Pooled Samples Research Articles

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

BackgroundSingle-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary population-scale analytical strategy. Many algorithms can deconvolve these tumors using single-cell profiles to infer their composition. While experimental choices do not change the true underlying composition of the tumor, they can affect the measurements produced by the assay.ResultsWe generated a dataset of high-grade serous ovarian tumors with paired expression profiles from using multiple strategies to examine the extent to which experimental factors impact the results of downstream tumor deconvolution methods. We find that pooling samples for single-cell sequencing and subsequent demultiplexing has a minimal effect. We identify dissociation-induced differences that affect cell composition, leading to changes that may compromise the assumptions underlying some deconvolution algorithms. We also observe differences across mRNA enrichment methods that introduce additional discrepancies between the two data types. We also find that experimental factors change cell composition estimates and that the impact differs by method.ConclusionsPrevious benchmarks of deconvolution methods have largely ignored experimental factors. We find that methods vary in their robustness to experimental factors. We provide recommendations for methods developers seeking to produce the next generation of deconvolution approaches and for scientists designing experiments using deconvolution to study tumor heterogeneity.

Future Perspectives for the Identification and Sequencing of Nicotinamide Adenine Dinucleotide-Capped RNAs.

Ribonucleic acid (RNA) is composed primarily of four canonical building blocks. In addition, more than 170 modifications contribute to its stability and function. Metabolites like nicotinamide adenine dinucleotide (NAD) were found to function as 5'-cap structures of RNA, just like 7-methylguanosine (m7G). The identification of NAD-capped RNA sequences was first made possible by NAD captureSeq, a multistep protocol for the specific targeting, purification, and sequencing of NAD-capped RNAs, developed in the authors' laboratory in the year 2015. In recent years, a number of NAD-RNA identification protocols have been developed by researchers around the world. They have enabled the discovery and identification of NAD-RNAs in bacteria, archaea, yeast, plants, mice, and human cells, and they play a key role in studying the biological functions of NAD capping. We introduce the four parameters of yield, specificity, evaluability, and throughput and describe to the reader how an ideal NAD-RNA identification protocol would perform in each of these disciplines. These parameters are further used to describe and analyze existing protocols that follow two general methodologies: the capture approach and the decapping approach. Capture protocols introduce an exogenous moiety into the NAD-cap structure in order to either specifically purify or sequence NAD-capped RNAs. In decapping protocols, the NAD cap is digested to 5'-monophosphate RNA, which is then specifically targeted and sequenced. Both approaches, as well as the different protocols within them, have advantages and challenges that we evaluate based on the aforementioned parameters. In addition, we suggest improvements in order to meet the future needs of research on NAD-modified RNAs, which is beginning to emerge in the area of cell-type specific samples. A limiting factor of the capture approach is the need for large amounts of input RNA. Here we see a high potential for innovation within the key targeting step: The enzymatic modification reaction of the NAD-cap structure catalyzed by ADP-ribosyl cyclase (ADPRC) is a major contributor to the parameters of yield and specificity but has mostly seen minor changes since the pioneering protocol of NAD captureSeq and needs to be more stringently analyzed. The major challenge of the decapping approach remains the specificity of the decapping enzymes, many of which act on a variety of 5'-cap structures. Exploration of new decapping enzymes or engineering of already known enzymes could lead to improvements in NAD-specific protocols. The use of a curated set of decapping enzymes in a combinatorial approach could allow for the simultaneous detection of multiple 5'-caps. The throughput of both approaches could be greatly improved by early sample pooling. We propose that this could be achieved by introducing a barcode RNA sequence before or immediately after the NAD-RNA targeting steps. With increased processing capacity and a potential decrease in the cost per sample, protocols will gain the potential to analyze large numbers of samples from different growth conditions and treatments. This will support the search for biological roles of NAD-capped RNAs in all types of organisms.

Sample Pooling: A Cost-Saving Strategy for SARS-CoV-2 Screening in Hospitalized Patients and Attending Relatives – Insights from a Secondary Care Hospital Amidst the Omicron Wave

Background: Pooled real-time reverse transcriptase polymerase chain reaction (rRT-PCR) for SARS-CoV-2 screening is cost- and labor-saving, but data during the Omicron wave are lacking. Objective: To examine a correlation between pooled rRT-PCR as a screening method for SARS-CoV-2 and community COVID-19 incidence. Materials and Methods: The authors retrospectively collected data on pooled rRT-PCR testing as a COVID-19 screening strategy between February 1 and April 30, 2022 in the present study center. Results: In comparison to performing single rRT-PCR testing, pooled rRT-PCR testing strategy reduced the numbers of rRT-PCR testing by 73.36%, 53.63%, and 54.7% in February, March, and April, respectively. The community COVID-19 incidence rate per day (CCIR) averaged 25.43, 48.12, and 80.96 per 100,000 population per day during February, March, and April, respectively. Conclusion: Small pooled rRT-PCR testing of up to five samples may be a cost-effective screening strategy among selected populations despite high CCIR during the Omicron wave. Keywords: Pooled rRT-PCR; Screening

Microbial Community Profiling from Natural Whey Starter to Mozzarella among Different Artisanal Dairy Factories in Apulia Region (Italy)

Mozzarella is one of the most popular unripened Apulian cheeses. Knowledge about microbial composition and variability of artisanal mozzarella and its production chain is increasingly growing. In this study, microbial communities from natural whey starters to end products from four renowned Apulian artisanal dairy factories have been explored by means of 16S metagenomics. The chemical properties of mozzarella samples were also detected and analyzed. Lactobacillus is the core acidifying component of the used starters, while some psychrophilic or contaminants bacteria appear in site-specific products. Biodiversity was found to be quite similar between the whey and mozzarella sample pools, while a significant variability among production sites (factories) has been detected. Furthermore, mozzarella microbial diversity seems to be in positive correlation with its lactic acid content. Targeted metagenomics would then be a powerful and relatively quick technique to characterize the microbiological variability of traditional milk-based foods.

TRANSLATION AND CROSS-CULTURAL ADAPTATION OF GENERIC SKILL SELF-ASSESSMENT INSTRUMENT FOR INDONESIAN UNDERGRADUATE MEDICAL STUDENTS

Background: There are various educational strategies that promote generic skills development in medical education; hence, there is a need for a valid and reliable instrument to assess them. This study aims to translate and adapt a generic skills self-assessment instrument developed by Groen et al.1 to assess Indonesian medical student’s generic skills in a classroom context.Methods: WHO's guidelines were used for the translation process, which consisted of: 1) forward translation, 2) expert panel review (using the Delphi method), 3) back translation, 4) pre-testing and cognitive interviews, and 5) the final version. Additional measures were employed to improve the translation accuracy, including proofreading (prior to step 2), expert panel review after step 3 and 4, and pilot testing along with psychometric testing after step 5. Backward translation was done by a professional translation service. Ten fourth-year students from Atma Jaya School of Medicine and Health Sciences were involved in step 4; meanwhile, we piloted the translated instrument to 35 other fourth-year students from the same sample pool. We also conducted an internal reliability test using Cronbach's alpha and construct validity test, including corrected total-item correlation and principal component analysis.Results: Steps 1-3 produced an Indonesian version of the generic skills assessment instrument with good face and content validity. Quantitative data analysis showed high internal reliability (Cronbach’s Alpha = .955) and acceptable item-total correlation (ranging from .345 to .757).Conclusion: Factor analysis showed 6 domains labelled as analytical skills, teamwork, communication skills, perseverance, social judgment, and global abstraction skills.

Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.

Temperature Elevation during Semen Delivery Deteriorates Boar Sperm Quality by Promoting Apoptosis.

Semen delivery practice is crucial to the efficiency of artificial insemination using high-quality boar sperm. The present study aimed to evaluate the effect of a common semen delivery method, a Styrofoam box, under elevated temperatures on boar sperm quality and functionality and to investigate the underlying molecular responses of sperm to the temperature rise. Three pooled semen samples from 10 Duroc boars (3 ejaculates per boar) were used in this study. Each pooled semen sample was divided into two aliquots. One aliquot was stored at a constant 17 °C as the control group. Another one was packaged in a well-sealed Styrofoam box and placed in an incubator at 37 °C for 24 h to simulate semen delivery on hot summer days and subsequently transferred to a refrigerator at 17 °C for 3 days. The semen temperature was continuously monitored. The semen temperature was 17 °C at 0 h of storage and reached 20 °C at 5 h, 30 °C at 14 h, and 37 °C at 24 h. For each time point, sperm quality and functionality, apoptotic changes, expression levels of phosphorylated AMPK, and heat shock proteins HSP70 and HSP90 were determined by CASA, flow cytometry, and Western blotting. The results showed that elevated temperature during delivery significantly deteriorated boar sperm quality and functionality after 14 h of delivery. Storage back to 17 °C did not recover sperm motility. An increased temperature during delivery apparently promoted the conversion of sperm early apoptosis to late apoptosis, showing a significant increase in the expression levels of Bax and Caspase 3. The levels of phosphorylated AMPK were greatly induced by the temperature rise to 20 °C during delivery but reduced thereafter. With the temperature elevation, expression levels of HSP70 and HSP90 were notably increased. Our results indicate that a temperature increase during semen delivery greatly damages sperm quality and functionality by promoting sperm apoptosis. HSP70 and HSP90 could participate in boar sperm resistance to temperature changes by being associated with AMPK activation and anti-apoptotic processes.

Epidemiology and molecular characterization of Theileria annulata in ticks collected from cattle in the central part of Tamil Nadu, India.

Tick-borne diseases are the most common in cattle in the tropical and subtropical regions of India and lead to substantial economic losses to small and marginal farmers. This study aimed to identify the diverse species of ticks infesting cattle in the central part of Tamil Nadu, India, and to assess the prevalence of Theileria annulata infection in various species of ticks through PCR. Out of 123 cross-bred and 105 native breed cattle examined for tick infestation, 40 (18%) and 29 (12.7%) cattle were infested with Ixodid ticks, respectively. The most prevalent tick species identified was Rhipicephalus microplus (n=589), followed by Hyalomma anatolicum (n=532), Hyalomma marginatum (n=145), Haemaphysalis intermedia (n=79), and Rhipicephalus haemophysaloides (n=1) found in the study area. The prevalence and intensity of the tick infestation were found to be higher in cross-bred (71.04%) than native breed cattle (28.96%), and there was no significant difference between the studied breeds (chi-square value =24; df =20; p value =0.24) was observed. However, a significant difference in the H. anatolicum tick infestation was observed between the Cauvery Delta (14.30%) and the North-Western (20%) zones of Tamil Nadu (p<0.05). DNA fragments of 193 bp derived from 18S rRNA gene sequences of T. annulata were amplified using species-specific primers. Of these, 16 out of 37 (43.2%) and 10 out of 39 (29%) pooled samples of H. anatolicum and 4 out of 18 (22.2%) and 1 out of 5 (20%) pooled samples of H. marginatum were found positive for T. annulata from the Cauvery Delta and North-Western zones, respectively. R. microplus, H. intermedia, and R. haemaphysaloides from these regions were negative. These findings confirm that H. anatolicum (52.17%) is the predominant vector for T.annulata rather than H. marginatum (18.84%), and the PCR is a useful method of determining the infection rates in ticks collected from animals carrying low levels of T. annulata piroplasms.

Diet of the sylvatic triatomine Mepraia spinolai: Association with Trypanosoma cruzi infection near human settlements

The proximity between infectious disease vector populations and human settlements, and the infection prevalence of vector populations can determine the rate of encounters between vectors and humans and hence infection risk. The diet of sylvatic triatomine vectors (kissing bugs) provides evidence about the host species involved in the maintenance of the protozoan Trypanosoma cruzi, the etiological agent of Chagas disease. Here, we characterized the diet of the Chilean endemic triatomine Mepraia spinolai using Next Generation Sequencing (NGS), and evaluated the relation between T. cruzi infection status and proximity to human settlements, with the proportion of human and human-associated (domestic and synanthropic) vertebrates in the diet. We sampled 28 M. spinolai populations, covering a latitudinal range of ∼800 km in Chile. For each population, genomic DNA was obtained from M. spinolai intestinal content. We assessed T. cruzi infection individually, and sequenced vertebrate cytochrome b to characterize the diet from infected and uninfected pooled samples. Human and human-associated animals were present in the diet of both T. cruzi-infected (13.50 %) and uninfected (10.43 %) kissing bugs. The proportion of human and human-associated vertebrates in the diet of infected M. spinolai was negatively associated with the distance from surrounding human settlements, but no relationship was detected for uninfected kissing bugs. This pattern could be related to alterations of kissing bug feeding behavior when infected by the protozoan. Our results highlight the relevance of developing a deeper knowledge of the wild transmission cycle of T. cruzi, thus advancing in the surveillance of vectors present in the natural environment near human settlements.

Detection of Selected Equine Respiratory Pathogens in Stall Samples Collected at a Multi-Week Equestrian Show during the Winter Months.

The aim of this study was to use environmental sampling to determine the frequency of detection of selected equine respiratory viruses and bacteria in horses attending a multi-week equestrian show during the winter months. At four time points during showing, environmental sponge samples were collected from all stalls on the property and tested for the presence of equine herpesvirus-1 (EHV-1), EHV-2, EHV-4, equine influenza virus (EIV), equine rhinitis B virus (ERBV), Streptococcus equi ss. equi (S. equi), and S. equi ss. zooepidemicus (S. zooepidemicus) using real-time PCR (PCR). Environmental sponges were collected from all 53 barns by using one sponge for up to 10 stalls. Further, 2/53 barns were randomly selected for individual stall sampling in order to compare the results between individual and pooled stall samples. A total of 333/948 (35.13%, 95% CI 32.09-38.26%) pooled environmental stall sponges tested PCR-positive for at least one of the selected respiratory pathogens. Streptococcus zooepidemicus was the most commonly detected pathogen in pooled samples (28.69%, 95% CI 25.83-31.69%), followed by EHV-2 (14.45%, 95% CI 12.27-16.85%), EHV-4 (1.37%, 95% CI 0.73-2.33%), and a very small percentage of pooled stall sponges tested PCR-positive for EHV-1, ERBV, EIV, and S. equi. In individual samples, 171/464 (36.85%, 95% CI 32.45-41.42%) environmental stall sponges tested PCR-positive for at least one of the selected pathogens, following a similar frequency of pathogen detection as pooled samples. The detection frequency of true respiratory pathogens from environmental samples was higher during the winter months compared to previous studies performed during spring and summer, and this testing highlights that such pathogens circulate with greater frequency during the colder months of the year. The strategy of monitoring environmental stall samples for respiratory pathogens circumvents the often labor-intensive collection of respiratory secretions from healthy horses and allows for a more efficient assessment of pathogen buildup over time. However, environmental stall testing for respiratory pathogens should not replace proper biosecurity protocols, but it should instead be considered as an additional tool to monitor the silent circulation of respiratory pathogens in at-risk horses.

Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as noninvasive biomarkers for the early detection of colorectal cancer and advanced adenomas

BackgroundEarly detection has proven to be the most effective strategy to reduce the incidence and mortality of colorectal cancer (CRC). Nevertheless, most current screening programs suffer from low participation rates. A blood test may improve both the adherence to screening and the selection to colonoscopy. In this study, we conducted a serum-based discovery and validation of cfDNA methylation biomarkers for CRC screening in a multicenter cohort of 433 serum samples including healthy controls, benign pathologies, advanced adenomas (AA), and CRC.ResultsFirst, we performed an epigenome-wide methylation analysis with the MethylationEPIC array using a sample pooling approach, followed by a robust prioritization of candidate biomarkers for the detection of advanced neoplasia (AN: AA and CRC). Then, candidate biomarkers were validated by pyrosequencing in independent individual cfDNA samples. We report GALNT9, UPF3A, WARS, and LDB2 as new noninvasive biomarkers for the early detection of AN. The combination of GALNT9/UPF3A by logistic regression discriminated AN with 78.8% sensitivity and 100% specificity, outperforming the commonly used fecal immunochemical test and the methylated SEPT9 blood test.ConclusionsOverall, this study highlights the utility of cfDNA methylation for CRC screening. Our results suggest that the combination methylated GALNT9/UPF3A has the potential to serve as a highly specific and sensitive blood-based test for screening and early detection of CRC.

Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: Prospection of peptides for vaccines and diagnostics.

The arrival of the Zika virus (ZIKV) in dengue virus (DENV)-endemic areas has posed challenges for both differential diagnosis and vaccine development. Peptides have shown promise in addressing these issues. The aim of this study was to identify the linear epitope profile recognized by serum samples from dengue and Zika patients in the E and NS1 proteins of DENV and ZIKV. This cross-sectional study included individuals of all ages with laboratory-confirmed DENV and ZIKV infections, who were selected through convenience sampling. The serum samples from dengue and Zika patients detected epitopes evenly distributed across the viral proteins in a peptide microarray platform. However, several epitopes were located within "epitope hotspots", characterized by clusters of peptides recognized in more than 30% of the sub-arrays analyzed using individual or pooled serum samples. The serum samples from dengue and Zika patients showed a high level of cross-reactivity with peptides in the DENV and ZIKV proteins. Analysis using an additional peptide microarray platform, which contained peptides selected based on the results of the initial screening, revealed that two DENV and one ZIKV peptide, highly specific to their related viruses, were located within the epitope hotspots; however, they presented low detection rates (32.5, 35.0, and 28.6%, respectively). In addition, two DENV peptides detected at similarly high rates by both dengue and Zika patients were also found within the epitope hotspots. These hotspots contain several immunodominant epitopes that are recognized by a larger number of individuals when compared to 15-amino acid (aa) sequence peptides. Thus, epitope hotspots may have greater potential to serve as antigens in diagnostic tests and vaccine development than peptides composed of only 15 amino acids.

Preliminary study on prevalence of hemoprotozoan parasites harbored by Stomoxys (Diptera: Muscidae) and tabanid flies (Diptera: Tabanidae) in horse farms in Nakhon Si Thammarat province, Southern Thailand.

Stomoxys and tabanid flies are of medical and veterinary importance because they play crucial roles in disease transmission as mechanical vectors of various hemopathogens. However, its role as a hemoprotozoan parasite vector in horse farms has not been studied. Therefore, we investigated the occurrence of hemoprotozoan parasites belonging to the genera Babesia, Theileria, and Trypanosoma in Stomoxys and tabanid flies using conventional polymerase chain reaction (PCR) and DNA sequencing. All samples (Stomoxys and tabanid flies) were collected using an Nzi trap for three consecutive days each month from November 2022 to March 2023. The flies were morphologically identified to the species level and separated according to sex. Individual (for tabanid flies) or pooled samples (consisting of three specimens of Stomoxys flies of the same species and sex collected from the same site) were used for DNA extraction. Conventional PCR was used to screen for hemoprotozoan parasite DNA, followed by Sanger sequencing to identify the species. In total, 189 biting flies were collected, including four species of Stomoxys (Stomoxys bengalensis, Stomoxys calcitrans, Stomoxys indicus, and Stomoxys sitiens) and five species of tabanids (Atylotus cryptotaxis, Chrysops dispar, Tabanus megalops, Tabanus mesogaeus, and Tabanus rubidus). Stomoxys calcitrans was the most prevalent species, accounting for 58.7% (n = 111) of the collected flies. Ten (12.4%) of the 81 samples (individuals and pools) analyzed by PCR were positive for the 18S rRNA gene of the Theileria/Babesia species. Trypanosoma DNA was not detected in any sample. After performing Basic Local Alignment Search Tool searches and a phylogenetic analysis, only six samples (7.4%), including S. calcitrans (n = 2), S. sitiens (n = 2), T. megalops (n = 1), and A. cryptotaxis (n = 1), were found to be infected with Theileria sinensis. Furthermore, apicomplexan parasites, namely, Mattesia spp. and Colpodella spp., were found on S. indicus, the fungus Meira spp. was found on S. calcitrans, and the pathogenic green alga Helicosporidium spp. was found on A. cryptotaxis. This study is the first to report a variety of Stomoxys and tabanid flies collected from horse farms in Thailand, which were found to be infected with Theileria and Colpodella species that affect mammals, suggesting that Stomoxys and tabanid flies can be used to confirm the presence of hemoprotozoan parasites in the study area. Understanding the presence of hemoprotozoa in flies could help design vector control programs and manage various diseases in the study area.

Inferring the distribution of norovirus in individual oysters below the limit of quantification by pooled sampling.

Norovirus (NoV) in oysters is a food safety risk of much concern. In order to assess the risk of the exposure, the distribution of the number of NoV copies contained in each oyster should be acquired first for comprehensively quantifying the associated risks. However, the part of the distribution below the limit of quantification cannot be obtained directly by laboratory detecting methods, which hampers accurate assessment. To tackle this challenging problem, a systematic method (Distribution Inference Method by Pooled Sampling) is proposed to infer the unobservable part of distribution based upon all measurements of the pooled samples with n=2. Using convolutional integrals and real-coded genetic algorithm for inferring, this method has neither requirements for the type or properties of the original distribution, nor requirements for historical data, even nor requirements for the relationship between observable and unobservable parts of the distribution. A series of experiments were conducted on simulated datasets of a variety of types, including normal distribution, uniform distribution, gamma distribution, lognormal distribution, zero-inflated Poisson distribution, their combinations, and even their splicing, covering common distribution types in oyster NoV scenario and more general scenarios. The results show that almost all inferred simulation data and their original counterparts passed Kolmogorov-Smirnov tests, which implies that they are essential of the same distribution. Based on this method, a ready-to-use web system was developed for researchers to infer their original distribution with pooled-sampling measurements from the detection of NoV or even other substances.

Judgments of Learning Following Retrieval Practice Produce Minimal Reactivity Effect on Learning of Education-Related Materials.

Testing (i.e., retrieval practice) is one of the most powerful strategies to boost learning. A recent study observed an incidental finding that making judgments of learning (JOLs) following retrieval practice further enhanced learning of education-related texts to a medium extent (Cohen's d = 0.44) by comparison with retrieval practice itself, suggesting that making JOLs may serve as an easy-to-implement educational intervention to improve the benefits of testing. Three experiments (one pre-registered) were conducted to test the replicability of Ariel et al.'s incidental finding and to further determine whether making JOLs following retrieval practice reactively enhances the benefits of testing for text learning. The three experiments consistently provided Bayesian evidence supporting no reactivity effect of JOLs following retrieval practice, regardless of whether the replication experiments were conducted in a laboratory (Experiment 1) or online (Experiments 2 and 3), whether the stimuli were presented in the same language (Experiments 2 and 3) or not (Experiment 1), and whether participants were recruited from the sample pool (Experiment 2) or not (Experiments 1 and 3) as in the original study. These null findings imply that making JOLs cannot be utilized as a practical strategy to enhance the benefits of testing for learning of educationally related materials. Possible explanations for the null reactivity effect of JOLs following retrieval practice are discussed.

Isotopic and proteomic evidence for communal stability at Pre-Pottery Neolithic Jericho in the Southern Levant

As one of the key, long-term occupied sites in the Southern Levant, Jericho was one of the most important early Neolithic centres to witness social and economic changes associated with the domestication of plants and animals. This study applies strontium (87Sr/86Sr), oxygen (δ18O) and carbon (δ13C) isotope analyses to the enamel of 52 human teeth from Pre-Pottery Neolithic (PPN) layers of Jericho to directly study human diet and mobility and investigate the degree of consolidation and the flexibility of social organization of Jericho society in the PPN period. The results indicate only two non-local individuals out of the 44 sampled inhabitants identified by strontium isotope analysis and are consistent with the presence of a largely sedentary community at PPN Jericho with no evidence for large-scale migration. We also construct strontium spatial baselines (87Sr/86Sr map) with local 87Sr/86Sr signatures for the sites across the Southern Levant based on systematic compilation and analysis of available data. In addition, we apply proteomic analysis of sex-specific amelogenin peptides in tooth enamel for sex estimation of the sampled individuals (n = 44), the results of which showed a sex-biased ratio (more male than female detected in this sample pool) in Jericho society during the PPN period, which may be due to the limited sample size or selective ritual practices like particular burial zones used for specific groups. We also pretreated a batch of human bone samples recovered from PPNB Jericho for stable carbon and nitrogen isotope analyses for dietary investigations. However, the extracted collagen showed poor preservation and no valid δ13C or δ15N data were obtained.

Quality testing of mifepristone and misoprostol in 11 countries.

Previous studies have demonstrated quality concerns with misoprostol. Mifepristone, however, has not been extensively assessed for quality. Between 2020 and 2021, Concept Foundation and the International Planned Parenthood Federation conducted a study to determine the quality of these medical abortion drugs in low- and middle-income countries (LMIC). The collection of batch samples of misoprostol and mifepristone was carried out by trained sampling agents in selected LMIC. Single drug packs and combipacks were sampled. A World Health Organization prequalified laboratory conducted testing method verifications and subsequent sample analysis. Tests included identification, assay, related substances, and content uniformity for misoprostol, and identification, assay, related substances, and dissolution for mifepristone. Samples were collected from Burkina Faso, Cambodia, Democratic Republic of Congo, India, Kyrgyzstan, Moldova, Nepal, Nigeria, Pakistan, Uganda and Vietnam. Sixty-four pooled batch samples were tested, consisting of 31 combipacks, 26 misoprostol-only and seven mifepristone-only products. Overall, 54.7% of samples were non-compliant with one or more of the specifications, representing 51.6% of combipack products, 57.1% of misoprostol tablets analyzed and 23.7% of mifepristone tablets. One falsified misoprostol-only product was found. The present study confirms that a significant problem still exists in relation to the quality of medical abortion drugs in LMIC. For misoprostol, our findings suggest that historical concerns around primary packaging may have been largely resolved but that manufacturing processes for both finished product and active pharmaceutical ingredient need to be improved. The present study also provides evidence of mifepristone quality issues.

Short-chain fatty acids levels in human milk are not affected by holder pasteurization and high hydrostatic pressure processing.

Sterilized donor milk (DM) is frequently used for feeding preterm infants. To date, the effect of different modes of DM sterilization on short-chain fatty acids (SCFAs) remains unknown. We aimed to quantify SCFAs in DM samples after two types of milk sterilization: the Holder pasteurization (HoP) and a high hydrostatic pressure (HP) processing. Eight pooled DM samples were sterilized by HoP (62.5°C for 30 min) or processed by HP (350 MPa at 38°C). Raw DM was used as control. Six SCFAs were quantified by gas chromatography/mass spectrometry. Compared to raw milk, both HoP and HP treatment did not significantly modulate the concentration of acetate, butyrate, propionate and isovalerate in DM. Valerate and isobutyrate were undetectable in DM samples. In conclusion, both HoP and HP processing preserved milk SCFAs at their initial levels in raw human milk.

B-097 Storage Stability of HbA1c in Whole Blood Tubes at Room Temperature on the Abbott Alinity c Clinical Chemistry System

Abstract Background Hospital laboratories frequently receive requests to order additional tests on an existing specimen. For this reason, laboratories routinely save specimens after initial testing has been completed for a defined period of time. The current literature lacks specific information regarding HbA1c stability in whole blood and the effects of red blood cell settling. In addition, literature references are not inclusive of various conditions which can cause gaps in data collection such as samples in queue for prolonged periods. To obtain information on prolonged storage of whole blood tubes, HbA1c was assessed for storage at room temperature (RT) (20–25°C) for up to 4 hours on the Alinity c system. In addition, potential carryover from a whole blood to a serum sample was assessed. Methods A minimum of 40 whole blood sample pools (approx. 8 mLs) were prepared from remnant samples. Sample pools were mixed, aliquoted, and stored at RT on the Alinity c system. The samples were tested as a single replicate continuously for up to 4 hours without mixing (minimum of 20 cycles) and compared to the baseline sample values. Carryover from a whole blood to a glucose serum sample was assessed after 4 hours continuous testing of whole blood to mimic a high volume testing laboratory. The stability of each HbA1c sample and carryover into a glucose sample were evaluated by comparing the mean absolute or percent difference from the respective sample baseline measurement. The allowed deviation from baseline was 5%. Results After 4 hours at RT, the whole blood cells had settled to approximately 50% from the top of the tube. The red blood cell settling had no significant impact on the results. Within sample precision for the 20 cycles of repetitive testing was &amp;lt;/ = 1%. The 48 individual samples showed insignificant difference from the baseline value, with a mean change of 1.0% (Range 0–3.2%). Sample carryover from the whole blood samples to a serum glucose sample was not significant (2.71 Baseline vs 2.64 first replicate). Conclusion This study demonstrated that the storage stability of HbA1c is stable for up to 4 hours at RT on the Alinity c system.

B-181 Multi-centre Analytical Performance Evaluation of the EXENTâ Solution for Identification and Quantitation of Monoclonal Immunoglobulins

Abstract Background Current routine methodologies for monoclonal immunoglobulin measurements may not be sufficiently sensitive to reflect the depth of response seen in patients since the introduction of novel therapies; mass spectrometry may offer a valuable, sensitive alternative approach. Here we describe the preliminary analytical performance characteristics of the EXENT® solution (in development by The Binding Site, part of Thermo Fisher scientific) that combines specific immunoprecipitation steps and mass spectrometry for the identification and quantification of IgG, IgA and IgM intact monoclonal immunoglobulins. Each intact monoclonal immunoglobulin clone can be tracked using its unique m/z value. Methods The Lower Limit of Measuring Interval (LLMI) was established for each immunoglobulin type following EP17-A2:2012. Linearity studies were performed according to CLSI EP06-A2:2020 using high and low pools of IgG, IgA, and IgM monoclonal samples and with additional linearity testing below 1 g/L for each specificity to more effectively demonstrate low-end linearity. Within run, between run, between analyzer, between lot and total precision for M protein concentrations and for molecular mass (m/z) of the monoclonal peaks were assessed according to CLSI EP5-A3-2014. Interference was tested following ED3:2018 using 20 potential interferents against 7 samples including high and low IgG, IgA and IgM monoclonal samples. Results The initial indication of the EXENT solution performance, in development, are set out below. Results suggest an analytical sensitivity of the assays around 15 mg/L at the LLMI for all specificities. Linearity over a range of 0.014–88.9 g/L for IgG, 0.011–68.4 g/L for IgA, and 0.11–74.2 g/L for IgM. Coefficients of variation (CVs) for M protein concentrations in precision studies were &amp;lt;15% for all specificities and samples. Mass/charge values were within ±1.1 to ±1.5 m/z in total precision studies, and within ±2.7 to ±3.9 m/z in between lot precision studies, respectively, for M proteins with an m/z value ranging from 11 360.6 to 11 698.5 m/z. No significant interference effects were observed when testing the 20 interferents including intralipid (20 g/L), triglyceride (15 g/L), bilirubin (400 mg/L), rheumatoid factor (200 IU/mL) and haemoglobin (10 g/L). Conclusion The new EXENT solution demonstrates the potential for a wide measuring interval and the ability to detect M proteins with very low concentration. Also, it could provide stable and reproducible performance for the detection and typing of monoclonal immunoglobulins.