Optimization of ultracentrifugation-based method to enhance the purity and proteomic profiling depth of plasma-derived extracellular vesicles and particles.

Circulating extracellular vesicles and particles (EVPs) are being investigated as potential biomarkers for early cancer detection, prognosis, and disease monitoring. However, the suboptimal purity of EVPs isolated from peripheral blood plasma has posed a challenge of in-depth analysis of the EVP proteome. Here, we compared the effectiveness of different methods for isolating EVPs from healthy donor plasma, including ultracentrifugation (UC)-based protocols, phosphatidylserine-Tim4 interaction-based affinity capture (referred to as "PS"), and several commercial kits. Modified UC methods with an additional UC washing or size exclusion chromatography step substantially improved EVP purity and enabled the detection of additional proteins via proteomic mass spectrometry, including many plasma membrane and cytoplasmic proteins involved in vesicular regulation pathways. This improved performance was reproduced in cancer patient plasma specimens, resulting in the identification of a greater number of differentially expressed EVP proteins, thus expanding the range of potential biomarker candidates. However, PS and other commercial kits did not outperform UC-based methods in improving plasma EVP purity. PS yielded abundant contaminating proteins and a biased enrichment for specific EVP subsets, thus unsuitable for proteomic profiling of plasma EVPs. Therefore, we have optimized UC-based protocols for circulating EVP isolation, which enable further in-depth proteomic analysis for biomarker discovery.

Large Language Model-Based Responses to Patients' In-Basket Messages.

Importance: Virtual patient-physician communications have increased since 2020 and negatively impacted primary care physician (PCP) well-being. Generative artificial intelligence (GenAI) drafts of patient messages could potentially reduce health care professional (HCP) workload and improve communication quality, but only if the drafts are considered useful. Objectives: To assess PCPs' perceptions of GenAI drafts and to examine linguistic characteristics associated with equity and perceived empathy. Design, Setting, and Participants: This cross-sectional quality improvement study tested the hypothesis that PCPs' ratings of GenAI drafts (created using the electronic health record [EHR] standard prompts) would be equivalent to HCP-generated responses on 3 dimensions. The study was conducted at NYU Langone Health using private patient-HCP communications at 3 internal medicine practices piloting GenAI. Exposures: Randomly assigned patient messages coupled with either an HCP message or the draft GenAI response. Main Outcomes and Measures: PCPs rated responses' information content quality (eg, relevance), using a Likert scale, communication quality (eg, verbosity), using a Likert scale, and whether they would use the draft or start anew (usable vs unusable). Branching logic further probed for empathy, personalization, and professionalism of responses. Computational linguistics methods assessed content differences in HCP vs GenAI responses, focusing on equity and empathy. Results: A total of 16 PCPs (8 [50.0%] female) reviewed 344 messages (175 GenAI drafted; 169 HCP drafted). Both GenAI and HCP responses were rated favorably. GenAI responses were rated higher for communication style than HCP responses (mean [SD], 3.70 [1.15] vs 3.38 [1.20]; P = .01, U = 12 568.5) but were similar to HCPs on information content (mean [SD], 3.53 [1.26] vs 3.41 [1.27]; P = .37; U = 13 981.0) and usable draft proportion (mean [SD], 0.69 [0.48] vs 0.65 [0.47], P = .49, t = -0.6842). Usable GenAI responses were considered more empathetic than usable HCP responses (32 of 86 [37.2%] vs 13 of 79 [16.5%]; difference, 125.5%), possibly attributable to more subjective (mean [SD], 0.54 [0.16] vs 0.31 [0.23]; P < .001; difference, 74.2%) and positive (mean [SD] polarity, 0.21 [0.14] vs 0.13 [0.25]; P = .02; difference, 61.5%) language; they were also numerically longer (mean [SD] word count, 90.5 [32.0] vs 65.4 [62.6]; difference, 38.4%), but the difference was not statistically significant (P = .07) and more linguistically complex (mean [SD] score, 125.2 [47.8] vs 95.4 [58.8]; P = .002; difference, 31.2%). Conclusions: In this cross-sectional study of PCP perceptions of an EHR-integrated GenAI chatbot, GenAI was found to communicate information better and with more empathy than HCPs, highlighting its potential to enhance patient-HCP communication. However, GenAI drafts were less readable than HCPs', a significant concern for patients with low health or English literacy.

Lymphopenia in the Adult Population With Fontan Physiology: A Potential New Marker for Disease Assessment.

Background: Patients with complex congenital heart disease and Fontan palliation frequently develop extracardiac disease, including hematologic abnormalities, such as lymphopenia. However, the clinical implications of this finding are poorly understood and are therefore the topic of this investigation. Methods: Patients with Fontan physiology in our centre (1999-2018) were evaluated for the presence and impact of lymphopenia. The cohort was divided into a group with lymphopenia (L) (2 consecutive absolute lymphocyte counts ≤ 1∗103 K/ µL) and a group who had never had lymphopenia (NL). Clinical characteristics and hospital admissions (762 patient-years) were evaluated. Results: In 62 adult patients with Fontan physiology (aged 34 ± 9 years; 32 women [52%]), the patients who developed lymphopenia earliest did so 8 years after Fontan completion, with up to 60% of patients developing lymphopenia by 30 years. Lymphopenia was found to be associated with portal hypertension (varices, ascites, splenomegaly, and thrombocytopenia [VAST] score)-NL: 0 (0-2) vs L: 2 (0-4), P < 0.0001). A total of 76 heart failure and 81 arrhythmia-associated admissions occurred per 1000 patient-years. At 40 years post-Fontan, the probability of a heart failure admission was higher in the L group (L: 51 [86%] vs NL: 8 [14%], P < 0.01). Conclusions: Adult patients with Fontan physiology and lymphopenia demonstrated portal hypertension and lymphatic dysfunction more commonly, perhaps suggesting that this may be a marker of Fontan congestion and early Fontan failure. Further investigation into the relationship between lymphopenia, clinical outcomes, and Fontan function is needed.

Contexte: Chez les patients atteints d'une cardiopathie congénitale complexe ayant subi une intervention de Fontan, il est fréquent de voir apparaître des maladies extracardiaques, dont des anomalies hématologiques, comme la lymphopénie. Cependant, les implications cliniques de cette observation sont mal comprises et font donc l'objet de cette étude. Méthodologie: La présence et l'impact d'une lymphopénie ont été évalués chez des patients présentant une physiologie de Fontan dans notre centre (1999-2018). La cohorte a été divisée en un groupe composé de sujets atteints de lymphopénie (L) (2 mesures consécutives du nombre absolu de lymphocytes ≤ 1 x 103 K/µL) et un groupe de sujets n'ayant jamais présenté de lymphopénie (NL). Les caractéristiques initiales et les hospitalisations (762 années-patients) ont été évaluées. Résultats: Chez 62 adultes présentant une physiologie de Fontan (âgés de 34 ± 9 ans; 32 femmes [52 %]), la lymphopénie est apparue au plus tôt 8 ans après l'intervention de Fontan, avant 30 ans chez jusqu'à 60 % des patients. La lymphopénie a été associée à l'hypertension portale (score varices, ascite, splénomégalie et thrombocytopénie [VAST]) ­ NL : 0 (0-2) vs L : 2 (0-4), p < 0,0001. Au total, il y a eu 76 hospitalisations pour insuffisance cardiaque et 81 pour arythmie pour 1000 années-patients. Quarante ans après l'intervention de Fontan, la probabilité d'une hospitalisation pour insuffisance cardiaque était plus élevée dans le groupe L que dans le groupe NL (L : 51 [86 %] vs NL : 8 [14 %], p < 0,01). Conclusions: L'hypertension portale et la dysfonction lymphatique étaient plus fréquentes chez les adultes présentant une physiologie de Fontan et une lymphopénie, ce qui laisse peut-être entendre que ce pourrait être un marqueur d'une congestion et d'une défaillance précoce du système Fontan. D'autres recherches sur le lien entre la lymphopénie, les issues cliniques et la fonction du système Fontan sont nécessaires.

Compliant Solid Polymer Electrolytes (SPEs) for Enhanced Anode-Electrolyte Interfacial Stability in All-Solid-State Lithium-Metal Batteries (LMBs).

Practical application of high energy density lithium-metal batteries (LMBs) has remained elusive over the last several decades due to their unstable and dendritic electrodeposition behavior. Solid polymer electrolytes (SPEs) with sufficient elastic modulus have been shown to attenuate dendrite growth and extend cycle life. Among different polymer architectures, network SPEs have demonstrated promising overall performance in cells using lithium metal anodes. However, fine-tuning network structures to attain adequate lithium electrode interfacial contact and stable electrodeposition behavior at extended cycling remains a challenge. In this work, we designed a series of comb-chain cross-linker-based network SPEs with tunable compliance by introducing free dangling chains into the SPE network. These dangling chains were used to tune the SPE ionic conductivity, ductility, and compliance. Our results demonstrate that increasing network compliance and ductility improves anode-electrolyte interfacial adhesion and reduces voltage hysteresis. SPEs with 56.3 wt % free dangling chain content showed a high Coulombic efficiency of 93.4% and a symmetric cell cycle life 1.9× that of SPEs without free chains. Additionally, the improved anode compliance of these SPEs led to reduced anode-electrolyte interfacial resistance growth and greater capacity retention at 92.8% when cycled at 1C in Li|SPE|LiFePO4 half cells for 275 cycles.

Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets.

Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes. Notably, cholangiocarcinoma cell lines are stratified into distinct lineage subtypes based on biliary or dual biliary/hepatocyte marker signatures, associated with dependency on specific lineage survival factors. Transcriptional analysis of patient specimens demonstrates the prognostic significance of these lineage subtypes. Additionally, we delineate strategies to enhance targeted therapies or to overcome resistance in cell lines with key driver gene mutations. Furthermore, clustering based on dependencies and proteomics data elucidates unexpected functional relationships, including a BTC subgroup with partial squamous differentiation. Thus, this cell line atlas reveals potential therapeutic targets in molecularly defined BTCs, unveils biologically distinct disease subtypes, and offers a vital resource for BTC research.

Electrochemical sensing at the fingertips: Wearable glove-based sensors for detection of 4-nitrophenol, picric acid and diazepam.

A wearable glove-based sensor is a portable and practical approach for onsite detection/monitoring of a variety of chemical threats. Herein, we report a flexible and sensitive wearable sensor fabricated on the nitrile glove fingertips by stencil-printing technique. The working electrodes were modified with multiwalled carbon nanotubes (MWCNTs)/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) for sensitive and real-time analyses of hazardous or chemical treats, as picric acid (PA) explosive, diazepam (DZ) as drug-facilitated crimes and the emerging pollutant 4-nitrophenol (4-NP). The multi-sensing platform towards PA, 4-NP, and DZ offers the ability of in-situ qualitative and quantitative analyses of powder and liquid samples. A simple sampling by touching or swiping the fingertip sensor on the sample or surface under investigation using an ionic hydrogel combined with fast voltammetry measurement provides timely point-of-need analyses. The wearable glove-based sensor uses the square wave voltammetry (SWV) technique and exhibited excellent performance to detect PA, 4-NP, and DZ, resulting in limits of detection (LOD) of 0.24 µM, 0.35 µM, 0.06 µM, respectively, in a wide concentration range (from 0.5 µM to 100 µM). Also, we obtained excellent manufacturing reproducibility with relative standard deviations (RSD) in the range of 3.65%-4.61% using 7 different wearable devices (n = 7) and stability in the range of 4.86%-6.61% using different electrodes stored for 10 days at room temperature (n = 10), demonstrating the excellent sensor-to-sensor reproducibility and stability for reliable in-field measurements. The stretchable sensor presented great mechanical robustness, supporting up to 80 bending or stretching deformation cycles without significant voltammetric changes. Collectively, our wearable glove-based sensor may be employed for analyses of chemical contaminants of concern, such as explosives (PA), drugs (DZ), and emerging pollutants (4-NP), helping in environmental and public safety control.

Has Management of Intrahepatic Cholangiocarcinoma Evolved with the Evidence? Trends and Practice Patterns from the National Cancer Database.

BACKGROUND: Management of intrahepatic cholangiocarcinoma (IHC) has advanced in recent decades, including randomized trial evidence supporting systemic therapy in the palliative and adjuvant setting. Mounting observational evidence suggests resection of IHC with multifocal disease (IHC-MF) or lymph node metastasis (IHC-LNM) should be limited. It is unknown how real-world practice has evolved in light of research advances. This study characterizes trends in management and outcomes of IHC without distant metastasis. METHODS: We queried the National Cancer Database (NCDB) for patients treated for IHC without distant metastasis (M0) and identified subgroups with lymph node (cN1) or multifocal hepatic involvement (cT2b). Two-sided Cochran-Armitage tests evaluated trends in initial treating modality and perioperative chemotherapy. Logistic regression evaluated associations with choice of initial treating modality. Overall survival (OS) was evaluated by using Kaplan-Meier methods. RESULTS: Between 2004 and 2020, 11,368 patients were treated for IHC without extrahepatic metastasis. Forty-three percent underwent resection. Initial management shifted from resection towards radiation or systemic therapy in IHC-MF and IHC-LNM. Use of perioperative chemotherapy increased from 39% pre-2010 to 70% in 2018-2020 (p < 0.001), most often delivered postoperatively. Across the entire cohort, median OS improved from 16 (95% confidence interval [CI] 15-18) to 27 months (95% CI 26-29). More modest improvements were observed in IHC-MF and IHC-LNM. CONCLUSIONS: Use of perioperative chemotherapy has been widely adopted, predating randomized trial evidence in the adjuvant setting. Initial management of IHC-MF and IHC-LNM has shifted from resection to systemic and/or radiation therapy. While OS has improved overall, outcomes of IHC-MF and IHC-LNM remain poor, warranting further investigation.

Case of a CIC::DUX4 fusion gene in a vascular neoplasm extends the spectrum of CIC-rearranged sarcomas.

CIC-rearranged sarcomas comprise a group of exceptionally aggressive round-cell sarcomas. These tumors most commonly demonstrate CIC::DUX4 fusion and show similar histopathology to Ewing sarcomas, though lesions mimicking vascular neoplasms have recently been described. Here, we describe a case of a patient with CIC::DUX4 fusion sarcoma identified using RNA-based molecular testing who was initially diagnosed with an endothelial neoplasm. The tumor showed extensive vasoformative growth, complete WT1 negativity, and global positive staining for ERG, CD31, and DUX4 by immunohistochemistry. Methylation testing of the tumor clustered more closely with angiosarcomas than with CIC-rearranged sarcomas. Our findings suggest that CIC::DUX4 fused neoplasms may demonstrate a more diverse phenotypic range than previously appreciated and offer evidence that both molecular and immunohistochemical studies are needed for accurate diagnosis.

The benefits of preoperative smoking cessation on abdominal wall reconstruction outcomes: An examination of abstinent versus never smokers.

INTRODUCTION: Active smoking is related to wound and respiratory complications following abdominal wall reconstruction (AWR), but no AWR studies directly compare outcomes of abstinent-smokers (AS), fulfilling four-weeks of smoking cessation, to non-smokers (NS). METHODS: Prospectively maintained institutional database was queried for all AWR between 2012 and 2019. AS and NS were included. Primary outcomes were wound and respiratory complications; secondary outcome was recurrence. Standard statistical analyses were performed. RESULTS: Evaluation included 1088 patients, 305 AS and 783 NS. AS had a lower BMI (31.3 vs 32.7 â€‹kg/m2; P â€‹= â€‹0.004) but increased ASA Class III (51.5% vs 34.5 â€‹%, P â€‹= â€‹0.009), COPD (8.9% vs 4.0 â€‹%, P â€‹= â€‹0.001), comorbidities (6.3 vs 4.7, P < 0.001), and wound class (Class III/IV: 25.3% vs 15.8 â€‹%, P â€‹= â€‹0.003). AS had increased defect size (229 vs 209.1 â€‹cm2; P â€‹= â€‹0.023), use of component separation (CST) (52.5% vs 43.8 â€‹%; P â€‹= â€‹0.010) and hospital stay (6.6 vs 6.2 days, P â€‹= â€‹0.015). Postoperative wound, mesh, and pulmonary infection, respiratory failure, and recurrence were similar. On multivariable regression, wound class and complications predicted recurrence. BMI, panniculectomy and CST predicted wound complications. BMI, CST, and wound class predicted respiratory complications. CONCLUSION: Despite greater patient and hernia complexity, smoking cessation appears to result in similar outcomes to never-smokers in this AWR population.

Identification of neural-relevant toxcast high-throughput assay intended gene targets: Applicability to neurotoxicity and neurotoxicant putative molecular initiating events.

The US EPA's Toxicity Forecaster (ToxCast) is a suite of high-throughput in vitro assays to screen environmental toxicants and predict potential toxicity of uncharacterized chemicals. This work examines the relevance of ToxCast assay intended gene targets to putative molecular initiating events (MIEs) of neurotoxicants. This effort is needed as there is growing interest in the regulatory and scientific communities about developing new approach methodologies (NAMs) to screen large numbers of chemicals for neurotoxicity and developmental neurotoxicity. Assay gene function (GeneCards, NCBI-PUBMED) was used to categorize gene target neural relevance (1 = neural, 2 = neural development, 3 = general cellular process, 3 A = cellular process critical during neural development, 4 = unlikely significance). Of 481 unique gene targets, 80 = category 1 (16.6 %); 16 = category 2 (3.3 %); 303 = category 3 (63.0 %); 97 = category 3 A (20.2 %); 82 = category 4 (17.0 %). A representative list of neurotoxicants (548) was researched (ex. PUBMED, PubChem) for neurotoxicity associated MIEs/Key Events (KEs). MIEs were identified for 375 compounds, whereas only KEs for 173. ToxCast gene targets associated with MIEs were primarily neurotransmitter (ex. dopaminergic, GABA)receptors and ion channels (calcium, sodium, potassium). Conversely, numerous MIEs associated with neurotoxicity were absent. Oxidative stress (OS) mechanisms were 79.1 % of KEs. In summary, 40 % of ToxCast assay gene targets are relevant to neurotoxicity mechanisms. Additional receptor and ion channel subtypes and increased OS pathway coverage are identified for potential future assay inclusion to provide more complete coverage of neural and developmental neural targets in assessing neurotoxicity.

Area Deprivation and Disease Severity in Adult Patients With Discoid Lupus Erythematosus.

Importance: The association of area deprivation with outcomes in discoid lupus erythematosus (DLE) remains poorly understood. Objective: To determine the association between US Census block measures of deprivation and disease severity in adult patients with DLE. Design, Setting, and Participants: This cross-sectional study included 154 patients with DLE seen between January 1, 2007, and January 1, 2024, at a single-center referral-based specialty rheumatologic-dermatology clinic in Philadelphia, Pennsylvania. Patients were aged 18 to 73 years and were enrolled in the University of Pennsylvania's Cutaneous Lupus Erythematosus Database study. Data were analyzed between January 1, 2024, and May 8, 2024. Exposures: Residence in a highly disadvantaged area as geocoded by a state area deprivation index (ADI). Main Outcomes and Measures: The main outcome was DLE disease severity as codified by the validated Cutaneous Lupus Erythematosus Disease Area and Severity Index (CLASI) damage and activity scores. Results: A total of 154 adult patients with DLE (128 women [83%] and 26 men [17%]; mean [SD] age, 43 [13] years; 6 [4%] Asian individuals, 98 [64%] Black individuals, 2 [1%] Hispanic individuals, 46 [30%] White individuals, and 2 individuals [1%] with other race or ethnicity; 78 [51%] with an ADI >5; 43 who currently smoked [28%];and 56 [36%] with concurrent systemic lupus erythematosus) were included in the analysis. By multivariable logistic regression, residence within communities with an ADI greater than 5 was associated with nearly 4-fold greater odds of moderate to severe damage (odds ratio [OR], 3.90; 95% CI, 1.27-12.69] and activity (OR, 3.31; 95% CI, 1.27-9.44). Concurrent cigarette smoking was similarly associated with greater odds of moderate to severe damage (OR, 3.15; 95% CI, 1.09-10.29). After controlling for ADI and other confounders, race was not significantly associated with DLE disease severity. Conclusions and Relevance: The results of this cross-sectional study suggest that geospatial disadvantage is associated with DLE disease severity independent of race. This invites a paradigm shift that considers the social context within which racial disparities are observed, highlighting the potential for geographically targeted interventions and policy changes to improve patient outcomes in DLE.

Exploring the efficacy of pyrethroid incorporated nets for the control of stored product moth species: immediate and delayed effects on Ephestia kuehniella and Plodia interpunctella (Lepidoptera: Pyralidae).

Insect pests pose a significant threat to stored commodities, necessitating the exploration of alternative pest management strategies. Long-lasting insecticide-incorporated nets (LLINs) have emerged as a promising tool, offering selectivity and reduced ecological impact compared to conventional chemical approaches. However, their efficacy against Ephestia kuehniella Zeller and Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae), cosmopolitan stored product moth species, has remained underexplored. This study investigated the immediate and delayed effects of 2 commercial pyrethroid-incorporated nets, Carifend (0.34% α-cypermethrin) and D-Terrence (0.4% deltamethrin), on the adult and larval stages. Both LLINs demonstrated high efficacy in controlling E. kuehniella and P. interpunctella, with mortality rates reaching up to 100% depending on exposure and post-exposure durations. Particularly, rapid knockdown was observed with D-Terrence net inducing 100% of adults in P. interpunctella after 30 min exposure. LLINs achieved almost 100% immediate mortality rate against adults after just 1 day of exposure. In addition, immediate rates of affected individuals reached as high as 81% and 91% in E. kuehniella and P. interpunctella larvae, respectively, following just 5 h of exposure to the D-Terrence. Different responses were observed between the adult and larval stages, with larvae exhibiting higher tolerance and potential for recovery from the affected phase after short exposures. There were increasing mortality rates after greater exposure to LLIN. Findings highlight the potential of LLINs as a pest management tool in storage facilities against these important stored product moths. Understanding the responses between life stages and the significance of delayed effects is crucial for optimizing LLIN deployment strategies.

Identification of 6-Anilino Imidazo[4,5-c]pyridin-2-ones as Selective DNA-Dependent Protein Kinase Inhibitors and Their Application as Radiosensitizers.

The dominant role of non-homologous end-joining in the repair of radiation-induced double-strand breaks identifies DNA-dependent protein kinase (DNA-PK) as an excellent target for the development of radiosensitizers. We report the discovery of a new class of imidazo[4,5-c]pyridine-2-one DNA-PK inhibitors. Structure-activity studies culminated in the identification of 78 as a nM DNA-PK inhibitor with excellent selectivity for DNA-PK compared to related phosphoinositide 3-kinase (PI3K) and PI3K-like kinase (PIKK) families and the broader kinome, and displayed DNA-PK-dependent radiosensitization of HAP1 cells. Compound 78 demonstrated robust radiosensitization of a broad range of cancer cells in vitro, displayed high oral bioavailability, and sensitized colorectal carcinoma (HCT116/54C) and head and neck squamous cell carcinoma (UT-SCC-74B) tumor xenografts to radiation. Compound 78 also provided substantial tumor growth inhibition of HCT116/54C tumor xenografts in combination with radiation. Compound 78 represents a new, potent, and selective class of DNA-PK inhibitors with significant potential as radiosensitizers for cancer treatment.

Extrahepatic Cholangiocarcinoma: Genomic Variables Associated With Anatomic Location and Outcome.

PURPOSE: This study aimed to define genomic differences between perihilar cholangiocarcinoma (PCA) and distal cholangiocarcinoma (DCA) and identify genomic determinants of survival. MATERIALS AND METHODS: Consecutive patients with ECA with tissue for targeted next-generation sequencing were analyzed, stratified by anatomic site (PCA/DCA), disease extent, and treatment. Associations between genomic alterations, clinicopathologic features, and outcomes were analyzed using Cox proportional hazards regression to compare survival. RESULTS: In total, 224 patients diagnosed between 2004 and 2022 (n = 127 PCA; n = 97 DCA) met inclusion criteria. The median survival was 29 months (43 after resection and 17 from diagnosis for unresectable disease). Compared with PCA, DCA was enriched in TP53alt (alterations; 69% v 33%; Q < 0.01), epigenetic pathway alterations (45% v 29%; Q = 0.041), and had more total altered pathways (median 3 v 2; Q < 0.01). KRASalt frequency was similar between PCA (36%) and DCA (37%); however, DCA was enriched in KRAS G12D (19% v 9%; P = .002). No other clinicopathologic or genomic variables distinguished subtypes. In resected patients, no genomic alterations were associated with outcome. However, in unresectable patients, CDKN2Aalt (hazard ratio [HR], 2.59 [1.48 to 4.52]) and APCalt (HR, 5.11 [1.96 to 13.3]) were associated with reduced survival. For the entire cohort, irresectability (HR, 3.13 [2.25 to 4.36]), CDKN2Aalt (HR, 1.80 [1.80 to 2.68]), and APCalt (HR, 2.00 [1.04 to 3.87]) were associated with poor survival. CONCLUSION: CDKN2Aalt and APCalt were associated with poor survival in ECA, primarily in advanced disease. As PCA and DCA were genetically similar, coanalysis of PCA and DCA in future genomic studies is reasonable.

Precision arbovirus serology with a pan-arbovirus peptidome.

Arthropod-borne viruses represent a crucial public health threat. Current arboviral serology assays are either labor intensive or incapable of distinguishing closely related viruses, and many zoonotic arboviruses that may transition to humans lack any serologic assays. In this study, we present a programmable phage display platform, ArboScan, that evaluates antibody binding to overlapping peptides that represent the proteomes of 691 human and zoonotic arboviruses. We confirm that ArboScan provides detailed antibody binding information from animal sera, human sera, and an arthropod blood meal. ArboScan identifies distinguishing features of antibody responses based on exposure history in a Colombian cohort of Zika patients. Finally, ArboScan details epitope level information that rapidly identifies candidate epitopes with potential protective significance. ArboScan thus represents a resource for characterizing human and animal arbovirus antibody responses at cohort scale.

Association of neighborhood disadvantage with cognitive function and cortical disorganization in an unimpaired cohort.

Objective: Neighborhood disadvantage is associated with worse health and cognitive outcomes. Morphological similarity network (MSN) is a promising approach to elucidate cortical network patterns underlying complex cognitive functions. We hypothesized that MSNs could capture intricate changes in cortical patterns related to neighborhood disadvantage and cognitive function, potentially explaining some of the risk for later life cognitive impairment among individuals who live in disadvantaged contexts. Methods: This cross-sectional study included cognitively unimpaired participants (n=524, age=62.96±8.377, gender (M:F)=181:343, ADI(L:H) =450,74) from the Wisconsin Alzheimer's Disease Research Center or Wisconsin Registry for Alzheimer's Prevention. Neighborhood disadvantage status was obtained using the Area Deprivation Index (ADI). Cognitive performance was assessed through six tests evaluating memory, executive functioning, and the modified preclinical Alzheimer's cognitive composite (mPACC). Morphological Similarity Networks (MSN) were constructed for each participant based on the similarity in distribution of cortical thickness of brain regions, followed by computation of local and global network features. We used linear regression to examine ADI associations with cognitive scores and MSN features. The mediating effect of MSN features on the relationship between ADI and cognitive performance was statistically assessed. Results: Neighborhood disadvantage showed negative association with category fluency, implicit learning speed, story recall and mPACC scores, indicating worse cognitive function among those living in more disadvantaged neighborhoods. Local network features of frontal and temporal brain regions differed based on ADI status. Centrality of left lateral orbitofrontal region showed a partial mediating effect between association of neighborhood disadvantage and story recall performance. Conclusion: Our findings suggest differences in local cortical organization by neighborhood disadvantage, which also partially mediated the relationship between ADI and cognitive performance, providing a possible network-based mechanism to, in-part, explain the risk for poor cognitive functioning associated with disadvantaged neighborhoods. Future work will examine the exposure to neighborhood disadvantage on structural organization of the brain.

uafR: An R package that automates mass spectrometry data processing.

Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/µl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.