bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-145 An R Shiny App for Automated Peak Deconvolution, Interpretation, and Quantitation of Monoclonal Proteins Using Capillary Electrophoresis Immunotyping Data
Authors: Cotten S 
Published: September 2023

Abstract

Background
Machine learning methods have been utilized to train algorithms for interpretation of immunofixation electrophoresis. This work developed an R Shiny app for immunotyping (IT) data capable of deconvoluting discrete peaks in overlapping backgrounds and automatic quantitation of monoclonal proteins. Unlike machine learning which obfuscates decision making, each step of this deconvolution and quantitation process is displayed to the end user.

Methods
Individual traces for 1315 previously interpreted IT results were used in the study. A modified Levenberg-Marquardt algorithm using 50 sets of randomized start parameters was used for deconvolution. Primitive peak features such as height, FWHM, AUC and retention time were used to match heavy and light chain deconvoluted peaks for interpretation. The matched peak with the largest AUC was compared to reviewer interpretation and peak quantitation. Repeatability of quantitation was evaluated through 10 consecutive rounds of deconvolution. Code was written for end user visualization in Shiny or batch processing in base R.

Results
Deconvolution was successful for 97.2% (1279/1315) of specimens. Agreement between the software and reviewer interpretation was 90.6% (11 927/13 150) across all deconvolutions and was consistent for 84.7% of samples in all 10 rounds of deconvolution. Discordant interpretation in 15.3% of samples was often attributed to splitting of large peaks with sharp maximums, large percentage (but small absolute) changes in calculated AUC for monoclonal proteins under 0.5 g/dL, or drifting baseline signal between channels. Mean and median percent CV for consecutive rounds of monoclonal quantitation was 5.9% and 1.16% respectively (protein range 0.02–4.5 g/dL). Deming regression of reviewer vs software quantitation had a calculated slope of 0.728 and Pearson’s r coefficient of 0.933.

Conclusion
Deconvolution and automatic quantitation of monoclonal protein peaks is possible using the Levenberg-Marquardt algorithm for immunotyping data. Future work aims to improve interpretation agreement with reviewers using more advanced ranking of matched peaks.
B-161 Mass Spectrometric Assay for the Early Diagnosis of Barth Syndrome
Authors: Byeon S , Vernon H , Oglesbee D , Pandey A 
Published: September 2023

Abstract

Background
Barth syndrome (BTHS) is an inborn error of phospholipid metabolism caused by pathogenic variants in the TAFAZZIN gene locus on a chromosome X. TAFAZZIN encodes a phospholipid transacylase enzyme, tafazzin, that promotes cardiolipin (CL) remodeling. Deficiency of tafazzin activity in BTHS results in accumulation of monolysocardiolipin (MLCL) and decreased abundance of mature CL, making an increased ratio of MLCL to CL as a diagnostic marker for BTHS. 52:2-MLCL to 72:8-CL in dried-blood spot (DBS) has been used for provisional identification BTHS using LC-MS/MS. A development of multiplexed method that targets several species of MLCL and CL can enhance the diagnosis of BTHS.

Methods
A targeted LC-MS/MS with scheduled multiple reaction monitoring (MRM) mode in negative electrospray ionization was developed using a triple quadrupole MS. DBS from patients with BTHS were obtained at Johns Hopkins University and provided by Barth Syndrome Foundation while control DBS were provided by Biochemical Genetics Laboratory at Mayo Clinic. Internal standards and chloroform:methanol (1:1, v/v) were added to DBS (1/8″ diameter) and sonicated. Supernatants were collected and dried under nitrogen gas. Followed by reconstitution in methanol, samples were subjected to LC-MS/MS analysis.

Results
More than 20 species of MLCL and CL species having various fatty acyl chains were detected and quantified. Remodeled CL species were decreased while MLCL and nascent CL species were found to be increased in known patients of BTHS (n = 8) compared to controls (n = 8). Notably, several ratios of lipids including 52:2-MLCL/72:8-CL and 54:2-MLCL/70:6-CL showed &gt;300-fold elevation in the patients.

Conclusion
Various species of MLCL and CL that can be used to diagnose BTHS can be measured from an easily accessible specimen such as DBS using this method.
B-218 Role of Delta Tocotrienol and Resveratrol Supplementation in Regulation of Micro RNAs in Patients With Metabolic Syndrome: A Randomized Controlled Trial
Authors: Khan D A , Fatima S 
Published: September 2023

Abstract

Background
Micro-RNAs (miRNAs) are involve in the regulation of central obesity, insulin resistance, inflammation and dyslipidemia in development of MetS. δ-tocotrienol and resveratrol improve the insulin resistance, inflammation and clinico-biochemical parameters in the patients with MetS.

Objective
To determine the effect of δ-tocotrienol and Resveratrol Mixture (TRM) supplementation for 24 weeks in comparison with placebo, on the relative expression of metabolic related miR-130b, miR-221, miR-15b-, miRNA-122, and miR-376b in the patients with MetS.

Methods
This randomized placebo-controlled trial was conducted at AFIP, NUMS, Pakistan. A total of 82 adult MetS patients, aged 18 to 60 years of both genders, were enrolled and randomly grouped into TRM (n = 41) and Placebo (n = 41). The TRM group was given 400 mg capsules of (δ-tocotrienol 250 mg; Resveratrol 150 mg), and placebo received 400 mg cellulose capsules twice daily for 24 weeks. miRNA was extracted by Trizole L S reagent with cel-miR-39 (Spike-In control). The cDNA was prepared by Reverse Transcriptase Kit. miRNAs expression profile was done by using qRT-PCR Kit (Qiagen) protocol on the Rotor-Gene.

Results
The TRM supplementation significantly (P &lt; 0.001) upregulated miR-130b-5p (3.05fold), miR-221-5p (2.45fold), and downregulated miR-122-5p by 2.22fold as compared to placebo after 24 weeks. No significant difference was observed in miR-15b-5p and miR-376b-5p.
Furthermore, patients in the TRM group had significant (P &lt; 0.05) correlation in improvement of MetS biomarkers and miRNAs including hs-CRP, miR-130b; miR-221, TNF-α; miR-221, fasting plasma glucose, miR-122, triglyceride and miR-130b with waist circumference. No significant side effect was reported.

Conclusion
TRM daily supplementation in addition to dietary restriction, is effective in the improvement of the metabolic syndrome components by upregulation of miR-130b-5p involve in central obesity, inflammation; miR-221-5p by decreasing insulin resistance and downregulation of miRNA 122 to improve dyslipidemia in the patients with MetS.
B-241 A Novel Approach to Develop Multiplex Loop Mediated Amplification (LAMP) Assays
Authors: Chander Y , Mead D 
Published: September 2023

Abstract

Background
Loop mediated amplification (LAMP) technology is a sensitive, accurate and rapid method for point-of-care (POC) molecular diagnostic detection. One disadvantage is that current LAMP methods can detect only one target per reaction whereas in a standard real-time PCR assay, multiple targets (3–4) can be detected in a single reaction. This is because current methods of detection for amplification products in a LAMP assay are not sequence-specific. Common detection methods include turbidity, use of color-changing dye or intercalating dye in the reaction mix, gel electrophoresis, etc. These methods are not sequence-specific and, thus, unable to differentiate between targets if amplified in a single tube, with the exception of lateral flow devices or melt analysis, which add time, complexity, and cost. To overcome this challenge, we have developed a novel method which simplifies development of multiplex LAMP without use of any additional primers/probes/reagents or steps.

Methods
Triplex RT-LAMP assay was developed for rapid detection of foot-and-mouth disease virus (FMDV) at POC. For this, LAMP primers targeting two different regions of 3D pol gene of FMDV were designed. For use as internal control (IC), LAMP primers were also designed targeting a conserved region of the bovine 18S rRNA gene. For multiplexing, best performing primer sets for each target were labelled with a unique fluorophore at 5′ end and a quencher (BHQ-1) at 3′ end. FMDV-1 primers were labeled with Cy5 fluorophore, FMDV-2 primers were labelled with Texas Red (TxR) fluorophore, and 18S rRNA with FAM fluorophore. Triplex RT-LAMP assay was performed using a specially formulated Multiplex Isothermal Master Mix but without any intercalating dye added to the mix. All 3 primer mixes were added to the Master Mix and reactions were carried out in a real-time thermocycler at 72°C for 30 min, with data collected every 30 seconds. Reaction kinetics were monitored as an increase in fluorescence associated with the accumulation of double-stranded DNA in respective channels (FAM for 18S rRNA, Cy5 for FMDV-1, and TxR for FMDV-2).
Assay sensitivity was determined by testing 10-fold serial dilution of respective template, individually as well as mixed together.

Results
Results obtained showed feasibility of triplex RT-LAMP assay for simultaneous detection of 3 targets in a single reaction. Sensitivity and specificity of triplex RT-LAMP was comparable to control reactions (RT-LAMP assay with intercalating dye) for each target. No cross reactivity or non-specific amplification was observed with any of the primer designs.

Conclusions
This newly developed method allows detection of up to 3 targets in a single reaction without affecting the assay performance. This method is much easier to develop and optimize than previously reported methods as it uses standard LAMP primers without need of any additional primers/probes.
B-248 Rapid PCR Method for Sexually Transmitted Infection (STI) Multiplex Testing Based on Novel Microfluidic Chip
Authors: Lee S , Park J , Koo H , Kim D , Park J , Lee D 
Published: September 2023

Abstract

Background
qPCR is being widely used for STI (Sexually Transmitted Infection) testing as the most sensitive and accurate diagnostic method. Genesystem developed a novel qPCR-based diagnostic platform, called Genoplex chip, which enables the simultaneous detection of multiple sexually transmitted pathogens with a single test. Genoplex chip realized high multiplex detection (up to 14 pathogens by a single pipetting), making it easy and fast to process more targets than conventional qPCR. In this study, Genoplex chip was used for diagnosing sexually transmitted infection(STI) to verify the usefulness in diagnostics.

Methods
Genoplex chip is a flat-shaped microfluidic chip where target-specific primers and probes are prelabeled free from contamination. This chip has 1 well for negative control and 9 connected wells for target detection. By a single pipetting into the inlet hole, samples are loaded and spread into every well of this microfluidic chip since all the wells are connected to each other. We completed performance validation of this new chip with STI diagnosis. Primers and probes for identifying STI pathogens are prelabeled on the inner surface of the Genoplex chip. We can detect and identify 12 major pathogens of STI, which are Chlamydia trachomatis (CT), Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), Mycoplasma genitalium (MG), Neisseria gonorrhoeae (NG), Trichomanas vaginalis (TV), Ureaplasma parvum (UP), Gardnerella vaginalis (GV), Candida albicans (CA), Treponema pallidum (TP), Herpes simplex virus type 1 (HSV1) and Herpes simplex virus type 2 (HSV2) by using these probes. Amplification of the target genes was performed by Genechecker UF-300 PCR System.

Results
We estimated 50 copies of 12 STI pathogens by qPCR process in 40 min. We also confirmed that there was no contamination and no interference in 12 targets.

Conclusion
With Genoplex chip, various targets can be quantitatively detected in one sample and more accurate results can be provided in efficient way. This novel system gives an opportunity to overcome the limitations of current molecular diagnostics by innovative multiplex detection technology. Therefore, it is expected that the Genoplex chip system will attract attention in the molecular diagnostics market.
B-249 Usefulness of Simultaneous Detection of Germline and Somatic Variants From Different Specimen Types by Next-generation Sequencing
Authors: Han M , Kim J 
Published: September 2023

Abstract

Background
Genetic variants detection by next-generation sequencing (NGS) from tumor specimen only is considered limited in diagnosis due to difficulties in discriminating somatic variants from germline ones. It will be even more helpful in diagnosing patients with cancer if we perform NGS analysis from specimen of both tumor and blood. This study shows the usefulness of simultaneous detection of germline and somatic variants from different specimen types by NGS.

Methods
NGS panel assay designed for solid tumor composed of 80 genes was conducted for detection of both somatic and germline variants. DNA samples extracted from both buffy coat of whole blood and formalin-fixed paraffin-embedded (FFPE) specimen from 4 patients with renal cancer and 3 patients with ovarian cancer were used in assay. We compared results from both specimen and finalized somatic and germline variants detected.

Results
In 4 patients specimen with renal cell carcinoma, we were able to rule out germline variants from somatic variants by analysis of NGS assay from both specimen types. Genes ruled out for germline variants of uncertain significance (tier 3) or higher levels are ARID1B: c.1031C&gt;T, p.A344V, ERBB2: c.3430G&gt;C, p.D1144H, BRCA2: c.3220A&gt;T, p.S1074C, POLE: c.2974G&gt;A, p.A992T, EP300: c.1666A&gt;G, p.M556V, EP300: c.2539C&gt;T, p.P847S, ERBB3: c.1115C&gt;G, p.P372R, BAP1: c.1124A&gt;T, p.E375V. In 3 patients with ovarian cancer, genes ruled out are EGFR: c.739G&gt;C, p.D247H, MET: c.4172A&gt;T, p.D1391V, PBRM1: c.2678A&gt;G, p.Y893C, SETD2: c.1208G&gt;A, p.S403N, AKT1: c.1373T&gt;C, p.M458T, FGFR3: c.160G&gt;A, p.G54R, KMT2C: c.9530G&gt;A, p.R3177H, SMARCB1: c.1116G&gt;A, p.T372T. All variants confirmed are tier 3 level of clinical significance.

Conclusion
According to the results of this study, we were able to exclude germline variants form somatic ones in NGS assay reports for cancer patients. This study shows the usefulness of simultaneous detection of germline and somatic variants from different specimen types by NGS.
B-269 Plasmodium Detection: Sera, Blood, Do They All Work?
Authors: Franco-Marín E , Ulloa G , Dehesa-García B , Santolalla M , Lescano A , García-Manrique B , Mayor P , Mayor A , Alonso H 
Published: September 2023

Abstract

Background
When diagnosing malaria, testing employs blood samples using either microscopy, the current gold standard or molecular diagnostic tests (more sensitive but significantly more expensive). In Plasmodium spp. screening programs in at-risk populations where there are not many resources available, dried blood on filter paper is used to ease transport, storage and preservation of the sample. Although Plasmodium detection studies using blood serum as a sample are available, it isn´t always as sensitive as using whole blood-based sampling, as the concentration of DNA in plasma is proportional to the level of parasitaemia. This study aims to confirm the differences in sensitivity using both samples, demonstrating the importance of choosing the right type of sample to use for diagnosis.

Methods
The study was carried out using the VIASURE Malaria Real Time PCR Detection Kit with sera and blood samples from 94 inhabitants from Nueva Esperanza community in the Peruvian Amazon collected between 2007 and 2020, establishing a comparative analysis between matrixes. Nucleic acid extraction was performed using the QIAamp DNA Mini Kit from QIAGEN and the VIASURE assay was performed using QuantStudio®6 Flex Real-Time PCR System thermocycler (Thermo Fisher Scientific) and the BioRad CFX96TM Real-Time PCR Detection System for analysing peripheral blood samples and the BioRad CFX96TM Real-Time PCR Detection System for analysing sera.

Results
From the total of samples, only 5 sera (5.31%) showed amplification of Plasmodium spp., whereas from blood samples, 30 resulted to be Plasmodium spp-positive. Therefore, 26.59% of detection is lost when serum is used as a sample, as opposed to blood.

Conclusion
After this analysis it could be concluded that malaria detection sensitivity is appreciably higher for blood samples than for sera samples. Thus, serum samples aren´t the best choice for Plasmodium spp. testing and whole blood-based matrixes are preferable for this diagnosis. These results reinforce the idea of the importance of the sample type when diagnosing different pathogens, as well as the relevance of a confirming comparative analysis when similar sample types are involved.
B-284 Evaluating the Range of Serum Neurofiament Light Chain at Different Ages in Chinese
Authors: Guo S , Meng Z , Tang M , Ren Y , Ying B 
Published: September 2023

Abstract

Background
Neurofilament light chain (NFL) has recently been identified as a sensitive biomarker for diagnosis and prognosis in many neurological diseases. However, studies focused on NFL levels ranges in healthy individuals remain few, especially in the Chinese population. The clarification of the reference range among healthy individuals at different ages would be useful for further clinical utility.

Objectives
To evaluate the serum neurofilament light chain range at different ages in healthy Chinese and analyze the potential contributing factors for NFL levels.

Methods
Healthy individuals undergoing rigorous cognitive and neuroimaging detection were enrolled. Serum samples and plasma samples of different anticoagulants were collected for NFL levels detection by the ultra-sensitive Simoa HD-1 platform. The tendency of NFL levels to change with age and potential influence factors were analyzed.

Results
We enrolled three hundred and ninety-nine healthy participants. The positive correlation between serum NFL levels and age was observed and the regression formula was further established. There were no statistical differences between the &lt;20 years group and the 20–29 years group (P = 0.2512), as well as the 60–69 years group and the 70–79 years group (P = 0.0528) and differences,were statistically significant among the remaining pairwise groups. We further observed the positive correlation between serum tNFL levels and age was 0.76 in total (P &lt; 0.0001). The NFL levels between the serum and heparin plasma are statistically different and there was no statistical difference between the serum and plasma of other anticoagulants.

Conclusions
The age-related change pattern was uncovered, providing important assistance for the clinical use of NFL to monitor the potential neurological alterations for people of different ages.
B-359 Bap1 Overexpression Enhances Epithelial-mesenchymal Transition in Cholangiocarcinoma
Authors: You H , Liao W , Huang W 
Published: September 2023

Abstract

Background
BRCA1-associated protein 1 (BAP1) is a nuclear protein that considered as a tumor suppressor by its involvement in DNA double-strand-break repair. However, BAP1 overexpression was observed in many kinds of cancer, such as intrahepatic cholangiocarcinoma (iCCA).

Methods and Results
Formalin-fixed paraffin-embedded cancer tissues were acquired from the archive of the Department of Pathology, Chang Gung Memorial Hospital at Kaohsiung, Taiwan. In this study, we identified 23.8% cytoplasmic BAP1 overexpression and 20.8% nuclear BAP1 overexpression cases in 101 iCCA patients. There were significant correlations between cytoplasmic expression of BAP1 with tumor growth pattern (P = 0.005), T classification (P = 0.006), and clinical AJCC seventh staging (P &lt; 0.001). In cell models (iCCA cell line RBE), overexpressed BAP1 were accumulated in cytoplasm. The translatome profile suggested that BAP1 overexpression may promote the migratory and invasive capacities of iCCA cells. In-vitro assays validated that BAP1 overexpression enhanced cell migration and invasion. Furthermore, we found that BAP1 overexpression induced epithelial-mesenchymal transition (EMT) in iCCA cells, showing E-cadherin and fibronection down-regulation and vimentin up-regulation.

Conclusion
These findings indicated that cytoplasmic BAP1 overexpression increased migratory and invasive capacities in iCCA cells, at least in part, via enhanced EMT regulations. Based on these findings, cytoplasmic BAP1 expression could be a candidate predictor for metastasis of iCCA.
Cancer Screening, Incidental Detection, and Overdiagnosis
Authors: Welch H Gilbert , Bergmark Regan 
Published: September 2023

Abstract

Background
In the past, patients were only diagnosed with cancer because they had symptoms. Now, because of screening and incidental detection, some patients are diagnosed with cancer when they are asymptomatic. While this shift is typically viewed as desirable, it has produced an unfortunate side-effect: it is now possible to be diagnosed with a cancer not destined to cause symptoms or death—a phenomenon labeled as overdiagnosis.

Content
We begin with a brief introduction to the heterogeneity of cancer progression: at one extreme, some cancers are already systemic by the time they are detectable; at the other, some grow extremely slowly or even regress. The ensuing sections describe the evidence that the pursuit of earlier detection has led to overdiagnosis. Although rarely confirmed in an individual, overdiagnosis is readily identifiable in a long-term follow-up of a randomized trial of screening. Furthermore, 2 population signatures for overdiagnosis exist: (a) rising incidence coupled with stable mortality and (b) rising early-stage incidence coupled with stable late-stage incidence. Finally, we review the misleading feedback produced by overdiagnosis—such as rising 5-year survival rates and more cancer survivors. This feedback is erroneously interpreted as reinforcing the value of early detection, encourages more screening/incidental detection and, ironically, promotes more overdiagnosis.

Summary
Overdiagnosis is an unintended consequence of the desire to detect cancer early. Given the evolving understanding that tumor biology and host response are more relevant to prognosis than early vs late diagnosis, it is time to challenge the assertion that early diagnosis is always the best approach to curing cancer.