to long-term (stand succession) and short-term (nitrogen deposition) influences. At the same time, several environmental factors (e.g. tree damage and scarring, distance to valley, topography, and stand age) had little influence on these same lichen communities. We recommend further use of epiphytic lichens as bioindicators of dynamic forest conditions.
Melatonin Absence Leads to Long-Term Leptin Resistance and Overweight in Rats

Melatonin (Mel), a molecule that conveys photoperiodic information to the organisms, is also involved in the regulation of energy homeostasis. Mechanisms of action of Mel in the energy balance remain unclear; herein we investigated how Mel regulates energy intake and expenditure to promote a proper energy balance. Male Wistar rats were assigned to control, control + Mel, pinealectomized (PINX) and PINX + Mel groups. To restore a 24-h rhythm, Mel (1 mg/kg) was added to the drinking water exclusively during the dark phase for 13 weeks. After this treatment period, rats were subjected to a 24-h fasting test, an acute leptin responsiveness test and cold challenge. Mel treatment reduced food intake, body weight, and adiposity. When challenged to 24-h fasting, Mel-treated rats also showed reduced hyperphagia when the food was replaced. Remarkably, PINX rats exhibited leptin resistance; this was likely related to the capacity of leptin to affect body weight, food intake, and hypothalamic signal-transducer and activator of transcription 3 phosphorylation, all of which were reduced. Mel treatment restored leptin sensitivity in PINX rats. An increased hypothalamic expression of agouti-related peptide (Agrp), neuropeptide Y, and Orexin was observed in the PINX group while Mel treatment reduced the expression of Agrp and Orexin. In addition, PINX rats presented lower UCP1 protein levels in the brown adipose tissue and required higher tail vasoconstriction to get a proper thermogenic response to cold challenge. Our findings reveal a previously unrecognized interaction of Mel and leptin in the hypothalamus to regulate the energy balance. These findings may help to explain the high incidence of metabolic diseases in individuals exposed to light at night.
Mine Waste and Acute Warming Induce Energetic Stress in the Deep-Sea Sponge Geodia atlantica and Coral Primnoa resedeaformis; Results From a Mesocosm Study

There is the potential for climate change to interact with pollution in all of the Earth’s oceans. In the fjords of Norway, mine tailings are released into fjords generating suspended sediment plumes that impact deep-sea ecosystems. These same deep-sea ecosystems are expected to undergo periodic warming as climate change increases the frequency of down-welling events in fjords. It remains unknown how a polluted deep-sea ecosystem would respond to down-welling because multiple stressors will often interact in unpredictable ways. Here, we exposed two deep-sea foundation species; the gorgonian coral Primnoa resedaeformis and the demosponge Geodia atlantica to suspended sediment (10 mg L-1) and acute warming (+ 5 °C) in a factorial mesocosm experiment for 40 days. Physiology (respiration, nutrient flux) and cellular responses (lysosomal cell stability) were measured for both the coral and sponge. Exposure to elevated suspended sediment reduced metabolism, supressed silicate uptake and induced cellular instability of the sponge G. atlantica. However, combining sediment with warming caused G. atlantica to respire and excrete nitrogen at a greater rate. For the coral P. resedaeformis, suspended sediments reduced O:N ratios after 40 days, however, warming had a greater effect on P. resedaeformis physiology compared to sediment. Warming increased respiration, nitrogen excretion, and cellular instability which resulted in lower O:N ratios. We argue that suspended sediment and warming can act alone and also interact to cause significant harm to deep-sea biota, however responses are likely to be species-specific. Warming and pollution could interact in the deep-sea to cause mortality to the coral P. resedaeformis and to a lesser extent, the sponge G. atlantica. As foundation species, reducing the abundance of deep sea corals and sponges would likely impact the ecosystems they support.
Knowledge of Orthodontics as a Dental Specialty: A Preliminary Survey among LASUCOM Students

Background: Awareness of malocclusion and the need to make corrections has increasingly becomes prevalent among our population. However, very few patients have presented in the orthodontic clinics with referrals from medical practitioners, an indication that the primary caregivers may be deficient in the knowledge of orthodontic practice. Objective: To assess the knowledge of orthodontics and the awareness of the effects of malocclusion on the general well-being, among medical students at the Lagos State University College of Medicine (LASUCOM). Materials and Methods: This cross-sectional study was conducted using a self-administered questionnaire. A total of 85 medical students in the institution participated in the study. Data entry and analysis was done using Epi info version 3.5. Frequency counts were generated for all variables and measures of central tendency for numerical variables. Results: All participants were medical students. Majority (75.3%) were in their clinical years while 24.7% were in their preclinical years. Only 45.9% of the respondents had heard of the term “orthodontics” and only 20% correctly answered that orthodontics involves malocclusion and its management. Concerning the treatment procedures used in orthodontic clinics, 54.1% of them selected rearrangement of teeth. When asked to identify the appliances used in orthodontics, 49.4% selected dentures, 40% selected removable appliances, and 57.7% selected braces. Most of the respondents (81.2%) agreed that as medical doctors they would refer patients for orthodontic care, while 3.5% were undecided and 15.3% disagreed. Conclusion: The medical students surveyed had limited knowledge of orthodontics as a specialty and also knew very little about the impact of malocclusion on the well-being of the individual. They would, therefore, benefit from basic education in orthodontics to stimulate their interest in the specialty and improve their ability to refer patients appropriately.
Serologic Evidence of Powassan Virus Infection in Patients with Suspected Lyme Disease

Powassan virus (POWV) lineage II is an emerging tickborne flavivirus with an unknown seroprevalence in humans. In a Lyme disease–endemic area, we examined the seroreactivity to POWV in 2 patient cohorts and described the clinical features of the POWV-seroreactive patients. POWV disease might be less neuroinvasive than previously thought.
Cellular Immune Responses against Simian T-Lymphotropic Virus Type 1 Target Tax in Infected Baboons

ABSTRACT There are currently 5 million to 10 million human T-lymphotropic virus type 1 (HTLV-1)-infected people, and many of them will develop severe complications resulting from this infection. A vaccine is urgently needed in areas where HTLV-1 is endemic. Many vaccines are best tested in nonhuman primate animal models. As a first step in designing an effective HTLV-1 vaccine, we defined the CD8+ and CD4+ T cell response against simian T-lymphotropic virus type 1 (STLV-1), a virus closely related to HTLV-1, in olive baboons (Papio anubis). Consistent with persistent antigenic exposure, we observed that STLV-1-specific CD8+ T cells displayed an effector memory phenotype and usually expressed CD107a, gamma interferon (IFN-γ), and tumor necrosis factor alpha (TNF-α). To assess the viral targets of the cellular immune response in STLV-1-infected animals, we used intracellular cytokine staining to detect responses against overlapping peptides covering the entire STLV-1 proteome. Our results show that, similarly to humans, the baboon CD8+ T cell response narrowly targeted the Tax protein. Our findings suggest that the STLV-1-infected baboon model may recapitulate some of the important aspects of the human response against HTLV-1 and could be an important tool for the development of immune-based therapy and prophylaxis. IMPORTANCE HTLV-1 infection can lead to many different and often fatal conditions. A vaccine deployed in areas of high prevalence might reduce the incidence of HTLV-1-induced disease. Unfortunately, there are very few animal models of HTLV-1 infection useful for testing vaccine approaches. Here we describe cellular immune responses in baboons against a closely related virus, STLV-1. We show for the first time that the immune response against STLV-1 in naturally infected baboons is largely directed against the Tax protein. Similar findings in humans and the sequence similarity between the human and baboon viruses suggest that the STLV-1-infected baboon model might be useful for developing a vaccine against HTLV-1.