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ABSTRACT: This article describes the regulatory and evidence requirements necessary for the authorization of antimethanogenic feed additives (AMFA) aimed at mitigating enteric methane (CH4) emissions from ruminants. It outlines the legislation and legal procedures in Australia, Canada, the European Union, New Zealand, South Korea, the United Kingdom, and the United States as illustrative examples, offering insights for applicants seeking authorization. Additionals objectives are to highlight consequential similarities and differences in regulations and evidence requirements and offer recommendations for scientists and applicants. The pivotal role that scientific evidence plays in the evaluation and approval processes is emphasized, along with the need for applicants and researchers to understand and adhere to the specific regulations of each jurisdiction. Feed additives are regulated to ensure their safety for animals, humans, and the environment, and to verify their effectiveness for the intended use of enteric CH4 mitigation. Regulations cover various aspects, including ingredient safety, manufacturing practices, product labeling, and the establishment of permissible limits for certain substances to ensure their safe use in animal feed. Compliance with these regulations is mandatory, and they are enforced by regulatory agencies within each jurisdiction, aiming to protect animal health, promote food safety, and prevent misleading claims and unsafe practices. The assessment processes involve evaluating scientific evidence submitted by applicants, along with evaluations of quality control procedures, and record-keeping practices. The major difference in regulations is that each jurisdiction developed unique criteria to legally classify AMFA, making it challenging to satisfy all legal classifications with a single set of criteria for scientific evidence. However, numerous similarities and a universal reliance on the concept of intended use indicate consistency across all jurisdictions on the need for robust evidence for efficacy, safety, and product quality and documentation even if the type, size, duration, and location of the studies they require differ. Recommendations are made for both scientists and applicants, emphasizing the importance of designing, conducting, and reporting scientific evaluations transparently, using validated standards and methods, and communicating with regulatory bodies to ensure compliance with regulations and evidence requirements.

Abstract The primary cilium is a hair-like organelle that hosts molecular machinery for various developmental and homeostatic signaling pathways. Its alteration can cause rare ciliopathies such as the Bardet-Biedl and Joubert syndromes, but is also linked to Alzheimer’s disease, clinical depression, and autism spectrum disorder. These afflictions are caused by disturbances in a wide variety of genes but a common phenotype amongst them is cognitive impairment. While cilia-mediated neural function has been widely examined in early neurodevelopment, their function in the adult brain is not well understood. To help elucidate the role of cilia in neural activity, we temporally induced the ablation of IFT88, a gene encoding the intraflagellar transport 88 protein which is neccessary for ciliogenesis, in adult mice before performing memory-related behavioral assays and electroencephalogram/electromyogram (EEG/EMG) recordings. Inducible IFT88 KO mice exhibited severe learning deficits in trace fear conditioning and Morris water maze tests. They had strongly affected brainwave activity both under isoflurane induced anesthesia and during normal activity. And additionally, inducible IFT88 KO mice had altered sleep architecture and attenuated phase-amplitude coupling, a process that underlies learning and memory formation. These results highlight the growing significance of primary cilia for healthy neural function in the adult brain.

Abstract Pediatric low-grade gliomas (pLGGs) exhibit heterogeneous prognoses and variable responses to treatment, leading to tumor progression and adverse outcomes in cases where complete resection is unachievable. Early prediction of treatment responsiveness and suitability for immunotherapy has the potential to improve clinical management and outcomes. Here, we present a radiogenomic analysis of pLGGs, integrating MRI and RNA sequencing data. We identify three immunologically distinct clusters, with one group characterized by increased immune activity and poorer prognosis, indicating potential benefit from immunotherapies. We develop a radiomic signature that predicts these immune profiles with over 80% accuracy. Furthermore, our clinicoradiomic model predicts progression-free survival and correlates with treatment response. We also identify genetic variants and transcriptomic pathways associated with progression risk, highlighting links to tumor growth and immune response. This radiogenomic study in pLGGs provides a framework for the identification of high-risk patients who may benefit from targeted therapies.

Abstract New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that substantially affect the transmission rate, both within and outside the Spike protein. The mutations that we infer to have the largest effects on transmission are strongly supported by experimental evidence from prior studies. Importantly, our model detects lineages with increased transmission even at low frequencies. As an example, we infer significant transmission advantages for the Alpha, Delta, and Omicron variants shortly after their appearances in regional data, when they comprised only around 1-2% of sample sequences. Our model thus facilitates the rapid identification of variants and mutations that affect transmission from genomic surveillance data.

Abstract The legacy effects of crop diversity on maize (Zea mays L.) tissue nutrient composition, weed community structure, and intensity of weed-crop competition were assessed through a field experiment at two sites in the northeastern United States. Fields were conditioned with crop diversity gradients from summer 2016 to spring 2019. The crop diversity gradients ranged from a single cultivar to sixteen intercropped cultivars (four species, four cultivars per species) and were established in organic annual and perennial cropping systems. Following the three-year conditioning phase, maize was planted across the entire experiment, and each conditioning-phase diversity treatment was split into weed-free, ambient-weed, moderate-weed, and heavy-weed treatments. Within each cropping system, the effect of crop diversity legacy on weed-crop competition was negligible. In contrast, weed-crop competition varied between the maize grown in soil conditioned by the annual and perennial cropping systems.

Abstract Quantum key distribution (QKD) is one of the major applications of quantum information technology. It can provide ultra‐secure key distribution with security guaranteed by the laws of quantum physics. Quantum key distribution is necessary to protect data transmission from quantum computing attacks in future communication networks. The laws of quantum mechanics dictate that as opposed to microwave frequencies, quantum coherence is preserved at room temperatures for terahertz (THz) frequencies. This makes the THz band a promising solution for room‐temperature QKD implementation in future wireless communication networks. The authors present the principles of continuous variable QKD (CV‐QKD) systems and review the latest developments in the design and analysis of CV‐QKD systems operating at microwave and THz frequencies. The authors also discuss how multiple‐input multiple‐output transmission can be incorporated into the quantum communications framework to improve the secret key rates and increase the coverage distances of the THz CV‐QKD system. Furthermore, major hardware challenges that must be surmounted to practically realise THz CV‐QKD systems are highlighted.

This essay considers the positioning of univer­sities as community partners amid uncertain—and for many—unsettling political times. An argument is made for universities to reflect on contemporary trends and to orient their missions to these trends. Inevitably, this work requires universities to think clearly and decisively about ‘what they are good at’ vis-à-vis the needs of the community—regardless of how communities are defined.Universities already advance different stakehold­ers’ core aims and values. But even deeper engage­ment is needed as popular allegiance to democracy shows signs of wear. Distinctive strengths of univer­sities as providers of public goods are considered. The need to step-up community partnerships, as a value-maximization strategy, is highlighted. The question of how partnerships relate to the long-term survival of universities is contemplated.

Analyzing the local microenvironment of tumor cells can provide significant insights into their complex interactions with their cellular surroundings, including immune cells. By quantifying the prevalence and distances of certain immune cells in the vicinity of tumor cells through a neighborhood analysis, patterns may emerge that indicate specific associations between cell populations. Such analyses can reveal important aspects of tumor-immune dynamics, which may inform therapeutic strategies. This method enables an in-depth exploration of spatial interactions among different cell types, which is crucial for research in oncology, immunology, and developmental biology. We introduce an R Markdown script called SNAQ™ (Single-cell Spatial Neighborhood Analysis and Quantification), which conducts a neighborhood analysis on immunofluorescent images without the need for extensive coding knowledge. As a demonstration, SNAQ™ was used to analyze images of pancreatic ductal adenocarcinoma. Samples stained for DAPI, PanCK, CD68, and PD-L1 were segmented and classified using QuPath. The resulting CSV files were exported into RStudio for further analysis and visualization using SNAQ™. Visualizations include plots revealing the cellular composition of neighborhoods around multiple cell types within a customizable radius. Additionally, the analysis includes measuring the distances between cells of certain types relative to others across multiple regions of interest. The R Markdown files that comprise the SNAQ™ algorithm and the input data from this paper are freely available on the web at https://github.com/AryehSilver1/SNAQ.

Bulk increases in nucleobase oxidation, most commonly manifesting as the guanine (G) nucleobase modification 8-oxo-7,8-dihydroguanine (8-oxoG), have been linked to several disease pathologies. Elucidating the effects of RNA oxidation on cellular homoeostasis is limited by a lack of effective tools for detecting specific regions modified with 8-oxoG. Building on a previously published method for studying 8-oxoG in DNA, we developed ChLoRox-Seq, which works by covalently functionalizing 8-oxoG sites in RNA with biotin. Importantly, this method enables antibody-free enrichment of 8-oxoG-containing RNA fragments for Next Generation Sequencing-based detection of modified regions transcriptome-wide. We demonstrate the high specificity of ChLoRox-Seq for functionalizing 8-oxoG over unmodified nucleobases in RNA and benchmark this specificity to a commonly used antibody-based approach. Key advantages of ChLoRox-Seq include: (1) heightened resolution of RNA oxidation regions (e.g. exon-level) and (2) lower experimental costs. By applying ChLoRox-Seq to mRNA extracted from human lung epithelial cells (BEAS-2B) after exposure to environmentally relevant stress, we observe that 8-oxoG modifications tend to cluster in regions that are G-rich and within mRNA transcripts possessing longer 5’ UTR and CDS regions. These findings provide new insight into the complex mechanisms that bias the accumulation of RNA oxidation across the transcriptome. Notably, our analysis suggests the possibility that most mRNA oxidation events are probabilistically driven and that mRNAs that possess more favourable intrinsic properties are prone to incur oxidation events at elevated rates. ChLoRox-Seq can be readily applied in future studies to identify regions of elevated RNA oxidation in any cellular model of interest.

Abstract Common hypotheses for the biomechanical cause underlying neonatal retinal hemorrhage include elevated intracranial pressure (ICP) inducing venous outflow obstruction and retinal deformation. A finite element computational model of the eye, optic nerve, and orbit was simulated with particular attention to the retinal vessels to analyze stress and strain on these structures during external head compression associated with normal vaginal delivery. Pressure from maternal contractions displaced the eye backward into the orbit, and the stiff optic nerve sheath provided localized resistance to this posterior displacement at its insertion point, resulting in tensile strain of 2.5% in the peripapillary (central) retina. Correspondingly, retinal vessels experienced tensile stress of up to 2.3 kPa near the optic nerve insertion point and opposing compressive stress of up to 3.2 kPa further away. The optic nerve was longitudinally compressed and experienced a mean radial tensile strain of 2.0%. Overall, forces associated with maternal labor resulted in a pattern of eye deformation that stretched the central retina in this simulation, mirroring the classical posterior localization of neonatal retinal hemorrhage. The optic nerve increased modestly in diameter despite rising ICP, suggesting retinal deformation is a more likely mechanism for retinal hemorrhage than occlusion of the central retinal vein.

Abstract Specific Emitter Identification (SEI) has been put forward as an Internet of Things (IoT) Physical Layer Security (PLS) approach for its abilities to detect, characterize, and identify wireless emitters by exploiting distinct, inherent, and unintentional features in their transmitted signals. Since its introduction, a significant amount of work has been conducted; however, most assume the emitters are passive and their identifying signal features are immutable and challenging to mimic. This suggests the emitters are reluctant and incapable of developing and implementing effective SEI countermeasures; however, Deep Learning (DL) has been shown capable of learning emitter-specific features directly from their raw in-phase and quadrature signal samples, while Software-Defined Radios (SDRs) are capable of manipulating these signal samples. Based on these capabilities, it is fair to question the ease at which an emitter can effectively mimic the SEI features of another or manipulate its own to hinder or defeat SEI. This work considers SEI mimicry using three signal features mimicking countermeasures; “off-the-self” DL; two SDRs of different sizes, weights, power, and cost (SWaP-C); handcrafted and DL-based SEI processes, and assessment of an SEI mimicry countermeasure in a “coffee shop” deployment. Our results show “off-the-shelf” DL algorithms, and SDR enables SEI mimicry; however, adversary success is hindered by: (i) the use of decoy emitter preambles, (ii) the use of a denoising autoencoder and (iii) SDR SWaP-C constraints.

Abstract Ureolysis-induced calcium carbonate precipitation (UICP) is a biomineral solution where the urease enzyme converts urea and calcium into calcium carbonate. The resulting biomineral can bridge gaps in fractured shale, reduce undesired fluid flow, limit fracture propagation, better store carbon dioxide, and potentially enhance well efficiency. The mechanical properties of shale cores were investigated using a modified Brazilian indirect tensile strength test. An investigation of intact shale using Eagle Ford and Wolfcamp cores was conducted at varying temperatures. Results show no significant difference between shale types (average tensile strength = 6.19 MPa). Eagle Ford displayed higher strength at elevated temperature, but temperature did not influence Wolfcamp. Comparatively, cores with a single, lengthwise heterogeneous fracture were sealed with UICP and further tested for tensile strength. UICP was delivered via a flow-through method which injected 20–30 sequential patterns of ureolytic microorganisms and UICP-promoting fluids into the fracture until permeability reduced by three orders of magnitude or with an immersion method which placed cores treated with guar gum and UICP-promoting fluids into a batch reactor, demonstrating that guar gum is a suitable inclusion and may reduce the number of flow-through injections required. Tensile results for both delivery methods were variable (0.15–8 MPa), and in some cores the biomineralized fracture split apart, possibly due to insufficient sealing and/or heterogeneity in the composite UICP-shale cores. Notably in other cores the biomineralized fracture remained intact, demonstrating more cohesion than the surrounding shale, indicating that UICP may produce a strong seal for subsurface application.

Abstract Background Monitoring is a crucial part of trial conduct and ensures that participants’ data is fairly represented, and future healthcare information is enhanced. This project aims to improve trial monitoring by creating a trial monitoring plan (TMP) template with input from individuals experienced in monitoring clinical trials. Methods A review of monitoring plans received from UK Clinical Research Collaboration (UKCRC) registered clinical trials units (CTU)s created the basis for a preliminary TMP template and a Delphi survey. The TMP template was finalised after 2 rounds of a Delphi survey and a two-part consensus meeting including trialists with experience and expertise in monitoring clinical trials. Results We received 31 monitoring plans from UKCRC-registered CTUs and reviewed over 800 monitoring items for inclusion in a TMP template, selecting items based on guidelines such as Good Clinical Practice (GCP) and our monitoring experiences. For certain items, further expert input was required. A total of 66 items were chosen for a Delphi survey involving 47 participants from 25 UK CTUs and industry. After the first round, all 66 items were retained, and six additional items were suggested by Delphi participants. In the second round, 37 items reached consensus for inclusion in the TMP template. The Delphi process was followed by a consensus meeting with 9 participants from 9 UK CTUs and industry. Participants in the consensus meeting voted on the 32 further items that had not reached the definition of consensus within the Delphi, regarding each item’s inclusion in or exclusion from the TMP template. The voting resulted in 18 items being excluded, leaving 14 items to be included in the TMP template. The process overall resulted in a standardised TMP template with input from many individuals with interest, experience, or expertise in monitoring clinical trials. Conclusion A TMP template was developed building on the currently used monitoring plans and with input from those experienced in clinical trial monitoring. Using a centrally developed good quality TMP template should contribute towards maintaining consistency in monitoring standards across all CTUs, resulting in higher research quality and improved quality assurance. Its use should provide reassurance to participants that their participation is carefully monitored to ensure that their data or any samples provided are treated with confidentiality, integrity, and respect and that their rights and well-being are protected.

Background: Reverse total shoulder arthroplasty (rTSA) demonstrates favorable long-term data and has outpaced anatomic total shoulder arthroplasty and hemiarthroplasty as the most-performed shoulder arthroplasty procedure. As indications and outcomes continue to favor rTSA, patients may turn to the internet as an efficient modality to answer various questions or concerns. This study investigates online patient questions pertaining to rTSA and the quality of the websites providing information. Hypotheses: (1) Questions will pertain to surgical indications, timeline of recovery, and postoperative restrictions; (2) the quality and transparency of online information is largely heterogenous. Methods: Three rTSA searches were entered into the Google Web Search. Questions under the “People also ask” tab were expanded sequentially and 100 consecutive results for each query were included for analysis (300 in total). Questions were categorized based on Rothwell’s Classification and subcategorized by topic. Websites were categorized by source. Website quality was evaluated by the Journal of the American Medical Association (JAMA) Benchmark Criteria. Results: Most questions fell into the Rothwell Fact category (49.7%). The most common question topics were Timeline of Recovery (17.3%), Specific Activities (14.7%), and Restrictions (11.3%). The least common question topics were Anatomy/Function (0.0%), Cost (0.3%), and Diagnoses/Evaluation (0.3%). The most common websites were Medical Practice (45.0%), Academic (22.3%), and Single Surgeon (12.3%). PubMed articles consisted of 41.2% of Government websites. The average JAMA score for all websites was 1.48 ± 1.27. Government websites had the highest JAMA score (3.11 ± 1.01) and constituted 55.9% of all websites with a score of 4/4. Medical Practice websites had the lowest JAMA score (0.99 ± 0.91). Conclusion: Patients are interested in the timeline of recovery, ability to perform specific activities after surgery, and short-term and long-term restrictions following rTSA. Although all patients will benefit from education on ways to perform activities of daily living while abiding by postoperative restrictions, physicians should set preoperative expectations regarding return-to-activity following rTSA in younger, more active patients. Finally, surgeons should provide patients with physical booklets and online information available on their websites to avoid reliance on low-quality online sources.

ABSTRACT: The evaluation of dairy cow feed efficiency using residual feed intake accounts for known energy sinks. However, behavioral traits may also contribute to the variation in feed efficiency. Our objective was to estimate the heritability and repeatability of behavioral traits and their genetic correlations with feed efficiency and its components in lactating Holstein cows. The first dataset consisted of 36,075 daily rumination and lying time records collected using a SMARTBOW ear-tag accelerometer (Zoetis, Parsippany, NJ) and 6,371 weekly feed efficiency records of 728 cows from the University of Wisconsin–Madison. The second dataset consisted of 59,155 daily activity records, measured as number of steps, recorded by pedometers (AfiAct; SAE Afikim, Kibbutz Afikim, Israel) and 8,626 weekly feed efficiency records of 635 cows from the University of Florida. Feed efficiency and its components included DMI, change in BW, metabolic BW, secreted milk energy, and residual feed intake. The statistical models included the fixed effect of cohort, lactation number, and days in milk, and the random effects of animal and permanent environment. Heritability estimates for behavioral traits using daily records were 0.19 ± 0.06 for rumination and activity, and 0.37 ± 0.07 for lying time. Repeatability estimates for behavioral traits using daily data ranged from 0.56 ± 0.02 for activity to 0.62 ± 0.01 for lying time. Both heritability and repeatability estimates were larger when weekly records instead of daily records were used. Rumination and activity had positive genetic correlations with residual feed intake (0.40 ± 0.19 and 0.31 ± 0.22, respectively) and lying time had a negative genetic correlation with this residual feed intake (−0.27 ± 0.11). These results indicate that more efficient cows tend to spend more time lying and less time active. Additionally, less efficient cows tend to eat more and therefore also tend to ruminate longer. Overall, sensor-based behavioral traits are heritable and genetically correlated with feed efficiency and its components and, therefore, they could be used as indicators to identify feed-efficient cows within the herd.

Abstract In preclinical studies, p53 loss of function impacts chemotherapy response, but this has not been consistently validated clinically. We trained a TP53-loss phenocopy gene expression signature from pan-cancer clinical samples in the TCGA. In vitro, the TP53-loss phenocopy signature predicted chemotherapy response across cancer types. In a clinical dataset of 3003 breast cancer samples treated with neoadjuvant chemotherapy, the TP53-loss phenocopy samples were 56% more likely to have a pathologic complete response (pCR), with a significant association between TP53-loss phenocopy and pCR in both ER positive and ER negative tumors. In an independent clinical validation in the I-SPY2 trial (N = 987), we confirmed the association with neoadjuvant chemotherapy pCR and found higher rates of chemoimmunotherapy response in TP53-loss phenocopy tumors compared to non-TP53-loss phenocopy tumors (64% vs. 28%). The TP53-loss phenocopy signature predicts chemotherapy response across cancer types in vitro, and in a proof-of-concept clinical validation is associated with neoadjuvant chemotherapy response across multiple clinical breast cancer cohorts.

Abstract The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base interactions additionally determine the ONECUT2-DNA binding energetics. These findings provide insights into the cooperative DNA binding by CUT-homeodomain proteins.

Abstract Background Chronic pain from peripheral neuromas is difficult to manage and often requires surgical excision, though intraoperative identification of neuromas can be challenging due to anatomical ambiguity. Mechanical manipulation of the neuroma during surgery can elicit a characteristic “startle sign”, which can help guide surgical management. However, it is unknown how anesthetic management affects detection of the startle sign. Methods We performed a retrospective cohort study of 73 neuroma excision surgeries performed recently at Massachusetts General Hospital. Physiological changes in the anesthetic record were analyzed to identify associations with a startle sign event. Anesthesia type and doses of pharmacological agents were analyzed between startle sign and no-startle sign groups. Results Of the 64 neuroma resection surgeries included, 13 had a startle sign. Combined intravenous and inhalation anesthesia (CIVIA) was more frequently used in the startle sign group vs. no-startle sign group (54% vs. 8%), while regional blockade with monitored anesthetic care was not associated with the startle sign group (12% vs. 0%), p = 0.001 for anesthesia type. Other factors, such as neuromuscular blocking agents, ketamine infusion, remifentanil infusion, and intravenous morphine equivalents showed no differences between groups. Conclusions Here, we identified hypothesis-generating descriptive differences in anesthetic management associated with the detection of the neuroma startle sign during neuroma excision surgery, suggesting ways to deliver anesthesia facilitating detection of this phenomenon. Prospective trials are needed to further validate the hypotheses generated.

Abstract This topical issue, Computational Approaches for Cyber Social Threats, showcases cutting-edge research that employs computational methods to tackle the pressing challenges of cyber social threats—such as fake news, disinformation, cyberbullying, hate speech, and online radicalization. In an increasingly interconnected digital landscape, these threats significantly jeopardize societal stability by eroding public trust, intensifying polarization, and widening social divides. The theme “Information Integrity During Crises” is highlighted to underscore the critical role of reliable information during global crises, when the spread of misinformation and disinformation is particularly pervasive. With a collection of nine outstanding papers, this topical issue advances our comprehension of how computational tools can address cyber social threats and protect information integrity during crises.

The Global Emerging Infections Surveillance (GEIS) program is the only Department of Defense (DoD) organization that coordinates global surveillance for emerging infectious diseases that affect US military forces operating in the United States or foreign locations. Since 1997, the GEIS program has focused on surveilling pathogens likely to affect military operations and the health of service members. The foundation of the GEIS program is the long-standing, mutually beneficial relationships between the DoD overseas laboratories and their host-country partners and militaries. Through centralized programmatic support, the GEIS program provides the infrastructure needed for a rapid and scalable response to emerging threats. The GEIS program continues to enhance and evolve its initiatives to provide timely, reliable information to decision-makers in the DoD. The GEIS program has been and will continue to be a vital source of actionable biosurveillance information during infectious disease events of global public health concern.

Since its establishment in 1997, the US Department of Defense (DoD) Global Emerging Infections Surveillance (GEIS) program has provided support for infectious disease pandemic preparedness and response. The GEIS program has shown the value of having a central hub responsible for coordinating a global network of DoD laboratories that conduct surveillance for militarily relevant infectious disease threats. The program has supported the establishment and maintenance of capabilities for collecting, characterizing, and reporting on major infectious disease events, including the COVID-19 pandemic and mpox outbreak. The GEIS program enables the US government to mitigate infectious disease threats to DoD mission readiness and to effectively respond to pathogens worldwide. Continued investment in maintaining the GEIS program and its network is critical for timely detection and response to future emerging infectious disease threats in various populations within locations where gaps in US government or host-nation surveillance might exist.

Abstract The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. “Digital Microbes” are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.

Abstract The study of cooperating genes in cancer can lead to mechanistic understanding and identifying potential therapeutic targets. To facilitate these types of studies, we developed a new dual-inducible system utilizing the tetracycline- and cumate-inducible systems driving HES3 and the PAX3::FOXO1 fusion-oncogene, respectively, as cooperating genes from fusion-positive rhabdomyosarcoma. With this model, we can independently induce expression of either HES3 or PAX3::FOXO1, as well as simultaneously induce expression of both genes. This new model will allow us to further investigate the cooperation between HES3 and PAX3::FOXO1 including the temporal requirements for genetic cooperation. Functionally, we show that dual-induction of PAX3::FOXO1 and HES3 modifies sphere formation in a HEK293T-based system. More broadly, this lentiviral dual-inducible system can be adapted for any cooperating genes (overexpression or knockdown), allowing for independent, simultaneous, or temporally controlled gene expression.

Abstract Background A genotype-by-environment (G × E) interaction is defined as genotypes responding differently to different environments. In salmonids, G × E interactions can occur in different rearing conditions, including changes in salinity or temperature. However, water flow, an important variable that can influence metabolism, has yet to be considered for potential G × E interactions, although water flows differ across production stages. The salmonid industry is now manipulating flow in tanks to improve welfare and production performance, and expanding sea pen farming offshore, where flow dynamics are substantially greater. Therefore, there is a need to test whether G × E interactions occur under low and higher flow regimes to determine if industry should consider modifying their performance evaluation and selection criteria to account for different flow environments. Here, we used genotype-by-sequencing to create a genomic-relationship matrix of 37 Chinook salmon, Oncorhynchus tshawytscha, families to assess possible G × E interactions for production performance under two flow environments: a low flow regime (0.3 body lengths per second; bl s−1) and a moderate flow regime (0.8 bl s−1). Results Genetic correlations for the same production performance trait between flow regimes suggest there is minimal evidence of a G × E interaction between the low and moderate flow regimes tested in this study, for Chinook salmon reared from 82.9 ± 16.8 g ( $${\overline{\text{x}}}$$ x ¯ ± s.d.) to 583.2 ± 117.1 g ( $${\overline{\text{x}}}$$ x ¯ ± s.d.). Estimates of genetic and phenotypic correlations between traits did not reveal any unfavorable trait correlations for size- (weight and condition factor) and growth-related traits, regardless of the flow regime, but did suggest measuring feed intake would be the preferred approach to improve feed efficiency because of the strong correlations between feed intake and feed efficiency, consistent with previous studies. Conclusion This new information suggests that Chinook salmon families do not need to be selected separately for performance across different flow regimes. However, further studies are needed to confirm this across a wider range of fish sizes and flows. This information is key for breeding programs to determine if separate evaluation groups are required for different flow regimes that are used for production (e.g., hatchery, post smolt recirculating aquaculture system, or offshore).

Abstract Glycan-mediated interactions play a crucial role in biology and medicine, influencing signalling, immune responses, and disease pathogenesis. However, the use of glycans in biosensing and diagnostics is limited by cross-reactivity, as certain glycan motifs can be recognised by multiple biologically distinct protein receptors. To address this specificity challenge, we report the enzymatic synthesis of a 150-member library of site-specifically fluorinated Lewisx analogues (‘glycofluoroforms’) using naturally occurring enzymes and fluorinated monosaccharides. Subsequent incorporation of a subset of these glycans into nanoparticles or a microarray revealed a striking spectrum of distinct binding intensities across different proteins that recognise Lewisx. Notably, we show that for two proteins with unique binding sites for Lewisx, glycofluoroforms exhibited enhanced binding to one protein, whilst reduced binding to the other, with selectivity governed by fluorination patterns. We finally showcase the potential diagnostic utility of this approach in glycofluoroform-mediated bacterial toxin detection by lateral flow.

Abstract The lymphatic system consists of a vessel network lined by specialized lymphatic endothelial cells (LECs) that are responsible for tissue fluid homeostasis and immune cell trafficking. The mechanisms for organ-specific LEC responses to environmental cues are not well understood. We found robust lymphangiogenesis during influenza A virus infection in the adult mouse lung. We show that the number of LECs increases twofold at 7 days post-influenza infection (dpi) and threefold at 21 dpi, and that lymphangiogenesis is preceded by lymphatic dilation. We also show that the expanded lymphatic network enhances fluid drainage to mediastinal lymph nodes. Using EdU labeling, we found that a significantly higher number of pulmonary LECs are proliferating at 7 dpi compared to LECs in homeostatic conditions. Lineage tracing during influenza indicates that new pulmonary LECs are derived from preexisting LECs rather than non-LEC progenitors. Lastly, using a conditional LEC-specific YAP/TAZ knockout model, we established that lymphangiogenesis, fluid transport and the immune response to influenza are independent of YAP/TAZ activity in LECs. These findings were unexpected, as they indicate that YAP/TAZ signaling is not crucial for these processes.

Abstract Genomic alterations in fibroblast growth factor receptor (FGFR) genes are present in a small number of metastatic pancreatic ductal adenocarcinomas (PDAC) and may represent an emerging subgroup of patients likely to benefit from FGFR targeted therapies. Here we present four FGFR2 fusion-positive metastatic PDAC patients who exhibited durable responses or disease control to FGFR kinase inhibitors. Utilizing our custom FGFR focused cell-free DNA assay, FGFR-Dx, we serially monitored variant allele fractions of FGFR2 fusions during FGFR inhibitor treatment and observed dynamic changes correlating with clinical responses. Genomic analysis of 30,229 comprehensively profiled pancreatic cancers revealed FGFR1-3 fusions in 245 cases, an incidence of 0.81%. FGFR fusions were generally mutually exclusive from other known oncogenes. Our findings provide clinical evidence for identifying and treating FGFR2 fusion-positive PDAC patients with FGFR targeted therapy.

Abstract Mount Rainier has had at least 11 large lahars over the last 6,000 years, including one occurring without evidence of eruptive activity. This prompted the creation of a lahar detection system that uses a combination of seismic, infrasound, and tripwires. We test a laser rangefinder placed on a river channel bank for detecting and confirming mass movements flowing past a station as an alternative to the physical tripwires. After testing the device at an experimental debris-flow flume, the laser rangefinder successfully captured a small debris flow on Mount Rainier in 2023, confirming its effectiveness as a lahar detection and monitoring tool. Over the 2-month deployment at Mount Rainier, we find that spurious recordings in the laser rangefinder data (noise) tend to correlate with high humidity, and that periods of noise do not correlate with increased co-located seismic amplitude. Therefore, the impact of the noise on future alarms can be mitigated by coupling a laser rangefinder alarm with that of independent datasets.

In 2018/2019, two large Guillain–Barré Syndrome (GBS) outbreaks took place in Peru. Here, we report a comprehensive analysis of biological samples from GBS patients from the 2019 outbreak. We applied metagenomic, microbiologic, and serological analyses to different biological samples collected from GBS patients. Further phenotypic and genomic characterization was conducted on Campylobacter jejuni isolates from GBS samples. Microbiologic and metagenomic analyses revealed several patients with multiple co-infections, yet no common infectious agents were found other than C. jejuni. Four C. jejuni isolates were isolated from rectal swabs. Twenty-one patients had detectable IgG serum antibodies related to C. jejuni, of whom seven had IgM antibodies. Genomic analyses showed that these four strains were clonal (ST2993) and contained the class A lipooligosaccharide biosynthesis locus. These results further support the idea that that C. jejuni is the etiological agent that triggered the GBS outbreak in Peru in 2019 and that the strains are not restricted to Peru, hence could be regarded as a broad public health concern. Furthermore, though we cannot delineate the role played by co-infections in GBS development, results obtained herein highlight metagenomic analysis as a potential new tool for depicting a yet unknown area of research in GBS.

Abstract Myocardial ischemia causes the release of bradykinin, which activates afferent nerve endings in the ventricular epicardium. This elicits a sympathetically mediated increase in arterial pressure and heart rate, referred to as the cardiogenic sympathetic afferent reflex. The rostroventrolateral medulla (RVLM) is a key sympathetic brain stem site for regulating cardiovascular activity. This study aimed to determine the importance of non‐barosensitive nociception sympathetic activity and the role of glutamate receptor activation of RVLM neurons in the cardiogenic sympathetic afferent reflex. We tested the hypothesis that inhibition of barosensitive sympathetic activity attenuates but does not abolish the reflex response to cardiac visceral afferents. Renal sympathetic nerve activity (RSNA), arterial pressure, and heart rate responses to epicardial bradykinin application were recorded in anesthetized rats before and after bilateral RVLM microinjection of either GABAA agonist muscimol, ionotropic glutamate receptor antagonist kynurenic acid, N‐methyl‐d‐aspartate (NMDA) receptor antagonist 2‐amino‐5‐ phosphonopentanoic acid (AP5), or non‐NMDA antagonist 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX). Baroreceptor loading‐induced inhibition of barosensitive activity attenuated the bradykinin‐induced RSNA response (93 ± 14% increase) and tachycardia (18 ± 3 bpm). While RVLM muscimol microinjection abolished the RSNA response (1.6 ± 4.2% from baseline, 0.49 ± 0.38 μV*s), surprisingly, it did not abolish the tachycardia (27 ± 4 bpm). Kynurenic acid microinjection blocked the arterial pressure and RSNA responses, while AP5 or CNQX only attenuated the responses. These data suggest that nociception‐sensitive sympathetic activity that does not appear to be barosensitive is also involved in the cardiogenic sympathetic afferent reflex. Importantly, while muscimol and kynurenic acid abolished the arterial pressure and RSNA response, neither affected the tachycardia, suggesting an alternate cardiac pathway independent of RVLM.

A lesser tuberosity osteotomy (LTO) is commonly performed during total shoulder arthroplasty to access the glenohumeral joint. Healing of the LTO is critical to optimizing the outcome of the procedure and is enhanced by a repair that provides stability and compression across the osteotomy site. The purpose of this article is to describe a technique that uses a tensionable suture construct to repair the LTO during anatomic total shoulder arthroplasty using a stemless humeral component. The technique involves passing a row of high-tensile sutures through bone tunnels lateral to the osteotomy site (transosseous sutures) and another row of sutures through the humeral implant (implant sutures). One limb of each bone tunnel suture is then tied to its corresponding limb of implant suture and the remaining free strands of the tied sutures are manually tensioned and tied to each other. This technique is an efficient and reproducible method for creating compression and stability across the osteotomy site that facilitates bony healing.

Abstract Plasmodium falciparum is the main causative agent of malaria, a deadly disease that mainly affects children under five years old. Artemisinin-based combination therapies have been pivotal in controlling the disease, but resistance has arisen in various regions, increasing the risk of treatment failure. The non-mevalonate pathway is essential for the isoprenoid synthesis in Plasmodium and provides several under-explored targets to be used in the discovery of new antimalarials. 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of the pathway. Despite its importance, there are no structures available for any Plasmodium spp., due to the complex sequence which contains large regions of high disorder, making crystallisation a difficult task. In this manuscript, we use cryo-electron microscopy to solve the P. falciparum DXPS structure at a final resolution of 2.42 Å. Overall, the structure resembles other DXPS enzymes but includes a distinct N-terminal domain exclusive to the Plasmodium genus. Mutational studies show that destabilization of the cap domain interface negatively impacts protein stability and activity. Additionally, a density for the co-factor thiamine diphosphate is found in the active site. Our work highlights the potential of cryo-EM to obtain structures of P. falciparum proteins that are unfeasible by means of crystallography.

Abstract Correctly identifying perturbed biological pathways is a critical step in uncovering basic disease mechanisms and developing much-needed therapeutic strategies. However, whether current tools are optimal for unbiased discovery of relevant pathways remains unclear. Here, we create “Benchmark” to critically evaluate existing tools and find that most function sub-optimally. We thus develop the “Pathway Ensemble Tool” (PET), which outperforms existing methods. Deploying PET, we identify prognostic pathways across 12 cancer types. PET-identified prognostic pathways offer additional insights, with genes within these pathways serving as reliable biomarkers for clinical outcomes. Additionally, normalizing these pathways using drug repurposing strategies represents therapeutic opportunities. For example, the top predicted repurposed drug for bladder cancer, a CDK2/9 inhibitor, represses cell growth in vitro and in vivo. We anticipate that using Benchmark and PET for unbiased pathway discovery will offer additional insights into disease mechanisms across a spectrum of diseases, enabling biomarker discovery and therapeutic strategies.

Abstract The ATR kinase responds to elevated levels of single-stranded DNA (ssDNA) to activate the G2/M checkpoint, regulate origin utilization, preserve fork stability, and allow DNA repair to ensure genome integrity. The intrinsic replication stress in cancer cells makes this pathway an attractive therapeutic target. The ssDNA that drives ATR signaling is sensed by the ssDNA-binding protein replication protein A (RPA), which acts as a platform for ATRIP recruitment and subsequent ATR activation by TopBP1. We have developed chemical RPA inhibitors (RPAi) that block RPA-ssDNA interactions (RPA-DBi) and RPA protein–protein interactions (RPA-PPIi); both activities are required for ATR activation. Here, we biochemically reconstitute the ATR kinase signaling pathway and demonstrate that RPA-DBi and RPA-PPIi abrogate ATR-dependent phosphorylation of target proteins with selectivity advantages over active site ATR inhibitors. We demonstrate that RPA post-translational modifications (PTMs) impact ATR kinase activation but do not alter sensitivity to RPAi. Specifically, phosphorylation of RPA32 and TopBP1 stimulate, while RPA70 acetylation does not affect ATR phosphorylation of target proteins. Collectively, this work reveals the RPAi mechanism of action to inhibit ATR signaling that can be regulated by RPA PTMs and offers insight into the anti-cancer activity of ATR pathway-targeted cancer therapeutics.

Abstract The objective of this review is to survey radiomics signatures for detecting pathological extracapsular extension (pECE) on magnetic resonance imaging (MRI) in patients with prostate cancer (PCa) who underwent prostatectomy. Scientific Literature databases were used to search studies published from January 2007 to October 2023. All studies related to PCa MRI staging and using radiomics signatures to detect pECE after prostatectomy were included. Systematic review was performed according to Preferred Reporting Items for Systematic Review and Meta-analyses (PRISMA). The risk of bias and certainty of the evidence was assessed using QUADAS-2 and the radiomics quality score. From 1247 article titles screened, 16 reports were assessed for eligibility, and 11 studies were included in this systematic review. All used a retrospective study design and most of them used 3 T MRI. Only two studies were performed in more than one institution. The highest AUC of a model using only radiomics features was 0.85, for the test validation. The AUC for best model performance (radiomics associated with clinical/semantic features) varied from 0.72–0.92 and 0.69–0.89 for the training and validation group, respectively. Combined models performed better than radiomics signatures alone for detecting ECE. Most of the studies showed a low to medium risk of bias. After thorough analysis, we found no strong evidence supporting the clinical use of radiomics signatures for identifying extracapsular extension (ECE) in pre-surgery PCa patients. Future studies should adopt prospective multicentre approaches using large public datasets and combined models for detecting ECE. Critical relevant statement The use of radiomics algorithms, with clinical and AI integration, in predicting extracapsular extension, could lead to the development of more accurate predictive models, which could help improve surgical planning and lead to better outcomes for prostate cancer patients. Protocol of systematic review registration PROSPERO CRD42021272088. Published: https://doi.org/10.1136/bmjopen-2021-052342 . Key Points Radiomics can extract diagnostic features from MRI to enhance prostate cancer diagnosis performance. The combined models performed better than radiomics signatures alone for detecting extracapsular extension. Radiomics are not yet reliable for extracapsular detection in PCa patients. Graphical Abstract

Abstract Microeukaryotes are key contributors to marine carbon cycling. Their physiology, ecology, and interactions with the chemical environment are poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle Clio, microbial communities along a 1050 km transect in the western North Atlantic Ocean were surveyed at 10–200 m vertical depth increments to capture metabolic signatures spanning oligotrophic, continental margin, and productive coastal ecosystems. Microeukaryotes were examined using a paired metatranscriptomic and metaproteomic approach. Here we show a diverse surface assemblage consisting of stramenopiles, dinoflagellates and ciliates represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m, and fungal proteins emerging in waters >3000 m. In the broad microeukaryote community, nitrogen stress biomarkers were found at coastal sites, with phosphorus stress biomarkers offshore. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, and nutrients.

Abstract Programmed cell death 1 (PD-1) is a premier cancer drug target for immune checkpoint blockade (ICB). Because PD-1 receptor inhibition activates tumor-specific T-cell immunity, research has predominantly focused on T-cell-PD-1 expression and its immunobiology. In contrast, cancer cell-intrinsic PD-1 functional regulation is not well understood. Here, we demonstrate induction of PD-1 in melanoma cells via type I interferon receptor (IFNAR) signaling and reversal of ICB efficacy through IFNAR pathway inhibition. Treatment of melanoma cells with IFN-α or IFN-β triggers IFNAR-mediated Janus kinase-signal transducer and activator of transcription (JAK/STAT) signaling, increases chromatin accessibility and resultant STAT1/2 and IFN regulatory factor 9 (IRF9) binding within a PD-1 gene enhancer, and leads to PD-1 induction. IFNAR1 or JAK/STAT inhibition suppresses melanoma-PD-1 expression and disrupts ICB efficacy in preclinical models. Our results uncover type I IFN-dependent regulation of cancer cell-PD-1 and provide mechanistic insight into the potential unintended ICB-neutralizing effects of widely used IFNAR1 and JAK inhibitors.

Abstract Rare genetic diseases are typically studied in referral populations, resulting in underdiagnosis and biased assessment of penetrance and phenotype. To address this, we develop a generalizable method of genotype inference based on distant relatedness and deploy this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. We identify 9 LQT5 families referred to a single specialty clinic, each carrying p.Asp76Asn, the most common LQT5 variant. We uncover recent common ancestry and a single shared haplotype among probands. Application to a non-referral population of 69,819 BioVU biobank subjects identifies 22 additional subjects sharing this haplotype, which we confirm to carry p.Asp76Asn. Referral and non-referral carriers have prolonged QT interval corrected for heart rate (QTc) compared to controls, and, among carriers, the QTc polygenic score is independently associated with QTc prolongation. Thus, our innovative analysis of shared chromosomal segments identifies undiagnosed cases of genetic disease and refines the understanding of LQT5 penetrance and phenotype.

Abstract With increasing pace, crystalline open frameworks are moving to larger scale, mature applications that stretch as broadly as catalysis, separation, water purification, adsorption, sensing, biomineralization and energy storage. A particular challenge in this development can be the unexpected variation in material properties from batch to batch, even when a cursory analysis would indicate that no process changes occurred. Our team has lived this journey in many larger projects where pilot scale production of metal-organic frameworks for use in devices has been a key milestone and suffered the difficulties of unexpected performance departures. In this Perspective, we aim to share some of the learning outcomes in the hope that it will further speed development in the field.

Recent discoveries of massive galaxies existing in the early universe, as well as apparent anomalies in Ωm and H0 at high redshift, have raised sharp new concerns for the ΛCDM model of cosmology. Here, we address these problems by using new solutions for the Einstein field equations of relativistic compact objects originally found by Ni. Applied to the universe, the new solutions imply that the universe’s mass is relatively concentrated in a thick outer shell. The interior space would not have a flat, Minkowski metric, but rather a repulsive gravitational field centered on the origin. This field would induce a gravitational redshift in light waves moving inward from the cosmic shell and a corresponding blueshift in waves approaching the shell. Assuming the Milky Way lies near the origin, within the KBC Void, this redshift would make H0 appear to diminish at high redshifts and could thus relieve the Hubble tension. The Ni redshift could also reduce or eliminate the requirement for dark energy in the ΛCDM model. The relative dimness of distant objects would instead arise because the Ni redshift makes them appear closer to us than they really are. To account for the CMB temperature–redshift relation and for the absence of a systematic blueshift in stars closer to the origin than the Milky Way, it is proposed that the Ni redshift and blueshift involve exchanges of photon energy with a photonic spacetime. These exchanges in turn form the basis for a cosmic CMB cycle, which gives rise to gravity and an Einsteinian cosmological constant, Λ. Black holes are suggested to have analogous Ni structures and gravity/Λ cycles.

Thermal green protein Q66E (TGP-E) has previously shown increased thermal stability compared to thermal green protein (TGP), a thermal stable fluorescent protein produced through consensus and surface protein engineering. In this paper, we describe the protein crystal structure of TGP-E to 2.0 Å. This structure reveals alterations in the hydrogen bond network near the chromophore that may result in the observed increase in thermal stability. We compare the very stable TGP-E protein to the structure of a yellow mutant version of this protein YTP-E E148D. The structure of this mutant protein reveals the rationale for the observed low quantum yield and directions for future protein engineering efforts.

Background Use of pulmonary vein isolation (PVI) to treat atrial fibrillation continues to increase. Despite great interest in leveraging administrative data for real‐world analyses, contemporary procedural codes for identifying PVI have not been evaluated. Methods and Results In this observational retrospective cohort study, inpatient PVIs were identified among US Medicare fee‐for‐service beneficiaries using Current Procedural Terminology (CPT) code 93656 in Carrier Line Files. Each patient was matched with their claims from Medicare Provider Analysis and Review to compare CPT with International Classification of Diseases, Tenth Revision, Procedure Coding System (ICD‐10‐PCS) claims submitted by health care facilities to bill for PVIs. We performed the reverse for commonly matched ICD‐10‐PCS codes, to identify corresponding CPT‐billed procedures. Finally, we reviewed institutional cases for additional comparison of CPT and ICD‐10‐PCS assignation for PVI. We identified 25 617 inpatient PVIs from January 2017 to December 2021, of which 18 165 (71%) were linked to Medicare Provider Analysis and Review. Of these, 16 672 (92%) were billed as ICD‐10‐PCS 02583ZZ: “Destruction of Conduction Mechanism, Percutaneous Approach.” The reverse process yielded heterogeneous results: among 75 003 procedures billed as ICD‐10‐PCS 02583ZZ, only 15 691 (21%) matched with CPT 93656 (PVI), as several other unrelated procedures were billed under this ICD‐10‐PCS code. Institutional case review confirmed the greater specificity of CPT codes. Conclusions The ICD‐10‐PCS code associated with CPT‐billed PVI procedures actually referred to ablation of the atrioventricular junction. Yet this ICD‐10‐PCS code also matched with a wide range of other procedures distinct from PVI. We conclude that ICD‐10‐PCS codes alone are not sensitive nor specific for identifying PVI in claims and cannot be reliably used in isolation for health services research on this important procedure.

Coastal lagoons are productive ecosystems supporting diverse biota but are susceptible to altered flow regimes and nutrient enrichment. The Coorong Lagoon in South Australia faces significant threats from reduced freshwater inputs and eutrophication, with the keystone macrophyte species, Ruppia tuberosa, generally in a state of decline. Identifying management strategies to guide their recovery has proven complicated due to the complex environmental requirements across life stages. This study aimed to develop a novel phenology-based habitat suitability model for quantifying the overall probability of reproductive success, based on salinity, water depth, light availability, temperature and filamentous algae presence. High-resolution predictions from a coupled hydrodynamic-habitat suitability model were validated against individual life stage data and reproductive outcomes (sexual and asexual) under both typical and atypical (La Niña) climatic conditions, achieving statistically significant (P < 0.05) correlation coefficients for all life stages under typical conditions. Results revealed considerable inter-annual variability in total areas suitable for reproduction between 2018 and 2022, primarily influenced by salinity and light availability during early stages (germination and sprouting) and reproductive stage. 2018 had the largest suitable areas for reproduction, while 2021 had the smallest. Under typical conditions, the central part of the lagoon was identified as a high conservation value area for R. tuberosa, offering optimal conditions for both sexual and asexual reproduction. This study highlights the importance of incorporating phenology into habitat models and demonstrates how such models can guide management decisions aiming at restoring not just the adult plant phase but also ensuring reproductive success and long-term resilience of the R. tuberosa community.

Summary: Outside acoustic communication, little is known about how animals coordinate social turn taking and how the brain drives engagement in these social interactions. Using Siamese fighting fish (Betta splendens), we discover dynamic visual features of an opponent and behavioral sequences that drive visually driven turn-taking aggressive behavior. Lesions of the telencephalon show that it is unnecessary for coordinating turn taking but is required for persistent participation in aggressive interactions. Circumscribed lesions of the caudal dorsomedial telencephalon (cDm; the fish pallial amygdala) recapitulated the telencephalic lesions. Furthermore, ventral telencephalic regions and the thalamic preglomerular complex, all of which project to cDm, show increased activity during aggressive interactions. Our work highlights how dynamic visual cues shape the rhythm of social interactions at multiple timescales. The results point to the vertebrate pallial amygdala as a region with an evolutionarily conserved role in regulating the persistence of emotional states, including those that promote engagement in social interactions.

A key issue in landscape management, whether public or private, is the mitigation of disturbance events that impact vegetation, ecosystem health, and thus ecosystem services (ESs). Although many studies have found significant tree mortality due to insect infestations, there is still insufficient understanding of how these infestations alter ESs and their associated economic values. Addressing this research gap can assist forest managers and decision-makers in refining and implementing adaptive management practices and policies, while enhancing the resilience of forests and their ESs. We investigated the impacts of bark beetle outbreaks on three ESs (timber provisioning, water retention, and carbon sequestration) in the Lake Tahoe region of Northern California and Northern Nevada. Using the landscape simulation model LANDIS-II, we examined differences between a business-as-usual management scenario and an enhanced management scenario with respect to the amount of aboveground tree biomass and ESs impacted by beetle outbreaks. Since insect infestation is also influenced by climate, each of the two management scenarios considered three different climate scenarios: a scenario with average historical climate (no climate change); a warmer, wetter scenario from the Model for Interdisciplinary Research on Climate (MIROC); and a hotter, drier scenario from the Centre National de Recherches Météorologiques (CNRM). Results show that a warmer and drier climate results in more severe beetle-induced tree mortality than a wetter and cooler climate, resulting in greater negative impacts to ESs. The estimated loss of ES value is approximately $0.2 to $0.8 million USD per year. Enhanced management is more capable than business-as-usual practices to prevent beetle damages to trees and ESs.

Phosphatidic acid phosphatase (PAP) is an evolutionarily conserved eukaryotic enzyme that catalyzes the Mg2+-dependent dephosphorylation of phosphatidic acid to produce diacylglycerol. The product and substrate of PAP are key intermediates in the synthesis of triacylglycerol and membrane phospholipids. PAP activity is associated with lipid-based cellular defects indicating the enzyme is an important target for regulation. We identified that the antidepressant sertraline is a novel inhibitor of PAP. Using Saccharomyces cerevisiae Pah1 as a model PAP, sertraline inhibited the activity by a noncompetitive mechanism. Sertraline also inhibited the PAP activity of human lipin 1 (α, β, and γ), an orthologue of Pah1. The inhibitor constants of sertraline for the S. cerevisiae and human PAP enzymes were 7-fold and ∼2-fold, respectively, lower than those of propranolol, a commonly used PAP inhibitor. Consistent with the inhibitory mechanism of sertraline and propranolol, molecular docking of the inhibitors predicts that they interact with non-catalytic residues in the haloacid dehalogenase-like catalytic domain of Pah1. The Pah1-CC (catalytic core) variant, which lacks regulatory sequences, was inhibited by both drugs in accordance with molecular docking data. That Pah1 is a physiological target of sertraline in S. cerevisiae is supported by the observations that the overexpression of PAH1 rescued the sertraline-mediated inhibition of pah1Δ mutant cell growth, the lethal effect of overexpressing Pah1-CC was rescued by sertraline supplementation, and that a sublethal dose of the drug resulted in a 2-fold decrease in TAG content.

Efficient chiral resolution is highly important in the food, pharmaceutical and agriculture industries because of the distinctive biological or pharmaceutical properties of enantiomers. Membrane-assisted chiral separation, which has the potential advantages of low cost and high yield, has attracted significant research attention, but the fabrication of high-quality chiral membranes displaying both high selectivity and high flux of enantiomers is still a challenge. Covalent organic frameworks (COFs), a class of porous materials with high porosity and diverse functionalities, are promising for the development of high-performance chiral separation membranes; however, these materials have yet to be developed. In this work, we demonstrated the in situ growth of a chiral TpPa-1 (cTpPa-1) membrane on polymer substrates via chiral induction. The resulting cTpPa-1@PAN membrane displayed a maximum enantioselectivity of 99.3 ​% ee for resolving limonene racemates with a flux of 5.5 ​mmol ​m−2 ​h−1. Furthermore, the effects of feed solvent polarity on membrane performance, the versatility of cTpPa-1 for making chiral composite membranes, and the mechanisms associated with cTpPa-1-based membranes were studied and are discussed.

Myocardial ischemia causes the production and release of metabolites such as bradykinin, which stimulates cardiac spinal sensory afferents, causing chest pain and an increase in sympathetic activity referred to as the cardiogenic sympathetic afferent reflex. While the brain stem nuclei, such as the nucleus tractus solitarius and rostral ventrolateral medulla, are essential in the cardiogenic sympathetic afferent reflex, the role of other supramedullary nuclei in the cardiogenic sympathetic afferent reflex are not clear. The dorsomedial hypothalamic nucleus (DMH) is involved in cardiovascular sympathetic regulation and plays an important role in the sympathetic response to stressful stimuli. In this study, we determined the role of DMH in the cardiogenic sympathetic afferent reflex. To do this we measured arterial pressure, heart rate, and renal sympathetic nerve activity (RSNA) responses to epicardial bradykinin (10 μg/mL) in anesthetized Sprague Dawley rats before and after bilateral DMH microinjection (50 nL) of either the GABAA agonist muscimol (0.5 nmol) to inhibit or the antagonist bicuculline (40 pmol) to disinhibit activity. Muscimol inhibition elicited a modest, albeit significant, reduction in basal arterial pressure and heart rate and attenuated the arterial pressure and heart rate reflex response to epicardial bradykinin. However, it did not change the magnitude of the reflex. Bicuculline disinhibition of the DMH increased basal arterial pressure, heart rate, and RSNA but did not augment the response to epicardial bradykinin. These results suggest that sympathetic activity derived from the DMH does not play an important role in the cardiogenic sympathetic afferent reflex in Sprague Dawley rats.