Shape Of Pattern Research Articles

Модель обработки и классификации сигналов ЭКГ на основе интеграции CNN, LSTM и метода двойного внимания

Heart rhythm abnormalities diagnosis or classification via electrocardiogram (ECG) in the field of signal processing is regarded as a challenging problem. Classifying ECG signals under the rules of the "Association for the Advancement of Medical Instrumentation (AAMI)" and the inter-patient scheme increases the difficulty of the challenge. AAMI classifies the ECG signal into the following categories: N, S, V, F, and Q. The S category is difficult to detect since its shape pattern is like the N category. To overcome these challenges, this study proposes a novel, robust, end-to-end, and efficient model for ECG signal classification by integrating the "Convolutional Neural Network (CNN)", "Long Short-Term Memory (LSTM)" and dual attention techniques. The architecture of the model includes an encoder-decoder unit built from LSTMs and a dual attention unit with two levels: the first is based on Squeeze-and-Excitation (SE) networks that are incorporated into CNN sections, and they are responsible for weighting the Local Heartbeat Shape Pattern (LHSP) features caught by CNN sections, while the second is based on the Bahdanau scheme, which is incorporated into the encoder-decoder unit, and it is responsible for weighting the Global Heartbeat (GH) features caught by the LSTMs. The suggested model can extract the distinctive features that balance local and global information for optimizing the ECG signal diagnosis. The presented approach is superior to previous methods in the literature and comparable to a cardiologist's performance. The introduced model attained the following F1-Scores: 99.12%, 99.89%, 96.48%, and 99.89% for classifying F, V, S, and N beats, respectively.

Molecular-scale kinetic Monte Carlo simulation of pattern formation in photoresist materials for EUV nanolithography

A kinetic Monte Carlo (KMC) simulation tool for modeling the pattern formation process in photoresist materials for extreme ultraviolet (photon energy 92 eV) nanolithography is presented. The availability of such a tool should support the progress toward novel materials and experimental procedures that lead to an improved pattern resolution. The molecular-scale simulations describe the process in a stochastic and mechanistic manner and include the excitation of high-energy electrons upon light absorption, the creation of a charged-particle cloud, electron-induced chemical degradation of the photoresist molecules, the resulting bond formation between neighboring degraded molecules, and a chemical development step after which a pattern of the remaining non-dissolved molecules is obtained. The method is applied to the application-relevant class of Sn-oxocore photoresist materials and uses their known electronic structure and optical electron energy loss function. The validity of the approach is tested by comparing measured and simulated total electron yield spectra and photoelectron spectra. A demonstration of the method is given by calculating the dose and pitch dependent average shape and stochastic variability (line edge roughness) of line patterns that are obtained for rectangular and sine-wave illumination, assuming various scenarios that determine how molecular-scale degradation will lead to bond creation. We show how from these simulations the ultimate pattern resolution can be deduced. The findings are analyzed systematically using results of KMC simulations that reveal the size of the cloud of degraded molecules around a point of absorption (blur length) and that further reveal the sensitivity to uniform illumination (contrast curves), and using percolation theory. We find that KMC modeling captures the consequences of the strong gradients in the density of degraded molecules and of the stochasticity of the patterning process that simplified models do not include, leading to a significantly improved view of the final pattern quality.

A sectional classification of Diplazium Sw. (Athyriaceae), based on plastid genomic, nuclear ribosomal, and morphological evidence

AbstractThe twinsorus‐fern genus Diplazium represents one of the most diverse genera within the lady‐fern family Athyriaceae, encompassing over 300 species, with the highest species diversity concentrated in tropical Asia and the Neotropics. Despite recent progress in phylogenetic studies of Diplazium, the infrageneric classification of this fern group remains challenging, particularly in D. subg. Callipteris. In this study, we explored the phylogenetic relationships within Diplazium using plastid (plastome and amplicon sequences) and nuclear ribosomal data, based on an extensive species sampling. Our phylogenetic analyses, using plastid and nuclear ribosomal datasets, congruently support 4 major clades and 12 subclades. Although deep relationships along the backbone were consistently well resolved using plastomes, nuclear ribosomal genomes and three concatenated plastid markers, cyto‐nuclear discordance was detected within subclades of D. subg. Callipteris. Considering our phylogenetic framework, we propose a classification of Diplazium with a particular focus on sectional delimitation. This classification comprises 4 previously recognized subgenera, and introduces 12 newly established sections. Our infrageneric divisions receive additional support from non‐molecular evidence, including stipe scales, leaf architecture, pinna/pinnule shape, indument and venation patterns, sori and spore features, and geographical distributions.

Nail Disorders as clues to systemic disease.

Disorders of the nail unit can provide important clues to underlying systemic diseases. Onychodystrophy or nail abnormalities include altered nail color, shape, or texture, with morphology and growth patterns often related to local anatomic factors such as edema, vascular supply, and neurologic innervation. Associated pain or loss of function can also affect daily activities. Because nail changes may be due to a range of systemic diseases, we chose to provide a systems-based broad overview of the common nail findings in patients with internal disease.

Analysis of the Characteristics of Mesh with Complex Knitting Patterns for Spaceborne Reflector Antennas

Metallic mesh with complex woven structures is commonly used as the surface in large aperture spaceborne reflector antennas. To study the electrical properties of mesh surfaces characterized by intricate patterns, this paper presents a method for building models to analyze complex meshes. High Frequency Structure Simulator and Computer Simulation Technology (CST) simulation of the reflection coefficients, with Astrakhan’s formulation as a reference, confirm that applying the wire-grid model in CST using the tetrahedral mesh type provides sufficiently accurate results. Furthermore, the rectangular periodic wire-grid model is simulated in CST, and its results are compared with those of Astrakhan’s formulation. Correlations between reflection characteristics and influence factors, including mesh opening size, wire diameter, nature of wire contact, and wave incident angle, are investigated. To exemplify the applicability of the wire-grid model to complex mesh with irregular pattern shapes, the reflection coefficients of a warp-knitted gold-coated molybdenum mesh woven by multi-wires are measured and compared to the simulated results from the wire-grid model. The results prove that the method proposed in this paper is suitable for modeling metal mesh with complex weave patterns.

Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies.

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation by distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60km2 per generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

Compact metasurface antenna for Sub-6 GHz applications with isolated n77/n78 bands using CSRR

Abstract A compact (0.35 λ0× 0.35 λ0 where λ0 is free space wavelength at the lower resonance frequency 3.50 GHz) bio-inspired tulip flower-shaped antenna (TFSA) is proposed. A double negative (DNG) metamaterial complementary split ring resonator (CSRR) is introduced near the feed in the hybrid triangular-circular patch which inserts a notch-band (4.20-4.38 GHz) in the wide bandwidth (3.15-7.05 GHz) and makes the antenna response dual-band. Consequently, this results in in-band interference reduction in 5G-Sub-6 GHz applications. A slotted FSS is placed at a distance of 28.507 mm beneath the monopole-reduced ground of the antenna to enhance the reduced gain from 4.39 dBi to 7.22 dBi. A further gain is improved to 12.84 dBi by placing a full copper surface (0.35 λ0× 0.35 λ0) as the reflector layer is placed below FSS at 1.6 mm. Finally, prototyped TFSA with FSS and reflector model achieve a dual bands reflection coefficient response (3.15-4.20 GHz): n77/n78, and (4.38-7.03 GHz): n46/n47/n96/n102/n79. The antenna reflection coefficient is tested using Keysight 14 GHz FieldFox Microwave Analyzer N9916A, and radiation patterns in the E-plane and H-plane are measured using an 18 GHz anechoic chamber. The comparison of simulated results with measured results is found an excellent match in bandwidth and with shapes of gain radiation patterns. The reflector and FSS jointly make the radiation pattern strong in the E-plane above the TFSA radiator. The antenna is well suited for n77/n78 (3.30-4.20 GHz), n79(4.40-4.99 GHz), n46 (5150-5925MHz), n47 (5855 – 5925MHz), n96/n102 (5925-6425MHz), 5.8 GHz HiperLAN, WiMAX 3.5GHz applications. An electrical equivalent circuit model of the proposed TFSA antenna is presented and validated using ADS software.

Operando Li-ion distribution measurement of all-solid-state batteries by Compton-scattered x rays

We report operando measurements of the Li-ion distribution in the anode and cathode of a coin-type all-solid-state battery in the charged and discharged states via Compton scattering using high-energy synchrotron radiation x-ray analysis. From the line shape pattern analysis of the Compton scattering x-ray spectrum, we accurately observed the Li-ion distribution within the cathode and anode during the charging/discharging of a real coin-shaped battery in an SUS casing. This study discusses the difference in Li-ion distribution between the cathode and anode and compares the Li-ion distribution of the battery after 20 charge–discharge cycles with those of a fresh battery.

Bioclimatic variables affect seed mass and seedling traits of four Gymnocalycium (Cactaceae) species along elevational gradients

Differences in climatic factors associated with elevation can lead to natural selection for local adaptation in species with a wide distribution range, with some regenerative characteristics changing along the gradient. Most Cactaceae species occur in heterogeneous environments, mainly in mountains. The increasing severity of environmental conditions along elevational gradients could affect seed size, influencing seedling growth. The main aims of the study were to analyse whether seed mass, and seedling size and shape are related to elevational gradients in different populations of four species of the genus Gymnocalycium and to evaluate the relationship between seed mass and bioclimatic variables. Populations of four species of Gymnocalycium (G. andreae, G. erinaceum, G. monvillei and G. mostii) were sampled; the populations were located along three different elevation gradients, with each population corresponding to an elevational class (extremes and intermediate sites). At each elevational site, mature fruits were collected and seed mass and seedling traits were measured. A shape index was calculated by dividing height by width. A value of 1 represents 'globose' seedlings, while increasing values indicate that the seedlings become 'columnar'. The Pearson correlation coefficient was calculated to analyse the relationship between seed mass and seedling size variables. Linear models were used to analyse seed size and seedling shape. First, with elevation as a predictor and then for seed mass, the 19 bioclimatic variables were extracted from WorldClim. The results show that seed mass was positively correlated with seedling shape index, and with seedling height and width. Differences in seed mass among populations were explained by the species and the gradient where they lived, as well as by the environmental variables mean temperature of the coldest quarter, precipitation of the wettest month, and precipitation of the driest month. In conclusion, the intraspecific analyses of the four Gymnocalycium species revealed that the seedling shape patterns were similar across all species in relation to elevation. However, seed mass varied with elevation differently for each species. These findings suggest that each species possesses unique characteristics that enable them to thrive in varying climatic conditions along elevational gradients.

Analysis pipeline to quantify uterine gland structural variations.

Technical advances in whole tissue imaging and clearing have allowed 3D reconstruction of exocrine uterine glands deep-seated in the endometrium. However, there are limited gland structure analysis platforms to analyze these imaging data sets. Here, we present a pipeline for segmenting and analyzing uterine gland shape. Using our segmentation methodology, we derive metrics to describe gland length, shape, and branching patterns. We then quantify gland behavior with respect to organization around the embryo and proximity of each gland to the uterine lumen. We apply this image analysis pipeline to uterine glands at the peri-implantation time points of a mouse pregnancy. Our analysis reveals that at the time of embryo or egg entry into the uterus, glands show changes in length, tortuosity, and proximity to the uterine lumen while gland branch number stays the same. Eventually, these shape changes aid in reorganization of the glands around the embryo implantation site. We further apply our analysis pipeline to human and guinea pig uterine glands, extending feasibility to other mammalian species. This work serves as a resource for researchers to extract quantitative and reproduciblemorphological features from three-dimensional uterine gland images to reveal insights about functional and structural patterns.

NIMG-02. DEVELOPING A RADIOMIC HIERARCHICAL GAUSSIAN PROCESS BOOSTING MODEL TO PREDICT PRIMARY TUMOR ORIGIN FROM MULTICENTRIC LONGITUDINAL MRI DATA OF BRAIN METASTASES

Abstract Focal neurologic deficits due to brain metastases might be the initial presentation in patients with cancer. Common approaches to investigate the occult primary malignancy include a whole-body PET-CT, whole-body MRI, studying tumor markers, or histopathological examination. Most of these modalities are expensive, time-consuming, invasive, and delay treatment. The field of radiomics leverages quantitative features extracted from images to improve the decision-making process in clinical practices. Although not easily understandable, these features are proxies for the tumor’s shape, contour, texture, and intensity patterns. They can help understand tumor heterogeneity, predict tumor behavior, and assess treatment response. We propose a robust radiomic workflow using longitudinal MRI data from 914 high-resolution imaging studies from 12 different centers (Ocaña-Tienda et al. (2023), Ramakrishnan et al. (2023), Wang et al. (2023)) to predict the origin of brain metastases from brain MRI scans. After using ensemble feature selection methods, we trained three fixed-effects and one mixed-effects multiclass classification model to account for longitudinal data. Fixed-effects logistic regression and support vector kernel models performed the worst (AUC 0.74 and 0.75, respectively), while the random forest performed better (AUC 0.97). The mixed-effects hierarchical Gaussian process boosting (GPBoost) model performed the best with an accuracy of 85.8%, precision of 85.4%, sensitivity of 85.8%, specificity of 95.7%, and an AUC of 0.98. In one-versus-rest classification, the GPBoost model identified the primary tumor as melanoma with the highest accuracy (96.1%) and non-small cell lung cancer with the lowest accuracy (89.0%). Developing such models holds great promise in reducing patient and institutional costs, improving time to effective treatment, and enhancing overall survival rates through personalized therapy approaches. In the future, we hope that incorporating newer patient data and refining the model to improve external validity would enable more accurate and generalizable predictions, leading to better clinical outcomes across diverse populations.

Importance of habit and environmental characteristics in shaping patterns of richness and range size of ferns and lycophytes in the Atlantic Forest.

Ferns and lycophytes, the two spore-bearing lineages of vascular plants, share a unique life cycle, and because of several morpho-ecophysiological similarities, are usually investigated as a unit, but they may have distinct ecological and environmental responses. Understanding the diversity and distribution patterns of ferns and lycophytes separately is essential for designing effective conservation strategies. We assessed species richness and range sizes using range-diversity analyses and investigated environmental (climatic, edaphic) and ecological (endemism, habit diversity, specialization) predictors of these range and richness metrics using generalized linear models. The central region of the Atlantic Forest primarily contained areas with fern and lycophyte species with high richness and small ranges; the northern and southern extremes of the forest had species with low richness and larger ranges. Fern richness was associated with a combination of environmental and ecological variables; lycophyte richness was associated only with ecological variables. Range sizes were positively related to habit diversity for both ferns and lycophytes, but the effect of environmental variables differed between the two lineages. Critical areas were primarily not within protected areas. Fern range sizes and richness were influenced by a combination of ecological and environmental factors such as temperature, precipitation, and soil variables; only ecological variables influenced lycophyte richness and range sizes. The effects of these factors must be considered separately for the two lineages due to their different responses to stressors. Conservation efforts should increase in the species-rich-low-range areas that are outside protected areas to protect these low-range species.

Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images.

Understanding the dynamic states and transitions of heterogeneous cell populations is crucial for addressing fundamental biological questions. High-content imaging provides rich datasets, but it remains increasingly difficult to integrate and annotate high-dimensional and time-resolved datasets to profile heterogeneous cell population dynamics in different microenvironments. Using hepatic stellate cells (HSCs) LX-2 as model, we proposed a novel analytical strategy for image-based integration and annotation to profile dynamics of heterogeneous cell populations in 2D/3D microenvironments. High-dimensional features were extracted from extensive image datasets, and cellular states were identified based on feature profiles. Time-series clustering revealed distinct temporal patterns of cell shape and actin cytoskeleton reorganization. We found LX-2 showed more complex membrane dynamics and contractile systems with an M-shaped actin compactness trend in 3D culture, while they displayed rapid spreading in early 2D culture. This image-based integration and annotation strategy enhances our understanding of HSCs heterogeneity and dynamics in complex extracellular microenvironments.

Ultrasonographic technique and appearance of the coelomic organs in crocodilians

IntroductionCrocodilians have significant ecological, conservational, and economic roles. They are also commonly raised for commercial purposes and kept as zoological specimens. Although ultrasonography has been used in zoological contexts for health assessments of crocodilians, published studies on a detailed ultrasonography protocol and ultrasonographic anatomy are lacking. This study aimed to establish a standardized ultrasonography protocol and pictorial reference of the ultrasonographic appearances of the coelomic organs of crocodilians.MethodsA total of 7 crocodilians comprising 4 different species were included in this study. The crocodilians were manually restrained and underwent a non-contrasted and contrasted computed tomography (CT) scan, followed by an ultrasonography (USG) examination. Ultrasound fusion imaging technique enabled greater confidence in establishing a clear organ localization and correlation between modalities by visualizing the same anatomy from the same view angle.ResultsThe heart, caudal vena cava, liver, fat body (steatotheca), spleen, stomach, duodenal loops, pancreas, kidneys, testes, ovaries and cloaca were visualized in all species. Longitudinal and transverse images of the coelomic structures were acquired when possible. The ultrasonographic characteristics of the coelomic organs, including transducer positioning, acoustic window and approach, shape, size, marginations, and echo pattern were documented.DiscussionThe findings of this study provided a useful ultrasonographic protocol and anatomical reference of the coelomic organs in crocodilians. Invaluable insights into the practicality and adequacy of ultrasonography in evaluating the coelomic structures of crocodilians as part of health assessment and disease diagnosis were also discussed.

From side‐work to main task: Housing, status, and Tibetan labour migration in Qinghai, China

AbstractAcross China, as in other parts of the world, urbanisation has accelerated at an unprecedented scale over the past 15 years. In farming areas of Qinghai in western China, large‐scale rural–urban movement of Tibetan villagers began around 2010 – a time when state‐led housing subsidy projects were launched. Drawing on ethnographic field research and focusing on the older cohort of rural Tibetan migrants to Xining, the largest city on the Tibetan Plateau, this article explores the complexities and linkages between state‐led housing subsidy projects, status, and Tibetan labour migration. It examines how housing and family status intersect to shape patterns of Tibetan labour migration and gendered divisions of labour. This study highlights an important but less explored factor in migration studies: in my research sites, the recent large‐scale Tibetan labour migration to cities has been driven by the desire to build new houses to secure family status as a result of the motives and social pressure created by state‐led housing subsidy projects.

Помехи неоднозначности сигналов космических РСА при использовании круглой зеркальной антенны

Reflector antennas are quite widely used in radar devices, including space-borne synthetic aperture radars (SARs). One of the problems of such SARs is to ensure the unambiguous measurement of the Doppler frequency of received signals. The shape of the Doppler spectrum of the echo signal is determined by the shape of the antenna pattern in the azimuthal plane. Thus, in general, the narrower the pattern (the larger the antenna size), the lower the level of the interference signal received at the side peaks of the ambiguity function. However, a significant increase in the antenna size is limited by the difficulties of its placement on the SAR launcher, which is especially important for small spacecraft. On the other hand, the required beam width in the elevation plane must satisfy two conditions: ensuring swath and ambiguity detuning. The time ambiguity interval is equal to half the distance of radio wave propagation during the pulse repetition interval. A technical contradiction arises between reducing the level of azimuthal and elevation ambiguity of SAR. The purpose of the article is estimation of azimuth and range ambiguities in a space-based SAR using a circular reflector antenna. In this regard, the material in the article is relevant. We consider a normal looking view which is performed using X-band space-borne SAR. The reasons for the emergence of ambiguities are considered. The necessary mathematical calculations are presented and calculations are made of the projection of circular antenna pattern and the achievable levels of azimuth and range ambiguity for space-based SARs. The obtained values were compared with similar data for a rectangular antenna. An analysis of the influence of the viewing angle and pulse repetition frequency on the ambiguity level was carried out. The results obtained make it possible to estimate the range and azimuth ambiguity level in space-borne SAR and present requirements for the need and level of additional suppression.

Environmental associations and the paleoecological significance of the genus Pyxidicula Ehrenberg,1838 and Pyxidicula muskegii sp. nov. in the Hudson and James Bay region peatlands, Canada

An environmental proxy routinely used in paleoecological studies of peatlands is testate amoebae, which are used to infer successional and hydrological shifts through time. However, since many species of protists globally remain undescribed, important ecological information about community assemblages and their interaction with environmental conditions in both the past and present has potential gaps. During the analysis of testate amoeba assemblages from peat cores across the Hudson and James Bay region of Canada, a testate amoeba that has not been formally described was discovered with high abundance in subfossil assemblages (up to 50%). We describe this new species, Pyxidicula muskegii sp. nov., using morphometric measurements of tests from these peat core records and demonstrate its environmental preferences using modern samples collected from the same region. The hemispheric shape and irregular areolar surface pattern on the test, along with its preference for lawns in both fens and bogs, support that P. muskegii is a new species. This species is also found in much lower relative abundance in modern samples (<3%) than in paleo-peat core records. This difference in modern and paleo-assemblage suggests that there is a taphonomic bias in their relative abundance with depth, which we attribute to their organic test that is less prone to decomposition. Therefore, it is critical to include rare taxa within future transfer function models to incorporate their environmental tolerances and improve model predictions.

CT and MRI features of adrenal hemangioma: A study of 21 cases from two centers

PurposeTo retrospectively analyze the CT and MR imaging presentations of adrenal hemangioma (AH) and to strengthen the recognition for such tumors. Materials and methodsThis retrospective study enrolled 21 patients with 22 lesions histologically proven AH from two centers between October 2010 and November 2023. The clinical presentation and preoperative diagnosis were recorded. Two radiologists reviewed the CT and MR imaging features in consensus, including number, size, shape, boundary, attenuation, signal intensity, and dynamic enhancement pattern. ResultsThe study included nine men and twelve women (mean age 55.6 ± 12.5 years, range, 35–77 years) without hormone production. AH was unilateral in 19 cases, bilateral in 2 cases. The maximum diameter was more than 3 cm in 19/22(86 %). AHs had oval (10/22,45 %), round (5/22, 23 %), or (7/22, 32 %) multilocular shape, and well-defined boundary (18/22,82 %). On unenhanced CT, 11/20 (55 %) displayed peripheral iso-density and central hypo-intensity, 3/20 (15 %) heterogeneously hyper-density, 6/20 (30 %) hypodensity, and 14/20 (70 %) contained speckled calcification. On T2-weighted images, 7/12 (58 %) exhibited nodular hyper-intensity peripherally, markedly hyper-intensity centrally, and hypo-intense fibrotic scar in between, 5/12 (42 %) hyperintensity. On T1-weighted images, 6/12 (50 %) displayed center hyper-intensity surrounded by peripheral hypo-intensity,5/12 hypo-intensity, 1/11 (9 %) hyperintensity. On DWI, 7/12 (58 %) demonstrated peripheral hyper-intensity and central hypo-intensity, 5/12 (42 %) hyper-intensity. CT and MR imaging findings were suggestive of cystic change and necrosis (19/22,86 %, 4 cystic tumors), hemorrhage (15/22,68 %), fat (7/22, 33 %) within the tumors. CT and MR enhanced images showed peripheral nodular enhancement with (3/22,14 %) or without (13/22, 59 %) delayed central filling, nodular peripheral and center enhancement with progressive partial fill-in (2/22,9%), capsular and/or septal mild enhancement (4/22, 18 %), and capsule (16/22,73 %). The solid part was significantly enhanced, similar to the abdominal aorta (AA) with no statistical difference between the two (P > 0.05). ConclusionsSmall AHs (<3cm) have the typical imaging features of hemangioma. The imaging findings of large AHs were various, the combination of T2-hyperintense signal with inner hypo-intense fibrotic scar, speckled calcification, central extensive necrosis and hemorrhage, and nodular peripheral enhancement with persistently slight further contrast accumulation may contribute to suggest the possibility. Cystic AH should be considered as a differential diagnosis for cystic adrenal masses.

Cis-regulatory Variation in Relation to Sex and Sexual Dimorphism in Drosophila melanogaster.

Much of sexual dimorphism is likely due to sex-biased gene expression, which results from differential regulation of a genome that is largely shared between males and females. Here, we use allele-specific expression to explore cis-regulatory variation in Drosophila melanogaster in relation to sex. We develop a Bayesian framework to infer the transcriptome-wide joint distribution of cis-regulatory effects across the sexes. We also examine patterns of cis-regulatory variation with respect to two other levels of variation in sexual dimorphism: (i) across genes that vary in their degree of sex-biased expression and (ii) among tissues that vary in their degree of dimorphism (e.g. relatively low dimorphism in heads vs. high dimorphism in gonads). We uncover evidence of widespread cis-regulatory variation in all tissues examined, with female-biased genes being especially enriched for this variation. A sizeable proportion of cis-regulatory variation is inferred to have sex-specific effects, with sex-dependent cis effects being much more frequent in gonads than in heads. Finally, we find some genes where 1 allele contributes to more than 50% of a gene's expression in heterozygous males but <50% of its expression in heterozygous females. Such variants could provide a mechanism for sex-specific dominance reversals, a phenomenon important for sexually antagonistic balancing selection. However, tissue differences in allelic imbalance are approximately as frequent as sex differences, perhaps suggesting that sexual conflict may not be particularly unique in shaping patterns of expression variation.

Contrasting the role of historic factors in phylogeograpic patterns in the native Johnny darter (Etheostoma nigrum) and invasive round goby (Neogobius melanostomus) in lower michigan.

Round goby (Neogobius melanostomus) is an invasive fish present in all five Great Lakes and is becoming increasingly common in their tributaries. Johnny darter (Etheostoma nigrum) is a native species that often coexists with N. melanostomus. In this work, historic factors are addressed as a source of genomic variation in study populations of these species. To do this, patterns of variation in the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) were characterized for both species throughout Lower Michigan. Populations of N. melanostomus and E. nigrum were sampled from 17 localities representing both eastern and western basins of Lower Michigan to test the hypothesis that populations differ between the eastern and western basins of the Great Lakes. Neogobius melanostomus populations were largely homogenous with no significant differences detected among populations or between the eastern and western basins. Additionally, N. melanostomus exhibited no evidence of overarching historical genetic structure, consistent with the recent invasion and rapid expansion of this species. Etheostoma nigrum exhibited significant differentiation among local populations; however, similarity among mtDNA haplotypes indicated that differences among populations are recent, suggesting that local forces are a more important factor in shaping patterns of variation than historical factors. Contrary to predictions, there were no significant differences detected between the eastern and western basins of the Great Lakes; however, construction of a neighbor-joining tree with F ST estimates revealed clustering of populations by basin with some anomalies. These anomalies may be the result of recent stream capture events facilitating gene flow between the two basins.