bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical Performance Evaluation of BioRad’s Unassayed Multiqual, Immunoassay Plus and Assayed Multiqual InteliQ Tube-Based Quality Control Materials
Authors: Laryea Erving T , Mitchell Kelsey , Standford Eric , Hernandez Julia , Wiencek Joesph R 
Published: November 2023

Abstract

Introduction
Quality control (QC) practices commonly require aliquoting of liquid material into sample cups prior to analysis. Recently, newer tube-based QC has become available that can be scanned directly onto the analyzer without additional aliquoting. In this study, we evaluate the performance of the BioRad’s Unassayed Multiqual (Mutiqual), Immunoassay (IA) Plus and Assayed InteliQ Muliqual (InteliQ) tube-based QC material. Materials and

Methods
The analytical performance of Multiqual, IA Plus and InteliQ materials were compared over 14 days at three concentrations on an Abbott Alinity ci analyzer system. The analysis included 20 unique clinical chemistry and 4 immunoassay analytes. For an applied comparison, all QC materials were analyzed using the same lot on multiple days, times, and by various laboratory team members (n=10). The means, standard deviations (SD) and coefficient of variation (CV) were calculated for each analyte. Minimum acceptable allowable imprecision (I) specifications were set using the biological variation (BV) database from European Federation for Laboratory Medicine (EFLM), which was calculated for each analyte using the equation I = 0.75*CV within-subject. Sample cups used for Multiqual and IA plus were also calculated to determine consumable waste for these materials over the study period and extrapolated for a year.

Results
Multiqual, IA Plus and InteliQ CVs for each analyte were compared to the EFLM BV database and showed comparable results for most analytes studied. Most analytes demonstrated &lt; 5% CV over the 14-day period for InteliQ except alkaline phosphatase, bicarbonate, total bilirubin, and triiodothyronine for either 1, 2 or 3 levels. Total bilirubin and free thyroxine were outside this CV for Multiqual and IA Plus. In addition, minimum acceptable allowable imprecision goals from EFLM were not met for several analytes that were included in InteliQ such as albumin, alkaline phosphatase, aspartate aminotransferase, calcium, bicarbonate, chloride, and sodium. Multiqual and IA plus analytes that did not meet imprecision goals were bicarbonate, chloride, sodium, and free thyroxine, respectively. A total of 84 sample cups were needed to perform Multiqual and IA plus QC analysis over the study period or approximately 2184 over a year.

Conclusion
Multiqual, IA Plus and InteliQ QC materials provide similar analytical performance although each material had some analytes that did not meet acceptable imprecision limits defined by EFLM. Implementation of new tube-based QC materials can reduce sample cup consumables and may reduce technologist time required to aliquot Multiqual and IA Plus.
A rare case of compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait (-alpha3.7) presented with spurious hypoxemia and moderate hemolytic anemia
Authors: Marhatta Adwait , Fang Yanan , Mulvey Joseph , Campbell Sean , Choudhuri Jui 
Published: November 2023

Abstract
We present a case of a 27-year-old female at 27 weeks of gestation, who presented at the emergency department for vaginal spotting. She was also found to have low oxygenation on pulse oximetry of approximately 82% at room air. Her SpO2 did not improve with O2 supplement. She had a similar presentation a month before, with mild light-headedness and low oxygenation. However, two repeated air blood gas (ABG) findings were normal for oxygen saturation. Hemoglobinopathy was suspected due to the disparity. She was anemic during her presentation, with hemoglobin 8.3 g/dl, RBC count 3.36 million/ul, MCV 81 fl and MCH 24.7 pg. Additional workup showed increased reticulocyte count, decreased haptoglobin, negative direct Coombs test, negative G6PD test, and no evidence of a PNH clone. Capillary hemoglobin electrophoresis showed HbA 59.8%, HbS 34.5%, HbA2 3.6% and a small peak (2.1%) in the Z8 zone with a trailing edge at HbF window. HPLC revealed an “unknown peak” of 8.2% with a retention time of 1.93 minutes as well as the HbS peak. There was also a tiny additional A2 peak unresolved from the main A2 peak. Alpha globin gene sequencing revealed one copy of the -alpha3.7 alpha-globin deletion and one copy of Hb Lansing variant in the alpha2-globin gene. This is consistent with the compound Hemoglobin Lansing/Hemoglobin S coinherited with alpha thalassemia trait. Hemoglobin Lansing is a rare unstable alpha hemoglobin variant with mutation of c.264C&gt;G resulting with a substitution of His by Gln at codon 87. The mutation was first discovered in the alpha 2 gene. Then the same mutation was found in alpha 1 gene later and named as Hemoglobin Lansing-Ramathibodi. To the best of our knowledge, this is the first reported case of Hemoglobin Lansing with alpha thalassemia trait (-alpha3.7) and HbS. Spuriously low pulse oximetry measurements have previously been reported in Hb Lansing variants. It was speculated to be due to different absorption spectra of Hb Lansing which is under study now. The patient also presented with hemolytic anemia. The exact cause was undetermined yet although it might be related to her hemoglobinopathy. Mild hemolytic anemia was reported in two cases of co-inheritance of Lansing-Ramathibodi and Hb Pakse (a non-deletional alpha thalassemia) but not in the members of the same family with Hb Lansing alone. It was also reported that some unstable alpha chain variants, when associated with another alpha thalassemia defect, present with a more severe phenotype including hemolytic anemia even though essentially asymptomatic in a heterozygous state.
CytogeneticsComparability of Beckman Coulter Access Cardiac Troponin I Assays
Authors: Stanek Caroline , Martin Deirdra , Lima Jose , Cao Liyun 
Published: November 2023

Abstract
Cardiac troponins (cTn) are the most sensitive and specific biomarkers of myocardial injury. The rise and/or fall of cardiac troponins above the 99th percentile of the upper reference limit (URL) is required in the assessment of acute myocardial infarction. In our institution, high sensitivity troponin I (hsTnI) is performed on four Access 2 Immunoassay Systems and three DXI 800 Access Immunoassay Systems. As a regional medical center, we accept patients from outside hospitals where contemporary cardiac troponin I (cTnI) were performed. The results from different assays and platforms may disagree and lead to incorrect explanation of the results as false rise and/or fall of cTn. To harmonize results among these assays, we analyzed the variation between the two assays of cTnI and hsTnI, and the concordance of same assay hsTnI on different instruments using patient specimens. To investigate the between-method variance, 424 patient specimens with troponin levels ranging from 0-23370 ng/L were used to measure both cTnI and hsTnI on DXI 800 instruments. To investigate the within-method agreement, 43 patient specimens with troponin levels ranging from 2-114394 ng/L were used to measure hsTnI on Access 2 and DXI instruments. The between-method comparison of cTnI and hsTnI on DXI showed a slope of 1.003 with intercept of -43.31 and correlation coefficient (CC) of 0.9590. The mean bias was -5.1%, which was within the analytical imprecision range determined in our laboratory (2.2%-10.7%). However, comparison of cTnI and hsTnI in patients with troponin &lt;20ng/L (n=103), the 99th percentile of the URL for males, showed the slope was 1.325 with intercept of -0.97 and CC of 0.7462. The mean bias was 1.91 (21.53%), which was much larger than the analytical imprecision. This is consistent with the fact that cTnI results are not reliable at the lower level due to the imprecision problem. Comparison of cTnI and hsTnI in patients with troponin &gt;20ng/L (n=321) showed the slope was 1.006 with intercept of –60.09 and CC of 0.9576. The mean bias was -54.30 (-5.23%), which was within the analytical imprecision range. The within-method comparison of hsTnI on Access 2 and DXI 800 showed the slope was 1.138 with intercept of -633.0 and CC of 0.9888. The mean bias was 2126.4 (10.6%), within the analytical imprecision range. These data indicate that cTnI results above the 99th percentile URL are comparable with hsTnI results if both are tested on DXI 800, and hsTnI results tested on Access 2 and DXI 800 are comparable. Thus, to use the cardiac troponins assay properly, we suggest the laboratory report cardiac troponins with the assay and instrument names to reduce confusion during results comparison.
Exploration and utilization of novel aldoxime, nitrile, and nitro compounds metabolizing enzymes from plants and arthropods
Authors: Yamaguchi Takuya 
Published: November 2023

ABSTRACT
Aldoxime (R1R2C=NOH) and nitrile (R−C≡N) are nitrogen-containing compounds that are found in species representing all kingdoms of life. The enzymes discovered from the microbial “aldoxime-nitrile” pathway (aldoxime dehydratase, nitrile hydratase, amidase, and nitrilase) have been thoroughly studied because of their industrial importance. Although plants utilize cytochrome P450 monooxygenases to produce aldoxime and nitrile, many biosynthetic pathways are yet to be studied. Cyanogenic millipedes accumulate various nitrile compounds, such as mandelonitrile. However, no such aldoxime- and nitrile-metabolizing enzymes have been identified in millipedes. Here, I review the exploration of novel enzymes from plants and millipedes with characteristics distinct from those of microbial enzymes, the catalysis of industrially useful reactions, and applications of these enzymes for nitrile compound production.
ExRec: a python pipeline for generating recombination-filtered multi-locus datasets
Authors: McCarthy Potter Sam , Jennings W Bryan 
Published: November 2023

Abstract

Summary
ExRec (Exclusion of Recombined DNA) is a dependency-free Python pipeline that implements the four-gamete test to automatically filter out recombined DNA blocks from thousands of DNA sequence loci. This procedure helps all loci better meet the “no intralocus recombination” assumption common to many coalescent-based analyses in population genomic, phylogeographic, and shallow-scale phylogenomic studies. The user-friendly pipeline contains five standalone applications—four file conversion scripts and one main script that performs the recombination filtering procedures. The pipeline outputs recombination-filtered data in a variety of common formats and a tab-delimited table that displays descriptive statistics for all loci and the analysis results. A novel feature of this software is that the user can select whether to output the longest nonrecombined sequence blocks from recombined loci (current best practice) or randomly select nonrecombined blocks from loci (a newer approach). We tested ExRec with six published phylogenomic datasets that ranged in size from 27 to 2237 loci and came in a variety of input file formats. In all trials the data could be easily analyzed in only seconds for the smaller datasets and &lt;30 min for the largest using a simple laptop computer.

Availability and implementation
ExRec was written in Python 3 under the MIT license. The program applications, user manual (including step-by-step tutorials), and sample data are freely available at https://github.com/Sammccarthypotter/ExRec.
ProteinMAE: masked autoencoder for protein surface self-supervised learning
Authors: Yuan Mingzhi , Shen Ao , Fu Kexue , Guan Jiaming , Ma Yingfan , Qiao Qin , Wang Manning 
Published: November 2023

Abstract

Summary
The biological functions of proteins are determined by the chemical and geometric properties of their surfaces. Recently, with the booming progress of deep learning, a series of learning-based surface descriptors have been proposed and achieved inspirational performance in many tasks such as protein design, protein–protein interaction prediction, etc. However, they are still limited by the problem of label scarcity, since the labels are typically obtained through wet experiments. Inspired by the great success of self-supervised learning in natural language processing and computer vision, we introduce ProteinMAE, a self-supervised framework specifically designed for protein surface representation to mitigate label scarcity. Specifically, we propose an efficient network and utilize a large number of accessible unlabeled protein data to pretrain it by self-supervised learning. Then we use the pretrained weights as initialization and fine-tune the network on downstream tasks. To demonstrate the effectiveness of our method, we conduct experiments on three different downstream tasks including binding site identification in protein surface, ligand-binding protein pocket classification, and protein–protein interaction prediction. The extensive experiments show that our method not only successfully improves the network’s performance on all downstream tasks, but also achieves competitive performance with state-of-the-art methods. Moreover, our proposed network also exhibits significant advantages in terms of computational cost, which only requires less than a tenth of memory cost of previous methods.

Availability and implementation
https://github.com/phdymz/ProteinMAE.
Limited clinical validity of univariate resting-state EEG markers for classifying seizure disorders
Authors: Faiman Irene , Sparks Rachel , Winston Joel S , Brunnhuber Franz , Ciulini Naima , Young Allan H , Shotbolt Paul 
Published: November 2023

Abstract
Differentiating between epilepsy and psychogenic non-epileptic seizures presents a considerable challenge in clinical practice, resulting in frequent misdiagnosis, unnecessary treatment and long diagnostic delays. Quantitative markers extracted from resting-state EEG may reveal subtle neurophysiological differences that are diagnostically relevant. Two observational, retrospective diagnostic accuracy studies were performed to test the clinical validity of univariate resting-state EEG markers for the differential diagnosis of epilepsy and psychogenic non-epileptic seizures. Clinical EEG data were collected for 179 quasi-consecutive patients (age &gt; 18) with a suspected diagnosis of epilepsy or psychogenic non-epileptic seizures who were medication-naïve at the time of EEG; 148 age- and gender-matched patients subsequently received a diagnosis from specialist clinicians and were included in the analyses. Study 1 is a hypothesis-driven study testing the ability of theta power and peak alpha frequency to classify people with epilepsy and people with psychogenic non-epileptic seizures, with an advanced machine learning pipeline. The next study (Study 2) is data-driven; a high number of quantitative EEG features are extracted and a similar machine learning approach as Study 1 assesses whether previously unexplored univariate EEG measures show promise as diagnostic markers. The results of Study 1 suggest that EEG markers that were previously identified as promising diagnostic indicators (i.e. theta power and peak alpha frequency) have limited clinical validity for the classification of epilepsy and psychogenic non-epileptic seizures (mean accuracy: 48%). The results of Study 2 indicate that identifying univariate markers that show good correlation with a categorical diagnostic label is challenging (mean accuracy: 45–60%). This is due to a considerable overlap in neurophysiological features between the diagnostic classes considered in this study, and to the presence of more dominant EEG dynamics such as alterations due to temporal proximity to epileptiform discharges. Markers that were identified in the context of previous epilepsy research using visually normal resting-state EEG were found to have limited clinical validity for the classification task of distinguishing between people with epilepsy and people with psychogenic non-epileptic seizures. A search for alternative diagnostic markers uncovered the challenges involved and generated recommendations for further research.
Risk factors for COVID-19 hospitalization and mortality in patients with chronic kidney disease: a nationwide cohort study
Authors: Artborg Angelica , Caldinelli Aurora , Wijkström Julia , Nowak Alexandra , Fored Michael , Stendahl Maria , Evans Marie , Rydell Helena 
Published: November 2023

ABSTRACT

Background
Several studies have demonstrated an increased risk of severe coronavirus disease 2019 (COVID-19) in chronic kidney disease (CKD) patients. However, few have investigated the impact of CKD stage and dialysis modality. The primary aim of this study was to investigate the association between CKD stage, dialysis modality and risk of severe COVID-19. Secondly, we aimed to study the impact of comorbidities and drugs on the risk of severe COVID-19 in the CKD population.

Methods
This nationwide observational study was based on data from the Swedish Renal Registry and three other national registries. Patients with non-dialysis CKD stage 3b–5 or dialysis on 1 January 2020 were included and followed until 31 December 2021. The primary outcome was COVID-19 hospitalization; the secondary outcome was COVID-19 mortality. Associations were investigated using logistic regression models, adjusting for confounders.

Results
The study population comprised 7856 non-dialysis CKD patients and 4018 dialysis patients. The adjusted odds ratios (aOR) for COVID-19 hospitalization and mortality were highest in the dialysis group [aOR 2.24, 95% confidence interval (CI) 1.79–2.81; aOR 3.10, Cl 95% 2.03–4.74], followed by CKD 4 (aOR 1.33, 95% CI 1.05–1.68; aOR 1.66, Cl 95% 1.07–2.57), as compared with CKD 3b. No difference in COVID-19 outcomes was observed between patients on hemodialysis and peritoneal dialysis. Overall comorbidity burden was one of the strongest risk factors for severe COVID-19 and the risk was also increased in patients prescribed insulin, proton pump inhibitors, diuretics, antiplatelets or immunosuppressants.

Conclusions
Worsening CKD stage and comorbidity are independent risk factors for severe COVID-19 in the Swedish CKD population.
All-cause and immune checkpoint inhibitor–associated acute kidney injury in immune checkpoint inhibitor users: a meta-analysis of occurrence rate, risk factors and mortality
Authors: Chen Jia-Jin , Lee Tao-Han , Kuo George , Yen Chieh-Li , Lee Cheng-Chia , Chang Chih-Hsiang , Tu Kun-Hua , Chen Yung-Chang , Fang Ji-Tseng , Hung Cheng-Chieh , Yang Chih-Wei , Chou Wen-Chi , Chi Ching-Chi , Tu Yu-Kang , Yu Yang Huang- 
Published: November 2023

ABSTRACTBackgroundImmune checkpoint inhibitors (ICIs) have been associated with acute kidney injury (AKI). However, the occurrence rate of ICI-related AKI has not been systematically examined. Additionally, exposure to proton pump inhibitors (PPIs) and non-steroidal anti-inflammatory drugs (NSAIDs) were considered as risk factors for AKI, but with inconclusive results in ICI-related AKI. Our aim was to analyse the occurrence rate of all-cause AKI and ICI-related AKI and the occurrence rates of severe AKI and dialysis-requiring AKI, and to determine whether exposure to PPIs and NSAIDs poses a risk for all-cause and ICI-related AKI.MethodsThis study population was adult ICI recipients. A systematic review was conducted by searching MEDLINE, Embase and PubMed through October 2023. We included prospective trials and observational studies that reported any of the following outcomes: the occurrence rate of all-cause or ICI-related AKI, the relationship between PPI or NSAID exposure and AKI development or the mortality rate in the AKI or non-AKI group. Proportional meta-analysis and pairwise meta-analysis were performed. The evidence certainty was assessed using the Grading of Recommendations Assessment, Development and Evaluation framework.ResultsA total of 120 studies comprising 46 417 patients were included. The occurrence rates of all-cause AKI were 7.4% (14.6% from retrospective studies and 1.2% from prospective clinical trials). The occurrence rate of ICI-related AKI was 3.2%. The use of PPIs was associated with an odds ratio (OR) of 1.77 [95% confidence interval (CI) 1.43–2.18] for all-cause AKI and an OR of 2.42 (95% CI 1.96–2.97) for ICI-related AKI. The use of NSAIDs was associated with an OR of 1.77 (95% CI 1.10–2.83) for all-cause AKI and an OR of 2.57 (95% CI 1.68–3.93) for ICI-related AKI.ConclusionsOur analysis revealed that approximately 1 in 13 adult ICI recipients may experience all-cause AKI, while 1 in 33 adult ICI recipients may experience ICI-related AKI. Exposure to PPIs and NSAIDs was associated with an increased OR risk for AKI in the current meta-analysis.
Nur77 influences immunometabolism to regulate the release of proinflammatory cytokines and the formation of lipid bodies during Mycobacterium tuberculosis infection of macrophages
Authors: Birari Pankaj , Mal Soumya , Majumder Debayan , Sharma Arun K , Kumar Manish , Das Troyee , Ghosh Zhumur , Jana Kuladip , Gupta Umesh D , Kundu Manikuntala , Basu Joyoti 
Published: November 2023

Abstract
Infection of macrophages with Mycobacterium tuberculosis induces innate immune responses designed to clear the invading bacterium. However, bacteria often survive within the intracellular environment by exploiting these responses triggered by macrophages. Here, the role of the orphan nuclear receptor Nur77 (Nr4a1) in regulating the response of macrophages infected with M. tuberculosis (Mtb) has been delineated. Nur77 is induced early during infection, regulates metabolism by binding directly at the promoter of the TCA cycle enzyme, isocitrate dehydrogenase 2 (IDH2), to act as its repressor, and shifts the balance from a proinflammatory to an anti-inflammatory phenotype. Depletion of Nur77 increased transcription of IDH2 and, consequently, the levels of intracellular succinate, leading to enhanced levels of the proinflammatory cytokine IL-1β. Further, Nur77 inhibited the production of antibacterial nitric oxide and IL-1β in a succinate dehydrogenase (SDH)-dependent manner, suggesting that its induction favors bacterial survival by suppressing bactericidal responses. Indeed, depletion of Nur77 inhibited the intracellular survival of Mtb. On the other hand, depletion of Nur77 enhanced lipid body formation, suggesting that the fall in Nur77 levels as infection progresses likely favors foamy macrophage formation and long-term survival of Mtb in the host milieu.
King Henry VII and the case of the missing treaty: Anglo-Hungarian crusading diplomacy reconsidered
Authors: Gauthier Charlotte 
Published: November 2023

Abstract
Henry VII of England has never been considered a ‘crusader king’; his monetary contributions towards anti-Ottoman crusading have been characterized by his biographers as little more than bribes designed to constrain the ambitions of would-be pretenders to the English throne. However, an unpublished Anglo-Hungarian treaty of alliance calls such simplistic explanations into question, showing that after the death of his son Arthur, prince of Wales, in spring 1502, Henry VII attempted to insert England into a pan-European platform of anti-Ottoman alliances using the provision of crusade financing as a diplomatic lever. This article shows just how Henry VII’s ‘crusade diplomacy’ worked in practice, arguing for a reassessment of what has long appeared to be the settled question of Henry VII’s foreign policy aims and demonstrating the centrality of the ‘Turkish question’ to early sixteenth-century European diplomacy.