Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-Infected Children Living in Central Africa Have Low Persistence of Antibodies to Vaccines Used in the Expanded Program on Immunization

Background The Expanded Program on Immunization (EPI) is the most cost-effective measures to control vaccine-preventable diseases. Currently, the EPI schedule is similar for HIV-infected children; the introduction of antiretroviral therapy (ART) should considerably prolong their life expectancy. Methods and Principal Findings To evaluate the persistence of antibodies to the EPI vaccines in HIV-infected and HIV-exposed uninfected children who previously received these vaccines in routine clinical practice, we conducted a cross-sectional study of children, aged 18 to 36 months, born to HIV-infected mothers and living in Central Africa. We tested blood samples for antibodies to the combined diphtheria, tetanus, and whole-cell pertussis (DTwP), the measles and the oral polio (OPV) vaccines. We enrolled 51 HIV-infected children of whom 33 were receiving ART, and 78 HIV-uninfected children born to HIV-infected women. A lower proportion of HIV-infected children than uninfected children had antibodies to the tested antigens with the exception of the OPV types 1 and 2. This difference was substantial for the measles vaccine (20% of the HIV-infected children and 56% of the HIV-exposed uninfected children, p<0.0001). We observed a high risk of low antibody levels for all EPI vaccines, except OPV types 1 and 2, in HIV-infected children with severe immunodeficiency (CD4+ T cells <25%). Conclusions and Significance Children were examined at a time when their antibody concentrations to EPI vaccines would have still not undergone significant decay. However, we showed that the antibody concentrations were lowered in HIV-infected children. Moreover, antibody concentration after a single dose of the measles vaccine was substantially lower than expected, particularly low in HIV-infected children with low CD4+ T cell counts. This study supports the need for a second dose of the measles vaccine and for a booster dose of the DTwP and OPV vaccines to maintain the antibody concentrations in HIV-infected and HIV-exposed uninfected children.
Signal diffusion and the mitigation of social exploitation in pneumococcal competence signalling

Quorum sensing (QS) in bacteria is thought to enable populations of cells to coordinately and cooperatively regulate gene expression for traits that confer group benefits. While this view has strong empirical and theoretical support, it is increasingly appreciated that QS under natural conditions may be incapable of monitoring bacterial numbers and, furthermore, that QS is evolutionarily unstable owing to conflicts of interest among competing cells. An alternative hypothesis, termed diffusion sensing (DS), proposes that autoinducer secretion monitors the diffusive properties of the local environment, with benefits that are directly realized by individual cells rather than populations. Here, we test central predictions of this hypothesis using the competence signalling system of Streptococcus pneumoniae as our model, which regulates the induction of natural transformation by the secretion and detection of a small diffusible peptide, CSP (competence-stimulating peptide). By experimentally manipulating the diffusive properties of the growth medium, we found that there is no fixed quorum for competence induction. Instead, induction cell density scales with diffusivity. In agreement with QS and DS expectations, we show that the benefit of signal exploitation by mutant cells that can use but not secrete CSP is strongly frequency-dependent. However, we also find that the magnitude of this benefit declines significantly as diffusion is reduced, a result more consistent with the predictions of DS. Together, these data provide strong support for the DS hypothesis for autoinducer response systems. More specifically, our results imply that autonomous rather than group benefits should be sought in order to more completely understand the role and evolution of CSP signalling in pneumococci.
Biological and Physical Properties of the Suckling Mouse Cataract Agent Grown in Chicken Embryos

Experiments were carried out with the suckling mouse cataract agent (SMCA) in an attempt to better characterize the nature of this agent. Despite the fact that high titers of SMCA were found in the chorioallantoic fluid of inoculated chicken embryos, the agent did not replicate in chicken embryo epithelial cell cultures. SMCA did not interfere with Sindbis virus plaque formation and was not inhibited by chicken interferon or polyinosinic-polycytidylic acid. The agent was relatively resistant to high pH and osmotic shock but was inactivated by low pH. Electron micrographs of negatively stained particles concentrated and semipurified from infected chicken embryo chorioallantoic fluids revealed pleomorphic particles ranging from approximately 70 to 400 nm in diameter. SMCA was resistant to kanamycin, novobiocin, and sodium aurothiomalate.
Prediction of Learning Curves in Machine Translation

Parallel data in the domain of interest is the key resource when training a statistical machine translation (SMT) system for a specific purpose. Since ad-hoc manual translation can represent a significant investment in time and money, a prior assesment of the amount of training data required to achieve a satisfactory accuracy level can be very useful. In this work, we show how to predict what the learning curve would look like if we were to manually translate increasing amounts of data. We consider two scenarios, 1) Monolingual samples in the source and target languages are available and 2) An additional small amount of parallel corpus is also available. We propose methods for predicting learning curves in both these scenarios.
Membrane fission by protein crowding

Significance The division of membrane-bound compartments into smaller, separate volumes is essential to cells. The process of membrane fission is required for the separation of two membrane compartments. The prevailing view has been that to drive fission, proteins must contain specific structural features such as curved scaffolds and wedge-like membrane insertions. In contrast, this work demonstrates a more general mechanism, in which crowding among membrane-bound proteins drives fission. Like a compressed gas, collisions among crowded proteins generate pressure that can stretch, bend, and ultimately disrupt membrane surfaces, leading to fission. The discovery of this mechanism broadens our perspective on membrane fission by demonstrating how any protein, independent of its structure, can assist in this essential cellular process. Membrane fission, which facilitates compartmentalization of biological processes into discrete, membrane-bound volumes, is essential for cellular life. Proteins with specific structural features including constricting rings, helical scaffolds, and hydrophobic membrane insertions are thought to be the primary drivers of fission. In contrast, here we report a mechanism of fission that is independent of protein structure—steric pressure among membrane-bound proteins. In particular, random collisions among crowded proteins generate substantial pressure, which if unbalanced on the opposite membrane surface can dramatically increase membrane curvature, leading to fission. Using the endocytic protein epsin1 N-terminal homology domain (ENTH), previously thought to drive fission by hydrophobic insertion, our results show that membrane coverage correlates equally with fission regardless of the hydrophobicity of insertions. Specifically, combining FRET-based measurements of membrane coverage with multiple, independent measurements of membrane vesiculation revealed that fission became spontaneous as steric pressure increased. Further, fission efficiency remained equally potent when helices were replaced by synthetic membrane-binding motifs. These data challenge the view that hydrophobic insertions drive membrane fission, suggesting instead that the role of insertions is to anchor proteins strongly to membrane surfaces, amplifying steric pressure. In line with these conclusions, even green fluorescent protein (GFP) was able to drive fission efficiently when bound to the membrane at high coverage. Our conclusions are further strengthened by the finding that intrinsically disordered proteins, which have large hydrodynamic radii yet lack a defined structure, drove fission with substantially greater potency than smaller, structured proteins.
Systematic review: monotherapy with antitumour necrosis factor α agents versus combination therapy with an immunosuppressive for IBD

The treatment of IBD has evolved significantly over the past 15 years. Historically, steroids and immunosuppressive drugs, such as methotrexate (MTX), azathioprine (AZA) and 6-mercaptopurine (6-MP) had been the mainstay of therapy. When infliximab (IFX) was approved for the treatment of Crohn's disease, it began the era of trying to understand how best to optimise our available treatment options. Initially, antitumour necrosis factor (anti-TNF) agents were used after immunosuppressives failed. Then, evidence showed that using AZA together with IFX early in the disease course was more effective than the typical sequential treatment algorithm.1 With the addition of newer anti-TNF drugs and development of different treatment regimens,2–5 there are still significant questions related to the most effective therapeutic strategy. Perhaps the most controversial of these questions is when to use anti-TNF monotherapy versus combination therapy with 6-MP, AZA or MTX. When considering patients with rheumatoid arthritis, where anti-TNF therapy also has a demonstrated efficacy, it is clear from randomised controlled trials (RCT) that the use of combination therapy improves clinical outcomes.6 Although it is logical that a similar benefit should exist in IBD, the evidence base upon which to make decisions is less robust, leading to patient and provider concerns regarding the balance between efficacy and toxicity. Providers have two sources of data to rely upon when addressing this concern with IBD patients, RCTs and observational data. RCTs are more rigorous, generally have better patient follow-up, and more often include prospective measurement of study end-points using well-accepted and often validated outcome measures. For this reason, RCTs result in a relatively robust assessment of key outcome measures such as clinical response, remission and mucosal healing. Although the data from RCTs may not directly translate to the ‘real world’,7 whatever generalisability is lost due to the application of strict inclusion …
Operating theatre time, where does it all go? A prospective observational study

Objective To assess the accuracy of surgeons and anaesthetists in predicting the time it will take them to complete an operation or procedure and therefore explain some of the difficulties encountered in operating theatre scheduling. Design Single centre, prospective observational study. Setting Plastic, orthopaedic, and general surgical operating theatres at a level 1 trauma centre serving a population of about 370 000. Participants 92 operating theatre staff including surgical consultants, surgical registrars, anaesthetic consultants, and anaesthetic registrars. Intervention Participants were asked how long they thought their procedure would take. These data were compared with actual time data recorded at the end of the case. Primary outcome measure Absolute difference between predicted and actual time. Results General surgeons underestimated the time required for the procedure by 31 minutes (95% confidence interval 7.6 to 54.4), meaning that procedures took, on average, 28.7% longer than predicted. Plastic surgeons underestimated by 5 minutes (−12.4 to 22.4), with procedures taking an average of 4.5% longer than predicted. Orthopaedic surgeons overestimated by 1 minute (−16.4 to 14.0), with procedures taking an average of 1.1% less time than predicted. Anaesthetists underestimated by 35 minutes (21.7 to 48.7), meaning that, on average, procedures took 167.5% longer than they predicted. The four specialty mean time overestimations or underestimations are significantly different from each other (P=0.01). The observed time differences between anaesthetists and both orthopaedic and plastic surgeons are significantly different (P<0.05), but the time difference between anaesthetists and general surgeons is not significantly different. Conclusion The inability of clinicians to predict the necessary time for a procedure is a significant cause of delay in the operating theatre. This study suggests that anaesthetists are the most inaccurate and highlights the potential differences between specialties in what is considered part of the “anaesthesia time. ”
Evaluating complex interventions: Perspectives and issues for health behaviour change interventions

Objective: Health behaviour change interventions (HBCIs), used in health education, health promotion, patient education and psychotherapy areas, are considered complex interventions. The objective of this article is to discuss the value and limitations of using randomised clinical trials (RCTs) to asses HBCIs. Methods: A scoping review of the literature was conducted to identify the main challenges of using RCTs for evaluating HBCIs. The issues were illustrated by case studies selected from research conducted by our multidisciplinary team. Results: In complex interventions, effects are produced not only by the intervention, but are strongly linked to context. Issues relating to transferability of results are therefore critical, and require adjustments to the RCT model. Sampling bias, biases related to the experimental conditions and biases due to the absence of double-blindness were examined and illustrated by case studies. Conclusion: The results underline the importance of a multidisciplinary approach. They call for adapted or alternative evaluation models that overcome the limitations of RCTs.
GSC-based spatial voice activity detection for enhanced speech coding in the presence of competing speech

An array of microphones is used for both noise suppression and spatial voice activity detection (SVAD). A generalized sidelobe canceler (GSC) is employed for robust adaptive interference rejection and the signals within the GSC are also exploited to provide speech activity detection for the desired signal. The SVAD shows promising results for the difficult case of an interfering speaker.
Animal biology and pathology / Biologie et pathologie animales Clutch size: a major sex ratio determinant in fig pollinating wasps?

Under local mate competition, sex ratio theory predicts that increasing numbers of ovipositing females (foundresses) on a site should lead to higher proportions of males in their broods. Fig pollinators have confirmed this prediction. It is also predicted that with decreasing clutch size, solitary foundresses should produce increasing proportions of sons. We show this to be true. Further, when several females compete, brood size decreases. As a result, the proportion of males increases, and this could provide a mechanistic explanation of sex ratio response to numbers of colonizing females. Therefore, sex ratio data on fig wasps need to be reassessed to determine whether females ‘count’ other foundresses, as is generally accepted, or whether they simply ‘count’ the number of eggs that they lay. To cite this article: F. Kjellberg et al., C. R. Biologies 328 (2005).
Sickness absence as a risk marker of future disability pension: the 10-town study

Sickness absence is increasingly recognised as a measure of ill health. Studies have examined associations between absence, morbidity, and mortality,1–3 but less is known about the status of sickness absence as a risk marker for future disability retirement,4–6 the focus of this study. Participants selected from the on-going Finnish 10-town study4 comprised all 46 569 full time municipal employees who had a job contract lasting a minimum of three full consecutive years between 1 January 1990 and 31 December 2000, and were below 55 at the end of the follow up, the age before which medical causes exclusively determine granting of disability pension for municipal employees in Finland. We obtained sickness absence records from employers’ registers for a fixed three year period of employment (the length of exposure assessment period was the same for all participants). The start of this period varied between 1 January 1990 and 1 January 1998 depending on the date when the job contract began. For those employees who had a job contract of more than three years, absences for the first three years were included in the analysis. We determined disability retirements from the end of the assessment period for …
A Spatial Web Graph Model with Local Influence Regions

We present a new stochastic model for complex networks, based on a spatial embedding of the nodes, called the spatial preferred attachment (SPA) model. In the SPA model, nodes have influence regions of varying size, and new nodes may link to a node only if they fall within its influence region. The spatial embedding of the nodes models the background knowledge or identity of the node, which will influence its link environment. In our model, nodes can determine their link environment based only on local knowledge of the network. We prove that our model gives a power-law in-degree distribution, with exponent in [2,∞) depending on the parameters, and with concentration for a wide range of in-degree values.
Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species.
AbYSS: Adapting Scatter Search to Multiobjective Optimization

We propose the use of a new algorithm to solve multiobjective optimization problems. Our proposal adapts the well-known scatter search template for single-objective optimization to the multiobjective domain. The result is a hybrid metaheuristic algorithm called Archive-Based hYbrid Scatter Search (AbYSS), which follows the scatter search structure but uses mutation and crossover operators from evolutionary algorithms. AbYSS incorporates typical concepts from the multiobjective field, such as Pareto dominance, density estimation, and an external archive to store the nondominated solutions. We evaluate AbYSS with a standard benchmark including both unconstrained and constrained problems, and it is compared with two state-of-the-art multiobjective optimizers, NSGA-II and SPEA2. The results obtained indicate that, according to the benchmark and parameter settings used, AbYSS outperforms the other two algorithms as regards the diversity of the solutions, and it obtains very competitive results according to the convergence to the true Pareto fronts and the hypervolume metric.
Local Synchronization of a Complex Network Model

This paper introduces a novel complex network model to evaluate the reputation of virtual organizations. By using the Lyapunov function and linear matrix inequality approaches, the local synchronization of the proposed model is further investigated. Here, the local synchronization is defined by the inner synchronization within a group which does not mean the synchronization between different groups. Moreover, several sufficient conditions are derived to ensure the local synchronization of the proposed network model. Finally, several representative examples are given to show the effectiveness of the proposed methods and theories.
Distributed Power Allocation for Cooperative Wireless Network Localization

Device-to-device (D2D) communication in cellular networks is a promising concept that permits cooperation among mobile devices not only to increase data throughput but also to enhance localization services. In those networks, the allocation of transmitting power plays a critical role in determining network lifetime and localization accuracy. Meanwhile, it is a challenging task for implementation in cooperative D2D networks, since each device has only imperfect estimates of local network parameters in distributed settings. In this paper, we establish an optimization framework for robust power allocation in cooperative wireless network localization, and develop distributed power allocation strategies. In particular, we decompose the power allocation problem into infrastructure and cooperation phases, show the sparsity property of the optimal power allocation, and develop efficient power allocation strategies. Simulation results show that these strategies can achieve significant performance improvement in localization accuracy compared to the uniform strategies.
The Relationship of Gamma Immunoglobin (IgG) Density and Apgar Score in Normal Term Pregnancy

The transfer of maternal IgG provides the neonate with humoral immunity during early life. The population of transferred IgG or IgG density (IgGρ) was estimated to find out if it has any relevance to the condition of an infant 1-5 minutes after birth or APGAR score which gives an insight into the state of health of the infant and thus its chances of survival and its milestone of development. Ex-vivo, term placenta of forty euthyroid mothers, the maternal serum, and cord blood were used to estimate the IgGρ in both maternal and cord blood by taking blood samples from the antecubital vein of the mother and from the umbilical cord (mixed blood) immediately after birth; having determined the APGAR score within 1-5 minutes post-partum. The findings featured the following: the mean APGAR score (10); mean IgGρ of the neonates (11.94 ± 0.12mg/100ml of blood); mean IgGρ of the maternal blood (10.9 ± 0.29/100ml). The difference however, was not statistically significant (P>0.05). The findings provide evidence suggesting that IgGρ, not only relates to, but determines APGAR score of the neonates. Keywords : APGAR score, IgG density, Term placenta, Cord blood