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Clinical Chemistry     Full-text available via subscription   (Followers: 53, SJR: 2.281, CiteScore: 3)
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Clinical Chemistry
Journal Prestige (SJR): 2.281
Citation Impact (citeScore): 3
Number of Followers: 53  
 
  Full-text available via subscription Subscription journal
ISSN (Print) 0009-9147 - ISSN (Online) 1530-8561
Published by AACC Homepage  [1 journal]
  • Liquid Biopsy to Catch the Epigenetic Changes in Endometrial Cancer

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      Authors: Alix-Panabières C; Pantel K.
      Pages: 745 - 747
      Abstract: The liquid biopsy (LB) concept was introduced and coined for the first time in 2010 (1) for circulating tumor cells and rapidly extended to other circulating biomarkers such as circulating tumor DNA (ctDNA), circulating cell-free RNA (noncoding and messenger RNA), extracellular vesicles (exosomes), circulating microRNA, and tumor-educated platelets, as well as the immune cells (2). Moreover, this concept has been expanded to other body fluids, including urine, cerebrospinal fluid, bone marrow, saliva, or sputum (2).
      PubDate: Thu, 24 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac043
      Issue No: Vol. 68, No. 6 (2022)
       
  • Repeat Expansion Disorders: Bridging the Gap

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      Authors: Kirk EP.
      Pages: 748 - 750
      Abstract: There are nearly 50 known genetic conditions that can be described as repeat expansion disorders (1). The defining characteristic of such conditions is a mutational mechanism (often the only known mutational mechanism) which is an increase in the size of a repeated DNA motif. Most commonly, this is a triplet repeat, but some conditions have larger repeated sequences, with the longest identified to date being a 24-base octapeptide repeat in exon 2 of PRNP (2). Most, but not all, repeat expansion disorders have neurological phenotypes as their main or only manifestation.
      PubDate: Wed, 01 Jun 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac047
      Issue No: Vol. 68, No. 6 (2022)
       
  • Taking the Next Step in Metagenomic Infectious Disease Diagnostics

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      Authors: Gaston D; Simner P.
      Pages: 751 - 753
      Abstract: molecular diagnosticsmicrobiologyinfectious disease
      PubDate: Sat, 12 Feb 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac007
      Issue No: Vol. 68, No. 6 (2022)
       
  • Women in Laboratory Medicine: A Q&A on Diversity and Inclusion

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      Authors: Ayala-Lopez N; Peck Palmer O, Parnas M, et al.
      Pages: 754 - 760
      Abstract: Women leaders and scientists have made significant contributions to laboratory medicine. Notably, 2 women, Mary H. McKenna and Miriam Reiner, were among the 9 founders of AACC in 1948; however, women in clinical chemistry still encounter biases and microaggressions. A concern is how these obstacles impact women’s progression through their career. Representation of women in leadership positions is low, and many women experience gender bias. Thus, there is still work to be done to address the challenges women face in their careers in medicine.
      PubDate: Fri, 20 May 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac068
      Issue No: Vol. 68, No. 6 (2022)
       
  • Fetomaternal Microchimerism and Amniotic Fluid Stem Cells: The Current
           State of Knowledge

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      Authors: Rosner M; Hengstschläger M.
      Pages: 761 - 764
      Abstract: During gestation, fetal cells migrating into the mother’s body can contribute to the regeneration of maternal tissues. Recent publications round out the overall view that fetal stem cells from the amniotic fluid could be an origin of this phenomenon.
      PubDate: Wed, 01 Jun 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac056
      Issue No: Vol. 68, No. 6 (2022)
       
  • Perplexingly High Tacrolimus Concentrations in a Renal Transplant Patient
           with HIV

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      Authors: Higgins V; Kapur B, Beriault D, et al.
      Pages: 765 - 768
      PubDate: Thu, 31 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac062
      Issue No: Vol. 68, No. 6 (2022)
       
  • Commentary on Perplexingly High Tacrolimus Concentrations in a Renal
           Transplant Patient with HIV

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      Authors: Goyal N.
      Pages: 768 - 769
      Abstract: The authors describe a 56-year-old female, with a history of HIV/22, treated with the protease inhibitors ritonavir and darunavir, who developed critically high tacrolimus concentrations following introduction of the drug in the early post-transplant period. Tacrolimus, a calcineurin inhibitor (CNI), is primarily metabolized in the intestine and liver by CYP3A4, whose activity is severely inhibited by protease inhibitors. In evaluating potential transplant recipients, it is always important to perform a careful review of prescription and over-the-counter medications because of the narrow therapeutic index of immunosuppression medications and risk of drug–drug interactions. This approach is especially important in patients with HIV because of the significant interaction of antiretrovirals with CNIs and mammalian target of rapamycin (mTOR) inhibitors, the backbone of transplant immunosuppressive regimen. It is important to work closely with the patient’s HIV physician to find an alternative antiretroviral regimen. In cases of resistance and limited HIV treatment options, an alternative immunosuppression regimen or starting CNIs at significantly reduced doses should be considered.
      PubDate: Fri, 01 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac063
      Issue No: Vol. 68, No. 6 (2022)
       
  • Commentary on Perplexingly High Tacrolimus Concentrations in a Renal
           Transplant Patient with HIV

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      Authors: Heger N.
      Pages: 769 - 770
      Abstract: Cytochrome P450 3A5 (CYP3A5) genotype is a primary determinant of tacrolimus blood concentration (1). Extensive and intermediate metabolizers may require 1.5–2 times the recommended starting tacrolimus dose, whereas poor metabolizers can start with the standard recommended dose. CYP3A5 genotyping is generally not performed routinely, and while there is no direct evidence of improved clinical outcomes, knowing genotype prior to initiation of tacrolimus therapy achieves target concentrations more quickly than through therapeutic drug monitoring alone (1). Inducers and inhibitors of CYP3A4/5 can have profound effects on drug metabolism. The product label for extended-release tacrolimus, sold by Astellas Pharma Canada (Advagraf XL), specifically warns about the use of the CYP3A inhibitor ritonavir (prescribed to the patient as HIV-1 treatment), because it may result in tacrolimus-associated adverse reactions through increased tacrolimus blood concentrations (2).
      PubDate: Fri, 01 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac064
      Issue No: Vol. 68, No. 6 (2022)
       
  • Angiogenic Biomarkers for Risk Stratification in Women with Preeclampsia

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      Authors: Docheva N; Arenas G, Nieman K, et al.
      Pages: 771 - 781
      Abstract: AbstractBackgroundPreeclampsia is a leading cause of maternal and neonatal mortality and morbidity worldwide. Diagnosis of the condition is currently limited to utilization of nonspecific signs and symptoms. However, identification of potential pathogenic biomarkers may support earlier diagnosis and ultimately improved prognosis.ContentThe current models of preeclampsia suggest that the disease has components of abnormal placentation, a degree of angiogenic imbalance and endothelial dysfunction. Angiogenic factors such as soluble fms-like tyrosine kinase-1 and soluble endoglin increase while placental growth factor concentrations decrease in the circulation weeks before the onset of the disease. Multiple studies have looked at the capacity of angiogenic factors for the prediction of preeclampsia and adverse pregnancy outcomes.SummaryThe goal of this review is to focus on the role of angiogenic factors in the pathogenesis of preeclampsia and use of angiogenic biomarkers for risk stratification, diagnosis, and prognosis of the disease.
      PubDate: Sat, 29 Jan 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvab281
      Issue No: Vol. 68, No. 6 (2022)
       
  • Highly Specific Droplet-Digital PCR Detection of Universally Methylated
           Circulating Tumor DNA in Endometrial Carcinoma

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      Authors: Beinse G; Borghese B, Métairie M, et al.
      Pages: 782 - 793
      Abstract: AbstractBackgroundNo circulating biomarker is available for endometrial carcinoma (EC). We aimed to identify DNA positions universally hypermethylated in EC, and to develop a digital droplet PCR (ddPCR) assay for detection of hypermethylated circulating tumor DNA (meth-ctDNA) in plasma from patients with EC.MethodsDNA positions hypermethylated in EC, and without unspecific hypermethylation in tissue/cell types releasing circulating cell-free DNA in plasma, were identified in silico from TCGA/Gene Expression Omnibus (GEO) data. A methylation-specific ddPCR (meth-ddPCR) assay following bisulfite conversion of DNA extracted from plasma was optimized for detection of meth-ctDNA according to dMIQE guidelines. Performances were validated on a retrospective cohort (n = 78 tumors, n = 30 tumor-adjacent tissues), a prospective pilot cohort (n = 33 stage I–IV patients), and 55 patients/donors without cancer.ResultsHypermethylation of zinc finger and SCAN domain containing 12 (ZSCAN12) and/or oxytocin (OXT) classified EC samples from multiple noncancer samples with high diagnostic specificity/sensitivity [>97%; area under the curve (AUC) = 0.99; TCGA/GEO tissues/blood samples]. These results were confirmed in the independent retrospective cohort (AUC = 0.99). Meth-ddPCR showed a high analytical specificity (limit of blank = 2) and sensitivity (absolute lower threshold of detection = 50 pgmethDNA/mLplasma). In the pilot cohort, meth-ctDNA was detected in pretreatment plasma samples from 9/11 and 5/20 patients with advanced and non-advanced EC, respectively. 2 of 9 patients had ctDNA detected after macroscopic complete surgery and experienced progression within 6 months. No healthy donors had any copy of hypermethylated DNA detected in plasma.ConclusionsMeth-ddPCR of ZSCAN12/OXT allows a highly specific and sensitive detection of ctDNA in plasma from patients with EC and appears promising for personalized approaches for these patients.
      PubDate: Tue, 22 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac020
      Issue No: Vol. 68, No. 6 (2022)
       
  • Single-Tube Screen for Rapid Detection of Repeat Expansions in Seven
           Common Spinocerebellar Ataxias

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      Authors: Lian M; Limwongse C, Yoon C, et al.
      Pages: 794 - 802
      Abstract: AbstractBackgroundThe autosomal dominantly inherited and genetically heterogeneous spinocerebellar ataxias (SCAs) exhibit highly similar clinical presentations. Many are caused by repeat expansions, of which at least 8 involve CAG repeats. Repeat expansion detection is the only method to confirm disease status in symptomatic individuals. We present a novel strategy to simultaneously screen for the presence of CAG repeat expansion in the genes responsible for SCAs 1, 2, 3, 6, 7, 12, and dentatorubral-pallidoluysian atrophy using a simplified single-tube assay.MethodsThe method employs differentially labeled locus-specific primers and a common triplet-primed primer. Amplified products from each locus are distinguished by a combination of the product size and the fluorophore tag. The upper size limit of the normal allele range was used as the cutoff for distinguishing normal from potentially affected samples, with repeat expansion detected by presence of electrophoretic peaks extending beyond the cutoff.ResultsBlinded evaluation of the assay on 60 genotype-known DNA samples correctly detected repeat expansion in the expected SCA repeat locus for all 31 DNA samples.ConclusionsIn principle, this strategy can be applied to the simultaneous screening of any group of disease genes sharing the same repetitive units and/or their reverse complement.
      PubDate: Wed, 09 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac011
      Issue No: Vol. 68, No. 6 (2022)
       
  • The Effect of Preanalytical and Physiological Variables on Cell-Free DNA
           Fragmentation

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      Authors: van der Pol Y; Moldovan N, Verkuijlen S, et al.
      Pages: 803 - 813
      Abstract: AbstractBackgroundAssays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve the performance of liquid biopsy. However, preanalytic and physiological differences between individuals on fragmentomic analysis are poorly defined.MethodsWe analyzed the impact of collection tube, plasma processing time, and physiology on the size distribution of cfDNA, their genome-wide representation, and sequence diversity at the cfDNA fragment ends using shallow whole-genome sequencing.ResultsNeither different stabilizing collection tubes nor processing times affected the cfDNA fragment sizes, but could impact the genome-wide fragmentation patterns and fragment-end sequences of cfDNA. In addition, beyond differences depending on the gender, the physiological conditions tested between 63 individuals (age, body mass index, use of medication, and chronic conditions) minimally influenced the outcome of fragmentomic methods.ConclusionsFragmentomic approaches have potential for implementation in the clinic, pending clear traceability of analytical and physiological factors.
      PubDate: Wed, 16 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac029
      Issue No: Vol. 68, No. 6 (2022)
       
  • Using Both Plasma and Urine Donor-Derived Cell-Free DNA to Identify
           Various Renal Allograft Injuries

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      Authors: Chen X; Qiu J, Wu Z, et al.
      Pages: 814 - 825
      Abstract: AbstractBackgroundThis study was designed to investigate the association between donor-derived cell-free DNA (dd-cfDNA) and renal allograft injuries.MethodsThis single-center study enrolled 113 adult kidney transplant recipients with kidney biopsies. Plasma and urine dd-cfDNA was detected by target region capture sequencing.ResultsPlasma dd-cfDNA fraction was increased in multiple types of injuries, but most significantly in antibody-mediated rejection. Plasma dd-cfDNA fraction in isolated antibody-mediated rejection (1.94%, IQR: 1.15%, 2.33%) was higher than in T cell-mediated rejection (0.55%, IQR: 0.50%, 0.73%, P = 0.002) and negative biopsies (0.58%, IQR: 0.42%, 0.78%, P < 0.001), but lower than in mixed rejection (2.49%, IQR: 1.16%, 4.90%, P = 0.342). Increased urine dd-cfDNA concentration was associated with several types of injury, but most significantly with BK polyomavirus-associated nephropathy. Urine dd-cfDNA concentration in BK polyomavirus-associated nephropathy (12.22 ng/mL, IQR: 6.53 ng/mL, 31.66 ng/mL) was respectively higher than that in T cell-mediated rejection (5.24 ng/mL, IQR: 3.22 ng/mL, 6.99 ng/mL, P = 0.001), borderline change (3.93 ng/mL, IQR: 2.45 ng/mL, 6.30 ng/mL, P < 0.001), and negative biopsies (3.09 ng/mL, IQR: 1.94 ng/mL, 5.05 ng/mL, P < 0.001). Plasma dd-cfDNA fraction was positively associated with glomerulitis (r = 0.365, P < 0.001) and peri-tubular capillaritis (r = 0.344, P < 0.001), while urine dd-cfDNA concentration correlated with tubulitis (r = 0.302, P = 0.002).ConclusionsBoth plasma and urine dd-cfDNA are sensitive markers for renal allograft injuries. The interpretation of a specific disease by dd-cfDNA should be combined with other clinical indicators.
      PubDate: Wed, 01 Jun 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac053
      Issue No: Vol. 68, No. 6 (2022)
       
  • Optimized Sequencing Adaptors Enable Rapid and Real-Time Metagenomic
           Identification of Pathogens during Runtime of Sequencing

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      Authors: Zhang D; Zhang J, Du J, et al.
      Pages: 826 - 836
      Abstract: AbstractBackgroundMetagenomic next-generation sequencing (mNGS) offers the promise of unbiased detection of emerging pathogens. However, in indexed sequencing, the sequential paradigm of data acquisition, demultiplexing, and analysis restrain read assignment in advance and real-time analysis, resulting in lengthy turnaround time for clinical metagenomic detection.MethodsWe described the utility of internal-index adaptors with different lengths of barcode in multiplex sequencing. The base composition for each position within these adaptors was well-balanced to ensure nucleotide diversity and optimal sequencing performance and to achieve the early assignment of reads by first sequencing the barcodes. Combined with an automated library preparation device, we delivered a rapid and real-time bioinformatics pathogen identification solution for the Illumina NextSeq platform. The diagnostic performance was evaluated by testing 153 lower respiratory tract specimens using mNGS in comparison to culture, 16S/internal transcribed spacer amplicon sequencing, and additional PCR-based tests.ResultsBy calculating the average F1 scores of all read lengths under different threshold values, we established the optimal threshold for pathogens identification, and found that 36 bp was the optimal shortest read length for rapid mNGS analysis. Rapid detection had a negative percentage agreement and positive percentage agreement of 100% and 85.1% for bacteria and 97.4% and 80.3% for fungi, when compared to a composite standard. The rapid mNGS solution enabled accurate pathogen identification in about 9.1 to 10.1 h sample-to-answer turnaround time.ConclusionsOptimized internal index adaptors combined with a real-time analysis pipeline provide a potential tool for a first-line test in critically ill patients.
      PubDate: Tue, 15 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac024
      Issue No: Vol. 68, No. 6 (2022)
       
  • Analytical Validation of a Novel 6-Gene Signature for Prediction of
           Distant Recurrence in Estrogen Receptor-Positive, HER2-Negative,
           Early-Stage Breast Cancer

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      Authors: Loughman T; Barron S, Wang C, et al.
      Pages: 837 - 847
      Abstract: AbstractBackgroundOncoMasTR is a recently developed multigene prognostic test for early-stage breast cancer. The test has been developed in a kit-based format for decentralized deployment in molecular pathology laboratories. The analytical performance characteristics of the OncoMasTR test are described in this study.MethodsExpression levels of 6 genes were measured by 1-step reverse transcription-quantitative PCR on RNA samples prepared from formalin-fixed, paraffin-embedded (FFPE) breast tumor specimens. Assay precision, reproducibility, input range, and interference were determined using FFPE-derived RNA samples representative of low and high prognostic risk scores. A pooled RNA sample derived from 6 FFPE breast tumor specimens was used to establish the linear range, limit of detection, and amplification efficiency of the individual gene expression assays.ResultsThe overall precision of the OncoMasTR test was high with an SD of 0.16, which represents less than 2% of the 10-unit risk score range. Test results were reproducible across 4 testing sites, with correlation coefficients of 0.94 to 0.96 for the continuous risk score and concordance of 86% to 96% in low-/high-risk sample classification. Consistent risk scores were obtained across a > 100-fold RNA input range. Individual gene expression assays were linear up to quantification cycle values of 36.0 to 36.9, with amplification efficiencies of 80% to 102%. Test results were not influenced by agents used during RNA isolation, by low levels of copurified genomic DNA, or by moderate levels of copurified adjacent nontumor tissue.ConclusionThe OncoMasTR prognostic test displays robust analytical performance that is suitable for deployment by local pathology laboratories for decentralized use.
      PubDate: Mon, 21 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac028
      Issue No: Vol. 68, No. 6 (2022)
       
  • Towards a New Qualitative Screening Assay for Synthetic Cannabinoids Using
           Metabolomics and Machine Learning

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      Authors: Streun G; Steuer A, Poetzsch S, et al.
      Pages: 848 - 855
      Abstract: AbstractBackgroundSynthetic cannabinoids (SCs) are steadily emerging on the drug market. To remain competitive in clinical or forensic toxicology, new screening strategies including high-resolution mass spectrometry (HRMS) are required. Machine learning algorithms can detect and learn chemical signatures in complex datasets and use them as a proxy to predict new samples. We propose a new screening tool based on a SC-specific change of the metabolome and a machine learning algorithm.MethodsAuthentic human urine samples (n = 474), positive or negative for SCs, were used. These samples were measured with an untargeted metabolomics liquid chromatography (LC)–quadrupole time-of-flight-HRMS method. Progenesis QI software was used to preprocess the raw data. Following feature engineering, a random forest (RF) model was optimized in R using a 10-fold cross-validation method and a training set (n = 369). The performance of the model was assessed with a test (n = 50) and a verification (n = 55) set.ResultsDuring RF optimization, 49 features, 200 trees, and 7 variables at each branching node were determined as most predictive. The optimized model accuracy, clinical sensitivity, clinical specificity, positive predictive value, and negative predictive value were 88.1%, 83.0%, 92.7%, 91.3%, and 85.6%, respectively. The test set was predicted with an accuracy of 88.0%, and the verification set provided evidence that the model was able to detect cannabinoid-specific changes in the metabolome.ConclusionsAn RF approach combined with metabolomics enables a novel screening strategy for responding effectively to the challenge of new SCs. Biomarkers identified by this approach may also be integrated in routine screening methods.
      PubDate: Tue, 22 Mar 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac045
      Issue No: Vol. 68, No. 6 (2022)
       
  • Partial Postponement of the Application of the In Vitro Diagnostic Medical
           Devices Regulation in the European Union

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      Authors: Vogeser M; Brüggemann M, Lennerz J, et al.
      Pages: 856 - 857
      PubDate: Wed, 01 Jun 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac048
      Issue No: Vol. 68, No. 6 (2022)
       
  • A Child with Developmental Regression and Electroencephalographic
           Abnormalities

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      Authors: Çıkı K; Yıldız Y, Güleray Lafcı N, et al.
      Pages: 858 - 860
      PubDate: Mon, 11 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvab284
      Issue No: Vol. 68, No. 6 (2022)
       
  • Increased Mean Cell Hemoglobin Concentration

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      Authors: Cook S.
      Pages: 861 - 862
      Abstract: hematologyhemoglobinelectrolytes
      PubDate: Mon, 11 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvab253
      Issue No: Vol. 68, No. 6 (2022)
       
  • Pain, Pain, Go Away: Exploring the Role of the Immune System in Regulating
           Chronic Pain

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      Authors: Rogers K; Merrill A.
      Pages: 863 - 863
      Abstract: Pain, in the appropriate context, is an essential component of life. It alerts us to danger, promotes healing, and plays a critical psychological role in normal growth and development. Chronic pain, in contrast, is physically and emotionally debilitating, and lies at the heart of some of the greatest challenges to our modern society. According to the Centers for Disease Control and Prevention, approximately 1 in 5 Americans suffer from chronic pain, costing an estimated $560 billion annually due to lost productivity, direct healthcare expenditures, and disability. Furthermore, well-intentioned efforts to combat chronic pain have contributed to an opioid crisis that has claimed an estimated 500 000 lives and continues to ravage vulnerable communities. Here we highlight recent studies seeking to better understand the physiologic underpinning of pain by examining the close relationship between the peripheral nervous system and cells of the immune system.
      PubDate: Mon, 11 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac013
      Issue No: Vol. 68, No. 6 (2022)
       
  • Everyday People

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      Authors: Annesley T.
      Pages: 864 - 865
      Abstract: When I was in college, I attended a Nobel Conference where Norman Borlaug spoke on the world food problem. When Borlaug approached the stage, I was unaware that I was in the presence of a man who would be credited with saving more than 1 billion lives. Dr. Borlaug had successfully developed wheat varieties with stable disease resistance, the ability to grow in diverse conditions across many geographic climates, and extremely high yield. These new wheat varieties prevented hunger and starvation around the world and helped create what is now known as the “Green Revolution.” Borlaug’s astounding accomplishment resulted in his receipt of the Nobel Peace Prize in 1970.
      PubDate: Wed, 01 Jun 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac052
      Issue No: Vol. 68, No. 6 (2022)
       
  • Leila with Her First Book

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      Authors: Rifai N.
      Pages: 866 - 867
      Abstract: Fig. 1Leila with her first book. 16x23 cm watercolor.
      PubDate: Mon, 11 Apr 2022 00:00:00 GMT
      DOI: 10.1093/clinchem/hvac010
      Issue No: Vol. 68, No. 6 (2022)
       
 
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