Comprehensive Catalog Research Articles

Learning-based methods for adaptive informative path planning

Adaptive informative path planning (AIPP) is important to many robotics applications, enabling mobile robots to efficiently collect useful data about initially unknown environments. In addition, learning-based methods are increasingly used in robotics to enhance adaptability, versatility, and robustness across diverse and complex tasks. Our survey explores research on applying robotic learning to AIPP, bridging the gap between these two research fields. We begin by providing a unified mathematical problem definition for general AIPP problems. Next, we establish two complementary taxonomies of current work from the perspectives of (i) learning algorithms and (ii) robotic applications. We explore synergies, recent trends, and highlight the benefits of learning-based methods in AIPP frameworks. Finally, we discuss key challenges and promising future directions to enable more generally applicable and robust robotic data-gathering systems through learning. We provide a comprehensive catalog of papers reviewed in our survey, including publicly available repositories, to facilitate future studies in the field.

Advancing Technical Debt Management in Software Systems with a Comprehensive TD Indicator and Question Catalog

The Technical Debt (TD) metaphor was introduced over three decades ago and continues to challenge software development projects. Despite its recognized importance, there is a lack of comprehensive catalog that not only lists TD types and indicators but also elucidates them. This paper significantly extends our previous work by presenting a detailed catalog of TD types and indicators, enriched with specific assessment questions and in-depth explanations for each indicator. We had extracted and refined TD categories from both academic and gray literature to assemble a list of 120 TD indicators across 10 distinct TD types. For each indicator, we provide detailed description and at least two tailored assessment questions in this version, to aid in the practical evaluation of technical debt. This enhanced catalog is designed to advance the specification and management of technical debt in software development, offering practitioners clear, actionable insights for assessing and addressing TD.

Massively parallel characterization of regulatory elements in the developing human cortex.

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.

Smart Unary Multilevel Marketing

The "Raksham" project stands as a cutting-edge Unilevel Marketing platform meticulously engineered to promote and distribute Raksham Ayurvedic health-conscious products. Harnessing a sophisticated amalgamation of HTML, CSS, JavaScript, MySQL, and PHP technologies, Raksham orchestrates a seamless and intuitive interface for interactions between distributors and end-users, redefining the paradigm of online marketing and sales. The Admin Portal emerges as the nerve center of Raksham, furnishing distributors with an array of powerful tools and features to streamline their operations. These include dynamic dashboards that furnish real-time insights into team performance, robust profile management capabilities, streamlined package enrollment processes, agile payment systems for seamless financial transactions, and sophisticated team management functionalities. These tools empower distributors to monitor their business performance meticulously, manage their teams effectively, and orchestrate secure and efficient financial transactions with ease. On the end-user front, Raksham presents a captivating and user-centric interface designed to enhance the shopping experience and foster customer engagement. Through features like intuitive messenger services facilitating seamless communication between users and distributors, comprehensive product catalogs showcasing the diverse range of Raksham products, and streamlined order tracking mechanisms, Raksham ensures that end-users can navigate the platform effortlessly, make informed purchasing decisions, and track their orders with convenience. The strategic integration of these features within Raksham's technological infrastructure not only augments operational efficiencies for distributors but also enhances user satisfaction and engagement among end-users. By leveraging state-of-the-art technologies and a user-centric design philosophy, Raksham solidifies its position as a formidable contender in the realm of Ayurvedic health-conscious products, poised to revolutionize the landscape of online marketing and sales in this domain. Keywords: The Advertising, Business ,Social , Network Service, Internet, Data Mining, Website

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition.

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.

A text mining analysis of European banks' and insurers' disclosures on climate‐related risks

AbstractThis paper empirically analyzes sustainability‐related disclosures of listed European banks and insurance companies by focusing on transition risks, physical risks as well as stranded assets as a possible consequence of transition and physical risks. We employ a text mining analysis and apply a comprehensive keyword catalog to 142 firms. The dataset used for the analysis comprises 852 annual and 551 sustainability reports, covering a sample period from 2017 to 2022. Our results show that disclosure on climate‐related risks considerably increases over the examined period, but that reporting on stranded assets is still in early stages. Moreover, European insurers report more on climate‐related risks relative to the number of analyzed tokens than banks. Finally, statistical evidence suggests that larger banks and insurers with above‐median market capitalization exhibit significantly more word hits on climate‐related risks as compared to smaller firms.

Catalog of the Chrysomelinae (Coleoptera: Chrysomelidae) deposited in the entomological collections of the Museu Paraense Emílio Goeldi (MPEG) and the Universidade do Estado do Pará (UEPA), Belém, Brazil

A comprehensive catalog is provided for most leaf beetles belonging to the Chrysomelinae subfamily, which are housed in the collections of two institutions in the state of Pará, located in northern Brazil: The Museu Paraense Emílio Goeldi (MPEG) and the Universidade do Estado do Pará (UEPA). The catalog includes detailed geographic distribution data for all species, along with new records and photographs (including two paratypes of Cryptostetha pereirai Bechyně, 1958, with descriptions of the aedeagus and spermatheca). Furthermore, information is provided on host plants, parasites, parasitoids, and predators associated with certain species.

Mapping and functional characterization of structural variation in 1060 pig genomes

BackgroundStructural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.ResultsWe present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV’s impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies.ConclusionsThis SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

The role of gaming for information, education and communication of AMR: full review of online education resources.

The first objective of the Global Action Plan on antimicrobial resistance (AMR) is to improve awareness and understanding of AMR through effective communication, education and training. Towards this several efforts have been made to create AMR awareness resources. The aim of these resources is to inform the public about responsible antibiotic use and drive positive behavioural change. Digital media and specifically games can serve as unique innovative platforms in public communication programmes. This study focuses on compiling and evaluating game-based AMR resources. Recognizing the engaging and creative potential of games as learning tools, the primary objective of this study was to identify games that can be used, individually or in combination depending on their unique focus and gameplay experience, for AMR awareness. Furthermore, games are evaluated on five objective criteria and recommendations are made towards further development of gaming resources towards AMR awareness. Meticulous curation was performed to mine information, education and communication resources, with a primary focus on games for AMR awareness and evaluating them based on game design and gameplay, AMR content and learning, engagement and replay appeal, learning outcomes, and level of difficulty and challenges. In this study, we selected 12 AMR games. Our evaluations, spanning various gamification elements and interactive parameters, informed recommendations for future AMR resource development, including multilevel game design, varied graphics, simple-to-understand rules, sustained challenge and a sense of reward, among others. This study generated the first-ever comprehensive catalogue of AMR games that may assist public communication programmes for AMR awareness. Evaluation of these games led to actionable design recommendations for future resources towards effective communication of AMR complexity, enhanced learning and awareness.

Abstract GS03-09: Characterization and proposed therapeutic exploitation of fusion RNAs in metastatic breast cancers

Abstract BACKGROUND: Large-scale genomic studies such as The Cancer Genome Atlas (TCGA) and Pan-Cancer Analysis of Whole Genomes (PCAWG) show that the breast cancer (BrCa) genome is dominated by structural variation (SV) rather than single base pair mutations, producing a fertile environment for gene fusions. In this study, we implement a rigorous, expression-based approach to create a comprehensive landscape of fusion RNAs in metastatic breast cancer (MBC). We find fusion RNAs—many of which are novel involving known oncogenes—are surprisingly common in the advanced setting and credential their use as base-editing therapeutic targets. METHODS: Two retrospective cohorts of MBC RNA-sequencing data were analyzed— Dana-Farber Cancer Institute CCPM (n = 252 cases, 276 specimens), MichiganCSER (n = 171 cases, 190 specimens)—with a Fusion MetaCaller that integrates 5 unsupervised fusion-finding algorithms. Fusion RNAs identified in at least 2 callers (High-Confidence) and absent in RNA-seq from normal tissue (Cancer-Specific) were classified as HCCS-Fusions. Further removal of common artifactual fusions was performed using public databases. Expression of each HCCS-Fusion was quantified using a supervised method (FusionInspector)—expressed HCCS-Fusions were defined as having a Fusion Fragment Per Million (FFPM) value > 0.1 and at least 10% of read counts mapping to the fusion breakpoint versus the flanking 5’ or 3’ partners’ exons. Normalized gene-level expression abundances were calculated to correlate transcriptomic features (gene expression, PAM50) with fusion RNAs. Recurrent, potentially pathogenic fusion RNAs were annotated using OncoKB and outlier expressed fusions (Q3 FFPM + [1.5 X IQR]) were interrogated. RESULTS: The frequency of HCCS-Fusions differed between subtypes with basal BrCa harboring the most per tumor followed by Her2, LumB and LumA—with a median HCCS-Fusion count of 13, 12, 7, 4 respectively. 64.5% of cases harbored a HCCS-Fusion in an OncoKB cancer-related gene. The most recurrent fusions involving a cancer-related gene were 5’ ESR1 fusions (14 cases)—all with in-frame breakpoints near exon6/7, disrupting ESR1’s ligand binding domain. 13 of 14 ESR1 fusions were called in Luminal B (LumB) metastases (Fisher’s exact enrichment p < 0.005 vs other subtypes)—defining an ESR1 fusion frequency of 6.5% in LumB disease. Beyond ESR1, we identify recurrent, low-frequency (2-4 cases) in-frame kinase fusions involving FGFR2, ADK, TLK2, PRKCA, BRAF, CHKA, CSNK1D, NEK11, TNIK—some potentially targetable with FDA-approved small molecule inhibitors—as well as recurrent, predicted loss-of-function fusion RNAs in NF1, MSI2, USP32, PTEN, and CDH1. Lastly, 33.6% of cases harbored at least one outlier expressed fusion RNA; including highly expressed in-frame fusions involving known BrCa mediators such as ERBB2, BRCA1, ARID1B, RPS6KB1/2, PIK3R3, AXIN1, TGFB1/2, FOXP1, PAK1, and CREBBP. CONCLUSIONS: Taken together, these results demonstrate that fusion RNAs in MBC—some recurrent, many highly expressed and unique to individual tumors—are common. We create the most comprehensive catalog of ESR1 fusions in MBC, better define their frequency, discover their enrichment in LumB-like tumors, and will discuss clinicopathologic and transcriptomic features associated with ESR1 fusion positive disease. We identify druggable fusions that would likely be missed by current testing standards, find recurrent loss-of-function fusion RNAs, and show that over one-third of metastatic cases harbor at least one outlier expressed fusion—many of which involve BrCa-related genes. In summary, we propose that fusion RNAs are a driving and perhaps overlooked mechanism of tumor evolution in therapy-resistant disease and postulate fusion transcripts present a compelling therapeutic opportunity in MBC. Preliminary data targeting fusion RNA breakpoints using a novel RNA base-editing approach will be discussed. Citation Format: Nolan Priedigkeit, Alinés Lebrón-Torres, Janny Liao, Jean-Baptiste Alberge, Stefania Morganti, Jakob Weiss, Jorge Gomez Tejeda Zanudo, Albert Grinshpun, Melissa Hughes, Karla Helvie, Kerry Sendrick, Kyleen Nguyen, Sarah Strauss, Janet Files, Maxwell Lloyd, Nikhil Wagle, Chip Stewart, Eric Winer, Bruce Johnson, Yvonne Li, Rinath Jeselsohn, Sara Tolaney, Daniel Abravanel, Nancy Lin, Heather Parsons, Gad Getz, Steffi Oesterreich, Adrian Lee, Todd Golub. Characterization and proposed therapeutic exploitation of fusion RNAs in metastatic breast cancers [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr GS03-09.

Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia.

A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat.

The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.

Telomere-to-telomere genome assembly of Oldenlandia diffusa.

We report the complete telomere-to-telomere genome assembly of Oldenlandia diffusa which renowned in traditional Chinese medicine, comprising 16 chromosomes and spanning 499.7Mb. The assembly showcases 28 telomeres and minimal gaps, with a total of only five. Repeat sequences constitute 46.41% of the genome, and 49,701 potential protein-coding genes have been predicted. Compared with O. corymbosa, O. diffusa exhibits chromosome duplication and fusion events, diverging 20.34 million years ago. Additionally, a total of 11 clusters of terpene synthase have been identified. The comprehensive genome sequence, gene catalog, and terpene synthase clusters of O. diffusa detailed in this study will significantly contribute to advancing research in this species' genetic, genomic, and pharmacological aspects.

The APO-K2 Catalog. II. Accurate Stellar Ages for Red Giant Branch Stars across the Milky Way

We present stellar age determinations for 4661 red giant branch stars in the APO-K2 catalog, derived using mass estimates from K2 asteroseismology from the K2 Galactic Archaeology Program and elemental abundances from the Apache Point Galactic Evolution Experiment survey. Our sample includes 17 of the 19 fields observed by K2, making it one of the most comprehensive catalogs of accurate stellar ages across the Galaxy in terms of the wide range of populations spanned by its stars, enabling rigorous tests of Galactic chemical evolution models. Taking into account the selection functions of the K2 sample, the data appear to support the age−chemistry morphology of stellar populations predicted by both inside-out and late-burst scenarios. We also investigate trends in age versus stellar chemistry and Galactic position, which are consistent with previous findings. Comparisons against APOKASC-3 asteroseismic ages show agreement to within ∼3%. We also discuss offsets between our ages and spectroscopic ages. Finally, we note that ignoring the effects of α-enhancement on stellar opacity (either directly or with the Salaris metallicity correction) results in an ∼10% offset in age estimates for the most α-enhanced stars, which is an important consideration for continued tests of Galactic models with this and other asteroseismic age samples.

A systematic approach for threat and vulnerability analysis of unmanned aerial vehicles

The proliferation of Unmanned Aerial Vehicles (UAVs) is expected to experience a substantial rise in the next years, driven by their ever-increasing application across various domains. However, ensuring secure communication between UAVs and their ground stations is crucial to prevent the unauthorized disclosure of sensitive information that could jeopardize the mission’s integrity when exploited by malicious actors. Despite this importance, several UAV systems currently operate based on open-source command and control technologies, which have overlooked several security considerations while focusing on availability and safety. To address this concern, this study conducts a comprehensive security assessment of UAV-based systems starting with a systematic literature review whose main purpose is building a comprehensive catalog of threats associated with this technology. Particular attention has been paid to the MAVlink protocol, an open-source protocol commonly utilized for telemetry and command and control for multiple UAVs. Therefore, drawing upon the built catalog, a threat modeling and penetration testing technique has been employed to examine the MAVlink implementation on a real UAV. A threat model developed for a specific case study is also presented, leading to the discovery of four new vulnerabilities, some of which were successfully exploited through attacks. By shedding light on these vulnerabilities, this work seeks to encourage further investigation and research to develop robust security mechanisms for UAV communication systems. It is imperative to address these vulnerabilities proactively to enhance the overall security posture and safeguard against potential threats in the UAV ecosystem.

Assessing experimental silvicultural treatments enhancing structural complexity in a central European forest – BEAST time‐series analysis based on Sentinel‐1 and Sentinel‐2

AbstractAssessing the dynamics of forest structure complexity is a critical task in times of global warming, biodiversity loss and increasing disturbances in order to ensure the resilience of forests. Recent studies on forest biodiversity and forest structure emphasize the essential functions of deadwood accumulation and diversification of light conditions for the enhancement of structural complexity. The implementation of an experimental patch‐network in managed broad‐leaved forests within Germany enables the standardized analysis of various aggregated and distributed treatments characterized through diverse deadwood and light structures. To monitor the dynamics of enhanced forest structure complexity as seasonal and trend components, dense time‐series from high spatial resolution imagery of Sentinel‐1 (Synthetic‐Aperture Radar, SAR) and Sentinel‐2 (multispectral) are analyzed in time‐series decomposition models (BEAST, Bayesian Estimator of Abrupt change, Seasonal change and Trend). Based on several spatial statistics and a comprehensive catalog on spectral indices, metrics from Sentinel‐1 (n = 84) and Sentinel‐2 (n = 903) are calculated at patch‐level. Metrics best identifying the treatment implementation event are assessed by change point dates and probability scores. Heterogeneity metrics of Sentinel‐1 VH and Sentinel‐2 NMDI (Normalized Multi‐band Drought Index) capture the treatment implementation event most accurately, with clear advantages for the identification of aggregated treatments. In addition, aggregated structures of downed or no deadwood can be characterized, as well as more complex standing structures, such as snags or habitat trees. To conclude, dense time‐series of complementary high spatial resolution sensors have the potential to assess various aggregated forest structure complexities, thus supporting the continuous monitoring of forest habitats and functioning over time.

Gene regulatory networks underlying sulfate deficiency responses in plants.

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.

Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8.

The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.

A comprehensive catalog of refactoring strategies to handle test smells in Java-based systems

A comprehensive catalog of refactoring strategies to handle test smells in Java-based systems

Comprehensive Proteomics Analysis of the Hemolymph Composition of Sugar-Fed Aedes aegypti Female and Male Mosquitoes.

In arthropods, hemolymph carries immune cells and solubilizes and transports nutrients, hormones, and other molecules that are involved in diverse physiological processes including immunity, metabolism, and reproduction. However, despite such physiological importance, little is known about its composition. We applied mass spectrometry-based label-free quantification approaches to study the proteome of hemolymph perfused from sugar-fed female and male Aedes aegypti mosquitoes. A total of 1403 proteins were identified, out of which 447 of them were predicted to be extracellular. In both sexes, almost half of these extracellular proteins were predicted to be involved in defense/immune response, and their relative abundances (based on their intensity-based absolute quantification, iBAQ) were 37.9 and 33.2%, respectively. Interestingly, among them, 102 serine proteases/serine protease-homologues were identified, with almost half of them containing CLIP regulatory domains. Moreover, proteins belonging to families classically described as chemoreceptors, such as odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), were also highly abundant in the hemolymph of both sexes. Our data provide a comprehensive catalogue of A. aegypti hemolymph basal protein content, revealing numerous unexplored targets for future research on mosquito physiology and disease transmission. It also provides a reference for future studies on the effect of blood meal and infection on hemolymph composition.