bluuebunny/crossref_metadata_2025 huggingface dataset:
B-300 Importance of Clinical Chemistry and Metabolism Parameters for the Management of Patient With Chronic Nitrous Oxide Intoxication
Authors: Grzych G , Gernez E , Marchand D , Deheul S , Zerimech F , Masso V , Bennis A , Diesnis R , Joncquel M , Kim I , Niguet J , Guichard J , Girot M , Tard C
Published: September 2023

Background

Recreational use of nitrous oxide (N2O) has increased exponentially recently and leads to severe neurological disorders. A recent report from European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) showed that the recreational use of N2O is a growing and became a major health issue in Europe. For biological monitoring, serum or urine N2O assays are not routinely performed because they do not allow to ensure a real exposure due to the very short half-life of this gas in the body. Functional disorders of vitamin B12 metabolism, characteristic of N2O intoxication, could be explored by two markers: homocysteine (Hcys) and methylmalonic acid (MMA). We experimented here, management of N2O abused patient thanks to functional markers as Hcys and MMA.

Methods

We collected clinical and biological data from patients with declared chronic N2O consumption. The patients treated in Lille University Hospital between september 2020 and december 2022 were included in the study. The clinical evaluation included the Peripheral Neuropathy Disability (PND) score which was evaluated by a neurologist.

Results

Our study included 202 patients with N2O abused, Globally, plasma functional markers concentration are increased in case on consumption (Table). We noticed that clinical sign of patient evaluated by PND score correlated with plasma MMA (P-value < 0.01) but not with plasma hcys (P-value > 0.05).

Conclusion

The use of functional markers as Hcys and MMA makes it possible to follow the metabolic disturbances of nitrous oxide abused patients and evaluated clinical outcomes. However, in view of the thrombotic risk related to high Hcys and the need to quickly adapt the nutritional treatment, biological and in particular Hcys, current reporting time is not satisfactory using mass spectrometry method. Hence, our medical laboratory aim to improve our method evaluating immunoassay techniques in order to reduce the turnaround time while maintaining analytical reliability.
B-305 A Novel Dilute-n-shoot Method for Quantitating Isotonitazene and Desmetonitazene in Human Urine By LC/MS
Authors: Simms P J
Published: September 2023

Background

Isonitazene is a benzimidazole derived opioid analgesic drug related to etonitazene, which has been sold as a designer drug. According to doctors isotonitazene has the potency of 20–200 times of fentanyl. The side effects of isotonitazene are like fentanyl and has been linked to many fatalities in Europe and the US. It has led to a number of overdoses through secondhand contact, by smelling or coming in contact with skin. It is slowly replacing fentanyl as the deadliest street drug in the US. We developed a dilute-n-shoot method that would test for isotonitazene and its metabolite metodesnitazene in human urine. This method used filtration to remove unwanted particulates and protein. It reduces the number of steps needed to prepare samples for liquid chromatography/mass spectrometry analysis compared to methods that require centrifugation. This assay allows for easier training of staff. In addition, it is easily adaptable to increase sample load.

Method

Isotonitazene and metodesnitazene urine samples were prepared for LC/MS analysis by diluting them 1:20 in 0.1% formic acid in water. These samples were spiked with internal standard and filtered through a 0.2 μm Captiva 96-well filter plate. Isotonitazene and metodesnitazene concentrations were measured using LC/MS in the positive ion mode. The separation was obtained using a phenylhexyl UPLC column, 50 × 2.1 mm, 1.8 μm, along with a 50:50 acetonitrile/methanol/water formic acid gradient mobile phase.

Results

The separation was completed in a proximately 4.5 min with good resolution between isotonitazene and metodesnitazene. Validation studies demonstrated that this method was linear from 2 to 100 ng/mL, with r2 ≥ 0.990 for both isotonitazene and metodesnitazene. Interday and intraday precision for both analytes were acceptable, with CV values < 5.0%. Accuracy measurements at 5, 25 and 80 ng/mL gave results where the percent difference was ≤20% for the 4 ng/mL concentration and ≤15% for the 25 and 80 ng/mL. A study of interfering compounds showed that there were no interferences that would affect the accuracy of isotonitazene and metodesnitazene. Recovery studies showed that > 90% of each analyte was recovered from the filtration step. The LOQ was determined to be 2 ng/mL and the LOD was determined to be 0.5 ng/mL. The reportable range was determined to be 2 to 200 ng/mL. The results of this validation will be discussed in detail in this poster.

Conclusion

The method was linear and precise for both analytes over a range of 2 to 100 ng/mL. The method was reproducible and easy to use. Isotonitazene and metodesnitazene could easily be quantitated in human urine using this method.
B-338 A Clinical Research LC-MS/MS Method for the Analysis of Immunosuppressant Drugs in Whole Blood Using Capitainer B Devices
Authors: Balloch S , Calton L , Hammond G
Published: September 2023

Background

Traditional laboratory analysis of the immunosuppressant drugs cyclosporine, everolimus, sirolimus and tacrolimus is well-established in clinical research. However there remains a need for individuals to undergo an invasive, time-consuming and disruptive process under the supervision of trained staff in order to collect a sufficient volume of whole blood for laboratory analysis. A reliable, remote sampling method may find utility in a clinical research setting. Here we describe the use of Capitainer® B qDBS devices to obtain analytically sensitive, precise and accurate data for cyclosporine, everolimus, sirolimus and tacrolimus analysis using small sample volumes. The Waters ACQUITY™ UPLC I-Class with Xevo™ TQ Absolute mass spectrometer was used to analyze these samples.

Methods

An in-house laboratory developed LC-MS/MS method to analyze all four immunosuppressants in a single ruin was developed. Waters MassTrak Immunosuppressant Calibrator and Control Sets (IVD) and whole blood External Quality Assurance samples (LGC, Bury, UK) were used in conjunction with Capitainer® B qDBS devices to assess the performance of the method. Samples were collected using Capitainer® B qDBS devices, and the sample (10 µL) extracted using solvent containing internal standards. A water/methanol/ammonium acetate gradient was used with a Waters C18 HSS SB column on a Waters ACQUITY™ UPLC™ I-Class and Xevo TQ Absolute Mass Spectrometer operating in positive electrospray ionization mode with run time of less than 2 min.

Results

Analytical sensitivity of the lowest calibrator at 1 ng/mL for everolimus, sirolimus and tacrolimus and 25 ng/mL for cyclosporine was demonstrated with S/N (PtP) > 10 across five analytical runs. We successfully demonstrated linearity of cyclosporine from 25–1500 ng/mL and everolimus, sirolimus and tacrolimus from 1–30 ng/mL, with r2 > 0.995 over five analytical runs. Total precision and repeatability across the four immunosuppressants (2, 8 and 22 ng/mL for everolimus, tacrolimus and tacrolimus; 150, 400 and 900 ng/mL for cyclosporine) with five replicates over five analytical runs (n = 25) was ≤15% CV. External quality assurance samples for all drugs met the scheme acceptance criteria, with mean bias ≤15% CV.

Conclusion

Using Capitainer® B qDBS devices and sample small volumes (10 µL) of whole blood, an in-house laboratory method was used to meet validation goals for analytical sensitivity, linearity, precision and accuracy for cyclosporine, everolimus, sirolimus and tacrolimus. Furthermore, the advantages conferred by volumetric absorptive microsampling, notably removing the requirement for travel and a venous blood draw and facilitating home sampling, render this technique applicable to clinical research. For Research Use Only. Not for Use in Diagnostic Procedures.
B-356 Advancements in Commercial Viability of a Blood Test for the Early Detection of Breast Cancer
Authors: Kehelpanalla C , Pascovici D , Li D , Heffernan K , David M , Huynh K , Lamoury G , Ekroos K , Meikle P J , Batarseh A M
Published: September 2023

Background

Mammography is the current diagnostic standard for breast cancer screening and monitoring. However, accessibility challenges, accuracy issues and patient discomfort all contribute to reduced patient compliance and utilization, resulting in a need for more effective diagnostic tools. A blood test to detect early-stage breast cancer is sought to increase the screening detection rate, provide more accurate monitoring tools, and improve outcomes for patients. We have previously reported a series of lipidomic studies and derived a lipid signature from plasma enriched extracellular vesicles (EVs) that effectively distinguished people with localized breast cancer from cancer-free controls. Here we report on a significant refinement to the test methodology allowing the assessment of the lipid signature directly from plasma samples and its performance, with the aim of advancing the commercial viability of the test as we move towards clinical application.

Methods

Lipids in EVs from fasted breast cancer and control blood samples (4 separate cohorts (n = 793)) were extracted and analysed by liquid chromatography-high resolution mass spectrometry (LC-HRAM-MS). Over 400 manually curated lipids were quantified. From these, an independent review and retrospective analysis of the data established a lipid signature. The lipid signature was modelled on each of the cohorts using leave-one-out internal cross-validation. Following variable selection, a lipid signature capable of distinguishing breast cancer samples from controls was derived. Furthermore, we investigated if the lipid signature can be assessed from plasma instead of EVs with the aim of further streamlining the process. We analysed the lipids in cancer and control plasma samples (n = 256) previously used for EV preparations, corresponding to patients from Cohorts 3 and 4, and applied the signature derived using EVs on plasma lipidomic data. NIST Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma was used for inter-laboratory quality control.

Results

Breast cancer subjects were differentiated from controls by the lipid signature with an area under the curve (AUC) of 0.77–0.89 across four cohorts. Assessing the signature directly from plasma, the test achieved a comparable AUC of 0.84. This improvement would make the test more clinically viable and easier to perform.

Conclusion

We derived a lipid signature, which shows high potential for distinguishing breast cancer samples from controls directly from plasma instead of EVs, reducing the test complexity. Ongoing studies will optimize the plasma lipidomic signature and prospectively compare the test against mammographic and pathological diagnoses.
B-360 Usefulness of the Ratios of CYFRA21-1 and p53 Autoantibody Immune Complexes to Their Free Antigens in Lung Cancer
Authors: Hong Y , Kim H , Lee J , Oh A , Kim H
Published: September 2023

Background

Autoantibodies against specific cancer-associated antigens are produced in the early stages of tumorigenesis. In lung cancer, the possibility of autoantibodies as diagnostic biomarkers has been proposed. This study was to evaluate the usefulness of novel DNA-guided sandwich immunoassay detecting CYFRA21-1 and p53 autoantibody immune complexes and their free antigens in diagnosis of lung cancer.

Methods

In total, 100 patients with lung cancer and 119 healthy controls were analyzed with 9G testTM Lung/Cancer (Biometrix Technology, South Korea) measuring plasma autoantibody immune complexes (CYFRA21-1 with anti-CYFRA21-1 autoantibody immune complex (CIC), p53 with anti-p53 autoantibody immune complex (PIC)) and their free antigens (CYFRA 21-1 and p53). The ratios of CIC to CYFRA21-1 (CIC/CYFRA21-1) and PIC to p53 (PIC/p53), and the multiplication of the two ratios, named as LC index were calculated.

Results

The levels of CIC and PIC were significantly increased in lung cancer compared with those in healthy control (P = 0.0062 and P = 0.0026, respectively), while free antigens didn’t distinguish between lung cancer and healthy control. The ratios CIC/CYFRA21-1 and PIC/p53 were significantly higher in lung cancer than those in healthy control (all, P < 0.0001). Diagnostic performances expressed as area under the curve (AUC) were higher in the ratios of autoantibody immune complexes to each free antigen (PIC/p53 and CIC/CYFRA21-1) than autoantibody immune complexes (PIC and CIC) (AUC; 0.887, 0.847 vs 0.618, 0.608, respectively). The most excellent diagnostic performance was proven with LC index at diagnostic cut-off 3.60, which showed 81% sensitivity and 95% specificity with 0.945 AUC (P < 0.001). It was more sensitive to early lung cancer than to advanced lung cancer (sensitivity 87.5% vs 72.7%).

Conclusion

The ratios of CIC to CYFRA21-1 and PIC to p53 are useful biomarkers in lung cancer diagnosis and the combination of the ratios, LC index could be complementary tool for lung cancer screening with radiological tests.
B-379 Analytical Performance of Two Tumor Marker Immunoassays on the Atellica CI 1900 Analyzer
Authors: Quintanilla M , Baldys A , Thakur K , Arrode-Bruses G , Rhea-McManus J , Leipold H
Published: September 2023

Background

The Atellica® CI 1900 Analyzer is an automated, mid-throughput, integrated chemistry and immunoassay analyzer utilizing both Atellica CH and Atellica IM assays. This study was designed to evaluate the analytical performance of the Atellica IM Carcinoembryonic Antigen (CEA) and Alpha Fetoprotein (AFP) assays* on the Atellica CI 1900 Analyzer.

Methods

The Atellica CI 1900 CEA and AFP assays use the same reagents and calibrators as the comparable Atellica IM assays. Precision and method comparison (MC) were used as performance indicators for the Atellica CI 1900 Analyzer. Precision studies were performed according to CLSI EP05-A3 using quality control, native, and contrived human serum samples. One aliquot of each sample pool was tested in duplicate in two runs per day ≥2 h apart on each analyzer for ≥20 days. MC studies were performed according to CLSI EP09-A3. Individual native and contrived human serum samples were analyzed using the Atellica IM assays on both the Atellica IM and Atellica CI 1900 Analyzers.

Results

Representative precision and MC results observed for each assay across indicated sample ranges are listed in the table. Slopes determined by the Deming linear regression model were approximately equal to 1.

Conclusion

Evaluation of the CEA and AFP assays using the Atellica CI 1900 Analyzer demonstrated good precision and equivalent performance compared to the same assays on the Atellica IM Analyzer.

*The products/features mentioned here are not commercially available in all countries. Their future availability cannot be guaranteed.
B-380 Drift of Freelite on Optilite
Authors: Griffiths M H , Kulasingam V , Cheng P L , Wang X Y , Schneider R J
Published: September 2023

Background

Serum free light chains (sFLC) which include kappa (KFLC), lambda (LFLC) and their ratio (K/L) are used for diagnosis and monitoring of plasma cell dyscrasias (PCDs). In 2002, the Binding Site Freelite assay established reference intervals (RIs) for KFLC, LFLC and K/L. Since that time, renal RIs have been proposed and drift for the Freelite assays has been reported. The objective of this study was to evaluate healthy and renal insufficiency population RIs and examine retrospective data to ascertain the reported assay drift.

Methods

260 serum samples were measured using the Freelite assay on the Optilite. Creatinine was measured on the Abbott Alinity and eGFR was calculated. Binding Site’s RIs for KFLC, LFLC and K/L were compared to samples with ≥60 eGFR and ≤59 eGFR samples were compared to the hypergammaglobulinemia population from a previous report in 2002. IFE was used to exclude samples with detectable monoclonal proteins. Retrospective data from University Health Network (UHN) was examined.

Results

The comparison results for the samples are in the tables below:

The data suggest that Freelite has drifted up approximately 300% for KFLC, 150% for LFLC and 200% for K/L. Using 220 000 data points from UHN and applying these recalibration factors, the normal KFLC vs LFLC bivariate distribution appears centered to the well-known ‘0.26–1.65’ K/L 100% diagnostic range.

Conclusions

Drift of Freelite is confirmed with this study and recalibration factors for Freelite are proposed which are lower KFLC values by 300% and lower LFLC values by 150% for K/L to be centered to 0.26–1.65. Institutions should review their data with Freelite on Optilite and any clinical data to confirm this finding. Drift of this magnitude has the potential to cause false positives for kappa and false negatives for lambda in the diagnosis and monitoring of PCDs.
B-389 Validation of One-step In-house RT-qPCR Method for Detecting MLL::AF4 Fusion
Authors: Marques F K , Zauli D A
Published: September 2023

Background

Rearrangements of mixed lineage leukemia gene (MLL) with 1 of >130 alternative partner genes is a recurrent cytogenetic finding in both acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) and is generally associated with a poor prognosis. Among the most common MLL rearrangement is t(4;11)(q21;q23), forming the MLL::AF4 (also known as KMT2A::AFF1) fusion gene. Unique among MLL rearrangements, MLL::AF4 is almost exclusively associated with pro-B cell ALL and is prototypical of infant ALL, where it carries a very poor prognosis. At least 10 different MLL-AF4 fusion transcripts have been found, due to break-points in different introns, some transcripts being more frequent in either adult or infant ALL. Fast and reliable diagnostic tests represent an important tool in clinical laboratories to detect these rearrangements and . In this context, this work aimed to validate a qualitative method to detect the main MLL::AF4 fusion isoforms.

Methods

We evaluated the performance of the Hs03043614_ft (e10e4, e9e4 and e9e5) and Hs03024412_ft (e11e4) inventoried TaqMan assays (Thermo Fisher Scientific). Total mRNA from negative and positive samples for each fusion was extracted by the TRIzol reagent according to the manufacturer’s instructions. All assays were performed using TaqMan RNA-to-Ct 1-Step kit (Thermo Fisher Scientific). The inventoried ABL1 assay (Thermo Fisher Scientific) was used as endogenous control. Using positive samples, negative samples and controls of each fusion were performed: sequence verification tests, standardization of RNA input, evaluation of reaction efficiency and determination of the detection limit (LOD). The performance of the assays was evaluated with ABL1 control separately from the fusions.

Results

Our results showed that both assays worked well for the detection of specific fusions. The best RNA input for the reactions was 200 ng. The efficiencies reactions were: a) with ABL1 in separate reactions: 92.6% and 110.0% for Hs03043614_ft and Hs03024412_ft assays, respectively; The literature recommends the limit of efficiency was between 90% and 110%. The LODs with ABL1 in separate reactions were 10−3 for both assays, respectively. There was no unspecific amplification in negative samples.

Conclusion

The TaqMan assays with RT one-step protocol evaluated are highly sensitive, fast, and reliable tools for detecting the most frequent MLL::AF4 fusion transcripts.
Acquired cardiovascular disease in adults with congenital heart disease
Authors: Brida Margarita , De Rosa Salvatore , Legendre Antoine , Ladouceur Magalie , Dos Subira Laura , Scognamiglio Giancarlo , Di Mario Carlo , Roos-Hesselink Jolien , Goossens Eva , Diller Gerhard , Gatzoulis Michael A
Published: September 2023

Rates of successful surgical repair and life expectancy for patients with congenital heart disease have increased dramatically in recent decades. Thanks to advances in diagnosis, treatment, and follow-up care, an ever-increasing number of individuals with congenital heart disease are reaching advanced age. The exposure to cardiovascular risk factors during their lifetime is modifying the outlook and late clinical trajectory of adult congenital heart disease (ACHD). Their disease burden is shifting from congenital to acquired, primarily atherosclerotic cardiovascular disease (ASCVD) with worrisome consequences. In addition, the complex background of ACHD often curbs appropriate preventive strategies by general practitioners or adult cardiologists. Comprehensive guidance for the prevention and management of acquired heart disease in ACHD patients is currently not available, as this topic has not been covered by the European Society of Cardiology (ESC) guidelines on cardiovascular disease prevention or the ESC guidelines for the management of ACHD. In this document, a state-of-the-art overview of acquired heart disease in ACHD patients and guidance on ASCVD prevention for both ACHD specialists and non-ACHD cardiologists are provided. The aim is to provide a clinical consensus statement to foster the development of a sustainable strategy for the prevention of ASCVD in a practical and simple-to-follow way in this ever-growing cardiovascular cohort, thus reducing their cardiovascular burden.
‘Un jugement politique’: race, policy and punishment in colonial Saint-Domingue before 1789
Authors: Christie Nancy , Gauvreau Michael
Published: September 2023

This article analyses the trial of Félicité, an enslaved woman in Port-au-Prince, who was convicted of theft and arson in 1787 and sentenced to be executed. The case is of interest to historians, as it is one of the few complete surviving records of slave testimony from Saint-Domingue. By examining the testimony of Félicité and a number of her fellow slaves and free people of colour, the case sheds new light on the sociability and economic life of urban slaves, explores the meaning of marronage, questions the extent to which racial solidarity existed between slaves and free people of colour and probes the assertions of recent scholarship regarding the use of slave testimony as autobiographical narrative. In addition, the article advances the argument that the outcome of the trial revealed a number of fault-lines within the white governing classes, particularly over the question of the intersection between humanitarianism and judicial decision-making.
A review of misfit functions for adjoint full waveform inversion in seismology
Authors: Gao Yajian , Tilmann Frederik , Rietbrock Andreas
Published: September 2023

In seismological full waveform inversion, the choice of misfit functions plays a critical role in quantifying the discrepancy between observed and synthetic data, affecting convergence rate and also final results. We revisit and compare six commonly used misfit functions, including cross-correlation time-shift (CC), least-square waveform difference (L2), multitaper time-shift (MT), exponentiated phase shift (EP), time–frequency phase shift (TF) and zero-lag cross-correlation coefficient (CCC), with respect to their definitions, adjoint sources and misfit kernels for velocity perturbations. Synthetic tests are performed for several canonical models.

First, we simulated wave propagation in a model with a single rectangular anomaly with sharp boundaries and a smoothed variant of that model. We analysed the resulting misfit kernels first for the P-wave phase, which is highly distorted in the sharp model due to strong heterogeneities, and mostly experiences traveltime perturbations in the smooth model. Second, we considered a model where a laterally limited region is subject to layered anomalies (low velocity in the middle crust and high velocity in the lower crust) and determine misfit kernels for S and surface waves in this model. Based on these two simplified seismological scenarios, we further perform iterative test inversions using different misfit functions.

Combining the features of misfit kernels and synthetic inversion results, we find that CCC, L2 and EP are the most effective at identifying the sharpness of velocity anomalies from the direct body waves and their scattered phases. Consequently, inversion based on those misfit measures yielded the best recovery in the inversion test. For surface and S waves from crustal sources, TF appears to be the most effective in constraining the heterogeneous structure in the crust but needs more iterations for convergence than other misfit functions.
N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes
Authors: Xie Yongjing , Butler Michael
Published: September 2023

Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%–40% and 10%–17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
The conceptualization and development of critical health literacy in children: a scoping review
Authors: Jenkins Catherine L , Sykes Susie , Wills Jane
Published: September 2023

The cognitive and social practices associated with critical health literacy, such as critical appraisal of health messages and participation in political processes to address wider determinants of health, are of lifelong benefit. Understanding how and where critical health literacy development can be supported early in the life course may improve health outcomes now and in the future. This scoping review focuses on how critical health literacy in children is conceptualized and the supportive environments available for its development. Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidelines are used in reporting. Evidence retrieved was eligible for inclusion if it contained a substantive conceptual or empirical study of critical health literacy in populations aged 7–11 (middle childhood). From the included 18 peer-reviewed and grey literature sources, schools are identified as the setting most associated with the development of critical health literacy in the target age group. However, the action-oriented dimension of critical health literacy is rarely supported in the school setting. The review concludes that further research is needed to clarify how and where to support children to develop critical health literacy in and outside of school settings.
Identification of a muscle-specific isoform of VMA21 as a potent actor in X-linked myopathy with excessive autophagy pathogenesis
Authors: Cocchiararo Ilaria , Cattaneo Olivia , Rajendran Jayasimman , Chabry Florent , Cornut Mélanie , Soldati Hadrien , Bigot Anne , Mamchaoui Kamel , Gibertini Sara , Bouche Axelle , Ham Daniel J , Laumonier Thomas , Prola Alexandre , Castets Perrine
Published: September 2023

Defective lysosomal acidification is responsible for a large range of multi-systemic disorders associated with impaired autophagy. Diseases caused by mutations in the VMA21 gene stand as exceptions, specifically affecting skeletal muscle (X-linked Myopathy with Excessive Autophagy, XMEA) or liver (Congenital Disorder of Glycosylation). VMA21 chaperones vacuolar (v-) ATPase assembly, which is ubiquitously required for proper lysosomal acidification. The reason VMA21 deficiencies affect specific, but divergent tissues remains unknown. Here, we show that VMA21 encodes a yet-unreported long protein isoform, in addition to the previously described short isoform, which we name VMA21-120 and VMA21-101, respectively. In contrast to the ubiquitous pattern of VMA21-101, VMA21-120 was predominantly expressed in skeletal muscle, and rapidly up-regulated upon differentiation of mouse and human muscle precursors. Accordingly, VMA21-120 accumulated during development, regeneration and denervation of mouse skeletal muscle. In contrast, neither induction nor blockade of autophagy, in vitro and in vivo, strongly affected VMA21 isoform expression. Interestingly, VMA21-101 and VMA21-120 both localized to the sarcoplasmic reticulum of muscle cells, and interacted with the v-ATPase. While VMA21 deficiency impairs autophagy, VMA21-101 or VMA21-120 overexpression had limited impact on autophagic flux in muscle cells. Importantly, XMEA-associated mutations lead to both VMA21-101 deficiency and loss of VMA21-120 expression. These results provide important insights into the clinical diversity of VMA21-related diseases and uncover a muscle-specific VMA21 isoform that potently contributes to XMEA pathogenesis.
Which airways should we treat? Structure–function relationships and estimation of the singular input modes from the forward model alone
Authors: Donovan Graham M
Published: September 2023

Structure–function relationships occur throughout the sciences. Motivated by optimization of such systems, we develop a framework for estimating the input modes from the singular value decomposition from the action of the forward operator alone. These can then be used to determine the input (structure) changes, which induce the largest output (function) changes. The accuracy of the estimate is determined by reference to the method of snapshots. The proposed method is demonstrated on several example problems, and finally used to approximate the optimal airway treatment set for a problem in respiratory physiology.
Preinfection Neutralizing Antibodies, Omicron BA.5 Breakthrough Infection, and Long COVID: A Propensity Score-Matched Analysis
Authors: Yamamoto Shohei , Matsuda Kouki , Maeda Kenji , Horii Kumi , Okudera Kaori , Oshiro Yusuke , Inamura Natsumi , Nemoto Takashi , Takeuchi Junko S , Li Yunfei , Konishi Maki , Tsuchiya Kiyoto , Gatanaga Hiroyuki , Oka Shinichi , Mizoue Tetsuya , Sugiyama Haruhito , Aoyanagi Nobuyoshi , Mitsuya Hiroaki , Sugiura Wataru , Ohmagari Norio
Published: September 2023

Background

Data are limited on the role of preinfection humoral immunity protection against Omicron BA.5 infection and long coronavirus disease (COVID) development.

Methods

We conducted nested case-control analysis among tertiary hospital staff in Tokyo who donated blood samples in June 2022 (1 month before Omicron BA.5 wave), approximately 6 months after receiving a third dose of COVID-19 mRNA vaccine. We measured live virus-neutralizing antibody titers against wild type and Omicron BA.5, and anti–receptor-binding domain (RBD) antibody titers at preinfection, and compared them between cases and propensity-matched controls. Among the breakthrough cases, we examined association between preinfection antibody titers and incidence of long COVID.

Results

Preinfection anti-RBD and neutralizing antibody titers were lower in cases than controls. Neutralizing titers against wild type and Omicron BA.5 were 64% (95% confidence interval [CI], 42%–77%) and 72% (95% CI, 53%–83%) lower, respectively, in cases than controls. Individuals with previous Omicron BA.1/BA.2 infections were more frequent among controls than cases (10.3% vs 0.8%), and their Omicron BA.5 neutralizing titers were 12.8-fold higher than infection-naive individuals. Among cases, preinfection antibody titers were not associated with incidence of long COVID.

Conclusions

Preinfection immunogenicity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may play a role in protecting against the Omicron BA.5 infection but not preventing long COVID.
Antiviral Susceptibility of Highly Pathogenic Avian Influenza A(H5N1) Viruses Circulating Globally in 2022–2023
Authors: Andreev Konstantin , Jones Jeremy C , Seiler Patrick , Kandeil Ahmed , Turner Jasmine C M , Barman Subrata , Rubrum Adam M , Webby Richard J , Govorkova Elena A
Published: September 2023

The antiviral susceptibility of currently circulating (2022–2023) highly pathogenic avian influenza (HPAI) A(H5N1) viruses was assessed by genotypic and phenotypic approaches. The frequency was low for neuraminidase (NA) and polymerase acidic (PA) substitutions associated with reduced inhibition by NA inhibitors (21/2698, 0.78%) or the PA inhibitor baloxavir (14/2600, 0.54%). Phenotypic testing of 22 clade 2.3.2.1a and 2.3.4.4b viruses revealed broad susceptibility to NA inhibitors and baloxavir for a conclusion that most contemporary HPAI A(H5N1) viruses retain susceptibility to antiviral drugs. Novel NA-K432E and NA-T438I substitutions (N2 numbering) were identified at elevated frequencies (104/2698, 3.85%) and caused reduced zanamivir and peramivir inhibition.
Improving the quality of hospital sterilization process using failure modes and effects analysis, fuzzy logic, and machine learning: experience in tertiary dental centre
Authors: En-Naaoui Amine , Aguezzoul Aicha , Kaicer Mohammed
Published: September 2023

Activities practiced in the hospital generate several types of risks. Therefore, performing the risk assessment is one of the quality improvement keys in the healthcare sector. For this reason, healthcare managers need to design and perform efficient risk assessment processes. Failure modes and effects analysis (FMEA) is one of the most used risk assessment methods. The FMEA is a proactive technique consisting of the evaluation of failure modes associated with a studied process using three factors: occurrence, non-detection, and severity, in order to obtain the risk priority number using fuzzy logic approach and machine learning algorithms, namely the support vector machine and the k-nearest neighbours. The proposed model is applied in the case of the central sterilization unit of a tertiary national reference centre of dental treatment, where its efficiency is evaluated compared to the classical approach. These comparisons are based on expert advice and machine learning performance metrics. Our developed model proved high effectiveness throughout the results of the expert’s vote (she agrees with 96% fuzzy-FMEA results against 6% with classical FMEA results). Furthermore, the machine learning metrics show a high level of accuracy in both training data (best rate is 96%) and testing data (90%). This study represents the first study that aims to perform artificial intelligence approach to risk management in the Moroccan healthcare sector. The perspective of this study is to promote the application of the artificial intelligence in Moroccan health management, especially in the field of quality and safety management.
Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge
Authors: Sharuddin Siti S , Ramli Norhayati , Yusoff Mohd Z M , Muhammad Nor A N , Ho Li S , Maeda Toshinari
Published: September 2023

Aims

This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers.

Methods and results

The POME final discharge, upstream (unpolluted by POME), and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterized. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae [Pr(>F) = 0.028], were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway, and amino acids among the predominant metabolisms identified (FDR < 0.05, PostFC > 4, and PPDE > 0.95). This was further validated through qualitative metabolomics, whereby amino acids were detected as the predominant metabolites.

Conclusions

The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.
Supplementation with rumen-inert fat in the growing phase altered adipogenic gene expression and the size and number of adipocytes in Hanwoo steers
Authors: Bharanidharan Rajaraman , Thirugnanasambantham Krishnaraj , Kim Jayeon , Xaysana Panyavong , Viengsakoun Napasirth , Ibidhi Ridha , Oh Joonpyo , Kim Na-Yeon , Beak Seok-Hyeon , Smith Stephen B , Kim Kyoung Hoon
Published: September 2023

We hypothesized that the provision of rumen-inert fat (RIF) to growing cattle (9 to 13 mo of age) would affect the expression of genes involved in lipid metabolism and thereby affect the size and number of adipocytes of steers slaughtered at 30 mo of age. Thirty steers with an average initial body weight (BW) of 239 ± 25 kg were allocated to six pens, balanced for BW and genetic merit for marbling, and assigned to one of two treatment groups: control (only basal diet) or test diet (basal diet with 200 g of RIF per day, on an as-fed basis) for 5 mo. Biopsy samples of longissimus lumborum (LM) muscle were then collected for analysis of fatty acid composition and gene expression. Both groups were then fed the same basal diets during the early and late fattening phases, without RIF, until slaughter (average shrunk BW = 759 kg). Supplementation with RIF increased the longissimus thoracis (LT) intramuscular fatty acid concentration at slaughter (P = 0.087) and numerically increased the quality grade score (P = 0.106). The LM intramuscular relative mRNA expression of genes such as PPARα, ZFP423 and SREBP1, FASN, SCD, FABP4, GPAT1, and DGAT2 were downregulated (P < 0.1) following RIF supplementation. Supplementation of RIF decreased (P < 0.1) diameter and concomitantly increased intramuscular adipocytes per viewing section at slaughter. This likely was caused by promotion of triacylglycerol hydrolysis during the growing phase. Another possible explanation is that the relative mRNA expression of gene ATGL was upregulated by RIF supplementation during the growing (P < 0.1) and the fattening phases (P < 0.05), while the genes associated with fatty acid uptake (FABP4) and esterification (DGAT2) were downregulated during the growing phase and upregulated (P < 0.1) during the fattening phase. This implies that the lipid turnover rate was higher for steers during the growing than fattening phase. This study demonstrated that RIF supplementation during the growing phase induced a carryover effect on the lipogenic transcriptional regulation involved in adipocyte lipid content of intramuscular adipose tissue; increased triacylglycerol hydrolysis during the growing phase subsequently was followed by increased lipid accumulation during the fattening phases.
Root and community inference on the latent growth process of a network
Authors: Crane Harry , Xu Min
Published: September 2023

Many statistical models for networks overlook the fact that most real-world networks are formed through a growth process. To address this, we introduce the Preferential Attachment Plus Erdős–Rényi model, where we let a random network G be the union of a preferential attachment (PA) tree T and additional Erdős–Rényi (ER) random edges. The PA tree captures the underlying growth process of a network where vertices/edges are added sequentially, while the ER component can be regarded as noise. Given only one snapshot of the final network G, we study the problem of constructing confidence sets for the root node of the unobserved growth process; the root node can be patient zero in an infection network or the source of fake news in a social network. We propose inference algorithms based on Gibbs sampling that scales to networks with millions of nodes and provide theoretical analysis showing that the size of the confidence set is small if the noise level of the ER edges is not too large. We also propose variations of the model in which multiple growth processes occur simultaneously, reflecting the growth of multiple communities; we use these models to provide a new approach to community detection.
Clonal aggregation of fluconazole-resistant Candida tropicalis isolated from sterile body fluid specimens from patients in Hefei, China
Authors: Wang Ying , Wan Xin , Zhao Li , Jin Peipei , Zhang Ju , Zhou Xin , Ye Naifang , Wang Xiaowei , Pan Yaping , Xu Liangfei
Published: September 2023

Candida tropicalis, a human conditionally pathogenic yeast, is distributed globally, especially in Asia-Pacific. The increasing morbidity and azole resistance of C. tropicalis have made clinical treatment difficult. The correlation between clonality and antifungal susceptibility of clinical C. tropicalis isolates has been reported. To study the putative correlation in C. tropicalis isolated from normally sterile body fluid specimens and explore the distinct clonal complex (CC) in Hefei, 256 clinical C. tropicalis isolates were collected from four teaching hospitals during 2016–2019, of which 30 were fluconazole-resistant (FR). Genetic profiles of 63 isolates, including 30 FR isolates and 33 fluconazole-susceptible (FS) isolates, were characterized using multilocus sequence typing (MLST). Phylogenetic analysis of the data was conducted using UPGMA (unweighted pair group method with arithmetic averages) and the minimum spanning tree algorithm. MLST clonal complexes (CCs) were analyzed using the goeBURST package. Among 35 differentiated diploid sequence types (DSTs), 16 DSTs and 1 genotype were identified as novel. A total of 35 DSTs were assigned to five major CCs based on goeBURST analysis. CC1 (containing DST376, 505, 507, 1221, 1222, 1223, 1226, and 1229) accounted for 86.7% (26/30) of the FR isolates. However, the genetic relationships among the FS isolates were relatively decentralized. The local FR CC1 belongs to a large fluconazole non-susceptible CC8 in global isolates, of which the putative founder genotype was DST225. The putative correlation between MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Hefei showed that DSTs are closely related to FR clones.
Shared and unique antibody and B cell profiles in HIV-positive and HIV-negative individuals with cryptococcal meningoencephalitis
Authors: Yoon Hyunah , Nakouzi Antonio S , Duong Van Anh , Hung Le Quoc , Binh Tran Quang , Tung Nguyen Le Nhu , Day Jeremy N , Pirofski Liise-anne
Published: September 2023

Host non-T cell markers to aid in the diagnosis of cryptococcal meningoencephalitis (CM) have not been identified. In this case-control study, we characterized antibody and B cell profiles in HIV-negative and HIV-positive Vietnamese individuals of the Kinh ethnicity recently diagnosed with CM and controls. The study included 60 HIV-negative with no known immunocompromising condition and 60 HIV-positive individuals, with 30 CM cases and 30 controls in each group. Participants were matched by age, sex, HIV serostatus, and CD4 count in the HIV-positive group. Plasma immunoglobulin (Ig) levels, including IgG1, IgG2, IgM, and IgA, Cryptococcus spp. glucuronoxylomannan (GXM)- and laminarin (branched ${\rm{\beta }}$-[1-3]-glucan)-binding IgG, IgM, IgA levels, and peripheral blood B cell subsets were measured. Logistic regression, principal component, and mediation analyses were conducted to assess associations between antibody, B cell levels, and CM. The results showed that GXM-IgG levels were higher and IgG1 and IgG2 were lower in CM cases than controls, regardless of HIV status. In HIV-negative individuals, IgG2 mediated an inverse association between CD19+CD27+CD43+CD5− (B-1b-like) cells and CM. In HIV-positive individuals, lower levels of IgA, laminarin-IgA, and CD19+CD27+IgM+IgD− (IgM+ memory B) cells were each associated with CM. The shared and distinct antibody and B cell profiles identified in HIV-negative and HIV-positive CM cases may inform the identification of non-T-cell markers of CM risk or unsuspected disease, particularly in HIV-negative individuals.
MF-Box: multifidelity and multiscale emulation for the matter power spectrum
Authors: Ho Ming-Feng , Bird Simeon , Fernandez Martin A , Shelton Christian R
Published: September 2023

We introduce MF-Box, an extended version of MFEmulator, designed as a fast surrogate for power spectra, trained using N-body simulation suites from various box sizes and particle loads. To demonstrate MF-Box’s effectiveness, we design simulation suites that include low-fidelity (LF) suites (L1 and L2) at 256 and $100 \, \rm {Mpc\, ~}h^{-1}$, each with 1283 particles, and a high-fidelity (HF) suite with 5123 particles at $256 \, \rm {Mpc\, ~}h^{-1}$, representing a higher particle load compared to the LF suites. MF-Box acts as a probabilistic resolution correction function, learning most of the cosmological dependencies from L1 and L2 simulations and rectifying resolution differences with just three HF simulations using a Gaussian process. MF-Box successfully emulates power spectra from our HF testing set with a relative error of $\lt 3~{{\ \rm per\ cent}}$ up to $k \simeq 7 \, h\rm {Mpc}{^{-1}}$ at z ∈ [0, 3], while maintaining a cost similar to our previous multifidelity approach, which was accurate only up to z = 1. The addition of an extra LF node in a smaller box significantly improves emulation accuracy for MF-Box at $k \gt 2 \, h\rm {Mpc}{^{-1}}$, increasing it by a factor of 10. We conduct an error analysis of MF-Box based on computational budget, providing guidance for optimizing budget allocation per fidelity node. Our proposed MF-Box enables future surveys to efficiently combine simulation suites of varying quality, effectively expanding the range of emulation capabilities while ensuring cost efficiency.