Search Results (75)

The reliability of passive samplers in measuring volatile organic compounds (VOCs) in indoor air depends on whether the uptake rate is constant given the environmental conditions and sampler exposure duration. The first phase of this study evaluated the performance of charcoal-based, solvent-extracted passive samplers (e.g., Radiello^® 130 passive samplers with white diffusive bodies) over exposure periods ranging from 1 week to 1 year in a test house with known vapor intrusion (VI). Chloroform %Bias values exceeded the ±30% acceptance criterion after 4 weeks exposure. Benzene, hexane, and trichloroethylene (TCE) concentrations were within the acceptance criterion for up to three months. Toluene and tetrachloroethylene (PCE), the two least volatile compounds, demonstrated uniform uptake rates over one year. In the second phase of this study, testing of the longer exposure times of 6 months and 1 year were evaluated with three additional passive samplers: Waterloo Membrane Sampler^TM (WMS^TM), SKC 575 with secondary diffusive cover, and Radiello^® 130 passive samplers with yellow diffusive bodies. The SKC 575 and Radiello^® 130 passive samplers produced acceptable results (%Bias ≤ 30%) over the 6-month exposure period, while the WMS^TM sampler results favored petroleum hydrocarbon more than chlorinated solvent uptake. After the 1-year exposure period, the passive sampler performances were acceptable under specific conditions of this study. The results suggest that all three samplers can produce acceptable results over exposure time periods beyond 30 days and up to a year for some compounds. Full article

Background/Objectives: An accurate evaluation of variant actionability is essential in cancer management. In Von Hippel–Lindau Syndrome (VHL), the interpretation of the germline variants is confounded by the presence of non-syndromic component tumors, such as clear cell renal cell carcinoma (ccRCC), hemangioblastoma, pheochromocytoma, and neuroendocrine tumors. These tumors frequently occur sporadically, without any association with VHL syndrome. The presence of these tumors in a patient with a germline VHL variant could lead to inaccurate attribution of these tumors to the germline variant and VHL syndrome. In our previous INT²GRATE (INTegrated INTerpretation of GeRmline And Tumor gEnomes) programs, we demonstrated that integrating tumor-derived and germline evidence offers a comprehensive approach for the accurate assessment of the germline variants in cancer syndromes. Methods/Results: Here, we present a novel INT²GRATE variant evidence framework (VEF) for evaluating the clinical actionability of the germline variants in VHL syndrome, offering an integrated approach that incorporates both constitutional and tumor data. We analyzed 2672 variants in the VHL gene and their associated tumors and clinical evidence to effectively distinguish between constitutional, sporadic, VHL differentials, and VHL allelic genetic conditions. The germline INT²GRATE variants, along with their comprehensive associated evidence, were made accessible in the first open-access INT²GRATE Variant data Portal. Conclusions: This novel and integrated approach to variant assessment and data sharing in hereditary cancer syndromes is essential in the clinical evaluation of genomic variants, advancing precision oncology, and improving patient care. Full article

Objectives: The COVID-19 pandemic has significantly impacted mental health worldwide. This study investigated the relationship between perceived COVID-19 threat and adjustment disorder (AjD) severity, examining self-compassion (SC) and experiential avoidance (EA) as potential moderators. Additionally, cluster analysis—a statistical method for grouping individuals based on similar psychological characteristics—was employed to identify distinct profiles of SC and EA and their associations with AjD, depression, and anxiety symptoms. Methods: A sample of 308 participants meeting AjD criteria completed measures assessing AjD severity (ADNM-20), depression (PHQ-9), anxiety (GAD-7), SC, EA, and perceived threat of COVID-19. Moderation analyses were performed using the PROCESS macro. Cluster analysis identified profiles based on SC and EA scores, with clusters compared on AjD, PHQ, and GAD symptom severity. Results: SC and EA moderated the relationship between perceived COVID-19 threat and AjD severity. Interestingly, individuals with high EA and low SC exhibited no significant association between perceived threat and AjD symptoms. Cluster analysis revealed four distinct profiles: (1) high SC and low EA, (2) average SC and EA, (3) low SC and low EA, and (4) low SC and high EA. Participants in the high SC/low EA cluster reported significantly lower levels of AjD, depression, and anxiety symptoms compared to those in the low SC/high EA cluster, who exhibited the highest symptom severity across all measures. Conclusions: Our findings suggest that individuals who relied on experiential avoidance and lacked self-compassion experienced less emotional distress related to pandemic-related worries, potentially shielding themselves from acute AjD symptoms. However, this strategy was associated with greater emotional distress, as those with high AE and SC exhibited more symptoms of AjD, depression, and anxiety. In contrast, individuals with low AE and high SC demonstrated significantly better psychological well-being. Full article

Numerous organisms, including animals, plants, fungi, protists, and bacteria, rely on toxins to meet their needs. Biological toxins have been classified into three groups: poisons transferred passively without a delivery mechanism; toxungens delivered to the body surface without an accompanying wound; and venoms conveyed to internal tissues via the creation of a wound. The distinctions highlight the evolutionary pathways by which toxins acquire specialized functions. Heretofore, the term venom has been largely restricted to animals. However, careful consideration reveals a surprising diversity of organisms that deploy toxic secretions via strategies remarkably analogous to those of venomous animals. Numerous plants inject toxins and pathogenic microorganisms into animals through stinging trichomes, thorns, spines, prickles, raphides, and silica needles. Some plants protect themselves via ants as venomous symbionts. Certain fungi deliver toxins via hyphae into infected hosts for nutritional and/or defensive purposes. Fungi can possess penetration structures, sometimes independent of the hyphae, that create a wound to facilitate toxin delivery. Some protists discharge harpoon-like extrusomes (toxicysts and nematocysts) that penetrate their prey and deliver toxins. Many bacteria possess secretion systems or contractile injection systems that can introduce toxins into targets via wounds. Viruses, though not “true” organisms according to many, include a group (the bacteriophages) which can inject nucleic acids and virion proteins into host cells that inflict damage rivaling that of conventional venoms. Collectively, these examples suggest that venom delivery systems—and even toxungen delivery systems, which we briefly address—are much more widespread than previously recognized. Thus, our understanding of venom as an evolutionary novelty has focused on only a small proportion of venomous organisms. With regard to this widespread form of toxin deployment, the words of the Sherman Brothers in Disney’s iconic tune, It’s a Small World, could hardly be more apt: “There’s so much that we share, that it’s time we’re aware, it’s a small world after all”. Full article

An ultrasound-responsive hydrogel system was developed that provides on-demand release when stimulated by focused ultrasound (fUS). Diels–Alder cycloadducts crosslinked polyethylene glycol (PEG) hydrogels and underwent a retrograde Diels–Alder reaction when exposed to fUS. Four-arm and eight-arm furan-based Diels–Alder hydrogel compositions were used to evaluate the link between the crosslinking density and the fUS-induced release and retention rates. PEG crosslinked with glutaraldehyde was also used as a non-Diels–Alder control hydrogel. By increasing the exposure time and the amplitude of fUS, the Diels–Alder-based hydrogels exhibited a correlative increase in the release of the entrapped BMP-2. Real-time B-mode imaging was used during fUS to visualize the on-demand degradation of the crosslinking matrix for the release of BMP-2. When monitored with a thermocouple, the increase in temperature observed was minimal in the area surrounding the sample during fUS stimulation, indicating fUS to be an external stimulus which could be used safely for spatiotemporally controlled release. PEG hydrogels were characterized using nuclear magnetic resonance, Fourier transform infrared spectroscopy, differential scanning calorimetry, thermogravimetric analysis, and compression testing. PEG degradation byproducts were evaluated for cytocompatibility in vitro. Overall, this study demonstrated that Diels–Alder-based PEG hydrogels can encapsulate BMP-2, undergo a retrograde reaction when externally stimulated with fUS, and release active BMP-2 to induce differentiation in human mesenchymal stem cells. Full article

Previous studies have shown that language learners’ auditory word recognition behavior provides evidence for independent contributions of perceptual and phonolexical representations, and learners’ patterns of auditory word recognition have been characterized as resulting from “fuzziness” or “imprecision” associated with these representations. More recently, it has been argued that representational “fuzziness” may in fact take various forms (e.g., neutralized, precise, ambiguous). The purpose of the present study is to further build on this line of work by elaborating additional logically possible scenarios by crossing larger sets of logically possible types of perceptual and phonolexical representational precision/imprecision, as an exercise in exploring the empirical and theoretical implications of our characterizations of representational fuzziness in language learners. We collect new empirical data for the purpose of demonstrating how we might evaluate auditory word recognition performance relative to this fuller set of predicted scenarios. We computed the set of hypothesized scenarios by crossing possible perceptual and lexical representations. We crossed four possible perceptual representations (NeutralizedC + NeutralizedV, NeutralizedC + PreciseV, PreciseC + NeutralizedV, or PreciseC + PreciseV) and six possible phonolexical representations (Neutralized, Ambiguous, Not X, Precise, Fuzzy Word, or Word Length), for a total of 24 scenarios, each accompanied by a set of predictions with respect to accuracy on an auditory word–picture matching test. We interpret the group and individual performance relative to these scenarios with the ultimate aim of better understanding the implications of our assumptions about the nature of perceptual and phonolexical representations relative to observed patterns of learner behavior. Our hope is that in computing this factorial typology of logically possible scenarios and demonstrating a starting point for how we might empirically evaluate its predictions, we set the stage for future research to refine the hypothesis space through empirical studies of auditory word processing in language learners. Full article

Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that plagued earlier sequencing methods, bioinformatics adopted an ambitious strategy involving high-throughput and highly automated assays. However, as the list of omics technologies continues to grow, the field of bioinformatics has changed in two fundamental ways. Despite enormous success in expanding our understanding of the biological world, the failure of bulk methods to account for biologically important variability among cells of the same or different type has led to a major shift toward single-cell and spatially resolved omics methods, which attempt to disentangle the conflicting signals contained in heterogeneous samples by examining individual cells or cell clusters. The second major shift has been the attempt to integrate two or more different classes of omics data in a single multimodal analysis to identify patterns that bridge biological layers. For example, unraveling the cause of disease may reveal a metabolite deficiency caused by the failure of an enzyme to be phosphorylated because a gene is not expressed due to aberrant methylation as a result of a rare germline variant. Conclusions: There is a fine line between superficial understanding and analysis paralysis, but like a detective novel, multi-omics increasingly provides the clues we need, if only we are able to see them. Full article

This study introduces a novel approach to analyze glycosidic linkages in unfractionated polysaccharides from alcohol-insoluble residues (AIRs) of five brown seaweed species. GC-MS analysis of partially methylated alditol acetates (PMAAs) enables monitoring and comparison of structural variations across different species, harvest years, and tissues with and without blanching treatments. The method detects a wide array of fucose linkages, highlighting the structural diversity in glycosidic linkages and sulfation position in fucose-containing sulfated polysaccharides. Additionally, this technique enhances cellulose quantitation, overcoming the limitations of traditional monosaccharide composition analysis that typically underestimates cellulose abundance due to incomplete hydrolysis of crystalline cellulose. The introduction of a weak methanolysis-sodium borodeuteride reduction pretreatment allows for the detection and quantitation of uronic acid linkages in alginates. Full article

The preS1 region of the large hepatitis B virus (HBV) surface protein is a crucial component in HBV infection; however, its impact on the development of hepatocellular carcinoma (HCC) remains unknown. This study investigated the relationship between serum preS1 levels and hepatocarcinogenesis in patients with chronic hepatitis B (CHB). The preS1 levels were measured in 531 patients with CHB without a history of HCC. Among the patients, 293 HBV carriers who had never received nucleotide/nucleoside analog (NA) therapy had their preS1 levels measured at their first visit (non-NA group), and 238 patients who had received NA therapy had their preS1 levels measured at the start of NA administration (NA group). The two groups had no significant differences in hepatitis B surface antigen (HBsAg) levels; however, the NA group’s preS1/HBsAg ratio was significantly higher. The preS1/HBsAg ratio was significantly different between patients with CHB not meeting the NA treatment criteria and patients with chronic hepatitis and cirrhosis who were eligible for NA treatment. The predictors of HCC development were analyzed, and the preS1/HBsAg ratio was identified in both groups. The preS1/HBsAg ratio could predict hepatocarcinogenesis in patients with CHB with or without NA administration. Full article

To clarify the risk factors for the aggravation of esophagogastric varices (EGVs) after hepatitis C virus (HCV) eradication with direct-acting antiviral (DAA) therapy, we enrolled 167 consecutive patients with HCV-related compensated cirrhosis who achieved a sustained virological response (SVR) after DAA therapy. During a median of 69 months, EGVs were aggravated in 42 (25%) patients despite SVR. The cumulative 1-, 3-, 5-, and 10-year aggravated EGV rates were 7%, 23%, 25%, and 27%, respectively. Multivariate analysis identified a platelet count < 11.0 × 10⁴/μL, LSM ≥ 18.0 kPa, total bile acid ≥ 33.0 μmol/L, and a diameter of left gastric vein (LGV) ≥ 5.0 mm at HCV eradication as independent risk factors for EGV aggravation post-SVR. In groups that met all of these risks, the cumulative EGV aggravation rates at 1, 3, and 5 years were 27%, 87%, and 91%, respectively. However, none of the patients who had only one or none of the risk factors experienced EGV aggravation. Platelet count, LSM, total bile acid, and diameter of LGV at HCV eradication were associated with aggravated EGV post-SVR. EGVs tend to worsen as two or more of these risk factors increase. Full article

The objectives of this paper are to investigate the trade-offs between a physically constrained neural network and a deep, convolutional neural network and to design a combined ML approach (“VarioCNN”). Our solution is provided in the framework of a cyberinfrastructure that includes a newly designed ML software, GEOCLASS-image (v1.0), modern high-resolution satellite image data sets (Maxar WorldView data), and instructions/descriptions that may facilitate solving similar spatial classification problems. Combining the advantages of the physically-driven connectionist-geostatistical classification method with those of an efficient CNN, VarioCNN provides a means for rapid and efficient extraction of complex geophysical information from submeter resolution satellite imagery. A retraining loop overcomes the difficulties of creating a labeled training data set. Computational analyses and developments are centered on a specific, but generalizable, geophysical problem: The classification of crevasse types that form during the surge of a glacier system. A surge is a glacial catastrophe, an acceleration of a glacier to typically 100–200 times its normal velocity. GEOCLASS-image is applied to study the current (2016-2024) surge in the Negribreen Glacier System, Svalbard. The geophysical result is a description of the structural evolution and expansion of the surge, based on crevasse types that capture ice deformation in six simplified classes. Full article

Bariatric surgery is associated with improved outcomes for several cancers, including breast cancer (BC), although the mechanisms mediating this protection are unknown. We hypothesized that elevated bile acid pools detected after bariatric surgery may be factors that contribute to improved BC outcomes. Patients with greater expression of the bile acid receptor FXR displayed improved survival in specific aggressive BC subtypes. FXR is a nuclear hormone receptor activated by primary bile acids. Therefore, we posited that activating FXR using an established FDA-approved agonist would induce anticancer effects. Using in vivo and in vitro approaches, we determined the anti-tumor potential of bile acid receptor agonism. Indeed, FXR agonism by the bile acid mimetic known commercially as Ocaliva (“OCA”), or Obeticholic acid (INT-747), significantly reduced BC progression and overall tumor burden in a pre-clinical model. The transcriptomic analysis of tumors in mice subjected to OCA treatment revealed differential gene expression patterns compared to vehicle controls. Notably, there was a significant down-regulation of the oncogenic transcription factor MAX (MYC-associated factor X), which interacts with the oncogene MYC. Gene set enrichment analysis (GSEA) further demonstrated a statistically significant downregulation of the Hallmark MYC-related gene set (MYC Target V1) following OCA treatment. In human and murine BC analyses in vitro, agonism of FXR significantly and dose-dependently inhibited proliferation, migration, and viability. In contrast, the synthetic agonism of another common bile acid receptor, the G protein-coupled bile acid receptor TGR5 (GPBAR1) which is mainly activated by secondary bile acids, failed to significantly alter cancer cell dynamics. In conclusion, agonism of FXR by primary bile acid memetic OCA yields potent anti-tumor effects potentially through inhibition of proliferation and migration and reduced cell viability. These findings suggest that FXR is a tumor suppressor gene with a high potential for use in personalized therapeutic strategies for individuals with BC. Full article

Island tameness results largely from a lack of natural predators. Because some insular rattlesnake populations lack functional rattles, presumably the consequence of relaxed selection from reduced predation, we hypothesized that the Santa Catalina Island, California, USA, population of the southern Pacific rattlesnake (Crotalus helleri, which possesses a functional rattle), would exhibit a decrement in defensive behavior relative to their mainland counterparts. Contrary to our prediction, rattlesnakes from the island not only lacked tameness compared to mainland snakes, but instead exhibited measurably greater levels of defensiveness. Island snakes attempted to bite 4.7 times more frequently as we endeavored to secure them by hand, and required 2.1-fold more time to be pinned and captured. When induced to bite a beaker after being grasped, the island snakes also delivered 2.1-fold greater quantities of venom when controlling for body size. The additional venom resulted from 2.1-fold larger pulses of venom ejected from the fangs. We found no effects of duration in captivity (2–36 months), which suggests an absence of long-term habituation of antipredator behaviors. Breeding bird surveys and Christmas bird counts indicated reduced population densities of avian predators on Catalina compared to the mainland. However, historical estimates confirmed that populations of foxes and introduced mammalian predators (cats and pigs) and antagonists (herbivorous ungulates) substantially exceeded those on the mainland in recent centuries, and therefore best explain the paradoxically exaggerated defensive behaviors exhibited by Catalina’s rattlesnakes. These findings augment our understanding of anthropogenic effects on the behaviors of island animals and underscore how these effects can negatively affect human safety. Full article

The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. This research sought to determine if these diets were associated with changes in the membranebound proteins that transport nutrients in the rumen epithelium (RE). Crossbred ewes (Poll Dorset × Merino) were fed W, PW, or PWL (50:50) fresh-cut forage ad libitum for 4 weeks. Average daily gain (ADG; p < 0.001) was highest in the W-fed lambs compared to the PW and PWL. Metabolisable energy intake (MEI) was higher in lambs fed W (p < 0.001) compared to PW and PWL. In pairwise comparisons of the PW and PWL diet group we found protein abundance was significantly (p < 0.05, FDR < 0.05, Benjamini p < 0.05) different in fatty acid metabolism, oxidative phosphorylation, and biosynthesis of cofactors pathways. There were not any differences in protein abundance related to nutrient transport or energy metabolism in the RE between W- vs. PW- and W- vs. PWL-fed lambs. However, in the PW- vs. PWL-fed lambs, there was a difference in the level of proteins regulating the metabolism of fatty acids and energy production in the mitochondria of the rumen epithelium. Full article

Rare familial spontaneous coronary artery dissection (SCAD) kindreds implicate genetic disease predisposition and provide a unique opportunity for candidate gene discovery. Whole-genome sequencing was performed in fifteen probands with non-syndromic SCAD who had a relative with SCAD, eight of whom had a second relative with extra-coronary arteriopathy. Co-segregating variants and associated genes were prioritized by quantitative variant, gene, and disease-level metrics. Curated public databases were queried for functional relationships among encoded proteins. Fifty-four heterozygous coding variants in thirteen families co-segregated with disease and fulfilled primary filters of rarity, gene variation constraint, and predicted-deleterious protein effect. Secondary filters yielded 11 prioritized candidate genes in 12 families, with high arterial tissue expression (n = 7), high-confidence protein-level interactions with genes associated with SCAD previously (n = 10), and/or previous associations with connective tissue disorders and aortopathies (n = 3) or other vascular phenotypes in mice or humans (n = 11). High-confidence associations were identified among 10 familial SCAD candidate-gene-encoded proteins. A collagen-encoding gene was identified in five families, two with distinct variants in COL4A2. Familial SCAD is genetically heterogeneous, yet perturbations of extracellular matrix, cytoskeletal, and cell–cell adhesion proteins implicate common disease-susceptibility pathways. Incomplete penetrance and variable expression suggest genetic or environmental modifiers. Full article