Low coverage whole genome sequencing of low-grade dysplasia strongly predicts colorectal cancer risk in ulcerative colitis.

Patients with inflammatory bowel disease (IBD) are at increased risk of colorectal cancer (CRC), and this risk increases dramatically in those who develop low-grade dysplasia (LGD). However, there is currently no accurate way to risk-stratify patients with LGD, leading to both over- and under-treatment of cancer risk. Here we show that the burden of somatic copy number alterations (CNAs) within resected LGD lesions strongly predicts future cancer development. We performed a retrospective multi-centre validated case-control study of n=122 patients (40 progressors, 82 non-progressors, 270 LGD regions). Low coverage whole genome sequencing revealed CNA burden was significantly higher in progressors than non-progressors (p=2×10-6 in discovery cohort) and was a very significant predictor of CRC risk in univariate analysis (odds ratio = 36; p=9×10-7), outperforming existing clinical risk factors such as lesion size, shape and focality. Optimal risk prediction was achieved with a multivariate model combining CNA burden with the known clinical risk factor of incomplete LGD resection. The measurement of CNAs in LGD lesions is a robust, low-cost and rapidly translatable predictor of CRC risk in IBD that can be used to direct management and so prevent CRC in high-risk individuals whilst sparing those at low-risk from unnecessary intervention.

A review of the direct targets of the cannabinoids cannabidiol, Δ9-tetrahydrocannabinol, N-arachidonoylethanolamine and 2-arachidonoylglycerol.

Marijuana has been used by humans for thousands of years for both medicinal and recreational purposes. This included the treatment of pain, inflammation, seizures, and nausea. In the 1960s, the structure of the principal psychoactive ingredient Δ9-tetrahydrocannabinol was determined, and over the next few decades, two cannabinoid receptors were characterized along with the human endocannabinoid system and what it affects. This includes metabolism, the cardiovascular and reproductive systems, and it is involved in such conditions as inflammation, cancer, glaucoma, and liver and musculoskeletal disorders. In the central nervous system, the endocannabinoid system has been linked to appetite, learning, memory, and conditions such as depression, anxiety, schizophrenia, stroke, multiple sclerosis, neurodegeneration, addiction, and epilepsy. It was the profound effectiveness of cannabidiol, a non-psychoactive ingredient of marijuana, to relieve the symptoms of Dravet syndrome, a severe form of childhood epilepsy, that recently helped spur marijuana research. This has helped substantially to change society's attitude towards this potential source of useful drugs. However, research has also revealed that the actions of endocannabinoids, such as anandamide and 2-arachidonoylglycerol, and the phytocannabinoids, tetrahydrocannabinol and cannabidiol, were not just due to interactions with the two cannabinoid receptors but by acting directly on many other targets including various G-protein receptors and cation channels, such as the transient receptor potential channels for example. This mini-review attempts to survey the effects of these 4 important cannabinoids on these currently identified targets.

Including Methane Emissions from Agricultural Ponds in National Greenhouse Gas Inventories.

Agricultural ponds are a significant source of greenhouse gases, contributing to the ongoing challenge of anthropogenic climate change. Nations are encouraged to account for these emissions in their national greenhouse gas inventory reports. We present a remote sensing approach using open-access satellite imagery to estimate total methane emissions from agricultural ponds that account for (1) monthly fluctuations in the surface area of individual ponds, (2) rates of historical accumulation of agricultural ponds, and (3) the temperature dependence of methane emissions. As a case study, we used this method to inform the 2024 National Greenhouse Gas Inventory reports submitted by the Australian government, in compliance with the Paris Agreement. Total annual methane emissions increased by 58% from 1990 (26 kilotons CH4 year-1) to 2022 (41 kilotons CH4 year-1). This increase is linked to the water surface of agricultural ponds growing by 51% between 1990 (115 kilo hectares; 1,150 km2) and 2022 (173 kilo hectares; 1,730 km2). In Australia, 16,000 new agricultural ponds are built annually, expanding methane-emitting water surfaces by 1,230 ha yearly (12.3 km2 year-1). On average, the methane flux of agricultural ponds in Australia is 0.238 t CH4 ha-1 year-1. These results offer policymakers insights into developing targeted mitigation strategies to curb these specific forms of anthropogenic emissions. For instance, financial incentives, such as carbon or biodiversity credits, can mobilize widespread investments toward reducing greenhouse gas emissions and enhancing the ecological and environmental values of agricultural ponds. Our data and modeling tools are available on a free cloud-based platform for other countries to adopt this approach.

Ultrabroadband two-dimensional electronic spectroscopy in the pump-probe geometry using conventional optics.

We report ultrabroadband two-dimensional electronic spectroscopy (2D ES) measurements obtained in the pump-probe geometry using conventional optics. A phase-stabilized Michelson interferometer provides the pump-pulse delay interval, τ1, necessary to obtain the excitation-frequency dimension. Spectral resolution of the probe beam provides the detection-frequency dimension, ω3. The interferometer incorporates active phase stabilization via a piezo stage and feedback from interference of a continuous-wave reference laser detected in quadrature. To demonstrate the method, we measured a well-characterized laser dye sample and obtained the known peak structure. The vibronic peaks are modulated as a function of the waiting time, τ2, by vibrational wave packets. The interferometer simplifies ultrabroadband 2D ES measurements and analysis.

Spatiotemporal dispersion compensation for a 200-THz noncollinear optical parametric amplifier.

A noncollinear optical parametric amplifier (NOPA) can produce few-cycle femtosecond laser pulses that are ideally suited for time-resolved optical spectroscopy measurements. However, the nonlinear-optical process giving rise to ultrabroadband pulses is susceptible to spatiotemporal dispersion problems. Here, we detail refinements, including chirped-pulse amplification (CPA) and pulse-front matching (PFM), that minimize spatiotemporal dispersion and thereby improve the properties of ultrabroadband pulses produced by a NOPA. The description includes a rationale behind the choices of optical and optomechanical components, as well as assessment protocols. We demonstrate these techniques using a 1 kHz, second-harmonic Ti:sapphire pump configuration, which produces ∼5-fs duration pulses that span from about 500 to 800 nm with a bandwidth of about 200 THz. To demonstrate the utility of the CPA-PFM-NOPA, we measure vibrational quantum beats in the transient-absorption spectrum of methylene blue, a dye molecule that serves as a reference standard.

Antiviral drug recognition and elevator-type transport motions of CNT3.

Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiviral drugs used in the treatment of coronavirus infections. We report high-resolution single-particle cryo-electron microscopy structures of bovine CNT3 complexed with antiviral nucleosides N4-hydroxycytidine, PSI-6206, GS-441524 and ribavirin, all in inward-facing states. Notably, we found that the orally bioavailable antiviral molnupiravir arrests CNT3 in four distinct conformations, allowing us to capture cryo-electron microscopy structures of drug-loaded outward-facing and drug-loaded intermediate states. Our studies uncover the conformational trajectory of CNT3 during membrane transport of a nucleoside analog antiviral drug, yield new insights into the role of interactions between the transport and the scaffold domains in elevator-like domain movements during drug translocation, and provide insights into the design of nucleoside analog antiviral prodrugs with improved oral bioavailability.

Performance of a novel spectroscopy-based tool for adjuvant therapy decision-making in hormone receptor-positive breast cancer: a validation study.

PURPOSE: Digistain Index (DI), measured using an inexpensive mid-infrared spectrometer, reflects the level of aneuploidy in unstained tissue sections and correlates with tumor grade. We investigated whether incorporating DI with other clinicopathological variables could predict outcomes in patients with early breast cancer. METHODS: DI was calculated in 801 patients with hormone receptor-positive, HER2-negative primary breast cancer and ≤ 3 positive lymph nodes. All patients were treated with systemic endocrine therapy and no chemotherapy. Multivariable proportional hazards modeling was used to incorporate DI with clinicopathological variables to generate the Digistain Prognostic Score (DPS). DPS was assessed for prediction of 5- and 10-year outcomes (recurrence, recurrence-free survival [RFS] and overall survival [OS]) using receiver operating characteristics and Cox proportional hazards regression models. Kaplan-Meier analysis evaluated the ability of DPS to stratify risk. RESULTS: DPS was consistently highly accurate and had negative predictive values for all three outcomes, ranging from 0.96 to 0.99 at 5 years and 0.84 to 0.95 at 10 years. DPS demonstrated statistically significant prognostic ability with significant hazard ratios (95% CI) for low- versus high-risk classification for RFS, recurrence and OS (1.80 [CI 1.31-2.48], 1.83 [1.32-2.52] and 1.77 [1.28-2.43], respectively; all P < 0.001). CONCLUSION: DPS showed high accuracy and predictive performance, was able to stratify patients into low or high-risk, and considering its cost and rapidity, has the potential to offer clinical utility.

"Mindset Matters": Perseverance, a balanced approach and structured support as facilitators of whole foods plant-based adoption.

Whole foods plant-based diets (WFPBD) show potential for preventing and addressing chronic diseases. However, concerns exist about their acceptability and feasibility. Research on firsthand WFPBD adoption experiences is limited but crucial for promoting dietary change. In a 12-week remotely delivered lifestyle modification program using an ad libitum WFPBD, twenty weight-loss seeking adults (ages 18-75) with overweight or obesity completed self-report surveys and semi-structured interviews via Zoom. The study aimed to explore: (1) experiences with WFPBD adoption; (2) factors that helped or hindered adherence; and (3) perceived salient benefits. Interviews were analyzed inductively through a conventional content analysis, and associations between variables examined with correlational analyses. Participants overall reported WFPBD adoption being a positive, new experience, with an equal number (30%) finding it easy/easier than expected as challenging. Key cited challenges included overwhelm, different eating habits in the household, and meal preparation. Key cited facilitators included adopting an incremental approach to dietary change, persisting after setbacks, and having simple go-to meals. Greater self-compassion and family support, and less sabotage from friends and family corresponded to greater dietary change (rs > 0.45, ps < .05). Participants valued accountability, structure, human support, nutrition psychoeducation and recipes in the program. Three categories emerged regarding perceived benefits of following the WFPBD: physical health benefits, improvements to eating habits, and greater perceived control/agency over health. Results indicate that future interventions should include psychological strategies alongside nutrition education to enhance self-efficacy, address household barriers, and combat feelings of overwhelm through sufficient structure, support, and meal preparation guidance. Messaging around WFPBD may benefit from discussing prevailing positive experiences with adoption, common benefits experienced, and options for an incremental approach given that feasibility and acceptability concerns may deter efforts.

Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2.

A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition. In mammals, organic cation transporter (OCT) subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and SLC22A2, respectively) are polyspecific transporters responsible for the uptake and clearance of structurally diverse cationic compounds in the liver and kidneys, respectively. Notably, it is well established that human OCT1 and OCT2 play central roles in the pharmacokinetics and drug-drug interactions of many prescription medications, including metformin. Despite their importance, the basis of polyspecific cationic drug recognition and the alternating access mechanism for OCTs have remained a mystery. Here we present four cryo-electron microscopy structures of apo, substrate-bound and drug-bound OCT1 and OCT2 consensus variants, in outward-facing and outward-occluded states. Together with functional experiments, in silico docking and molecular dynamics simulations, these structures uncover general principles of organic cation recognition by OCTs and provide insights into extracellular gate occlusion. Our findings set the stage for a comprehensive structure-based understanding of OCT-mediated drug-drug interactions, which will prove critical in the preclinical evaluation of emerging therapeutics.

Hepatocytes undergo punctuated expansion dynamics from a periportal stem cell niche in normal human liver.

BACKGROUND & AIMS: While normal human liver is thought to be generally quiescent, clonal hepatocyte expansions have been observed, though neither their cellular source nor their expansion dynamics have been determined. Knowing the hepatocyte cell of origin, and their subsequent dynamics and trajectory within the human liver will provide an important basis to understand disease-associated dysregulation. METHODS: Herein, we use in vivo lineage tracing and methylation sequence analysis to demonstrate normal human hepatocyte ancestry. We exploit next-generation mitochondrial sequencing to determine hepatocyte clonal expansion dynamics across spatially distinct areas of laser-captured, microdissected, clones, in tandem with computational modelling in morphologically normal human liver. RESULTS: Hepatocyte clones and rare SOX9+ hepatocyte progenitors commonly associate with portal tracts and we present evidence that clones can lineage-trace with cholangiocytes, indicating the presence of a bipotential common ancestor at this niche. Within clones, we demonstrate methylation CpG sequence diversity patterns indicative of periportal not pericentral ancestral origins, indicating a portal to central vein expansion trajectory. Using spatial analysis of mitochondrial DNA variants by next-generation sequencing coupled with mathematical modelling and Bayesian inference across the portal-central axis, we demonstrate that patterns of mitochondrial DNA variants reveal large numbers of spatially restricted mutations in conjunction with limited numbers of clonal mutations. CONCLUSIONS: These datasets support the existence of a periportal progenitor niche and indicate that clonal patches exhibit punctuated but slow growth, then quiesce, likely due to acute environmental stimuli. These findings crucially contribute to our understanding of hepatocyte dynamics in the normal human liver. IMPACT AND IMPLICATIONS: The liver is mainly composed of hepatocytes, but we know little regarding the source of these cells or how they multiply over time within the disease-free human liver. In this study, we determine a source of new hepatocytes by combining many different lab-based methods and computational predictions to show that hepatocytes share a common cell of origin with bile ducts. Both our experimental and computational data also demonstrate hepatocyte clones are likely to expand in slow waves across the liver in a specific trajectory, but often lie dormant for many years. These data show for the first time the expansion dynamics of hepatocytes in normal liver and their cell of origin enabling the accurate measurment of changes to their dynamics that may lead to liver disease. These findings are important for researchers determining cancer risk in human liver.

Molecular basis of polyspecific drug binding and transport by OCT1 and OCT2.

A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition 1, 2 . In mammals, organic cation transporter subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and SLC22A2, respectively) are polyspecific transporters responsible for the uptake and clearance of structurally diverse cationic compounds in the liver and kidneys, respectively 3, 4 . Notably, it is well established that human OCT1 and OCT2 play central roles in the pharmacokinetics, pharmacodynamics, and drug-drug interactions (DDI) of many prescription medications, including metformin 5, 6 . Despite their importance, the basis of polyspecific cationic drug recognition and the alternating access mechanism for OCTs have remained a mystery. Here, we present four cryo-EM structures of apo, substrate-bound, and drug-bound OCT1 and OCT2 in outward-facing and outward-occluded states. Together with functional experiments, in silico docking, and molecular dynamics simulations, these structures uncover general principles of organic cation recognition by OCTs and illuminate unexpected features of the OCT alternating access mechanism. Our findings set the stage for a comprehensive structure-based understanding of OCT-mediated DDI, which will prove critical in the preclinical evaluation of emerging therapeutics.

A 2023 Agenda for Substance Use Prevention and Treatment in the US.

In this Viewpoint, officials from the White House Office of National Drug Control Policy describe 3 actions that health care personnel can take to expand prevention and treatment of substance misuse and overdose.

Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines.

Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (µ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye.

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.

Dietary Restriction Impacts Peripheral Circadian Clock Output Important for Longevity in Drosophila.

Circadian clocks may mediate lifespan extension by caloric or dietary restriction (DR). We find that the core clock transcription factor Clock is crucial for a robust longevity and fecundity response to DR in Drosophila. To identify clock-controlled mediators, we performed RNA-sequencing from abdominal fat bodies across the 24 h day after just 5 days under control or DR diets. In contrast to more chronic DR regimens, we did not detect significant changes in the rhythmic expression of core clock genes. Yet we discovered that DR induced de novo rhythmicity or increased expression of rhythmic clock output genes. Network analysis revealed that DR increased network connectivity in one module comprised of genes encoding proteasome subunits. Adult, fat body specific RNAi knockdown demonstrated that proteasome subunits contribute to DR-mediated lifespan extension. Thus, clock control of output links DR-mediated changes in rhythmic transcription to lifespan extension.

Methotrexate recognition by the human reduced folate carrier SLC19A1.

Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division1,2. Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu3. The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell1,3, as well as chemotherapeutic agents such as methotrexate4-6. As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance4-8. Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC.

Identifying cultural differences in metacognition.

Some aspects of human metacognition, such as the ability to consciously evaluate our beliefs and decisions, are hypothesized to be culturally acquired. However, direct evidence for this claim is lacking. As an initial step toward answering this question, here we examine differences in metacognitive performance between populations matched for occupation (students), income, demographics and general intelligence but drawn from 2 distinct cultural milieus (Beijing, China and London, U.K.). Chinese participants showed more efficient metacognitive evaluation of perceptual decision-making task performance compared to U.K. participants. These differences manifested in boosts to postdecisional processing following error trials, despite no differences in first-order performance. In a second experiment, we directly replicate these findings and show that a metacognitive advantage generalizes to a task that replaces postdecision evidence with equivalent social advice. Together, our results are consistent with a proposal that metacognitive capacity is shaped via sociocultural interactions. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Do Cellphone Bans Save Lives? Evidence From Handheld Laws on Traffic Fatalities.

Distracted driving is one of the leading causes of fatal motor vehicle accidents in the United States. Policymakers in several states have responded to this phenomenon by implementing laws that restrict the use of handheld devices while operating a vehicle. In this paper, we utilize various quasi-experimental designs to estimate the impact of state-level handheld mandates on traffic fatalities. We find robust evidence that restricting the use of handheld devices while driving reduces daily traffic fatalities by 0.63 individuals in the short term. The results further indicate that while the magnitude of the impact is smaller in the long term, this policy is still effective at curbing traffic fatalities, saving more than 69 lives per state each year.

Remotely Delivered Behavioral Weight Loss Intervention Using an Ad Libitum Plant-Based Diet: Pilot Acceptability, Feasibility, and Preliminary Results.

BACKGROUND: Many traditional lifestyle interventions use calorie prescriptions, but most individuals have difficulty sustaining calorie tracking and thus weight loss. In contrast, whole food plant-based diets (WFPBDs) have previously shown significant weight loss without this issue. However, most WFPBD interventions are face-to-face and time-intensive, and do not leverage gold standard behavioral strategies for health behavior change. OBJECTIVE: This open pilot trial was the first to evaluate the feasibility of a fully featured, remotely delivered behavioral weight loss intervention using an ad libitum WFPBD. METHODS: Over 12 weeks, participants (N=15) with overweight or obesity received a newly designed program that integrated behavioral weight loss and a WFPBD prescription via weekly web-based modules and brief phone coaching calls. Assessments were performed at baseline, midtreatment (6 weeks), and after treatment (12 weeks). RESULTS: The intervention was rated as highly acceptable (mean 4.40 out of 5, SE 0.18), and attrition was low (6.7%). In all, intention-to-treat analyses revealed that 69% (10.4/15) of the participants lost 5% of their weight (mean -5.89, SE 0.68 kg). Predefined benchmarks for quality of life were met. CONCLUSIONS: A pilot digital behavioral weight loss intervention with a non-energy-restricted WFPBD was feasible, and the mean acceptability was high. Minimal contact time (80-150 minutes of study interventionist time per participant over 12 weeks) led to clinically relevant weight loss and dietary adherence for most participants (10.4/15, 69% and 11.8/15, 79%, respectively), and quality of life improvements (reliable change indices >1.53). We hope that this work will serve as a springboard for future larger scale randomized controlled studies evaluating the efficacy of such programs for weight loss, dietary change, and quality of life. TRIAL REGISTRATION: ClinicalTrials.gov NCT04892030; https://clinicaltrials.gov/ct2/show/NCT04892030.