Miracle-dz/UniFAR-FTUs huggingface dataset:
Intercalibration and Gaussian Process Modeling of Nighttime Lights Imagery for Measuring Urbanization Trends in Africa 2000-2013

Sub-Saharan Africa currently has the world’s highest urban population growth rate of any continent at roughly 4.2% annually. A better understanding of the spatiotemporal dynamics of urbanization across the continent is important to a range of fields including public health, economics, and environmental sciences. Nighttime lights imagery (NTL), maintained by the National Oceanic and Atmospheric Administration, offers a unique vantage point for studying trends in urbanization. A well-documented deficiency of this dataset is the lack of intra- and inter-annual calibration between satellites, which makes the imagery unsuitable for temporal analysis in their raw format. Here we have generated an ‘intercalibrated’ time series of annual NTL images for Africa (2000–2013) by building on the widely used invariant region and quadratic regression method (IRQR). Gaussian process methods (GP) were used to identify NTL latent functions independent from the temporal noise signals in the annual datasets. The corrected time series was used to explore the positive association of NTL with Gross Domestic Product (GDP) and urban population (UP). Additionally, the proportion of change in ‘lit area’ occurring in urban areas was measured by defining urban agglomerations as contiguously lit pixels of >250 km2, with all other pixels being rural. For validation, the IRQR and GP time series were compared as predictors of the invariant region dataset. Root mean square error values for the GP smoothed dataset were substantially lower. Correlation of NTL with GDP and UP using GP smoothing showed significant increases in R2 over the IRQR method on both continental and national scales. Urban growth results suggested that the majority of growth in lit pixels between 2000 and 2013 occurred in rural areas. With this study, we demonstrated the effectiveness of GP to improve conventional intercalibration, used NTL to describe temporal patterns of urbanization in Africa, and detected NTL responses to environmental and humanitarian crises. The smoothed datasets are freely available for further use.
The Group Delay and Suppression Pattern of the Cochlear Microphonic Potential Recorded at the Round Window

Background It is commonly assumed that the cochlear microphonic potential (CM) recorded from the round window (RW) is generated at the cochlear base. Based on this assumption, the low-frequency RW CM has been measured for evaluating the integrity of mechanoelectrical transduction of outer hair cells at the cochlear base and for studying sound propagation inside the cochlea. However, the group delay and the origin of the low-frequency RW CM have not been demonstrated experimentally. Methodology/Principal Findings This study quantified the intra-cochlear group delay of the RW CM by measuring RW CM and vibrations at the stapes and basilar membrane in gerbils. At low sound levels, the RW CM showed a significant group delay and a nonlinear growth at frequencies below 2 kHz. However, at high sound levels or at frequencies above 2 kHz, the RW CM magnitude increased proportionally with sound pressure, and the CM phase in respect to the stapes showed no significant group delay. After the local application of tetrodotoxin the RW CM below 2 kHz became linear and showed a negligible group delay. In contrast to RW CM phase, the BM vibration measured at location ∼2.5 mm from the base showed high sensitivity, sharp tuning, and nonlinearity with a frequency-dependent group delay. At low or intermediate sound levels, low-frequency RW CMs were suppressed by an additional tone near the probe-tone frequency while, at high sound levels, they were partially suppressed only at high frequencies. Conclusions/Significance We conclude that the group delay of the RW CM provides no temporal information on the wave propagation inside the cochlea, and that significant group delay of low-frequency CMs results from the auditory nerve neurophonic potential. Suppression data demonstrate that the generation site of the low-frequency RW CM shifts from apex to base as the probe-tone level increases.
A Critical Review of Recurrent Neural Networks for Sequence Learning

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been dicult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades rst yielded and then made practical these powerful learning models. When appropriate, we reconcile conicting notation and nomenclature. Our goal is to provide a selfcontained explication of the state of the art together with a historical perspective and references to primary research.
Range Scan Registration Using Reduced Deformable Models

We present an unsupervised method for registering range scans of deforming, articulated shapes. The key idea is to model the motion of the underlying object using a reduced deformable model. We use a linear skinning model for its simplicity and represent the weight functions on a regular grid localized to the surface geometry. This decouples the deformation model from the surface representation and allows us to deal with the severe occlusion and missing data that is inherent in range scan data. We formulate the registration problem using an objective function that enforces close alignment of the 3D data and includes an intuitive notion of joints. This leads to an optimization problem that we solve using an efficient EM‐type algorithm. With our algorithm we obtain smooth deformations that accurately register pairs of range scans with significant motion and occlusion. The main advantages of our approach are that it does not require user specified markers, a template, nor manual segmentation of the surface geometry into rigid parts.
Meeting iron needs for infants and children

Purpose of review Iron deficiency early in life is associated with impaired neurological development. This study reviews the latest research on how to best meet iron requirements in infants and children. Recent findings There is concurrent evidence that delayed cord clamping is well tolerated and improves infant iron stores. Iron supplements or enriched complementary foods starting before 6 months of life do not reduce iron deficiency prevalence in low-risk populations. However, for low birth weight infants, iron supplements before 6 months of life have long-term benefits. Iron deficiency anaemia (IDA) during the second half year of life is rare in countries with high compliance to iron-rich complementary foods, but remains a major problem globally. In high-risk populations, iron supplementation reduces IDA and possibly improves growth. However, increased risk of infections is a concern and optimal preventive strategies have not yet been determined. Finally, there is concurrent evidence that iron supplementation of anaemic school-aged children reduces IDA and possibly improves neuropsychological outcomes. Summary Interventions for prevention of iron deficiency should be prioritized in risk groups. However, the unclear long-term benefits and possible risk of adverse effects, particularly increased infections in developing countries, prompt further large-scale, double-blinded trials.
Cost of Exactly Simulating Quantum Entanglement with Classical Communication

We investigate the amount of communication that must augment classical local hidden variable models in order to simulate the behavior of entangled quantum systems. We consider the scenario where a bipartite measurement is given from a set of possibilities and the goal is to obtain exactly the same correlations that arise when the actual quantum system is measured. We show that, in the case of a single pair of qubits in a Bell state, a constant number of bits of communication is always sufficient — regardless of the number of measurements under consideration. We also show that, in the case of a system of n Bell states, a constant times 2 n bits of communication is necessary. PACS numbers: 03.67. Hk, 03.67. Lx
Simple Mechanisms for a Subadditive Buyer and Applications to Revenue Monotonicity

We study the revenue maximization problem of a seller with n heterogeneous items for sale to a single buyer whose valuation function for sets of items is unknown and drawn from some distribution D. We show that if D is a distribution over subadditive valuations with independent items, then the better of pricing each item separately or pricing only the grand bundle achieves a constant-factor approximation to the revenue of the optimal mechanism. This includes buyers who are k-demand, additive up to a matroid constraint, or additive up to constraints of any downward-closed set system (and whose values for the individual items are sampled independently), as well as buyers who are fractionally subadditive with item multipliers drawn independently. Our proof makes use of the core-tail decomposition framework developed in prior work showing similar results for the significantly simpler class of additive buyers. In the second part of the article, we develop a connection between approximately optimal simple mechanisms and approximate revenue monotonicity with respect to buyers’ valuations. Revenue non-monotonicity is the phenomenon that sometimes strictly increasing buyers’ values for every set can strictly decrease the revenue of the optimal mechanism. Using our main result, we derive a bound on how bad this degradation can be (and dub such a bound a proof of approximate revenue monotonicity); we further show that better bounds on approximate monotonicity imply a better analysis of our simple mechanisms.
A thrombospondin structural repeat containing rhoptry protein from Plasmodium falciparum mediates erythrocyte invasion

Host cell invasion by Plasmodium falciparum requires multiple molecular interactions between host receptors and parasite ligands. A family of parasite proteins, which contain the conserved thrombospondin structural repeat motif (TSR), has been implicated in receptor binding during invasion. In this study we have characterized the functional role of a TSR containing blood stage protein referred to as P. falciparum thrombospondin related apical merozoite protein (PfTRAMP). Both native and recombinant PfTRAMP bind untreated as well as neuraminidase, trypsin or chymotrypsin‐treated human erythrocytes. PfTRAMP is localized in the rhoptry bulb and is secreted during invasion. Adhesion of microneme protein EBA175 with its erythrocyte receptor glycophorin A provides the signal that triggers release of PfTRAMP from the rhoptries. Rabbit antibodies raised against PfTRAMP block erythrocyte invasion by P. falciparum suggesting that PfTRAMP plays an important functional role in invasion. Combination of antibodies against PfTRAMP with antibodies against microneme protein EBA175 provides an additive inhibitory effect against invasion. These observations suggest that targeting multiple conserved parasite ligands involved in different steps of invasion may provide an effective strategy forthe development of vaccines against blood stage malaria parasites.
Investigating Body Image Disturbance in Anorexia Nervosa Using Novel Biometric Figure Rating Scales: A Pilot Study

This study uses novel biometric figure rating scales (FRS) spanning body mass index (BMI) 13.8 to 32.2 kg/m2 and BMI 18 to 42 kg/m2 . The aims of the study were (i) to compare FRS body weight dissatisfaction and perceptual distortion of women with anorexia nervosa (AN) to a community sample; (ii) how FRS parameters are associated with questionnaire body dissatisfaction, eating disorder symptoms and appearance comparison habits; and (iii) whether the weight spectrum of the FRS matters. Women with AN (n = 24) and a community sample of women (n = 104) selected their current and ideal body on the FRS and completed additional questionnaires. Women with AN accurately picked the body that aligned best with their actual weight in both FRS. Controls underestimated their BMI in the FRS 14-32 and were accurate in the FRS 18-42. In both FRS, women with AN desired a body close to their actual BMI and controls desired a thinner body. Our observations suggest that body image disturbance in AN is unlikely to be characterized by a visual perceptual disturbance, but rather by an idealization of underweight in conjunction with high body dissatisfaction. The weight spectrum of FRS can influence the accuracy of BMI estimation. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.
Analysis of Human Cytomegalovirus-Encoded MicroRNA Activity during Infection

ABSTRACT MicroRNAs (miRNAs) are expressed in a wide variety of organisms, ranging from plants to animals, and are key posttranscriptional regulators of gene expression. Virally encoded miRNAs are unique in that they could potentially target both viral and host genes. Indeed, we have previously demonstrated that a human cytomegalovirus (HCMV)-encoded miRNA, miR-UL112, downregulates the expression of a host immune gene, MICB. Remarkably, it was shown that the same miRNA also downregulates immediate-early viral genes and that its ectopic expression resulted in reduced viral replication and viral titers. The targets for most of the viral miRNAs, and hence their functions, are still unknown. Here we demonstrate that miR-UL112 also targets the UL114 gene, and we present evidence that the reduction of UL114 by miR-UL112 reduces its activity as uracil DNA glycosylase but only minimally affects virus growth. In addition, we show that two additional HCMV-encoded miRNAs, miR-US25-1 and miR-US25-2, reduce the viral replication and DNA synthesis not only of HCMV but also of other viruses, suggesting that these two miRNAs target cellular genes that are essential for virus growth. Thus, we suggest that in addition to miR-UL112, two additional HCMV miRNAs control the life cycle of the virus.
Association of prenatal exposure to acetaminophen and coffee with childhood asthma

Some studies have suggested that maternal acetaminophen use during pregnancy is associated with asthma in the offspring, and coffee consumption may modify the toxicity of acetaminophen. We aim to examine whether pregnancy maternal acetaminophen use increases the risk for offspring asthma, and whether such a potential association could be modified by maternal coffee consumption.
The pendulum test for evaluating spasticity of the elbow joint.

OBJECTIVE To develop a modification of the pendulum test to allow evaluation of elbow spasticity. DESIGN The main difficulties of directly applying the conventional pendulum test to the elbow were the small inertia of the forearm and the uncomfortable posture. We designed an experimental apparatus similar to a clock pendulum and developed an elbow biomechanic model to measure objectively spasticity of the elbow joint. The model consisted of linear stiffness and damping and gravity contribution. SETTING A referral medical center in Taiwan. PARTICIPANTS Eleven stable stroke patients and 11 able-bodied subjects. INTERVENTIONS A custom-designed accessory apparatus to facilitate the pendulum test in elbow joints. MAIN OUTCOME MEASURES By using an optimization technique, we estimated parameters of the proposed elbow biomechanic model as the candidate indicators of spasticity. RESULTS The stiffness constant remained relatively consistent in all groups. Both the damping coefficient and damping ratio increased in the affected side of stroke patients and tended to increase with the severity of spasticity. Damping ratio had marginally better differentiation capability than the damping coefficient. CONCLUSIONS The damping ratio derived from the proposed model differentiated spasticity from normotonus and increased as spasticity increased.
Spatiotemporal Features of Early Neuronogenesis Differ in Wild-Type and Albino Mouse Retina

In albino mammals, lack of pigment in the retinal pigment epithelium is associated with retinal defects, including poor visual acuity from a photoreceptor deficit in the central retina and poor depth perception from a decrease in ipsilaterally projecting retinal fibers. Possible contributors to these abnormalities are reported delays in neuronogenesis (Ilia and Jeffery, 1996) and retinal maturation (Webster and Rowe, 1991). To further determine possible perturbations in neuronogenesis and/or differentiation, we used cell-specific markers and refined birth dating methods to examine these events during retinal ganglion cell (RGC) genesis in albino and pigmented mice from embryonic day 11 (E11) to E18. Our data indicate that relative to pigmented mice, more ganglion cells are born in the early stages of neuronogenesis in the albino retina, although the initiation of RGC genesis in the albino is unchanged. The cellular organization of the albino retina is perturbed as early as E12. In addition, cell cycle kinetics and output along the nasotemporal axis differ in retinas of albino and pigmented mice, both absolutely, with the temporal aspect of the retina expanded in albino, and relative to the position of the optic nerve head. Finally, blocking melanin synthesis in pigmented eyecups in culture leads to an increase in RGC differentiation, consistent with a role for melanin formation in regulating RGC neuronogenesis. These results point to spatiotemporal defects in neuronal production in the albino retina, which could perturb expression of genes that specify cell fate, number, and/or projection phenotype.
Systems biology: experimental design

Experimental design has a long tradition in statistics, engineering and life sciences, dating back to the beginning of the last century when optimal designs for industrial and agricultural trials were considered. In cell biology, the use of mathematical modeling approaches raises new demands on experimental planning. A maximum informative investigation of the dynamic behavior of cellular systems is achieved by an optimal combination of stimulations and observations over time. In this minireview, the existing approaches concerning this optimization for parameter estimation and model discrimination are summarized. Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed.
White matter damage and cognitive impairment after traumatic brain injury

White matter disruption is an important determinant of cognitive impairment after brain injury, but conventional neuroimaging underestimates its extent. In contrast, diffusion tensor imaging provides a validated and sensitive way of identifying the impact of axonal injury. The relationship between cognitive impairment after traumatic brain injury and white matter damage is likely to be complex. We applied a flexible technique—tract-based spatial statistics—to explore whether damage to specific white matter tracts is associated with particular patterns of cognitive impairment. The commonly affected domains of memory, executive function and information processing speed were investigated in 28 patients in the post-acute/chronic phase following traumatic brain injury and in 26 age-matched controls. Analysis of fractional anisotropy and diffusivity maps revealed widespread differences in white matter integrity between the groups. Patients showed large areas of reduced fractional anisotropy, as well as increased mean and axial diffusivities, compared with controls, despite the small amounts of cortical and white matter damage visible on standard imaging. A stratified analysis based on the presence or absence of microbleeds (a marker of diffuse axonal injury) revealed diffusion tensor imaging to be more sensitive than gradient-echo imaging to white matter damage. The location of white matter abnormality predicted cognitive function to some extent. The structure of the fornices was correlated with associative learning and memory across both patient and control groups, whilst the structure of frontal lobe connections showed relationships with executive function that differed in the two groups. These results highlight the complexity of the relationships between white matter structure and cognition. Although widespread and, sometimes, chronic abnormalities of white matter are identifiable following traumatic brain injury, the impact of these changes on cognitive function is likely to depend on damage to key pathways that link nodes in the distributed brain networks supporting high-level cognitive functions.
Admission Trends Over 8 Years for Diabetic Foot Ulceration in a Specialized Diabetes Unit in Cameroon

High rates of foot complications have been reported in people with diabetes in sub-Saharan Africa (SSA). However, there is a paucity of data in support of the changing pattern with time. We report here data on trends in hospitalization for foot ulceration over an 8-year consecutive period in a specialized diabetes unit in SSA. Admission and discharge registers of the diabetes and endocrine unit of the Yaounde Central hospital, Cameroon, were reviewed for the period 2000 through 2007. Data were collected on the status for diabetes, presence of foot ulcer, age, sex, duration of hospitalization, amputation, and deaths.We found that 1841 patients with diabetes were admitted during the study period. The prevalence of foot ulceration was 13% (95% confidence interval [CI] = 11%-15%) and varied significantly by year of study (P = .001). The mean duration of hospitalization significantly decreased with time. Foot ulcer was associated with 115% (95% CI = 87%-148%) more bed use than other conditions in diabetes. Foot ulcer was associated with a nonsignificantly lower risk of death or dropout, with evidence of some attenuation with time. With one exception, the amputation rate of 16% (95% CI = 11%-20%) was similar across years. Foot ulcer is a major cause of hospital admission and bed use for diabetes in Cameroon.