Miracle-dz/UniFAR-FTUs huggingface dataset:
Severe anaemia complicating HIV in Malawi; Multiple co-existing aetiologies are associated with high mortality

Background Severe anaemia is a major cause of morbidity and mortality in HIV-infected adults living in resource-limited countries. Comprehensive data on the aetiology is lacking and needed to improve outcomes. Methods HIV-infected adults with severe (haemoglobin ≤70g/l) or very severe anaemia (haemoglobin ≤50 g/l) were recruited at Queen Elizabeth Central Hospital, Blantyre, Malawi. Fifteen potential causes of severe anaemia of anaemia and associations with anaemia severity and mortality were explored. Results 199 patients were enrolled: 42.2% had very severe anaemia and 45.7% were on ART. Over two potential causes for anaemia were present in 94% of the patients; including iron deficiency (55.3%), underweight (BMI<20: 49.7%), TB-infection (41.2%) and unsuppressed HIV-infection (viral load >1000 copies/ml) (73.9%). EBV/CMV co-infection (16.5%) was associated with very severe anaemia (OR 2.8 95% CI 1.1-6.9). Overall mortality was high (53%; 100/199) with a median time to death of 16 days. Death was associated with folate deficiency (HR 2.2; 95% CI 1.2-3.8) and end stage renal disease (HR 3.2; 95% CI 1.6-6.2). Conclusion Mortality among severely anaemic HIV-infected adults is strikingly high. Clinicians must be aware of the urgent need for a multifactorial approach, including starting or optimising HIV treatment; considering TB treatment, nutritional support and attention to potential renal impairment.
Intuitionistic Fuzzy and Interval-Valued Intuitionistic Fuzzy Cosine Similarity Measures for Pattern Recognitions

Abstract In this work, considering the information carried by the membership degree and the nonmembership degree in intuitionistic fuzzy sets (IFSs) and interval-valued intuitionistic fuzzy sets (IVIFSs) as vector representations, in the vector space we propose novel cosine similarity measures for IFSs based on the cosine similarity measure (angular coefficient) between Fuzzy Sets and cosine similarity measures between IVIFSs based on the extension of cosine similarity measures between IFSs. Then, applied examples for pattern recognitions are presented to demonstrate the efficiency of the proposed cosine similarity measures.
Modification of recombinant human epidermal growth factor (rh-EGF) expression vector by site-directed mutagenesis for therapeutic protein production

Recombinant human epidermal growth factor (rh-EGF) has high value in therapies for h-EGF deficiency-related diseases. The expression of the h-EGF gene was designed by using the pET21b(+) vector and Escherichia coli BL21(DE3) as the expression host. In a previous study, the sequence of a 6xHis tag without any restriction sites was fused to the h-EGF gene, yet it was not possible to obtain a purified and single rh-EGF by this approach. In this study, we modified the rh-EGF expression vector using site-directed mutagenesis (SDM) to remove the sequence of the 6xHis tag. The vector modification was carried out by inserting a stop codon and the EcoRI restriction site, along with deleting the 6xHis tag sequence. The results of PCR showed non-specific bands, while 2-step cycles PCR produced one non-specific band, and 3-step cycles PCR produced two non-specific bands. After purification of the PCR products, the SDM-recombinant plasmids treated for template plasmid-free product were transformed into E. coli DH5a. Even though the transformation efficiency was low, the planned gene mutations including the deletion of the 6xHis tag and insertion of the stop codon and EcoRI restriction site in plasmid pET21b(+) were successfully carried out. When using this modified vector in expression studies, rh-EGF of a similar size to that of the rh-EGF standard and approximately 1 kDa smaller than the rh-EGF-6xHis of the previous study was obtained.
Effects Of Environmental And Anthropogenic Factors On The Range Contraction Of Bird And Mammal Species

The largest contributor to biodiversity loss is habitat destruction caused by humans. A common consequence of habitat destruction is a reduction in the geographic range of a species. Little research has been done to separate the contribution of anthropogenic and environmental variables to the extinction or persistence of species that have experienced range contraction. In this thesis, I examined the relative effects of several variables (elevation, mean annual precipitation, mean annual temperature, human population density, distance from roads, and proportion of land converted to built-up land, cropland, and rangeland) on the geographic ranges of declining bird and mammal species from all continents except Antarctica. Species were examined separately to determine which variables might have influenced the contraction in the ranges of individual species. The results of each variable were compiled both by individual species and by continent. My results suggest environmental variables have a greater effect on species persistence and extinction than do the anthropogenic variables I tested. Mean annual precipitation was most often identified as having a positive or negative influence on species persistence. The findings of this study provide a comprehensive assessment of the effects of environmental and anthropogenic variables on the persistence of both individual species and all species from each of the 6 continents included in the analyses. These findings could allow conservation biologists to better predict areas where a declining species will persist, thereby enabling the prioritization of areas for the establishment of wildlife reserves.
Why do mutant allele frequencies in oncogenes peak around .40 and rapidly decrease?

The mutant allele frequencies in oncogenes peak around . 40 and rapidly decrease. In this article, we explain why this is the case. Invoking a key result from mathematical analysis in our model, namely, the inverse function theorem, we estimate the selection coefficients of the mutant alleles as a function of germline allele frequencies. Under complete dominance of oncogenic mutations, this selection function is expected to be linearly correlated with the distribution of the mutant alleles. We demonstrate that this is the case by investigating the allele frequencies of mutations in oncogenes across various cancer types, validating our model for mean effective selection. Consistent with the population genetics model of fitness, the selection function fits a gamma-distribution curve that accurately describes the trend of the mutant allele frequencies. While existing equations for selection explain evolution at low allele frequencies, our equations are general formulas for natural selection under complete dominance operating at all frequencies. We show that selection exhibits linear behaviour at all times, favouring dominant alleles with respect to the change in recessive allele frequencies. Also, these equations show, selection behaves like power law against the recessive alleles at low dominant allele frequencies.
Chromosome (mis)segregation is biased by kinetochore size

Summary: Aneuploidy, the gain or loss of chromosomes, arises through problems in chromosome segregation during mitosis or meiosis and has been implicated in cancer and developmental abnormalities in humans [1]. Possible routes to aneuploidy include a compromised spindle assembly checkpoint (SAC), cohesion defects, centrosome amplification, as well as improper kinetochore-microtubule attachments [2]. However, none of these established routes takes into account the intrinsic features of the kinetochore - the critical chromosomal interface with spindle microtubules. Kinetochore size and respective microtubule binding capacity varies between different animal and plant species [3-10], among different chromosomes from the same species (including humans) [3, 11-15], and in response to microtubule attachments throughout mitosis [16-18]. How kinetochore size impacts chromosome segregation remains unknown. Addressing this fundamental question in human cells is virtually impossible, because most of the 23 pairs of chromosomes cannot be morphologically distinguished, while detection of 2-3 fold differences in kinetochore size is limited by diffraction and cannot be resolved by conventional light microscopy in living cells. Here we used the unique cytological attributes of female Indian muntjac, the mammal with the lowest known chromosome number (n=3), to track individual chromosomes with distinct kinetochore sizes throughout mitosis. We found that chromosomes with larger kinetochores bi-orient more easily and are biased to congress to the equator in a motor-independent manner. However, they are also more prone to establish erroneous merotelic attachments and lag behind during anaphase. Thus, we uncovered an intrinsic kinetochore feature - size - as an important determinant of chromosome segregation fidelity.
Secondhand horror: effects of direct and indirect predator cues on behavior and reproduction of the bank vole

Risk recognition by prey is of paramount importance within the evolutionary arms race between predator and prey. Prey species are able to detect direct predator cues like odors and adjust their behavior appropriately. The question arises whether an indirect predation cue, such as the odor of scared individuals, can be detected by conspeci ﬁ cs and subsequently affects recipient behavior. Parents may also transfer their experience with predators to their offspring. In two experiments, we assessed how direct and indirect predation cues affect bank vole ( Myodes glareolus ) foraging behavior, reproduction, and pup ﬁ tness. Weasel ( Mustela nivalis ) odor served as the direct cue, whereas the odor of weasel-scared conspeci ﬁ cs, alarm pheromones, was used as an indirect cue and both of those were compared to a control odor, clean wood shavings. Alarm pheromones attracted female voles, measured as time in proximity to the treatment and foraging. Both predator odor and alarm pheromones enhanced reproduction compared to the control odor. Females treated with alarm pheromone had signi ﬁ cantly higher pregnancy rates, and pups from predator-treated mothers were signi ﬁ cantly heavier at birth. Our study provides two novel ideas. First, the impact of a predator can be socially transmitted. Second, predation risk likely triggers terminal investment in reproduction.
Generation of iPSCs by Nonintegrative RNA-Based Reprogramming Techniques: Benefits of Self-Replicating RNA versus Synthetic mRNA

The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is gaining in importance in the fields of regenerative medicine, tissue engineering, and disease modeling. Patient-specific iPSCs have as an unlimited cell source a tremendous potential for generating various types of autologous cells. For the future clinical applicability of these iPSC-derived cells, the generation of iPSCs via nongenome integrating methods and the efficient reprogramming of patients' somatic cells are required. In this study, 2 different RNA-based footprint-free methods for the generation of iPSCs were compared: the use of synthetic modified messenger RNAs (mRNAs) or self-replicating RNAs (srRNAs) encoding the reprogramming factors and GFP. Using both RNA-based methods, integration-free iPSCs without genomic alterations were obtained. The pluripotency characteristics identified by specific marker detection and the in vitro and in vivo trilineage differentiation capacity were comparable. Moreover, the incorporation of a GFP encoding sequence into the srRNA enabled a direct and convenient monitoring of the reprogramming procedure and the successful detection of srRNA translation in the transfected cells. Nevertheless, the use of a single srRNA to induce pluripotency was less time consuming, faster, and more efficient than the daily transfection of cells with synthetic mRNAs. Therefore, we believe that the srRNA-based approach might be more appropriate and efficient for the reprogramming of different types of somatic cells for clinical applications.
Temporal dynamic analysis of a mountain ecosystem based on multi‐source and multi‐scale remote sensing data

During the last decades, ecosystems have suffered a decline in natural resources due to climate change and anthropogenic pressure. Specifically, the European rabbit introduced by humans, as well as drought episodes, have led to a change in the vegetation structure of a mountainous ecosystem: Teide National Park in Spain. Teide managers studied, with field‐based traditional methods, how the two keystone vegetation species, Spartocytisus supranubius and Pterocephalus lasiospermus, have changed their dynamics in this vulnerable and heterogenic ecosystem. However, remote sensing is an important tool for classifying, monitoring, and managing large areas in a fast and economic way. This work proposes a methodological framework to monitor the changes produced in this protected area using multi‐source remote sensing imagery. The results strengthen and extend the analysis followed by the National Park managers, demonstrating that S. supranubius has decreased its population while P. lasiospermus has increased. Moreover, this study presents thematic maps of the species of interest, as well as its specific coverage at different dates, providing quantitative data difficult to get with traditional approaches.
The Synthesis of Basic Motion Regulator System for Quadrupedal Walking Vehicle and Its Experiments

Legged locomotion is considered to be superior to conventional wheeled vehicles with respect to the adaptability in the rough ground conditions. In the past score of years research experiments have been performed, but no practical walking vehicle has ever been realized. The authors have examined this problem and have come to the conclusion that one of the main reasons of the retarded advent of a practical walking vehicle lies in its mechanical aspects, and proposed a “3 dimensional cartesian
D3.4 BRAIN - Advanced SSVEP signal processing tools

Brain-computer interfaces (BCI) based on Steady State Visual EvokedPotential (SSVEP) can provide higher information transfer rate thanother BCI modalities. For the sake of safety and comfort, the frequency of the repetitive visual stimulus (RVS) necessary to elicit an SSVEP, should be higher than 30 Hz. However, in the frequency rangeabove 30 Hz, only a limited number of frequencies can elicit sufficiently strong SSVEPs for BCI purposes. Consequently, the conventionalapproach, consisting in presenting various repetitive visual stimuli having different frequency each, is not practical for SSVEP basedBCI functioning. Indeed this would bring low communication bitrates.In order to increase the number of possible repetitive visual stimuli, we consider modulating the phase of the stimulus instead of thefrequency. Thus, several stimuli, sharing the same frequency, but with different phase can be presented to the user. The approach presented in this document, to detect the phase of the stimulus is termedphase synchrony. It consists in using as feature, to identify a subject's focus of attention, the phase difference between the SSVEP and the stimulus. The phase is extracted through the Hilbert transformapplied on an univariate signal resulting from spatially filteringthe electroencephalogram.
Subgraph-based Metamorphic Malwares Analysis

Malware authors commonly used code obfuscation to evade detection mechanisms. When this technique is applied to malwares, they can change their instruction sequence and also even their signature. These malwares which have same functionality and different appearance are able to evade signature-based AV products. Thus, AV venders paid large amount of cost to analyze and classify malware for generating new signature. In this paper, we propose a new approach for analyzing metamorphic malwares. The proposed mechanism first converts malware’s API call sequences to CodeGraph through dynamic analysis. After that, we extract all subgraphs and analyze how similar two malware’s behaviors are through subgraph similarity. To validate proposed mechanism, we use 46 real-world malwares include 20 variants. In evaluation, all metamorphic malwares are classified correctly, and similar module behaviors among different malwares are also discovered.
Light-induced indeterminacy alters shade avoiding tomato leaf morphology

Plants sense foliar shade of competitors and alter their developmental programs through the shade avoidance response. Internode and petiole elongation, and changes in overall leaf area and leaf mass per area, are the stereotypical architectural responses to foliar shade in the shoot. However, changes in leaf shape and complexity in response to shade remain incompletely, and qualitatively, described. Using a meta-analysis of >18,000 previously published leaflet outlines, we demonstrate that shade avoidance alters leaf shape in domesticated tomato and wild relatives. The effects of shade avoidance on leaf shape are subtle with respect to individual traits, but are combinatorially strong. We then seek to describe the developmental origins of shade-induced changes in leaf shape by swapping plants between light treatments. Leaf size is light-responsive late into development, but patterning events, such as stomatal index, are irrevocably specified earlier. Observing that shade induces increases in shoot apical meristem size, we then describe gene expression changes in early leaf primordia and the meristem using laser microdissection. We find that in leaf primordia shade avoidance is not mediated through canonical pathways described in mature organs, but rather the expression of KNOX and other indeterminacy genes, altering known developmental pathways responsible for patterning leaf shape. We also demonstrate that shade-induced changes in leaf primordium gene expression largely do not overlap with those found in successively initiated leaf primordia, providing evidence against classic hypotheses that shaded leaf morphology results from prolonged production of juvenile leaf types.
On a Miniature Free-Swimming Robotic Fish with Multiple Sensors

Bio-inspired robotic fish hold strong promise for underwater missions. This paper deals with the design and control issues of a miniature free-swimming robotic fish with multiple sensors. Specifically, a synthesized mechanical design scheme mainly relying on a two-link serial mechanism and a pair of mechanical pectoral fins is first presented. Next, a bio-inspired Central Pattern Generator (CPG) based control method aided by feedback information from multiple sensors of various types to achieve three-dimensional swimming is proposed. Finally, experimental results on the 35-centimetre-long robotic fish verify the efficacy of the proposed mechatronic design and control methods. It is found that the CPG control combined with sensory information greatly contributes to swimming ability and intelligence of the robotic fish.
TOWARDS A BETTER UNDERSTANDING OF THE EFFECTS OF PRAZIQUANTEL ON THE INTERACTION BETWEEN THE HELMINTH PARASITE SCHISTOSOMA MANSONI AND ITS MURINE HOST

Schistosomiasis is a neglected tropical disease (NTD) that infects 206 million individuals worldwide. This disease is caused by dioecious trematodes of the genus Schistosoma, and its pathology is associated with the large number of eggs that are released by the female. Entrapped eggs lead to host immune and inflammatory responses resulting in disease progression. Chemotherapy provides the main means of control and praziquantel (PZQ) is the only widely available drug that is used in all mass drug administration (MDA) programs. As the number of individuals receiving PZQ continues to grow, the development of PZQ resistance is a concern and increases as the drug pressure placed on the parasites increases. We employed Next Generation Sequencing (NGS) to provide transcriptomic data related to four areas of attention: 1) What is the effect of PZQ on the murine hostS. mansoni interaction, and how does PZQ effect S. mansoni in vivo? , 2) What is the effect at the molecular level of PZQ on male S. mansoni in vivo? , 3) What is the respective contribution of Rand Senantiomers to the S. mansoni transcriptomic response? , and 4) What is the
Phylogeography of Pulsatilla cernua (Ranunculaceae), a grassland species, in Japan

Abstract The genetic diversity and structure of Pulsatilla cernua, a continental‐grassland relict, were investigated using variations in chloroplast DNA (cpDNA) and microsatellites of nuclear DNA. In the analyses of three cpDNA regions, 17 haplotypes were found in 24 populations of P. cernua from Japan, Korea, and Russia. Although the route and time of migration between the continent of Asia and Japan could not be well resolved, the cpDNA haplotype network suggests the existence of several ancient lineages in Japan and a recent secondary migration from Japan to the continent. Microsatellite analyses did not indicate genetic structure among the Japanese populations, indicating the existence of gene flow across the distribution area until recently. These results indicate that the present fragmentation of P. cernua in Japan may reflect a rapid, recent reduction from a previously large, continuous distribution.
Particles: a naturally parallel approach to modeling

Particle-based technique that are being developed for the mechanical and visual modeling of complex nonrigid materials are described. These are motivated by both the goal of developing a real-time training simulator for arthroscopic surgery and the goal of developing an accurate model of cloth for automatic garment handling. In this approach a material is represented as a large collection of microscopic particles interacting with each other according to simple physical laws operating on a microscopic level. Since modeled materials derive their macroscopic properties from these microscopic interactions, the technique closely parallels the actual discrete structures of nature. The development of software tools for use in experimentation, which has been the focus of initial investigations, is discussed. <<ETX>>
Population genetics and phylogeography of the pygmy nuthatch in Southern California

I examined the population genetic structure, phylogeography, and subspecies structure of pygmy nuthatch (Sitta pygmaea') populations in southern California using mitochondrial DNA sequence data. Population genetic analyses indicate that pygmy nuthatch populations fragmented in the disjunct mountain ranges of southern California exhibit low but significant levels of genetic differentiation. These results correspond to phylogeographic analyses that further suggest that the isolation of pygmy nuthatch populations occurred recently, most likely at the beginning of the current interglacial period (~10,000-20,000 years ago). The mitochondrial DNA data also support a subspecific break between S. p. melanotis and S. p. leuconucha farther north than proposed subspecific breaks that are based upon morphological characters. These results are similar to patterns found in other bird populations exhibiting similar distributions in California and western North America.