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BackgroundHalyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.ResultsAnalysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.ConclusionsAvailability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

An amendment to this paper has been published and can be accessed via the original article.

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, involving both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning models have predominantly used transcriptome data with manually defined features to detect lncRNAs, however, they often underrepresent the abundance of lncRNAs and can be biased in their detection. Here we present a study using Natural Language Processing (NLP) models to identify plant lncRNAs from genomic sequences rather than transcriptomic data. The NLP models were trained to predict lncRNAs for seven model and crop species (Zea mays, Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max and Oryza sativa) using publicly available genomic references. We demonstrated that lncRNAs can be accurately predicted from genomic sequences with the highest accuracy of 83.4% for Z. mays and the lowest accuracy of 57.9% for B. rapa, revealing that genome assembly quality might affect the accuracy of lncRNA identification. Furthermore, we demonstrated the potential of using NLP models for cross-species prediction with an average of 63.1% accuracy using target species not previously seen by the model. As more species are incorporated into the training datasets, we expect the accuracy to increase, becoming a more reliable tool for uncovering novel lncRNAs. Finally, we show that the models can be interpreted using explainable artificial intelligence to identify motifs important to lncRNA prediction and that these motifs frequently flanked the lncRNA sequence.

The environment gametes perform in just before fertilization is increasingly recognized to affect offspring fitness, yet the contributions of male and female gametes and their adaptive significance remain largely unexplored. Here, we investigated gametic thermal plasticity and its effects on hatching success and embryo performance in Atlantic salmon (Salmo salar). Eggs and sperm were incubated overnight at 2°C or 8°C, temperatures within the optimal thermal range of this species. Crosses between warm- and cold-incubated gametes were compared using a full-factorial design, with half of each clutch reared in cold temperatures and the other in warm temperatures. This allowed disentangling single-sex interaction effects when pre-fertilization temperature of gametes mismatched embryonic conditions. Pre-fertilization temperature influenced hatch timing and synchrony, and matching sperm and embryo temperatures resulted in earlier hatching. Warm incubation benefited eggs but harmed sperm, reducing the hatching success and, overall, gametic thermal plasticity did not enhance offspring fitness, indicating vulnerability to thermal changes. We highlight the sensitivity of male gametes to higher temperatures, and that gamete acclimation may not effectively buffer against deleterious effects of thermal fluctuations. From an applied angle, we propose the differential storage of male and female gametes as a tool to enhance sustainability within the hatcheries.

Weeds pose a significant threat to agricultural production, leading to substantial yield losses and increased herbicide usage, with severe economic and environmental implications. This paper uses deep learning to explore a novel approach via targeted segmentation mapping of crop plants rather than weeds, focusing on canola (Brassica napus) as the target crop. Multiple deep learning architectures (ResNet-18, ResNet-34, and VGG-16) were trained for the pixel-wise segmentation of canola plants in the presence of other plant species, assuming all non-canola plants are weeds. Three distinct datasets (T1_miling, T2_miling, and YC) containing 3799 images of canola plants in varying field conditions alongside other plant species were collected with handheld devices at 1.5 m. The top performing model, ResNet-34, achieved an average precision of 0.84, a recall of 0.87, a Jaccard index (IoU) of 0.77, and a Macro F1 score of 0.85, with some variations between datasets. This approach offers increased feature variety for model learning, making it applicable to the identification of a wide range of weed species growing among canola plants, without the need for separate weed datasets. Furthermore, it highlights the importance of accounting for the growth stage and positioning of plants in field conditions when developing weed detection models. The study contributes to the growing field of precision agriculture and offers a promising alternative strategy for weed detection in diverse field environments, with implications for the development of innovative weed control techniques.

BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.ResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.ConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Molecular biomarkers correspond to all endogenous or exogenous biomolecules, whose presence or alteration in metabolic pathways indicate the response of a biological system to a disturbance caused by internal or external factors. The search for biomarkers has allowed deepening the knowledge of complex pathophysiological mechanisms of diseases, interactions with potential drugs, and the improvement of diagnostic and therapeutic tests, establishing itself as a central point in personalized medicine. In addition, the development of the omics sciences has fostered an increasing exploration in this field of research. This review presents essential and relevant concepts in biomarker research, explores the various definitions and classifications of biomarkers according to their purpose, the critical aspects to be considered in experimental design, the primary employed study models (in vivo, in vitro, and in silico) and the factors that have hindered their ultimate implementation. Finally, important, and current clinical and pharmacological research areas in which biomarker research play a central role are presented.

Abstract This study reports the optoelectronic characterization of few‐layer ReSe2field effect transistors at different pressures. The output curves reveal dominant n‐type behavior and a low Schottky barrier at the metal contacts. The transfer curves show a significant hysteresis that can be exploited in memory devices with an order ofmagnitude memory window and good cycling. The devices are dramatically affected by air pressure; their conductance and mobility increase with the lowering pressure that desorbs electronegative air molecules from the surface of the material. The photoresponse under white super‐continuum laser illumination reveals that the device exhibits positive photoconductivity (PPC) at ambient and low (≈1 mbar) pressure and negative photoconductivity (NPC) in a higher vacuum (≈10−4 mbar). The transition from PPC to NPC can be explained by considering that the photoresponse is affected by molecule desorption, which yields PPC at higher pressure, and defect trapping of photogenerated carriers, which can dominate at lower pressures. The transient behavior of the device exposed to laser pulses shows a faster response and a higher photodetection efficiency at ambient pressure, with the highest signal‐to‐noise ratio at the valley of the transfer curve between p‐ and n‐type conduction.

Introduction: Treatment with lorlatinib for patients with advanced ALK- and ROS1-rearranged NSCLC (ALK+ and ROS1+ NSCLC) is associated with a unique set of adverse events (AEs) often requiring dose reduction. However, the impact of dose reductions on outcomes remains unclear and is mainly limited to analyses from prospective studies of lorlatinib in the first-line setting. Methods: We reviewed the course of 144 patients with advanced ALK- or ROS1-rearranged NSCLC treated with lorlatinib in the second-line or later setting to assess the frequency of dose reductions resulting from treatment-related AEs (TRAEs) and the association between dose reductions and progression-free survival (PFS) and overall survival (OS). Results: A total of 58 patients (40%) had TRAE-related dose reductions, most (59%) owing to neurocognitive AEs or neuropathy. Among all patients, the median PFS was 8.1 months (95% confidence interval [CI]: 6.4–11.8); the median OS was 20.7 months (95% CI: 16.3–30.5). Among patients who were started on lorlatinib 100 mg/d (n = 122), a Cox regression model with the occurrence of a dose reduction as a time-dependent covariate indicated no association between dose reduction and PFS (hazard ratio = 0.86, 95% CI: 0.54–1.39) or OS (hazard ratio = 0.78, 95% CI: 0.47–1.30). Conclusions: Lorlatinib dose reductions were not associated with inferior clinical outcomes in this multicenter analysis. Prompt identification of lorlatinib TRAEs and implementation of dose reductions may help maximize tolerability without compromising outcomes.

Orphan crops are important sources of nutrition in developing regions and many are tolerant to biotic and abiotic stressors; however, modern crop improvement technologies have not been widely applied to orphan crops due to the lack of resources available. There are orphan crop representatives across major crop types and the conservation of genes between these related species can be used in crop improvement. Machine learning (ML) has emerged as a promising tool for crop improvement. Transferring knowledge from major crops to orphan crops and using machine learning to improve accuracy and efficiency can be used to improve orphan crops. Machine learning has emerged as a promising tool for crop improvement. Here, the authors review transferring knowledge from major crops to orphan crops and using machine learning to improve accuracy and efficiency of orphan crops breeding. [ABSTRACT FROM AUTHOR]

Crop disease detection is important due to its significant impact on agricultural productivity and global food security. Traditional disease detection methods often rely on labour‐intensive field surveys and manual inspection, which are time‐consuming and prone to human error. In recent years, the advent of imaging technologies coupled with machine learning (ML) algorithms has offered a promising solution to this problem, enabling rapid and accurate identification of crop diseases. Previous studies have demonstrated the potential of image‐based techniques in detecting various crop diseases, showcasing their ability to capture subtle visual cues indicative of pathogen infection or physiological stress. However, the field is rapidly evolving, with advancements in sensor technology, data analytics and artificial intelligence (AI) algorithms continually expanding the capabilities of these systems. This review paper consolidates the existing literature on image‐based crop disease detection using ML, providing a comprehensive overview of cutting‐edge techniques and methodologies. Synthesizing findings from diverse studies offers insights into the effectiveness of different imaging platforms, contextual data integration and the applicability of ML algorithms across various crop types and environmental conditions. The importance of this review lies in its ability to bridge the gap between research and practice, offering valuable guidance to researchers and agricultural practitioners. [ABSTRACT FROM AUTHOR]

Few evidence-based trainings exist on how to equip healthcare providers, particularly nurses, with the skills to engage in cost of care conversations with patients/caregivers to mitigate the impact of cancer-related financial toxicity. This study evaluated a pilot training developed in collaboration with Triage Cancer® to prepare oncology nurses to identify and assist patients/caregivers facing financial and/or legal barriers to care. Ten pediatric oncology nurses completed the training and pre/post-surveys on behaviors related to financial and legal need screening, frequency and comfort level of answering questions, knowledge, and behavior changes, along with training evaluation questions. At baseline, six nurses reported never screening for financial needs and nine for legal needs. Following the training, seven nurses stated they were likely to screen for financial/legal needs. At six months post-training, nurses had referred 85 patients/caregivers to financial/legal navigation services. Comfort levels in answering financial/legal questions increased by 6.5 points and knowledge scores increased by 1.7 points post-training. Most nurses recommended this training to other healthcare providers who work with patients with cancer and their caregivers. This study highlights the importance of providing oncology nurses with resources to engage in cost of care conversations and oncology financial legal navigation programs to mitigate the impact of cancer-related financial toxicity. [ABSTRACT FROM AUTHOR]

Background: Despite the critical role of faculty diversity in the persistence and academic experiences of undergraduate students as well as in the development of engineering innovations, women of color (WoC) faculty are still underrepresented in engineering programs across the United States. Purpose/Hypothesis: This study identifies whether the demographic composition of undergraduate engineering students is correlated with the representation of WoC faculty. It also highlights the institutional- and departmental-level factors that contribute to the race-gender diversification of the engineering professoriate. Design/Method: Informed by organizational demography as the theoretical framework, the methods include linear and logit regression analyses. Data come from the American Society for Engineering Education, the Integrated Postsecondary Education Data System, and the American Community Survey, and include engineering departmental-level observations across 345 institutions over 12 years. Results: Engineering departments that award more bachelor's degrees to women African American/Black undergraduate students are more likely to employ relatively more African American/Black women faculty. This positive relationship is also found among Asian Americans and Hispanics/Latinas. Conclusions: Research findings demonstrate the relationship between engineering undergraduate composition, as well as other departmental- and institutional-level factors, and the prevalence of WoC faculty. The findings highlight important areas for stakeholders and academic administrators to consider when developing strategies and programs to diversify the composition of engineering faculty.

BackgroundCyclodestructive procedures are often used in patients with refractory glaucoma who have failed to achieve lower intraocular pressure (IOP) from filtration procedures and maximal medical therapy. Destruction of the ciliary body helps to lower IOP by reducing aqueous humor formation. Of the many types of cyclodestructive procedures, laser cyclophotocoagulation (CPC) has become the most common surgical method for reducing aqueous inflow. Options for CPC are wide-ranging: they can be performed using a neodymium:yttrium-aluminum-garnet (Nd:YAG) or diode laser and laser energy can be delivered by either the contact or non-contact method. Another cyclodestructive procedure is endoscopic cyclophotocoagulation (ECP), which the ophthalmologist can use selectively to target the ciliary epithelium and ablate ciliary body tissue. There is debate regarding which cyclodestructive method is best and how they compare to other glaucoma surgeries.ObjectivesTo assess the relative effectiveness and safety of cyclodestructive procedures compared with other procedures in people with refractory glaucoma of any type and to assess the relative effectiveness and safety of individual cyclodestructive procedures compared with each other.Search methodsWe searched the Cochrane Central Register of Controlled Trials (CENTRAL) (which contains the Cochrane Eyes and Vision Trials Register) (2018, Issue 9); Ovid MEDLINE; Embase.com; PubMed; LILACS BIREME; ClinicalTrials.gov and the WHO ICTRP. The date of the search was 21 September 2018.Selection criteriaWe included randomized controlled trials or quasi-randomized trials in which participants underwent a secondary procedure for refractory glaucoma. We included trials with any laser type, route of administration, and laser settings. The primary comparison was any cyclodestructive procedure versus another glaucoma treatment, and the secondary comparisons were individual cyclodestructive procedures versus another cyclodestructive procedure.Data collection and analysisTwo review authors independently reviewed the titles and abstracts from the database searches, and after retrieving the full-text reports of those that were potentially relevant, classified the full-text articles as included or excluded. Two review authors independently extracted data from the included studies and assessed the risk of bias. Discrepancies were resolved by discussion or by consultation with a third review author when necessary.Main resultsWe included five trials reporting data for 330 eyes (326 participants). One study to had a low risk of bias for most domains and the other studies had an overall unclear risk of bias. This review includes four different comparisons: 1) ECP versus Ahmed implant, 2) micropulse CPC versus continuous-wave CPC; 3) CPC with a diode versus Nd:YAG laser; and 4) CPC with an Nd:YAG laser emitting 8J versus 4J.No study reported data for our primary outcome, change from baseline in pain severity as reported by the participant or change in number of pain medications.For our primary comparison, we included one trial that compared ECP with the Ahmed implant. At 12-month follow-up, the mean difference (MD) in IOPs between groups was -1.14 mmHg (95% confidence interval (CI) -4.21 to 1.93; 58 participants; low-certainty evidence (LCE)). At 24 months postintervention, we found very LCE suggesting that visual acuity may be better among participants in the ECP group than in the Ahmed implant group (MD -0.24 logMAR, 95% CI -0.52 to 0.04; 54 participants), and the difference in the mean number of glaucoma medications used by participants in each group was unclear (MD -0.50, 95% CI -1.17 to 0.17; 54 participants; very LCE). Reported adverse events in the ECP group (34 participants) were one case each of hypotony, phthisis bulbi, retinal detachment, and choroidal detachment; in the Ahmed implant group (34 participants) there was one case of endophthalmitis, two cases of retinal detachment, and six cases of choroidal detachment.Three types of comparisons from four included studies provided data for our secondary comparisons. In the study that compared micropulse with continuous-wave CPC, median IOP was reported to be similar between the two groups at all time points. At 18 months postintervention, the median number of IOP-lowering medications was reduced from two to one in both groups. One participant in the micropulse and two in the continuous group exhibited worsened visual acuity. One case of prolonged inflammation was seen in the micropulse group (23 participants). Seven cases of prolonged inflammation, five cases of hypotony, and one case of phthisis bulbi were seen in the continuous group (23 participants).Two studies compared CPC using a semiconductor diode versus an Nd:YAG laser. At 12 months postintervention, the MD in IOP was 1.02 mmHg (95% CI -1.49 to 3.53) in one study (LCE). The second study did not report mean IOP beyond three months of follow-up. Neither study reported the mean change in best-corrected visual acuity or number of glaucoma medications. Both studies reported hypotony as an adverse event in three participants in each study.One study compared different energy settings of the same Nd:YAG laser. At 12-month follow-up, visual acuity was unchanged or improved in 21 of 33 participants in the 8J group and 20 of 27 participants in the 4J group (risk ratio 0.86, 95% CI 0.61 to 1.21; very LCE). More participants in the 8J group reduced the number of medications taken compared with the 4J group (RR 1.49, 95% CI 0.76 to 2.91; 50 participants; very low-certainty evidence). The presence of fibrin or hyphema were seen in five participants who received 8J and none who received 4J. There was a severe anterior chamber reaction in 11 of 26 (42%) participants who received 8J of energy and 2 of 21 (10%) participants who received 4J of energy.Authors' conclusionsEvidence from five studies included in this review was inconclusive as to whether cyclodestructive procedures for refractory glaucoma result in better outcomes and fewer complications than other glaucoma treatments, and whether one type of cyclodestructive procedure is better than another. The most commonly reported adverse events across all five studies were hypotony and phthisis bulbi. Large, well-designed randomized controlled trials are needed. Patient-reported outcomes such as pain and quality of life should be considered as primary outcomes or important secondary outcomes of future trials.