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Background: Colon cancers are categorized into mismatch repair deficient/microsatellite unstable (MSI-H) and mismatch repair proficient/microsatellite stable (MSS) cancers. This study aims to compare the disease characteristics and trends in the utilization of cancer therapies across different age groups and stages in these two groups. Methods: MSI-H and MSS colon adenocarcinomas from 2010 to 2016 were identified using the National Cancer Database. We compared patient and disease characteristics between the two groups and evaluated the use of adjuvant chemotherapy across age groups and cancer stages. Within MSI-H and MSS groups, we conducted a landmark analysis after propensity score matching for adjuvant chemotherapy versus no chemotherapy to determine its effect on survival. Results: Of the 542,368 patients that met inclusion criteria, 120,751 (22%) had mismatch repair results available-out of these 96,928 (80%) had MSS colon cancers while 23,823 (19.7%) had MSI-H cancers. MSI-H disease had a bimodal age distribution (<40 years = 22%; ≥75 years = 26%) and was frequent among females (22%) and non-Hispanic Whites (20%). Among those < 65 years, 15% of low-risk stage 2 MSI-H patients and 40% of high-risk stage 2 MSI-H patients received adjuvant chemotherapy. More than two-thirds of stage 3 patients <65 years received adjuvant chemotherapy in both groups. After conducting propensity-score matching for age, gender, and co-morbidities, we found that adjuvant chemotherapy use had a trend towards lower overall survival (OS) in low-risk stage 2 MSI-H (HR = 1.8 [95% CI, 0.8-4.02]) and high-risk stage 2 MSI-H (HR = 1.42 [95% CI, 0.96-2.12]) groups. Adjuvant chemotherapy significantly improved OS in stage 3 colon cancer patients irrespective of microsatellite status or risk category of disease. Conclusions: MSI-H colon cancer had bimodal age distribution. Among stage 2 MSI-H patients <65 years, a notable proportion received adjuvant chemotherapy. Among MSI-H stage 2 patients, adjuvant chemotherapy use was associated with lower survival while it significantly improved survival for stage 3 patients, irrespective of MSI status.

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Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor occupancy during neural progenitor cell differentiation. We show thousands of enhancers undergo rapid, transient accessibility changes associated with distinct periods of transcription factor expression. However, most DNA methylation changes are unidirectional and delayed relative to chromatin dynamics, creating transiently discordant epigenetic states. Genome-wide detection of 5-hydroxymethylcytosine further revealed active demethylation begins ahead of chromatin and transcription factor activity, while enhancer hypomethylation persists long after these activities have dissipated. We demonstrate that these timepoint specific methylation states predict past, present and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to mediate short and long-term enhancer regulation during cell fate specification.

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South Asia's Eastern Indo-Gangetic Plains (EIGP) is home to approximately 450 million people. This region is characterized by the highest global concentration of rural poverty and a predominant reliance on agriculture for nutritional sustenance and economic livelihoods. Agriculture in the EIGP is highly cereal-centric, making crop diversification indispensable for its development. This data article is part of the research conducted by an interdisciplinary team of researchers analysing the status and determinants of crop diversification in South Asia's EIGP. The data presented here were collected from 1,400 farm households across 72 communities in eight locations within the EIGP of India, Nepal, and Bangladesh during the year 2023. The research employed a simple random sampling method for empirical data collection. The primary agricultural decision-makers were given a tailored questionnaire comprising seven modules. These modules sought comprehensive data on livelihood practices, changes in agriculture, aspirations, diet, food security, mechanization, demographics, and asset ownership. The questionnaire was translated from English into Nepali and Bangla to facilitate a thorough understanding of the farmers' livelihoods in the study areas. The survey successfully ended with 1400 properly filled and captured questionnaires, which was quite representative. The cross-sectional data presented here describe location-specific farm-level crop distribution, enabling the analysis of geographic variations in crop diversification. The generation of this dataset addresses a significant gap in the availability of information on the current state of crop diversification in the EIGP, offering a foundational baseline for future research and interventions by regional governments and development partners. We employed the Herfindahl-Hirschman Index (HHI) to calculate crop diversification and a Tobit Regression Model to identify the region-specific determinants of crop diversification. The dataset is hereby made available as it is considered vital for regional policy and practical recommendations.

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BACKGROUND: Unicompartmental knee replacements (UKRs) are performed by surgeons at various stages in training with varying levels of supervision, but we do not know if this is a safe practice with comparable outcomes to consultant-performed UKR. The aim of this study was to use registry data for England and Wales to investigate the association between surgeon grade (consultant, or trainee), the senior supervision of trainees (supervised by a scrubbed consultant, or not), and the risk of revision surgery following UKR. METHODS AND FINDINGS: We conducted an observational study using prospectively collected data from the National Joint Registry for England and Wales (NJR). We included adult patients who underwent primary UKR for osteoarthritis (n = 106,206), recorded in the NJR between 2003 and 2019. Exposures were the grade of the operating surgeon (consultant, or trainee) and whether or not trainees were directly supervised by a consultant during the procedure (referred to as "supervised by a scrubbed consultant"). The primary outcome was all-cause revision surgery. The secondary outcome was the number of procedures revised for the following specific indications: aseptic loosening/lysis, infection, progression of osteoarthritis, unexplained pain, and instability. Flexible parametric survival models were adjusted for patient, operation, and healthcare setting factors. We included 106,206 UKRs in 91,626 patients, of which 4,382 (4.1%) procedures were performed by a trainee. The unadjusted cumulative probability of failure at 15 years was 17.13% (95% CI [16.44, 17.85]) for consultants, 16.42% (95% CI [14.09, 19.08]) for trainees overall, 15.98% (95% CI [13.36, 19.07]) for trainees supervised by a scrubbed consultant, and 17.32% (95% CI [13.24, 22.50]) for trainees not supervised by a scrubbed consultant. There was no association between surgeon grade and all-cause revision in either crude or adjusted models (adjusted HR = 1.01, 95% CI [0.90, 1.13]; p = 0.88). Trainees achieved comparable all-cause survival to consultants, regardless of the level of scrubbed consultant supervision (supervised: adjusted HR = 0.99, 95% CI [0.87, 1.14]; p = 0.94; unsupervised: adjusted HR = 1.03, 95% CI [0.87, 1.22]; p = 0.74). Limitations of this study relate to its observational design and include: the potential for nonrandom allocation of cases by consultants to trainees; residual confounding; and the use of the binary variable "surgeon grade," which does not capture variations in the level of experience between trainees. CONCLUSIONS: This nationwide study of UKRs with over 16 years' follow up demonstrates that trainees within the current training system in England and Wales achieve comparable all-cause implant survival to consultants. These findings support the current methods by which surgeons in England and Wales are trained to perform UKR.

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Cognitive resilience describes the phenomenon of individuals evading cognitive decline despite prominent Alzheimer's disease neuropathology. Operationalization and measurement of this latent construct is non-trivial as it cannot be directly observed. The residual approach has been widely applied to estimate CR, where the degree of resilience is estimated through a linear model's residuals. We demonstrate that this approach makes specific, uncontrollable assumptions and likely leads to biased and erroneous resilience estimates. We propose an alternative strategy which overcomes the standard approach's limitations using machine learning principles. Our proposed approach makes fewer assumptions about the data and construct to be measured and achieves better estimation accuracy on simulated ground-truth data.

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Magnetic fields have been used to uniformly align the lyotropic chiral nematic (cholesteric) liquid crystalline (LC) phase of biopolymers to a global orientation and optical appearance. Here, we demonstrate that, in contrast, weak and patterned magnetic field gradients can create a complex optical appearance with the variable spatial local organization of needle-like magnetically decorated cellulose nanocrystals. The formation of optically patterned thin films with left- and right-handed chiral and achiral regions is observed and related to local magnetic gradient-driven vortices during LC suspension flow. We trace the localized flow directions of the magnetically decorated nanocrystals during evaporation-induced assembly, demonstrating how competing evaporation and field-induced localized flow affect the twisted organization within magnetically induced vortices. The simulations suggested that localized twisting inversion originates from the interplay between the direction and strength of the local-depth-related magnetic gradients and the receding front through peripheral magnetic gaps. We propose that this finding will lead to magnetically patterned photonic films.

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PURPOSE: The purpose of this study was to explore self-perceived changes in athlete journey trajectory, or shifts, after ACLR that facilitate or hinder physical activity participation among youth. METHODS: Ten participants were included in this study at a median of 5.9 years after adolescent ACLR. Using an interpretive phenomenological methodology, semi-structured interviews with each participant were recorded and transcribed verbatim. Data collection focused on participants' lived experiences of reintegration to physical activity after ACLR. Thematic analyses were guided by the procedures of the constant comparative method. RESULTS: Nineteen distinct shifts were identified from participants' perspectives, categorized into the main classification scheme of 1) environmental shifts (extrinsic demands, built environment, social network), 2) psychological shifts (expectations, motivation, meaning of sports, accountability, priorities, athlete identity, mental health, confidence, knowledge, character, participation mentality), and 3) physical shifts (movement competence, sport participation, physical activity, normalization, knee health). Factors perceived to induce shifts were categorized as natural, injury-driven, or life transition-driven. CONCLUSION: In the years following adolescent ACLR, young athletes experience physical, psychological, and environment shifts that impact physical activity participation. These findings provide important insight for future work that aims to optimize physical activity outcomes after an injury-related disruption in the athlete journey.

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OBJECTIVE: Long-term outcomes after multi-valve cardiac surgery remain under-evaluated. METHODS: Medicare administrative claims from 2008-2019 identified beneficiaries undergoing multi-valve surgery. Operative characteristics were doubly-adjudicated using International Classification of Diseases and Current Procedural Technology codes. A multivariable flexible parametric model evaluated predictors of survival; regression standardization was performed to predict standardized survival probabilities (SSP) at varying percentiles of annual valvar volume. RESULTS: Of 476,092 cardiac surgeries involving the aortic (AVS), mitral (MVS), or tricuspid (TVS) valve, 63,083 (13.3%) were identified as involving multi-valve surgery: 22,884 MVS+TVS, 30,697 AVS+MVS, 3,443 AVS+TVS and 6,059 AVS+MVS+TVS. Surgery occurred at 1,157 hospitals by 2,922 surgeons. Annual valvar volume (total AVS+MVS+TVS) was tallied for surgeons and hospitals. Median survival varied substantially by type of multi-valve surgery: 8.09 [7.90-8.24] years in MVS/TVS, 6.65 [6.49-6.81] years in AVS/MVS, 5.77 [5.37-6.13] in AVS/TVS, and 6.02 [5.64-6.38] in AVS/MVS/TVS. SSPs were calculated across combined hospital/surgeon volume percentiles; the median SSP increased with increasing percentile of combined hospital/surgeon volume: 5%tile: 5.77 [5.58,5.98], 25%tile: 6.18 [6.07,6.28], 50%tile: 6.56 [6.44,6.68], 75%tile: 6.86 [6.75,6.97], and 95%tile: 7.58 [7.34,7.83] years, respectively. CONCLUSIONS: Survival varied significantly by type of multi-valve surgery, worsened with addition of concomitant interventions and improved substantially with increasing annual hospital and surgeon volume. Hospital volume was associated with an improved early hazard for death that abated beyond 3 months post-surgery), while surgeon volume was associated with an improved hazard for death that persisted even beyond the first post-operative year. Consideration should be given to referring multi-valve cases to high-volume hospitals and surgeons.

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Infections caused by Gram-negative bacteria are leading causes of mortality worldwide. Due to the rise in antibiotic resistant strains, there is a desperate need for alternative strategies to control infections caused by these organisms. One such approach is the prevention of infection through vaccination. While live attenuated and heat-killed bacterial vaccines are effective, they can lead to adverse reactions. Newer vaccine technologies focus on utilizing polysaccharide or protein subunits for safer and more targeted vaccination approaches. One promising avenue in this regard is the use of proteins released by the Type 5 secretion system (T5SS). This system is the most prevalent secretion system in Gram-negative bacteria. These proteins are compelling vaccine candidates due to their demonstrated protective role in current licensed vaccines. Notably, Pertactin, FHA, and NadA are integral components of licensed vaccines designed to prevent infections caused by Bordetella pertussis or Neisseria meningitidis. In this review, we delve into the significance of incorporating T5SS proteins into licensed vaccines, their contributions to virulence, conserved structural motifs, and the protective immune responses elicited by these proteins.

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Introduction: Alternative lengthening of telomeres (ALT) occurs in sarcomas and ALT cancers share common mechanisms of therapy resistance or sensitivity. Telomeric DNA C-circles are self-primed circular telomeric repeats detected with a PCR assay that provide a sensitive and specific biomarker exclusive to ALT cancers. We have previously shown that 23% of high-risk neuroblastomas are of the ALT phenotype. Here, we investigate the frequency of ALT in Ewing's family sarcoma (EFS), rhabdomyosarcoma (RMS), and osteosarcoma (OS) by analyzing DNA from fresh frozen primary tumor samples utilizing the real-time PCR C-circle Assay (CCA). Methods: We reviewed prior publications on ALT detection in pediatric sarcomas. DNA was extracted from fresh frozen primary tumors, fluorometrically quantified, C-circles were selectively enriched by isothermal rolling cycle amplification and detected by real-time PCR. Results: The sample cohort consisted of DNA from 95 EFS, 191 RMS, and 87 OS primary tumors. One EFS and 4 RMS samples were inevaluable. Using C-circle positive (CC+) cutoffs previously defined for high-risk neuroblastoma, we observed 0 of 94 EFS, 5 of 187 RMS, and 62 of 87 OS CC+ tumors. Conclusions: Utilizing the ALT-specific CCA we observed ALT in 0% of EFS, 2.7% of RMS, and 71% of OS. These data are comparable to prior studies in EFS and OS using less specific ALT markers. The CCA can provide a robust and sensitive means of identifying ALT in sarcomas and has potential as a companion diagnostic for ALT targeted therapeutics.

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Characterization of the interference patterns observed in B-mode images (i.e., speckle statistics) is a valuable tool in tissue characterization. However, changes in echo amplitudes unrelated to speckle, including power loss due to attenuation and diffraction, can bias these metrics, undermining their utility. Tissue with high attenuation such as the uterine cervix are especially affected. The purpose of this study was to demonstrate and quantify the effects of attenuation and diffraction on speckle statistics and to propose methods of compensation. Analysis was performed on simulated diffuse scattering phantoms of varying attenuation with simulated transducers at 9 and 5 MHz center frequency. Application in the in vivo macaque cervix using a clinical scanner is also presented. Nakagami and homodyned K distribution parameters were calculated in parameter estimation regions (PERs) of varying size within simulations and experiments. Changes in speckle statistics parameters with respect to PER size and depth were compared with and without two different compensation schemes. It has been shown that compensation for attenuation and diffraction is necessary to produce speckle statistics estimates that do not depend on medium attenuation or PER size. Reducing the dependence on these factors connects speckle statistics estimates more closely with the microstructure of the probed medium.

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The intramolecular through-space NMR spectroscopic effect of steric compression is related to intramolecular through-space van der Waals repulsion. The electron cloud of a proton can be pushed away by the electron cloud of a nearby proton or functional group. As the electron population of the sterically compressed proton is decreased (therefore deshielded), the chemical shift sharply moves downfield, which may result in ambiguity for the proton signal assignment. Also, the conformation of the local area of the sterically compressed proton can be altered by the steric repulsion, therefore, the coupling constant/coupling pattern of a sterically compressed proton could be influenced. This review summarizes and presents the impacts on the chemical shift and coupling constant by the 1H NMR spectroscopic effect of steric compression extracted from the reported examples from the 1950s to 2021.

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The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.

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Inferring the 3D structure and conformation of disordered biomolecules, e.g., single stranded nucleic acids (ssNAs), remains challenging due to their conformational heterogeneity in solution. Here, we use escape-time electrometry (ETe) to measure with sub elementary-charge precision the effective electrical charge in solution of short to medium chain length ssNAs in the range of 5-60 bases. We compare measurements of molecular effective charge with theoretically calculated values for simulated molecular conformations obtained from Molecular Dynamics simulations using a variety of forcefield descriptions. We demonstrate that the measured effective charge captures subtle differences in molecular structure in various nucleic acid homopolymers of identical length, and also that the experimental measurements can find agreement with computed values derived from coarse-grained molecular structure descriptions such as oxDNA, as well next generation ssNA force fields. We further show that comparing the measured effective charge with calculations for a rigid, charged rod-the simplest model of a nucleic acid-yields estimates of molecular structural dimensions such as linear charge spacings that capture molecular structural trends observed using high resolution structural analysis methods such as X-ray scattering. By sensitively probing the effective charge of a molecule, electrometry provides a powerful dimension supporting inferences of molecular structural and conformational properties, as well as the validation of biomolecular structural models. The overall approach holds promise for a high throughput, microscopy-based biomolecular analytical approach offering rapid screening and inference of molecular 3D conformation, and operating at the single molecule level in solution.

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Background: Poor long-term recovery outcomes after treatment (e.g., readmission to inpatient treatment) are common among individuals with substance use disorders (SUDs). In-person mindfulness-based treatments (MBTs) are efficacious for SUDs and may improve recovery outcomes. However, existing MBTs for SUD have limited public health reach, and thus scalable delivery methods are needed. A digitally-delivered MBT for SUDs may hold promise. Methods: We recently developed Mindful Journey, a smartphone app-based adjunctive MBT for improving long-term recovery outcomes. In this paper, we present details on the app and describe the protocol for a single-site pilot feasibility randomized controlled trial of Mindful Journey. In this trial, individuals (n = 34) in an early phase of outpatient treatment for SUDs will be randomized to either treatment-as-usual (TAU) plus Mindful Journey, or TAU only. The trial will focus on testing the feasibility (e.g., engagement) and acceptability of the app (e.g., perceived usability and helpfulness for recovery), as well as feasibility of study procedures (e.g., assessment completion). The trial will incorporate ecological momentary assessment before and after treatment to assess mechanisms in real-time, including mindfulness, craving, difficulties with negative emotion regulation, and savoring. To examine the sensitivity to change of outcomes (substance use, substance-related problems, and psychological distress) and mechanism variables (noted above), we will test within-treatment-condition changes over time. Discussion: The proposed pilot trial will provide important preliminary data on whether Mindful Journey is feasible and acceptable among individuals with SUDs. Trial registration: ClinicalTrials.gov NCT05109507.

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Background Histotripsy is a nonthermal, nonionizing, noninvasive, focused US technique that relies on cavitation for mechanical tissue breakdown at the focal point. Preclinical data have shown its safety and technical success in the ablation of liver tumors. Purpose To evaluate the safety and technical success of histotripsy in destroying primary or metastatic liver tumors. Materials and Methods The parallel United States and European Union and England #HOPE4LIVER trials were prospective, multicenter, single-arm studies. Eligible patients were recruited at 14 sites in Europe and the United States from January 2021 to July 2022. Up to three tumors smaller than 3 cm in size could be treated. CT or MRI and clinic visits were performed at 1 week or less preprocedure, at index-procedure, 36 hours or less postprocedure, and 30 days postprocedure. There were co-primary end points of technical success of tumor treatment and absence of procedure-related major complications within 30 days, with performance goals of greater than 70% and less than 25%, respectively. A two-sided 95% Wilson score CI was derived for each end point. Results Forty-four participants (21 from the United States, 23 from the European Union or England; 22 female participants, 22 male participants; mean age, 64 years ± 12 [SD]) with 49 tumors were enrolled and treated. Eighteen participants (41%) had hepatocellular carcinoma and 26 (59%) had non-hepatocellular carcinoma liver metastases. The maximum pretreatment tumor diameter was 1.5 cm ± 0.6 and the maximum post-histotripsy treatment zone diameter was 3.6 cm ± 1.4. Technical success was observed in 42 of 44 treated tumors (95%; 95% CI: 84, 100) and procedure-related major complications were reported in three of 44 participants (7%; 95% CI: 2, 18), both meeting the performance goal. Conclusion The #HOPE4LIVER trials met the co-primary end-point performance goals for technical success and the absence of procedure-related major complications, supporting early clinical adoption. Clinical trial registration nos. NCT04572633, NCT04573881 Published under a CC BY 4.0 license. Supplemental material is available for this article. See also the editorial by Nezami and Georgiades in this issue.

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