Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmodium vivax Sporozoite Challenge in Malaria-Naïve and Semi-Immune Colombian Volunteers

Background Significant progress has been recently achieved in the development of Plasmodium vivax challenge infections in humans, which are essential for vaccine and drug testing. With the goal of accelerating clinical development of malaria vaccines, the outcome of infections experimentally induced in naïve and semi-immune volunteers by infected mosquito bites was compared. Methods Seven malaria-naïve and nine semi-immune Colombian adults (n = 16) were subjected to the bites of 2–4 P. vivax sporozoite-infected Anopheles mosquitoes. Parasitemia levels, malaria clinical manifestations, and immune responses were assessed and compared. Results All volunteers developed infections as confirmed by microscopy and RT-qPCR. No significant difference in the pre-patent period (mean 12.5 and 12.8 days for malaria-naïve and malaria-exposed, respectively) was observed but naïve volunteers developed classical malaria signs and symptoms, while semi-immune volunteers displayed minor or no symptoms at the day of diagnosis. A malaria-naïve volunteer developed a transient low submicroscopic parasitemia that cured spontaneously. Infection induced an increase in specific antibody levels in both groups. Conclusion Sporozoite infectious challenge was safe and reproducible in semi-immune and naïve volunteers. This model will provide information for simultaneous comparison of the protective efficacy of P. vivax vaccines in naïve and semi-immune volunteers under controlled conditions and would accelerate P. vivax vaccine development. Trial Registration clinicaltrials.gov NCT01585077
Influence of Glutathione S-Transferase M1 and T1 Genotypes on Larynx Cancer Risk among Korean Smokers

Abstract Glutathione S-transferase (GST) isoenzymes are involved in the detoxification of major carcinogens present in tobacco smoke. It is thus conceivable that deficiency in GST activity due to homozygous deletions of the GSTM1 and GSTT1 genes (the null genotypes) may modulate susceptibility to smoking-induced cancers. The influence of the GSTM1 and GSTT1 null genotypes on larynx cancer risk among the Korean population were evaluated using peripheral blood DNA from 82 larynx cancer patients and 63 healthy controls, all of whom were male current smokers. Increased larynx cancer risk was related to the GSTM1 null genotype (odds ratio (OR)=3.53, 95% confidence interval (CI)=1.27−9.83). The OR associated with the GSTT1 null genotype was also increased, but did not reach statistical significance (OR=1.83, 95% CI=0.70−4.79). Individuals lacking both the GSTM1 and GSTT1 genes were at a significantly higher risk for larynx cancer than individuals with both genes present (OR=4.04, 95% CI=1.33−12.30). These data confirm that the GSTM1 null genotype is an important risk modifier for larynx cancer among Korean smokers and combined GSTM1 and GSTT1 null genotypes could be a useful predictor of genetic susceptibility to larynx cancer.
A Negative Regulatory Loop between MicroRNA and Hox Gene Controls Posterior Identities in Caenorhabditis elegans

MicroRNAs (miRNAs) have been found to regulate gene expression across eukaryotic species, but the function of most miRNA genes remains unknown. Here we describe how the analysis of the expression patterns of a well-conserved miRNA gene, mir-57, at cellular resolution for every minute during early development of Caenorhabditis elegans provided key insights in understanding its function. Remarkably, mir-57 expression shows strong positional bias but little tissue specificity, a pattern reminiscent of Hox gene function. Despite the minor defects produced by a loss of function mutation, overexpression of mir-57 causes dramatic posterior defects, which also mimic the phenotypes of mutant alleles of a posterior Hox gene, nob-1, an Abd homolog. More importantly, nob-1 expression is found in the same two posterior AB sublineages as those expressing mir-57 but with an earlier onset. Intriguingly, nob-1 functions as an activator for mir-57 expression; it is also a direct target of mir-57. In agreement with this, loss of mir-57 function partially rescues the nob-1 allele defects, indicating a negative feedback regulatory loop between the miRNA and Hox gene to provide positional cues. Given the conservation of the miRNA and Hox gene, the regulatory mechanism might be broadly used across species. The strategy used here to explore mir-57 function provides a path to dissect the regulatory relationship between genes.
Dealing with incongruence in phylogenomic analyses

Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent. We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
Heterogeneity in Breast Cancer and the Problem of Relevance of Findings

Many attempts are made to identify critical genetic events responsible for the development and progression of breast cancer. There is increasing evidence that breast cancer is a heterogeneous disease, both, phenotypically as well as with respect to its molecular biologically. It is, therefore, extremely difficult to establish a diagnostically and prognostically relevant tumourigenesis model. Emerging new techniques such as microarrays, will provide us with a wealth of additional data over the next years. The precise sampling of tumour material in clearly defined histopathological lesions will be a prerequisite for the assignment of specific genetic alterations to defined stages of breast disease.
The Hemodynamic Effects of Ephedrine on the Onset Time of Rocuronium in Pigs

Several studies have found a correlation between the onset time of muscle relaxants, cardiac index, and muscle blood flow. Ephedrine increases these hemodynamic variables and shortens onset time of rocuronium in humans. Our aim in this animal study was to determine the effect of ephedrine on the onset time of rocuronium, cardiac index, and muscle blood flow after administration of thiopental. At predefined measuring points, mean arterial blood pressure and cardiac index were measured invasively and onset time was determined mechanomyographically. Twenty-four pigs were randomly assigned to three groups. Group I received etomidate and subsequently rocuronium (2 × 95% effective dose). Instead of etomidate, Group II received thiopental. In Group III, ephedrine 100 &mgr;g/kg was given before thiopental; additionally, muscle blood flow was measured (fluorescent microspheres). Although there were differences in hemodynamics between Groups I and II, this was not reflected in different onset times of rocuronium. In Group III, ephedrine compensated the thiopental-induced decrease of mean arterial blood pressure, cardiac index, and muscle blood flow, but no significant shortening of onset time (Group I: 74 ± 21 s; Group II: 71 ± 24; Group III: 69 ± 22 s) was found. Our results demonstrated that ephedrine-related increases in cardiac index and blood flow did not shorten onset time of rocuronium in healthy pigs.
Automatic Semantic Annotation of Real-World Web Images

As the number of Web images is increasing at a rapid rate, searching them semantically presents a significant challenge. Many raw images are constantly uploaded with little meaningful direct annotations of semantic content, limiting their search and discovery. In this paper, we present a semantic annotation technique based on the use of image parametric dimensions and metadata. Using decision trees and rule induction, we develop a rule-based approach to formulate explicit annotations for images fully automatically, so that by the use of our method, semantic query such as "sunset by the sea in autumn in New York" can be answered and indexed purely by machine. Our system is evaluated quantitatively using more than 100,000 Web images. Experimental results indicate that this approach is able to deliver highly competent performance, attaining good recall and precision rates of sometimes over 80%. This approach enables a new degree of semantic richness to be automatically associated with images which previously can only be performed manually.
Collateral Circulation in the Limb

ARRiS AND GALE lectures dealing with blood vessels given in the last ten years number as many as all those which concerned them in the preceding century. This is a clear indication of increasing interest in the blood vessels, as witness also the present stirring developments in the surgery of the cardiovascular system. Despite, or more properly perhaps because of, the exciting nature of some of these developments, it may not be out of place to emphasise here, in the strongest terms, the importance of the study of the behaviour of collateral circulations in the field of the diseases resulting in arterial obstruction; indeed it might, with some justice, present a claim for first place. Moreover, it involves fundamental problems of blood vessel growth.
Application of the fractal fragmentation model to the fill of natural shear zones

Statistical descriptions of the frequency size distribution of rock fragments are summarised in the introduction. It is shown, that not all soils exhibit fractal frequency size distribution. A physical process leading to the scale invariant frequency size distribution of material sheared under constrained conditions is then described from the micro-mechanical point of view. The material from natural shear zones in silty shales is examined in the framework of this theory and it is shown that this theory may be relevant. Finally some possible applications for geotechnical engineering are discussed.
Senescing grass crops as regional sources of reactive volatile organic compounds

[1] Grass crop species, rice and sorghum, that are widely grown in the southeastern Texas region were analyzed for release of biogenic volatile organic compounds (VOCs) in simulated leaf-drying/senescence experiments. VOC release was measured by both online proton transfer reaction mass spectrometry (PTR-MS) and proton transfer ion trap mass spectrometry (PIT-MS) methods, and it was demonstrated that these two grass crops release a large variety of oxygenated VOCs upon drying under laboratory conditions primarily from leaves and not from stems. VOC release from paddy rice varieties was much greater than from sorghum, and major VOCs identified by gas chromatography PTR-MS included methanol, acetaldehyde, acetone, n-pentanal, methyl propanal, hexenol, hexanal, cis-3-hexenal, and trans-2-hexenal. The latter four VOCs, all C6 compounds known to be formed in wounded leaves, were the major volatiles released from drying rice leaves; smaller but substantial amounts of acetaldehyde were observed in all drying experiments. Online detection of VOCs using PIT-MS gave results comparable to those obtained with PTR-MS, and use of PIT-MS with collision-induced dissociation of trapped ions allowed unambiguous determination of the ratios of cis- and trans-hexenals during different phases of drying. As rice is one of the largest harvested crops on a global scale, it is conceivable that during rice senescence releases of biogenic VOCs, especially the reactive C6 wound VOCs, may contribute to an imbalance in regional atmospheric oxidant formation during peak summer/fall ozone formation periods. A county-by-county estimate of the integrated emissions of reactive biogenic VOCs from sorghum and rice production in Texas suggests that these releases are orders of magnitude lower than anthropogenic VOCs in urban areas but also that VOC emissions from rice in southeastern coastal Texas may need to be included in regional air quality assessments during periods of extensive harvesting.
Structure and protein environment of the retinal chromophore in light- and dark-adapted bacteriorhodopsin studied by solid-state NMR.

Our previous solid-state 13C NMR studies on bR have been directed at characterizing the structure and protein environment of the retinal chromophore in bR568 and bR548, the two components of the dark-adapted protein. In this paper, we extend these studies by presenting solid-state NMR spectra of light-adapted bR (bR568) and examining in more detail the chemical shift anisotropy of the retinal resonances near the ionone ring and Schiff base. Magic angle spinning (MAS) 13C NMR spectra were obtained of bR568, regenerated with retinal specifically 13C labeled at positions 12-15, which allowed assignment of the resonances observed in the dark-adapted bR spectrum. Of particular interest are the assignments of the 13C-13 and 13C-15 resonances. The 13C-15 chemical resonance for bR568 (160.0 ppm) is upfield of the 13C-15 resonance for bR548 (163.3 ppm). This difference is attributed to a weaker interaction between the Schiff base and its associated counterion in bR568. The 13C-13 chemical shift for bR568 (164.8 ppm) is close to that of the all-trans-retinal protonated Schiff base (PSB) model compound (approximately 162 ppm), while the 13C-13 resonance for bR548 (168.7 ppm) is approximately 7 ppm downfield of that of the 13-cis PSB model compound. The difference in the 13C-13 chemical shift between bR568 and bR548 is opposite that expected from the corresponding 15N chemical shifts of the Schiff base nitrogen and may be due to conformational distortion of the chromophore in the C13 = C14-C15 bonds. (ABSTRACT TRUNCATED AT 250 WORDS)
Profit maximization for multiple products in online social networks

Information propagation in online social networks (OSNs), which helps shaping consumers' purchasing decisions, has received a lot of attention. The ultimate goal of marketing and advertising in OSNs is to massively influence audiences and enlarge the number of product adoptions. Most of existing works focus on maximizing the influence of a single product or promoting the adoption of one product in competing campaigns. However, in reality, the majority of companies produce various products for supplying customers with different needs. Therefore, it is truly significant and also challenging to wisely distribute limited budget across multiple products in viral marketing. In this paper, we investigate a Profit Maximization with Multiple Adoptions (PM2A) problem, which aims at maximizing the overall profit across all products. The natural greedy fails to provide a bounded result. In order to select high quality seeds for information propagation, we first proposed the PMCE algorithm, which has a ratio 1/2 (1 - 1/e2). Moreover, we further improve this ratio to (1-1/e) by proposing the PMIS algorithm. Comprehensive experiments on three real social networks are conducted. And results show that our algorithms outperform other heuristics, and better distribute the budget in terms of profit maximization.
Activation of Sphingosine 1-Phosphate Receptor 1 Enhances Hippocampus Neurogenesis in a Rat Model of Traumatic Brain Injury: An Involvement of MEK/Erk Signaling Pathway

Among sphingosine 1-phosphate receptors (S1PRs) family, S1PR1 has been shown to be the most highly expressed subtype in neural stem cells (NSCs) and plays a crucial role in the migratory property of NSCs. Recent studies suggested that S1PR1 was expressed abundantly in the hippocampus, a specific neurogenic region in rodent brain for endogenous neurogenesis throughout life. However, the potential association between S1PR1 and neurogenesis in hippocampus following traumatic brain injury (TBI) remains unknown. In this study, the changes of hippocampal S1PR1 expression after TBI and their effects on neurogenesis and neurocognitive function were investigated, focusing on particularly the extracellular signal-regulated kinase (Erk) signaling pathway which had been found to regulate multiple properties of NSCs. The results showed that a marked upregulation of S1PR1 occurred with a peak at 7 days after trauma, revealing an enhancement of proliferation and neuronal differentiation of NSCs in hippocampus due to S1PR1 activation. More importantly, it was suggested that mitogen-activated protein kinase-Erk kinase (MEK)/Erk cascade was required for S1PR1-meidated neurogenesis and neurocognitive recovery following TBI. This study lays a preliminary foundation for future research on promoting hippocampal neurogenesis and improving TBI outcome.
A 32.75-Gb/s Voltage-Mode Transmitter With Three-Tap FFE in 16-nm CMOS

This paper describes a 32.75-Gb/s voltage-mode transmitter (TX) with three-tap feed forward equalization that is fabricated in a 16-nm FinFET CMOS technology. The TX uses a dual regulator architecture to allow independent control of output swing, output common-mode, and equalization. A hybrid impedance control scheme is presented where the total number of driver slices is used for coarse impedance control, and analog loop-based voltage control is used for fine impedance control of the TX. A finite-impulse response compensation circuit to compensate for the data dependent current due to equalization is also presented. The TX consumes 120.8 mW with 0.9- and 1.2-V supplies, provides 0.25–0.9 Vpp output swing, and achieves total jitter of 6.49 ps–pp and random jitter of 220 fs–rms at 32.75 Gb/s with bit error rate of 1e-12.
Cross-Species Interaction between Rapidly Evolving Telomere-Specific Drosophila Proteins

Telomere integrity in Drosophila melanogaster is maintained by a putative multisubunit complex called terminin that is believed to act in analogy to the mammalian shelterin complex in protecting chromosome ends from being recognized as sites of DNA damage. The five proteins supposed to form the terminin complex are HP1-ORC associated protein, HP1-HOAP interacting protein, Verrocchio, Drosophila Telomere Loss/Modigliani and Heterochromatic Protein 1. Four of these proteins evolve rapidly within the Drosophila genus. The accelerated evolution of terminin components may indicate the involvement of these proteins in the process by which new species arise, as the resulting divergence of terminin proteins might prevent hybrid formation, thus driving speciation. However, terminin is not an experimentally proven entity, and no biochemical studies have been performed to investigate its assembly and action in detail. Motivated by these facts in order to initiate biochemical studies on terminin function, we attempted to reconstitute terminin by co-expressing its subunits in bacteria and investigated the possible role of the fast-evolving parts of terminin components in complex assembly. Our results suggest formation of stable subcomplexes of terminin, but not of the whole complex in vitro. We found that the accelerated evolution is restricted to definable regions of terminin components, and that the divergence of D. melanogaster Drosophila Telomere Loss and D. yakuba Verrocchio proteins does not preclude their stable interaction.
Active living in the trucking sector: environmental barriers and health promotion strategies.

BACKGROUND As one of the most underserved segments of the U.S. labor force, truck drivers have been associated with a series of morbid conditions intimately linked to their occupational milieux, their mostly unhealthful nutritional intake and sedentary lifestyles, and their resulting excess weight-gain. METHODS This paper reports data from a baseline assessment of 25 trucking work settings located around interstate highways I-40 and I-85 in North Carolina. It examines how the environmental attributes of these work settings influence the physical and recreational activity behaviors of truckers, compares findings with those from other occupational environments, and brings to the fore a new health promotion paradigm for trucking worksites. RESULTS Findings support growing empirical and anecdotal evidence that trucking work settings remain not only active-living deserts, but overall unhealthful places. A scan of physical, social, and information environments within trucking worksites as well as physical environments of surrounding communities reveal only meager opportunities for physical and recreational activity for truckers. CONCLUSION This paper places the highly underserved population of truckers firmly within the discourse of worksite health promotion, and calls for comprehensive multistakeholder wellness strategies that address a multitude of risk factors linked to the occupational context.
The high spontaneous mutation rate: is it a health risk?

The human mutation rate for base substitutions is much higher in males than in females and increases with paternal age. This effect is mainly, if not entirely, due to the large number of cell divisions in the male germ line. The mutation-rate increase is considerably greater than expected if the mutation rate were simply proportional to the number of cell divisions. In contrast, those mutations that are small deletions or rearrangements do not show the paternal age effect. The observed increase with the age of the father in the incidence of children with different dominant mutations is variable, presumably the result of different mixtures of base substitutions and deletions. In Drosophila, the rate of mutations causing minor deleterious effects is estimated to be about one new mutation per zygote. Because of a larger number of genes and a much larger amount of DNA, the human rate is presumably higher. Recently, the Drosophila data have been reanalyzed and the mutation-rate estimate questioned, but I believe that the totality of evidence supports the original conclusion. The most reasonable way in which a species can cope with a high mutation rate is by quasi-truncation selection, whereby a number of mutant genes are eliminated by one "genetic death. "