Miracle-dz/UniFAR-FTUs huggingface dataset:
Allele Frequency–Based and Polymorphism-Versus-Divergence Indices of Balancing Selection in a New Filtered Set of Polymorphic Genes in Plasmodium falciparum

Signatures of balancing selection operating on specific gene loci in endemic pathogens can identify candidate targets of naturally acquired immunity. In malaria parasites, several leading vaccine candidates convincingly show such signatures when subjected to several tests of neutrality, but the discovery of new targets affected by selection to a similar extent has been slow. A small minority of all genes are under such selection, as indicated by a recent study of 26 Plasmodium falciparum merozoite-stage genes that were not previously prioritized as vaccine candidates, of which only one (locus PF10_0348) showed a strong signature. Therefore, to focus discovery efforts on genes that are polymorphic, we scanned all available shotgun genome sequence data from laboratory lines of P. falciparum and chose six loci with more than five single nucleotide polymorphisms per kilobase (including PF10_0348) for in-depth frequency–based analyses in a Kenyan population (allele sample sizes >50 for each locus) and comparison of Hudson–Kreitman–Aguade (HKA) ratios of population diversity (π) to interspecific divergence (K) from the chimpanzee parasite Plasmodium reichenowi. Three of these (the msp3/6-like genes PF10_0348 and PF10_0355 and the surf4.1 gene PFD1160w) showed exceptionally high positive values of Tajima's D and Fu and Li's F indices and have the highest HKA ratios, indicating that they are under balancing selection and should be prioritized for studies of their protein products as candidate targets of immunity. Combined with earlier results, there is now strong evidence that high HKA ratio (as well as the frequency-independent ratio of Watterson's θ/K) is predictive of high values of Tajima's D. Thus, the former offers value for use in genome-wide screening when numbers of genome sequences within a species are low or in combination with Tajima's D as a 2D test on large population genomic samples.
Guidance of young children

I. DEVELOPMENTALLY APPROPRIATE CHILD GUIDANCE: ESSENTIAL ELEMENTS. 1. Understanding Child Development: The Foundation for Developmentally Appropriate Child Guidance. 2. Guiding with Positive Discipline and an Authoritative Caregiving Style. 3. Positive Discipline Strategies: Direct Guidance. 4. Developmentally Appropriate Practices (DAP) and Early Childhood Classroom Management. II. SPECIAL TOPICS IN CHILD GUIDANCE. 5. Guiding Children in Times of Stress. 6. Guiding Children Toward a Healthy Sense of Self and Self-Esteem. 7. Guiding Young Children's Understanding and Management of Anger. 8. Understanding and Guiding Aggressive Children. 9. Prosocial Behavior: Guiding Its Development. III. DEVELOPING An "ECLECTIC" APPROACH TO CHILD GUIDANCE. 10. Child-Guidance Theories and Their Strategies. 11. The Decision-Making Model of Child Guidance: An "Eclectic" Approach. Appendix: Review of Major Positive Discipline Strategies. Name Index. Subject Index.
Does Woman + a Network = Career Progression?

Question: I am an ambitious and talented junior manager who has recently been hired by FAB plc, a large multinational company. I am also a woman and, as part of my induction pack, have received an invitation to join FABFemmes — the in-company women's network. I don't think my gender has been an obstacle to my success thus far and so I don't really feel the need to join. But on the other hand I don't want to turn my back on something that might offer me a useful source of contacts to help me advance up the career ladder. What would be the best thing to do? — Ms Ambitious, UK
Can We Do Better?

Clinicians have at their disposal a variety of instruments with which to evaluate the risk presented by sex offenders. These measures yield similar predictive potency, and combining them does not appear to enhance prediction. The present study examined whether classification and regression tree analysis could identify new combinations of predictors that would improve predictive validity. Items from seven actuarial instruments were used to construct classification trees. Overall, classification trees achieved slightly higher predictive accuracy than did actuarial instruments. In addition, these analyses highlight the heterogeneity among sex offenders. Despite this improvement, one should consider the incorporation of other predictors into the instruments—including dynamic factors, protective factors, and measures with strong theoretical justification.
The impact of secondary tasks on drivers during naturalistic driving: Analysis of EEG dynamics

Driver distraction is a significant cause of accidents leading to injuries and fatalities on the roadway. Driving is a complex task and demands continuous visual and cognitive attention on the primary task of driving. Drivers are at risk of responding more slowly or less suitable to intricate and dynamically changing situations that entail their complete attention. Therefore, monitoring and detection of driver distraction can directly facilitate decreasing the costs associated with roadway disasters. There has been much research effort toward developing automatic detectors of drivers' distraction state. Many approaches were based on analyzing the driving behavior or using camera-based techniques to monitor and evaluate driver distraction. However, besides the issues with privacy and consumer adoption, there are limitations with how early they can detect the signs of distraction. Neurophysiological signals such as Electroencephalogram (EEG) and brain activity analysis have been extensively used to understand the precursors of distraction at the physiological level to develop systems to alert the drivers well in advance. The objective of this study is to take a step toward establishing a systematic framework to extract effective descriptors and to measure the impact of in-vehicle secondary tasks on driver cognitive state during naturalistic driving by capturing the changes in EEG dynamics. We employed our wearable data acquisition platform to collect wireless EEG data from six subjects during a naturalistic driving session and investigated six potentially distracting stimuli. We present a standard analysis framework to examine the impact of various EEG signal pre-processing, feature extraction, and classification methods in order to detect driver engagement in a secondary task with high accuracy (98.99 ± 1.2%) solely based on their recorded EEG.
Cortical Specialization for Higher Cognitive Functions: Beyond the Maturational Model

Most research in adult neuropsychology is concerned with attributing cognitive functions to particular regions of the cerebral neocortex. Few, however, consider the more fundamental question of how this structural and functional specialization develops within the neocortex. Part of the reason for the neglect of this question is the assumption that the regional functional specification of neocortex is a maturational process under tight genetic control. Closer inspection of the available evidence from developmental neurobiology, however, suggests that, at least for higher cognitive functions in humans, this assumption is incorrect (see Johnson, 1997, for review). Thus, there is a need to understand the mechanisms underlying cortical specialization during preand postnatal life in human infants and children. Explaining this process is not only important for basic science but offers the opportunity of fresh perspectives on developmental disorders and educational strategies. During the last quarter of the century, there has been an increasing effort to relate postnatal brain development in human infants and children to changes in cognitive and perceptual capacities. However, much of the work has been based on a general maturational framework, in which it is assumed that as particular cortical regions mature they allow or enable new cognitive functions. A related assumption has been that there is a progression of maturation from posterior to anterior regions, with the visual cortex being functional from shortly after birth and the frontal lobes being the last parts of cortex to become functional. This posterior to anterior assumption is largely based on evidence from neuroanatomical studies (see Johnson, 1997, for review), but it is assumed to have direct functional consequences. The general maturational framework underlies many of our current models
Proteome analysis of a Lactococcus lactis strain overexpressing gapA suggests that the gene product is an auxiliary glyceraldehyde 3‐phosphate dehydrogenase

The sequence of the genome from the Lactococcus lactis subspecies lactis strain IL1403 shows the presence of two reading frames, gapA and gapB, putatively encoding glyceraldehyde 3‐phosphate dehydrogenase (GAPDH). Previous proteomic analysis of the L. lactis subspecies cremoris strain MG1363 has revealed two neighbouring protein spots, GapBI and GapBII, with amino terminal sequences identical to the product of gapA from the L. lactis subspecies cremoris strain LM0230 and that of the two IL1403 sequences. In order to assign the two protein spots to their respective genes we constructed an L. lactis strain that overexpessed the gapA gene derived from MG1363 upon nisin induction. Compared to the wild‐type, the overexpressing strain had a 3.4‐fold elevated level of specific GAPDH activity when grown in the presence of nisin. In both MG1363 and the gapA overexpressing strain the GAPDH activity was specific for NAD. No NADP dependent activity was detected. Proteome analysis of the gapA overexpressing strain revealed two new protein spots, GapAI and GapAII, not previously detected in proteome analysis of MG1363. Results from mass spectrometry analysis of GapA and GapB and comparison with the deduced protein sequences for the GAPDH isozymes from the genome sequence of strain IL1403 allowed us to assign GapA and GapB to their apparent IL1403 homologues encoded by gapA and gapB, respectively. Furthermore, we suggest that a homologue of a gapB product, represented by GapB, is the main source of GAPDH activity in L. lactis during normal growth.
Pedagogical distance: explaining misalignment in student-driven online learning activities using Activity Theory

This paper provides an Activity Theory analysis of two online student-driven interactive learning activities to interrogate assumptions that such groups can effectively learn in the absence of the teacher. Such an analysis conceptualises learning tasks as constructed objects that drive pedagogical activity. The analysis shows a disconnect between the codified curriculum plan and its actual enactment, and a misalignment of interpretations of the object by different participants in the activity. We name this ‘pedagogical distance’. We argue that a teaching presence is important to guide both student and tutor interpretations of the learning task, and offer suggestions for decreasing pedagogical distance.
Financial Integration, Financial Development, and Global Imbalances

Global financial imbalances can result from financial integration when countries differ in financial markets development. Countries with more advanced financial markets accumulate foreign liabilities in a gradual, long‐lasting process. Differences in financial development also affect the composition of foreign portfolios: countries with negative net foreign asset positions maintain positive net holdings of nondiversifiable equity and foreign direct investment. Three observations motivate our analysis: (1) financial development varies widely even among industrial countries, with the United States on top; (2) the secular decline in the U.S. net foreign asset position started in the early 1980s, together with a gradual process of international financial integration; (3) the portfolio composition of U.S. net foreign assets features increased holdings of risky assets and a large increase in debt.
Host country nationals as socializing agents: a social identity approach

A major challenge facing Multinational Enterprises (MNEs) is finding ways to increase the success rates of managers assigned overseas. Our paper draws upon social identity theory to develop a model that focuses on the role of host country nationals (HCNs) in determining the adjustment of expatriate managers. Specifically, our model proposes attributes of the expatriate and the HCN that can increase the salience of national identity and outgroup categorization of expatriates by the HCNs. We also suggest how outgroup categorization interacts with a number of situational factors to influence the role of HCNs as socializing agents for expatriate newcomers. Finally, we propose that the socializing behaviors HCNs may display or withhold from the expatriate will affect the adjustment of the expatriate. Our model highlights the often-overlooked partners in the expatriate adjustment process and emphasizes the need for MNEs to be cognizant of the social dynamics between HCNs and expatriates in the host location. Copyright © 2007 John Wiley & Sons, Ltd.
Rapidly Progressive Aphasic Dementia with Motor Neuron Disease: A Distinctive Clinical Entity

The association of motor neuron disease (MND) with rapidly progressive aphasic dementia has been recognized as a distinct clinical syndrome within the group of frontotemporal dementias (FTDs). Although the clinical and neuropsychological features of this syndrome have been defined, a small number of post-mortem studies have been published with heterogeneous neuropathological findings. We performed cognitive, neuro-imaging and neuropathological studies on a 71-year-old male with rapidly progressive aphasic dementia and MND. We initially found a selective non-fluent aphasia associated with hypoperfusion of the left frontotemporal cortex. Proton magnetic resonance spectroscopy revealed an asymmetric change of brain metabolites, with greater changes in the left temporal lobe. The bulbar manifestations of MND occurred over the following 6 months, and the patient died of bronchopneumonia. The neuropathological examination revealed loss of neurons in the hypoglossal nucleus and anterior horns of the cervical spinal cord with microvacuolation and dot-like ubiquitin-positive deposits in the frontoparietotemporal cortex, but no changes suggestive of Alzheimer’s, Pick’s or Lewy body disease. These findings support the conclusion that MND with rapidly progressive aphasic dementia is a distinctive clinical entity within the group of FTD-MND.
No Association between 5-HTTLPR and Harm Avoidance in Korean College Students

There have been numerous studies on the association between 5-HTTLPR (polymorphisms in the promoter region of the serotonin transporter gene) and anxiety-related personality traits, with conflicting results. In this study, we administered Korean version of the Temperament and Character Inventory (K-TCI) to a sample of 158 Korean college students and genotyped for the 5-HTTLPR in order to compare the TCI dimensional scores including harm avoidance according to the 5-HTTLPR genotype and sex. We could not find the association between 5-HTTLPR and harm avoidance and other TCI measures. Considering known allele frequencies differences of 5-HTTLPR among different ethnic groups, further cross-cultural studies with a larger sample would be needed.
On reproducibility and traceability of simulations

Reproducibility of experiments is the pillar of a rigorous scientific approach. However, simulation-based experiments often fail to meet this fundamental requirement. In this paper, we first revisit the definition of reproducibility in the context of simulation. Then, we give a comprehensive review of issues that make this highly desirable feature so difficult to obtain. Given that experimental (in-silico) science is only one of the many applications of simulation, our analysis also explores the needs and benefits of providing the simulation reproducibility property for other kinds of applications. Coming back to scientific applications, we give a few examples of solutions proposed for solving the above issues. Finally, going one step beyond reproducibility, we also discuss in our conclusion the notion of traceability and its potential use in order to improve the simulation methodology.
Edinburgh Research Explorer Development of a high density 600K SNP genotyping array for chicken

, , Abstract Background: High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species. Results: We report here the development of a 600 K Affymetrix W Axiom W HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10 – 15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome ( Gallus_gallus_4.0 ) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium ( P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses. Conclusions: This Affymetrix W Axiom W array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.
Optimal Energy Balanced Data Gathering in Wireless Sensor Networks

Unbalanced energy consumption is an inherent problem in wireless sensor networks where some nodes may be overused and die out early, resulting in a short network lifetime. In this paper, we investigate the problem of balancing energy consumption for data gathering sensor networks. Our key idea is to exploit the tradeoff between hop-by-hop transmission and direct transmission to balance energy dissipation among sensor nodes. By assigning each node a transmission probability which controls the ratio between hop-by-hop transmission and direct transmission, we formulate the energy consumption balancing problem as an optimal transmission probability allocation problem. We discuss this problem for both chain networks and general networks. Moreover, we present the solution to compute the optimal number of sections in terms of maximizing the network lifetime. Numerical results demonstrate that our methods outperform the traditional hop-by-hop and direct transmission schemes and achieve significant lifetime extension especially for dense sensor networks.
A central dip in the macular pigment spatial profile is associated with age and smoking.

PURPOSE To investigate the relationship between specific macular pigment (MP) spatial profiles and risk factors for age-related macular degeneration (AMD). METHODS The MP spatial profile of 484 healthy subjects was measured with customized heterochromatic flicker photometry (cHFP) and categorized into one of two profile types: typical exponential or atypical "central dip. " Data on risk factors for AMD were obtained with a general health and lifestyle questionnaire. Dietary and serum concentrations of lutein (L) and zeaxanthin (Z) were also assessed. RESULTS The presence of the central dip MP spatial profile was significantly more common in older subjects (the mean ± SD age of subjects with a central dip MP spatial profile was 46.9 ± 12 years, whereas the mean age of subjects with a typical MP spatial profile was 41.8 ± 12 years; P = 0.004) and in current cigarette smokers (P = 0.031). Also, there was a significant age-related decline in central MP optical density (MPOD; 0.25° retinal eccentricity), but in the men only (r = -0.146, P = 0.049). CONCLUSIONS A central dip in the MP spatial profile, seen in older subjects and in cigarette smokers, may represent an undesirable feature of macular pigmentation. Further research is needed in this area.
Dual mechanism for presynaptic modulation by axonal metabotropic glutamate receptor at the mouse mossy fibre‐CA3 synapse

1 To investigate mechanisms responsible for the presynaptic inhibitory action mediated by the axonal group II metabotropic glutamate receptor (mGluR) at the mossy fibre‐CA3 synapse, we used a quantitative fluorescence measurement of presynaptic Ca2+ in mouse hippocampal slices. 2 Bath application of the group II mGluR‐specific agonist (2S,1′R,2′R,3′R)‐2‐(2,3‐dicarboxycyclopropyl)glycine (DCG‐IV, 1 μM) reversibly suppressed the presynaptic Ca2+ influx (to 55·2 ± 4·6 % of control, n= 5) as well as field EPSPs recorded simultaneously (to 3·1 ± 2·0 %). Presynaptic fibre volley was not affected by 1 μM DCG‐IV. 3 A quantitative analysis of the inhibition of presynaptic Ca2+ influx and field EPSP suggested that DCG‐IV suppressed the field EPSP to a greater extent than would be expected if the suppression were solely due to a decrease in the presynaptic Ca2+ influx. 4 DCG‐IV at 1 μM suppressed the mean frequency (to 73·8 ± 3·9 % of control, n= 11), but not the mean amplitude (to 97·0 ± 3·5 %), of miniature EPSCs recorded from CA3 neurones using the whole‐cell patch‐clamp technique. 5 These results suggest that group II mGluR‐mediated suppression is due both to a reduction of presynaptic Ca2+ influx and downregulation of the subsequent exocytotic machinery.