Miracle-dz/UniFAR-FTUs huggingface dataset:
How Can the Operating Environment for Nutrition Research Be Improved in Sub-Saharan Africa? The Views of African Researchers

Optimal nutrition is critical for human development and economic growth. Sub-Saharan Africa is facing high levels of food insecurity and only few sub-Saharan African countries are on track to eradicate extreme poverty and hunger by 2015. Effective research capacity is crucial for addressing emerging challenges and designing appropriate mitigation strategies in sub-Saharan Africa. A clear understanding of the operating environment for nutrition research in sub-Saharan Africa is a much needed prerequisite. We collected data on the barriers and requirements for conducting nutrition research in sub-Saharan Africa through semi-structured interviews with 144 participants involved in nutrition research in 35 countries in sub-Saharan Africa. A total of 133 interviews were retained for coding. The main barriers identified for effective nutrition research were the lack of funding due to poor recognition by policymakers of the importance of nutrition research and under-utilisation of research findings for developing policy, as well as an absence of research priority setting from within Africa. Current research topics were perceived to be mainly determined by funding bodies from outside Africa. Nutrition researchers argued for more commitment from policymakers at national level. The low capacity for nutrition research was mainly seen as a consequence of insufficient numbers of nutrition researchers, limited skills and a poor research infrastructure. In conclusion, African nutrition researchers argued how research priorities need to be identified by African stakeholders, accompanied by consensus building to enable creating a problem-driven national research agenda. In addition, it was considered necessary to promote interactions among researchers, and between researchers and policymakers. Multidisciplinary research and international and cross-African collaboration were seen as crucial to build capacity in sub-Saharan nutrition research.
Inference of temporally varying Bayesian Networks

Motivation: When analysing gene expression time series data, an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Although some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data. Results: Here, we present a method that allows us to infer regulatory network structures that may vary between time points, using a set of hidden states that describe the network structure at a given time point. To model the distribution of the hidden states, we have applied the Hierarchical Dirichlet Process Hidden Markov Model, a non-parametric extension of the traditional Hidden Markov Model, which does not require us to fix the number of hidden states in advance. We apply our method to existing microarray expression data as well as demonstrating is efficacy on simulated test data. Contact: thomas.thorne@imperial.ac. uk
Foot placement relies on state estimation during visually guided walking.

As we walk, we must accurately place our feet to stabilize our motion and to navigate our environment. We must also achieve this accuracy despite imperfect sensory feedback and unexpected disturbances. In this study we tested whether the nervous system uses state estimation to beneficially combine sensory feedback with forward model predictions to compensate for these challenges. Specifically, subjects wore prism lenses during a visually guided walking task, and we used trial-by-trial variation in prism lenses to add uncertainty to visual feedback and induce a reweighting of this input. To expose altered weighting, we added a consistent prism shift that required subjects to adapt their estimate of the visuomotor mapping relationship between a perceived target location and the motor command necessary to step to that position. With added prism noise, subjects responded to the consistent prism shift with smaller initial foot placement error but took longer to adapt, compatible with our mathematical model of the walking task that leverages state estimation to compensate for noise. Much like when we perform voluntary and discrete movements with our arms, it appears our nervous systems uses state estimation during walking to accurately reach our foot to the ground. NEW & NOTEWORTHY Accurate foot placement is essential for safe walking. We used computational models and human walking experiments to test how our nervous system achieves this accuracy. We find that our control of foot placement beneficially combines sensory feedback with internal forward model predictions to accurately estimate the body's state. Our results match recent computational neuroscience findings for reaching movements, suggesting that state estimation is a general mechanism of human motor control.
On the geometry of broad emission region in quasars

We study the geometry of the Hβ broad emission region by comparing the M BH values derived from Hβ through the virial relation with those obtained from the host galaxy luminosity in a sample of 36 low-redshift (z ∼ 0.3) quasars. This comparison lets us infer the geometrical factor f needed to deproject the line-of-sight velocity component of the emitting gas. The wide range off values we found, together with the strong dependence off on the observed linewidth, suggests that a disc-like model for the broad-line region is preferable to an isotropic model, both for radio-loud and radio-quiet quasars. We examined similar observations of the C iv line and found no correlation in the width of the two lines. Our results indicate that an inflated disc broad-line region, in which the Carbon line is emitted in a flat disc while Hβ is produced in a geometrically thick region, can account for the observed differences in the width and shape of the two emission lines.
Cognitive therapy for the prevention of suicide attempts: a randomized controlled trial.

CONTEXT Suicide attempts constitute a major risk factor for completed suicide, yet few interventions specifically designed to prevent suicide attempts have been evaluated. OBJECTIVE To determine the effectiveness of a 10-session cognitive therapy intervention designed to prevent repeat suicide attempts in adults who recently attempted suicide. DESIGN, SETTING, AND PARTICIPANTS Randomized controlled trial of adults (N = 120) who attempted suicide and were evaluated at a hospital emergency department within 48 hours of the attempt. Potential participants (N = 350) were consecutively recruited from October 1999 to September 2002; 66 refused to participate and 164 were ineligible. Participants were followed up for 18 months. INTERVENTION Cognitive therapy or enhanced usual care with tracking and referral services. MAIN OUTCOME MEASURES Incidence of repeat suicide attempts and number of days until a repeat suicide attempt. Suicide ideation (dichotomized), hopelessness, and depression severity at 1, 3, 6, 12, and 18 months. RESULTS From baseline to the 18-month assessment, 13 participants (24.1%) in the cognitive therapy group and 23 participants (41.6%) in the usual care group made at least 1 subsequent suicide attempt (asymptotic z score, 1.97; P = .049). Using the Kaplan-Meier method, the estimated 18-month reattempt-free probability in the cognitive therapy group was 0.76 (95% confidence interval [CI], 0.62-0.85) and in the usual care group was 0.58 (95% CI, 0.44-0.70). Participants in the cognitive therapy group had a significantly lower reattempt rate (Wald chi2(1) = 3.9; P = . 049) and were 50% less likely to reattempt suicide than participants in the usual care group (hazard ratio, 0.51; 95% CI, 0.26-0.997). The severity of self-reported depression was significantly lower for the cognitive therapy group than for the usual care group at 6 months (P= .02), 12 months (P = .009), and 18 months (P = .046). The cognitive therapy group reported significantly less hopelessness than the usual care group at 6 months (P = .045). There were no significant differences between groups based on rates of suicide ideation at any assessment point. CONCLUSION Cognitive therapy was effective in preventing suicide attempts for adults who recently attempted suicide.
Fast and Exact: ADMM-Based Discriminative Shape Segmentation with Loopy Part Models

In this work we use loopy part models to segment ensembles of organs in medical images. Each organ's shape is represented as a cyclic graph, while shape consistency is enforced through inter-shape connections. Our contributions are two-fold: firstly, we use an efficient decomposition-coordination algorithm to solve the resulting optimization problems: we decompose the model's graph into a set of open, chain-structured, graphs each of which is efficiently optimized using Dynamic Programming with Generalized Distance Transforms. We use the Alternating Direction Method of Multipliers (ADMM) to fix the potential inconsistencies of the individual solutions and show that ADMM yields substantially faster convergence than plain Dual Decomposition-based methods. Secondly, we employ structured prediction to encompass loss functions that better reflect the performance criteria used in medical image segmentation. By using the mean contour distance (MCD) as a structured loss during training, we obtain clear test-time performance gains. We demonstrate the merits of exact and efficient inference with rich, structured models in a large X-Ray image segmentation benchmark, where we obtain systematic improvements over the current state-of-the-art.
Individual differences in semantic and structural errors in children’s memory for sentences

Children with poor reading comprehension in spite of good reading accuracy (poor comprehenders), have unimpaired phonological short-term memory and show normal memory for lists of words. The present paper explores poor comprehenders’ immediate memory for meaningful sentences. Poor comprehenders were worse at sentence repetition than controls and an error analysis revealed a qualitative difference in the nature of errors made by the two groups. The groups made a similar proportion of errors which altered the sentence structure; however, the poor comprehenders’ errors were more likely to alter the meaning of the target sentence than those made by the controls. This finding is discussed in terms of the educational implications of poor memory for meaning-based information in poor comprehenders.
Microjansky Radio Sources in DC 0107–46 (Abell 2877)

The cluster DC 0107-46 (Abell 2877) lies within the Phoenix Deep Survey, made at 1.4 GHz with the Australia Telescope Compact Array. Of 89 known optical cluster members, 70 lie within the radio survey area. Of these 70 galaxies, 15 (21%) are detected, with luminosities as faint as 1.0 × 1020 W Hz-1. Spectroscopic observations are available for 14/15 of the radio-detected cluster galaxies. Six galaxies show only absorption features and are typical low-luminosity active galactic nucleus (AGN) radio sources. One galaxy hosts a Seyfert 2 nucleus, two are star-forming galaxies, and the remaining five may be star-forming galaxies, AGNs, or both.
Fast Kernel Classifiers with Online and Active Learning

Very high dimensional learning systems become theoretically possible when training examples are abundant. The computing cost then becomes the limiting factor. Any efficient learning algorithm should at least take a brief look at each example. But should all examples be given equal attention? This contribution proposes an empirical answer. We first present an online SVM algorithm based on this premise. LASVM yields competitive misclassification rates after a single pass over the training examples, outspeeding state-of-the-art SVM solvers. Then we show how active example selection can yield faster training, higher accuracies, and simpler models, using only a fraction of the training example labels.
Inhibition of diabetic leukostasis and blood-retinal barrier breakdown with a soluble form of a receptor for advanced glycation end products.

PURPOSE The interaction of advanced glycation end products (AGEs) with their receptors is hypothesized to be involved in the development of diabetic retinopathy. In the present study, the role of an AGE receptor, RAGE, was investigated in the development of diabetic retinopathy in vivo. METHODS C57/BJ6 and RAGE-transgenic mice that carried human RAGE genetic DNA under the control of the murine flk-1 promoter were made diabetic with streptozocin. Three months after the onset of diabetes, the soluble form of RAGE (sRAGE) or mouse serum albumin was injected intraperitoneally at 100 mug/d for 14 consecutive days. After the final injection, blood-retinal barrier breakdown, retinal leukostasis, expression of VEGF and ICAM-1, and expression of RAGE in the retina were investigated. RESULTS Blood-retinal barrier breakdown and increased leukostasis were associated with the experimental diabetes in the C57/BJ6 mice. These changes were significantly augmented in RAGE-transgenic mice. The blood-retinal barrier breakdown and leukostasis in the diabetic C57/BJ6 and RAGE-transgenic mice were accompanied by increased expression of VEGF and ICAM-1 in the retina. The systemic administration of sRAGE significantly inhibited blood-retinal barrier breakdown, leukostasis, and expression of ICAM-1 in the retina in both the diabetic C57/BJ6 and RAGE-transgenic mice. The expression of RAGE was slightly increased in the retinal vessels in diabetic or RAGE-transgenic mice. Furthermore, a strong induction of RAGE was observed in the retinal vessels of diabetic RAGE-transgenic mice. CONCLUSIONS This study further demonstrates the role of the AGEs and RAGE axis in blood-retinal barrier breakdown and the retinal leukostasis, which are characteristic clinical symptoms of diabetic retinopathy. Furthermore, these data demonstrate that blocking AGE bioactivity may be effective for the treatment of diabetic retinopathy.
Many Faces of Expertise: Fusiform Face Area in Chess Experts and Novices

The fusiform face area (FFA) is involved in face perception to such an extent that some claim it is a brain module for faces exclusively. The other possibility is that FFA is modulated by experience in individuation in any visual domain, not only faces. Here we test this latter FFA expertise hypothesis using the game of chess as a domain of investigation. We exploited the characteristic of chess, which features multiple objects forming meaningful spatial relations. In three experiments, we show that FFA activity is related to stimulus properties and not to chess skill directly. In all chess and non-chess tasks, experts' FFA was more activated than that of novices' only when they dealt with naturalistic full-board chess positions. When common spatial relationships formed by chess objects in chess positions were randomly disturbed, FFA was again differentially active only in experts, regardless of the actual task. Our experiments show that FFA contributes to the holistic processing of domain-specific multipart stimuli in chess experts. This suggests that FFA may not only mediate human expertise in face recognition but, supporting the expertise hypothesis, may mediate the automatic holistic processing of any highly familiar multipart visual input.
Hierarchical Sparse Spectral Clustering For Image Set Classification

We present a structural matching technique for robust classification based on image sets. In set based classification, a probe set is matched with a number of gallery sets and assigned the label of the most similar set. We represent each image set by a sparse dictionary and compute a similarity matrix by matching all the dictionary atoms of the gallery and probe sets. The similarity matrix comprises the sparse coding coefficients and forms a fully connected directed graph. The nodes of the graph are the dictionary atoms and the edges are the sparse coefficients. The graph is converted to an undirected graph with positive edge weights and spectral clustering is used to cut the graph into two balanced partitions using the normalized cut algorithm. This process is repeated until the graph reduces to critical and non-critical partitions. A critical partition contains atoms with the same gallery label along with one or more probe atoms whereas a noncritical partition either consists of only probe atoms or atoms with multiple gallery labels with no probe atom. Using the critical partitions, we define a novel set based similarity measure and assign the probe set the label of the gallery set with maximum similarity. The proposed algorithm is applied to image set based face recognition using two standard databases. Comparison with existing techniques shows the validity and robustness of our algorithm in the presence of outlier images.
A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies

BACKGROUND Personalized cancer treatments depend on the determination of a patient's genetic status according to known genetic profiles for which targeted treatments exist. Such genetic profiles must be scientifically validated before they is applied to general patient population. Reproducibility of findings that support such genetic profiles is a fundamental challenge in validation studies. The percentage of overlapping genes (POG) criterion and derivative methods produce unstable and misleading results. Furthermore, in a complex disease, comparisons between different tumor subtypes can produce high POG scores that do not capture the consistencies in the functions. RESULTS We focused on the quality rather than the quantity of the overlapping genes. We defined the rank value of each gene according to importance or quality by PageRank on basis of a particular topological structure. Then, we used the p-value of the rank-sum of the overlapping genes (PRSOG) to evaluate the quality of reproducibility. Though the POG scores were low in different studies of the same disease, the PRSOG was statistically significant, which suggests that sets of differentially expressed genes might be highly reproducible. CONCLUSIONS Evaluations of eight datasets from breast cancer, lung cancer and four other disorders indicate that quality-based PRSOG method performs better than a quantity-based method. Our analysis of the components of the sets of overlapping genes supports the utility of the PRSOG method.
Determination of the Charge Collection Efficiency in Neutron Irradiated Silicon Detectors

The charge collected from p-type silicon strip sensors irradiated to SuperLHC fluences has been determined with a beta source using fast front-end electronics. The bias voltage dependence of the collected charge and the hit detection efficiency have been measured before and after accelerated annealing. Predictions of the performance at the SuperLHC are derived.
Will caching at base station improve energy efficiency of downlink transmission?

Caching popular contents at the base station (BS) can reduce the end-to-end delay of service and the cost of cellular networks. Yet it is unknown whether introducing cache to BS can improve the energy efficiency (EE) of downlink systems. With BS caching, energy consumption for backhauling can be reduced, but caches will also consume energy. In this paper, we analyze the EE of two kinds of networks with a macro BS or multiple non-coordinated pico BSs with caches, where the impact of content popularity and request arrival density are considered. Analytical and simulation results show that introducing cache can improve the EE if the file catalog size is not too large and placing the caches at the pico BSs is more energy efficient.
Uncertainties in isoprene photochemistry and emissions: implications for the oxidative capacity of past and present atmospheres and for climate forcing agents

Abstract. Isoprene and its oxidation products are major players in the oxidative chemistry of the troposphere. Current understanding of the factors controlling biogenic isoprene emissions and of the fate of isoprene oxidation products in the atmosphere has been evolving rapidly. We use a climate–biosphere–chemistry modeling framework to evaluate the sensitivity of estimates of the tropospheric oxidative capacity to uncertainties in isoprene emissions and photochemistry. Our work focuses on two climate transitions: from the Last Glacial Maximum (LGM, 19 000–23 000 years BP) to the preindustrial (1770s) and from the preindustrial to the present day (1990s). We find that different oxidants have different sensitivities to the uncertainties tested in this study. Ozone is relatively insensitive, whereas OH is the most sensitive: changes in the global mean OH levels for the LGM-to-preindustrial transition range between −29 and +7 % and those for the preindustrial-to-present-day transition range between −8 and +17 % across our simulations. We find little variability in the implied relative LGM–preindustrial difference in methane emissions with respect to the uncertainties tested in this study. Conversely, estimates of the preindustrial-to-present-day and LGM-to-preindustrial changes in the global burden of secondary organic aerosol (SOA) are highly sensitive. We show that the linear relationship between tropospheric mean OH and tropospheric mean ozone photolysis rates, water vapor, and total emissions of NOx and reactive carbon – first reported in Murray et al. (2014) – does not hold across all periods with the new isoprene photochemistry mechanism. This study demonstrates how inadequacies in our current understanding of isoprene emissions and photochemistry impede our ability to constrain the oxidative capacities of the present and past atmospheres, its controlling factors, and the radiative forcing of some short-lived species such as SOA over time.
Does Institutional Change in Universities Influence High-Tech Entrepreneurship? Evidence from China's Project 985

This paper contributes to institutional theory on cognitive and normative institutional change targeted at altering beliefs, behaviors, and ultimately firm performance. Prior work emphasizes institutional changes where the ideas and beliefs originate from those within the institutional context. Under examined are cases of institutional changes in beliefs and behaviors imposed from outside of the context, which may result in inconsistencies among cognitive, normative, and regulatory institutional pillars. Project 985 was a program implemented by the Chinese government that provided funding for a set of universities to build new research centers. We found that graduates of these universities subsequently expressed greater beliefs in innovation and founded more high-tech ventures, but that entrepreneurs influenced by the reform were not as financially successful as entrepreneurs who founded firms before the reform or from non-985 universities. We explain this surprising finding as caused by the fact that Project 985 was institutionally inconsistent with China’s broader institutional environment. An important implication is that institutional changes may alter beliefs and behavior, but they must be consistent with the broader institutional environment to improve firm performance.