Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite

Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite—the deadliest of those that cause malaria—is able to develop resistance to antimalarial drugs, thwarting present efforts to control it. Genome-wide association studies (GWAS) provide a critical hypothesis-generating tool for understanding how this occurs. However, in P. falciparum, the limited amount of linkage disequilibrium hinders the power of traditional array-based GWAS. Here, we demonstrate the feasibility and power improvements gained by using whole-genome sequencing for association studies. We analyzed data from 45 Senegalese parasites and identified genetic changes associated with the parasites’ in vitro response to 12 different antimalarials. To further increase statistical power, we adapted a common test for natural selection, XP-EHH (cross-population extended haplotype homozygosity), and used it to identify genomic regions associated with resistance to drugs. Using this sequence-based approach and the combination of association and selection-based tests, we detected several loci associated with drug resistance. These loci included the previously known signals at pfcrt, dhfr, and pfmdr1, as well as many genes not previously implicated in drug-resistance roles, including genes in the ubiquitination pathway. Based on the success of the analysis presented in this study, and on the demonstrated shortcomings of array-based approaches, we argue for a complete transition to sequence-based GWAS for small, low linkage-disequilibrium genomes like that of P. falciparum.
Pulmonary Hypertension Is Associated with Mortality and Cardiovascular Events in Chronic Kidney Disease Patients

Background: We evaluated the prevalence, determinants and prognosis value of pulmonary hypertension (PH) in non-dialysis chronic kidney disease (CKD) patients. Methods: This is a prospective study with stages 3-5 non-dialysis-dependent CKD patients. PH was estimated by Doppler echocardiography and defined as a pulmonary artery systolic pressure above 35 mm Hg. Results: Three hundred fifty-three patients were recruited, of whom 94 (26.6%) had PH. Prevalence of PH increased with the decline of renal function: 21.6, 24.1, and 31.7% in stages 3, 4, and 5, respectively. Independent predictors of PH were age, estimated glomerular filtration rate (eGFR), history of cardiovascular (CV) events, the presence of an arteriovenous fistulae (AVF), and left ventricular (systolic and diastolic) dysfunction. Over a median follow-up of 22 months, 71 patients died (20%). After multivariate adjustment for age, gender, previous CV disease, diastolic and systolic dysfunction, PH remained as an independent predictor of all-cause mortality (hazards ratio [HR] 1.84, 95% CI 1.06-3.18, p = 0.02). One hundred patients (28%) had a new onset CV event. After adjustment for age, gender, previous CV disease, systolic and diastolic dysfunction, PH maintains its independent association with CV events (HR 2.77, 95% CI 2.00-3.25, p < 0.001). Conclusions: PH prevalence rises as kidney function declines. Main determinants of PH are age, eGFR, previous CV disease, the presence of an AVF and left ventricular systolic or diastolic dysfunction. PH is an independent predictor of all-cause mortality and CV events.
Dynamic Friction Models for Longitudinal Road / Tire Interaction : Experimental Results

A new dynamic friction force model for the longitudinal road/tire interaction for wheeled ground vehicles is validated via experiments with an actual passenger vehicle. Contrary to common static friction/slip maps, this new dynamic friction model is able to accurately capture the transient behavior of the friction force observed during transitions between braking and acceleration. A velocitydependent, steady-state expression of the friction force vs. the slip coefficient also allows easy tuning of the model parameters by comparison with steady-state experimental data. Our experimental results validate the accuracy of this new tire friction model in predicting the friction force during transient vehicle motion.
ep 2 00 2 Integrable Flows in c = 1 String Theory

In these notes we review the method to construct integrable deformations of the compactified c = 1 bosonic string theory by primary fields (momentum or winding modes), developed recently in collaboration with S. Alexandrov and V. Kazakov. The method is based on the formulation of the string theory as a matrix model. The flows generated by either momentum or winding modes (but not both) are integrable and satisfy the Toda lattice hierarchy*.
Network Games with Perfect Complements

The model presented here examines the case of games played on networks where an agent’s decision to undertake some costly investment is perfectly complementary with the decisions of his neighbors. Equilibrium actions of individual agents are found to depend on a measure of their network centrality known as their coreness. High levels of investment depend on the existence of densely connected subgroups within the network known in the sociology literature as k-cores. Peripheral nodes who inhabit sparsely connected areas of the network will be unable to support high levels of investment, even if they themselves have low costs and high degrees. Supplementary results which describe the structure of optimal networks and the relationship between coreness and Bonacich centrality are also presented. Potential applications of this framework include models of human capital investment within firms, costly information transmission, user engagement in social networking products, and bandwidth allocation decisions in large autonomous networks. ∗Department of Economics, University of Warwick, Coventry, United Kingdom. Contact: a.harkins@warwick.ac. uk
Enhanced Pitch Sensitivity in Individuals with Autism: A Signal Detection Analysis

Past research has shown a superiority of participants with high-functioning autism over comparison groups in memorizing picture-pitch associations and in detecting pitch changes in melodies. A subset of individuals with autism, known as musical savants, is also known to possess absolute pitch. This superiority might be due to an abnormally high sensitivity to fine-grained pitch differences in sounds. To test this hypothesis, psychoacoustic tasks were devised so as to use a signal detection methodology. Participants were all musically untrained and were divided into a group of 12 high-functioning individuals with autism and a group of 12 normally developing individuals. Their task was to judge the pitch of pure tones in a same-different discrimination task and in a high-low categorization task. In both tasks, the obtained psychometric functions revealed higher pitch sensitivity for subjects with autism, with a more pronounced advantage over control participants in the categorization task. These findings confirm that pitch processing is enhanced in high-functioning autism. Superior performance in pitch discrimination and categorization extends previous findings of enhanced visual performance to the auditory domain. Thus, and as predicted by the enhanced perceptual functioning model for peaks of ability in autism (Mottron & Burack, 2001), autistic individuals outperform typically developing population in a variety of low-level perceptual tasks.
Outcomes of Electrical Burns at Chris Hani Baragwanath Burn Centre in South Africa

Background: The significant morbidity of electrical burn injuries is well described in the medical literature, especially in the form of major limb amputations. Reported mortality rates are generally described as low, especially in the more recent analyses Patients presenting factors, mortality characteristics and morbidity factors (length of stay in hospital and in ICU, procedures performed, organ support factors). These were recorded in an Excel spreadsheet and statistical analysis was done. Aims: The study aims was to determine the epidemiology, the morbidity and the mortality of electrical burns in a local South African setting. Method: A retrospective record review was conducted of electrical burn cases at Chris Hani Baragwanath Hospital Adult Burns Unit in the last 15 years, from January 1995 to April 2010. Results: There were 101 patients with electrical burns in the period studied, comprising 7% of total burns admissions. 91% were males. The mean age was 30, 0 and the mean length of stay was 31, 0 days. Mechanism was divided as follows: 37% suspected or documented cable theft, 4% lightning, 10% domestic or informal occupational accidents, and the remainder unspecified. Mean body surface area burn was 19, 9%. 13 patients died during their hospital admission (12, 9%). 19 patients required ICU (29, 7%) and stayed between 2 to 31 days there. Major amputation rate was 16, 9%. 8 fasciotomies, 71 sloughectomies/debridements and 38 skin grafts were performed. Conclusion: A very large proportion of electrical burns in South Africa are probably due to cable-theft related injuries. Mortality from electrical injuries is significantly higher than international data and morbidity remains significant. This may be due to constraints in ICU resources. This may also be due to severity of injuries. Prevention strategies should be refined and implemented to reduce the burden of disease.
Harmonic maps into conic surfaces with cone angles less than $2\pi$

We prove the existence and uniqueness of harmonic maps in degree one homotopy classes of closed, orientable surfaces of positive genus, when the target has conic points with cone angles less than $2\pi$. For a cone point $p$ of cone angle less than or equal $\pi$ we show that one can minimize, uniquely, in the relative homotopy class of a homeomorphism sending a fixed point $q$ in the domain to $p$. The latter can be interpreted as minimizing maps from punctured Riemann surfaces.
A shift from offline to online: Adolescence, the internet and social participation

ABSTRACT Adolescents’ social participation is increasingly taking place in virtual settings, including social media, but there is no longer a distinct boundary between online and offline social participation. Furthermore, online social participation is becoming a societal concern, with internet use identified as impacting social and emotional well-being. This qualitative descriptive study explored the occupational nature of online social participation amongst Irish adolescents aged 9-16 years old. Data were collected through three focus groups. Four themes that captured the nature of the Internet as a setting for social participation were identified: a) building relationships and connections, b) identity experimentation and construction, c) cyber culture and virtual norms, and d) overuse and unsociable behaviour. The study provides insights into how adolescents experience and organise their social occupations in online settings and how these unfold into offline ‘reality’. While online social participation expands social experiences and connections, face-to-face experiences were more valued. There is an imperative to research online-offline social participation to develop a broader understanding of this evolving, contemporary occupation.
Sample Preservation, DNA or RNA Extraction and Data Analysis for High-Throughput Phytoplankton Community Sequencing

Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affected the results of the NGS analysis. A mock community was pooled from phytoplankton species with variation in nucleus size and cell wall hardness. Although the study showed potential for studying Lugol-preserved sample collections, it demonstrated critical challenges in the DNA-based phytoplankton analysis in overall. The 18S rRNA gene sequencing output was highly affected by the variation in the rRNA gene copy numbers per cell, while sample preservation and nucleic acid extraction methods formed another source of variation. At the top, sequence-specific variation in the data quality introduced unexpected bioinformatics bias when the sliding-window method was used for the quality trimming of the Ion Torrent data. While DNA-based analyses did not correlate with biomasses or cell numbers of the mock community, rRNA-based analyses were less affected by different RNA extraction procedures and had better match with the biomasses, dry weight and carbon contents, and are therefore recommended for quantitative phytoplankton analyses.
8 Language and Aging

Language in old age has been an active research area since early experimental investigations in cognitive aging (e.g., Craik & Masani, 1967; Riegel & Riegel, 1964). This is undoubtedly because of the profound importance of language throughout the lifespan not only in cognition, but in social interactions as well. Declines in language processing, such as increased difficulty in understanding spoken language or in producing a word while speaking, undermine older adults’ ability and desire to communicate, and can erode evaluation of their language competence by themselves and by others (e.g., Hummert, Garstka, Ryan, & Bonnesen, 2004; Ryan, See, Meneer, & Trovato, 1994). Negative self-appraisal promotes withdrawal from social interaction, and negative appraisal by others promotes their use of oversimplified speech to older adults (Hummert et al., 2004; Kemper, Finter-Urczyk, Ferrell, Harden, & Billington, 1998). This downward cycle highlights the practical significance of identifying patterns of change in language during adulthood and old age, especially since there is good news about aging in this research. The aging pattern is characterized by stability and improvement during adulthood in some language functions, unlike other cognitive abilities such as episodic or working memory which are characterized by quite uniform age-related decrements. Research on language processing has also played an important role in the development of theory in cognitive aging (e.g., Baltes, Staudinger, & Lindenberger, 1999; Burke, Mackay, & James, 2000; DeDe, Caplan, Kemptes, & Waters, 2004; Hasher, Lustig, & Zacks, in press; Kemper, 2006;
Creative Destruction and Firm-Specific Performance

We investigate underlying factors that explain increases in the heterogeneity of firmspecific stock returns and fundamentals. Heterogeneity is significantly higher in traditional manufacturing and non-manufacturing industries that are more information technology (IT) intensive in our sample period. We hypothesise that IT is associated with creative destruction, which widens the performance difference between winner and loser firms. Our results suggest recent findings of rising firm-specific variation in U.S. stocks may partially reflect an accelerating pace of creative destruction; and of greater firmspecific variation in richer and faster growing countries may, in part, be due to more intensive creative destruction in those economies. They thus support the approach to endogenous growth theory in Aghion and Howitt (1992, 1998), Aghion et al. (2004, 2005), and Acemoglu et al. (1997, 2003, 2005).
The Effect of Sensorimotor Replacement on Smoking Cessation and Craving

Current treatments for smoking cessation such as nicotine replacement therapy or varenicline address the primary reinforcer of smoking (nicotine), but sensorimotor stimuli (e.g. smell/taste of smoke, inhaling/exhaling, airway sensations, holding the cigarette) may act as secondary reinforcers and also contribute to smoking reward. Addressing both these aspects of smoking may help to enhance smoking cessation treatment. The aim of this review was to examine whether sensorimotor replacement can help to alleviate craving and aid smoking cessation. Three sensorimotor replacement products were examined: non-nicotine inhalators/aerosols, de-nicotinised cigarettes and electronic cigarettes. The current research suggests that sensorimotor replacement may enhance the efficacy of nicotine replacement therapy, but is unlikely to be useful if used alone. Electronic cigarettes may be the most promising approach, due to the combination of nicotine delivery and sensorimotor input.
Older women’s experiences, identities and coping strategies for dealing with a problem-drinking male family member*

Abstract Aims: In this study, we highlight the identities and actions of women with a problem-drinking relative by analysing autobiographies of women born between the 1920s and the 1950s. We ask how women describe their relationship and the problems arising because of a significant other’s drinking and how they cope with these problems. Methods: In the analysis, we pay attention to the power dynamics between family members. We, first, trace what kind of positions or identities the protagonists take in relation to the drinker. Second, we examine what kinds of harms and emotional reactions significant other’s drinking causes. Third, we consider how writers identify or take distance from events described in the autobiographies. Findings: Our analysis reveals four main identities and coping strategies: the positions of victim, helper, boundary setter and fighter. The victim and helper positions often entail women’s weakness and oppressed role, while the positions of boundary setter and fighter express women’s own power and reflexivity in action. Conclusions: Knowledge of the identities and coping strategies is important for understanding the power aspects of a relationship and developing appropriate support for women suffering from family member’s drinking.
Ambigüedad de rol, satisfacción laboral y ciudadanía organizacional en el sector público: un estudio de mediación multinivel

This study aimed to examine the mediating effect of job satisfaction in the relationship between role ambiguity and organizational citizenship behavior (OCB) according to the “HEalthy and Resilient Organization” model in two local corporations. A multilevel analysis of mediation was employed to examine the relationship between these variables, controlling for the effect of employee division. The sample consisted of a total of 340 employees. The results indicate that job satisfaction exhibits a total mediation in the relationship between role ambiguity and OCB of public employees. These results indicate the importance of employees’ well-being to decrease negative effects of role ambiguity in public employees’ performance.
Differentiating Intimate Partner Homicide From Other Homicide: A Swedish Population-Based Study of Perpetrator, Victim, and Incident Characteristics

Objective: Intimate partner homicides (IPHs) continue to be widespread and constant over time when compared with other types of homicide. Yet research addressing IPH particularly within the European context, is limited. The question of whether perpetrators of partner-related violence differ from offenders of general violence has been raised in research. In light of inconsistent findings and ongoing debate, the aim was to identify sociodemographic and criminological characteristics in perpetrators and victims of IPH, and to determine whether they differ from other types of homicides in Sweden. Method: This retrospective study was based on national data of all male-perpetrated homicides (N = 211) in Sweden committed between 2007 and 2009. Characteristics of IPH (n = 46) and non-IPH (n = 165) were compared and analyzed by conducting bivariate and multiple logistic regressions. Results: Perpetrators of IPH were older, more likely to be employed, less likely to have been convicted, and had less persistent criminal histories. Perpetrators of IPH were also less likely to be intoxicated at the time of the offense; nonetheless, intoxication was a common feature among victims and perpetrators in both groups. Further, perpetrators of partner-related homicides are substantially more likely to commit suicide. Conclusion: The present study illustrates critical differences between IPH and non-IPH perpetrators. As hypothesized, IPH perpetrators were less socially disadvantaged, less likely to have past criminal offenses, and more likely to commit suicide following the homicidal act. This study demonstrates that perpetrators of IPH constitute a separate subtype and, conceptually, ought to be treated separately.
Effects of Image Charges on the Scavenging of Aerosol Particles by Cloud Droplets and on Droplet Charging and Possible Ice Nucleation Processes

Abstract Previous calculations of the rate at which falling droplets in clouds collide with aerosols have led to the conclusion that except in thunderclouds any electrical charges on the aerosols or droplets have little effect on the collision rate. However, it had been assumed that the aerosols would have only a few elementary charges on them, whereas it is now known that at the tops of nonthunderstorm clouds the evaporating droplets may have several hundred elementary charges on them and that much of this charge remains on the residual aerosol for 5 min or so after the evaporation. Also, most previous calculations neglected image charge forces that provide strong attraction at close range even when droplet and aerosol have charges of the same sign and of comparable magnitude. The authors present numerical calculations showing that electrical effects dominate collision rates for charged evaporation aerosols. The calculations are for the size range of 0.1- to 1.0-μm radius with the collision efficiency co.
Product Diversity and Spectrum of Choice in Hospital ePrescribing Systems in England

Background ePrescribing systems have considerable potential for improving healthcare quality and safety. With growing expectations about the benefits of such systems, there is evidence of widespread plans to implement these systems in hospitals in England where hitherto they have had a low uptake. Given the international drive away from developing home-grown to systems to procuring commercial applications, we aimed to identify available ePrescribing systems in England and to use the findings to develop a taxonomy of the systems offered by suppliers. Methods and Findings We undertook a scoping review of the published and grey literature, and conducted expert interviews with vendors, healthcare organisations and national ePrescribing experts in order to identify the spectrum of available systems, identify and map their key features, and then iteratively develop and validate a taxonomy of commercial ePrescribing systems available to English hospitals. There is a wide range of available systems including 13 hospital-wide applications and a range of specialty systems. These commercial applications can be grouped into four sub-categories: standalone systems, modules within integrated systems, functionalities spread over several modules, and specialty systems. The findings also reveal that apart from four packaged applications (two of which are specialty systems), all other systems have none or less than two live implementations across England. Conclusions The wide range of products developed in the last few years by different national and international suppliers, and the low uptake of these products by English hospitals indicate that the English ePrescribing market is still in its infancy. This market is undergoing rapid cycles of change, both with respect to the number of suppliers and their diversity of offerings. Constant renewal of knowledge is needed on the status of this evolving market, encompassing the products development and adoption, to assist implementation decisions and facilitate market maturity.