Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Neurovirulence of African and Asian Genotype Zika Virus Isolates in Outbred Immunocompetent Mice

Abstract. Although first isolated almost 70 years ago, Zika virus (ZIKV; Flavivirus, Flaviviridae) has only recently been associated with significant outbreaks of disease in humans. Several severe ZIKV disease manifestations have also been recently documented, including fetal malformations, such as microcephaly, and Guillain–Barré syndrome in adults. Although principally transmitted by mosquitoes, sexual transmission of ZIKV has been documented. Recent publications of several interferon receptor knockout mouse models have demonstrated ZIKV-induced disease. Herein, outbred immunocompetent CD-1/ICR adult mice were assessed for susceptibility to disease by intracranial (i.c.) and intraperitoneal (i.p.) inoculation with the Ugandan prototype strain (MR766; African genotype), a low-passage Senegalese strain (DakAr41524; African genotype) and a recent ZIKV strain isolated from a traveler infected in Puerto Rico (PRVABC59; Asian genotype). Morbidity was not observed in mice inoculated by the i.p. route with either MR766 or PRVABC59 for doses up to 6 log10 PFU. In contrast, CD-1/ICR mice inoculated i.c. with the MR766 ZIKV strain exhibited an 80–100% mortality rate that was age independent. The DakAr41524 strain delivered by the i.c route caused 30% mortality, and the Puerto Rican ZIKV strain failed to elicit mortality but did induce a serum neutralizing immune response in 60% of mice. These data provide a potential animal model for assessing neurovirulence determinants of different ZIKV strains as well as a potential immunocompetent challenge model for assessing protective efficacy of vaccine candidates.
Hyperparameter Optimization for Effort Estimation

Software analytics has been widely used in software engineering for many tasks such as generating effort estimates for software projects. One of the "black arts" of software analytics is tuning the parameters controlling a data mining algorithm. Such hyperparameter optimization has been widely studied in other software analytics domains (e.g. defect prediction and text mining) but, so far, has not been extensively explored for effort estimation. Accordingly, this paper seeks simple, automatic, effective and fast methods for finding good tunings for automatic software effort estimation. We introduce a hyperparameter optimization architecture called OIL (Optimized Inductive Learning). We test OIL on a wide range of hyperparameter optimizers using data from 945 software projects. After tuning, large improvements in effort estimation accuracy were observed (measured in terms of standardized accuracy). From those results, we recommend using regression trees (CART) tuned by different evolution combine with default analogy-based estimator. This particular combination of learner and optimizers often achieves in a few hours what other optimizers need days to weeks of CPU time to accomplish. An important part of this analysis is its reproducibility and refutability. All our scripts and data are on-line. It is hoped that this paper will prompt and enable much more research on better methods to tune software effort estimators.
CRISPR/Cas9 knockouts reveal genetic interaction between strain-transcendent erythrocyte determinants of Plasmodium falciparum invasion

Significance During malaria infections, Plasmodium falciparum parasites invade RBCs. Identification of host factors for parasite invasion guides the development of vaccines and host-targeted therapeutics. Here we describe the development of an in vitro culture system for the functional analysis of RBC determinants using the immortal erythroleukemia cell line JK-1. JK-1 cells can be induced to differentiate synchronously, support parasite invasion, and are amenable to genetic manipulation. Using this system, we validated two host factors, basigin and CD44, as strain-transcendent host factors for parasite invasion, and we demonstrated a functional interaction between these two proteins. The ability to perform gene editing to produce RBC mutants will augment our ability to study malaria infection. During malaria blood-stage infections, Plasmodium parasites interact with the RBC surface to enable invasion followed by intracellular proliferation. Critical factors involved in invasion have been identified using biochemical and genetic approaches including specific knockdowns of genes of interest from primary CD34+ hematopoietic stem cells (cRBCs). Here we report the development of a robust in vitro culture system to produce RBCs that allow the generation of gene knockouts via CRISPR/Cas9 using the immortal JK-1 erythroleukemia line. JK-1 cells spontaneously differentiate, generating cells at different stages of erythropoiesis, including terminally differentiated nucleated RBCs that we term “jkRBCs. ” A screen of small-molecule epigenetic regulators identified several bromodomain-specific inhibitors that promote differentiation and enable production of synchronous populations of jkRBCs. Global surface proteomic profiling revealed that jkRBCs express all known P. falciparum host receptors in a similar fashion to cRBCs and that multiple P. falciparum strains invade jkRBCs at comparable levels to cRBCs and RBCs. Using CRISPR/Cas9, we deleted two host factors, basigin (BSG) and CD44, for which no natural nulls exist. BSG interacts with the parasite ligand Rh5, a prominent vaccine candidate. A BSG knockout was completely refractory to parasite invasion in a strain-transcendent manner, confirming the essential role for BSG during invasion. CD44 was recently identified in an RNAi screen of blood group genes as a host factor for invasion, and we show that CD44 knockout results in strain-transcendent reduction in invasion. Furthermore, we demonstrate a functional interaction between these two determinants in mediating P. falciparum erythrocyte invasion.
Reduced patient anxiety as a result of radiation therapist‐led psychosocial support: a systematic review

Up to 49% of patients attending radiation therapy appointments may experience anxiety and distress. Anxiety is heightened during the first few visits to radiation oncology. Radiation therapists (RT) are the only health professionals in direct daily contact with patients during treatment, placing them in a unique position to explore patients’ psychosocial needs. This review aims to synthesise literature regarding the effect of RT‐led psychosocial support on patient anxiety. In May 2015, we searched the following electronic databases: Medline, PsycINFO, Embase, CINAHL, PubMed and Cochrane library. Radiation therapy‐specific journals were hand‐searched, and reference lists of identified studies searched. This review complies with Preferred Reporting Items for Systematic Reviews and Meta‐analyses (PRISMA) guidelines. The search identified 263 articles, of which 251 were excluded based on non‐English language, duplicate article or relevance. A total of 12 articles involving 1363 patients were included and categorised into three broad themes: ‘Patient Perspectives’ 3 articles, ‘Patient Information and Education’ 5 articles and ‘Screening and Needs Assessment’ 4 articles. Two publications referred to the same sample and data. Quality ratings were mixed, with one study rated ‘high’ quality, seven ‘moderate’ and four ‘low’. Methodological weaknesses were identified in relation to workflow, sample size and responder bias. RTs have a role in psychosocial support through increased communication and information sharing, which can benefit both patients and staff. RT‐led practices such as relationship building, patient education sessions and screening and needs assessments are feasible and can reduce anxiety.
Opening the Black Box Lessons From Research on Immersive Jewish Service-Learning Programs for Young Adults

Short-term, immersive, Jewish service-learning (IJSL) programs have emerged as a key communal strategy to encourage Jewish young adults to engage in service and see their volunteer work as a Jewish act. Utilizing two years of multi-method research, this article opens the “black box” of IJSL pedagogy, suggesting that group cohesion, quality of service work, interactions with community members, learning sessions, Jewish observance, and follow-up programming are critical to participant outcomes, including connections between Jewish identity and service and plans to engage in future volunteer work and to volunteer under Jewish auspices. The article also explores the limitations of current recruitment paradigms, which often result in gender-imbalanced groups with a history of strong Jewish engagement. It recommends that the IJSL fi eld engage in a process of external scanning for innovative ideas, foster a culture of experimentation and “demonstration projects,” and integrate feedback systems into planning and decision making.
A Novel Pore-Forming Toxin in Type A Clostridium perfringens Is Associated with Both Fatal Canine Hemorrhagic Gastroenteritis and Fatal Foal Necrotizing Enterocolitis

A role for type A Clostridium perfringens in acute hemorrhagic and necrotizing gastroenteritis in dogs and in necrotizing enterocolitis of neonatal foals has long been suspected but incompletely characterized. The supernatants of an isolate made from a dog and from a foal that died from these diseases were both found to be highly cytotoxic for an equine ovarian (EO) cell line. Partial genome sequencing of the canine isolate revealed three novel putative toxin genes encoding proteins related to the pore-forming Leukocidin/Hemolysin Superfamily; these were designated netE, netF, and netG. netE and netF were located on one large conjugative plasmid, and netG was located with a cpe enterotoxin gene on a second large conjugative plasmid. Mutation and complementation showed that only netF was associated with the cytotoxicity. Although netE and netG were not associated with cytotoxicity, immunoblotting with specific antisera showed these proteins to be expressed in vitro. There was a highly significant association between the presence of netF with type A strains isolated from cases of canine acute hemorrhagic gastroenteritis and foal necrotizing enterocolitis. netE and netF were found in all cytotoxic isolates, as was cpe, but netG was less consistently present. Pulsed-field gel electrophoresis showed that netF-positive isolates belonged to a clonal population; some canine and equine netF-positive isolates were genetically indistinguishable. Equine antisera to recombinant Net proteins showed that only antiserum to rNetF had high supernatant cytotoxin neutralizing activity. The identifica-tion of this novel necrotizing toxin is an important advance in understanding the virulence of type A C. perfringens in specific enteric disease of animals.
The occurrence of dental caries is associated with atherosclerosis

OBJECTIVE: Previous studies have suggested that marginal periodontitis is a risk factor for developing atherosclerosis. The objective of this study was to determine whether caries may also be associated with atherosclerosis. METHODS: The computed tomography data sets of 292 consecutive patients, 137 women and 155 men with a mean age of 54.1±17.3 years, were analyzed. Caries were quantified based on the number of decayed surfaces of all the teeth, and periodontitis was quantified on the basis of the horizontal bone loss in the jaw. The presence of chronic apical periodontitis (CAP) was assessed, and the aortic atherosclerotic burden was quantified using a calcium scoring method. RESULTS: The patients with <1 caries surfaces/tooth had a lower atherosclerotic burden (0.13±0.61 mL) than patients with ≥1 caries surfaces/tooth. The atherosclerotic burden was greater in patients with a higher number of lesions with pulpal involvement and more teeth with chronic apical periodontitis. In the logistical regression models, age (Wald 49.3), number of caries per tooth (Wald 26.4), periodontitis (Wald 8.6), and male gender (Wald 11) were found to be independent risk factors for atherosclerosis. In the linear regression analyses, age and the number of decayed surfaces per tooth were identified as influencing factors associated with a higher atherosclerotic burden, and the number of restorations per tooth was associated with a lower atherosclerotic burden. CONCLUSION: Dental caries, pulpal caries, and chronic apical periodontitis are associated positively, while restorations are associated inversely, with aortic atherosclerotic burden. Prospective studies are required to confirm these observations and answer the question of possible causality.
ICT and Language Teacher Development in the Global South: A New Materialist Discourse Analysis

In this article, I present insights from a discourse analytic study in which I examined publications that emerged from a teacher development program in Bangladesh. The program, known as English in Action, utilizes information and communication technologies to deliver professional development activities to English-language teachers. Now in its 8th year, the program claims great success in developing teachers’ pedagogical knowledge and capacity. The primary purpose of this article is to analyze the discourses that this program uses to claim success. Building on Hargreaves and Fullan's (1992) three integrated approaches to teacher development, I analyzed a large corpus of texts. I drew on the recent scholarship on new materialism to guide the analysis. The findings suggest that most of the discourses that English in Action uses are detached from the material reality in which teachers live, learn, and work. I conclude the article with a call for using a new materialist lens to read dominant discourses about ICT-use in teacher professional development.
Development of large area polycrystalline diamond detectors for fast timing application of high-energy heavy-ion beams

We have studied the effects of electrode fabrication and detector capacitance on the time resolution of large area electronic grade polycrystalline chemical vapour deposited diamond sensors that are suitable for time of flight measurements of heavy ions at relativistic velocities. Sensors were prepared both in house, with Al or Au metal contacts, and commercially fabricated with Au/diamond-like carbon contacts. He, Ar and a mixture of Ne and O beams at 16.3, 33.5 and 21-23 MeV/u, respectively were used on these devices whilst arranged in transmission geometry. Signal processing only began over one meter away from the sensors. The present approach, where we have large-area/large capacitance multi-strip detectors with processing electronics at some distance from the target, is compatible with anticipated space limitations in particle- identification and tracking setups at existing and planned nuclear fragmentation facilities. In a systematic study under these conditions, we demonstrate that the time resolution is limited by detector capacitance and energy deposition in the sensors. An intrinsic time resolution σ = (44±5) ps was achieved for a diamond detector of ∼ 14 pF capacitance. We conclude that, once further refinements are made, a large area time of flight detection system using polycrystalline diamond detectors would be able to provide time resolutions better than 40 ps, approaching the requirement for particle-identification in relativistic fragmentation experiments, such as those at the facility for antiproton and ion research, FAIR. © 2012 IOP Publishing Ltd and Sissa Medialab srl.
Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species’ vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: N^b was a linear (r2 = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw N^b based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems).
Support for School-to-school Networks: How Networking Teachers Perceive Support Activities of a Local Coordinating Agency

ABSTRACT External support by a local coordinating agency facilitates the work of school-to-school networks. This study provides an innovative theoretical framework to analyse how support provided by local education offices for school-to-school networks is perceived by the participating teachers. Based on a quantitative survey and qualitative interview data from a networking project in eight German districts, we argue that in order to enable networks to work independently on innovative reforms, local coordinating agencies should focus on autonomy support, such as training on network management, and on support aimed at establishing significance, i.e. through vision and goal setting.
Maxwell Chern-Simons Solitons from Type IIB String Theory

We study various three-dimensional supersymmetric Maxwell Chern-Simons solitons by using type IIB brane configurations. We give a systematic classification of soliton spectra such as topological BPS vortices and nontopological vortices in an $\mathcal{N}=2,3$ supersymmetric Maxwell Chern-Simons system via the branes of type IIB string theory. We identify the brane configurations with the soliton spectra of the field theory and obtain nice agreement with field theory aspects. We also discuss possible brane constructions for BPS domain wall solutions.
Imagerie mentale et alexithymie chez les psychopathes incarcérés

Le deficit en imagerie mentale constitue une des caracteristiques cliniques de la psychopathie (Cleckley, 1976; McCord & McCord, 1964). Sur base de leur score a l'echelle de psychopathie de Hare (1991), des sujets incarceres ont ete repartis dans un groupe « psychopathe » et un groupe « controle ». Ces deux groupes ont ete compares dans de trois etudes qui testent l'hypothese d'un deficit en imagerie mentale chez les psychopathes. La premiere etude examine l'imagerie par l'evocation d'un souvenir emotionnel. La seconde examine l'imagerie en rapport avec les caracteristiques cliniques de l'alexithymie. La troisieme etude examine la vivacite de l'imagerie dans sept modalites sensorielles. Les resultats de ces trois etudes confirment dans l'hypothese d'un deficit global en imagerie mentale chez les psychopathes. Les implications therapeutiques sont envisagees.
Predicting Employee Work Engagement Levels, Determinants and Performance Outcome: Empirical Validation in the Context of an Information Technology Organization

Extensive research has been devoted to examining the predictability of various determinant factors of work engagement (WE). One of the significant conclusions from this research suggests that employee expectations of the job and their feeling of fulfilment at work determine the nature of engagement initiatives. Hence, there is a need to understand the employees’ work context. This context may also include intra- and inter-group relationships within the workplace setting. This research attempts to explain the nature and extent of WE by examining the variability in engagement levels of employees working in an information technology (IT) organization augmented with a framework tested using structural equation modelling (SEM). A sample comprising 100 responses was collected using multistage sampling method. The results show that on an average, employees are moderately engaged at work. Organizational culture (OC) acts as a significant determinant of transformational leadership (TL) and WE. Further, TL resulted in a positive significant effect on job performance (JP), while an engaged employee is likely going to be a high-performing employee in the organization.
Factors Associated with Elevated ALT in an International HIV/HBV Co-Infected Cohort on Long-Term HAART

Background Previous studies have demonstrated that hepatitis B virus (HBV) infection increases the risk for ALT elevations in HIV-HBV co-infected patients during the first year of HAART; however, there is limited data on the prevalence of ALT elevations with prolonged HAART in this patient group. Methods/Principal findings To identify factors associated with ALT elevations in an HIV-HBV co-infected cohort receiving prolonged HAART, data from 143 co-infected patients on HAART enrolled in an international HIV-HBV co-infected cohort where ALT measurements were obtained every 6 months was analysed. A person-visit analysis was used to determine frequency of ALT elevation (≥2.5×ULN) at each visit. Factors associated with ALT elevation were determined using multivariate logistic regression with generalized estimating equations to account for correlated data. The median time on HAART at the end of follow-up was 5.6 years (range 0.4–13.3) years. During follow-up, median ALT was 36 U/L with 10.6% of person-visits classified as having ALT elevation. Most ALT elevations were grade 2 (86.5%), with only 13.5% of all ALT elevations grade 3 or higher. Univariate associations with ALT elevation (p<0.05) included history of AIDS, HBV DNA ≥2,000 IU/ml, HBeAg positive, study visit CD4 <200 cells/ml and nadir CD4 <200 cells/ml. In the multivariate analysis, only study visit CD4 <200 cells/ml (OR 2.07, 95%CI 1.04–4.11, p = 0.04) and HBeAg positive status (OR 2.22, 95%CI 1.03–4.79, p = 0.04) were independently associated with ALT elevation. Conclusions In this HIV-HBV co-infected cohort, elevated ALT after >1 year of HAART was uncommon, and severe ALT elevations were rare. HIV-HBV co-infected patients on long-term HAART who are either HBeAg positive or have a CD4 count of <200 cells/ml are at increased risk for ALT elevations.
USER DESIGN OF CUSTOMIZED PRODUCTS

User design offers tantalizing potential benefits to manufacturers and consumers, including a closer match of products to user preferences, which should result in a higher willingness to pay for goods and services. There are two fundamental approaches that can be taken to user design: parameterbased systems and needs-based systems. With parameter-based systems, users directly specify the values of design parameters of the product. With needs-based systems, users specify the relative importance of their needs, and an optimization algorithm recommends the combination of design parameters that is likely to maximize user utility. Through an experiment in the domain of consumer laptop computers, we show that for parameter-based systems, outcomes, including measures for comfort and fit, increase in the expertise of the user. We also show that for novices, the needs-based interface results in better outcomes than the parameter-based interface.