bluuebunny/crossref_metadata_2025 huggingface dataset:
Hebbian learning of stimulus-response associations using transcranial magnetic stimulation
Authors: Held Leslie , Cracco Emiel , Bardi Lara , Kiraga Maggie , Cristianelli Elio , Brass Marcel , Abrahamse Elger L. , Braem Senne
Published: July 2023

Classical conditioning states that the systematic co-occurrence of a neutral stimulus with an unconditioned stimulus can cause the neutral stimulus to, over time, evoke the same response as the unconditioned stimulus. On a neural level, Hebbian learning suggests that this type of learning occurs through changes in synaptic plasticity when two neurons are simultaneously active, resulting in increased connectivity between them. Inspired by learning theories, we here investigated whether the mere co-activation of visual stimuli and stimulation of the primary motor cortex using transcranial magnetic stimulation (TMS) would result in stimulus-response associations that can impact future behaviour. During a learning phase, we repeatedly paired the presentation of a specific colour (but not other colours) with a TMS pulse over the motor cortex. Next, participants performed a two-alternative forced choice task where they had to categorize simple shapes and we studied whether the shapes’ task-irrelevant colour (and its potentially associated involuntary motor activity) affected the required motor response. Participants showed more errors on incongruent trials for stimuli that were previously paired with high intensity TMS pulses, but only when tested on the same day. Using a drift diffusion model for conflict tasks, we further demonstrate that this interference occurred early, and gradually increased as a function of associated TMS intensity. Taken together, our findings show that the human brain can learn stimulus-response associations using externally induced motor cortex stimulation.
Chronic chemogenetic activation of hippocampal progenitors enhances adult neurogenesis and modulates anxiety-like behavior and fear extinction learning
Authors: Maheshwari Megha , Singla Aastha , Rawat Anoop , Banerjee Toshali , Pati Sthitapranjya , Shah Sneha , Maiti Sudipta , Vaidya Vidita A.
Published: July 2023

Adult hippocampal neurogenesis is a lifelong process that involves the integration of newborn neurons into the hippocampal network, and plays a role in cognitive function and the modulation of mood-related behavior. Here, we sought to address the impact of chemogenetic activation of adult hippocampal progenitors on distinct stages of progenitor development, including quiescent stem cell activation, progenitor turnover, differentiation and morphological maturation. We find that hM3Dq-DREADD-mediated activation of nestin-positive adult hippocampal progenitors recruits quiescent stem cells, enhances progenitor proliferation, increases doublecortin-positive newborn neuron number, accompanied by an acceleration of differentiation and morphological maturation, associated with increased dendritic complexity. Behavioral analysis indicated anxiolytic behavioral responses in transgenic mice subjected to chemogenetic activation of adult hippocampal progenitors at timepoints when newborn neurons are predicted to integrate into the mature hippocampal network. Furthermore, we noted an enhanced fear memory extinction on a contextual fear memory learning task in transgenic mice subjected to chemogenetic activation of adult hippocampal progenitors. Our findings indicate that hM3Dq-DREAD-mediated chemogenetic activation of adult hippocampal progenitors impacts distinct aspects of hippocampal neurogenesis, associated with the regulation of anxiety-like behavior and fear memory extinction.
MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer
Authors: Sakellaropoulos Theodore , Do Catherine , Jiang Guimei , Cova Giulia , Meyn Peter , Dimartino Dacia , Ramaswami Sitharam , Heguy Adriana , Tsirigos Aristotelis , Skok Jane A
Published: July 2023

Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connecting them with their target genes remains challenging. Here, we present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies clusters of highly ranked CREs, referred to as ‘hubs’, which contribute to the regulation of multiple genes and significantly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet-identified CREs represent a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.
Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake
Authors: Ferrari Alessandra , Whang Emily , Xiao Xu , Kennelly John P. , Romartinez-Alonso Beatriz , Mack Julia J. , Weston Thomas , Chen Kai , Kim Youngjae , Tol Marcus J. , Bideyan Lara , Nguyen Alexander , Gao Yajing , Cui Liujuan , Bedard Alexander H. , Sandhu Jaspreet , Lee Stephen D. , Fairall Louise , Williams Kevin J. , Song Wenxin , Munguia Priscilla , Russell Robert A. , Martin Martin G. , Jung Michael E. , Jiang Haibo , Schwabe John W.R. , Young Stephen G. , Tontonoz Peter
Published: July 2023

Intestinal cholesterol absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1), the target of the drug ezetimibe (EZ), assists in the initial step of dietary cholesterol uptake. However, how cholesterol moves downstream of NPC1L1 is unknown. Here we show that Aster-B and Aster-C are critical for non-vesicular cholesterol movement in enterocytes, bridging NPC1L1 at the plasma membrane (PM) and ACAT2 in the endoplasmic reticulum (ER). Loss of NPC1L1 diminishes accessible PM cholesterol in enterocytes and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate cholesterol at the PM and display evidence of ER cholesterol depletion, including decreased cholesterol ester stores and activation of the SREBP-2 transcriptional pathway. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, we show that the Aster pathway can be targeted with a small molecule inhibitor to manipulate dietary cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption.

One-Sentence Summary

Identification of a targetable pathway for regulation of dietary cholesterol absorption
A framework for Frizzled-G protein coupling and implications to the Wnt-PCP signaling pathways
Authors: Zhang Zhibin , Lin Xi , Wei Ling , Wu Yiran , Xu Lu , Wu Lijie , Wei Xiaohu , Wang Arthur , Zhao Suwen , Zhu Xiangjia , Xu Fei
Published: July 2023

The ten Frizzled receptors (FZDs) are essential in Wnt signaling and play important roles in embryonic development and tumorigenesis. Among these, FZD6 is closely associated with lens development. Understanding FZD activation mechanism is key to unlock these emerging targets. Here we present the cryo-EM structures of FZD6 and FZD3 which are known to relay non-canonical Wnt-PCP (planar cell polarity) signaling pathways as well as FZD1 in their G protein-coupled (active) and G protein-free (inactive) states, respectively. Comparison of the three inactive/active pairs unveiled a shared activation framework among all ten FZDs. Mutagenesis along with imaging and functional analysis on the human lens epithelial tissues suggested potential crosstalk between G-protein binding and Wnt-PCP signaling pathways. Together, this study provides an integrated understanding of FZD structure and function, and lays the foundation for developing therapeutic modulators to activate or inhibit FZD signaling for a range of disorders including cancers and cataracts.
Impact of COVID-19 on the cascade of care for tuberculosis: A systematic review
Authors: Fapohunda Tomiwa , Mapahla Lovemore , Taha Reham Amin Khidir , Chivese Tawanda
Published: July 2023

Objectives

To describe the impact of the COVID-19 pandemic on the TB care cascade.

Methods

In this systematic review, the Cochrane library, Scopus, CINAHL, Ebscohost, and PubMed databases were comprehensively searched from the onset of the pandemic, till May 5th, 2022. Eligible studies were those reporting on changes in the TB cascade of care one year before and one year during the COVID-19 pandemic. Due to the expected differences in the contexts of the included studies, a narrative synthesis was conducted.

Results

Twenty-seven studies, from Asia, North America, Africa, South America, and Europe were included. TB screening decreased by between 1% - 50%, and multidrug resistance tuberculosis (MDR-TB) screening decreased by between 15%-17%. Diagnostic delay increased by between 35 - 45 days, contact tracing decreased by up to 36.1%, and case notification decreased by between 3%-63%. TB treatment enrolment decreased by between 16%-35.0%, treatment completion decreased by around 8.0% and treatment success decreased by up to 17.0%.

Conclusion

COVID-19 had a detrimental impact on the TB care cascade and these findings suggest a need for policies to protect healthcare systems for TB and other communicable diseases in future health emergencies.

Protocol registration - PROSPERO: CRD42021272456

Ethics approval

This systematic review used data from published studies and aggregated data, thus, ethics approval was not required.
Increased interhemispheric functional connectivity during non-dominant hand movement in right-handed subjects
Authors: Tsurugizawa Tomokazu , Taki Ai , Zalesky Andrew , Kasahara Kazumi
Published: July 2023

Hand preference is one of the behavioral expressions of lateralization in the brain. Previous fMRI studies, using conventional task-based functional MRI (fMRI), investigated the lateralization of brain function, and several regions including the motor cortex, putamen, thalamus, and cerebellum were activated during the single-hand movement. However, lateralization of functional connectivity related to hand preference has not been investigated. Here, we used the generalized psychophysiological interaction (gPPI) approach to investigate the alteration of functional connectivity during single-hand movement from the resting state in right-hand subjects. The functional connectivity in interhemispheric motor-related regions including the supplementary motor area, putamen, precentral gyrus, and cerebellum was significantly increased during non-dominant hand movement, while functional connectivity was not increased during dominant hand movement. The general linear model (GLM) showed activation in the left supplementary motor area, left precentral gyrus, and right cerebellum during right hand movement and activation in the right supplementary motor area, right precentral gyrus, and left cerebellum during left hand movement. These results indicate that a combination of GLM and gPPI analysis can detect the lateralization of hand preference more clearly in right-handed subjects.
Microengineering 3D Collagen Matrices with Tumor-Mimetic Gradients in Fiber Alignment
Authors: Joshi Indranil M. , Mansouri Mehran , Ahmed Adeel , Simon Richard A. , Bambizi Poorya Esmaili , Desa Danielle E. , Elias Tresa M. , Brown Edward B. , Abhyankar Vinay V.
Published: July 2023

In the tumor microenvironment (TME), collagen fibers facilitate tumor cell migration through the extracellular matrix. Previous studies have focused on studying the responses of cells on uniformly aligned or randomly aligned collagen fibers. However, the in vivo environment also features spatial gradients in alignment, which arise from the local reorganization of the matrix architecture due to cell-induced traction forces. Although there has been extensive research on how cells respond to graded biophysical cues, such as stiffness, porosity, and ligand density, the cellular responses to physiological fiber alignment gradients have been largely unexplored. This is due, in part, to a lack of robust experimental techniques to create controlled alignment gradients in natural materials. In this study, we image tumor biopsy samples and characterize the alignment gradients present in the TME. To replicate physiological gradients, we introduce a first-of-its-kind biofabrication technique that utilizes a microfluidic channel with constricting and expanding geometry to engineer 3D collagen hydrogels with tunable fiber alignment gradients that range from sub-millimeter to millimeter length scales. Our modular approach allows easy access to the microengineered gradient gels, and we demonstrate that HUVECs migrate in response to the fiber architecture. We provide preliminary evidence suggesting that MDA-MB-231 cell aggregates, patterned onto a specific location on the alignment gradient, exhibit preferential migration towards increasing alignment. This finding suggests that alignment gradients could serve as an additional taxis cue in the ECM. Importantly, our study represents the first successful engineering of continuous gradients of fiber alignment in soft, natural materials. We anticipate that our user-friendly platform, which needs no specialized equipment, will offer new experimental capabilities to study the impact of fiber-based contact guidance on directed cell migration.
Efficient Functions for Energetic Least-Cost Analysis over Land and Water in thelbmechpackage forR
Authors: Mejía Ramón Andrés G.
Published: July 2023

Current least-cost tools for behavioral scientists are computationally insufficient and lack methods to independently derive animal-specific energetic cost functions based on locational data. Moreover, topologically-valid approaches only measure the biomechanical cost of movement, when sometimes net metababolical expediture may be a more-important consideration. In this paper, I first derive generalizable cost functions for energetic expenditure for any arbitrary biped or quadruped, versus the currently-employed regressed functions with limited cross-taxa or behavioral mode applicability. I then describe the cost-distance functions of the R package lbmech, designed to (1) regress the parameters describing behavioral sensitivity to slope from GPS tracking data; and (2) calculate the costs of movement in terms of time, kinetic work, and net metabolic expenditure. Finally, I demonstrate the utility of this package using publicly-available GPS, ocean current velocity, and elevation data from the Balearic Islands of Spain. This approach greatly facilitates the collection of field-based data given the reliance on GPS data. Moreover, it allows us to identify and consider individual- and group-level effects and variances that may lead to differential movement-related fitness with evolutionary consequences.
A Robust Combination Test Using the Normal Distribution, with Application to Phylogenetic Inference
Authors: Haque Md Rejuan , Kubatko Laura
Published: July 2023

Combination tests are used to combine P-values from individual studies to test a global null hypothesis. These types of tests can also be applied to combine P-values from testing separate null hypotheses within the same study in cases for which the procedure for testing a global null hypothesis is unavailable. One such application of a combination test is to detect the presence of hybrid species within a set of species. Although many combination tests have been proposed in the literature, there is no uniformly most powerful test applicable for all conditions. For instance, in the hybrid detection application, it is expected that only a few of the species within a set species might have truly arisen via hybridization, and thus when tested, only a few of the individual P-values are expected to be significant. Thus, a desirable property of a combination test for this situation is to be able to reject the global null hypothesis even if only a small fraction of the individual P-values are significant. In this paper, we propose a new combination test based on the normal distribution that assigns weight to each test adaptively, thereby providing powerful results even when only a small fraction of the individual null hypotheses are false. A comprehensive simulation study, as well as real data applications, demonstrate that the proposed test is powerful in detecting false global null hypotheses under several situations for which existing tests have low power.
IFNγ modestly contributes to disease progression in theNdufs4(-/-) model of Leigh syndrome while IP10 is dispensable
Authors: Hanaford Allison R , Khanna Asheema , James Katerina , Truong Vivian , Liao Ryan , Chen Yihan , Mulholland Michael , Kayser Bernhard , Hsieh Erin Shien , Sedensky Margaret , Morgan Phil , Kalia Vandana , Sarkar Surojit , Johnson Simon C
Published: July 2023

Leigh syndrome (LS) is the most common pediatric presentation of genetic mitochondrial disease. LS is a multi-system disease characterized by severe neurologic and metabolic abnormalities. The defining feature of the disease is the presence of symmetric, bilateral, progressive necrotizing lesions in the brain stem, cerebellum, and basal ganglia. The pathogenic mechanisms underlying disease initiation and progression in LS have yet to be elucidated. Recent evidence demonstrates that the immune system plays a key role in LS pathogenesis. Treatment with the macrophage-depleting Csf1r inhibitor pexidartinib prevents disease in theNdufs4(-/-) mouse model of LS, but the mechanisms leading to immune activation and governing disease progression remain to be elucidated. In recent work, the cytokines IFNγ and IFNγ-induced protein 10 (IP10) were found to be significantly elevated inNdufs4(-/-) brainstem. Given their role as macrophage-activating factors, here we sought to assess the role of IFNγ and IP10 in LS using by generatingNdufs4(-/-)/Ifng(-/-) andNdufs4(-/-)/IP10(-/-) double knockout lines. We find that IP10 alone does not significantly impact the onset or progression of disease in theNdufs4(-/-) model, while IFNγ loss significantly, but modestly, improves survival. These data indicate that IFNγ contributes to pathology, but that IFNγ and IP10 are both dispensable for overall disease course of LS. Our findings support some role for IFNγ targeting therapies in the management of mitochondrial disease, but suggest they may provide only modest benefits, at least in LS.
Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity
Authors: Ooi Amanda , Esau Luke E. , Pugachev Artyom , Groen Arnoud , Mfarrej Sara , Salunke Rahul P. , Subudhi Amit K. , Ben-Rached Fathia , Alofi Fadwa , Alsomali Afrah , Alquthami Khaled , Khogeer Asim , Hashem Anwar M. , Almontashiri Naif , Magistretti Pierre J. , Hala Sharif , Pain Arnab
Published: July 2023

An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.
Periodontitis promotes bacterial extracellular vesicle-induced neuroinflammation in the brain and trigeminal ganglion
Authors: Ha Jae Yeong , Seok Jiwon , Kim Suk-Jeong , Jung Hye-Jin , Ryu Ka-Young , Nakamura Michiko , Jang Il-Sung , Hong Su-Hyung , Lee Youngkyun , Lee Heon-Jin
Published: July 2023

Gram-negative bacteria derived extracellular vesicles (EVs), also known as outer membrane vesicles, have attracted significant attention due to their pathogenic roles in various inflammatory diseases. We recently demonstrated that EVs secreted by the periodontopathogenAggregatibacter actinomycetemcomitans(Aa) can cross the blood–brain barrier (BBB) and that their extracellular RNA cargo can promote the secretion of proinflammatory cytokines, such as IL-6 and TNF-α, in the brain. To gain more insight into the relationship between periodontal disease (PD) and neuroinflammatory diseases, we investigated the effect of Aa EVs in a mouse model of ligature-induced PD. When EVs were administered through intragingival injection or EV-soaked gel, proinflammatory cytokines were strongly induced in the brains of PD mice. The use of TLR (Toll-like receptor)-reporter cell lines andMyD88knockout mice confirmed that the increased release of cytokines was triggered by Aa EVs via TLR4 and TLR8 signaling pathways and their downstream MyD88 pathway. Furthermore, the injection of EVs through the epidermis and gingiva resulted in the direct retrograde transfer of Aa EVs from axon terminals to the cell bodies of trigeminal ganglion (TG) neurons and the subsequent activation of TG neurons. We also found that the Aa EVs changed the action potential of TG neurons. These findings suggest that EVs derived from periodontopathogens such as Aa might be involved in pathogenic pathways for neuroinflammatory diseases, neuropathic pain, and other systemic inflammatory symptoms as a comorbidity of periodontitis.

Author summary

Extracellular vesicles (EVs) secreted from bacterial cells play a key role in microbe-host cell communication. Bacterial EVs (bEVs) may be closely linked to the pathogenesis underlying neuroinflammatory diseases. In the current experiments, bEVs caused the brain to release proinflammatory cytokines by activating the host TLR signaling pathway. This induction of neuroinflammation was significantly more prominent in the periodontitis disease model, implying a substantial link between periodontal and neuroinflammatory diseases through bEVs. We also show that bEVs are translocated to the neuronal cell body via retrograde axonal transport, where they directly activate neuronal proinflammatory signals (Fig 8). Our findings reveal that bEVs are a pathogenic pathway for neurological conditions potentially linked to periodontitis, such as Alzheimer’s disease and trigeminal neuropathic pain.
Pasa: Leverage population pangenome graph to scaffold prokaryote genome assemblies
Authors: Do Van Hoan , Nguyen Son Hoang , Le Duc Quang , Nguyen Tam Thi , Nguyen Canh Hao , Ho Tho Huu , Nam Vo Sy , Nguyen Trang , Nguyen Hoang Anh , Cao Minh Duc
Published: July 2023

Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the art in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.
Improving the Circularization Efficiency, Stability and Translatability of Circular RNA by circDesign
Authors: Xu Congcong , Zhang Liang , Wang Weiyun , Tang Yuying , Wang Qiuhe , An Jinqi , Xu Heng , Ge Yun , Zhu Hanfei , Wang He , Li Bin , Wang Xiaotian , Qiu Xuhui , Shen Mingyun , Chen Geng , Shen Haifa , Huang Liang , Li Hangwen
Published: July 2023

Synthetic circular RNA (circRNA) has recently emerged as the next generation RNA technology for vaccine and drug development, featuring its uniqueness in a closed-loop structure and cap-independent translation mechanism. However, rational design and optimization of circRNA to improve its stability and protein coding potential remains challenging due to lack of structure prediction tool and sequence design algorithm for endless circular-shaped RNA. In this study, we presented circDesign, a computational approach to achieve optimal design of the circRNA with enhanced circularization efficiency, stability, and translatability. Using rabies virus glycoprotein (RABV-G) and varicella-zoster virus (VZV) glycoprotein gE as the exemplified antigens, we demonstrated that optimized circRNAs encoding corresponding antigens exhibited higher stability and protein translation efficiencyin vitro. Formulated by proprietary delivery system lipopolyplex (LPP), the optimized circRNA vaccines encoding RABV-G or VZV gE antigen further elicited enhanced humoral and cellularin vivoimmune responses in mice. Taken together, this circular RNA design approach provided a general strategy to leverage the capability of circRNA as next generation vaccines or therapeutics.
Evidence for multiscale multiplexed representation of visual features in EEG
Authors: Karimi-Rouzbahani Hamid
Published: July 2023

Distinct neural processes are often encoded across distinct time scales of neural activations. However, it has remained unclear if this multiscale coding strategy is also implemented for separate features of the same process. One difficulty is that the conventional methods of time scale analysis provide imperfect estimations of time scales when several components are active during a single process. Developing a novel decoding-based time scale estimation method, we detected distinct time scales for simultaneously present features of visual stimuli in electroencephalography. We observed that orientation and colour of grating stimuli were encoded in shorter whereas the spatial frequency and contrast of those stimuli were encoded in longer time scales. The conventional autocorrelation-based estimation of time scale was unable to detect these distinguishable time scales. These results provide new evidence for a multiscale multiplexed neural code in the human visual system and introduces a flexible method for estimating neural time scales.
Structural, Social, and Contextual factors influencing COVID-19 vaccine uptake: A qualitative methods study among Healthcare Workers and Older People in Uganda
Authors: Slivesteri Sande , Ssali Agnes , Bahemuka Ubaldo M , Nsubuga Denis , Muwanga Moses , Nsereko Chris , Ssemwanga Edward , Robert Asaba , Seeley Janet , Elliott Alison , Ruzagira Eugene
Published: July 2023

Background

The COVID-19 vaccine rollout program in Uganda was launched in March 2021 with Healthcare Workers (HCWs), older persons (≥50 years), and persons with chronic conditions as priority groups for vaccination. To inform the vaccine rollout efforts, we set out to explore the social and structural factors that influenced the uptake of COVID-19 vaccines among HCWs and older people in Uganda.

Methods

Between September and October 2021, we conducted 33 in-depth interviews with 25 HCWs aged 21–63 years from three hospitals from two districts in the central region of Uganda and eight older people from communities in Wakiso district. Selection was purposive based on sex, occupation, education, cadre of HCWs (doctors, nurses, laboratory technologist, hospital support staff, administrator) and vaccination status. We explored participants’ knowledge, beliefs, personal experiences, barriers, and facilitators to vaccine uptake and suggestions for future COVID-19 vaccine rollout. Interviews were audio-recorded, data was transcribed and translated from the local language, coded, and analysed by themes.

Results

Twenty-two of the 25 (88%) HCWs and 3 of the 8 (38%) older people had received at least one dose of the COVID-19 vaccine at the time of interview.

The structural facilitating factors to vaccine uptake included access to correct information, fear of a risky work environment, and mandatory vaccination requirements especially for frontline HCWs. Old age, chronic health conditions, and the fear of death are contextual facilitating factors, while influence from leaders was the main social facilitating factor.

Myths and misconceptions about COVID-19 vaccines and the fear of side effects were common social barriers to vaccine uptake among HCWs and older people. Long distances to vaccination centres, vaccine stock-outs, and long queues at the vaccination centres were specific barriers to vaccine uptake for older people. The prerequisite of signing a consent form was a specific structural barrier for the HCWs. Transport challenges linked to long distances to the vaccination centres, for older people, and having underlying chronic health conditions, for both older people and HCWs, were the reported contextual factors.

Conclusion

Future roll out of new vaccines should have a comprehensive information dissemination strategy about the vaccines. Improved access to vaccines through community outreaches, reliable vaccine supply and addressing vaccine misinformation, may enhance COVID-19 vaccine uptake in Uganda and other future mass vaccination campaigns.
Evaluating Large Language Models in Extracting Cognitive Exam Dates and Scores
Authors: Zhang Hao , Jethani Neil , Jones Simon , Genes Nicholas , Major Vincent J. , Jaffe Ian S. , Cardillo Anthony B. , Heilenbach Noah , Ali Nadia Fazal , Bonanni Luke J. , Clayburn Andrew J. , Khera Zain , Sadler Erica C. , Prasad Jaideep , Schlacter Jamie , Liu Kevin , Silva Benjamin , Montgomery Sophie , Kim Eric J. , Lester Jacob , Hill Theodore M. , Avoricani Alba , Chervonski Ethan , Davydov James , Small William , Chakravartty Eesha , Grover Himanshu , Dodson John A. , Brody Abraham A. , Aphinyanaphongs Yindalon , Masurkar Arjun , Razavian Narges
Published: July 2023

Importance

Large language models (LLMs) are crucial for medical tasks. Ensuring their reliability is vital to avoid false results. Our study assesses two state-of-the-art LLMs (ChatGPT and LlaMA-2) for extracting clinical information, focusing on cognitive tests like MMSE and CDR.

Objective

Evaluate ChatGPT and LlaMA-2 performance in extracting MMSE and CDR scores, including their associated dates.

Methods

Our data consisted of 135,307 clinical notes (Jan 12th, 2010 to May 24th, 2023) mentioning MMSE, CDR, or MoCA. After applying inclusion criteria 34,465 notes remained, of which 765 underwent ChatGPT (GPT-4) and LlaMA-2, and 22 experts reviewed the responses. ChatGPT successfully extracted MMSE and CDR instances with dates from 742 notes. We used 20 notes for fine-tuning and training the reviewers. The remaining 722 were assigned to reviewers, with 309 each assigned to two reviewers simultaneously. Inter-rater-agreement (Fleiss’ Kappa), precision, recall, true/false negative rates, and accuracy were calculated. Our study follows TRIPOD reporting guidelines for model validation.

Results

For MMSE information extraction, ChatGPT (vs. LlaMA-2) achieved accuracy of 83% (vs. 66.4%), sensitivity of 89.7% (vs. 69.9%), true-negative rates of 96% (vs 60.0%), and precision of 82.7% (vs 62.2%). For CDR the results were lower overall, with accuracy of 87.1% (vs. 74.5%), sensitivity of 84.3% (vs. 39.7%), true-negative rates of 99.8% (98.4%), and precision of 48.3% (vs. 16.1%). We qualitatively evaluated the MMSE errors of ChatGPT and LlaMA-2 on double-reviewed notes. LlaMA-2 errors included 27 cases of total hallucination, 19 cases of reporting other scores instead of MMSE, 25 missed scores, and 23 cases of reporting only the wrong date. In comparison, ChatGPT’s errors included only 3 cases of total hallucination, 17 cases of wrong test reported instead of MMSE, and 19 cases of reporting a wrong date.

Conclusions

In this diagnostic/prognostic study of ChatGPT and LlaMA-2 for extracting cognitive exam dates and scores from clinical notes, ChatGPT exhibited high accuracy, with better performance compared to LlaMA-2. The use of LLMs could benefit dementia research and clinical care, by identifying eligible patients for treatments initialization or clinical trial enrollments. Rigorous evaluation of LLMs is crucial to understanding their capabilities and limitations.
Hepatitis C risk score as a tool to identify infected individuals: A demonstration study in Egypt
Authors: El-Khoury Rayane , Chemaitelly Hiam , Alaama Ahmed S. , Hermez Joumana G. , Nagelkerke Nico , Abu-Raddad Laith J.
Published: July 2023

Hepatitis C virus (HCV) infection is a global health challenge. By the end of 2021, WHO estimated that less than quarter of global HCV infections were diagnosed. There is a need for a public health tool that can facilitate identification of infected persons and linking them to testing and treatment. We derived and validated a risk score to identify infected persons in Egypt and provided a demonstration of its utility. The 2008 and 2014 Egypt Demographic and Health Surveys were used to derive two risk scores using multivariable logistic regression. Both scores showed similar dependence on sex, age, and type of place of residence. Both risk scores demonstrated high and similar areas under the curve of 0.77 (95% CI: 0.76-0.78) and 0.78 (95% CI: 0.77-0.80), respectively. For the 2008 Risk Score, sensitivity was 73.7%, specificity was 68.5%, positive predictive value (PPV) was 27.8%, and negative predictive value (NPV) was 94.1%. For the 2014 Risk Score, sensitivity was 64.0%, specificity was 78.2%, PPV was 22.2%, and NPV was 95.7%. Each score was validated by applying it to a different survey database than the one used to derive it. Implementation of HCV risk scores is an effective strategy to identify carriers of HCV infection and to link them to testing and treatment at low cost to national programs.
A curated census of pathogenic and likely pathogenic UTR variants and evaluation of deep learning models for variant effect prediction
Authors: Bohn Emma , Lau Tammy , Wagih Omar , Masud Tehmina , Merico Daniele
Published: July 2023

Variants in 5’ and 3’ untranslated regions (UTR) contribute to rare disease. While predictive algorithms to assist in classifying pathogenicity can potentially be highly valuable, the utility of these tools is often unclear, as it depends on carefully selected training and validation conditions. To address this, we developed a high-confidence set of pathogenic (P) and likely pathogenic (LP) variants and assessed deep learning (DL) models for predicting their molecular effect. 3’ and 5’ UTR variants documented as P or LP (P/LP) were obtained from ClinVar and refined by reviewing the annotated variant effect and reassessing evidence of pathogenicity following published guidelines. Prediction scores from sequence-based DL models were compared between three groups: P/LP variants acting though the mechanism for which the model was designed (model-matched), those operating through other mechanisms (model-mismatched), and putative benign variants. PhyloP was used to compare conservation scores between P/LP and putative benign variants. 295 3’ and 188 5’ UTR variants were obtained from ClinVar, of which 26 3’ and 68 5’ UTR variants were classified as P/LP. Predictions by DL models achieved statistically-significant differences when comparing model-matched P/LP variants to both putative benign variants and model-mismatched P/LP variants, as well as when comparing all P/LP variants to putative benign variants. PhyloP conservation scores were significantly higher among P/LP compared to putative benign variants for both the 3’ and 5’ UTR. In conclusion, we present a high-confidence set of P/LP 3’ and 5’ UTR variants spanning a range of mechanisms and supported by detailed pathogenicity and molecular mechanism evidence curation. Predictions from DL models further substantiate these classifications. These datasets will support further development and validation of DL algorithms designed to predict the functional impact of variants that may be implicated in rare disease.
Drug-coated versus conventional balloons to improve recanalization of a coronary chronic total occlusion after failed attempt
Authors: Amat-Santos Ignacio J. , Marengo Giorgio , Ybarra Luiz F. , Fernández-Diaz Jose Antonio , Regueiro Ander , Gutiérrez Alejandro , Martín-Moreiras Javier , Sánchez-Luna Juan Pablo , González-Gutiérrez Jose Carlos , Fernandez-Cordon Clara , Carrasco-Moraleja Manuel , Rinfret Stéphane
Published: July 2023

Background

Chronic total occlusion (CTO) plaque modification (CTO-PM) is often used for unsuccessful CTO interventions.

Methods

Multicenter, prospective study including consecutive patients with failed CTO recanalization. At the end of the failed procedure, patients received either conventional (CB) or drug-coated balloon (DCB) or at the operator’s discretion for CTO-PM and underwent new attempt of CTO recanalization ∼3 months later.

Results

A total of 55 patients were enrolled (DCB: 22; CB 33), with a median age of 66 years. Median J-score was 3 and CCS angina class III-IV was present in 40% of the patients. After the first CTO-PCI attempt no in hospital cardiac deaths were registered, with 3.6% rates of in-hospital myocardial infarction. The success rate of the second CTP PCI attempt was 86.8%, with periprocedural complication rate of 5.7% and without difference between DCB and CB groups. Compared with CB, in the DCB group, the second CTO-PCI required a shorter median fluoroscopy time (33 vs 60min, p<0.001), lower contrast volume (170 vs 321cc, p<0.001) and lower radiation dose (1.7 vs 3.3Gy, p<0.001). At 1-year follow up outcomes were comparable between the 2 strategies, target lesion failure occurred in 5.7% and major adverse cardiovascular events in 11.2%.

Conclusions

PM after CTO recanalization failure is safe and warrants high success rates when 2ndattempt is performed. A DCB strategy for CTO-PM does not seem to ensure higher success or better clinical outcomes, but its use was associated with simpler staged procedures.
The Hidden Biocatalytic Potential of the Old Yellow Enzyme Family
Authors: White David W. , Iamurri Samantha , Keshavarz-Joud Parisa , Blue Tamra , Copp Janine , Lutz Stefan
Published: July 2023

The rapid advancement of sequencing technology has created an immense reservoir of protein sequence-function information that has yet to be fully utilized for fundamental or biocatalytic applications. For example, ene reductases from the ‘old yellow enzyme’ (OYE) family catalyze the asymmetric hydrogenation of activated alkenes with enhanced stereoselectivity - key transformations for sustainable production of pharmaceutical and industrial synthons. Despite the proven biocatalytic application, the OYE family remains relatively underexplored with only 0.1% of identified members having any experimental characterization. Here, a platform of integrated bioinformatics and synthetic biology techniques was employed to systematically organize and screen the natural diversity of the OYE family. Using protein similarity networks, the known and unknown regions of the >115,000 members of the OYE family were broadly explored to identify phylogenetic and sequence-based trends. From this analysis, 118 novel enzymes were characterized across the family to broadly explore and expand the biocatalytic performance and substrate scope of known OYEs. Over a dozen novel enzymes were identified exhibiting enhanced catalytic activity or altered stereospecificity. Beyond well-established ene reduction, we detected widespread occurrence of oxidative chemistry amongst OYE family members at ambient conditions. Crystallography studies of selected OYEs yielded structures for two enzymes, contributing to a better understanding of their unique performance. Their structures revealed an unusual loop conformation within a novel OYE subclass. Overall, our study significantly expands the known functional and chemical diversity of OYEs while identifying superior biocatalysts for asymmetric reduction and oxidation.
The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain
Authors: van Vlimmeren Anne E. , Voleti Rashmi , Chartier Cassandra A. , Jiang Ziyuan , Karandur Deepti , Humphries Preston A. , Lo Wan-Lin , Shah Neel H.
Published: July 2023

Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C- terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

Significance Statement

The protein tyrosine phosphatase SHP2 is mutated in a variety of human diseases, including several cancers and developmental disorders. Most mutations in SHP2 hyperactivate the enzyme by destabilizing its auto-inhibited state, but several disease-associated mutations do not conform to this mechanism. We show that one such mutation, T42A, alters the ligand binding specificity of the N-terminal regulatory domain of SHP2, causing the mutant phosphatase to be more readily activated by certain upstream signals than the wild-type phosphatase. Our findings reveal a novel mode of SHP2 dysregulation that will improve our understanding of pathogenic signaling. Our study also illustrates how mutations distal to the specificity-determining region of a protein can alter ligand binding specificity.
MKP1 promotes nonalcoholic steatohepatitis by suppressing AMPK activity through LKB1 nuclear retention
Authors: Qiu Bin , Lawan Ahmed , Xirouchaki Chrysovalantou E. , Yi Jae-Sung , Robert Marie , Zhang Lei , Brown Wendy , Fernández-Hernando Carlos , Yang Xiaoyong , Tiganis Tony , Bennett Anton M.
Published: July 2023

Nonalcoholic steatohepatitis (NASH) is triggered by hepatocyte death through activation of caspase 6, as a result of decreased adenosine monophosphate (AMP)-activated protein kinase-alpha (AMPKα) activity. Increased hepatocellular death promotes inflammation which drives hepatic fibrosis. We show that the nuclear-localized mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP1) is upregulated in NASH patients and in NASH diet fed mice. The focus of this work was to investigate whether and how MKP1 is involved in the development of NASH. Under NASH conditions increased oxidative stress, induces MKP1 expression leading to nuclear p38 MAPK dephosphorylation and decreased liver kinase B1 (LKB1) phosphorylation at a site required to promote LKB1 nuclear exit. Hepatic deletion of MKP1 in NASH diet fed mice released nuclear LKB1 into the cytoplasm to activate AMPKα and prevent hepatocellular death, inflammation and NASH. Hence, nuclear-localized MKP1-p38 MAPK-LKB1 signaling is required to suppress AMPKα which triggers hepatocyte death and the development of NASH.
Guiding a language-model based protein design method towards MHC Class-I immune-visibility profiles for vaccines and therapeutics
Authors: Gasser Hans-Christof , Oyarzun Diego , Rajan Ajitha , Alfaro Javier
Published: July 2023

Proteins have an arsenal of medical applications that include disrupting protein interactions, acting as potent vaccines, and replacing genetically deficient proteins. While therapeutics must avoid triggering unwanted immune-responses, vaccines should support a robust immune-reaction targeting a broad range of pathogen variants. Therefore, computational methods modifying proteins’ immunogenicity without disrupting function are needed. While many components of the immune-system can be involved in a reaction, we focus on Cytotoxic T-lymphocytes (CTLs). These target short peptides presented via the MHC Class I (MHC-I) pathway. To explore the limits of modifying the visibility of those peptides to CTLs within the distribution of naturally occurring sequences, we developed a novel machine learning technique,CAPE-XVAE. It combines a language model with reinforcement learning to modify a protein’s immune-visibility. Our results show thatCAPE-XVAEeffectively modifies the visibility of the HIV Nef protein to CTLs. We contrastCAPE-XVAEtoCAPE-Packer, a physics-based method we also developed. Compared toCAPE-Packer, the machine learning approach suggests sequences that draw upon local sequence similarities in the training set. This is beneficial for vaccine development, where the sequence should be representative of the real viral population. Additionally, the language model approach holds promise for preserving both known and unknown functional constraints, which is essential for the immune-modulation of therapeutic proteins. In contrast,CAPE-Packer, emphasizes preserving the protein’s overall fold and can reach greater extremes of immune-visibility, but falls short of capturing the sequence diversity of viral variants available to learn from. Source code:https://github.com/hcgasser/CAPE(Tag:CAPE 1.1)