Machine learning in biological physics: From biomolecular prediction to design.

Machine learning has been proposed as an alternative to theoretical modeling when dealing with complex problems in biological physics. However, in this perspective, we argue that a more successful approach is a proper combination of these two methodologies. We discuss how ideas coming from physical modeling neuronal processing led to early formulations of computational neural networks, e.g., Hopfield networks. We then show how modern learning approaches like Potts models, Boltzmann machines, and the transformer architecture are related to each other, specifically, through a shared energy representation. We summarize recent efforts to establish these connections and provide examples on how each of these formulations integrating physical modeling and machine learning have been successful in tackling recent problems in biomolecular structure, dynamics, function, evolution, and design. Instances include protein structure prediction; improvement in computational complexity and accuracy of molecular dynamics simulations; better inference of the effects of mutations in proteins leading to improved evolutionary modeling and finally how machine learning is revolutionizing protein engineering and design. Going beyond naturally existing protein sequences, a connection to protein design is discussed where synthetic sequences are able to fold to naturally occurring motifs driven by a model rooted in physical principles. We show that this model is "learnable" and propose its future use in the generation of unique sequences that can fold into a target structure.

The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.

Protein evolution is guided by structural, functional, and dynamical constraints ensuring organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes that lack translational activity due to sequence degradation and thus over time have undergone "devolution." Previously pseudogenized genes sometimes regain their protein-coding function, suggesting they may still encode robust folding energy landscapes despite multiple mutations. We study both the physical folding landscapes of protein sequences corresponding to human pseudogenes using the Associative Memory, Water Mediated, Structure and Energy Model, and the evolutionary energy landscapes obtained using direct coupling analysis (DCA) on their parent protein families. We found that generally mutations that have occurred in pseudogene sequences have disrupted their native global network of stabilizing residue interactions, making it harder for them to fold if they were translated. In some cases, however, energetic frustration has apparently decreased when the functional constraints were removed. We analyzed this unexpected situation for Cyclophilin A, Profilin-1, and Small Ubiquitin-like Modifier 2 Protein. Our analysis reveals that when such mutations in the pseudogene ultimately stabilize folding, at the same time, they likely alter the pseudogenes' former biological activity, as estimated by DCA. We localize most of these stabilizing mutations generally to normally frustrated regions required for binding to other partners.

Linear Bloch-Siegert phase-encoded low-field MRI: RF coils, pulse sequence, and image reconstruction.

Conventional B 0 $$ {B}_0 $$ gradient systems have several weaknesses including high cost and bulk. As a step towards addressing these while providing new degrees of freedom for spatial encoding and system design in Magnetic Resonance Imaging (MRI), a radio frequency (RF) gradient encoding system and pulse sequence for phase encoding using the Bloch-Siegert (BS) shift were developed. Optimized BS spatial encoding coils with bucking windings (counter-wound loops) were designed and constructed, along with compatible homogeneous imaging coils for excitation and signal reception. Two coil systems were developed: one for phantom imaging and a second for human wrist imaging. BS phase-encoded imaging and BS RF pulse simulations were performed. Pulse sequences were designed for linear stepping in k-space and implemented on a 47.5-mT scanner to image resolution phantoms in both coil setups. Reconstructions were performed using both the full B 1 + $$ {B}_1^{+} $$ -based encoding fields for each BS pulse amplitude and using inverse discrete Fourier transforms. A B 0 $$ {B}_0 $$ gradient was used for frequency encoding during signal readout, and the third axis was projected. Specific absorption ratio (SAR) calculations were performed for the wrist coil to determine the safety of BS-based RF encoding for B 0 $$ {B}_0 $$ fields in the low field MRI regime. The optimized RF spatial encoding coils resulted in higher linearity ( R 2 = 0.9981 $$ {R}^2=0.9981 $$ and 0.9921 in the phantom and wrist coils, respectively) than coils used in previous work. The phantom and wrist imaging coils were validated in simulations and experimentally to produce a peak B 1 + = 1.35 $$ {B}_1^{+}=1.35 $$ G and 0.8 G with 12-W input power, respectively, in the field-of-view (length = 11 cm) used for imaging. Nominal imaging resolutions of 5.22 and 7.21 mm were, respectively, achieved by the two-coil systems in the RF phase-encoded dimension. Coil systems, pulse sequences, and image reconstructions were developed for linear RF phase encoding using the BS shift and validated using a 47.5-mT open low field scanner, establishing a key component required for B 0 $$ {B}_0 $$  gradient-free imaging at low B 0 $$ {B}_0 $$  field strengths.

Correlation of Ablation Volume with Renal Function Loss after Cryoablation in Solitary Functioning Kidneys.

PURPOSE: To determine the degree of renal function deterioration after renal cryoablation in patients with a solitary functioning kidney on the basis of ablation volume. MATERIALS AND METHODS: Over a 15-year period, 81 percutaneous cryoablations were performed in solitary functioning kidneys. After exclusion of patients with baseline end-stage renal disease (ESRD) and insufficient follow-up, analysis was performed on 65 procedures in 52 patients (40 men; mean age, 63.5 years). The postcryoablation renal function was based on the lowest serum creatinine within 6 months after procedure. Renal function change was defined as percentage glomerular filtration rate (GFR) change. Volumetric analysis was performed on the target lesion, renal parenchyma, and ablation zone. RESULTS: The median tumor diameter was 2.0 cm (range, 0.8-4.7 cm). The median baseline GFR decreased from 56.4 mL/min/1.73 m2 (range, 17.5-89.7 mL/min/1.73 m2) to 46.9 mL/min/1.73 m2 (range, 16.5-89.7 mL/min/1.73 m2) at median of 95 days (P < .001), equating to a -7.9% median renal function change (range, -45.0% to +30.7%). All patients had Stage 2 or worse chronic kidney disease, and baseline function did not correlate with renal function change. The median volume of ablated parenchyma was 19.7 mL (range, 2.4-87.3 mL), equating to 8.1% (range, 0.7%-37.2%) of total parenchyma. The volume of parenchymal volume ablated correlated significantly with renal function loss, whereas age, hypertension, and diabetes mellitus did not. No patient developed ESRD within 1 year after cryoablation. CONCLUSIONS: Cryoablation in solitary functioning kidneys resulted in a modest reduction in renal function, even in patients with chronic kidney disease and ablations up to 20% of renal parenchymal volume.

Screening persistent organic pollutants for effects on testosterone and estrogen synthesis at human-relevant concentrations using H295R cells in 96-well plates.

Many persistent organic pollutants (POPs) are suspected endocrine disruptors and it is important to investigate their effects at low concentrations relevant to human exposure. Here, the OECD test guideline #456 steroidogenesis assay was downscaled to a 96-well microplate format to screen 24 POPs for their effects on viability, and testosterone and estradiol synthesis using the human adrenocortical cell line H295R. The compounds (six polyfluoroalkyl substances, five organochlorine pesticides, ten polychlorinated biphenyls and three polybrominated diphenyl ethers) were tested at human-relevant levels (1 nM to 10 µM). Increased estradiol synthesis, above the OECD guideline threshold of 1.5-fold solvent control, was shown after exposure to 10 µM PCB-156 (153%) and PCB-180 (196%). Interestingly, the base hormone synthesis varied depending on the cell batch. An alternative data analysis using a linear mixed-effects model that include multiple independent experiments and considers batch-dependent variation was therefore applied. This approach revealed small but statistically significant effects on estradiol or testosterone synthesis for 17 compounds. Increased testosterone levels were demonstrated even at 1 nM for PCB-74 (18%), PCB-99 (29%), PCB-118 (16%), PCB-138 (19%), PCB-180 (22%), and PBDE-153 (21%). The MTT assay revealed significant effects on cell viability after exposure to 1 nM of perfluoroundecanoic acid (12%), 3 nM PBDE-153 (9%), and 10 µM of PCB-156 (6%). This shows that some POPs can interfere with endocrine signaling at concentrations found in human blood, highlighting the need for further investigation into the toxicological mechanisms of POPs and their mixtures at low concentrations relevant to human exposure.

Temperature-Pressure Swing Process for Reactive Carbon Capture and Conversion to Methanol: Techno-Economic Analysis and Life Cycle Assessment.

A model was developed to conduct techno-economic analysis (TEA) and life cycle assessment (LCA) for reactive carbon capture (RCC) and conversion of carbon dioxide (CO2) to methanol. This RCC process is compared to a baseline commercialized flue gas CO2 hydrogenation process. An ASPEN model was combined with existing TEA and LCA models into a larger TEA/LCA framework in Python. From preliminary experimental data, the model found a levelized cost of $0.79/kg methanol for the baseline process and $0.99/kg for the RCC process. The cradle-to-gate carbon intensity of the baseline process was 0.50 kg-CO2e/kg-methanol, compared to 0.55 kg-CO2e/kg-methanol for the RCC process. However, water consumption for RCC (10.21 kg-H2O/kg-methanol) is greatly reduced compared to the baseline (12.89 kg-H2O/kg-methanol). Future improvements in hydrogen electrolysis costs will benefit the RCC. A target H2/methanol mass ratio of 0.26 was developed for RCC laboratory experiments to reduce methanol cost below the baseline. If a ratio of 0.24 can be achieved, a levelized cost of $0.76/kg methanol is projected, with a carbon intensity of 0.42 kg-CO2e/kg-methanol.

High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage.

In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.

Maternal pre-pregnancy BMI influences the associations between bisphenol and phthalate exposures and maternal weight changes and fat accumulation.

BACKGROUND: Bisphenols and phthalates are two classes of endocrine-disrupting chemicals (EDCs) thought to influence weight and adiposity. Limited research has investigated their influence on maternal weight changes, and no prior work has examined maternal fat mass. We examined the associations between exposure to these chemicals during pregnancy and multiple maternal weight and fat mass outcomes. METHODS: This study included a sample of 318 women enrolled in a Canadian prospective pregnancy cohort. Second trimester urinary concentrations of 2 bisphenols and 12 phthalate metabolites were quantified. Self-reported and measured maternal weights and measured skinfold thicknesses were used to calculate gestational weight gain, 3-months and 3- to 5-years postpartum weight retention, late pregnancy fat mass gain, total postpartum fat mass loss, and late postpartum fat mass retention. Adjusted robust regressions examined associations between chemicals and outcomes in the entire study population and sub-groups stratified by pre-pregnancy body mass index (BMI). Bayesian kernel machine regression examined chemical mixture effects. RESULTS: Among women with underweight or normal pre-pregnancy BMIs, MBzP was negatively associated with weight retention at 3- to 5-years postpartum (B = -0.04, 95%CI: -0.07, -0.01). Among women with overweight or obese pre-pregnancy BMIs, MEHP and MMP were positively associated with weight retention at 3-months and 3- to 5-years postpartum, respectively (B's = 0.12 to 0.63, 95%CIs: 0.02, 1.07). DEHP metabolites and MCNP were positively associated with late pregnancy fat mass gain and late postpartum fat mass retention (B's = 0.04 to 0.18, 95%CIs: 0.001, 0.32). Further, the mixture of EDCs was positively associated with late pregnancy fat mass gain. CONCLUSION: In this cohort, pre-pregnancy BMI was a key determinant of the associations between second trimester exposure to bisphenols and phthalates and maternal weight changes and fat accumulation. Investigations of underlying physiological mechanisms, windows of susceptibility, and impacts on maternal and infant health are needed.

Utilizing generative conversational artificial intelligence to create simulated patient encounters: a pilot study for anaesthesia training.

PURPOSE OF THE STUDY: Generative conversational artificial intelligence (AI) has huge potential to improve medical education. This pilot study evaluated the possibility of using a 'no-code' generative AI solution to create 2D and 3D virtual avatars, that trainee doctors can interact with to simulate patient encounters. METHODS: The platform 'Convai' was used to create a virtual patient avatar, with a custom backstory, to test the feasibility of this technique. The virtual patient model was set up to allow trainee anaesthetists to practice answering questions that patients' may have about interscalene nerve blocks for open reduction and internal fixation surgery. This tool was provided to anaesthetists to receive their feedback and evaluate the feasibility of this approach. RESULTS: Fifteen anaesthetists were surveyed after using the tool. The tool had a median score [interquartile range (IQR)] of 9 [7-10] in terms of how intuitive and user-friendly it was, and 8 [7-10] in terms of accuracy in simulating patient responses and behaviour. Eighty-seven percent of respondents felt comfortable using the model. CONCLUSIONS: By providing trainees with realistic scenarios, this technology allows trainees to practice answering patient questions regardless of actor availability, and indeed from home. Furthermore, the use of a 'no-code' platform allows clinicians to create customized training tools tailored to their medical specialties. While overall successful, this pilot study highlighted some of the current drawbacks and limitations of generative conversational AI, including the risk of outputting false information. Additional research and fine-tuning are required before generative conversational AI tools can act as a substitute for actors and peers.

Healthcare transition in pediatric neurosurgery: lessons learned from a pilot program for patients with hydrocephalus and spina bifida.

OBJECTIVE: The pediatric neurosurgical community has increasingly recognized the importance of healthcare transition, the process of moving a patient from a pediatric to an adult model of care. However, surveys of pediatric neurosurgeons have revealed that few institutions have formal transition programs. Here, the authors share their preliminary experience with the development of a formal transition pilot program for patients with spina bifida and/or hydrocephalus. METHODS: Patients 18 years of age or older with a diagnosis of spina bifida and/or hydrocephalus who were followed by a pediatric neurosurgeon at Connecticut Children's from January 2017 to December 2023 and were recommended to transition to an adult neurosurgeon were retrospectively reviewed. Patients in the informal transition program (ITP) cohort (i.e., the recommendation to transition was made before the formal transition program [FTP] was developed in early 2020) were compared with those in the FTP cohort. RESULTS: Twenty-two patients met inclusion criteria with 7 (31.8%) in the ITP cohort and 15 (68.2%) in the FTP cohort. The median age at the time of the recommendation to transition was similar in both ITP and FTP cohorts (24 [IQR 20-35] years vs 25 [IQR 24-27] years, respectively). Four (57.1%) patients in the ITP cohort had a confirmed visit with an adult neurosurgeon, compared with 13 (86.7%) patients in the FTP cohort (p = 0.274). One patient in the ITP cohort with a failed transition returned to pediatric neurosurgical care, and 1 patient in the FTP cohort required a shunt revision by an adult neurosurgeon within 1 year of the recommendation to transition. CONCLUSIONS: Healthcare transition is recognized as a priority within pediatric neurosurgery, but structured, formal transition programs remain underdeveloped. The authors' preliminary experience with a pilot transition program demonstrated that patients who underwent a formal transition were more likely to successfully establish care with an adult neurosurgeon and trended toward less resource utilization.

Midwives' support for parents following stillbirth: How they practise and resources they need from a phenomenological perspective.

AIM: To explore the perceptions and experiences of midwives caring for couples who experience a stillbirth. DESIGN: Qualitative study based on Gadamer's hermeneutic phenomenology. METHODS: This study was conducted with midwives (n = 18) at the birth unit of a third-level public hospital in Jaén (Spain) in 2023. Personal semi-structured interviews were recorded in audio for later transcription by two researchers following steps described by Fleming. RESULTS: Two themes were identified as important aspects of the practise of midwives in a situation of the birth of a stillborn child: (1) the importance of each action of the midwife, and (2) the availability of resources determines the care provided. CONCLUSIONS: Having a stillbirth is a very complex experience, in which the psychological support and human and material resources involved are the basic tool for the care of these families. Acknowledging limitations of the available resources, the assistance and care provided by midwives are in line with the clinical practice guidelines, which can have an emotional impact on them. IMPLICATIONS FOR THE PROFESSION AND/OR PATIENT CARE: The care to be provided in stillbirth requires appropriate human and material resources for these families. Midwifery and nursing professionals are in a unique position for acting in cases of families with a stillbirth, updated protocols and, in general, the coordination of the different agents involved within the healthcare system. WHAT PROBLEM DID THE STUDY ADDRESS?: The midwives´ experiences in cases which end with the delivery of a stillborn. WHAT WERE THE MAIN FINDINGS?: Each action of the midwife is as important as the availability of resources to offer the most appropriate care. WHERE AND ON WHOM WILL THE RESEARCH HAVE AN IMPACT?: In each woman who receives the care of a midwife who attends the birth of a stillborn. REPORTING METHOD: COREQ checklist. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution occurred for this study as this research focused on exploring staffs' perspectives from the specific viewpoint of their personal experience.

Repeat Exchange Autologous Cranioplasty for Recurrent Benign Osteoma: Meta-analysis and Literature Review.

Osteomas are benign bony lesions that can occur throughout the craniofacial skeleton. Surgical excision can be an effective treatment, as recurrence is relatively uncommon. Outside of incomplete resection, causes of recurrence are poorly documented, especially in the pediatric population. Exchange cranioplasty is an autologous reconstructive surgical option for patients of all ages, and it can be effective in the treatment of large calvarial osteomas. Recurrent lesions of the cranioplasty site have not been well described in the literature, with only 3 documented reports. In this study, we present a unique case of a recurrent osteoma at the site of a prior exchange cranioplasty. The authors also provide a systematic review of the literature for recurrent osteomas and highlight causes and conclusions for these lesions. Utilizing the PRISMA guidelines, a systematic review of articles published across databases was performed to identify accounts of recurrent osteomas at prior cranioplasty sites. Our systematic review illustrates that recurrent osteomas overlying different cranioplasty biomaterials is a rare entity and is due to incomplete resection of the galea and periosteum during the index procedure. Biomaterial selection for the pediatric population requires careful consideration before reconstruction. Though limited by 3 articles previously published and without a direct link to recurrence, long-term studies are needed to further guide biomaterial selection in the pediatric population to evaluate potential recurrences.

Bypassing the Identification: MS2Quant for Concentration Estimations of Chemicals Detected with Nontarget LC-HRMS from MS2 Data.

Nontarget analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is now widely used to detect pollutants in the environment. Shifting away from targeted methods has led to detection of previously unseen chemicals, and assessing the risk posed by these newly detected chemicals is an important challenge. Assessing exposure and toxicity of chemicals detected with nontarget HRMS is highly dependent on the knowledge of the structure of the chemical. However, the majority of features detected in nontarget screening remain unidentified and therefore the risk assessment with conventional tools is hampered. Here, we developed MS2Quant, a machine learning model that enables prediction of concentration from fragmentation (MS2) spectra of detected, but unidentified chemicals. MS2Quant is an xgbTree algorithm-based regression model developed using ionization efficiency data for 1191 unique chemicals that spans 8 orders of magnitude. The ionization efficiency values are predicted from structural fingerprints that can be computed from the SMILES notation of the identified chemicals or from MS2 spectra of unidentified chemicals using SIRIUS+CSI:FingerID software. The root mean square errors of the training and test sets were 0.55 (3.5×) and 0.80 (6.3×) log-units, respectively. In comparison, ionization efficiency prediction approaches that depend on assigning an unequivocal structure typically yield errors from 2× to 6×. The MS2Quant quantification model was validated on a set of 39 environmental pollutants and resulted in a mean prediction error of 7.4×, a geometric mean of 4.5×, and a median of 4.0×. For comparison, a model based on PaDEL descriptors that depends on unequivocal structural assignment was developed using the same dataset. The latter approach yielded a comparable mean prediction error of 9.5×, a geometric mean of 5.6×, and a median of 5.2× on the validation set chemicals when the top structural assignment was used as input. This confirms that MS2Quant enables to extract exposure information for unidentified chemicals which, although detected, have thus far been disregarded due to lack of accurate tools for quantification. The MS2Quant model is available as an R-package in GitHub for improving discovery and monitoring of potentially hazardous environmental pollutants with nontarget screening.

Evaluating atezolizumab in patients with urinary tract squamous cell carcinoma (AURORA): study protocol for a single arm, open-label, multicentre, phase II clinical trial.

BACKGROUND: Bladder and urinary tract cancers account for approximately 21,000 new diagnoses and 5,000 deaths annually in the UK. Approximately 90% are transitional cell carcinomas where advanced disease is treated with platinum based chemotherapy and PD-1/PD-L1 directed immunotherapy. Urinary tract squamous cell carcinoma (UTSCC) accounts for about 5% of urinary tract cancers overall making this a rare disease. We have yet to establish definitive systemic treatment options for advanced UTSCC. Preliminary translational data, from UTSCC patient tumour samples, indicate high PD-L1 expression and tumour infiltrating lymphocytes in a proportion of cases. Both of these features are associated with differential gene expression consistent with a tumour/immune microenvironment predicted to be susceptible to immune checkpoint directed immunotherapy which we will evaluate in the AURORA trial. METHODS: AURORA is a single arm, open-label, multicentre,UK phase II clinical trial. 33 patients will be recruited from UK secondary care sites. Patients with UTSCC, suitable for treatment with palliative intent, will receive atezolizumab PD-L1 directed immunotherapy (IV infusion, 1680 mg, every 28 days) for one year if tolerated. Response assessment, by cross sectional imaging will occur every 12 weeks. AURORA uses a Simon's 2-stage optimal design with best overall objective response rate (ORR, by RECIST v1.1) at a minimum of 12 weeks from commencing treatment as the primary endpoint. Secondary endpoints will include overall survival, progression-free survival, duration of response, magnitude of response using waterfall plots of target lesion measurements, quality of life using the EORTC QLQ-C30 tool, safety and tolerability (CTCAE v5) and evaluation of potential biomarkers of treatment response including PD-L1 expression. Archival tumour samples and blood samples will be collected for translational analyses. DISCUSSION: If this trial shows atezolizumab to be safe and effective it may lead to a future late phase randomised controlled trial in UTSCC. Ultimately, we hope to provide a new option for treatment for such patients. TRIAL REGISTRATIONS: EudraCT Number: 2021-001995-32 (issued 8th September 2021); ISRCTN83474167 (registered 11 May 2022); NCT05038657 (issued 9th September 2021).

Intravascular Ultrasound-Guided Transvenous Biopsy of Retroperitoneal Lymph Nodes: Diagnostic Accuracy and Safety Compared with CT-Guided Percutaneous Biopsy.

PURPOSE: To compare the diagnostic accuracy and adverse event rates of intravascular ultrasound (US)-guided transvenous biopsy (TVB) versus those of computed tomography (CT)-guided percutaneous needle biopsy (PNB) for retroperitoneal (RP) lymph nodes. MATERIALS AND METHODS: In this single-institution, retrospective study, 32 intravascular US-guided TVB procedures and a sample of 34 CT-guided PNB procedures for RP lymph nodes where targets were deemed amenable to intravascular US-guided TVB were analyzed. Procedural metrics, including diagnostic accuracy, defined as diagnostic of malignancy or a clinically verifiable benign result, and adverse event rates were compared. RESULTS: The targets of intravascular US-guided TVB were primarily aortocaval (47%, 15/32) or precaval (34%, 11/32), whereas those of CT-guided PNB were primarily right pericaval (44%, 15/34) or retrocaval (44%, 15/34) (P < .001). The targets of intravascular US-guided TVB averaged 2.4 cm in the long axis (range, 1.3-3.7 cm) compared with 2.9 cm (range, 1.4-5.7 cm) for those of CT-guided PNB (P = .02). There was no difference in the average number of needle passes (3.8 for intravascular US-guided TVB vs 3.9 for CT-guided PNB; P = .68). The diagnostic accuracy was 94% (30/32) and the adverse event rate was 3.1% (1/32) for intravascular US-guided TVB, similar to those of CT-guided PNB (accuracy, 91% [31/34]; adverse event rate, 2.9% [1/34]). CONCLUSIONS: Intravascular US-guided TVB had a diagnostic accuracy and adverse event rate similar to CT-guided PNB for RP lymph nodes, indicating that intravascular US-guided TVB may be as safe and effective as conventional biopsy approaches for appropriately selected targets.

Intravascular Ultrasound Guidance for Transjugular Intrahepatic Portosystemic Shunt Creation Reduces Laboratory Markers of Acute Liver Injury.

PURPOSE: To compare the laboratory markers of acute liver injury after transjugular intrahepatic portosystemic shunt (TIPS) creation performed using intravascular ultrasound (IVUS) guidance with those using other techniques. MATERIALS AND METHODS: This single-center, retrospective study examined 293 TIPS procedures performed between 2014 and 2022 (160 men; mean age, 57.4 years; 71.7% with ascites, 158 with IVUS). Laboratory changes on postprocedural day (PPD) 1 were classified based on Common Terminology Criteria for Adverse Events (CTCAE) grades and were compared between IVUS and non-IVUS cases. RESULTS: IVUS cases had a lower baseline Model for End-Stage Liver Disease (MELD) score (12.5 vs 13.7, P = .016), higher pre- (16.8 vs 15.2, P = .009), and post-TIPS (6.6 vs 5.4 mm Hg, P < .001) pressure gradient, smaller stent diameter (9.2 vs 9.9 mm, P < .001), and fewer needle passes (2.4 vs 4.2, P < .001). IVUS predicted a lower PPD 1 CTCAE grade for aspartate transaminase (8.0% vs 22.2% grade ≥ 2, P = .010), alanine transaminase (ALT) (2.2% vs 7.1%, P = .017), and bilirubin (9.4% vs 26.2%, P < .001), findings confirmed using multivariable regression and propensity score analysis. IVUS predicted fewer adverse events (1.3% vs 8.1%, P = .008) and an increased likelihood of PPD 1 discharge (81% vs 59%, P = .004). IVUS was not associated with differences in PPD 30 MELD scores or 30-day survival; however, higher PPD 1 ALT (ß = 1.96, P = .008) and bilirubin levels (ß = 1.38, P = .004) predicted larger PPD 30 MELD score increase. Higher increases in ALT level predicted worse 30-day survival (hazard ratio, 1.93; P = .021). CONCLUSION: IVUS resulted in less laboratory evidence of acute liver injury immediately following TIPS creation.

Phospholipid Removal for Enhanced Chemical Exposomics in Human Plasma.

The challenge of chemical exposomics in human plasma is the 1000-fold concentration gap between endogenous substances and environmental pollutants. Phospholipids are the major endogenous small molecules in plasma, thus we validated a chemical exposomics protocol with an optimized phospholipid-removal step prior to targeted and non-targeted liquid chromatography high-resolution mass spectrometry. Increased injection volume with negligible matrix effect permitted sensitive multiclass targeted analysis of 77 priority analytes; median MLOQ = 0.05 ng/mL for 200 µL plasma. In non-targeted acquisition, mean total signal intensities of non-phospholipids were enhanced 6-fold in positive (max 28-fold) and 4-fold in negative mode (max 58-fold) compared to a control method without phospholipid removal. Moreover, 109 and 28% more non-phospholipid molecular features were detected by exposomics in positive and negative mode, respectively, allowing new substances to be annotated that were non-detectable without phospholipid removal. In individual adult plasma (100 µL, n = 34), 28 analytes were detected and quantified among 10 chemical classes, and quantitation of per- and polyfluoroalkyl substances (PFAS) was externally validated by independent targeted analysis. Retrospective discovery and semi-quantification of PFAS-precursors was demonstrated, and widespread fenuron exposure is reported in plasma for the first time. The new exposomics method is complementary to metabolomics protocols, relies on open science resources, and can be scaled to support large studies of the exposome.

Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows.

Nontarget mass spectrometry has great potential to reveal patterns of water contamination globally through community science, but few studies are conducted in low-income countries, nor with open-source workflows, and few datasets are FAIR (Findable, Accessible, Interoperable, Reusable). Water was collected from urban and rural rivers around Dhaka, Bangladesh, and analyzed by liquid chromatography high-resolution mass spectrometry in four ionization modes (electrospray ionization ±, atmospheric pressure chemical ionization ±) with data-independent MS2 acquisition. The acquisition strategy was complementary: 19,427 and 7365 features were unique to ESI and APCI, respectively. The complexity of water pollution was revealed by >26,000 unique molecular features resolved by MS-DIAL, among which >20,000 correlated with urban sources in Dhaka. A major wastewater treatment plant was not a dominant pollution source, consistent with major contributions from uncontrolled urban drainage, a result that encourages development of further wastewater infrastructures. Matching of deconvoluted MS2 spectra to public libraries resulted in 62 confident annotations (i.e., Level 1-2a) and allowed semiquantification of 42 analytes including pharmaceuticals, pesticides, and personal care products. In silico structure prediction for the top 100 unknown molecular features associated with an urban source allowed 15 additional chemicals of anthropogenic origin to be annotated (i.e., Level 3). The authentic MS2 spectra were uploaded to MassBank Europe, mass spectral data were openly shared on the MassIVE repository, a tool (i.e., MASST) that could be used for community science environmental surveillance was demonstrated, and current limitations were discussed.

Novel Per- and Polyfluoroalkyl Substances Discovered in Cattle Exposed to AFFF-Impacted Groundwater.

The leaching of per- and polyfluoroalkyl substances (PFASs) from Australian firefighting training grounds has resulted in extensive contamination of groundwater and nearby farmlands. Humans, farm animals, and wildlife in these areas may have been exposed to complex mixtures of PFASs from aqueous film-forming foams (AFFFs). This study aimed to identify PFAS classes in pooled whole blood (n = 4) and serum (n = 4) from cattle exposed to AFFF-impacted groundwater and potentially discover new PFASs in blood. Thirty PFASs were identified at various levels of confidence (levels 1a-5a), including three novel compounds: (i) perfluorohexanesulfonamido 2-hydroxypropanoic acid (FHxSA-HOPrA), (ii) methyl((perfluorohexyl)sulfonyl)sulfuramidous acid, and (iii) methyl((perfluorooctyl)sulfonyl)sulfuramidous acid, belonging to two different classes. Biotransformation intermediate, perfluorohexanesulfonamido propanoic acid (FHxSA-PrA), hitherto unreported in biological samples, was detected in both whole blood and serum. Furthermore, perfluoroalkyl sulfonamides, including perfluoropropane sulfonamide (FPrSA), perfluorobutane sulfonamide (FBSA), and perfluorohexane sulfonamide (FHxSA) were predominantly detected in whole blood, suggesting that these accumulate in the cell fraction of blood. The suspect screening revealed several fluoroalkyl chain-substituted PFAS. The results suggest that targeting only the major PFASs in the plasma or serum of AFFF-exposed mammals likely underestimates the toxicological risks associated with exposure. Future studies of AFFF-exposed populations should include whole-blood analysis with high-resolution mass spectrometry to understand the true extent of PFAS exposure.

Associations between the chemical exposome and pregnancy induced hypertension.

Exposure to environmental chemicals has been linked to an increased risk of pregnancy-induced hypertension (PIH). This prospective cohort study examined the associations between PIH and maternal chemical exposure to four classes of chemicals (i.e., phthalates, bisphenols, perfluoroalkyl acids, non-essential metals and trace minerals). Participants included 420 pregnant women from the Alberta Pregnancy Outcomes and Nutrition (APrON) cohort who had data available on diagnosed PIH and environmental chemical exposure. Twelve phthalate metabolites, two bisphenols, eight perfluoroalkyl acids and eleven non-essential metals or trace minerals were quantified in maternal urine or blood samples collected in the second trimester of pregnancy. Associations between the urinary and blood concentrations of these chemicals and PIH were assessed using multiple logistic and LASSO regression analyses in single- and multi-chemical exposure models, respectively. Thirty-five (8.3%) participants were diagnosed with PIH. In single chemical exposure models, two phthalate metabolites, mono-methyl phthalate (MMP) and monoethyl phthalate (MEP), three perfluoroalkyl acids, perfluoroheptanoic acid (PFHpA), perfluorononanoic acid (PFNA), and perfluorodecanoic acid (PFDA), and one metal, manganese, were associated with increased odds of PIH. The metabolites of di (2-ethylhexyl) phthalate (DEHP) and the molar sum of these metabolites, as well as antimony, displayed trend associations (p < 0.10). In multi-chemical exposure models using LASSO penalized regressions and double-LASSO regressions, MEP (AOR: 1.43, 95% CI: 1.09-1.88, p = 0.009) and PFNA (AOR: 2.03, 95% CI: 1.01-4.07, p = 0.04) were selected as the chemicals most highly associated with PIH. These findings suggest that maternal levels of phthalates and perfluoroalkyl acids may be associated with the diagnosis on PIH. Future research should consider both individual and multi-chemical exposures when examining predictors of PIH and other maternal cardiometabolic health disorders, such as preeclampsia, eclampsia, HELLP syndrome, and gestational diabetes.