Search Results (203)

Massively parallel or next-generation sequencing (NGS) has enabled the genetic characterization of cancer patients, allowing the identification of somatic and germline variants associated with their diagnosis, tumor classification, and therapy response. Despite its benefits, NGS testing is not yet available in the Chilean public health system, rendering it both costly and time-consuming for patients and clinicians. Using a retrospective cohort of 67 formalin-fixed, paraffin-embedded (FFPE) colorectal cancer (CRC) samples, we aimed to implement the identification, annotation, and prioritization of relevant actionable tumor somatic variants in our laboratory, as part of the public health system. We compared two different library preparation methodologies (amplicon-based and capture-based) and different bioinformatics pipelines for sequencing analysis to assess advantages and disadvantages of each one. We obtained 80.5% concordance between actionable variants detected in our analysis and those obtained in the Cancer Genomics Laboratory from the Universidad de Chile (62 out of 77 variants), a validated laboratory for this methodology. Notably, 98.4% (61 out of 62) of variants detected previously by the validated laboratory were also identified in our analysis. Then, comparing the hybridization capture-based library preparation methodology with the amplicon-based strategy, we found ~94% concordance between identified actionable variants across the 15 shared genes, analyzed by the TumorSec^TM bioinformatics pipeline, developed by the Cancer Genomics Laboratory. Our results demonstrate that it is entirely viable to implement an NGS-based analysis of actionable variant identification and prioritization in cancer samples in our laboratory, being part of the Chilean public health system and paving the way to improve the access to such analyses. Considering the economic realities of most Latin American countries, using a small NGS panel, such as TumorSec^TM, focused on relevant variants of the Chilean and Latin American population is a cost-effective approach to extensive global NGS panels. Furthermore, the incorporation of automated bioinformatics analysis in this streamlined assay holds the potential of facilitating the implementation of precision medicine in this geographic region, which aims to greatly support personalized treatment of cancer patients in Chile. Full article

We performed a diagnostic disease investigation on a wild smallmouth bass (Micropterus dolomieu) with skin ulcers that was collected from Lake Oahe, South Dakota, following reports from anglers of multiple fish with similar lesions. Gross and histologic lesions of ulcerative dermatitis, myositis, and lymphocytolysis within the spleen and kidneys were consistent with largemouth bass virus (LMBV) infection. LMBV was detected by conventional PCR in samples of a skin ulcer, and the complete genome sequence of the LMBV (99,184 bp) was determined from a virus isolate obtained from a homogenized skin sample. A maximum likelihood (ML) phylogenetic analysis based on the major capsid protein (MCP) gene alignment supported the LMBV isolate (LMBV-SD-2023) as a member of the species Ranavirus micropterus1, branching within the subclade of LMBV isolates recovered from North American largemouth (Micropterus salmoides) and smallmouth bass. This is the first detection of LMBV in wild smallmouth bass from South Dakota. The ultrastructure of the LMBV isolate exhibited the expected icosahedral shape of virions budding from cellular membranes. Viral nucleic acid in infected cells was visualized via in situ hybridization (ISH) within dermal granulomas, localized predominantly at the margin of epithelioid macrophages and central necrosis. Further sampling is needed to determine the geographic distribution, affected populations, and evolutionary relationship between isolates of LMBV. Full article

What can hybridity teach us? The answer I posit is–like water–to embrace movement in all its forms. We are currently experiencing the sixth mass extinction event on earth and yet few scholars give prolonged attention to how we are to sustainably move our human inheritances forward on this increasingly uninhabitable planet. Reflecting on the work of transnational poets, specifically South Korean poet Kim Hyesoon translated through Korean American poet Don Mee Choi and Lebanese American poet Etel Adnan, we are reminded of the myriad ways in which humans can move and survive in a foreign yet familiar world. This paper finds its support in the confluence of transnational contemporary feminist poetics, formalism, environmentalism, and posthumanism. Through the use of various critical discourses, this paper considers how movement and its hybrid capacities offer a new understanding of contemporary North American poetics. In this sense, a poem should be viewed as a dynamic temporal cybernetic system, a vessel, full of energy, simultaneously pulsing with the changing movements and constrictions of everyday life. Full article

A high-throughput sequencing-based grapevine metagenomic survey was conducted across all grape-growing Canadian provinces (British Columbia, Ontario, Nova Scotia, and Québec) with the objective of better understanding the grapevine virome composition. In total, 310 composite grapevine samples representing nine Vitis vinifera red; five V. vinifera white; seven American–French red; and five white hybrid cultivars were analyzed. dsRNA, enriched using two different methods, was used as the starting material and source of viral nucleic acids in HTS. The virome status on the distribution and incidence in different regions and grapevine cultivars is addressed. Results from this study revealed the presence of 20 viruses and 3 viroids in the samples tested. Twelve viruses, which are in the regulated viruses list under grapevine certification, were identified in this survey. The major viruses detected in this survey and their incidence rates are GRSPaV (26% to 100%), GLRaV-2 (1% to 18%), GLRaV-3 (15% to 63%), GRVFV (0% to 52%), GRGV (0% to 52%), GPGV (3.3% to 77%), GFkV (1.5% to 31.6%), and GRBV (0% to 19.4%). This survey is the first comprehensive virome study using viral dsRNA and a metagenomics approach on grapevine samples from the British Columbia, Ontario, Nova Scotia, and Quebec provinces in Canada. Results from this survey highlight the grapevine virome distribution across four major grapevine-growing regions and their cultivars. The outcome of this survey underlines the need for strengthening current management options to mitigate the impact of virus spread, and the implementation of a domestic grapevine clean plant program to improve the sanitary status of the grapevine ecosystem. Full article

This article demonstrates the enabling influence of mixed-genre (or hybrid) poetries by North American women on recent poetry by Irish women poets, specifically in the past decade. Using a compositional/practice-based framework of interruption, the article provides an overview and analysis of interruptive strategies in a number of exemplary texts, including Don’t Let Me Be Lonely by Claudia Rankine, Jane: A Murder by Maggie Nelson, and Zong! by M. NourbeSe Philip in the North American context and ISDAL by Susannah Dickey, The Sun is Open by Gail McConnell, and MOTHERBABYHOME by Kimberly Campanello, among others. This comparative approach encompasses close readings and analysis of particular compositional approaches evident in both national contexts, in addition to the use of archival sources, news-reporting, and aesthetic strategies of interruption. The article suggests that “a poetics of material interruption” is at play in poetries on both sides of the Atlantic, gesturing towards marginalising forces of gender and colonisation, thus linking to themes prevalent in the above poetries in both Irish and North American contexts. The author poses a “poetics of material interruption” in the aesthetics and composition of the above mixed-genre poetries, perhaps arising from their interactions with the material conditions to which they respond. Full article

The systematics and phylogeny of the most speciose genus (Leopardus) of the felidae have historically been contentious and problematic. These issues have been compounded with the recent advancement of genetic techniques that make it possible to detect events such as incomplete lineage sorting (ILS), punctual historical ancestral introgression (PHAI), and repetitive introgression or recent hybridization (RI-RH). Each of these events have noteworthily affected the Leopardus genus. One Leopardus taxon (Leopardus tigrinus, herein called tigrina) has been especially complex from a phylogenetic point of view. In the last decade, one new species has been reported (L. guttulus) and two other new species likely exist within the tigrinas (L. emiliae and L. pardinoides). However, the most surprising find was the discovery of a new and not previously reported tigrina, the Nariño cat, from the southern Andean region of Colombia (2023). Later that same year, a new paper criticized the discovery. In response to that criticism, herein, we provide new molecular genetics results of the Nariño cat as well as new insights into the molecular phylogeny of the tigrinas inside the Leopardus genus: (1) In this new work, we analyzed the mtND5 gene of Nariño cat samples collected over four years (2001, 2007, 2017, 2023) as well as analyzed mitogenomes of Nariño cat samples collected in three different years (2001, 2017, 2023). The temporal Nariño cat samples (2001, 2007, 2017, 2023) refer to samples taken from a single specimen across different years. Based on these analyses, data from 2001 and 2007 represent the most reliable information. In contrast, samples from 2017 and 2023 may be contaminated with DNA from the Pampas cat and tigrina, respectively. (2) On the other hand, based on sequencing the mtND5 gene of 164 specimens of Leopardus, northern Andean and Central American tigrinas (37 specimens) are divided into at least six different groups (without counting the Nariño cat). Based on our analysis of sequenced mitogenomes of 102 specimens (including 34 northern Andean and Central American tigrinas) of the Leopardus genus, there are at least eight different groups of tigrinas (without counting the Nariño cat). Henceforth, there are strong datasets which support the existence of multiple lineages within the presumed “a priori” northern Andean tigrina and thus much of the genetic diversity of this wild cat has gone unnoticed. There are a series of potential taxa that have gone unnoticed due to a lack of sampling of this polyphyletic Andean feline. Full article

The way literature scholars read now has been under scrutiny for over a decade. The same long decade has seen an explosion in experimental literatures that make reading in the literary-critical sense a matter for poets: a poet’s hybrid, whose disturbance of genre is claimed by publishers as the writing’s main attraction. This paper explores the disturbance of literary criticism in the work of contemporary North American poets, Maureen N. McLane and Lisa Robertson. Asking how these poets read now, the paper argues that an exchange of powers between analysis and performance reorients criticism toward a hybrid ‘dramatic’ mode, activist in its sensibilities and committed to a redistribution of agencies by style and form. Far from deepening the divide between creative and academic criticism, these poets model the significance of composition, prosody, and voice for critical writing of all kinds. Full article

In American Hybrid (2009), Cole Swenson describes hybrid poetics as a reconciliation between the two dominant poetic traditions of the 20th century, which might be called lyric and experimental (xx–xxi). More recently, however, “hybrid” refers to any work blurring boundaries between poetry and other genres. This is most notable in the ever-increasing interest in the lyric essay but also in the constant revision of contemporary elegy as anti-elegy. In Poetry of Mourning, Jahan Ramazani defines anti-elegy in terms of its refusal of consolation and instead its seeking of more melancholic mourning. Subsequently, as noted by Bardazzi, Binetti, and Culler, “Elegy remains a poetic genre and yet, it has also developed a ‘mode of discourse’ that moves beyond its literary borders and finds its expressions in entangled intra-actions between the most diverse range of elegiac objects”. In the early 21st century, hybrid elegy represents the collision of two major changes in American culture: the changing nature of American death rituals and the increasingly intermedial literary landscape. Drawing on examples from Nox by Anne Carson and Ghost Of by Diane Khoi Nguyen, an elegiac version of the hyper-personalized American death ritual is inscribed in assemblages of images and text on the page. When read as a personalized American death ritual, the hybrid elegy materializes its own tradition and poetics, which are expressed in the poetic constraints of assemblage and recognizable in their reliance on elegiac repetition. Full article

This essay explores how the concept of enfreakment can be used to analyze older adult characters in late 1970s US American theatre, focusing on D.L. Coburn’s The Gin Game and Tennessee Williams’s This is the Peaceable Kingdom. These tragicomedies reflect societal fears and stigmas surrounding aging, linking back to the historical context of freak shows. Enfreakment intersects with themes of otherness and ableism, highlighting the sensationalism associated with freak culture. The social construction of P.T. Barnum’s freak and older adults as non-hybrids (Haim Hazan) shares common ground. Using a comparative approach and close reading, this research reveals that the fictional nursing home setting limits freedom and produces both repulsion and compassion through its residents, showcasing invective as a protocol of enfreakment. Full article

Rock imagery in the Puebloan region of the American Southwest often combines elements from different animal, human, plant, and natural sources. Blended elements may depict or refer to other-wordly states of existence or to creation narratives. Beings with combined elements can shift from shapes familiar in the present world and transport the viewer’s frame of reference to the spirit world. Puebloan belief in layering worlds below and above the present world is an important underlying social construct. Other worlds, especially those below, refer to past mythical times when animals and humans existed in primordial forms or were not fully formed, or may refer to the land of the dead or the underworld. Certain animal forms may have been selected because they are spirit guides, have specific powers, or were guardian-gods of cardinal directions. Some animals, such as birds, were chosen as messengers of prayers or offerings, while others (such as bears) had healing powers. The placement of images on the landscape or in relation to natural features imparts added power to the imagery. Ambiguity and multiple meanings also enhance these powers and incorporate concepts of emergence and transformation. Some images refer to the transformation that occurs when dancers wear kachina masks and then assume the attributes of those kachinas. Examples will be presented from images dating to the pre-European contact period (1300 to 1540 AD) found at Petroglyph National Monument, in the central Rio Grande valley of New Mexico. Comparisons to painted wall murals in kivas (ceremonial rooms) made during the same time period are presented. Full article

This paper presents deep learning models—specifically, Long Short-Term Memory (LSTM) networks and hybrid Convolutional Neural Network–LSTM (CNN-LSTM) with a Copula-Based Random Forest (CBRF) model to estimate Heterogeneous Treatment Effects (HTEs) in survival analysis. The proposed method is designed to capture non-linear relationships and temporal dependencies in clinical and genomic data, with a particular focus on exploring how treatment effects vary by race as a moderating factor. Using breast cancer data from the TCGA-BRCA dataset, which includes both clinical variables and gene expression profiles, we filter the data to focus on two racial groups: Black or African American and White. Dimensionality reduction is performed using Principal Component Analysis (PCA). We compare the CNN-LSTM, LSTM, and CBRF models under three weighting strategies—no weights, Horvitz–Thompson (HT) weights, and Inverse Probability of Treatment Weighting (IPTW)—for predicting treatment effects. Model performance is evaluated using Root Mean Squared Error (RMSE), Mean Absolute Error (MAE), Concordance statistic (C-statistic), Average Treatment Effect (ATE), and Conditional Average Treatment Effect (CATE) by race. The CNN-LSTM model consistently outperforms the others, achieving the lowest prediction errors and highest discrimination, particularly under IPTW. Among the weighting strategies, IPTW yields the most substantial improvements in model performance and bias reduction. Importantly, race-specific treatment effects exhibit notable variation: CNN-LSTM estimates a slightly higher CATE for Black individuals under IPTW. Overall, CNN-LSTM with IPTW is recommended for robust and equitable causal inference, especially in racially stratified settings. Full article

The phytoremediation capacity of three common poplar species, white poplar (Populus alba L.), Lombardy poplar (Populus nigra ’Italica’), and Euro-American hybrid poplar (Populus × euramericana (Dode) Guinier cl. I-214), grown in a middle-sized city with a continental climate in Serbia was analyzed. For this purpose, 15 polycyclic aromatic hydrocarbons (PAHs), 10 polychlorinated biphenyls (PCBs), and 6 heavy metals (HMs) were tracked in leaves and one-year-old branches. P. × euramericana showed the highest PAH uptake capacity, with concentrations of 821.40 ng g⁻¹ dry weight (DW) and 453.64 ng g⁻¹ DW in leaves and branches, respectively. Likewise, P. euramericana accumulated the highest levels of PCBs in leaves (364.53 ng g⁻¹ DW). Additionally, P. nigra ‘Italica’ demonstrated the greatest accumulation potential for HMs, particularly zinc, with 310.10 µg g⁻¹ DW in leaves. Leaves accumulated ~30% more pollutants compared with branches. Significant differences in pollutant uptake capacities were found among species and plant organs. These findings highlight the importance of species selection in phytoremediation and clarify the role of poplar species in accumulating pollutants to mitigate urban pollution. Finally, this study provides valuable insights for future phytoremediation strategies using poplars, especially in urban environments with similar conditions. Full article

This study explores rhythm metrics as a sociolinguistic marker in Philippine English (PhE), addressing gaps in understanding rhythmic variation in Southeast Asian Englishes. It aims to uncover how rhythmic patterns reflect sociolectal identities within a multilingual context. Using acoustic data from 30 participants in Manila, rhythm metrics (%V, ΔV, ΔC, nPVI, and rPVI) were analyzed to examine rhythmic tendencies. The findings reveal distinct patterns: PhE acrolect aligns with stress-timed rhythms of general American English, PhE basilect reflects syllable-timed features similar to Spanish, and PhE mesolect occupies a hybrid position blending elements of both. By emphasizing rhythm as a key identifier of sociolectal variation, this study advances the understanding of linguistic diversity in World Englishes and provides a novel framework for exploring identity in multilingual settings. Full article

In order to realize green and low-carbon transformation, some ports have explored the path of sustainable equipment upgrading by adjusting the energy structure of yard cranes in recent years. However, there are multiple uncertainties in the investment process of hydrogen-powered yard cranes, and the existing valuation methods fail to effectively deal with these dynamic changes and lack scientifically sound decision support tools. To address this problem, this study constructs a multi-factor real options model that integrates the dynamic uncertainties of hydrogen price, carbon price, and technology maturity. In this study, a geometric Brownian motion is used for hydrogen price simulation, a Markov chain model with jump diffusion term and stochastic volatility is used for carbon price simulation, and a learning curve method is used to quantify the evolution of technology maturity. Aiming at the long investment cycle of ports, a hybrid option strategy of “American and European” is designed, and the timing and scale of investment are dynamically optimized by Monte Carlo simulation and least squares regression. Based on the empirical analysis of Qingdao Port, the results show that the optimal investment plan for hydrogen-powered yard cranes project under the framework of a multi-factor option model is to use an American-type option to maintain moderate flexibility in the early stage, and to use a European-type option to lock in the return in the later stage. The study provides decision support for the green development of ports and enhances economic returns and carbon emission reduction benefits. Full article

The classification of agricultural products is of great importance for quality control, optimized marketing, efficient logistics, research progress, consumer satisfaction, and sustainability. Dragon fruit has many varieties that need to be identified quickly and accurately for packaging and marketing. Considering the increasing demand for dragon fruit, it is obvious that an automated classification system has significant commercial and scientific value by increasing sorting efficiency and reducing manual labor costs. This study aimed to classify four commonly produced dragon fruit varieties according to their color, mechanical, and physical properties using machine learning models. Data were collected from 224 dragon fruits (53 American beauty, 57 Dark star, 65 Vietnamese white, and 49 Pepino dulce variety). Classification was performed using measurable physical and mechanical properties obtained through digital image processing, colorimetry, electronic weighing, and stress–strain testing. These methods provided objective and reproducible data collection for the models. Three models—Random Forest, Gradient Boosting, and Support Vector Classification—were implemented and their performances were evaluated using accuracy, precision, recall, Matthews’s correlation coefficient, Cohen’s Kappa, and F1-Score. The Random Forest model showed the highest performance in all metrics, achieving 98.66% accuracy, while the Support Vector Classification model had the lowest success. The superior performance of the Random Forest model can be attributed to its ability to handle complex, nonlinear relationships among multiple variables while preventing overfitting through ensemble learning. However, potential challenges in dragon fruit classification include variations due to environmental factors, genetic variation, and hybridization. Future research can focus on incorporating biochemical or genetic markers and improving real-time classification for industrial applications. Full article