bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-exercise Estimated Cardiorespiratory Fitness and Mortality Among Adults With Hypertension
Authors: Zhu Yong-Jian , Fu Wan-Rong , Lu Wen-Jie , Wang Xu-Le , Wang Xi , Shan Ying-Guang , Zheng Xiao-Lin , Li Ran , Peng Meng , Pan Liang , Qiu Jing , Qin Xiao-Fei , Sun Guo-Ju , Wang Lu , Dong Jian-Zeng , Xiao Li-Li , Qiu Chun-Guang
Published: October 2024

BACKGROUND

The non-exercise estimated cardiorespiratory fitness (eCRF) has been recognized as an important predictor of mortality among the general population. This study sought to evaluate the relationship between eCRF and mortality from all causes, cardiovascular disease (CVD), and cancer in hypertensive adults.

METHODS

We included 27,437 adults with hypertension from the National Health and Nutrition Examination Survey (NHANES) III and 10 NHANES cycles from 1999 to 2018. Multivariate Cox proportional hazard models were used to assess the hazard ratios and 95% confidence intervals (CIs) of eCRF for mortality.

RESULTS

A total of 8,023 deaths were recorded throughout a median 8.6-year follow-up, including 2,338 from CVD, and 1,761 from cancer. The eCRF with per 1 metabolic equivalent increase was linked to decreased risk of all-cause (adjusted HR 0.78, 95% CI: 0.75–0.81) and CVD mortality (adjusted HR 0.79, 95% CI: 0.74–0.84), rather than cancer mortality (adjusted HR 0.94, 95% CI: 0.86–1.03). Moreover, a stronger protective effect of eCRF was observed for females (HR 0.66 (95% CI: 0.62–0.72) versus HR 0.78 (95% CI: 0.73–0.83), Pinteraction < 0.001 for all-cause mortality; HR 0.70 (95% CI: 0.61–0.80;) versus HR 0.82 (95% CI: 0.73–0.92), Pinteraction = 0.026 for CVD mortality) compared with males. Findings did not significantly differ in subgroup analyses and sensitivity analyses.

CONCLUSIONS

Among adults with hypertension, eCRF was inversely related to all-cause and CVD mortality, but not cancer mortality. A significant interaction effect existed between sex and eCRF. Further studies are needed to verify this association in different populations.
FormatAEG: a framework for bypassing ASLR defense and automated exploitation of format string vulnerability
Authors: Xu Shenglin , Jiang Zhiyuan , Wang Yongjun , Xie Peidai
Published: October 2024

The format string vulnerability is a common software vulnerability. A well-constructed format string can read and modify arbitrary memory addresses, causing serious system problems. Existing automated exploit generation solutions for format string vulnerability are unable to cope with the limitations imposed by the vulnerability defense mechanism Address Space Layout Randomization (ASLR) and the program itself on vulnerability exploitation. In this paper, to address the above challenges, we propose FormatAEG, the first automatic exploitation framework for format string vulnerabilities that can bypass ASLR defense and the program's own constraints. Specifically, we first proposed an arbitrary address reading and writing method based on a format string vulnerability, which can modify the target address data by directly arranging the target address or automatically searching and utilizing the pointer chain in the stack. Then, we propose a vulnerability reentry method based on global offset table (GOT) hijacking, which hijacks the program control flow by modifying function addresses in the GOT, making the vulnerability reentrant. In the experimental section, we evaluated FormatAEG using 20 Capture The Flag programs from top international tournaments and two real-world programs with format string vulnerabilities. The evaluation results show that with ASLR defense turned on, FormatAEG successfully detects format string vulnerability in 19 of these programs and generates exploit code for 15 of them. Compared with existing tools, FormatAEG detected 11 more format string vulnerabilities and generated 13 more exploit codes.
Probabilistic bias analysis for exposure misclassification of household income by neighbourhood in a cohort of individuals with colorectal cancer
Authors: Davis Laura E , Banack Hailey R , Calderon-Anyosa Renzo , Strumpf Erin C , Mahar Alyson L
Published: October 2024

Introduction

Despite poor agreement, neighbourhood income is used as a proxy for household income, due to a lack of data availability. We quantified misclassification between household and neighbourhood income and demonstrate quantitative bias analysis (QBA) in scenarios where only neighbourhood income is available in assessing income inequalities on colorectal cancer mortality.

Methods

This was a retrospective study of adults with colorectal cancer diagnosed 2006–14 from Statistics Canada’s Canadian Census Health and Environment Cohort. Neighbourhood income quintiles from Statistics Canada were used. Census household income quintiles were used to determine bias parameters and confirm results of the QBA. We calculated positive and negative predictive values using multinomial models, adjusting for age, sex and rural residence. Probabilistic QBA was conducted to explore the implication of exposure misclassification when estimating the effect of income on 5-year mortality.

Results

We found poor agreement between neighbourhood and household income: positive predictive values ranged from 21% to 37%. The bias-adjusted risk of neighbourhood income on 5-year mortality was similar to the risk of mortality by household income. The bias-adjusted relative risk of the lowest income quintile compared with the highest was 1.42 [95% simulation interval (SI) 1.32–1.53] compared with 1.46 [95% confidence interval (CI) 1.39–1.54] for household income and 1.18 (95% CI 1.12–1.24) for neighbourhood income.

Conclusion

QBA can be used to estimate adjusted effects of neighbourhood income on mortality which represent household income. The predictive values from our study can be applied to similar cohorts with only neighbourhood income to estimate the effects of household income on cancer mortality.
Barriers and facilitators of the use of clinical informatics resources to facilitate pharmacogenomic implementation in resource-limited settings
Authors: Bosic-Reiniger Jade , Martin James L , Brown Karen E , Anderson Heather D , Blackburn Hayley , Kao David P , Trinkley Katy E , Woodahl Erica L , Aquilante Christina L
Published: October 2024

Objective

Understand perceived barriers to and facilitators of using clinical informatics applications for pharmacogenomic (PGx) implementation in resource-limited settings.

Materials and Methods

We conducted a qualitative research study using a semi-structured interview guide informed by the Consolidated Framework for Implementation Research (CFIR). Interview questions assessed CFIR contextual determinants related to: electronic health record (EHR) infrastructure; clinical informatics personnel and resources; EHR integration of PGx test results; PGx clinical decision support (CDS) tools; institutional resources; and partner receptivity. Transcripts were coded and analyzed to identify themes.

Results

We interviewed 24 clinical informaticists and executive leaders working in rural or underserved health care settings in Montana (n = 15) and Colorado (n = 9) and identified three major themes: (1) EHR infrastructure limitations, (2) insufficient supporting resources, and (3) unique contextual considerations for resource-limited settings. EHR infrastructure limitations included limited agency related to EHR build and interoperability concerns. Theme 1 highlighted challenges associated with integrating structured data into the EHR and inadequate vendor support. Theme 2 included limited familiarity with PGx across the care team, cost concerns, and allocation of non-financial resources. Theme 3 highlighted perceptions about the clinical utility of PGx within rural and underrepresented populations. Potential facilitators, such as being able to act nimbly, were found to coexist among the reported barriers.

Discussion and Conclusion

Our results provide insight into the clinical informatics infrastructure in resource-limited settings and identify unique considerations for clinical informatics-facilitated PGx implementation. Future efforts in these settings should consider innovative partnerships and strategies to leverage facilitators and minimize barriers associated with integrating PGx CDS applications.
The impact of exogenous vasoactive intestinal polypeptide on inflammatory responses and mRNA expression of tight junction genes in lambs fed a high-grain diet
Authors: Mia Golam K , Hawley Emma , Yusuf Mustapha , Amat Samat , Ward Alison K , Keller Wanda L , Dorsam Glenn , Swanson Kendall C
Published: October 2024

This study assessed the impact of administering vasoactive intestinal polypeptide (VIP) on inflammation and intestinal VIP and tight junction mRNA expression in lambs fed grain-based finishing diets. Sixteen wether lambs (69.6 ± 1.9 kg) were individually housed, adapted to a corn-based diet containing no forage, and randomly assigned to 2 treatment groups. Lambs were intraperitoneally injected every other day for 28 d with either saline (0.9% NaCl) with no VIP (n = 8; control) or saline with VIP (n = 8; 1.3 nmol/kg BW). Blood samples were collected weekly for analysis of cytokine concentrations, and on days 0 and 28 for lipopolysaccharide (LPS), and LPS-binding protein (LBP) concentrations. Upon completion of the treatment period, lambs were euthanized and gastrointestinal tissues, including rumen, jejunum, cecum, and colon samples, were collected for analysis of the expression of tight junction mRNA (claudin-1, claudin-4, occludin, and ZO-1), endogenous VIP, and VIP receptor (VPAC-1). No treatment effects (P ≥ 0.38) were observed for VIP and VPAC-1 mRNA expression in the colon. Supplementation with VIP did not influence (P ≥ 0.28) the expression of claudin-1, claudin-4, occludin, and ZO-1 tight junction mRNA in the rumen, jejunum, cecum, and colon. Lambs treated with VIP had greater (P ≤ 0.01) plasma concentrations of the anti-inflammatory cytokines, IL-10 and IL-36RA. There were treatment-by-day interactions observed (P ≤ 0.02) for concentrations of the pro-inflammatory cytokines, MIP-1α and MIP-1β. Lambs that did not receive VIP had greater serum concentrations of LPS (P = 0.05) than the lambs receiving VIP. These data suggest that VIP administration may not influence tight junction mRNA expression but may decrease LPS concentrations and thus inflammation in lambs fed a grain-based diet.
Rare case of concomitant coronary artery bypass grafting and open abdominal aortic aneurysm repair
Authors: Pastore Dakota , Higgins Sabrina , James Taylor , Hooda Zamaan , Shenasen Pasha , Therionos Alexios , Bustamante John Paul , Beniwal Jagbir , Connolly Mark , Danks John
Published: October 2024

Coronary artery disease occurs when coronary vessels are unable to supply adequate oxygen to the myocardium, while an abdominal aortic aneurysm (AAA) is a dilatation of the abdominal aorta. Both conditions have similar risk factors such as smoking and hypertension. If these disease processes become severe and are left untreated, life-threatening consequences may occur. We present a 71-year-old male with prior myocardial infarction and an infrarenal AAA that underwent a rare combined procedure of coronary artery bypass grafting (CABG) and open AAA repair surgery. The CABG involved grafting the left internal mammary artery and saphenous vein to coronary arteries while the AAA repair used an 18-mm bifurcated aortic graft. Combined CABG and open AAA repair is complex and rare, but aims to reduce mortality and prevent aneurysm rupture in patients with severe comorbid conditions. The patient’s positive postoperative outcome highlights the procedure’s efficacy in select cases.
The Effect of Online Music Therapy Interventions on Reducing Stress Levels in Small Hotel Managers: A Mixed-Methods Pilot Study
Authors: Dungsirisangthong Pichaya , Boonyam Treetip , Chiengchana Natee , Buranaprapuk Ampai
Published: October 2024

The rapidly changing business environment and increasing uncertainties due to the coronavirus disease 2019 pandemic since 2020 have led to heightened stress levels among managers. This study employed a mixed-method design to examine the effects of online music therapy interventions on reducing stress levels in small hotel managers. Thirteen managers participated in the online music therapy program, which consisted of six weekly music therapy sessions and self-guided music interventions for practice during the week. The music therapy interventions included music-assisted relaxation, improvisation, music listening with drawing, moving with music, song discussion, songwriting, and singing. The intake questionnaire collected participants’ demographic information and musical backgrounds. The Thai Perceived Stress Scale-10 (T-PSS-10) and Visual Analog Scale of Stress (VAS-S) were used to measure perceived stress levels. A paired t-test analysis compared the average participants’ perceived stress scores between pre and post-tests. Results demonstrated a significant reduction in perceived stress scores. Both the VAS-S for music therapy interventions and self-guided music interventions showed significant decreases after participation in each music therapy session and self-guided practice. In conclusion, online music therapy interventions can effectively reduce the perceived stress levels of managers facing uncertainty in small hotel businesses.
9New Materialism
Authors: Taylor Colleen
Published: October 2024

This review essay focuses on how the year’s work in new materialism builds on a vibrant discourse in literary studies and nascent, growing trends in postcolonial and indigenous new materialisms. A variety of new materialist works published in 2023, from the monographs Earthly Things: Immanence, New Materialisms, and Planetary Thinking and The Garden Politic: Global Plants and Botanical Nationalism in Nineteenth-Century America, to the journal article ‘New Materialism and Posthumanism in Roman Archaeology’, explore the ways in which the pillars of new materialist thought, such as the agentic capacity of vibrant matter, ‘speaking objects’, and entanglement, can lead to decolonial revelations about human culture and history. The essay is grouped according to common themes addressed in this year’s body of work: 1. Introduction; 2. Literature and Beyond; 3. Colonial Plants and Enslaved Objects; 4. New Materialism and Eco-Marxism; 5. Immanence and Planetary Thinking; 6. New (Materialist) Topics of Conversation in Science; and 7. Conclusion. The varied scholarship surveyed points to the conclusion that what was once seen as new materialism’s ethical weakness—its focus on matter over human beings—is now becoming a decolonial strength.
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome
Authors: Richardson Miles , Zhao Shijie , Sheth Ravi U. , Lin Liyuan , Qu Yiming , Lee Jeongchan , Moody Thomas , Ricaurte Deirdre , Huang Yiming , Velez-Cortes Florencia , Urtecho Guillaume , Wang Harris H.
Published: October 2024

The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or “spatial hubs” dominated byBacteroideceae,Ruminococceae, andLachnospiraceaefamilies. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.

One Sentence Summary

High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
Authors: Rahmaninejad Hadi , Xiao Yao , Tortora Maxime M.C. , Fudenberg Geoffrey
Published: October 2024

In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between neighboring topologically associating domains, and elevated contact frequency between convergent CTCF barriers across the genome. However, recentin vivomeasurements present a puzzle: reported residence times for CTCF on chromatin are in the range of a few minutes, while lifetimes for cohesin are much longer. Can the observed features of genome folding result from the action of relatively transient barriers? To address this question, we developed a dynamic barrier model, where CTCF sites switch between bound and unbound states with rates that can be directly compared with biophysical measurements. Using this model, we investigated how barrier dynamics would impact observables for a range of experimental genomic and imaging datasets, including ChIP-seq, Hi-C, and microscopy. We found the interplay of CTCF and cohesin binding timescales influence the strength of each of these features, leaving a signature of barrier dynamics even in the population-averaged snapshots offered by genomic datasets. First, in addition to barrier occupancy, barrier bound times are crucial for instructing features of genome folding. Second, the ratio of boundary to extruder lifetime greatly alters simulated ChIP-seq and simulated Hi-C. Third, large-scale changes in chromosome morphology observed experimentally after increasing extruder lifetime require dynamic barriers. By integrating multiple sources of experimental data, our biophysical model argues that CTCF barrier bound times effectively approach those of cohesin extruder lifetimes. Together, we demonstrate how models that are informed by biophysically measured protein dynamics broaden our understanding of genome folding.
DeepFocus: A Transnasal Approach for Optimized Deep Brain Stimulation of Reward Circuit Nodes
Authors: Guo Yuxin , Forssell Mats , Kusyk Dorian M. , Jain Vishal , Swink Isaac , Corcoran Owen , Lee Yuhyun , Goswami Chaitanya , Whiting Alexander C. , Cheng Boyle C. , Grover Pulkit
Published: October 2024

Objective

Transcranial electrical stimulation (TES) is an effective technique to modulate brain activity and treat diseases. However, TES is primarily used to stimulate superficial brain regions and is unable to reach deeper targets. The spread of injected currents in the head is affected by volume conduction and the additional spreading of currents as they move through head layers with different conductivities, as is discussed in [1]. In this paper, we introduce DeepFocus, a technique aimed at stimulating deep brain structures in the brain’s “reward circuit” (e.g. the orbitofrontal cortex, Brodmann area 25, amygdala, etc.).

Approach

To accomplish this, DeepFocus utilizes transnasal electrode placement (under the cribriform plate and within the sphenoid sinus) in addition to electrodes placed on the scalp, and optimizes current injection patterns across these electrodes. To quantify the benefit of DeepFocus, we develop the DeepROAST simulation and optimization platform. DeepROAST simulates the effect of complex skull-base bones’ geometries on the electric fields generated by DeepFocus configurations using realistic head models.

It also uses optimization methods to search for focal and efficient current injection patterns, which we use in our simulation and cadaver studies.

Main Results

In simulations, optimized DeepFocus patterns created larger and more focal fields in several regions of interest than scalp-only electrodes. In cadaver studies, DeepFocus patterns created large fields at the medial orbitofrontal cortex (OFC) with magnitudes comparable to stimulation studies, and, in conjunction with established cortical stimulation thresholds, suggest that the field intensity is sufficient to create neural response, e.g. at the OFC.

Significance

This minimally invasive stimulation technique can enable more efficient and less risky targeting of deep brain structures to treat multiple neural conditions.
Beyond the CTCT: Remote Structural Changes After VIM-MRgFUS in Essential Tremor
Authors: Krauß Jonas , Upadhyay Neeraj , Purrer Veronika , Borger Valeri , Daamen Marcel , Maurer Angelika , Schmeel Carsten , Radbruch Alexander , Wüllner Ullrich , Boecker Henning
Published: October 2024

Introduction

Essential tremor (ET) is a progressive disorder characterized by altered network connectivity between the cerebellum, thalamus, and cortical regions. Magnetic Resonance-guided Focused Ultrasound (MRgFUS) of the ventral intermediate nucleus (VIM) is an effective, minimally invasive treatment for ET. Increasing clinical use in ET facilitates research on structural changes after thalamic lesions.

Methods

Forty-six patients with medication-resistant ET underwent unilateral VIM-MRgFUS. Voxel-based morphometry was applied to investigate Gray Matter Volume (GMV) changes over a time span of 6 months in the whole brain and the thalamus in particular to investigate local and distant effects.

Results

Clinically, contralateral tremor significantly decreased by 68 % at 6 months following MRgFUS. In addition to local changes in thalamic nuclei (VIM, ventral lateral posterior, centromedian thalamus and pulvinar), VBM revealed remote GMV decreases in the ipsilesional insula and the anterior cingulate cortex as well as the contralesional middle occipital gyrus. Increased GMV was found in both temporal gyri. There was no significant correlation between regional GMV declines and tremor improvement. However, temporal volume increases were associated with improved motor-related functional abilities and quality of life outcomes.

Conclusion

Our findings implicate distributed structural changes following unilateral VIM-MRgFUS. Structural losses could reflect Wallerian degeneration of VIM output neurons or plasticity due to decreased sensory input following tremor improvement.
Chemo-Profiling by UPLC-QTOF-MS, GC-MS/MS analysis andIn VitroBioactivity Assessment ofDesmodium gangeticumDC
Authors: Jagtap Mamata A. , Magdum Aditya B. , Lugade Vishwajit V. , Kamble Pratik S. , Jayannawar Dayanand P. , Nimbalkar Mansingraj S. , Patil Swaroopa A.
Published: October 2024

Desmodium gangeticumDC., commonly known as Shalparni, and a member of the Fabaceae family, is a small shrub native to tropical and subtropical regions. The active principles of this plant are primarily concentrated in its roots, which are traditionally used in various medicinal formulations. This study aimed to identify alternative sources of raw material by evaluating the biochemical analysis and bioactivity profiling of both fresh and dried plant parts—roots, leaves, and stems. Extracts were prepared using methanol, ethanol, and distilled water and subjected to phytochemical, antioxidant, anti-inflammatory (HRBC membrane stabilization), and antibacterial assays. Additionally, chemical profiling was performed using FTIR, GC-MS/MS, and UPLC-Q-TOF-MS. This is the first report onD. gangeticumas one of the Dashmoola plants for its biochemical analysis, bioactivity, and chemoprofiling of the entire plant. Results indicated that the GC-MS/MS analysis identified 25 volatile compounds in leaves, whereas the roots contained 21. These compounds included fatty acids, ketones, hydrocarbons, alcohols, and esters. UPLC-Q-TOF-MS analysis revealed a diverse array of bioactive compounds: 287 in aqueous leaf extracts and 192 in aqueous root extracts, many of which were identified as bioactive agents. Notably, the leaf extracts exhibited a higher number of bioactive compounds compared to the roots, highlighting the plant’s diverse bioactive compounds in different tissues. The study demonstrates that both the leaves and roots ofD. gangeticumcontain significant therapeutic compounds. Therefore, the leaves could serve as a sustainable alternative to roots as raw material for medicinal preparations, contributing to the conservation of this plant in its natural habitat.
The thermotolerant Arabian killifish,Aphanius dispar, as a novel infection model for human fungal pathogens
Authors: Minhas Rashid , Bedekovic Tina , Veale Teigan , John Larissa L. H. , Hamied Atyaf Saied , Scrase Elliott , Read Sienna , Davies Chantelle , Gifford Hugh , Farrer Rhys , Bates Steven , Brand Alexandra C. , Ramsdale Mark , Kudoh Tetsuhiro
Published: October 2024

Candida albicans: a fungal pathogen, can cause superficial and fatal infections in humans. An important virulence factor inC. albicansdissemination is the transformation from yeast to an invasive hyphal form, which is favoured at human body temperature. Zebrafish, a useful model for studyingC. albicansinfections, cannot survive at 37°C. Arabian killifish,Aphanius dispar, an emerging teleost model can tolerate temperatures up to 40 °C for up to 12 days (independent feeding time) allowing for longer analysis compared to zebrafish. This study introducesA. disparas a thermo-relevant and a more accurate reporter of the virulence mechanisms relevant toC. albicansas a human pathogen. UsingA. dispar, we tested virulence at human skin (30 °C), body temperature (37 °C) and a high fever condition (40°C). Infection byC. albicansat 37°C and 40°C significantly increased virulence, reduced survival of AKF embryos and formed invasive hyphal network compared to 30 °C. Two mutant strains ofC. albicans. pmr1Δ(with aberrant cell surface glycans) exhibited reduced virulence at 37°C, whereasrsr1Δ (lacking a cell polarity marker) showed less virulence at 30 °C. Additionally, anti-fungal treatment rescued AKF survival in a dose-dependent manner, indicating AKF’s potential forin vivodrug testing. Our data indicates the quantitative and qualitative importance of examining virulence traits at physiologically relevant temperatures and demonstrates an equivalence to findings for systemic infection derived in mouse models. TheA. disparembryo therefore provides an excellentin vivomodel system for assessing virulence, drug-testing, and real-time imaging of host-pathogen interactions.

Significance Statement

The virulence of many pathogens is dependent on host temperature. We demonstrate that theA. disparembryo provides an excellent new thermo-relevant alternative to zebrafish and mouse models, which have limitations in terms of the range of temperatures that can be assessed in real-time. In this study, we have assessedC. albicanstemperature-based virulence, focusing on human body and human skin temperatures (37, 40 and 30 °C, respectively) by examining different genetic backgrounds ofC. albicansstrains. The results indicate differentC. albicansstrains with genetic background show varied virulence depending on temperature indicating importance of examination of virulence mechanisms at physiological temperatures.
Estimating the mean: behavioral and neural correlates of summary representations for time intervals
Authors: Otsuka Taku , Karsilar Hakan , van Rijn Hedderik
Published: October 2024

Our behavior is guided by the statistical regularities in the environment. Prior research on temporal context effects has demonstrated the dynamic processes through which humans adapt to the environment’s temporal regularities. However, learning temporal regularities not only entails dynamic adaptation to traces of previous individual events but also often requires the extraction and retention of summary statistics (e.g., the mean) of temporal distributions. To investigate these summary representations for temporal distributions and to test their sensitivity to distributional changes, we explicitly asked participants to extract the mean of different distributions of time intervals, which shared the same mean but varied in their variability specifically operationalized by the width and presentation frequency of the intervals. Our findings showed that the variability of the estimated mean increased with the distributions’ variability, even though the actual mean remained constant. We further examined how such learning of temporal distributions modulates EEG signals during subsequent temporal judgments. Analysis revealed that the contingent negative variation (CNV), predictive of single-trial RTs, was correlated with how much individuals’ estimates of the mean were affected by the distributions’ variability. Conversely, the post-interval P2 was not modulated by the distributions but predicted participants’ responses, suggesting that P2 reflects the perceived duration of an interval. Taken together, our results demonstrate not only that humans can accurately estimate the mean of a temporal distribution, but also that the representation of the mean becomes more uncertain as the variability of the distribution increases, as reflected neurally in the preparation-related CNV during temporal decisions.
Whole-Process 3D ECM-Encapsulated Organoid-Based Automated High-Throughput Screening Platform Accelerates Drug Discovery for Rare Diseases
Authors: Xu Zhaoting , Yang Hui , Zhou Yuru , Dzakah Emmanuel Enoch , Zhao Bing
Published: October 2024

The use of organoids, especially patient-derived organoids, for high-throughput screening (HTS) is widely accepted due to their ability to mimic the three-dimensional (3D) structure, function, and drug responses of in vivo tissues. However, the complexity of handling extracellular matrix (ECM) components with traditional HTS devices leads to the utilization of suspension cultures in matrix-free or matrix-low conditions during HTS, which can alter their transcriptomic landscape and drug responses. Here, we develop a whole-process 3D ECM-encapsulated organoid-based automated HTS (wp3D-OAHTS) platform, which enables the rapid and accurate generation of uniformly distributed 3D cell-matrix mixture domes at the center of each well in 96-well plates. This approach replicates the process of manual organoid culture but with superior stability and reproducibility. Utilizing this platform, we screened 2,802 compounds on neuroendocrine cervical cancer organoids, a rare malignancy with significant unmet clinical needs. We identified 7 top hits that display strong anti-tumor effects with remarkably low half-maximal inhibitory concentration (IC50) and validated the in vivo efficacy of Quisinostat 2HCl. Additionally, we demonstrated that employing 3D ECM-encapsulated organoid cultures for HTS, rather than suspended cultures, provides optimal conditions for drug discovery. Our wp3D-OAHTS platform significantly improves the rapidity and efficiency of new drug discovery for rare diseases.
Integrated scFv identification and CAR T cell generation for AML targeting in vivo
Authors: Müller-Tidow Carsten , Liu Yi , Lauk Annika , Sedloev David , Brysting Josephine , Cetin Ela , Liu Chunan , Moennig Maximilian , Luft Thomas , Yun Haiyang , Schmitt Michael , Sauer Tim , Zhou Fengbiao , Rohde Christian
Published: October 2024

Cancer immunotherapy has witnessed remarkable advancements, especially in the development of chimeric antigen receptor (CAR) T cell therapy. Here, we integrated single-chain variable fragment (scFv) development with CAR T cell generation based on a newly developed scFv phagemid library. High-throughput long-read PacBio sequencing identified 4.5 x 107 unique full-length scFv proteins within the generated library. In a proof of principle, we screened for scFvs targeting C-type lectin-like molecule-1 (CLL1) with subsequent cloning into a third generation retroviral CAR backbone. Functional assays revealed the specificity and potency of these CAR T cells in targeting CLL1-positive AML cells in vitro. In vivo studies reduced tumor burden and improved survival rates compared to controls. Taken together, screening for tumor specific scFvs against CLL1 can rapidly generate AML specific CAR T cells with effective tumor killing in vivo.
Recursive Cleaning for Large-scale Protein Data via Multimodal Learning
Authors: Jiang Zixuan , Zhang Sitao , Cao Jiahang , Zhang Qiang , Liu Shiyi , Fang Yuetong , Zhang Lingfeng , Qing Rui , Xu Renjing
Published: October 2024

Abstract

Reliable datasets and high-performance models work together to drive significant advancements in protein representation learning in the era of Artificial Intelligence. The size of protein models and datasets has grown exponentially in recent years. However, the quality of protein knowledge and model training has suffered from the lack of accurate and efficient data annotation and cleaning methods. To address this challenge, we introduceProtAC, which corrects largeProtein datasets with a scalableAutomaticCleaning framework that leverages both sequence and functional information through multimodal learning. To fulfill data cleaning, we propose the Sequence-Annotation Matching (SAM) module in the model, which filters the functional annotations that are more suitable for the corresponding sequences. Our approach is a cyclic process consisting of three stages: first pretraining the model on a large noisy dataset, then finetuning the model on a small manually annotated dataset, and finally cleaning the noisy dataset using the finetuned model. Through multiple rounds of “train-finetune-clean” cycles, we observe progressive improvement in protein function prediction and sequenceannotation matching. As a result, we achieve(1)a state-of-the-art (SOTA) model that outperforms competitors with fewer than 100M parameters, evaluated on multiple function-related downstream tasks, and(2)a cleaned UniRef50 dataset containing ∼50M proteins with well-annotated functions. Performing extensive biological analysis on a cleaned protein dataset, we demonstrate that our model is able to understand the relationships between different functional annotations in proteins and that proposed functional annotation revisions are reasonable.
WNT-mediating TCF/LEF transcription factor gene expression in early human pluripotency and cell lineages differs from the rodent paradigm
Authors: Ross Connor , Azami Takuya , Salonna Marika , Gyuris Richard , Nichols Jennifer , Hoppler Stefan
Published: October 2024

Embryonic stem cell research has uncovered different requirements for WNT/β-catenin signalling in human naïve pluripotent cells compared to the mouse paradigm. It is therefore important to study WNT/β-catenin signalling directly in models of early human development. Since TCF/LEF factors mediate the regulation of target genes downstream of WNT/β-catenin signalling, we studied the expression and protein localisation of the four TCF/LEF genes by analysingin vitro“snapshots” of human development, leveraging naïve and primed pluripotent cells as well as extraembryonic and early embryonic cell lineages. Strikingly, we comprehensively confirm clear differences between mouse and human pluripotent stem cells, suggesting species-specific requirements for WNT signalling that may reflect differences in states of pluripotency. Human naïve ES cells express very low TCF7L1, unlike their mouse counterparts. TCF7L2 is robustly expressed in human naïve ES-derived trophectoderm cells. In human primed pluripotent stem cells, activation of WNT/β-Catenin signalling is required to induce expression of bothTCF7andLEF1, concomitant with hallmark gastrulation markers. This expression of human TCF/LEF genes benchmarks differential requirements for WNT/β-catenin signalling throughout early human embryo development that requires further investigation.
Amplification of disease by nutrient addition: Testing mechanisms from individual to community levels
Authors: Green Elizabeth T. , Heckman Robert W. , Mitchell Charles E.
Published: October 2024

Nutrient supply can amplify disease epidemics through mechanisms from individual to community levels. Within host individuals, nutrient addition can drive pathogen replication or growth. Across a host population, nutrient addition can drive disease transmission by increasing host growth and abundance relative to defense. Furthermore, such effects may be influenced by pathogen species interactions. Understanding how nutrients impact disease epidemics requires a framework that integrates these mechanisms across biological levels. To build such a framework, we conducted a field experiment in an old field on tall fescue,Lolium arundinaceum, and used structural equation models to integrate multiple hypothesized mechanisms. Nutrient addition (NPK fertilizer) increased brown patch disease but was best modeled as a direct path and not mediated by host abundance. To expand our framework, we also re-analyzed a previous experiment. That experiment reproduced the direct path from nutrients to disease, and added an indirect path mediated by host population abundance. Nutrient addition also increased foliar nitrogen, consistent with individual-level mechanism, but this did not increase disease. Brown patch decreased with burden of another disease, anthracnose, independently of nutrients. These results partially support both individual- and population-level hypotheses, emphasizing the importance of considering multiple biological levels underlying impacts of abiotic change.
RiboTag RNA Sequencing Identifies Local Translation of HSP70 In Astrocyte Endfeet After Cerebral Ischemia
Authors: Shim Bosung , Ciryam Prajwal , Tosun Cigdem , Serra Riccardo , Tsymbalyuk Natalia , Keledjian Kaspar , Gerzanich Volodymyr , Simard J. Marc
Published: October 2024

Brain ischemia causes disruption in cerebral blood flow and blood-brain barrier (BBB) integrity which are normally maintained by the astrocyte endfeet. Emerging evidence points to dysregulation of the astrocyte translatome during ischemia, but its effects on the endfoot translatome are unknown. In this study, we aimed to investigate the early effects of ischemia on the astrocyte endfoot translatome in a rodent model of cerebral ischemia-reperfusion. To do so, we immunoprecipitated astrocyte-specific tagged ribosomes (RiboTag IP) from mechanically isolated brain microvessels. In mice subjected to middle cerebral artery occlusion and reperfusion and contralateral controls, we sequenced ribosome-bound RNAs from perivascular astrocyte endfeet and identified 205 genes that were differentially expressed in the translatome after ischemia. Pathways associated with the differential expressions included proteostasis, inflammation, cell cycle, and metabolism. Transcription factors whose targets were enriched amongst upregulated translating genes included HSF1, the master regulator of the heat shock response. The most highly upregulated genes in the translatome were HSF1-dependentHspa1aandHspa1b, which encode the inducible HSP70. We found that HSP70 is upregulated in astrocyte endfeet after ischemia, coinciding with an increase in ubiquitination across the proteome. These findings suggest a robust proteostasis response to proteotoxic stress in the endfoot translatome after ischemia. Modulating proteostasis in endfeet may be a strategy to preserve endfeet function and BBB integrity after ischemic stroke.
A Novel Genomic Rearrangement in theAmaranthus palmeriExtrachromosomal Circular DNA Provides Dual Herbicide Resistance to Glyphosate and Glufosinate
Authors: Carvalho-Moore Pâmela , Borgato Ednaldo A. , Cutti Luan , Porri Aimone , Meiners Ingo , Lerchl Jens , Norsworthy Jason K. , Patterson Eric L.
Published: October 2024

Amplification of chloroplastic glutamine synthetase (GS2) has been characterized as one of the resistance mechanisms in glufosinate-resistantAmaranthus palmeriaccession (MSR2). Previously, the overamplification of the glyphosate-resistance gene, 5-enolpyruvylshikimate-3-phosphate (EPSPS), inA. palmeriwas determined to be driven by an extrachromosomal circular DNA (eccDNA). Here, a novel eccDNA is described that carries both glyphosate and glufosinate-ammonium target site due to co-duplication of their chromosomic native region, conferring resistance. BesidesEPSPS, the novel replicon has a region replaced by a fragment carrying theGS2isoforms (GS2.1andGS2.2) and other genes. The co-existence of eccDNA carrying onlyEPSPSwas confirmed in MSR2 samples harboring dual targeting eccDNA. The genomic structure ofGS2andEPSPSamplification was also assessed in a different glufosinate-resistantA. palmeriaccession (MSR1) along with MSR2. The accessions showed distinctGS2.1andGS2.2amplification patterns suggesting the existence of diverse replicons that were not assembled here. TheEPSPSwas amplified in both accessions, and a correlation was observed with theGS2isoforms in MSR2, further supporting the co-existence of these genes in the same replicon. These findings shed light on the complexity of eccDNA formation in plant systems, with the collection and accumulation of extra pieces of DNA.
Oxygen chemoreceptor inhibition by dopamine D2receptors in isolated zebrafish gills
Authors: Reed Maddison , Jonz Michael G.
Published: October 2024

Dopamine is an essential modulator of oxygen sensing and control of ventilation and was the first neurotransmitter described in the carotid body. Little is known of the evolutionary significance of dopamine in oxygen sensing, or whether it plays a similar role in anamniotes. In the model vertebrate, zebrafish (Danio rerio), presynaptic dopamine D2receptor expression was demonstrated in gill neuroepithelial cells (NECs)—analogues of mammalian oxygen chemoreceptors; however, a mechanism for dopamine and D2in oxygen sensing in the gills had not been defined. The present study tested the hypothesis that presynaptic D2receptors provide a feedback mechanism that attenuates the chemoreceptor response to hypoxia. Using an isolated gill preparation from Tg(elavl3:GCaMP6s) zebrafish, we measured hypoxia-induced changes in intracellular Ca2+concentration ([Ca2+]i) in NECs and postsynaptic neurons. Activation of D2with dopamine or specific D2agonist, quinpirole, decreased hypoxic responses in NECs; whereas D2antagonist, domperidone, had the opposite effect. Addition of SQ22536, an adenylyl cyclase (AC) inhibitor, decreased the effect of hypoxia on [Ca2+]i, similar to dopamine. Activation of AC by forskolin partially recovered the suppressive effect of dopamine on the Ca2+response to hypoxia. Further, we demonstrate that the response to hypoxia in postsynaptic sensory neurons was dependent upon innervation with NECs, and was subject to modulation by activation of presynaptic D2. Our results provide the first evidence of neurotransmission of the hypoxic signal at the NEC-nerve synapse in the gill and suggest that a presynaptic, modulatory role for dopamine in oxygen sensing arose early in vertebrate evolution.

Key points

For the first time, we present an experimental model that permits imaging of intracellular Ca2+in identified vertebrate oxygen chemoreceptors using GCaMP in a whole/intact sensing organ.

The hypoxic response of zebrafish chemoreceptors is attenuated by dopamine through a mechanism involving D2receptors and adenylyl cyclase.

Zebrafish oxygen chemoreceptors send a hypoxic signal to postsynaptic (sensory) neurons.

Postsynaptic neuronal responses to hypoxia are modulated by presynaptic D2receptors, suggesting a link between chemoreceptor inhibition by dopamine and modulation of the hypoxic ventilatory response.

Our results suggests that a modulatory role for dopamine in oxygen sensing arose early in vertebrate evolution.
Dnajc3(HSP40) Enhances Axon Regeneration in the Mouse Optic Nerve
Authors: Wang Jiaxing , Li Ying , Struebing Felix L. , Jardines Sandra , Lin Su-Ting , Lin Fangyu , Geisert Eldon E.
Published: October 2024

A forward genetics approach was used to identify genomic elements enhancing axon regeneration in the BXD recombinant mouse strains. Axon regeneration was induced by knocking downPtenin retinal ganglion cells (RGCs) using adeno-associated virus (AAV) to deliver an shRNA followed by an intravitreal injection of Zymosan with CPT-cAMP that produced a mild inflammatory response. RGC axons were damaged by optic nerve crush (ONC). Following a 12-day survival period, regenerating axons were labeled by intravitreal injection of Cholera Toxin B (CTB) conjugated with Alexa Fluor 647. Two days later, labeled axons within the optic nerve were examined to determine the number of regenerating axons and the distance they traveled down the optic nerve. The analysis revealed a surprising difference in the amount of axonal regeneration across all 33 BXD strains. There was a 7.5-fold difference in the number of regenerating axons and a 4-fold difference in distance traveled by regenerating axons. These data were used to generate an integral map defining genomic loci modulating the enhanced axonal regeneration. A quantitative trait locus modulating axon regeneration was identified on Chromosome 14 (115 to 119 Mb). Within this locus were 16 annotated genes. Subsequent testing revealed that one candidate gene,Dnajc3, modulates axonal regeneration.Dnajc3encodes Heat Shock Protein 40 (HSP40), which is a molecular chaperone. Knocking downDnajc3in the high regenerative strain (BXD90) led to a decreased regeneration response, while overexpression ofDnajc3in a low regenerative strain (BXD34) resulted in an increased regeneration response. These findings suggest thatDnajc3not only increases the number of regenerating axons, it also increases the distance those axons travel. This may prove to be critical for functional recovery in large mammals, where the distance axons travel to their target is considerably longer than that of the mouse. Thus,Dnajc3may play a critical role for functional recovery in humans by increasing the number of regenerating axons and the distance the regenerating axons travel.
Ethanol drinking sex-dependently alters cortical IL-1β synaptic signaling and cognitive behavior in mice
Authors: Liss A , Siddiqi MT , Podder D , Scroger MV , Vessey G , Martin K , Paperny NM , Vo KT , Astefanous A , Belachew N , Idahor E , Varodayan FP
Published: October 2024

Individuals with alcohol use disorder (AUD) struggle with inhibitory control, decision making, and emotional processing. These cognitive symptoms reduce treatment adherence, worsen clinical outcomes, and promote relapse. Neuroimmune activation is a key factor in the pathophysiology of AUD, and targeting this modulatory system is less likely to produce unwanted side effects compared to directly targeting neurotransmitter dysfunction. Notably, the cytokine interleukin-1β (IL-1β) has been broadly associated with the cognitive symptoms of AUD, though the underlying mechanisms are not well understood. Here we investigated how chronic intermittent 24-hour access two bottle choice ethanol drinking affects medial prefrontal cortex (mPFC)-related cognitive function and IL-1 synaptic signaling in male and female C57BL/6J mice. In both sexes, ethanol drinking decreased reference memory and increased mPFC IL-1 receptor 1 (IL-1R1) mRNA levels. In neurons, IL-1β can activate either pro-inflammatory or neuroprotective intracellular pathways depending on the isoform of the accessory protein (IL-1RAcP) recruited to the IL-1R1 complex. Moreover, ethanol drinking sex-dependently shifted mPFC IL-1RAcP isoform gene expression and IL-1β regulation of mPFC GABA synapses, both of which may contribute to female mPFC resiliency and male mPFC susceptibility. This type of signaling bias has become a recent focus of rational drug development. Therefore, in addition to increasing our understanding of how IL-1β sex-dependently contributes to mPFC dysfunction in AUD, our current findings also support the development of a new class of pharmacotherapeutics based on biased IL-1 signaling.

Highlights

- Female mice consumed more ethanol, but were less cognitively impaired than males

- Ethanol altered IL-1β effects at mPFC GABA synapses, with females less sensitive than males

- Ethanol altered mPFCIl1rapmRNA to promote female neuroprotection and male neuroinflammation