Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping.

Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.

Association of aortic stiffness with abdominal vascular and coronary calcifications in patients with stage 3 and 4 chronic kidney disease.

RATIONALE AND OBJECTIVES: Increased central (aortic) arterial stiffness has hemodynamic repercussions that affect the incidence of cardiovascular and renal disease. In chronic kidney disease (CKD) there may be an increase in aortic stiffness secondary to multiple metabolic alterations including calcification of the vascular wall (VC). The objective of this study was to analyze the association of central aortic pressures and aortic stiffness with the presence of VC in abdominal aorta (AAC) and coronary arteries(CAC). MATERIALS AND METHODS: We included 87 pacientes with CKD stage 3 and 4. Using applanation tonometry, central aortic pressures and aortic stiffness were studied. We investigated the association of aortic pulse wave velocity (Pvc-f) and Pvc-f adjusted for age, blood pressure, sex and heart rate (Pvc-f index) with AAC obtained on lumbar lateral radiography and CAC assessed by multidetector computed tomography. AAC and CAC were scored according to Kauppila and Agatston methods, respecti-vely. For the study of the association between Pvc-f index, Kauppila score, Agatston score, central aortic pressures, clinical parameters and laboratory data, multiple and logistic regression were used. We investigated the diagnosis performance of the Pvc-f index for prediction of VC using receiver-operating characteristic (ROC). RESULTS: Pvc-f and Pvc-f index were 11.3 ± 2.6 and 10.6 m/s, respectively. The Pvc-f index was higher when CKD coexisted with diabetes mellitus (DM). AAC and CAC were detected in 77% and 87%, respectively. Albuminuria (ß = 0.13, p = 0.005) and Kauppila score (ß = 0.36, p = 0.001) were independently associated with Pvc-f index. In turn, Pvc-f index (ß = 0.39, p = 0.001), DM (ß = 0.46, p = 0.01), and smoking (ß = 0.53; p = 0.006) were associated with Kauppila score, but only Pvc-f index predicted AAC [OR: 3.33 (95% CI: 1.6-6.9; p = 0.001)]. The Kauppila score was independently associated with the Agatston score (ß = 1.53, p = 0.001). The presence of AAC identified patients with CAC with a sensitivity of 73%, a specificity of 100%, a positive predictive value of 100% and a negative predictive value of 38%. The Vpc-f index predicted the presence of CAC [OR: 3.35 (95% CI: 1.04-10.2, p = 0.04)]. In the ROC curves, using the Vpc-f index, the AUC for AAC and CAC was 0.82 (95%CI: 0.71-0.93, p = 0.001) and 0.81 (95% CI: 0.67-0.96, p = 0.02), respectively. CONCLUSIONS: When stage 3-4 CKD coexists with DM there is an increase in aortic stiffness determined by the Vpc-f index. In stage 3-4 CKD, AAC and CAC are very prevalent and both often coexist. The Vpc-f index is independently associated with AAC and CAC and may be useful in identifying patients with VC in these territories.

Analytical solutions for viscoelectric effects in electrokinetic nanochannels.

Understanding electrokinetic transport in nanochannels and nanopores is essential for emerging biological and electrochemical applications. The viscoelectric effect is an important mechanism implicated in the increase of local viscosity due to the polarization of a solvent under a strong electric field. However, most analyses of the viscoelectric effect have been limited to numerical analyses. In this work, we present a set of analytical solutions applicable to the physical description of viscoelectric effects in nanochannel electrokinetic systems. To achieve such closed-form solutions, we employ the Debye-Hückel approximation of small diffuse charge layer potentials compared to the thermal potential. We analyze critical parameters, including electroosmotic flow profiles, electroosmotic mobility, flow rate, and channel conductance. We compare and benchmark our analytical solutions with published predictions from numerical models. Importantly, we leverage these analytical solutions to identify essential thermophysical and nondimensional parameters that govern the behavior of these systems. We identify scaling parameters and relations among surface charge density, ionic strength, and nanochannel height.

A neural network model for rapid prediction of analyte focusing in isotachophoresis.

We present the development and demonstration of a neural network (NN) model for fast and accurate prediction of whether or not a chosen analyte is focused by an isotachophoresis (ITP) buffer system. The NN model is useful in the rapid evaluation of possible ITP chemistries applicable to analytes of interest. We trained and tested the NN model for univalent species based on extensive data sets of over 10,000 anionic and 10,000 cationic ITP simulations. The NN model uses as inputs the mobilities and the acid dissociation constants of leading electrolyte ion, trailing electrolyte ion, counterion, and a single analyte as well as the leading-to-counterion concentration ratio of the leading zone. The output then indicates whether the chosen electrolyte system yields stable ITP focusing of the analyte. The prediction accuracy of the NN model is over 97.7%. We demonstrate the applicability of the NN by validating its predictions with reported experimental data for anionic and cationic ITP. We have packaged the NN model in a free, web-based application named IONN (isotachophoresis on neural network), which can be used to rapidly screen ITP electrolyte systems.

Mucormicosis maxilar asociado a COVID-19, tratamiento médico-quirúrgico y manejo multidisciplinario. Reporte de caso / Maxillary mucormycosis associated with COVID-19, medical-surgical treatment and multidisciplinary management. Case report

Resumen Introducción: Durante la actual pandemia de COVID-19 múltiples complicaciones se han desarrollado posterior a la enfermedad, dentro de las cuales se encuentran las infecciones fúngicas, como la mucormicosis, que puede resultar directamente de la infección por COVID-19 y/o como efecto secundario de los fármacos utilizados en su tratamiento. La mucormicosis es una infección causada por un grupo de hongos llamados mucormycetes; a nivel rinocerebral se presenta con celulitis facial, cefalea, proptosis, movilización del diente afectado y secreción nasal. Reporte de caso: Se presenta a un paciente femenino de 57 años con antecedente de neumonía grave por COVID-19 con posterior desarrollo de absceso periodontal que ameritó extracción del segundo molar superior derecho con posterior formación de fistula. Se toma TC de macizo facial donde se evidencia erosión ósea con pérdida de la morfología habitual y en pared anterior del seno maxilar derecho. Se realiza biopsia reportando tejido óseo con elementos micóticos (hifas aseptadas) morfológicamente compatibles con mucor sp. Se realizó tratamiento con anfotericina B y hemimaxilectomia derecha. Actualmente se encuentra en tratamiento con pozaconazol, y lavados quirúrgicos. Conclusión: La enfermedad de COVID-19 es una enfermedad muy común actualmente a nivel mundial, por lo que es importante identificar y llevar un seguimiento de aquellas personas con factores de riesgo para desarrollar mucormicosis; el diagnóstico y un plan de tratamiento temprano es fundamental para evitar complicaciones, las cuales pueden originar un desenlace fatal.

Abstract Introduction: During the current pandemic of COVID-19 multiple complications have developed after the disease, among which are fungal infections, such as mucormycosis, which can result directly from COVID-19 infection and/or as a side effect of the drugs used in its treatment. Mucormycosis is an infection caused by a group of fungi called mucormycetes; at the rhinocerebral level it presents with facial cellulitis, headache, proptosis, mobilization of the affected tooth and nasal secretion. Case report: the following is a 57-year-old female patient with a history of severe pneumonia due to COVID-19 with subsequent development of periodontal abscess that merited extraction of the upper right second molar with subsequent fistula formation. The patient started an infection with the presence of purulent secretion in the extraction area of the right molar. A CT scan of the facial mass was taken showing bone erosion with loss of the usual morphology in the right upper maxillary bone and anterior wall of the right maxillary sinus, as well as a biopsy of the right maxilla reporting bone tissue with mycotic elements (aseptates hyphae) morphologically compatible with mucor sp. Treatment with amphotericin B and right hemimaxillectomy was performed. She is currently being treated with pozaconazole and surgical washings. Conclusion: COVID-19 disease is currently a very common disease worldwide, so it is important to identify and follow up those people with risk factors for developing mucormycosis; early diagnosis and treatment plan is essential to avoid complications, which can lead to a fatal outcome.

Quality improvements in radiation oncology clinical trials.

Clinical trials have become the primary mechanism to validate process improvements in oncology clinical practice. Over the past two decades there have been considerable process improvements in the practice of radiation oncology within the structure of a modern department using advanced technology for patient care. Treatment planning is accomplished with volume definition including fusion of multiple series of diagnostic images into volumetric planning studies to optimize the definition of tumor and define the relationship of tumor to normal tissue. Daily treatment is validated by multiple tools of image guidance. Computer planning has been optimized and supported by the increasing use of artificial intelligence in treatment planning. Informatics technology has improved, and departments have become geographically transparent integrated through informatics bridges creating an economy of scale for the planning and execution of advanced technology radiation therapy. This serves to provide consistency in department habits and improve quality of patient care. Improvements in normal tissue sparing have further improved tolerance of treatment and allowed radiation oncologists to increase both daily and total dose to target. Radiation oncologists need to define a priori dose volume constraints to normal tissue as well as define how image guidance will be applied to each radiation treatment. These process improvements have enhanced the utility of radiation therapy in patient care and have made radiation therapy an attractive option for care in multiple primary disease settings. In this chapter we review how these changes have been applied to clinical practice and incorporated into clinical trials. We will discuss how the changes in clinical practice have improved the quality of clinical trials in radiation therapy. We will also identify what gaps remain and need to be addressed to offer further improvements in radiation oncology clinical trials and patient care.

A critical review of microfluidic systems for CRISPR assays.

Reviewed are nucleic acid detection assays that incorporate clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics and microfluidic devices and techniques. The review serves as a reference for researchers who wish to use CRISPR-Cas systems for diagnostics in microfluidic devices. The review is organized in sections reflecting a basic five-step workflow common to most CRISPR-based assays. These steps are analyte extraction, pre-amplification, target recognition, transduction, and detection. The systems described include custom microfluidic chips and custom (benchtop) chip control devices for automated assays steps. Also included are partition formats for digital assays and lateral flow biosensors as a readout modality. CRISPR-based, microfluidics-driven assays offer highly specific detection and are compatible with parallel, combinatorial implementation. They are highly reconfigurable, and assays are compatible with isothermal and even room temperature operation. A major drawback of these assays is the fact that reports of kinetic rates of these enzymes have been highly inconsistent (many demonstrably erroneous), and the low kinetic rate activity of these enzymes limits achievable sensitivity without pre-amplification. Further, the current state-of-the-art of CRISPR assays is such that nearly all systems rely on off-chip assays steps, particularly off-chip sample preparation.

Probability of hospitalisation and death among COVID-19 patients with comorbidity during outbreaks occurring in Mexico City.

Background: We compared the probability of hospitalization and death caused by COVID-19 in patients with comorbidities during three periods defined for this study: first-wave (FW), interwave period (IP), and second-wave (SW) observed in Mexico City. Methods: In this registry-based study, we included individuals over 20 years of age. During the FW (symptomatic), the IP, and the SW (symptomatic and asymptomatic), participants were diagnosed using nasopharyngeal swabs. Symptomatic individuals with risk factors for serious disease or death were referred to the hospital. SARS-CoV-2 infection was defined by RT-qPCR in all hospitalized patients. All data were added to the SISVER database. Bayesian analysis and False Discovery Rate were used for further evaluation. Results: The study included 2 260 156 persons (mean age of 43.1 years). Of these, 8.6% suffered from DM, 11.6% arterial hypertension, and 9.7% obesity. Of the total, 666 694 persons tested positive (29.5%). Of the infected persons, a total of 85 587 (12.8%) were hospitalized: 24 023 in the FW; 16 935 in the IP, and 44 629 in the SW. Of the hospitalized patients, there were 42 979 deaths (50.2%), in the FW, 11 964 (49.8%), in the IP, 6794 (40.1%), and in the SW 24 221 (54.3%). The probability of death among individuals hospitalized with or without comorbidities increased consistently in all age groups. A significant increase in the Fatality Rate was observed in individuals with comorbidities (1.36E-19< = FDR< = 3.36E-2). A similar trend was also observed in individuals without comorbidities (1.03E-44< = FDR< = 5.58E-4). Conclusions: The data from this study show a considerable increase in the number of detected cases of infection between the FW and SW. In addition, 12.8% of those infected were hospitalized for severe COVID-19. A high mortality rate was observed among hospitalized patients (>50%). An age-dependent probability of death was observed with a positive trend in hospitalized patients with and without comorbidities.

Tumor microenvironment in non-melanoma skin cancer resistance to photodynamic therapy.

Non-melanoma skin cancer has recently seen an increase in prevalence, and it is estimated that this grow will continue in the coming years. In this sense, the importance of therapy effectiveness has increased, especially photodynamic therapy. Photodynamic therapy has attracted much attention as a minimally invasive, selective and repeatable approach for skin cancer treatment and prevention. Although its high efficiency, this strategy has also faced problems related to tumor resistance, where the tumor microenvironment has gained a well-deserved role in recent years. Tumor microenvironment denotes a wide variety of elements, such as cancer-associated fibroblasts, immune cells, endothelial cells or the extracellular matrix, where their interaction and the secretion of a wide diversity of cytokines. Therefore, the need of designing new strategies targeting elements of the tumor microenvironment to overcome the observed resistance has become evident. To this end, in this review we focus on the role of cancer-associated fibroblasts and tumor-associated macrophages in the resistance to photodynamic therapy. We are also exploring new approaches consisting in the combination of new and old drugs targeting these cells with photodynamic therapy to enhance treatment outcomes of non-melanoma skin cancer.

MLC performance prognosis using a degradation model based on trajectory log data from a daily test.

PURPOSE: This paper investigates the feasibility of implementing a predictive maintenance program for a multileaf collimator (MLC) based on data collected in trajectory logs (TLs) obtained by conducting a simple daily test, with the aim of minimizing unscheduled downtime. METHODS: A dynamic field test was designed, and the TLs generated in the course of daily administration in a linear accelerator were collected to evaluate trajectory deviations of the MLC leaves as well as interlocks (COL 420219/20, COL 420207/08) reported by the machine. During this evaluation, we observed that the trajectory deviations of some leaves increased up to a threshold value beyond which certain interlocks began to appear in treatment fields in those leaves. An exponential degradation model was therefore developed to predict this drift and determine each leaf's remaining useful life (RUL). Once the applicability of the model was confirmed, we added a second accelerator equipped with an MLC with the same configuration to validate the model. RESULTS: The model was able to predict certain COL 420219/20 interlocks resulting from primary readout/expected position discrepancies and to estimate each leaf's RUL. In total, 11 cases (8 interlocks + 3 potential interlocks avoided due to service interventions [27.3% of the total]) were detected over 7 days in advance, with no false positive results. Scheduling of service interventions several days prior to MLC failure would therefore be possible. When these types of interlocks were not predicted by the model, they were always generated by leaf motor failure. Consequently, intervention time could also be optimized by directly replacing the motor. During the study period, for these types of interlocks, our approach would have reduced downtime from 35.25 to 4.00 h (88.7%) and from 34.75 to 22.83 h (34.3%) for each accelerator, respectively. For COL 420207/08 interlocks, which are generated by primary/secondary readout discrepancies, no correlation with leaf trajectory deviation increases recorded in the TLs was found. Throughout the study period, these types of interlocks requiring service intervention, also mainly for motor replacement, represented a downtime of 9.50 h for the first accelerator (21.2% of total downtime) and by 4.33 h (11.1% of total downtime) for the second accelerator. CONCLUSION: This study demonstrates that by applying a predictive MLC maintenance program based on information collected in TLs, it is possible to predict certain interlocks and therefore schedule preemptive interventions to avoid their occurrence. This could optimize health-care delivery performance and minimize the loss of treatment sessions.

Detection and Discrimination of Single Nucleotide Polymorphisms by Quantification of CRISPR-Cas Catalytic Efficiency.

The specificity of CRISPR-Cas12 assays is attractive for the detection of single nucleotide polymorphisms (SNPs) implicated in, e.g., cancer and SARS-CoV-2 variants. Such assays often employ endpoint measurements of SNP or wild type (WT) activated Cas12 trans-cleavage activity; however, the fundamental kinetic effects of SNP versus WT activation remain unknown. We here show that endpoint-based assays are limited by arbitrary experimental choices (like used reporter concentration and assay duration) and work best for known target concentrations. More importantly, we show that SNP (versus WT) activation results in measurable kinetic shifts in the Cas12 trans-cleavage substrate affinity (KM) and apparent catalytic efficiency (kcat*/KM). To address endpoint-based assay limitations, we then develop an assay based on the quantification of Michaelis-Menten parameters and apply this assay to a 20 base pair WT target of the SARS-CoV-2 E gene. We find that the kcat*/KM measured for WT is 130-fold greater than the lowest kcat*/KM among all 60 measured SNPs (compared to a 4.8-fold for endpoint fluorescence of the same SNP). KM also offers a strong ability to distinguish SNPs, varies 27-fold over all the cases, and, importantly, is insensitive to the target concentration. Last, we point out trends among kinetic rates and SNP base and location within the CRISPR-Cas12 targeted region.

Liquid Heterostructures: Generation of Liquid-Liquid Interfaces in Free-Flowing Liquid Sheets.

Chemical reactions and biological processes are frequently governed by the structure and dynamics of the interface between two liquid phases, but these interfaces are often difficult to study due to the relative abundance of the bulk liquids. Here, we demonstrate a method for generating multilayer thin film stacks of liquids, which we call liquid heterostructures. These free-flowing layered liquid sheets are produced with a microfluidic nozzle that impinges two converging jets of one liquid onto opposite sides of a third jet of another liquid. The resulting sheet consists of two layers of the first liquid enveloping an inner layer of the second liquid. Infrared microscopy, white light reflectivity, and imaging ellipsometry measurements demonstrate that the buried liquid layer has a tunable thickness and displays well-defined liquid-liquid interfaces and that this inner layer can be only tens of nanometers thick. The demonstrated multilayer liquid sheets minimize the amount of bulk liquid relative to their buried interfaces, which makes them ideal targets for spectroscopy and scattering experiments.

Uncertainty Quantification of Michaelis-Menten Kinetic Rates and Its Application to the Analysis of CRISPR-Based Diagnostics.

Michaelis-Menten kinetics is an essential model to rationalize enzyme reactions. The quantification of Michaelis-Menten parameters can be very challenging as it is sensitive to even small experimental errors. We here present a quantification of the uncertainty inherent to the experimental determination of kinetic rate parameters for enzymatic reactions. We study the influence of several sources of uncertainty and bias, including the inner filter effect, pipetting errors, number of points in the Michaelis-Menten curve, and flat-field correction. Using Monte Carlo simulations and analyses of experimental data, we compute typical uncertainties of k c a t ${{k}_{cat}}$ , K M ${{K}_{M}}$ , and catalytic efficiency k c a t / K M ${{k}_{cat}/{K}_{M}}$ . As a salient example, we analyze the extraction of such parameters for CRISPR-Cas systems. CRISPR diagnostics have recently attracted much interest and yet reports of these enzymatic kinetic rates have been highly unreliable and inconsistent.

Lossless Medical Image Compression by Using Difference Transform.

This paper introduces a new method of compressing digital images by using the Difference Transform applied in medical imaging. The Difference Transform algorithm performs the decorrelation process of image data, and in this way improves the encoding process, achieving a file with a smaller size than the original. The proposed method proves to be competitive and in many cases better than the standards used for medical images such as TIFF or PNG. In addition, the Difference Transform can replace other transforms like Cosine or Wavelet.

Effect of the administration of different forms of vitamin D on central blood pressure and aortic stiffness, and its implication in the reduction of albuminuria in chronic kidney disease. / Efecto de la administración de diferentes formas de vitamina D en la presión arterial y rigidez aórticas, y su implicación en la reducción de la albuminuria en la enfermedad renal crónica.

BACKGROUND AND OBJECTIVES: Vitamin D(vitD) participates in phospho-calcium metabolism and exerts multiple pleiotropic effects. There is tissue 1-α (OH)ase that converts 25-OH cholecalciferol (25 (OH) D) in calcitriol that exerts autocrine and paracrine effects. 25 (OH)D deficiency could limit these tissue effects of vitD. The administration of nutritional vitD and the activator of the vitD receptor, paricalcitol, may promote beneficial effects on vascular and renal function. The objective of this work was to study in subjects with chronic kidney disease (CKD) the effect that the administration of different forms of vitD has on arterial function and albuminuria, and the possible relationship between the modifications of these variables. PATIENTS AND METHODS: We studied in 97 patients with CKD stages 3-4 the effect of the administration of cholecalciferol (group 2; n: 35) and paricalcitol (n: 31; group 3) on parameters derived from brachial blood pressure, aortic blood pressure and on aortic stiffness studied using carotid-femoral pulse velocity (Vpc-f), and on albuminuria. A group of patients with stages 3-4 CKD who did not receive vitD therapy served as a control group (n: 31; group 1). All parameters were studied at baseline and after the follow-up period which was 7 ± 2 months. RESULTS: In the baseline phase, no differences were observed between the groups in brachial systolic blood pressure (bSBP), central systolic blood pressure (SBP), brachial pulse pressure (bPP), and central pulse pressure (pCP) or in aortic stiffness that was increased in all groups with a baseline Vpc-f value of 10.5 (9.2-12.1) m/sec. The baseline albuminuria value in the grouped patients was 229 (43-876) mg / g (median (interquartile range)), with no differences between the groups. Serum calcium and phosphorus increased significantly in those treated with cholecal-ciferol (native vitD) and paricalcitol (active vitD). Parathormone (PTH) values decreased in those treated with paricalcitol.bPP and cPP decreased in all groups treated with native and active vitD. No significant changes in bPP and cPP were observed in the control group. Vpc-f did not change significantly in any of the groups, although the variation was quantitatively greater in group 3 (11.2±2 vs. 10.7±1.6 (P=.06)). No differences were observed in the changes in Vpc-f between the groups when adjusted to the baseline values of estimated glomerular filtration rate (eGFR), albuminuria, PTH, vitD, brachial and central blood pressure parameters, and their changes with treatment.Those who received treatment with native and active vitD presented a significant decrease in albuminuria of 17% (group 2) and 21% (group 3) compared to a 16% increase in the untreated group (group 1) (P=.01). A decrease in albuminuria ≥30% was observed more frequently in the groups treated with some form of vitD (group 2: 23%; group 3: 45%) than in the control group (13%) (P=.03). The decrease in albuminuria observed in the groups treated with any of the forms of vitD did not vary when the baseline values of the biochemical parameters of phosphorus-calcium metabolism, those of arterial function (PPb, PPc, Vpc-f) or its modifications were introduced as covariates. There was no significant correlation between changes in Vpc-f and albuminuria. In logistic regression, changes in arterial function parameters were also not explanatory for the ≥30% decrease in albuminuria. CONCLUSIONS: In patients with CKD stages 3-4, treated with RAS blockers and with residual albuminuria, the administration of or paricalcitol reduces brachial and aortic pulse pressures, and albuminuria. The decrease in albuminuria does not seem to be mediated, at least not decisively, by changes in central hemodynamics or aortic stiffness.

Electrochemical Methods for Water Purification, Ion Separations, and Energy Conversion.

Agricultural development, extensive industrialization, and rapid growth of the global population have inadvertently been accompanied by environmental pollution. Water pollution is exacerbated by the decreasing ability of traditional treatment methods to comply with tightening environmental standards. This review provides a comprehensive description of the principles and applications of electrochemical methods for water purification, ion separations, and energy conversion. Electrochemical methods have attractive features such as compact size, chemical selectivity, broad applicability, and reduced generation of secondary waste. Perhaps the greatest advantage of electrochemical methods, however, is that they remove contaminants directly from the water, while other technologies extract the water from the contaminants, which enables efficient removal of trace pollutants. The review begins with an overview of conventional electrochemical methods, which drive chemical or physical transformations via Faradaic reactions at electrodes, and proceeds to a detailed examination of the two primary mechanisms by which contaminants are separated in nondestructive electrochemical processes, namely electrokinetics and electrosorption. In these sections, special attention is given to emerging methods, such as shock electrodialysis and Faradaic electrosorption. Given the importance of generating clean, renewable energy, which may sometimes be combined with water purification, the review also discusses inverse methods of electrochemical energy conversion based on reverse electrosorption, electrowetting, and electrokinetic phenomena. The review concludes with a discussion of technology comparisons, remaining challenges, and potential innovations for the field such as process intensification and technoeconomic optimization.

Enzyme Kinetics and Detector Sensitivity Determine Limits of Detection of Amplification-Free CRISPR-Cas12 and CRISPR-Cas13 Diagnostics.

Interest in CRISPR-Cas12 and CRISPR-Cas13 detection continues to increase as these detection schemes enable the specific recognition of nucleic acids. The fundamental sensitivity limits of these schemes (and their applicability in amplification-free assays) are governed by kinetic rates. However, these kinetic rates remain poorly understood, and their reporting has been inconsistent. We quantify kinetic parameters for several enzymes (LbCas12a, AsCas12a, AapCas12b, LwaCas13a, and LbuCas13a) and their corresponding limits of detection (LoD). Collectively, we present quantification of enzyme kinetics for 14 guide RNAs (gRNAs) and nucleic acid targets for a total of 50 sets of kinetic rate parameters and 25 LoDs. We validate the self-consistency of our measurements by comparing trends and limiting behaviors with a Michaelis-Menten trans-cleavage reaction kinetics model. For our assay conditions, activated Cas12 and Cas13 enzymes exhibit trans-cleavage catalytic efficiencies between order 105 and 106 M-1 s-1. For assays that use fluorescent reporter molecules (ssDNA and ssRNA) for target detection, the kinetic rates at the current assay conditions result in an amplification-free LoD in the picomolar range. The results suggest that successful detection of target requires cleavage (by an activated CRISPR enzyme) of the order of at least 0.1% of the fluorescent reporter molecules. This fraction of reporters cleaved is required to differentiate the signal from the background, and we hypothesize that this required fraction is largely independent of the detection method (e.g., endpoint vs reaction velocity) and detector sensitivity. Our results demonstrate the fundamental nature by which kinetic rates and background signal limit LoDs and thus highlight areas of improvement for the emerging field of CRISPR diagnostics.

Isotachophoresis: Theory and Microfluidic Applications.

Isotachophoresis (ITP) is a versatile electrophoretic technique that can be used for sample preconcentration, separation, purification, and mixing, and to control and accelerate chemical reactions. Although the basic technique is nearly a century old and widely used, there is a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important because the interest and adoption of the technique has grown over the last two decades, especially with its implementation in microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory starting from physicochemical first-principles, including conservation of species, conservation of current, approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions that govern transport dynamics, with a strong emphasis on steady and unsteady transport. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles that govern the ITP focusing of weak and strong electrolytes; ITP dynamics in peak and plateau modes; a review of simulation tools, experimental tools, and detection methods; applications of ITP for on-chip separations and trace analyte manipulation; and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities and to provide a rigorous basis for the increased adoption of ITP in microfluidics.

Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer. Corrigendum.

A figure in the article by Huyke et al. [(2021), J. Synchrotron Rad. 28, 1100-1113] is corrected.

A modular and reconfigurable open-channel gated device for the electrokinetic extraction of cell-free DNA assays.

The high-efficiency separation and extraction of short fragments of cell-free DNA (cfDNA) remain challenging due to their low abundance and short lengths. This study presents a method for separating short cfDNA fragments, with lengths ranging from about 100 to 200 base pairs, from liquid human plasma samples into separable and extractable bands as solid agarose gel slabs. To achieve this, a novel millimeter-scale fluidic device is used for sample handling, transient isotachophoresis, and extraction. The device features open-to-atmosphere liquid chambers that define and manually actuated (i.e., movable) agarose-made gate valve structures. The agarose gates then define discrete zones for buffers, sample injection, DNA pre-concentration via isotachophoresis, size-based gel separation, and DNA-band extraction. As a demonstration of its efficacy, the device is applied to the enrichment and purification of M. tuberculosis genomic DNA fragments spiked in human plasma samples. This purified cfDNA is analyzed using the quantitative polymerase chain reaction (qPCR) of the IS6110 repetitive sequence in the M. tuberculosis genome. The data from this study demonstrates that high sensitivity can be achieved in cfDNA detection, as shown by the comparison with a typical solid-phase extraction method and buffer spiked with cfDNA. Evidence is presented that suggests plasma peptides generated by treatment of the sample with proteinase K acts as endogenous spacer molecules, which improve the resolution and purification of DNA relative to the marker dye and other contaminants that decrease the signal level in qPCR.