bluuebunny/crossref_metadata_2025 huggingface dataset:
B - 102 Neurocognitive Functioning of Patients Diagnosed with Sickle Cell Disease in Low-to-Middle Income Countries
Authors: Pinkett Bari L , Hankins Jane , Heitzer Andrew , Longoria Jennifer , Nesbitt Katherine , Wrigley Jordan
Published: September 2024

Objective

Sickle Cell Disease (SCD) is a monogenic blood disorder affecting the production of hemoglobin, a protein that carries oxygen to all vital organs in the body. As a result, insufficient oxygen delivery and cerebrovascular complications often occur which can affect neurocognitive performance. In low-to-middle-income countries (LMIC) where health care and treatment of the disease are harder to access, there is minimal neurocognitive surveillance. Our research aim was to evaluate the neurocognitive impact of SCD in children living in LMIC and establish which neurocognitive assessment measures are commonly used in SCD samples worldwide.

Data Selection

To analyze this, a librarian created search terms in studies from Embase, PubMed, Web of Science, Global Health CABI, ERIC, CINAHL, and PsycINFO. Studies that focused on participants with SCD of any genotype with a measure for cognitive/academic outcomes were included while commentaries and editorials were excluded. Two research assistants screened 1831 abstracts in Covidence, 52 abstracts were chosen for full-text review, and 18 articles were ultimately included for data extraction.

Data Synthesis

A systematic review was used to analyze these studies. Most of the studies were conducted in African and Middle Eastern countries and Brazil. Common measures included the Wechsler Intelligence Scale for Children or Adults. Information regarding cultural or language adaptations of neurocognitive measures was rarely reported. Several of the studies demonstrated that individuals with SCD have lower neurocognitive functioning compared to a non-SCD control group.

Conclusion

Further research is needed regarding the validity of neurocognitive measures used in LMIC among patients diagnosed with SCD.
B - 104 Cognition, Stigma, and Social and Occupational Functioning in First Episode Psychosis
Authors: Done Monica , Allen Daniel N , Cadiz Hazel , Condray Ruth , Gates-Woodyatt Jessica J
Published: September 2024

Objective

Among the many challenges faced by individuals experiencing their first episode of psychosis (FEP), commencement of public, self-, and structural stigma regarding their symptoms contributes to internalized shame, social exclusion, and discrimination. Individuals with FEP may experience rejection from friends, family, and community members due to misconceptions and fear surrounding mental illness, which can worsen mental health outcomes and hinder recovery. The aim of this study was to evaluate the extent of self-reported stigma and predictors in adults with a first episode of psychosis.

Method

We measured IQ, stigma, social and occupational functioning, race, sex, and symptoms of psychosis in a sample of 77 individuals with FEP (29% female, mean age 31.8 years).

Results

Multiple regression analysis indicated that psychotic symptoms delusions were significant predictors of stigma in the model, while race, IQ, sex, and functioning were not significant predictors. The model was statistically significant for symptoms of delusions (p < 0.05).

Conclusions

Initial findings indicate increased stigma is predicted by increased severity of delusional symptoms among individuals experiencing their first episode of psychosis. Surprisingly, other factors associated with stigma in more chronic illness were not significant predictors in the regression model. It may be that early in the course of psychotic illness, symptoms differentially contribute individuals’ perceptions of stigma by others. While these results offer preliminary insight, further research is necessary to explore additional factors uniquely associated with stigma in FEP, including contributors to internalized, public, and structural stigma, as well as interventions for decreasing negative impacts of stigma.
B - 109 Long-Term Cognitive Effects of Combined Opioid/Non-Opioid Use
Authors: Zolliecoffer Chandler J , Panchagnula Sreenath
Published: September 2024

Objective

Chronic pain is estimated to afflict 25–50% of community-dwelling older adults (Cravello et al., 2019). Despite the growing epidemic, opioids remain commonly prescribed analgesics, and approximately 10% of older adults with intermittent opioid use become chronic users (Ramachandran et al., 2021). This is concerning given an observed association between cognitive decline and prescription opioid use within this population (Warner et al., 2022). In efforts to reduce opioid consumption, opioid/non-opioid combinations have been used (Pergolizzi et al., 2023); however, the long-term cognitive impact of such alternatives has not been investigated. Thus, the current case report investigates the neurocognitive outcome following longtime opioid/non-opioid combination cessation in the context of chronic pain.

Method

A 69-year-old Black woman with approximate 30-year history of chronic pain underwent neuropsychological re-evaluation 2 years post-initial assessment and 1.5 years after stopping combined hydromorphone/clonidine use via intrathecal pump. Baseline MRI brain revealed mild diffuse atrophy and punctate nonspecific T2 white matter hyperintensities. CT head approximately 1 year later was unremarkable.

Results

Neuropsychological re-assessment approximately 2 years post-baseline evaluation revealed significantly declined performances on speed-mediated tasks (e.g., oral numeric sequencing, fluency) amid an otherwise grossly stable, albeit globally impaired, cognitive profile.

Conclusions

This study elucidates the impact of a 1.5-year period of abstinence from 13 years of combined intrathecal opioid/non-opioid use. Overall, results suggest that cognitive performance, even following this abstinence period, is not improved. Thus, while opioid/non-opioid therapies may reduce opioid exposure, deleterious cognitive effects persist. This study highlights the importance of non-opioid analgesics in efforts to attenuate cognitive impairment risk.
B - 115 How Training Conditions Impact Performance on a Theoretically-Derived Learning Instrument
Authors: Dixon Bradley J , Woodard John L
Published: September 2024

Objective

Few neuropsychological measures were developed using an explicit theory that accounts for individual performance. We developed a novel associative learning measure to address this limitation and investigated whether training conditions could influence accuracy and response time.

Methods

Fifty young, community-dwelling adult participants completed the novel relational learning task, which explicitly trained two stimulus pairs (A- > B, A- > C) and involved a single common stimulus. Participants identify six unique relationships between stimuli: trained relations (A- > B, A- > C), mutually entailed relations (B- > A, C- > A), and combinatorial relations (B- > C, C- > B). Participants were randomly assigned to a congruent (A is opposite B, A is opposite C) or incongruent (A is opposite B, B is the same as C) training condition and completed the procedure when stimuli were observably (e.g., color-coded shapes) or arbitrarily related (e.g., letters).

Results

Comparisons of accuracy between training conditions using Bayesian independent samples t-tests found moderate evidence of no reliable difference between training groups when stimuli were observably related (BF01 = 3.4, δ = 0.06) and arbitrarily related (BF01 = 3.5, δ = 0.03). Comparisons of response time found strong evidence that participants took longer to identify relations when receiving incongruent training when the stimuli were visually related (BF10 = 38.8, δ = 0.9) but inconclusive evidence when the stimuli were arbitrarily related (BF10 = 1.5, δ = 0.49) (See Table 1).

Conclusion

These findings suggest that manipulating training conditions does not appreciably impact the ability to identify relationships between stimuli accurately. However, training appears to increase the response time needed to identify visibly related stimuli accurately. While this is a promising theoretically-derived learning paradigm, further research is required for validation in clinical practice.
B - 117 Preliminary Validity for a Standardized Measure of Neuropsychological Testing Readiness: the Barnett-Coldiron Testing Readiness Inventory
Authors: Coldiron Allyson M , Killingsworth Derek C , Zamora Joel A , Bishop Kellee N , DiGiovanna Benjamin J , Motley John E , Arreola Langarica Ashley D , Guillory Logan A , Barnett Michael D
Published: September 2024

Objective

Neuropsychological testing requires specific conditions of the clinician, client, and setting for valid standardized measurement and clinical interpretation, and yet only effort/symptom validity and orientation are routinely assessed in a standardized manner. Many other conditions are agreed to impact testing performance, including the developed construct of testing readiness: internal client states that are appropriate for undergoing neuropsychological testing (e.g., well rested, not intoxicated) as well as atypical conditions that require accommodations (e.g., mobility limitations, colorblindness). This study examined the preliminary validity of a testing readiness self-report screening measure developed to standardize the assessment and reporting of this aspect of profile validity.

Method

Community-dwelling young adults (N = 58) and older adults (N = 35) were screened for psychological and cognitive well-being, and then completed the Barnett-Coldiron Testing Readiness Inventory (BCTRI), followed by a short neuropsychological battery.

Results

The BCTRI displayed good internal consistency (α = 0.84) with a skewed distribution (−1.57) expected of healthy, testing-ready participant samples, and the only difference in BCTRI scores between participant demographic groups was found in psychological symptoms between age cohorts (t[57.99] = 2.27, p = 0.03). Additionally, the BCTRI showed discriminative validity with established neuropsychological tests – including an effort test (p = 0.81) – as well as concurrent validity with screening measures of overlapping psychological constructs (r = 0.60, p < 0.001).

Conclusion

The BCTRI displayed preliminary validity for the standardized assessment of testing readiness, as an aspect of client profile validity for neuropsychological testing, and the measure’s easy interpretation and quantitative reporting method show potential utility for both clinical and research settings. Future studies will investigate cutoff scores for clinical use.
B - 122 A Preliminary Analysis of the Neuropsychological Evaluation of the UPSA (NEUPSA)
Authors: Peek Elizabeth , Miranda Alannah , Holloway Breanna , Raven Karli , Rosberg Holden , Minassian Arpi , Perry William
Published: September 2024

Objective

The UCSD Performance Skills Assessment (UPSA) is a well-established performance instrument created to evaluate functional outcomes. We applied a neuropsychological framework to the UPSA and created the Neuropsychological Evaluation of the UPSA (NEUPSA), assessing the cognitive processes that underlie the functional tasks in the UPSA. The study aimed to compare the executive function and attention components of the NEUPSA with a validated computerized cognitive assessment.

Methods

Participants were 86 adults drawn from the San Diego community. Participants completed the UPSA, 5 Choice CPT (5CCPT) which evaluates attention by calculating a d-prime score that assesses sustained attention, and the Iowa Gambling Task (IGT) which assesses risky decision making. We employed a Spearman’s correlation analysis with a 95% confidence interval to assess the strength of the relationship between NEUPSA attention scores and 5CCPT and IGT performance.

Results

NEUPSA subscores were significantly correlated with performance on computerized cognitive assessments. 5CCPT scores were positively correlated with NEUPSA attention scores (r = 0.24, p = 0.03). IGT scores were positively correlated with NEUPSA executive functioning scores (r = 0.23, p = 0.04).

Conclusion

These findings provide preliminary evidence that the NEUPSA assesses aspects of attention (i.e., sustained attention) and executive function (i.e., risky decision making). Further research, however, needs to be conducted on the validity of this measure and the utility in assessing neuropsychological function in clinical populations. Next steps include assessing NEUPSA performance in various non-healthy comparison populations. In this study, we emphasize the fundamental cognitive principles necessary for performance, offering a promising avenue for comprehending impaired functioning.
B - 125 Atypical Alzheimer’s Disease in a Highly Educated Individual: a Case Study
Authors: Jiang Yirou , DeVaughn Saskia , Peery Shelley
Published: September 2024

Objective

Early onset of atypical Alzheimer’s disease (ad) can be challenging to identify, especially in highly educated individuals. Protein deposits in neural areas other than the medial temporal lobe can be associated with a heterogeneous neurocognitive pattern. We present a case that highlights the value of biomarker studies in these individuals.

Method

A 67-year-old, right-handed female with 18 years of education presented with inefficient word retrieval and mental set loss, which emerged approximately two to three years prior. Symptoms worsened in the context of gabapentin use status post lung cancer resection without return to baseline with steady progression. Remaining medical history includes a 1.4 cm right parietal falcine meningioma, hyperlipidemia, and depression.

Results

In the context of high average premorbid functioning, challenges included complex executive functioning, subtle visuospatial deficits, and encoding and recall inefficiencies. Naming was low average. Neuroimaging revealed mild parietal and dorsal frontal atrophy, potentially age-appropriate, with no significant hippocampal atrophy.

Conclusions

The present case highlights the possibility of atypical protein deposits and neurocognitive pattern in a highly educated individual with the potential of an early onset ad process. The value of biomarkers and neuropsychological nuances will be of increasing relevance in the context of emerging amyloid therapies.
B - 132 Validation of the PCL-5 Symptom Severity Scale Embedded Symptom Validity Index in a Cross-Cultural Forensic Sample
Authors: Snodgrass Makenna , Schroeder Ryan W , Spector Jack , Bieu Rachel
Published: September 2024

Objective

Three embedded symptom validity indices were recently created for the PTSD Checklist for DSM-5 (PCL-5). The first, the PCL-5 Symptom Severity Scale (PSS), is derived from the PCL-5 total score, and preliminary findings have indicated its effectiveness in research and clinical samples. Our aim was to cross-validate this validity index in a cross-cultural forensic sample.

Method

Examinees were Macedonian and Kosovar contractors (N = 79) previously employed at military bases in Afghanistan and Iraq. Examinees underwent defense psychological examinations between 2018 and 2023 related to pursuit of federal workers compensation claims for PTSD. Testing was performed with translated instruments and administered with assistance from certified interpreters. Two sets of analyses were conducted in this study. In the first, examinees were categorized as valid or invalid responders based on their Trauma Symptom Inventory-II Atypical Response Scale (ATR) scores. In the second, validity status was categorized based on a more conservative criterion of failing 2+ validity tests.

Results

Receiver operating characteristic analyses were used to determine optimal cutoff scores and classification accuracy statistics for the PSS. The area under the curve was acceptable (0.77) in both analyses. When categorizing invalidity with the ATR, a PSS cutoff of 64 resulted in 95% specificity and 33% sensitivity. When categorizing invalidity by failure of 2+ validity tests, the PSS cutoff could be adjusted to 62 resulting in 90% specificity and 46% sensitivity.

Conclusion

Results of the current study are in line with those from previous research. These findings extend the utility of the PSS to a cross-cultural forensic sample.
B - 134 Validation of the Pcl-5 Rare Items Scale Embedded Symptom Validity Index in a Cross-Cultural Forensic Sample
Authors: Snodgrass Makenna , Schroeder Ryan , Spector Jack , Bieu Rachel
Published: September 2024

Objective

Recently, three embedded symptom validity indices were developed for the PTSD Checklist for the DSM-5 (PCL-5). The PCL-5 Rare Item (PRI) scale is one of those indices, which is calculated by summing examinee responses to infrequently endorsed item ratings. Preliminary findings indicate the PRI is effective in a research sample but potentially less effective in a clinical sample. The aim of the current study was to cross-validate the PRI in a cross-cultural forensic sample.

Method

Examinees were Macedonian and Kosovar contractors (N = 79). Contractors were previously employed at military bases in Afghanistan and Iraq. The examinees underwent defense psychological examinations related to pursuing federal workers compensation claims for PTSD. Examinations were conducted between 2018 and 2023 with appropriately translated instruments and assistance from certified interpreters. Two sets of analyses were performed for this study. First, examinees were categorized as responding validly or invalidly based on their Trauma Symptom Inventory-II Atypical Response Scale (ATR) scores. In a second set of analyses, validity status was based on a more conservative criterion of failing 2+ validity tests.

Results

Receiver operating characteristic analyses were employed. Area under the curve findings were acceptable (0.74) in both sets of analyses. When invalidity was based on the ATR, a PRI cutoff of 3 resulted in 95% specificity and 35% sensitivity. Similarly, when invalidity was determined by failure of 2+ validity tests, a PRI cutoff of 3 resulted in 95% specificity and 36% sensitivity.

Conclusion

Results of the current study support the utility of the PRI in a cross-cultural forensic sample.
B - 138 Factors Influencing Performance Validity Test (PVT) Performance in a Clinical Multiple Sclerosis Sample
Authors: Palmeri Maria J , Rose Nina , Foley Frederick , Seng Elizabeth
Published: September 2024

Objective

Performance Validity Test (PVT) failure, originally designed to assess malingering in forensic settings, is remarkably common in the clinical setting. Though there are potentially numerous explanations for PVT failure, there is a paucity of research investigating its frequency, and contributing factors, in patients with neurological disorders. We aimed to identify factors associated with PVT failure among patients with multiple sclerosis (MS).

Method

A hierarchical logistic regression was performed on a dataset containing neuropsychological assessment results of 32 males (23.5%), and 104 females (76.5%) with MS (N = 106, Mean age = 47.9) to evaluate associations between depression (Patient Health Questionnaire-9, PHQ-9), anxiety (Hospital Anxiety and Depression Scale, HADS-Anxiety) (step 1), fatigue (Fatigue Scale of Motor and Cognitive Functions, FSMC) (step 2), age/years of education (step 3), and PVT failure (Test of Memory Malingering, TOMM score < 45).

Results

The final model was significant and explained 40.8% of the variance in TOMM failure (χ2(6) = 21, p = 0.002). The odds of PVT failure increased by 22.1% (p = 0.04) for every 1 unit increase in z-score on the PHQ-9. The odds of PVT failure increased by 66.3% for every 1 point increase in total Cognitive Fatigue (p = 0.01). Age, education, HADS-Anxiety, and Motor-Fatigue were not significantly associated with TOMM failure.

Conclusion

It is commonly assumed that neurology patients who fail PVTs are seeking secondary gain (e.g., disability). This study provides some support for the hypothesis that psychological factors, such as depression and cognitive fatigue, may significantly contribute to PVT failure in some clinical populations.
B - 142 Reason to Forget Use of (Most) Digit Span Validity Measures in Aging Clinical Samples
Authors: Reese Caitlin S , Denney David A , Gonzalez Deborah M , Stohlman Shelby , Walls Brittany D , Ruchinskas Robert
Published: September 2024

Objective

The Digit Span (DS) subtest has survived every iteration of the Wechsler Adult Intelligence Scale (WAIS), and the reliable digit span (RDS forward+backward) is an established embedded performance validity test (PVT). The only known DS meta-analysis drew near equivalency between the WAIS-R and WAIS-III RDS and age-corrected scaled score (ACSS) validity cutoffs, recommending use of either. The WAIS-IV included a new DS sequencing subtest. Alternate and enhanced RDS measures, adding sequencing, were derived. However, aging samples often perseverate on sequencing. The aims of this study are to confirm and update the faulty use of the enhanced RDS in the aging, establish that use of the previously recommended DS ACSS cutoff (now including sequencing) is similarly faulty, and update all DS PVT cutoff specificities in a clinical aging sample.

Method

Memory Clinic data were taken from 350 individuals with neuropsychologist-neurologist consensus diagnoses including 111 individuals with early Alzheimer’s disease (ad), 181 with mild cognitive impairment (MCI; 99 amnestic; 82 non-amnestic) and 58 with subjective cognitive complaints (SCC).

Results

Most DS embedded PVTs (e.g., ACSS<6, Enhanced RDS < 11) present with poor specificity in aging clinical populations (e.g., Χ2 (3350) = 26.331,p = <0.001), while the traditional RDS (< 6) excludes sequencing and retains the best relative specificity (81–95%), as ad performs worst on sequencing (<0.001).

Conclusions

While prior research favored the DS ACSS in older individuals, this study provided support for the traditional RDS in a memory clinic population. Future directions include corroborating these findings using standalone PVTs and conducting an updated DS meta-analysis.
B - 144 Base Rates of Performance Validity Test Failure among Patients with Persistent COVID-Related Cognitive Concerns
Authors: Sedgwick Thomas A , Basurto Karen S , Finley John-Christopher A , Boulais Brooke M , Phillips Matthew S , Jennette Kyle J , Soble Jason H , Ellison Rachael L , Pliskin Neil H , Ulrich Devin M
Published: September 2024

Objective

Data on performance invalidity in neuropsychological evaluations among patients with SARS-CoV-2-related cognitive concerns is limited. This study investigated the base rates of performance validity test (PVT) failure among a sample of neuropsychological referrals with persistent cognitive concerns following SARS-CoV-2 infection.

Method

Data were collected from 62 patients (27% male, 73% female) with subjective cognitive concerns following SARS-Cov-2 infection. The sample included ethnoracially diverse adult patients (M = 44.1 years, SD = 12.53) with an average of 15 years of education (SD = 2.97) who underwent comprehensive neuropsychological evaluations including freestanding (Test of Memory Malingering, Trial 1 [TOMM T1]) and embedded (Wechsler Adult Intelligence Scale-4th Edition Digit Span Reliable Digit Span [WAIS-IV DS RDS]; California Verbal Learning Test-Brief Form Forced Choice [CVLT-BF FC]; Brief Visuospatial Memory Test Recognition-Discrimination [BVMT RD]; Stroop Word Reading T-Score [Stroop Word T]) PVTs.

Results

A majority of the sample (63%) passed all PVTs, 9.7% of the sample failed ≥2 PVTs suggesting invalidity, and 27.4% of the sample failed exactly one PVT. On embedded PVTs, failure rates were as follows: WAIS-IV DS RDS: 11.3%, CVLT-BF FC: 1.6%, BVMT Rec-Dis: 8.1%, and Stroop Word T: 8.1%. The failure rate on TOMM Trial 1 was 19.4%.

Conclusions

Patients presenting with persistent cognitive concerns following SARS-CoV-2 infection demonstrated relatively low overall invalidity rates using an empirically established cut-off (≥2). Further research is needed to confirm the generalizability of the present findings, as well as to explore the implications of failure on one PVT and the implications of failure on embedded versus freestanding PVTs in this population.
B - 146 An Analysis of Emotional Distress as a Predictor of Performance and Symptom Validity
Authors: Brandys Tyler , Kent George W , Clark Emilie , Naatz Lisa , Pyykkonen Ben
Published: September 2024

Objective

The current study examined the impact of emotional distress on measures of performance and symptom validity. It examined this relationship with the Victoria Symptom Validity Test (VSVT), the Wechsler Adult Intelligence Scale Fourth Edition (WAIS-IV) Reliable Digit span, and MMPI-2 FBS.

Data Selection

83 participants were assessed at a Midwest clinic. Inclusion criteria required the administration of relevant tests.

Data Synthesis

A Binary logistic regression indicated that emotional distress was not a significant predictor of group identification via symptom validity: VSVT Difficult Items (p = 0.55) and WAIS-IV reliable Digit Span (p = 0.56). However, the MMPI-2 variables of emotional distress (Scales, 1, 2, 3, and 7) were predictive of FBS classification (P = 0.01). Follow up independent samples t-test comparing validity classification identified group difference on MMPI-2 scales of 1, 2,3, and 7 were only significant for MMPI-2 FBS and not VSVT and WAIS-IV RDS.

Conclusions

The current analysis identified that emotional distress, as measured by 4 MMPI-2 clinical scales, did not significantly predict validity classification via VSVT Hard Items or WAIS-IV RDS. In contrast, emotional distress was predictive of symptom validity classification as identified by MMPI-2 FBS cut score. Significant group differences in emotional distress were evident on all 4 MMPI-2 scales assessed when classified by FBS cut score. These constructs should be understood as unique in their relationship to emotional distress, with PVTs not being impacted by the endorsement of emotional distress, but SVT was associated with the endorsement of emotional distress.
Utilization of duckweed-derived biomass for polyhydroxybutyrate production in Escherichia coli via dual enzymatic saccharification using amylase and cellulase complex
Authors: Ooi Toshihiko , Sato Rikako , Matsumoto Ken'ichiro
Published: September 2024

Duckweed is a rapid-growing plant with a high starch and low lignin content. The duckweed was saccharified via dual enzymatic treatment using amylase and cellulase complex. The duckweed-derived glucose was utilized for polyhydroxybutyrate (PHB) production in engineered Escherichia coli. In addition, the low concentration supplementation of the duckweed extract promoted cell growth compared to the analytical grade glucose.
Aurantiochytrium mutant strains exhibiting different colony colors altered the contents of squalene
Authors: Yang Tianjing , Kubo Shohei , Juntila Darryl Joy , Iwata Yasushi , Tomita Kanako , Hase Yoshihiro , Oono Yutaka , Araie Hiroya , Yoneda Kohei , Maeda Yoshiaki , Suzuki Iwane
Published: September 2024

Aurantiochytrium sp. 18W-13a, a marine heterotrophic protist belonging to the genus thraustochytrid, is known to accumulate high levels of squalene and carotenoids. Nowadays, the mutagenesis breeding of microorganisms is still widely practiced because the induced mutations of DNA do not involve the permanent integration of heterologous DNA sequences. Therefore, in this study, we focused on the improvement of squalene yield by mutagenesis breeding using Aurantiochytrium sp. 18W-13a. To bypass the massively laborious screening, we propose to use colony colors as the first criterion to screen mutants with high squalene accumulation, since the carotenoid and squalene synthetic pathways share an intermediate. We selected pale (white)-colored mutants after carbon ion irradiation. The white mutants exhibited larger squalene yields than twice as much of the original strain. The results clearly indicate that the present screening method with colony colors promises to obtain productive strains of squalene.
Batch-effect correction in single-cell RNA sequencing data using JIVE
Authors: Hastings Joseph , Lee Donghyung , O’Connell Michael J
Published: September 2024

Motivation

In single-cell RNA sequencing analysis, addressing batch effects—technical artifacts stemming from factors such as varying sequencing technologies, equipment, and capture times—is crucial. These factors can cause unwanted variation and obfuscate the underlying biological signal of interest. The joint and individual variation explained (JIVE) method can be used to extract shared biological patterns from multi-source sequencing data while adjusting for individual non-biological variations (i.e. batch effect). However, its current implementation is originally designed for bulk sequencing data, making it computationally infeasible for large-scale single-cell sequencing datasets.

Results

In this study, we enhance JIVE for large-scale single-cell data by boosting its computational efficiency. Additionally, we introduce a novel application of JIVE for batch-effect correction on multiple single-cell sequencing datasets. Our enhanced method aims to decompose single-cell sequencing datasets into a joint structure capturing the true biological variability and individual structures, which capture technical variability within each batch. This joint structure is then suitable for use in downstream analyses. We benchmarked the results against four popular tools, Seurat v5, Harmony, LIGER, and Combat-seq, which were developed for this purpose. JIVE performed best in terms of preserving cell-type effects and in scenarios in which the batch sizes are balanced.

Availability and implementation

The JIVE implementation used for this analysis can be found at https://github.com/oconnell-statistics-lab/scJIVE.
NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide–human leukocyte antigen complexes
Authors: Jiang Dawei , Xi Binbin , Tan Wenchong , Chen Zixi , Wei Jinfen , Hu Meiling , Lu Xiaoyun , Chen Dong , Cai Hongmin , Du Hongli
Published: September 2024

Motivation

Neoantigens, derived from somatic mutations in cancer cells, can elicit anti-tumor immune responses when presented to autologous T cells by human leukocyte antigen. Identifying immunogenic neoantigens is crucial for cancer immunotherapy development. However, the accuracy of current bioinformatic methods remains unsatisfactory. Surface and structural features of peptide–HLA class I (pHLA-I) complexes offer valuable insight into the immunogenicity of neoantigens.

Results

We present NeoaPred, a deep-learning framework for neoantigen prediction. NeoaPred accurately constructs pHLA-I complex structures, with 82.37% of the predicted structures showing an RMSD of < 1 Å. Using these structures, NeoaPred integrates differences in surface, structural, and atom group features between the mutant peptide and its wild-type counterpart to predict a foreignness score. This foreignness score is an effective factor for neoantigen prediction, achieving an AUROC (Area Under the Receiver Operating Characteristic Curve) of 0.81 and an AUPRC (Area Under the Precision-Recall Curve) of 0.54 in the test set, outperforming existing methods.

Availability and implementation

The source code is released under an Apache v2.0 license and is available at the GitHub repository (https://github.com/Dulab2020/NeoaPred).
Computational prediction of multiple antigen epitopes
Authors: Viswanathan Rajalakshmi , Carroll Moshe , Roffe Alexandra , Fajardo Jorge E , Fiser Andras
Published: September 2024

Motivation

Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable.

Results

Here, we introduce the antigen epitope prediction program ISPIPab that combines information from two feature-based methods and a docking-based method. We demonstrate that ISPIPab outperforms each of its individual classifiers as well as other state-of-the-art methods, including those designed specifically for epitope prediction. By combining the prediction algorithm with hierarchical clustering, we show that we can effectively capture epitopes that align with available experimental data while also revealing additional novel targets for future experimental investigations.
Once upon a time: exploring the biogeographic history of the largest endemic lizard family in the Neotropics (Squamata: Gymnophthalmidae)
Authors: Vásquez-Restrepo Juan D , Ribeiro‑Júnior Marco A , Sánchez-Pacheco Santiago J
Published: September 2024

Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages.
Adjusting for incomplete baseline covariates in randomized controlled trials: a cross-world imputation framework
Authors: Song Yilin , Hughes James P , Ye Ting
Published: September 2024

In randomized controlled trials, adjusting for baseline covariates is commonly used to improve the precision of treatment effect estimation. However, covariates often have missing values. Recently, Zhao and Ding studied two simple strategies, the single imputation method and missingness-indicator method (MIM), to handle missing covariates and showed that both methods can provide an efficiency gain compared to not adjusting for covariates. To better understand and compare these two strategies, we propose and investigate a novel theoretical imputation framework termed cross-world imputation (CWI). This framework includes both single imputation and MIM as special cases, facilitating the comparison of their efficiency. Through the lens of CWI, we show that MIM implicitly searches for the optimal CWI values and thus achieves optimal efficiency. We also derive conditions under which the single imputation method, by searching for the optimal single imputation values, can achieve the same efficiency as the MIM. We illustrate our findings through simulation studies and a real data analysis based on the Childhood Adenotonsillectomy Trial. We conclude by discussing the practical implications of our findings.
Global, regional and national burdens of acne vulgaris in adolescents and young adults aged 10–24 years from 1990 to 2021: a trend analysis
Authors: Zhu Zhou , Zhong Xiaoying , Luo Zhongyu , Liu Mingjuan , Zhang Hanlin , Zheng Heyi , Li Jun
Published: September 2024

Background

Acne vulgaris is a common skin condition affecting adolescents and young adults worldwide, yet data on the burden and trends of this disease remain limited. We aimed to investigate trends in the burden of acne vulgaris among adolescents and young adults aged 10–24 years at global, regional and national levels.

Methods

We retrieved data from the Global Burden of Disease Study 2021 for individuals aged 10–24 years in 204 countries and territories from 1990 to 2021. We analysed the numbers, age-standardized rates and average annual percentage changes (AAPCs) of the prevalence, incidence and disability-adjusted life years (DALYs) for acne vulgaris at the global, regional and national levels. Additionally, we examined these global trends by age, sex and Sociodemographic Index (SDI).

Results

Globally, the age-standardized prevalence rate of acne vulgaris among adolescents and young adults increased from 8563.4 per 100 000 population [95% uncertainty interval (UI) 7343.5–9920.1] in 1990 to 9790.5 (95% UI 8420.9–11 287.2) per 100 000 population in 2021, with an AAPC of 0.43 [95% confidence interval (CI) 0.41–0.46]. The age-standardized incidence rate and age-standardized DALY rate also showed a similar upward trend. Regionally, Western Europe had the highest age-standardized prevalence, incidence and DALY rates, while North Africa and the Middle East had the largest increase in these rates. By SDI quintile, the high SDI region had the highest age-standardized prevalence, incidence and DALY rates from 1990 to 2021, whereas the low-middle SDI region had the lowest burden of acne vulgaris but experienced the most significant increase in these rates. Globally, the age-standardized prevalence rate of acne vulgaris in 2021 was approximately 25% higher in young women than in young men (10 911.8 per 100 000 population vs. 8727.8 per 100 000 population). Among all age groups, adolescents aged 15–19 years had the highest age-specific prevalence rate, while adolescents aged 10–14 years experienced the largest increase from 1990 to 2021 (AAPC 0.50, 95% CI 0.48–0.52).

Conclusions

The burden of acne vulgaris among adolescents and young adults has continued to increase in nearly all countries since the 1990s. Managing this condition remains a significant challenge, necessitating more effective and targeted interventions to control the acne burden.
Patterns of treatment failure in patients with sinonasal squamous cell carcinoma after chemoradiotherapy
Authors: Wang Li , Wang Jie , Wang Tian , Li Yi , Song Xinmao
Published: September 2024

Objectives

To investigate the failure patterns based on precision radiation treatment and to determine the predictive factors of treatment failure for sinonasal squamous cell carcinoma (SNSCC) patients.

Methods

This was a retrospective study that included 214 cases of treatment failure from 441 consecutive patients. Two experienced radiation oncologists evaluated the tumour volume of cases with local recurrence. The 5-year overall survival (OS), progression-free survival (PFS) rates, and distant-metastasis-free survival (DMFS) were estimated. Investigations were performed on the factors that predicted local failure or distant metastasis.

Results

About 140 (31.7%) patients developed local recurrence, 24 (5.4%) experienced regional failure, and 65 (14.7%) underwent distant metastasis. In-field, marginal, and out-of-field failures occurred in 55.7% (78/140), 33.6% (47/140), and 10.7% (15/140) of patients with local recurrence, respectively. In logistic regression analysis, factors statistically significant for total local failure included treatment mode (P < .01), chemotherapy (P < .01), and surgical margins (P < .01). Primary tumours with poor differentiation (P = .018) and R2 resection margin (P = .009) were more prone to develop distant failure. The 5-year OS, PFS, and DMFS rates were 57.8%, 52.0%, and 56.7% for the whole cohort. In univariate and multivariate analysis, the skull base involvement was an independent predictor for poorer OS and PFS; orbital invasion was an independent predictor for poorer OS.

Conclusions

Local recurrence and distant metastasis were the most common failure modes. Treatment mode, chemotherapy, and surgical margins were related to local recurrence. Poor differentiation and R2 resection margin were predictors for distant failure.

Advances in knowledge

Local recurrence is the most common failure pattern in patients with SNSCC who accepted chemoradiotherapy, and marginal and out-of-field failures occurred in 44.3% of patients with local recurrence.
A national survey of interventional radiology trainees on peripheral and aortic endovascular training
Authors: Rao Mihir M , Zhong Jim , Mahay Usman , Haslam Philip , Patel Jai
Published: September 2024

Objectives

The development of technical skills in peripheral and aortic endovascular intervention is an essential part of interventional radiology (IR) training. Access to endovascular training remains contentious, with IR and vascular surgery (VS) trainees competing for opportunities. The Collaborative Peripheral and Aortic Endovascular Training Survey (CPAETS) aimed to evaluate IR trainees’ experiences, expectations, and barriers to endovascular training.

Methods

CPAETS was a joint survey between the British Society of Interventional Radiology and the Rouleaux Club (UK Vascular Trainees’ Association), open for 12 weeks and distributed to UK-based IR and VS trainees. This article focuses on IR trainee responses.

Results

Thirty-two responses were received from IR trainees across England, Scotland, and Wales. Overall, 59% of respondents were satisfied with their endovascular training. IR trainees reported less regular hands-on experience of aortic endovascular procedures (50%) compared to peripheral endovascular procedures (93%). Consequently fewer trainees (65%) felt confident in achieving the necessary aortic endovascular competencies by the end of their training, compared to peripheral procedures (89%).

Conclusion

Limited exposure to aortic endovascular procedures resulted in reduced confidence levels in performing aortic intervention as compared to peripheral procedures. Potential solutions to bridge some of these IR training gaps include greater pre-operative and post-operative presence, the use of simulators, and IR fellowships to ensure adequate training opportunities.

Advances in knowledge

This article provides a snapshot of the current gaps in IR endovascular training in the United Kingdom, with insight into solutions that can enable trainees to develop clinical and technical competencies required for IR consultant practice.
Accuracy of an artificial intelligence-enabled diagnostic assistance device in recognizing normal chest radiographs: a service evaluation
Authors: Kumar Amrita , Patel Puja , Robert Dennis , Kumar Shamie , Khetani Aneesh , Reddy Bhargava , Srivastava Anumeha
Published: September 2024

Objectives

Artificial intelligence (AI) enabled devices may be able to optimize radiologists’ productivity by identifying normal and abnormal chest X-rays (CXRs) for triaging. In this service evaluation, we investigated the accuracy of one such AI device (qXR).

Methods

A randomly sampled subset of general practice and outpatient-referred frontal CXRs from a National Health Service Trust was collected retrospectively from examinations conducted during November 2022 to January 2023. Ground truth was established by consensus between 2 radiologists. The main objective was to estimate negative predictive value (NPV) of AI.

Results

A total of 522 CXRs (458 [87.74%] normal CXRs) from 522 patients (median age, 64 years [IQR, 49-77]; 305 [58.43%] female) were analysed. AI predicted 348 CXRs as normal, of which 346 were truly normal (NPV: 99.43% [95% CI, 97.94-99.93]). The sensitivity, specificity, positive predictive value, and area under the ROC curve of AI were found to be 96.88% (95% CI, 89.16-99.62), 75.55% (95% CI, 71.34-79.42), 35.63% (95% CI, 28.53-43.23), and 91.92% (95% CI, 89.38-94.45), respectively. A sensitivity analysis was conducted to estimate NPV by varying assumptions of the prevalence of normal CXRs. The NPV ranged from 88.96% to 99.54% as prevalence increased.

Conclusions

The AI device recognized normal CXRs with high NPV and has the potential to increase radiologists’ productivity.

Advances in knowledge

There is a need for more evidence on the utility of AI-enabled devices in identifying normal CXRs. This work adds to such limited evidence and enables researchers to plan studies to further evaluate the impact of such devices.
How Family Group Conferencing Can Support a Contextual Safeguarding Response to Community-based Youth Harm: Lessons for Practice from a Participatory Study
Authors: Owens Rachael , Bradbury-Leather Vanessa
Published: September 2024

This article reports on a study that brought Family Group Conferencing (FGC) and Contextual Safeguarding together to create an innovative practice response to extra-familial harm. It took place as part of a wider research project into the implementation of Contextual Safeguarding—an ecological approach to creating safety for young people harmed outside the home. Whilst there is growing understanding in social care of the contextual dynamics of young people’s safeguarding needs beyond their homes, many remain unsure about what it means, in practice, for them to create safety in a context. Using data collected via participatory and embedded research methods, this article considers how FGCs were adapted to create responses to youth harm that shifted the focus from ‘family’ to ‘community’; addressed the ‘social conditions of harm’; and drew on practitioners’ existing FGC skills. It demonstrates conceptual alignment and practice benefits for bringing the two approaches together and argues that drawing on the value-base and skills of FGC coordinators has considerable potential. The article highlights three key elements that are needed to recreate similar responses, namely: organisational mandate/support; conceptual framework aligned to ecological theory; and skills and attributes that include facilitation, working restoratively and with authority in challenging situations.
A review of the genus Euterpe: botanical and genetic aspects of açai, the purple gold of the Amazon
Authors: Teixeira Bruno , Teixeira Gisele , Darnet Elaine , Schaller Hubert , Rogez Hervé , Darnet Sylvain
Published: September 2024

Achieving improved plant breeding is one of the most significant challenges facing efforts to ensure human nutrition and energy security over the next 30 years. The principal focus of plant breeding is to increase the production of conventional crops, but the domestication and breeding of lesser-known plants may also represent a source of food and energy. The African oil palm is an example of a cultivated plant that has reached the first rank of oil sources over the last four decades. Among palms, açai palm trees are highlighted due to the violet berries being commercialized internationally as functional foods. Açai palms are candidates for domestication and breeding and have a large area of cultivation. We reviewed the literature and technical reports concerning the açai genetic pool to detail the açai palm tree species and their biology, diversity centre, genetic resources, and existing breeding programmes.