De novo design of high-affinity binders of bioactive helical peptides.

Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

Metrologically Traceable Quantification of 3 Apolipoprotein E Isoforms in Cerebrospinal Fluid.

BACKGROUND: APOE genotype is associated with Alzheimer disease. Thus, the concentration of apolipoprotein E (apoE) isoforms in cerebrospinal fluid (CSF) could be altered in dementia. However, conflicting results have been obtained in different studies. Carefully validated and standardized assays could improve the interpretation of research findings, allow their replication in other laboratories, and generalize their application. METHODS: To evaluate this hypothesis, we aimed to develop, validate, and standardize a new measurement procedure using LC-MS/MS. Purified recombinant apoE protein standards (E2, E3, E4) were thoroughly characterized and used to assign the concentration of a matrix-matched calibration material that contained each apoE isoform, which ensured the metrological traceability of results. RESULTS: The assay of each isoform in human CSF was precise (≤11%CV) and of moderate throughput (approximately 80 samples per day). It demonstrated good linearity and parallelism for lumbar CSF, ventricular CSF, and bovine CSF. The use of an SI-traceable matrix-matched calibrator enabled precise and accurate measurements. There was no association observed between total apoE concentration and the number of Ɛ4 alleles in a cohort of 322 participants. However, the concentration of each isoform was significantly different in heterozygotes, with E4 > E3 > E2. Isoform concentrations were associated with cognitive and motor symptoms but contributed negligibly to a predictive model of cognitive impairment that included established CSF biomarkers. CONCLUSIONS: Our method simultaneously measures each apoE isoform in human CSF with excellent precision and accuracy. A secondary matrix-matched material has been developed and is available to other laboratories to improve interlaboratory agreement.

A Targeted Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Quantification of Peptides from the Carboxyl-terminal Region of Type III Procollagen, Biomarkers of Collagen Turnover.

BACKGROUND: The development of analytical approaches to help reduce the risk of growth hormone (GH) doping is important to fair competition and the health of athletes. However, the reliable detection of GH use remains challenging. The identification of novel biomarkers of GH administration could lead to a better understanding of the physiological response to GH, more sensitive detection of the illicit use of GH in sport, and better management of patients treated for GH disorders. METHODS: We developed a targeted liquid chromatography-tandem mass spectrometry method to simultaneously quantify the carboxyl-terminal propeptide of type III procollagen (P-III-CP) and type III collagen degradation products in human serum. Following proteolysis, we instituted a simple acid precipitation step to reduce digested sample complexity before peptide immunoenrichment, which improved the recovery of one target peptide from serum. We evaluated the concentration of each biomarker at different age ranges and after GH administration in healthy participants. RESULTS: The assay was linear over an estimated concentration range of 0.3 to1.0 nM and 0.1 to 0.4 nM for each surrogate peptide of P-III-CP and collagen fragments, respectively. Intra-day and inter-day coefficients of variation were ≤15%. Biomarker concentrations appeared to vary with age and to reflect age-specific collagen turnover. Moreover, their concentrations changed after GH administration. CONCLUSIONS: Our method quantifies the proteins belonging to the family of P-III-CP and type III collagen degradation products in human serum, which could be used to detect GH administration in athletes and better understand diseases involving GH therapy or altered type III collagen turnover.

Mainstream partial denitrification-anammox in sand and expanded clay deep-bed polishing filters under practical loading rates and backwashing conditions.

This study focused on evaluating the feasibility of expanded clay and sand as media types for mainstream partial denitrification-anammox (PdNA) in deep-bed single-media polishing filters under nitrogen and solids loading rates as well as backwash conditions similar to conventional denitrification filters. The surface roughness and iron content of the expanded clay were hypothesized to allow for enhanced anammox retention, nitrogen removal rates, and runtimes. However, under the tested loading rates and backwash conditions, no clear benefit of expanded clay was observed compared with conventional sand. This study showed the feasibility of PdNA in filters with both sand and expanded clay with PdN efficiencies of 76% and 77%, PdNA rates of 840 and 843 g N/m3 /d and TIN removal rates of 960 and 964 g N/m3 /d, respectively. Glycerol demands were 1.5-1.6 g COD added per g TIN removed , thus indicating potential carbon savings up to 75% compared with conventional denitrification. Overall, this study showed for the first time PdNA filters performing at nitrogen removal rates double that of previous PdNA studies under realistic conditions while providing insights into the media choice and backwashing conditions. Future research on expanded clay backwash conditions is needed to provide its full potential in PdNA filters. PRACTITIONER POINTS: Hydraulic and TSS loading rates similar to conventional denitrification can be applied in PdNA filters. Conventional sand can be used when retrofitting conventional denitrification filters into PdNA filters. Carbon savings up to 75% can be achieved with glycerol when retrofitting conventional filters into PdNA filters.

Media selection for anammox-based polishing filters: Balancing anammox enrichment and retention with filtration function.

Retrofitting conventional denitrification filters into partial denitrification-anammox (PdNA)- or anammox (AnAOB)-based filters will reduce the needs for external carbon addition. The success of AnAOB-based filters depends on anammox growth and retention within such filters. Studies have overlooked the importance of media selection and its impact on AnAOB capacity, head loss progression dynamics, and shear conditions applied onto the AnAOB biofilm. The objective of this study was to evaluate viable media types (10 types) that can enhance AnAOB rates for efficient nitrogen removal in filters. Given the higher backwash requirement and lower AnAOB capacity of the conventionally used sand, expanded clay (3-5 mm) was recommended for AnAOB-based filters in this study. Owing to its surface characteristics, expanded clay had higher AnAOB activity (304- vs. 104-g NH4 + -N/m2 /day) and higher AnAOB retention (43% more) than sand. Increasing the iron content of expanded clay to 37% resulted in an increase in zeta potential, which led to 56% more anammox capacity compared to expanded clay with 7% iron content. This work provides insight into the importance of media types in the growth and retention of AnAOB in filters, and this knowledge could be used as basis in the development of PdNA filters. PRACTITIONER POINTS: Expanded clay showed the lowest head loss buildup and most likely will result in longer runtime for full-scale PdNA applications The highest AnAOB rates were achieved in expanded clay types and sand compared with smaller media typically used in biofiltration Expanded clay resulted in better AnAOB retention under shear, whereas sand could not withstand shear and required more frequent backwashing Expanded clay iron coating enhanced AnAOB enrichment and retention, most likely due to increased surface roughness and/or positive charge.

Candidate High-Resolution Mass Spectrometry-Based Reference Method for the Quantification of Procalcitonin in Human Serum Using a Characterized Recombinant Protein as a Primary Calibrator.

Procalcitonin (PCT) is a widely used biomarker for rapid sepsis diagnosis and antibiotic stewardship. Variability of results in commercial assays has highlighted the need for standardization of PCT measurements. An antibody-free candidate reference measurement procedure (RMP) based on the isotope dilution mass spectrometry and protein calibration approach was developed and validated to quantify PCT in human serum. The method allows quantification of PCT from 0.25 to 13.74 µg/L (R > 0.998) with extension up to 132 µg/L after dilution of samples with PCT concentration above 13.74 µg/L. Intraday bias was between -3.3 and +5.7%, and interday bias was between -3.0 and -0.7%. Intraday precision was below 5.1%, and interday precision was below 4.0%. The candidate RMP was successfully applied to the absolute quantification of PCT in five frozen human serum pools. A recombinant PCT used as a primary calibrator was characterized by high-resolution mass spectrometry and amino acid analysis to establish traceability of the results to the SI units. This candidate RMP is fit to assign target values to secondary certified reference materials (CRMs) for further use in external quality assessment schemes to monitor the accuracy and comparability of the commercially available immunoassay results and to confirm the need for improving the harmonization of PCT assays. The candidate RMP will also be used to evaluate whether the correlation between the candidate RMP and immunoassays is sufficiently high. Overall, this candidate RMP will support reliable sepsis diagnosis and guide treatment decisions, patient monitoring, and outcomes.

The effects of NUDT15 and TPMT variants on mercaptopurine treatment in Vietnamese pediatric acute lymphoblastic leukemia patients.

6-mercaptopurine (6-MP) plays a critical role in the treatment of pediatric acute lymphoblastic leukemia (ALL). NUDT15 and TPMT gene variants have been strongly associated with myelotoxicity caused by using 6-MP. Therefore, the purpose of this study is to investigate the frequency of NUDT15 and TPMT polymorphisms, as well as the impact of NUDT15 variants on the use of 6-MP to treat pediatric ALL in Vietnam. Sanger sequencing was applied to detect NUDT15 and TPMT gene variants in 70 pediatric ALL patients. Duration of drug interruption, level of neutropenia, and 6-MP tolerance dose were recorded. NUDT15 variants were detected from 23 out of 70 (32.9%) patients. Three well-known haplotype variants were identified as NUDT15 *2 (p.V18_V19insGV and p.R139C), *3 (p.R139C), and *6 (p.V18_V19insGV); besides, a novel NUDT15 p.R11Q was not previously reported. The NUDT15 wild-type, heterozygous variant, and homozygous variant genotypes were 67.1%, 30.1%, and 2.8%, respectively. Two TPMT heterozygous polymorphisms were TPMT*3C and *6, accounted for 2.8%. Patients with intermediate and low activity NUDT15 were given the median 6-MP tolerance dose of 55.2 and 37.2 versus 69.5 mg/m2/day of patients with NUDT15 normal activity (p = 0.0001). Patients with homozygous variant diplotype were drastically sensitive to 6-MP, with an average dose intensity of 49.6%, compared to 73.6% and 92.7% of those with heterozygous and wild-type diplotype, respectively (p = 0.0001). Our results suggest that 6-MP dose adjustment should be based on NUDT15 variants in pediatric Vietnamese ALL patients.

Harmonization status of procalcitonin measurements: what do comparison studies and EQA schemes tell us?

Sepsis represents a global health priority because of its high mortality and morbidity. The key to improving prognosis remains an early diagnosis to initiate appropriate antibiotic treatment. Procalcitonin (PCT) is a recognized biomarker for the early indication of bacterial infections and a valuable tool to guide and individualize antibiotic treatment. To meet the increasing demand for PCT testing, numerous PCT immunoassays have been developed and commercialized, but results have been questioned. Many comparison studies have been carried out to evaluate analytical performance and comparability of results provided by the different commercially available immunoassays for PCT, but results are conflicting. External Quality Assessment Schemes (EQAS) for PCT constitute another way to evaluate results comparability. However, when making this comparison, it must be taken into account that the variety of EQA materials consist of different matrices, the commutability of which has not yet been investigated. The present study gathers results from all published comparison studies and results from 137 EQAS surveys to describe the current state-of-the-art harmonization of PCT results. Comparison studies globally highlight a significant variability of measurement results that nonetheless seem to have a moderate impact on medical decision-making. For their part, EQAS for PCT provides highly discrepant estimates of the interlaboratory CV. Due to differences in commutability of the EQA materials, the results from different peer groups could not be compared. To improve the informative value of the EQA data, the existing limitations such as non-harmonized conditions and suboptimal and/or unknown commutability of the EQA materials have to be overcome. The study highlights the need for commutable reference materials that could be used to properly evaluate result comparability and possibly standardize calibration, if necessary. Such an initiative would further improve the safe use of PCT in clinical routine.

Development of an antibody-free ID-LC MS method for the quantification of procalcitonin in human serum at sub-microgram per liter level using a peptide-based calibration.

The quantification of low abundant proteins in complex matrices by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains challenging. A measurement procedure based on optimized antibody-free sample preparation and isotope dilution coupled to LC-MS/MS was developed to quantify procalcitonin (PCT) in human serum at sub-microgram per liter level. A combination of sodium deoxycholate-assisted protein precipitation with acetonitrile, solid-phase extraction, and trypsin digestion assisted with Tween-20 enhanced the method sensitivity. Linearity was established through peptide-based calibration curves in the serum matrix (0.092-5.222 µg/L of PCT) with a good linear fit (R2 ≥ 0.999). Quality control materials spiked with known amounts of protein-based standards were used to evaluate the method's accuracy. The bias ranged from -2.6 to +4.3%, and the intra-day and inter-day coefficients of variations (CVs) were below 2.2% for peptide-based quality controls. A well-characterized correction factor was determined and applied to compensate for digestion incompleteness and material loss before the internal standards spike. Results with metrological traceability to the SI units were established using standard peptide of well-characterized purity determined by peptide impurity corrected amino acid analysis. The validated method enables accurate quantification of PCT in human serum at a limit of quantification down to 0.245 µg/L (bias -1.9%, precision 9.1%). The method was successfully applied to serum samples obtained from patients with sepsis. Interestingly, the PCT concentration reported implementing the isotope dilution LC-MS/MS method was twofold lower than the concentration provided by an immunoassay.

Malignant Melanoma of Anorectum: Two Case Reports.

Malignant melanoma of the anorectum is a rare disorder. Patients often present with local symptoms similar to benign diseases. The prognosis is very poor, and almost all patients die because of metastases. We report 2 female patients with unremarkable histories. Both of them received previous operations before visiting our center after they were diagnosed with anorectal malignant melanoma. One case underwent abdominoperineal resection and postoperative chemotherapy. The other had been treated with ultralow anterior resection followed by immunotherapy.

Evaluation of the necessity and the feasibility of the standardization of procalcitonin measurements: Activities of IFCC WG-PCT with involvement of all stakeholders.

Procalcitonin (PCT) is an important biomarker for sepsis diagnosis and management. To date, there is no higher-order reference measurement procedure (RMP) and certified reference material to achieve global standardization of results and results traceability to the SI units. Although efforts have been made to harmonize PCT results, a number of comparison studies and external quality assessment (EQA) schemes show conflicting results regarding results comparability and to date, equivalence of PCT results across the assays remains questionable in absence of studies relying on commutable EQA materials. In this context, the IFCC initiated activities to fill these gaps through the creation of the working group on standardization of PCT assays that gathers experts from National Metrology Institutes, calibration laboratories, clinicians, biologists, EQA providers and assay manufacturers. Among the activities, a higher order RMP and commutable reference materials are under development to build a robust reference measurement system (RMS). A commutability study is being organized to identify EQA materials that are fit for purpose to reliably estimate the current comparability of PCT results. This work will make it possible to evaluate the necessity and the feasibility for establishing and maintaining a new RMS for PCT assays, if deemed necessary.

Multi-Sensor Data Fusion in A Real-Time Support System for On-Duty Firefighters.

While working on fire ground, firefighters risk their well-being in a state where any incident might cause not only injuries, but also fatality. They may be incapacitated by unpredicted falls due to floor cracks, holes, structure failure, gas explosion, exposure to toxic gases, or being stuck in narrow path, etc. Having acknowledged this need, in this study, we focus on developing an efficient portable system to detect firefighter's falls, loss of physical performance, and alert high CO level by using a microcontroller carried by a firefighter with data fusion from a 3-DOF (degrees of freedom) accelerometer, 3-DOF gyroscope, 3-DOF magnetometer, barometer, and a MQ7 sensor using our proposed fall detection, loss of physical performance detection, and CO monitoring algorithms. By the combination of five sensors and highly efficient data fusion algorithms to observe the fall event, loss of physical performance, and detect high CO level, we can distinguish among falling, loss of physical performance, and the other on-duty activities (ODAs) such as standing, walking, running, jogging, crawling, climbing up/down stairs, and moving up/down in elevators. Signals from these sensors are sent to the microcontroller to detect fall, loss of physical performance, and alert high CO level. The proposed algorithms can achieve 100% of accuracy, specificity, and sensitivity in our experimental datasets and 97.96%, 100%, and 95.89% in public datasets in distinguishing between falls and ODAs activities, respectively. Furthermore, the proposed algorithm perfectly distinguishes between loss of physical performance and up/down movement in the elevator based on barometric data fusion. If a firefighter is unconscious following the fall or loss of physical performance, an alert message will be sent to their incident commander (IC) via the nRF224L01 module.

Two-dimensional complex shear modulus imaging of soft tissues by integration of Algebraic Helmoltz Inversion and LMS filter into dealing with noisy data: a simulation study.

Elasticity and viscosity of soft tissues can be obtained from the complex shear modulus imaging (CSMI). CSMI is often used not only to investigate the structure of tissues but also to detect tumors in tissues. One of the most popular ways to categorize the methods used in CSMI is into quasi-static and dynamic methods. In the dynamic method, a force excitation is used to create the shear wave propagation, and the particle velocities are measured to extract their amplitude and phase at spatial locations. These parameters are then employed to directly or indirectly estimate the Complex Shear Modulus (CSM) represented by elasticity and viscosity. Algebraic Helmholtz Inversion (AHI) algorithm provides the direct estimation of CSM using the Finite Difference Time Domain (FDTD) technique. The limitation of this method, however, is that the noise generated from measuring the particle velocity strongly degrades the accuracy of the estimation. To overcome this problem, we proposed in this paper an adaptive AHI (AAHI) algorithm that offers a good performance in CSMI with a mean error of 2.06%.

Development of temperature controller-integrated portable HIFU driver for thermal coagulation.

BACKGROUND: Temperature monitoring during high-intensity focused ultrasound (HIFU) therapy on tissue is essential to regulate the degree of thermal coagulation and to achieve the desired treatment outcomes eventually. The aim of the current study was to design and investigate the feasibility of a proportional-integral-derivative (PID) temperature controller-integrated portable HIFU driver for thermal coagulation. METHODS: A portable HIFU driver was designed and operated at a maximum output voltage of 50 V with pulse-width modulation signals at 2 MHz. The temperature of ex vivo bovine liver tissue was monitored using a K-type thermocouple during the 2-MHz HIFU exposure. RESULTS: The tissue temperature was maintained at 60 °C using a PID controller-integrated HIFU driver that modulated the output voltage during the 300-s HIFU exposure. The ex vivo testing demonstrated that the tissue temperature at the focal point approached the chosen temperature, i.e., 60 °C, within 70 s. The temperature was maintained with a deviation of less than 4 °C until the HIFU driver voltage was turned off at 300 s. CONCLUSIONS: The designed PID controller-integrated HIFU driver can be used as a small portable tool to regulate the tissue temperature in real time and achieve thermal coagulation via HIFU sonication.

Measurement of Human Gait Symmetry using Body Surface Normals Extracted from Depth Maps.

In this paper, we introduce an approach for measuring human gait symmetry where the input is a sequence of depth maps of subject walking on a treadmill. Body surface normals are used to describe 3D information of the walking subject in each frame. Two different schemes for embedding the temporal factor into a symmetry index are proposed. Experiments on the whole body, as well as the lower limbs, were also considered to assess the usefulness of upper body information in this task. The potential of our method was demonstrated with a dataset of 97,200 depth maps of nine different walking gaits. An ROC analysis for abnormal gait detection gave the best result ( AUC = 0.958 ) compared with other related studies. The experimental results provided by our method confirm the contribution of upper body in gait analysis as well as the reliability of approximating average gait symmetry index without explicitly considering individual gait cycles for asymmetry detection.

A Rare Colonic Metastasis Case from Hepatocellular Carcinoma.

BACKGROUND: Hepatocellularcarcinoma (HCC) metastasis include intrahepatic and extrahepatic metastasis. Similar to intrahepatic metastasis, extrahepatic metastases are not unusual in cases with HCC. However, colonic metastasis is infrequent. CASE REPORT: We describe a clinical case, he was diagnosed with HCC a year ago, treated with TACE (transarterialchemoembolisation), re-examined with abdominal pain and defecation disorder. The tests such as CT scan, colorectal endoscopy, fine needle aspiration (FNA) revealed secondary metastatic lesion of HCC in sigmoid colon. This is the first gastrointestinal (GI) tract metastatic we have encountered. CONCLUSION: HCC metastases of the colon are rare, especially cases of hematogenous spread. The prognosis of these patients is often very critical. Indications for surgical removal of the lesion may be used if the general situation of patient is acceptable.

Human gait symmetry assessment using a depth camera and mirrors.

It is proposed in this paper a reliable approach for human gait symmetry assessment using a Time-of-Flight (ToF) depth camera and two mirrors. The setup formed from these devices provides a sequence of 3D point clouds that is the input of our system. A cylindrical histogram is estimated for describing the posture in each point cloud. The sequence of such histograms is then separated into two sequences of sub-histograms representing two half-bodies. A cross-correlation technique is finally applied to provide values describing gait symmetry indices. The evaluation was performed on 9 different gait types to demonstrate the ability of our approach in assessing gait symmetry. A comparison between our system and related methods, that employ different input data types, is also provided.

Quantification of Idelalisib in Human Plasma by Ultra-Performance Liquid Chromatography Coupled to Mass Spectrometry in Negative Ionization Mode.

BACKGROUND: Idelalisib is the first orally active selective phosphatidylinositol 3-kinase delta inhibitor approved by Food and Drug Administration and European Medicines Agency in 2014 for the treatment of several types of blood cancer. Idelalisib is widely used as a monotherapy or in combination with rituximab, bendamustine, or ofatumumab with a significant efficacy. However, idelalisib has shown increased risk of infection and a higher frequency of serious adverse events. It may be useful to determine idelalisib concentration in human plasma to adjust dose and to manage adverse effects in clinical practice. METHODS: After a single-step protein precipitation of plasma samples, the chromatographic separation was performed using an ultra-high performance liquid chromatography system coupled with mass tandem spectrometry in a negative ionization mode using isotope-labeled internal standard. This method was validated by studies of its linearity, accuracy, imprecision, limit of quantification, recovery, matrix effect, selectivity, and stability. RESULTS: The quantification method was linear from 10 to 2500 ng/mL with a 5 ng/mL lower limit of quantification that encompasses the clinical range of drug concentration. The intraday and interday imprecisions were below 8.1% and 11.4%, respectively. The recoveries and matrix effect of idelalisib were 85.6% ± 1.2% and 95.7% ± 3.0%, respectively, which are consistent, precise, and reproducible (coefficient of variation % < 15%). Peak plasma concentration and trough plasma concentration ranges of idelalisib reached 1591-1937 ng/mL and 256.3-303.3 ng/mL, respectively, in 3 follicular lymphoma patients treated with idelalisib 150 mg twice a day. CONCLUSIONS: A robust and sensitive liquid chromatography-tandem mass spectrometry method was developed and validated to quantify idelalisib concentration in human plasma. This method was effectively applied to 3 follicular lymphoma patients.