Single-cell quantification of ribosome occupancy in early mouse development.

Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.

Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges.

Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).

ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation.

MOTIVATION: The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. The lack of well-validated bioinformatic pipelines for CH calling may contribute to lack of reproducibility in studies of CH. RESULTS: Here, we developed ArCH, an Artifact filtering Clonal Hematopoiesis variant calling pipeline for detecting single nucleotide variants and short insertions/deletions by combining the output of four variant calling tools and filtering based on variant characteristics and sequencing error rate estimation. ArCH is an end-to-end cloud-based pipeline optimized to accept a variety of inputs with customizable parameters adaptable to multiple sequencing technologies, research questions, and datasets. Using deep targeted sequencing data generated from six acute myeloid leukemia patient tumor: normal dilutions, 31 blood samples with orthogonal validation, and 26 blood samples with technical replicates, we show that ArCH improves the sensitivity and positive predictive value of CH variant detection at low allele frequencies compared to standard application of commonly used variant calling approaches. AVAILABILITY AND IMPLEMENTATION: The code for this workflow is available at: https://github.com/kbolton-lab/ArCH.

Who Do We Fail to Rescue after Pancreatoduodenectomy? Outcomes Among >4000 Procedures Expose Windows of Opportunity.

OBJECTIVE: Our investigation on in-hospital mortality after 4474 pancreatoduodenectomies aimed to identify time-dependent risks as well as windows of opportunity to rescue patients from complications. BACKGROUND: Pancreatoduodenectomy is generally considered a safe procedure with a 1-10% perioperative mortality based on complexity and surgical volume. Yet, patients are susceptible for life-threatening complications particularly with extended resections. Recognition of distinct vulnerabilities over time while patients recover is required to permit focused monitoring, sophisticated resource allocation, and greatest surgical safety. METHODS: Patients who deceased in-hospital after pancreatoduodenectomy between 2003-2021 were retrieved from the institutional pancreatectomy registry and analyzed in detail with respect to their postoperative course. RESULTS: Among 4474 pancreatoduodenectomies, 156 patients deceased in-hospital (3.5%). When assessing root causes of mortality, we observed 3 different clusters of complications which were postpancreatectomy-specific (47.4%), visceral vasculature-associated (25.6%), or cardiopulmonary in origin (23.7%). The median times of root cause onset in the 3 categories were postoperative day (POD) 9, POD 4.5 ( P =0.008) and POD 3 ( P <0.001), and medians of in-hospital mortality were POD 31, POD 18 ( P =0.009) and POD 8 ( P <0.001), respectively. Intervals between root cause onset and mortality varied with medians of 23 days, 11 days ( P =0.017), and 1 days ( P <0.001). The 3 categories were similarly distributed between different types of surgical complexity. CONCLUSION: Postpancreatectomy-specific complications prompt almost half of in-hospital mortalities after pancreatoduodenectomy, with rather long intervals for interventions to prevent failure to rescue. In contrast, visceral vasculature-related events and cardiopulmonary complications dominate early in-hospital mortalities with short intervals until mortality, demanding rigorous management of such events or preoperative conditioning. These data externally validate a previous high-volume initiative and highlight distinct windows of opportunity to optimize perioperative safety.

Lysine-homologue substitution: Impact on antimicrobial activity and proteolytic stability of cationic stapled heptapeptides.

Numerous natural antimicrobial peptides (AMPs) exhibit a cationic amphipathic helical conformation, wherein cationic amino acids, such as lysine and arginine, play pivotal roles in antimicrobial activity by aiding initial attraction to negatively charged bacterial membranes. Expanding on our previous work, which introduced a de novo design of amphipathic helices within cationic heptapeptides using an 'all-hydrocarbon peptide stapling' approach, we investigated the impact of lysine-homologue substitution on helix formation, antimicrobial activity, hemolytic activity, and proteolytic stability of these novel AMPs. Our results demonstrate that substituting lysine with ornithine enhances both the antimicrobial activity and proteolytic stability of the stapled heptapeptide AMP series, while maintaining low hemolytic activity. This finding underscores lysine-homologue substitution as a valuable strategy for optimizing the therapeutic potential of diverse cationic AMPs.

Digitizing translucent object appearance by validating computed optical properties.

The optical properties available for an object are most often fragmented and insufficient for photorealistic rendering of the object. We propose a procedure for digitizing a translucent object with sufficient information for predictive rendering of its appearance. Based on object material descriptions, we compute optical properties and validate or adjust this object appearance model based on comparison of simulation with spectrophotometric measurements of the bidirectional scattering-surface reflectance distribution function (BSSRDF). To ease this type of comparison, we provide an efficient simulation tool that computes the BSSRDF for a particular light-view configuration. Even with just a few configurations, the localized lighting in BSSRDF measurements is useful for assessing the appropriateness of computed or otherwise acquired optical properties. To validate an object appearance model in a more common lighting environment, we render the appearance of the obtained digital twin and assess the photorealism of our renderings through pixel-by-pixel comparison with photographs of the physical object.

Belgian dietitians' knowledge, perceptions and willingness-to-recommend of genetically modified food and organisms.

BACKGROUND: Dietitians play a critical role in the public's relationship with food and are often overlooked as an important stakeholder group in the general debate about sustainable food. Genetically modified organisms (GMOs) are one type of modern food source that could contribute to a more sustainable food system. This case study is the first to examine the knowledge, perception and willingness-to-recommend (WTR) genetically modified (GM) foods by dietitians in Europe. METHODS: An online survey was addressed to all members of the Flemish Association of Dietitians (Belgium) in 2021, resulting in a sample of 98 valid responses. Multivariate linear regression included sociodemographic, knowledge, and attitudinal factors as the independent variables to explain dietitians' WTR. RESULTS: Flemish dietitians had limited knowledge of GMOs; only about half of the GM questions were answered correctly. Most dietitians (53%-76%) would recommend GMOs with positive effects on human nutrition or sustainability, whereas few dietitians (19%-27%) would recommend other GMO applications. Trust in GMO information sources and perceived GM benefits significantly influenced a positive WTR of GM foods. Predominant negative information about GM foods was significantly associated with dietitians' low trust and WTR such foods. CONCLUSIONS: Countering the predominantly negative portrayal with more neutral and factual information could improve trust, which in turn could positively influence dietitians' perceptions towards GMOs. By further examining the knowledge and perception of dietitians worldwide GMOs and gene-edited products, new insights could be could gathered into the positioning of this underexposed stakeholder group.

A robust and accurate single-cell data trajectory inference method using ensemble pseudotime.

BACKGROUND: The advance in single-cell RNA sequencing technology has enhanced the analysis of cell development by profiling heterogeneous cells in individual cell resolution. In recent years, many trajectory inference methods have been developed. They have focused on using the graph method to infer the trajectory using single-cell data, and then calculate the geodesic distance as the pseudotime. However, these methods are vulnerable to errors caused by the inferred trajectory. Therefore, the calculated pseudotime suffers from such errors. RESULTS: We proposed a novel framework for trajectory inference called the single-cell data Trajectory inference method using Ensemble Pseudotime inference (scTEP). scTEP utilizes multiple clustering results to infer robust pseudotime and then uses the pseudotime to fine-tune the learned trajectory. We evaluated the scTEP using 41 real scRNA-seq data sets, all of which had the ground truth development trajectory. We compared the scTEP with state-of-the-art methods using the aforementioned data sets. Experiments on real linear and non-linear data sets demonstrate that our scTEP performed superior on more data sets than any other method. The scTEP also achieved a higher average and lower variance on most metrics than other state-of-the-art methods. In terms of trajectory inference capacity, the scTEP outperforms those methods. In addition, the scTEP is more robust to the unavoidable errors resulting from clustering and dimension reduction. CONCLUSION: The scTEP demonstrates that utilizing multiple clustering results for the pseudotime inference procedure enhances its robustness. Furthermore, robust pseudotime strengthens the accuracy of trajectory inference, which is the most crucial component in the pipeline. scTEP is available at https://cran.r-project.org/package=scTEP .

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data.

Gene regulatory network is a complicated set of interactions between genetic materials, which dictates how cells develop in living organisms and react to their surrounding environment. Robust comprehension of these interactions would help explain how cells function as well as predict their reactions to external factors. This knowledge can benefit both developmental biology and clinical research such as drug development or epidemiology research. Recently, the rapid advance of single-cell sequencing technologies, which pushed the limit of transcriptomic profiling to the individual cell level, opens up an entirely new area for regulatory network research. To exploit this new abundant source of data and take advantage of data in single-cell resolution, a number of computational methods have been proposed to uncover the interactions hidden by the averaging process in standard bulk sequencing. In this article, we review 15 such network inference methods developed for single-cell data. We discuss their underlying assumptions, inference techniques, usability, and pros and cons. In an extensive analysis using simulation, we also assess the methods' performance, sensitivity to dropout and time complexity. The main objective of this survey is to assist not only life scientists in selecting suitable methods for their data and analysis purposes but also computational scientists in developing new methods by highlighting outstanding challenges in the field that remain to be addressed in the future development.

Racial and ethnic differences in reported haemophilia death rates in the United States.

INTRODUCTION: People with haemophilia's life expectancies have improved over time. Whether progress has been experienced equitably is unknown. AIM: To examine recorded haemophilia death (rHD) rates according to race and ethnicity in the United States (US). METHODS: In this cohort study, rHDs were examined with US National Vital Statistics' 1999-2020 Multiple Cause-of-Death data. rHD was defined as having a haemophilia A (D66) or B (D67) ICD-10 code in the death certificate (underlying or multiple causes of death). Age-adjusted rHD rates were compared with age-adjusted rate ratios (aRR) and 95% Confidence Intervals (CI). RESULTS: There were 3115 rHDs in males with an rHD rate of 0.98 per 1 million males. Between 1999 and 2020, rHD rates declined by 46% in NH (Non-Hispanic) White, 44% in NH Black (aRR = 0.56, 95%CI 0.43, 0.74), and 42% in Hispanic (aRR = 0.58, 95%CI 0.39, 0.88) males. However, rHD rates remained higher and were on average 30% greater in NH Black versus NH White males (aRR = 1.30 95% CI 1.16, 1.46). Among males with rHD, the median age at death rose from 54.5 to 65.5 years between 1999 and 2020 and was 12 years lower in NH Black (56 years) versus NH White (68 years) males in 2010-2020. There were 930 females with rHD, with an age-adjusted rate of 0.22 per 1 million females, which was consistent between 1999 and 2020. CONCLUSION: Reported haemophilia-death rates improved in males across all race/ethnicities, but rates were higher Black versus White males. Given the inherent limitations of the current study's data source, further investigation of survival rates and disparities in haemophilia are needed.

Cross-sectional study evaluating the association of haemophilia-related distress and clinically relevant outcomes.

INTRODUCTION: In chronic diseases, disease-related distress can impact disease outcomes. Distress and haemophilia-related distress has been demonstrated in people with haemophilia (PwH). The association of haemophilia-related distress on disease outcomes among PwH is unknown. AIM: To study the association of haemophilia-related distress with haemophilia specific outcomes, including adherence to prophylactic therapy, the presence of a target joint, healthcare utilization and work-impairment. METHODS: In a cross-sectional study, adults with haemophilia A or B were enrolled in a study to validate the haemophilia-related distress questionnaire (HRDq). In this planned analysis, univariate and multivariate associations between the HRDq total score and disease outcomes were explored. RESULTS: The 114 participants in this analysis were male, mostly with haemophilia A (92%) and severe disease (52%) with a median age of 31.9 years. On univariate analysis, HRDq total score (5-point change) was associated with the presence of a target joint (P = .002), high healthcare utilization (P = .011), poor adherence (P = .033) and work-impairment (P ≤ .001). After adjustment for age, race, severity and other potential confounders, adherence (aß 0.33, 95% CI .17, .49) and work-impairment (aß 4.69, 95% CI 3.27-6.1) remained statistically significantly associated with HRDq total score. CONCLUSION: Haemophilia-related distress is associated with poor adherence to factor prophylaxis and work-impairment. The direction of the association (causation) is yet to be determined and requires future study.

Coma Recovery Scale-Revised Predicts Disability Rating Scale in Acute Rehabilitation of Severe Traumatic Brain Injury.

OBJECTIVE: To explore the prognostic value of the Coma Recovery Scale-Revised (CRS-R) in predicting disability outcomes in patients with severe traumatic brain injury using the Disability Rating Scale (DRS). DESIGN: Secondary analysis including linear and logistic regressions were performed. SETTING: Data were collected in a previous clinical trial. PARTICIPANTS: One hundred eighty-four participants across 3 countries (N=184). MAIN OUTCOME MEASURES: Disability Rating Scales. RESULTS: Analyses showed an inverse relation between CRS-R scores obtained at baseline and change in DRS scores at 6 weeks. Similarly, changes in CRS-R scores between baseline and 4 weeks were also found to have an inverse relation to change in DRS scores at 6 weeks. CONCLUSIONS: This study generates a tool that can be used to predict the probability that a patient with severe traumatic brain injury lands in 1 of 3 disability categories. The CRS-R may be useful in prognostication of disability in patients with severe traumatic brain injury.

CPA: a web-based platform for consensus pathway analysis and interactive visualization.

In molecular biology and genetics, there is a large gap between the ease of data collection and our ability to extract knowledge from these data. Contributing to this gap is the fact that living organisms are complex systems whose emerging phenotypes are the results of multiple complex interactions taking place on various pathways. This demands powerful yet user-friendly pathway analysis tools to translate the now abundant high-throughput data into a better understanding of the underlying biological phenomena. Here we introduce Consensus Pathway Analysis (CPA), a web-based platform that allows researchers to (i) perform pathway analysis using eight established methods (GSEA, GSA, FGSEA, PADOG, Impact Analysis, ORA/Webgestalt, KS-test, Wilcox-test), (ii) perform meta-analysis of multiple datasets, (iii) combine methods and datasets to accurately identify the impacted pathways underlying the studied condition and (iv) interactively explore impacted pathways, and browse relationships between pathways and genes. The platform supports three types of input: (i) a list of differentially expressed genes, (ii) genes and fold changes and (iii) an expression matrix. It also allows users to import data from NCBI GEO. The CPA platform currently supports the analysis of multiple organisms using KEGG and Gene Ontology, and it is freely available at http://cpa.tinnguyen-lab.com.

Genetic variations of antioxidant genes and their association with male infertility in Vietnamese men.

BACKGROUND: Antioxidant genes, such as superoxide dismutase (SOD), catalase (CAT), and nitric oxide synthase (NOS), play critical roles in spermatogenesis and sperm functions. Polymorphisms of antioxidant genes have been shown to be strongly associated with sperm quality which affects male fertility. METHODS: To investigate the association of antioxidant gene polymorphisms to male infertility in Vietnamese men, in this case-control study, using Sanger sequencing, we genotyped four variants SOD1:7958G>A, SOD2:c.47T>C, CAT:-262C>T, and NOS3:-786C>T. RESULTS AND CONCLUSIONS: We identified SOD1:7958GA genotype and NOS3:-786CT genotype in the infertility group were significantly higher than in the control with OR = 2.191 (95% CI: 1.226-3.915, p = 0.004) and OR = 3.135 (95% CI: 1.591-6.180, p < 0.001), respectively. We also detected that the frequency of the SOD2:c.47TC genotype was significantly higher in the male infertility group than in fertile men (OR = 1.941, 95% CI: 1.063-3.595, p = 0.029). Gene-gene interactions between the SNPs of SOD1, SOD2, and CAT might increase the risk of male infertility patients. In particular, patients carrying the SOD1:GA+AA, SOD2:TC+CC, and CAT:CT/TT genotype pattern have an increased risk of male infertility (OR = 7.614, p = 0.007). To our knowledge, this is the first study to evaluate the association between the SOD1:7958G>A polymorphism and male infertility. Further studies with larger sample sizes and more genes are needed to better assess the association between variants of antioxidant genes and male infertility.

Pancreaticoduodenectomy combined gastroduodenal collateral reconstruction and preservation due to median arcuate ligament syndrome: technical notes with two surgical cases report (with video).

INTRODUCTION: Pancreaticoduodenectomy in patients with CA stenosis due to median arcuate ligament often required carefully collateral pathways management to avoid hepatic ischemic complications. CASES PRESENTATION: Case 1: A 63-year-old man was referred to our department because of jaundice with distal common bile duct tumor. Pancreaticoduodenectomy with left posterior SMA first approach and circumferential lymphadenectomy was performed. Case 2: A 48-year-old man was referred to our department because of right-upper-quadrant abdominal pain with Vater tumor. Laparoscopic pancreaticoduodenectomy with left posterior SMA first approach and circumferential lymphadenectomy was performed. Postoperatively, in all two cases, three-dimensional reconstruction images showed developed collateral pathways around the pancreatic head, and the CA was stenosis in 75% and 70% due to MAL, respectively. Intraoperatively, in all two cases, we confirmed poor blood flow in the common hepatic artery (CHA) by palpation and observation. So that in the first case, we have decided to proceed a no-touch technique of GDA segmental resection en bloc with the tumor and reconstructed with an end-to-end GDA anastomosis; in the second cases, we have decided to proceed gastroduodenal collateral preservation. When preserving these collateral pathways, we confirmed that the PHA flow remained pulsatile as an indicator that the blood flow was adequate. CONCLUSION: Celiac axis stenosis was a rare but difficult-to-managed condition associated with pancreaticoduodenectomy. Collateral pathways management depends on variety of collateral pathways.

Blessing of the moon: cultural beliefs, birth timing and child health in Nepal.

In many South Asian contexts, specific dates are auspicious and inauspicious for health-related behaviours and outcomes. This study analysed the effect of lunar date-related auspicious beliefs in Nepal on childbirths and neonatal health outcomes. Using the daily birth records from a tertiary maternity hospital, we empirically examined whether births occurred disproportionally around full moon days. We found an average of 10.7 extra births on and before full moon days, with an average of 7.5 extra Caesarean deliveries on full moon days. We demonstrated that births occurring on or before the full moon day have poor neonatal health outcomes. However, a subsample analysis suggested better health outcomes for low-risk mothers and worse health outcomes for high-risk mothers. These findings suggest that low-risk mothers may move their deliveries to auspicious dates with fewer complications than high-risk mothers. The results emphasise the need for additional research to distinguish health service demand from supply influences on birth timing in Nepal.

European stakeholders' perspectives on implementation potential of precision weed control: the case of autonomous vehicles with laser treatment.

Weed control is a basic agricultural practice, typically achieved through herbicides and mechanical weeders. Because of the negative environmental impacts of these tools, alternative solutions are being developed and adopted worldwide. Following recent technical developments, an autonomous laser-based weeding system (ALWS) now offers a possible solution for sustainable weed control. However, beyond recent proof of performance, little is known about the adoption potential of such a system. This study assesses the adoption potential of ALWS, using a mixed-method approach. First, six macro-environmental factors regarding the adoption of ALWS were determined. This assessment is referred to as a Political, Economic, Social, Technological, Legal, Environmental (PESTLE) analysis and is conducted in a form of a literature review initiated by expert consultations. Second, a range of European stakeholders' perceptions of ALWS was evaluated in four focus-group discussions (n = 55), using a strengths, weaknesses, opportunities, threats (SWOT) analysis. The factors identified in the PESTLE and SWOT analyses were subsequently merged to provide a comprehensive overview of the adoption potential of ALWS. Labour reduction, precision treatment and environmental sustainability were found to be the most important advantages of ALWS. High costs and performance uncertainty were identified as the main weaknesses. To promote the adoption of ALWS, this study recommends the following: (1) Concrete performance results, both technical and economic, should be communicated to farmers. (2) Farmers' knowledge of precision agriculture should be improved. (3) Advantage should be taken of policies that are favourable towards non-chemical methods and the high demand for organic products. This article also extensively discusses regulatory barriers, the risks posed to the safety of both humans and the machines involved, technological challenges and requirements, and policy recommendations related to ALWS adoption.

Community-wide Screening for Tuberculosis in a High-Prevalence Setting.

BACKGROUND: The World Health Organization has set ambitious targets for the global elimination of tuberculosis. However, these targets will not be achieved at the current rate of progress. METHODS: We performed a cluster-randomized, controlled trial in Ca Mau Province, Vietnam, to evaluate the effectiveness of active community-wide screening, as compared with standard passive case detection alone, for reducing the prevalence of tuberculosis. Persons 15 years of age or older who resided in 60 intervention clusters (subcommunes) were screened for pulmonary tuberculosis, regardless of symptoms, annually for 3 years, beginning in 2014, by means of rapid nucleic acid amplification testing of spontaneously expectorated sputum samples. Active screening was not performed in the 60 control clusters in the first 3 years. The primary outcome, measured in the fourth year, was the prevalence of microbiologically confirmed pulmonary tuberculosis among persons 15 years of age or older. The secondary outcome was the prevalence of tuberculosis infection, as assessed by an interferon gamma release assay in the fourth year, among children born in 2012. RESULTS: In the fourth-year prevalence survey, we tested 42,150 participants in the intervention group and 41,680 participants in the control group. A total of 53 participants in the intervention group (126 per 100,000 population) and 94 participants in the control group (226 per 100,000) had pulmonary tuberculosis, as confirmed by a positive nucleic acid amplification test for Mycobacterium tuberculosis (prevalence ratio, 0.56; 95% confidence interval [CI], 0.40 to 0.78; P<0.001). The prevalence of tuberculosis infection in children born in 2012 was 3.3% in the intervention group and 2.6% in the control group (prevalence ratio, 1.29; 95% CI, 0.70 to 2.36; P = 0.42). CONCLUSIONS: Three years of community-wide screening in persons 15 years of age or older who resided in Ca Mau Province, Vietnam, resulted in a lower prevalence of pulmonary tuberculosis in the fourth year than standard passive case detection alone. (Funded by the Australian National Health and Medical Research Council; ACT3 Australian New Zealand Clinical Trials Registry number, ACTRN12614000372684.).

Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer.

Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.

Heck Reaction of 2-Oxyacrylates with Aryl Bromides: A Common Route to Monoaryl Pyruvates and Ortho Ester-Protected Monoaryl Pyruvates.

A palladium-catalyzed Heck reaction between 2-oxyacrylates and aryl bromides was developed, where DavePhos was a unique ligand that efficiently promoted the reaction. The products, 2-oxycinnamates, served as excellent precursors, providing synthetically useful monoaryl pyruvates or ortho ester-protected monoaryl pyruvates depending on the nature of the 2-oxy group. The formation of such ortho esters via alkoxide addition is novel, and computational studies identified a plausible mechanism with an oxyallyl zwitterion as the key intermediate.