Maternal Expression Relaxes Constraint on Innovation of the Anterior Determinant, bicoid

The origin of evolutionary novelty is believed to involve both positive selection and relaxed developmental constraint. In flies, the redesign of anterior patterning during embryogenesis is a major developmental innovation and the rapidly evolving Hox gene, bicoid (bcd), plays a critical role. We report evidence for relaxation of selective constraint acting on bicoid as a result of its maternal pattern of gene expression. Evolutionary theory predicts 2-fold greater sequence diversity for maternal effect genes than for zygotically expressed genes, because natural selection is only half as effective acting on autosomal genes expressed in one sex as it is on genes expressed in both sexes. We sample an individual from ten populations of Drosophila melanogaster and nine populations of D. simulans for polymorphism in the tandem gene duplicates bcd, which is maternally expressed, and zerknüllt (zen), which is zygotically expressed. In both species, we find the ratio of bcd to zen nucleotide diversity to be two or more in the coding regions but one in the noncoding regions, providing the first quantitative support for the theoretical prediction of relaxed selective constraint on maternal-effect genes resulting from sex-limited expression. Our results suggest that the accelerated rate of evolution observed for bcd is owing, at least partly, to variation generated by relaxed selective constraint

Excellent diagnostic characteristics for ultrafast gene profiling of DEFA1-IL1B-LTF in detection of prosthetic joint infections

The timely and exact diagnosis of prosthetic joint infection (PJI) is crucial for surgical decision-making. Intraoperatively, delivery of the result within an hour is required. Alpha-defensin lateral immunoassay of joint fluid (JF) is precise for the intraoperative exclusion of PJI; however, for patients with a limited amount of JF and/or in cases where the JF is bloody, this test is unhelpful. Important information is hidden in periprosthetic tissues that may much better reflect the current status of implant pathology. We therefore investigated the utility of the gene expression patterns of 12 candidate genes (TLR1, -2, -4, -6, and 10, DEFA1, LTF, IL1B, BPI, CRP, IFNG, and DEFB4A) previously associated with infection for detection of PJI in periprosthetic tissues of patients with total joint arthroplasty (TJA) (n = 76) reoperated for PJI (n = 38) or aseptic failure (n = 38), using the ultrafast quantitative reverse transcription-PCR (RT-PCR) Xxpress system (BJS Biotechnologies Ltd.). Advanced data-mining algorithms were applied for data analysis. For PJI, we detected elevated mRNA expression levels of DEFA1 (P < 0.0001), IL1B (P < 0.0001), LTF (P < 0.0001), TLR1 (P = 0.02), and BPI (P = 0.01) in comparison to those in tissues from aseptic cases. A feature selection algorithm revealed that the DEFA1-IL1B-LTF pattern was the most appropriate for detection/exclusion of PJI, achieving 94.5% sensitivity and 95.7% specificity, with likelihood ratios (LRs) for positive and negative results of 16.3 and 0.06, respectively. Taken together, the results show that DEFA1-IL1B-LTF gene expression detection by use of ultrafast qRT-PCR linked to an electronic calculator allows detection of patients with a high probability of PJI within 45 min after sampling. Further testing on a larger cohort of patients is needed.Web of Science5592697268

3D hindlimb joint mobility of the stem-archosaur Euparkeria capensis with implications for postural evolution within Archosauria.

Triassic archosaurs and stem-archosaurs show a remarkable disparity in their ankle and pelvis morphologies. However, the implications of these different morphologies for specific functions are still poorly understood. Here, we present the first quantitative analysis into the locomotor abilities of a stem-archosaur applying 3D modelling techniques. μCT scans of multiple specimens of Euparkeria capensis enabled the reconstruction and three-dimensional articulation of the hindlimb. The joint mobility of the hindlimb was quantified in 3D to address previous qualitative hypotheses regarding the stance of Euparkeria. Our range of motion analysis implies the potential for an erect posture, consistent with the hip morphology, allowing the femur to be fully adducted to position the feet beneath the body. A fully sprawling pose appears unlikely but a wide range of hip abduction remained feasible-the hip appears quite mobile. The oblique mesotarsal ankle joint in Euparkeria implies, however, a more abducted hindlimb. This is consistent with a mosaic of ancestral and derived osteological characters in the hindlimb, and might suggest a moderately adducted posture for Euparkeria. Our results support a single origin of a pillar-erect hip morphology, ancestral to Eucrocopoda that preceded later development of a hinge-like ankle joint and a more erect hindlimb posture

Dynamics and pattern formation in invasive tumor growth

In this work, we study the in-vitro dynamics of the most malignant form of the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor consists of the inner dense proliferating zone and the outer less dense invasive region. Experiments with different types of cells show qualitatively different behavior. Wild-type cells invade a spherically symmetric manner, but mutant cells are organized in tenuous branches. We formulate a model for this sort of growth using two coupled reaction-diffusion equations for the cell and nutrient concentrations. When the ratio of the nutrient and cell diffusion coefficients exceeds some critical value, the plane propagating front becomes unstable with respect to transversal perturbations. The instability threshold and the full phase-plane diagram in the parameter space are determined. The results are in a good agreement with experimental findings for the two types of cells.Comment: 4 pages, 4 figure

Identification of the connections in biologically inspired neural networks

We developed an identification method to find the strength of the connections between neurons from their behavior in small biologically-inspired artificial neural networks. That is, given the network external inputs and the temporal firing pattern of the neurons, we can calculate a solution for the strengths of the connections between neurons and the initial neuron activations if a solution exists. The method determines directly if there is a solution to a particular neural network problem. No training of the network is required. It should be noted that this is a first pass at the solution of a difficult problem. The neuron and network models chosen are related to biology but do not contain all of its complexities, some of which we hope to add to the model in future work. A variety of new results have been obtained. First, the method has been tailored to produce connection weight matrix solutions for networks with important features of biological neural (bioneural) networks. Second, a computationally efficient method of finding a robust central solution has been developed. This later method also enables us to find the most consistent solution in the presence of noisy data. Prospects of applying our method to identify bioneural network connections are exciting because such connections are almost impossible to measure in the laboratory. Knowledge of such connections would facilitate an understanding of bioneural networks and would allow the construction of the electronic counterparts of bioneural networks on very large scale integrated (VLSI) circuits

Adsorbate-induced surface stress, surface strain and surface reconstruction : S on Cu(100) and Ni(100)

Density functional theory (DFT) calculations have been applied to investigate the known difference in behaviour of S adsorption on Cu(100) and Ni(100). Both surfaces form a 0.25 ML (2 × 2) adsorption phase, but while at higher coverage a 0.5 ML c(2 × 2) phase forms on Ni(100), on Cu(100) only a reconstructed 0.47 ML (√17 × √17)R14° structure occurs. Calculations of the energy, structure, and surface stress of (2 × 2) and c(2 × 2) phases on both substrates show there is an energy advantage on both surfaces to form the higher coverage phase, but that both surfaces show local surface strain around the S atoms in the (2 × 2) phase, a phenomenon previously investigated only on Cu(100). More than forty different structural models of the Cu(100)(√17 × √17)R14°-S phase have been investigated. The pseudo-(100)c(2 × 2) structure previously proposed, containing 16 Cu adatoms per unit mesh in the reconstructed layer, is found to be less energetically favourable than many other possible structures, even after taking account of local structural relaxations. Significantly more favourable is a structure with 12 Cu adatoms per (√17 × √17)R14° unit mesh, previously proposed on the basis of scanning tunnelling microscopy (STM), and found to yield simulated STM images in good agreement with experiment. This model has all S atoms in local 4-fold coordinated hollows relative to the Cu atoms below, half being located above Cu adatoms with the remainder lying above the underlying outermost substrate layer. However, an alternative model with only 4 Cu adatoms and with half the S atoms at 3-fold coordinated sites on the periphery of the Cu adatom cluster, has an even lower energy and gives simulated STM images in excellent agreement with experiment

Ice Cores from the St. Elias Mountains, Yukon, Canada: Their Significance for Climate, Atmospheric Composition and Volcanism in the North Pacific Region

A major achievement in research supported by the Kluane Lake Research Station was the recovery, in 2001 –02, of a suite of cores from the icefields of the central St. Elias Mountains, Yukon, by teams of researchers from Canada, the United States, and Japan. This project led to the development of parallel, long (103 – 104 year) ice-core records of climate and atmospheric change over an altitudinal range of more than 2 km, from the Eclipse Icefield (3017 m) to the ice-covered plateau of Mt. Logan (5340 m). These efforts built on earlier work recovering single ice cores in this region. Comparison of these records has allowed for variations in climate and atmospheric composition to be linked with changes in the vertical structure and dynamics of the North Pacific atmosphere, providing a unique perspective on these changes over the Holocene. Owing to their privileged location, cores from the St. Elias Icefields also contain a remarkably detailed record of aerosols from various sources around or across the North Pacific. In this paper we review major scientific findings from the study of St. Elias Mountain ice cores, focusing on five main themes: (1) The record of stable water isotopes (δ18O, δD), which has unique characteristics that differ from those of Greenland, other Arctic ice cores, and even among sites in the St. Elias; (2) the snow accumulation history; (3) the record of pollen, biomass burning aerosol, and desert dust deposition; (4) the record of long-range air pollutant deposition (sulphate and lead); and (5) the record of paleo-volcanism. Our discussion draws on studies published since 2000, but based on older ice cores from the St. Elias Mountains obtained in 1980 and 1996

Multilingual assessment of early child development: Analyses from repeated observations of children in Kenya.

In many low- and middle-income countries, young children learn a mother tongue or indigenous language at home before entering the formal education system where they will need to understand and speak a countrys official language(s). Thus, assessments of children before school age, conducted in a nations official language, may not fully reflect a childs development, underscoring the importance of test translation and adaptation. To examine differences in vocabulary development by language of assessment, we adapted and validated instruments to measure developmental outcomes, including expressive and receptive vocabulary. We assessed 505 2-to-6-year-old children in rural communities in Western Kenya with comparable vocabulary tests in three languages: Luo (the local language or mother tongue), Swahili, and English (official languages) at two time points, 5-6&nbsp;weeks apart, between September 2015 and October 2016. Younger children responded to the expressive vocabulary measure exclusively in Luo (44%-59% of 2-to-4-year-olds) much more frequently than did older children (20%-21% of 5-to-6-year-olds). Baseline receptive vocabulary scores in Luo (β&nbsp;=&nbsp;0.26, SE&nbsp;=&nbsp;0.05, p&nbsp;&lt;&nbsp;0.001) and Swahili (β&nbsp;=&nbsp;0.10, SE&nbsp;=&nbsp;0.05, p&nbsp;=&nbsp;0.032) were strongly associated with receptive vocabulary in English at follow-up, even after controlling for English vocabulary at baseline. Parental Luo literacy at baseline (β&nbsp;=&nbsp;0.11, SE&nbsp;=&nbsp;0.05, p&nbsp;=&nbsp;0.045) was associated with child English vocabulary at follow-up, while parental English literacy at baseline was not. Our findings suggest that multilingual testing is essential to understanding the developmental environment and cognitive growth of multilingual children

Schroedinger operators with singular interactions: a model of tunneling resonances

We discuss a generalized Schr\"odinger operator in $L^2(\mathbb{R}^d), d=2,3$, with an attractive singular interaction supported by a $(d-1)$-dimensional hyperplane and a finite family of points. It can be regarded as a model of a leaky quantum wire and a family of quantum dots if $d=2$, or surface waves in presence of a finite number of impurities if $d=3$. We analyze the discrete spectrum, and furthermore, we show that the resonance problem in this setting can be explicitly solved; by Birman-Schwinger method it is cast into a form similar to the Friedrichs model.Comment: LaTeX2e, 34 page