Miracle-dz/UniFAR-FTUs huggingface dataset:
A Genome Wide Association Study of Plasmodium falciparum Susceptibility to 22 Antimalarial Drugs in Kenya

Background Drug resistance remains a chief concern for malaria control. In order to determine the genetic markers of drug resistant parasites, we tested the genome-wide associations (GWA) of sequence-based genotypes from 35 Kenyan P. falciparum parasites with the activities of 22 antimalarial drugs. Methods and Principal Findings Parasites isolated from children with acute febrile malaria were adapted to culture, and sensitivity was determined by in vitro growth in the presence of anti-malarial drugs. Parasites were genotyped using whole genome sequencing techniques. Associations between 6250 single nucleotide polymorphisms (SNPs) and resistance to individual anti-malarial agents were determined, with false discovery rate adjustment for multiple hypothesis testing. We identified expected associations in the pfcrt region with chloroquine (CQ) activity, and other novel loci associated with amodiaquine, quinazoline, and quinine activities. Signals for CQ and primaquine (PQ) overlap in and around pfcrt, and interestingly the phenotypes are inversely related for these two drugs. We catalog the variation in dhfr, dhps, mdr1, nhe, and crt, including novel SNPs, and confirm the presence of a dhfr-164L quadruple mutant in coastal Kenya. Mutations implicated in sulfadoxine-pyrimethamine resistance are at or near fixation in this sample set. Conclusions/Significance Sequence-based GWA studies are powerful tools for phenotypic association tests. Using this approach on falciparum parasites from coastal Kenya we identified known and previously unreported genes associated with phenotypic resistance to anti-malarial drugs, and observe in high-resolution haplotype visualizations a possible signature of an inverse selective relationship between CQ and PQ.
Manipulating Multimedia Materials

This chapter discusses a theoretical framework for designing multimedia in which manipulation, rather than perception, of objects plays the predominant role. The framework is based on research by cognitive psychologists and on Engelkamp’s (1998) multimodal model of action-based learning. Although the assumptions of Engelkamp’s model should be helpful for instructional design, they are not complete enough to include the additional demands of multimedia learning. These additional demands can result in unintended actions, involve sequences of related actions, and require reflection about domain-specific knowledge. Actions can be performed on either physical or virtual manipulatives, but virtual manipu-latives exist in idealized environments, support continuous transformations of objects, and allow for dynamic linking to other objects, symbols, and data displays. The use of manipulatives in the Building Blocks and Animation Tutor projects provide illustrations.
Drift of ocular alignment following strabismus surgery. Part 2: using adjustable sutures

Aim: To measure the drift of ocular alignment following strabismus surgery utilising adjustable sutures. Methods: 106 patients, aged 12 to 84 years, underwent adjustable suture strabismus surgery with a follow-up of 0.5–4 years (mean 24.3 months). Results: For all subjects measured on distant fixation, there was a mean undercorrection drift of 8.3 (SD 2.3) prism dioptres (PD) from week 1 to 48 months postoperatively (p = 0.005). Patients with exotropia demonstrated an undercorrection drift on distant fixation from week 1 to 2 years (mean 10.1 (3.5) PD, p = 0.023). Patients who underwent recession surgery developed a mean 9.1 (3.3) PD undercorrection drift from week 1 to 3 years (p = 0.031). Patients who had unilateral recession and resection surgery showed a mean 6.8 (2.9) PD undercorrection drift from week 1 to 18 months (p = 0.049). Patients with constant or intermittent postoperative stereopsis had a statistically significant undercorrection drift (⩽5.1 PD) at certain postoperative periods (p<0.042), while those without stereopsis had no significant drift. Conclusion: Most patients developed a general drift toward undercorrection, especially following recession or recession with resection surgery and those with exotropia. Surgeons should consider creating a mild overcorrection at the time of suture adjustment, while avoiding long-term diplopia.
Survey the relationship between five factor model and psychopathic personality in a sample of male prisoners in Iran

Most research into psychopathy among prisoners has almost entirely been based in Western countries, and it is unclear whether these research findings are applicable to other settings as well. The main aim of the current study was to survey the relationship between Five Factor Model and psychopathic personality in a sample of male prisoners in Iran. Participants (N = 202) completed the Hare Psychopathic Checklist: screening version (PCL: SV) and NEO Five Factors Inventory (NEO-FFI). The results were analyzed with Pearson correlation coefficient, regression, and t-test for the independent group. Results showed positive and significant correlation between psychopathy with extraversion and also negative and significant correlation between psychopathy with openness, agreeableness and conscientiousness. The comparison of psychopath prisoners with non-psychopath and non-prisoners showed that there were significant differences between groups in conscientiousness, agreeableness, openness; thus psychopath prisoner, in comparison with other groups, was lower in conscientiousness, agreeableness and openness. More research regarding the studied variables can render brighter data.
From Decision Procedures to Synthesis Procedures

Software synthesis is a technique for automatically generating code from a given specification. The goal of software synthesis is to make software development easier while increasing both the productivity of the programmer and the correctness of the produced code. In this paper we present an approach to synthesis that relies on the use of automated reasoning and decision procedures. First we describe how to generalize decision procedures into predictable and complete synthesis procedures.Here completeness means that the procedure is guaranteed to find code that satisfies the given specification. We illustrate the process of turning a decision procedure into a synthesis procedure using linear integer arithmetic as an example.However, writing a complete specification can be a tedious task,sometimes even harder than writing the code itself. To over come this problem, ideally the user could provide a few input-output examples, and then the code should be automatically derived.We outline how to broaden usability and applications of current software synthesis techniques. We conclude with an outlook on possible future research directions and applications of synthesis procedures.
Small-Maturity Asymptotics for the At-The-Money Implied Volatility Slope in Lévy Models

ABSTRACT We consider the at-the-money (ATM) strike derivative of implied volatility as the maturity tends to zero. Our main results quantify the behaviour of the slope for infinite activity exponential Lévy models including a Brownian component. As auxiliary results, we obtain asymptotic expansions of short maturity ATM digital call options, using Mellin transform asymptotics. Finally, we discuss when the ATM slope is consistent with the steepness of the smile wings, as given by Lee’s moment formula.
Observational constraints on pulsar wind theories

Two-dimensional, relativistic, MHD simulations of pulsar-wind powered nebulae provide strong constraints on the properties of the winds themselves. In particular, they confirm that Poynting flux must be converted into particle energy close to or inside the termination shock front, emphasising the puzzle known as the σ paradox. To distinguish between the different possible resolutions of this paradox, additional observational constraints are required. In this paper, I briefly discuss two recents developments in this respect: the modelling of high time-resolution optical polarimetry of the Crab pulsar, and the detection of the pulsar/Be star binary PSR 1259-63 in TeV energy gamma-rays.
Quality of Computationally Inferred Gene Ontology Annotations

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation.
A dynamic attention system that reorients to unexpected motion in real-world traffic environments

In this paper we propose a system architecture that extends the current state-of-the-art in computational visual attention by incorporating the biological concept of ventral attention. According to recent findings regarding the neurobiological foundations of attention, there exist two separate but interacting attention systems in the human brain: the dorsal attention system and the ventral attention system. As opposed to the well-known computational concepts of bottom-up and top-down saliency, which both correspond to the dorsal attention system, the ventral attention system is sensitive to behavior-relevant stimuli that are unexpected (i.e. not top-down salient), independent of their perceptual saliency (bottom-up saliency). This results in a dynamic interplay between top-down saliency, bottom-up saliency and ventral attention in the proposed system architecture, enabling the system to redirect its focus of attention to important stimuli while being absorbed in a task, even if their perceptual saliency is low. Our technical system instance implementing the proposed architecture integrates several state-of-the-art methods in a coherent system and concentrates on unexpected motion as a first technical account of ventral attention. In our experiments, we demonstrate that the ventral attention enables our system to detect and reorient to important situations in real-world traffic environments that are relevant for the behavior of driving.
Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of sRNAs in embryo dormancy maintenance and release in Larix leptolepis, we deciphered the endogenous “sRNAome” in dormant and germinated embryos. High-throughput sequencing of sRNA libraries showed that dormant embryos exhibited a length bias toward 24-nt while germinated embryos showed a bias toward 21-nt lengths. This might be associated with distinct levels of RNA-dependent RNA polymerase2 (RDR2) and/or RDR6, which is regulated by hormones. Proportions of miRNAs to nonredundant and redundant sRNAs were higher in germinated embryos than in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. We identified a total of 160 conserved miRNAs from 38 families, 3 novel miRNAs, and 16 plausible miRNA candidates, of which many were upregulated in germinated embryos relative to dormant embryos. These findings indicate that larches and possibly other gymnosperms have complex mechanisms of gene regulation involving miRNAs and other sRNAs operating transcriptionally and posttranscriptionally during embryo dormancy and germination. We propose that abscisic acid modulates embryo dormancy and germination at least in part through regulation of the expression level of sRNA-biogenesis genes, thus changing the sRNA components.
Landmark Recognition: State-of-the-Art Methods in a Large-Scale Scenario

The recognition of landmarks in images can help to manage large image collections and thus is desirable for many image retrieval ap- plications. A practical system has to be scalable with an increasing num- ber of landmarks. For the domain of landmark recognition we investigate state-of-the-art CBIR methods on an image dataset of 900 landmarks. Our experiments show that the kNN classier outperforms the SVM in a large-scale scenario. The examined visual phrase concept has shown not to be as eective as the classical Bag-of-Words approach although the most landmarks are objects with a relatively xed composition of their (nearby) parts.
Saving for your future self: The role of imaginary experiences

Abstract Despite increased longevity, many people fail to save the funds necessary to support their retirement. In an attempt both to elucidate and remedy this failing, research exploring the “future-self continuity” hypothesis has revealed that temporal discounting is decreased and saving increased when connections between one’s current and future self are strengthened. Here, we explored the possibility that a basic component of mental imagery – spatial visual perspective – may be an important determinant of people’s decisions to spend now or save for the future. The results of two experiments supported this prediction. Rates of saving were enhanced when a distant-future event was generated from a third-person vs. first-person vantage point, an effect that was mediated by visual bodily awareness during mental imagery.
Adiabatic invariants and mixmaster catastrophes

We present a rigorous analysis of the role and uses of the adiabatic invariant in the Mixmaster dynamical system. We propose a new invariant for the global dynamics which in some respects has an improved behaviour over the commonly used one. We illustrate its behaviour in a number of numerical results. We also present a new formulation of the dynamics via Catastrophe Theory. We find that the change from one era to the next corresponds to a fold catastrophe, during the Kasner shifts the potential is an Implicit Function Form whereas, as the anisotropy dissipates, the Mixmaster potential must become a Morse 0--saddle. We compare and contrast our results to many known works on the Mixmaster problem and indicate how extensions could be achieved. Further exploitation of this formulation may lead to a clearer understanding of the global Mixmaster dynamics.
Auditory Artificial Grammar Learning in Macaque and Marmoset Monkeys

Artificial grammars (AG) are designed to emulate aspects of the structure of language, and AG learning (AGL) paradigms can be used to study the extent of nonhuman animals' structure-learning capabilities. However, different AG structures have been used with nonhuman animals and are difficult to compare across studies and species. We developed a simple quantitative parameter space, which we used to summarize previous nonhuman animal AGL results. This was used to highlight an under-studied AG with a forward-branching structure, designed to model certain aspects of the nondeterministic nature of word transitions in natural language and animal song. We tested whether two monkey species could learn aspects of this auditory AG. After habituating the monkeys to the AG, analysis of video recordings showed that common marmosets (New World monkeys) differentiated between well formed, correct testing sequences and those violating the AG structure based primarily on simple learning strategies. By comparison, Rhesus macaques (Old World monkeys) showed evidence for deeper levels of AGL. A novel eye-tracking approach confirmed this result in the macaques and demonstrated evidence for more complex AGL. This study provides evidence for a previously unknown level of AGL complexity in Old World monkeys that seems less evident in New World monkeys, which are more distant evolutionary relatives to humans. The findings allow for the development of both marmosets and macaques as neurobiological model systems to study different aspects of AGL at the neuronal level.
Evolving the Behavior of Autonomous Agents in Strategic Combat Scenarios via SARSA Reinforcement Learning

Computational agents of commercial Real Time Strategic (RTS) games mostly have their behaviors designed via simple ad hoc and static techniques, which require manual definition of actions. Thus, such agents are not able to adapt themselves to diverse situations and their behavior becomes predictable along the game, enabling human players to eventually discover the strategies used by them. This work proposes a modeling approach for the use of SARSA reinforcement learning technique applied to combat situations in RTS games. This technique enables that computational agents evolve their combat behavior according to actions of opponents. The performance of this technique was evaluated using a Starcraft based simulator. The experiments showed that agents were able to improve their behavior, developing knowledge to decide about the best actions during different game states and using this knowledge in an efficient way to obtain better results in later battles.
Hanging off a bar

Exertion Games involve physical effort and as a result can facilitate physical health benefits. We present Hanging off a Bar, an action hero-inspired Exertion Game in which players hang off an exercise bar over a virtual river for as long as possible. Initial observations from three events with audiences ranging from the general public to expert game designers suggest that Hanging off a Bar can be engaging for players and facilitate intense exertion within seconds. Furthermore, we collected suggestions for what game elements players believe could entice them to increase their physical effort investment. These suggestions, combined with Hanging off a Bar as research vehicle due to the easy measurement of exertion through hanging time, enable future explorations into the relationship between digital game elements and physical exertion, guiding designers on how to support exertion in digital games.
Clinical applications of schizophrenia genetics: genetic diagnosis, risk, and counseling in the molecular era

Schizophrenia is a complex neuropsychiatric disease with documented clinical and genetic heterogeneity, and evidence for neurodevelopmental origins. Driven by new genetic technologies and advances in molecular medicine, there has recently been concrete progress in understanding some of the specific genetic causes of this serious psychiatric illness. In particular, several large rare structural variants have been convincingly associated with schizophrenia, in targeted studies over two decades with respect to 22q11.2 microdeletions, and more recently in large-scale, genome-wide case-control studies. These advances promise to help many families afflicted with this disease. In this review, we critically appraise recent developments in the field of schizophrenia genetics through the lens of immediate clinical applicability. Much work remains in translating the recent surge of genetic research discoveries into the clinic. The epidemiology and basic genetic parameters (such as penetrance and expression) of most genomic disorders associated with schizophrenia are not yet well characterized. To date, 22q11.2 deletion syndrome is the only established genetic subtype of schizophrenia of proven clinical relevance. We use this well-established association as a model to chart the pathway for translating emerging genetic discoveries into clinical practice. We also propose new directions for research involving general genetic risk prediction and counseling in schizophrenia.
Polarographic Electrode Measures of Cerebral Tissue Oxygenation: Implications for Functional Brain Imaging

The changes in blood flow, blood volume and oxygenation that accompany focal increases in neural activity are collectively referred to as the hemodynamic response and form the basis of non-invasive neuroimaging techniques such as blood oxygen level dependent (BOLD) functional magnetic resonance imaging. A principle factor influencing blood oxygenation, the cerebral metabolic rate of oxygen consumption is poorly understood and as such, data from imaging techniques are difficult to interpret in terms of the underlying neural activity. In particular how neurometabolic changes vary temporally, spatially and in magnitude remains uncertain. Furthermore knowledge of which aspects of neural activity are closely reflected by metabolic changes is essential for the correct interpretation of cognitive neuroscience studies in terms of information processing. Polarographic electrode measurements of cerebral tissue oxygenation in animal models following presentation of sensory stimuli have started to address these issues. Early studies demonstrated both increases and decreases in tissue oxygenation following neural activation. However a recent series of elegant studies in the cat visual system demonstrated a tight spatial and temporal coupling between evoked peri-synaptic activity and oxygen consumption following presentation of visual stimuli.
Object oriented approach for building extraction from high resolution satellite images

In this paper, an object oriented approach for automatic building extraction from high resolution satellite image is developed. Firstly, Single Feature Classification is applied on the high resolution satellite image. After that, the high resolution image is segmented by using the split and merge segmentation so that the pixels that are grouped as raster objects have probability attributes associated with them. Then different filters are applied on the image to remove the objects which are not of our interest. After filtering the segments, the output raster image is converted into vector image. After converting the raster image into vector image, the building objects are extracted on the basis of area. The cleanup methods are applied to smoothen the extracted buildings and also to increase the accuracy of extraction of buildings. Imagine Objective tool of ERDAS 2011 has been used. The approach is applied on three different satellite images. The extracted buildings are compared with the manually digitized buildings. For one satellite image it has picked up all the buildings with a slight change in the area of footprints of buildings. Only one patch of road is extracted as a building. For the other two satellite images, the overall accuracy is low as compared to the first satellite image. Some patches of road and ground are also extracted as buildings. The branching factor, miss factor, building detection percentage and quality percentage were also calculated for accuracy assessment. Nonetheless, the overall accuracy of building extraction with respect to area was found to be 85.38% in a set of 66 buildings, 73.81% in a set of 94 buildings and 70.64% in a set of 102 buildings.