bluuebunny/crossref_metadata_2025 huggingface dataset:
Incremental Accumulation of Linguistic Context in Artificial and Biological Neural Networks
Authors: Tikochinski Refael , Goldstein Ariel , Meiri Yoav , Hasson Uri , Reichart Roi
Published: January 2024

Accumulated evidence suggests that Large Language Models (LLMs) are beneficial in predicting neural signals related to narrative processing. The way LLMs integrate context over large timescales, however, is fundamentally different from the way the brain does it. In this study, we show that unlike LLMs that apply parallel processing of large contextual windows, the incoming context to the brain is limited to short windows of a few tens of words. We hypothesize that whereas lower-level brain areas process short contextual windows, higher-order areas in the default-mode network (DMN) engage in an online incremental mechanism where the incoming short context is summarized and integrated with information accumulated across long timescales. Consequently, we introduce a novel LLM that instead of processing the entire context at once, it incrementally generates a concise summary of previous information. As predicted, we found that neural activities at the DMN were better predicted by the incremental model, and conversely, lower-level areas were better predicted with short-context-window LLM.
Profiling Clinical Researchers Effectively using Embeddings and Clustering
Authors: Sharma Anika , Edelson Maxim , Kuo Tsung-Ting
Published: January 2024

Effective researcher profiling is key to support rapid research team formation. We developed a profiling method using (1) widely accessible publication titles, (2) document embedding vector representations to consider background, and (3) both general and specific types of datasets. Our results showed that the most similar researchers have cosine similarities of 0.287/0.258. Our preliminary results can support biomedical informaticians to expedite collaborative clinical studies, enhance research quality, and eventually improve patient healthcare outcomes.
Frailty, Mental Disorders, and Metabolic Syndrome: A Genetic Association and Mediation Mendelian Randomization Study
Authors: Deng Ming-Gang , Wang Kai , Nie Jia-Qi , Liu Fang , Liang Yuehui , Liu Jiewei
Published: January 2024

Objective

To examine the genetic associations of metabolic syndrome (MetS) with frailty and mental disorders [depression, schizophrenia (SCZ), and bipolar disorder (BIP)], along with causality between frailty and MetS and the mediating role of mental disorders.

Methods

The summary-level datasets were obtained from recent genome-wide association studies. The genetic correlation was explored from the perspectives of global and local genetic correlation. Univariate Mendelian Randomization (UMR) was used to investigate the causal link between frailty and metabolic syndrome (MetS), followed by multivariate MR to address the confounding effects of body mass index (BMI) and physical activity (PA). Finally, two-step MR analyses were conducted to examine whether the causal relationship was mediated by mental disorders.

Results

The global genetic correlation analyses presented MetS was positively associated with frailty and depression, but reversely related to SCZ. Similarly, MetS was locally correlated to frailty, depression, and SCZ in numerous genomic regions. The UMR demonstrated that fragile people have a higher likelihood of suffering from MetS (OR: 2.773, 95% CI: 1.455-5.286,p= 0.002), and reversely people with MetS tended to be more fragile (beta: 0.211, 95% CI: 0.180-0.241,p< 0.001). This bidirectional causal association still existed even after adjusting for BMI and PA. The mediation analyses implied this causality was mediated by depression, but not SCZ and BIP.

Conclusion

Our research provided evidence of genetic correlations between MetS and frailty, depression, and SCZ. Additionally, we discovered a bidirectional causality between frailty and MetS, with depression playing a significant mediating role.
cg05883128 (DDX60) and NR3C2 (CD4 T-cells and B-cells) to Be the Genetic Roots of Systemic Lupus Erythematosus
Authors: Zhang Zhengjun
Published: January 2024

Motivation

Systemic lupus erythematosus (SLE) is an autoimmune disease and a long-term condition affecting many body parts. Autoimmune diseases are affecting more people for reasons unknown, and the causes of these diseases remain a mystery.

Method

A newly introduced robust competing (risk) max-logistic regression classifier that can simultaneously perform subtype clustering and classification for disease diagnoses and predictions becomes a new hope to solve the mystery. We use this method in the study to discover critical DNA methylation CpG sites and genome genes, which lead to the highest accuracy and interpretability.

Results

The DNA methylation CpG site cg05883128 (DDX60) and gene NR3C2 are essentially responsible for SLE development. They can lead to 100% prediction accuracy together with a miniature set of other CpG sites and genes, respectively. cg05883128 (DDX60) reveals the LSE mechanism affecting many body parts. NR3C2 in CD4 T cells and B cells behaves reversely, leading to the cause of LSE and explaining the mechanism of the autoimmune disease.

Conclusions

This work represents a pioneering effort and intellectual discovery in applying the max-logistic competing risk factor model to identify critical genes for LSE, and the interpretability and reproducibility of the results across diverse populations suggest that the CpGs and DEGs identified can provide a comprehensive description of the transcriptomic features of SLE. The practical implications of this research include the potential for personalized risk assessment, precision diagnosis, and tailored treatment plans for patients.
The Impact of Normal Aging Out on Continuity of Treatment among Children and Adolescents Living with HIV in the PEPFAR Supported Program in Kenya
Authors: Odero Lydia , Chafetz Aaron , Gikura Mary , Goldstein Deborah , Golin Rachel , Kemunto Diana , Maina Nelly , Mutisya Immaculate , Muthoka Kennedy , Nganga Evelyn , Okegbe Tishina , Okutoyi Salome , Omoro Gonza , Siberry George , Wafula Rose , Achwoka Dunstan
Published: January 2024

Introduction

To reduce HIV-related morbidity and mortality among children and adolescents living with HIV, defined as those 0-14 years old, continuity of treatment is critical. Treatment continuity estimates among children and adolescents living with HIV lag adults. We sought to understand how aging out among children and adolescents living with HIV in Kenya impacts continuity of treatment.

Methods

A retrospective cohort analysis was performed on de-identified individual-level data from the Kenya National Data Warehouse for all clients who initiated and/or received antiretroviral therapy between the periods of Oct 1, 2018 and Sep 30, 2022 (US Government fiscal years 2019-2022). Children and adolescents living with HIV previously on antiretroviral therapy and those newly initiating antiretroviral therapy were included in the analysis. Outcomes included aging out of the cohort after turning 15 years old, interruption in treatment, return to treatment, and remaining active on treatment.

Results

The study analyzed client-level data for four US Government fiscal years 2019-2022. The number of active children and adolescents living with HIV on treatment at the end of fiscal year 2019 was 44,628. This changed to 48,218, 48,262, and 44,780 representing 8%, 0%, and -7% cohort growth/loss at the end of fiscal years 2020, 2021 and 2022, respectively. Among those who were on treatment at the beginning of each fiscal year, aging-out accounted for 47%, 39%, and 28% of the total losses for the periods 2020, 2021 and 2022, respectively. Interruptions in treatment accounted for proportions ranging from 5-9% among those active on treatment. Among the newly-initiated on treatment within each fiscal year, aging-out proportions ranged from 3%-5%. Among those who returned to treatment in each fiscal year, the proportions who remained active at the end of the fiscal year varied from 72%-76%.

Conclusions

This analysis suggests that normal aging-out results in underestimation of HIV treatment continuity for children and adolescents living with HIV. Routine aging out analyses can inform programs on their true rates of interruptions in treatment, as they work to achieve epidemic control among children and adolescents living with HIV.
Bystander intervention is associated with reduced mortality among injury victims in Cameroon
Authors: O’Connor Kathleen , Driban Matthew , Oke Rasheedat , Dissak-Delon Fanny Nadia , Magdalene Tanjong Signe Mary , Mirene Tchekep , Dieudonne Mbeya , Kinge Thompson , Njock Richard L. , Nkusu Daniel N. , Tsiagadigui Jean-Gustave , Edouka Cyrille , Wonja Catherine , Eisner Zachary , Delaney Peter , Julliard Catherine , Chichom-Mefire Alain , Christie S. Ariane
Published: January 2024

Introduction

Despite high injury mortality rates, Cameroon currently lacks a formal prehospital care system. In other sub-Saharan African low and middle-income countries, Lay First Responder (LFR) programs have trained non-medical professionals with high work-related exposure to injury in principles of basic trauma care. To develop a context-appropriate LFR program in Cameroon, we used trauma registry data to understand current layperson bystander involvement in prehospital care and explore associations between current non-formally trained bystander-provided prehospital care and clinical outcomes.

Methods

The Cameroon Trauma Registry (CTR) is a longitudinal, prospective, multisite trauma registry cohort capturing data on injured patients presenting to four hospitals in Cameroon. We assessed prevalence and patterns of prehospital scene care among all patients enrolled in a prospective, multisite trauma registry (Cameroon Trauma Registry (CTR)) in 2020. Associations between scene care, clinical status at presentation, and outcomes were tested using univariate and multivariate logistic regression. Injury severity was measured using the abbreviated injury score. Data were analyzed using Stata17.

Results

Of 2212 injured patients, 455 (21%) received prehospital care (PC) and 1699 (77%) did not receive care (NPC). Over 90% (424) of prehospital care was provided by persons without formal medical training. The most common prehospital interventions performed included bleeding control (370, 57%) and fracture immobilization (139, 21%). PC patients were more severely injured (p<0.001), had markers of increased socioeconomic status (p=0.01), and longer transport distances (p<0.001) compared to NPC patients. Despite increased severity of injury, patients who received PC were more likely to present with a palpable pulse (OR=6.2, p=0.02). Multivariate logistic regression adjusted for injury severity, socioeconomic status and travel distance found PC to be associated with reduced emergency department mortality (OR=0.14, p<0.0001).

Conclusions

Although prehospital injury care in Cameroon is rarely performed and is provided almost entirely by persons without formal medical training, prehospital intervention is associated with increased early survival after injury. Implementation of LFR training to strengthen the frequency and quality of prehospital care has considerable potential to improve trauma survival. LFR training in Cameroon should target commercial drivers given high work-related exposure to the injured and emphasize bleeding control interventions.
Factors associated with viral Load re-suppression after enhanced adherence counseling among recipients of care with an Initial high viral load result in RISE-supported facilities in five States in Nigeria
Authors: Obasa Gbenga Benjamin , Ijaiya Mukhtar , Okwor Ejike , Dare Babafemi , Emerenini Franklin , Anyanwu Prince , Akinjeji Adewale , Brickson Kate , Zech Jennifer , Ogundare Yemisi , Atuma Emmanuel , Strachan Molly , Fayorsey Ruby , Curran Kelly
Published: January 2024

This study explores factors influencing viral re-suppression among 1,607 recipients of HIV care in Nigeria who completed Enhanced Adherence Counseling (EAC) between July 2021 and June 2022. The analysis, part of the Reaching Impact, Saturation, and Epidemic Control (RISE) project, utilized routine program data from 132 health facilities. Results showed a 91% re-suppression rate post-EAC, with age and ART regimen type identified as significant factors. Adolescents (10-19 years) had a higher likelihood of re-suppression, while ROC on second-line regimens exhibited lower resuppression rates. These findings inform programmatic decisions to enhance HIV treatment outcomes in Nigeria.
Characteristics of Walk-In Clinic Physicians and Patients in Ontario, Canada: A Cross-Sectional Study
Authors: Lapointe-Shaw Lauren , Salahub Christine , Austin Peter C. , Bai Li , Banwatt Sundeep , Berthelot Simon , Bhatia R. Sacha , Bird Cherryl , Desveaux Laura , Kiran Tara , Lofters Aisha , Maclure Malcolm , Martin Danielle , McBrien Kerry A. , McCracken Rita K. , Paterson J. Michael , Rahman Bahram , Shuldiner Jennifer , Tadrous Mina , Terpou Braeden A. , Thakkar Niels , Wang Ruoxi , Ivers Noah M.
Published: January 2024

Objective

We aimed to describe family physicians who primarily practice in a walk-in clinic setting and compare them to family physicians who provide longitudinal care.

Design

A cross-sectional study that linked results from an annual physician survey (2019) to administrative healthcare data from Ontario, Canada. We compared the characteristics, practice patterns, and patients of physicians primarily working in a walk-in clinic setting, with family physicians providing longitudinal care.

Setting

Ontario, Canada.

Participants

Physicians who primarily worked in a walk-in clinic setting in 2019, as indicated by an annual physician survey.

Exposure

Whether the physician was a walk-in clinic physician or a family physician who provided longitudinal care.

Main Measures

Physician demographic and practice characteristics, as well as their patients’ demographic and healthcare utilization characteristics.

Results

Compared to the 9,137 family physicians practicing longitudinal care, the 597 physicians who self-identified as practicing primarily in walk-in clinics were more frequently male (67% vs. 49%) and could speak a language other than English or French (43% vs. 32%). Walk-in clinic physicians had more encounters with patients who were younger (M37 vs. 47 years), had lower levels of prior healthcare utilization (15% vs. 19% in highest band), who resided in large urban areas (87% vs. 77%), and in highly ethnically diverse neighborhoods (45% vs. 35%). Walk-in clinic physicians had more encounters with unattached patients (32% vs. 17%) and with patients attached to another physician outside their group (54% vs. 18%).

Conclusion

Physicians who primarily work in walk-in clinics saw many patients from historically underserved groups, and many patients who were attached to another family physician.
Data leakage in deep learning studies of translational EEG
Authors: Brookshire Geoffrey , Kasper Jake , Blauch Nicholas , Wu Yunan “Charles” , Glatt Ryan , Merrill David A. , Gerrol Spencer , Yoder Keith J. , Quirk Colin , Lucero Ché
Published: January 2024

A growing number of studies use deep neural networks (DNNs) to identify diseases from recordings of brain activity. DNN studies of electroencephalography (EEG) typically use cross-validation to test how accurately a model can predict the disease state of held-out test data. In these studies, segments of EEG data are often randomly assigned to the training or test sets. As a consequence, data from individual subjects appears in both training and test data. Could high test-set accuracy reflect leakage from subject-specific representations, rather than patterns that identify a disease? We address this question by testing the performance of DNN classifiers using segment-based holdout (where EEG segments from one subject can appear in both the training and test sets), and comparing this to their performance using subject-based holdout (where individual subjects’ data appears exclusively in either the training set or the test set). We compare segment-based and subject-based holdout in two EEG datasets: one classifying Alzheimer’s disease, and the other classifying epileptic seizures. In both datasets, we find that performance on previously-unseen subjects is strongly overestimated when models are trained using segment-based holdout. Next, we survey the literature and find that the majority of translational DNN-EEG studies use segment-based holdout, and therefore overestimate model performance on new subjects. In a hospital or doctor’s office, clinicians need to diagnose new patients whose data was not used in training the model; segment-based holdout, therefore, does not reflect the real-world performance of a translational DNN model. When evaluating how DNNs could be used for medical diagnosis, models must be tested on subjects whose data was not included in the training set.
Is there a difference in the satisfaction levels between professionals who have participated and those who have not participated in the TeleUTIP telemedicine project regarding their engagement in tele-education activities?
Authors: Moleda Constant Hilda M. R. , Jacovas Vanessa Cristina , Vinadé Chagas Maria Eulália , Cotta Matte Maria Cristina , Klever Emanuele König , Cunha Luciane , Mafalda Krauzer João Ronaldo , de Campos Moreira Taís , Cabral Felipe Cezar
Published: January 2024

Objective

The aim of this study is to introduce a distance education program and assess the satisfaction of health professionals.

Methods

A cross-sectional study was conducted in five public hospitals across different regions of Brazil. A total of 171 health professionals participated in a tele-education activity involving discussions of complex cases in a Case-Based Learning (CBL) format. Employee satisfaction was measured using the translated questionnaire Tele-Education Satisfaction Assessment Instrument (IAS-TE).

Results

The mean satisfaction score for participants was 4.6 on a 5-point Likert-type scale. Participants engaged in the telemedicine project (35.5%) reported significantly higher satisfaction (p<0.001) compared to their non-participating peers (n = 149, 64.5%). The IAS-TE exhibited a Cronbach’s alpha of 0.73, indicating good reliability, and demonstrated good homogeneity (KMO = 0.76, Bartlett’s test of sphericity = p<0.00).

Conclusion

Participants in the proposed activity expressed high levels of satisfaction. The findings suggest that satisfaction levels are elevated among professionals involved in the telemedicine project. The proposed satisfaction assessment instrument (IAS-TE) exhibits robust psychometric qualities and is suitable for evaluating other distance education activities. Future perspectives involve gaining a deeper understanding of strategies to enhance satisfaction for professionals who do not engage in activities using advanced technology.
WITHDRAWN: Impact of spatial clustering of cytotoxic and tumor infiltrating lymphocytes on overall survival in women with high grade serous ovarian cancer
Authors: Soupir Alex C. , Townsend Mary K. , Hathaway Cassandra A. , Nguyen Jonathan , Moran Segura Carlos , Saeed-Vafa Daryoush , Ospina Oscar E. , Peres Lauren C. , Conejo-Garcia Jose R. , Terry Kathryn L. , Tworoger Shelley S. , Fridley Brooke L.
Published: January 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to incorrect handling of multiple measures in the survival analyses. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Mechanical hyperalgesia and neuropathic pain qualities impart risk for chronic postoperative pain after total knee replacement
Authors: Vigotsky Andrew D. , Cong Olivia , Pinto Camila B , Barroso Joana , Perez Jennifer , Petersen Kristian Kjaer , Arendt-Nielsen Lars , Hardt Kevin , Manning David , Apkarian A. Vania , Branco Paulo
Published: January 2024

Total knee replacement (TKR) is the gold-standard treatment for end-stage chronic osteoarthritis pain, yet many patients report chronic postoperative pain after TKR. The search for preoperative predictors for chronic postoperative pain following TKR has been studied with inconsistent findings. This study investigates the predictive value of quantitative sensory testing (QST) and PainDETECT for postoperative pain 3, 6, and 12 months post-TKR. We assessed baseline and postoperative (3- and 6-months) QST measures in 77 patients with knee OA (KOA) and 41 healthy controls, along with neuropathic pain scores in patients (PainDETECT). QST parameters included pressure pain pressure threshold (PPT), pain tolerance threshold (PTT), conditioned pain modulation (CPM), and temporal summation (TS) using cuff algometry, alongside mechanical hyperalgesia, and mechanical temporal summation to repeated pinprick stimulation. Compared to healthy controls, KOA patients at baseline demonstrated hyperalgesia to pinprick stimulation at the medial OA-affected knee and cuff pressure on the ipsilateral calf. Lower cuff algometry PTT and mechanical pinprick hyperalgesia were associated with baseline KOA pain intensity. Moreover, baseline pinprick pain hyperalgesia explained 25% of variance in pain intensity 12 months post-TKR and preoperative neuropathic pain scores also captured 30% and 20% of the variance in postoperative pain at 6- and 12-months, respectively. A decrease in mechanical pinprick hyperalgesia from before surgery to 3 months after TKR was associated with lower postoperative pain at the 12 months post-TKR follow-up, and vice-versa. Our findings suggest that preoperative pinprick hyperalgesia and PainDETECT neuropathic-like pain symptoms show predictive value for the development of chronic post-TKR pain.
Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing
Authors: Shen Xiangyu , Chen Chunxu , Wang Yue , Zheng Wan , Zheng Jiahuan , Jones Amanda E. , Zhu Bing , Zhang Hao , Lyons Charles , Rijal Arjun , Moley James A. , Cao Gengsheng , Liu Kui , Winn Robert , Dickinson Amanda , Zhang Kai , Wang Hengbin
Published: January 2024

Ubiquitination of histone H2A at lysine 119 residue (H2AK119ub) plays critical roles in a wide range of physiological processes, including Polycomb gene silencing1,2, replication3–5, DNA damage repair6–10,Xinactivation11,12, and heterochromatin organization13,14. However, the underlying mechanism and structural basis of H2AK119ub remains largely elusive. In this study, we report that H2AK119ub nucleosomes have a unique composition, containing histone variants H2BC1 and H2AZ.2, and importantly, this composition is required for H2AK119ub and Polycomb gene silencing. Using the UAB domain of RSF1, we purified H2AK119ub nucleosomes to a sufficient amount and purity. Mass spectrometry analyses revealed that H2AK119ub nucleosomes contain the histone variants H2BC1 and H2AZ.2. A cryo-EM study resolved the structure of native H2AK119ub nucleosomes to a 2.6A resolution, confirming H2BC1 in one subgroup of H2AK119ub nucleosomes. Tandem GST-UAB pulldown, Flag-H2AZ.2, and HA-H2BC1 immunoprecipitation revealed that H2AK119ub nucleosomes could be separated into distinct subgroups, suggesting their composition heterogeneity and potential dynamic organization. Knockout or knockdown of H2BC1 or H2AZ.2 reduced cellular H2AK119ub levels, establishing H2BC1 and H2AZ.2 as critical determinants of H2AK119ub. Furthermore, genomic binding profiles of H2BC1 and H2AZ.2 overlapped significantly with H2AK119ub binding, with the most significant overlapping in the gene body and intergenic regions. Finally, assays in developing embryos reveal an interaction of H2AZ.2, H2BC1, and RING1Ain vivo. Thus, this study revealed, for the first time, that the H2AK119ub nucleosome has a unique composition, and this composition is required for H2AK119ub and Polycomb gene silencing.
The impact of struvite and ash recycling-derived fertilizers on microbial phosphorus mobilization capabilities and community structure in aLolium perennefield trial
Authors: Deinert Lea , Ashekuzzaman SM , Forrestal Patrick , Schmalenberger Achim
Published: January 2024

Rock phosphate is a non-renewable primary source for mineral phosphorus (P) fertilizers that intensive agriculture is highly dependent on. To avoid P fertilizer shortages and limit negative environmental impacts, circular economy approaches are needed with recycling-derived fertilizer (RDF) applications such as struvites and ashese. Hence, a grassland field trial was conducted with four RDFs, two struvites (potato wastewater, municipal wastewater) and two ashes (poultry-litter ash, sewage-sludge ash) at a P application rate of 40 kg P ha-1(n=5). The impact of the RDFs on the soil microbial P cycling community was compared to conventional mineral P-fertiliser and a P-free control. Topsoil samples were taken directly afterLolium perennegrass cuts at months three, fife and 15. Cultivable phosphonate and phytate utilizing bacteria, potential acid and alkaline phosphomonoesterase activity, andphoCandphoDcopy numbers responded stronger to seasonal effects than treatment effects. No significant overall effect of the fertilizer application was detected in the beta diversity of the bacterial and fungal communities after 15 months, but individual phylogenetic groups were affected by the treatments. The ash treatments demonstrated some distinguishing results across the bacterial and fungal community, with significantly higher relative abundance of Firmicutes and Rokubacteria and lower relative abundance of Actinobacteriota. Sewage-sludge ash had significantly lowest abundances of generaBacillusandBradyrhizobium(month 15s) that are well known for their P cycling abilities. The struvite RDFs either positively influenced the P cycling microbial community or did not affect it at all, while demonstrating better tri-calcium phosphate solubilizing capabilities after the 3 months harvest. These findings indicate that struvites could be a suitable replacement for conventional P fertilizers in the future.
Anticipatory emotions and academic performance: The role of boredom in a preservice teachers’ lab experience
Authors: Gómez-Ochoa de Alda Jesús A. , Marcos-Merino José María , Valares-Masa Cristina , Esteban-Gallego María Rocío
Published: January 2024

Affective experiences within academic contexts significantly influence educational outcomes. Despite this, the literature reveals a gap in generalising these effects to specific classroom activities, partly arising from the absence of suitable instruments to measure emotions in situational educational scenarios. Our study introduces an experience sampling method to measure sixteen discrete emotional states, deriving two scales for positive and negative activating emotions. Grounded in psychological and neuroscientific theories that integrate emotion with cognition, our research explores the interplay between prior knowledge, preservice teachers’ anticipatory situational emotions, and subsequent learning in an experimental science education context. Analysing data from 269 preservice teachers from diverse backgrounds (STEM and non-STEM) at the upper-secondary level, we found that negative activating emotions are often rooted in non-STEM backgrounds and exacerbated by limited prior science knowledge. These negative emotions impact achievement and learning primarily through the mediating role of boredom. Furthermore, our results indicate that the detrimental impact of boredom on achievement is significantly influenced by prior knowledge, with a more pronounced effect on students with lower levels. Given that emotions are amenable to intervention, our findings propose that specifically addressing boredom in students with low prior knowledge could amplify the benefits of educational strategies.
Enhanced legumain activity links progranulin deficiency to TDP-43 pathology in frontotemporal lobar degeneration
Authors: Robinson Sophie , Reich Marvin , Mühlhofer Maria-Teresa , Buschmann Katrin , Wauters Eline , Mühlhofer Quirin , Werner Georg , Ahles Andrea , Engelhardt Stefan , Krenner Claudia , Bartels Björn , Gutbier Simon , Reifschneider Anika , Riemenschneider Henrick , Reinheckel Thomas , Edbauer Dieter , Simon Matthew J. , Kariolis Mihalis S. , Logan Todd , Paolo Gilbert Di , Broeckhoven Christine Van , Damme Markus , Paquet Dominik , Haass Christian , Capell Anja
Published: January 2024

Loss-of-function mutations inGRNare a major cause of frontotemporal lobar degeneration (FTLD) with TDP-43-positive inclusions. Progranulin (PGRN) loss leads to lysosomal dysfunction, microglial hyperactivation, and TDP-43 deposition, yet the underlying pathomechanism remains unknown. We demonstrate that PGRN slows the maturation and limits the proteolytic activity of the lysosomal protease legumain (LGMN). Accordingly, LGMN activity is strongly elevated inGrnknockout (ko) mice, in human induced pluripotent stem cell-derivedGRNko microglia, and in FTLD-GRNpatients’ brain. Secreted microglial LGMN is internalized by neurons, where it mediates pathological processing of TDP-43, which is prevented by selective LGMN inhibition. In contrast, AAV-mediated overexpression of LGMN in mouse brains promotes TDP-43 processing, the aggregation of phosphorylated TDP-43 and increases plasma neurofilament light chain (NfL), a marker for neuronal loss. Our findings identify LGMN as a link between PGRN haploinsufficiency and TDP-43 pathology in FTLD-GRNand suggest LGMN as a therapeutic target.
DUALISTIC SAHA DOSE-DEPENDENT EFFECTS ON GLIAL-INFLAMMATORY RESPONSE
Authors: Mancino S. , Boraso M. , Galmozzi A. , De Fabiani E. , Crestani  , Viviani B.
Published: January 2024

Neuroinflammation comprises biochemical and cellular responses of the nervous system to injury, emerging as a central process in many neurological conditions. Although beneficial in nature, over-activation of the immune response may result in the production of neurotoxic factors that exacerbate the disease state. Due to the relevant role of histone acetylation in transcriptional regulation, inhibition of histone deacetylase (HDAC) activity plays a central role in the pathogenesis of inflammation. Here, we investigated the impact of HDACs inhibition in the regulation of the inflammatory response elicited by lipopolysaccharide (LPS) in glia cells using trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA). We observed that acute and prolonged exposure to low doses of TSA boosts the inflammatory response in glia cells. Conversely, TSA pre-treatment in cells exposed to LPS decreases inflammation. Additionally, we observed that low and high doses of SAHA exert opposite effects on LPS-induced inflammatory response. Low dose (100 nM) potentiates inflammatory response by increasing the production of pro-inflammatory cytokines tumour necrosis factor (TNF)-α and interleukin (IL) - 1β; and reducing the anti-inflammatory mediator IL-10. Nevertheless, 5 µM SAHA reverts the pro-towards anti-inflammatory profile.

To better characterize SAHA dualistic effects in glia cells, we generated comparative genome-wide gene expression data. Simultaneous exposure to 5 µM SAHA and LPS (10 ng/ml) alters the expression of 1628 genes, while the combination of 100 nM SAHA and LPS regulates the expression of 97 transcripts. Both doses of SAHA differentially regulate important pathways involved in cellular function maintenance, homeostasis, and survival.

Likewise, inhibition of the Janus Kinase - signal transducers and activators of the transcription (JAK/STAT) signalling pathway seems to mediate the anti-inflammatory effects of 5 µM SAHA. On the other hand, 100 nM SAHA increases pro-inflammatory cytokine levels possibly via modulation of the underlined feedback mechanisms triggered by IL-10 expression regulation.

Together, these results contribute to outline a comprehensive picture of the involvement of HDACs inhibitors (HDACi) in the onset or prevention of neuroinflammation, showing that their effects depend on cell types, HDACi dosage and specificity, and protocol used.
HSV-1 ICP0 Dimer Domain Adopts a Novel β-barrel Fold
Authors: McCloskey Erick , Kashipathy Maithri , Cooper Anne , Gao Philip , Johnson David K. , Battaile Kevin P. , Lovell Scott , Davido David J.
Published: January 2024

Infected cell protein 0 (ICP0) is an immediate-early regulatory protein of herpes simplex virus 1 (HSV-1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C-terminal dimer domain (residues 555-767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0’s dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C-terminus of ICP0 was purified from bacteria and analyzed by X-ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β-strands and two α-helices. Interestingly, two adjacent β-strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β-barrel-like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β-strands of each dimer, creating a “stacking” of the β-barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C-terminal SUMO-interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV-1 life cycle.
Quantitative assessment of Newcastle disease virus proteins interactions with all known mucin types of Chicken and Quail
Authors: Almhanna Hazem , Kumar Arun HS
Published: January 2024

Background

Newcastle Disease (ND), caused by the Newcastle Disease Virus (NDV) poses a significant threat to poultry, leading to severe economic losses. Understanding the molecular interactions between NDV proteins and avian mucins is crucial for developing targeted interventions.

Material and Methods

In this study, twelve NDV proteins were systematically assessed for their interactions with sixteen quail and eight chicken mucin types, revealing diverse and species-specific binding patterns.

Results

High-affinity interactions between mucins (Muc5A, Muc5B, and Muc6) and NDV hemagglutinin-neuraminidase, was observed in addition to significant interactions with NDV fusion glycoprotein. Notably, chicken Muc4 displayed mid-range interactions exclusively with NDV fusion glycoprotein, highlighting potential species-specific differences in viral entry mechanisms between quails and chickens. Furthermore, the study investigated the number of binding sites on NDV proteins and chicken/quail mucins. Chicken Muc5B emerged as a standout with the highest number (20) of binding sites, suggesting its crucial role in NDV infection. The binding site analysis identified key regions in NDV fusion glycoprotein and hemagglutinin-neuraminidase, indicating potential targets for vaccine development.

Conclusion

This study provides a foundation for future research into optimizing diagnostic approaches and therapeutic strategies for NDV infections. Validation of these interactions with real-world clinical data, coupled with an exploration of tissue-specific mucin expression patterns, could further enhance our understanding of host-virus dynamics. The identified interactions offer promising avenues for developing vaccines that target specific binding sites, thereby contributing to the effective control and prevention of Newcastle Disease in poultry populations.
Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag
Authors: Brumbaugh-Reed Ellen H. , Aoki Kazuhiro , Toettcher Jared E.
Published: January 2024

Biomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function—dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles, a major question in cell biology and drug development. Here we report an optogenetic approach to selectively dissolve a condensate of interest in a reversible and spatially controlled manner. We show that light-gated recruitment of maltose-binding protein (MBP), a commonly used solubilizing domain in protein purification, results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP, showing that disrupting condensation of the oncogenic fusion protein FUS-CHOP results in reversion of FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
G-quadruplexes inHaloferax volcanii
Authors: Aktary Zackie , Cucchiarini Anne , Vesco Guglielmo , Noury Dorian , Jourdain Thomas , Verga Daniela , Mahou Pierre , Olivier Nicolas , Valková Natalia , Porubiaková Otilia , Brázda Václav , Bouvier Marie , Kwapisz Marta , Clouet-d’Orval Béatrice , Allers Thorsten , Lestini Roxane , Mergny Jean-Louis , Guittat Lionel
Published: January 2024

The archaeal domain is a taxonomically rich component of microbial communities that inhabit a wide range of habitats on Earth, including the human body. Phylogenomic analyses have indicated that archaea represent the closest known relatives of eukaryotes, thus suggesting that eukaryotes may have evolved from an archaeal ancestor. G-quadruplex structures (G4), formed by guanine rich sequences, are among the most intensively studied local DNA/RNA structures and regulate key biological processes such as replication and gene expression. A bioinformatics analysis of the genome of the salt-loving archaeaH. volcaniirevealed a large number of potential G4 sequences (PQS). Biophysical analyses showed that a representative panel of these sequences form stable G4 structures under physiological conditionsin vitro. In addition, immunofluorescence experiments using the G4-specific antibody, BG4, detected G4sin vivoat the single-cell level with super-resolution microscopy. Moreover, we directly visualized G4 in exponentially growing or stationary cells both at the DNA and RNA levels. G4s were also observed in the RNA and DNA of the hyperthermophile archaeonT. barophilus. Finally, we identified helicases potentially involved in G4 unfolding. Together, withH. volcaniias a new model, our work helps to fill the gap between bacteria and eukaryotic organisms for G4 studies and will aid in uncovering the evolutionary history of G4 structures in the tree of life.
Annotation-free prediction of microbial dioxygen utilization
Authors: Flamholz Avi I. , Goldford Joshua E. , Larsson Elin M. , Jinich Adrian , Fischer Woodward W. , Newman Dianne K.
Published: January 2024

Aerobes require dioxygen (O2) to grow; anaerobes do not. But nearly all microbes — aerobes, anaerobes, and facultative organisms alike — express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2utilization has wide-ranging effects on microbes: aerobes typically have larger genomes, encode more O2-utilizing enzymes, and tend to use different amino acids in their proteins. Here we show that these effects permit high-quality prediction of O2utilization from genome sequences, with several models displaying >70% balanced accuracy on a ternary classification task wherein blind guessing is only 33.3% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genome sequence content — e.g. triplets of amino acids — perform about as well as intensive annotation-based algorithms, enabling the rapid processing of global-scale sequence data to predict aerobic physiology. To demonstrate the utility of efficient physiological predictions we estimated the prevalence of aerobes and anaerobes along a well-studied O2gradient in the Black Sea, finding strong quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We therefore suggest that statistical methods like ours can be used to estimate, or “sense,” pivotal features of the environment from DNA sequencing data.

Importance

We now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology — an organism’s capacity to engage metabolically with its environment — may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without first annotating genes, e.g. by considering only the amino acids in protein sequences. Annotation-free algorithms enabled rapid characterization of natural samples, demonstrating a quantitative correspondence between sequences and local O2levels. These results suggest that DNA sequencing can be repurposed as a multi-pronged chemical sensor, estimating concentrations of O2and other key facets of complex natural settings.
Segmentation-free measurement of locomotor frequency in Caenorhabditis elegans using image invariants
Authors: Ji Hongfei , Chen Dian , Fang-Yen Christopher
Published: January 2024

An animal's locomotor rate is an important indicator of its motility. In studies of the nematode C. elegans, assays of the frequency of body bending waves have often been used to discern the effects of mutations, drugs, or aging. Traditional manual methods for measuring locomotor frequency are low in throughput and subject to human error. Most current automated methods depend on image segmentation, which requires high image quality and is prone to errors. Here, we describe an algorithm for automated estimation of C. elegans locomotor frequency using image invariants, i.e., shape-based parameters that are independent of object translation, rotation, and scaling. For each video frame, the method calculates a combination of 8 Hu's moment invariants and a set of Maximally Stable Extremal Regions (MSER) invariants. The algorithm then calculates the locomotor frequency by computing the autocorrelation of the time sequence of the invariant ensemble. Results of our method show excellent agreement with manual or segmentation-based results over a wide range of frequencies. We show that compared to a segmentation-based method that analyzes a worm's shape and a method based on video covariance, our technique is more robust to low image quality and background noise. We demonstrate the system's capabilities by testing the effects of serotonin and serotonin pathway mutations on C. elegans locomotor frequency.
Mouse Auditory Cortex Undergoes Asynchronous Maturation in the Right and Left Hemispheres
Authors: Reid Ashlan , Neophytou Demetrios , Levy Robert , Oviedo Hysell V.
Published: January 2024

Despite the significance of lateralized auditory processing in human cognition, there are limited studies in animal models exploring the developmental mechanisms of this cortical specialization. Here, we find that cellular and network signs of maturity in the Auditory Cortex (ACx) appear earlier in the right hemisphere in male mice. We further demonstrate that persistent, experience dependent map reorganization is confined to the hemisphere that is actively maturing and can be differentially engaged by temporally limited manipulations of the sensory environment. Our data suggests that differential timing in hemisphere development could lead to lateralized auditory functioning.
Osmotic stress response of the coral and oyster pathogenVibrio coralliilyticus: acquisition of catabolism gene clusters for the compatible solute and signaling moleculemyo-inositol
Authors: Boas Lichty Katherine E. , Loughran Rachel M. , Ushijima Blake , Richards Gary P. , Boyd E. Fidelma
Published: January 2024

Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known as osmolytes. The osmotic stress response and compatible solutes used by the coral and oyster pathogenVibrio coralliilyticuswere unknown. In this study, we showed that to alleviate osmotic stressV. coralliilyticusbiosynthesized glycine betaine (GB) and transported into the cell choline, GB, ectoine, dimethylglycine, and dimethylsulfoniopropionate, but notmyo-inositol.Myo-inositol is a stress protectant and a signaling molecule that is biosynthesized and used by algae. Bioinformatics identifiedmyo-inositol (iol) catabolism clusters inV. coralliilyticusand otherVibrio, Photobacterium, Grimontia,andEnterovibriospecies. Growth pattern analysis demonstrated thatV. coralliilyticusutilizedmyo-inositol as a sole carbon source, with a short lag time of 3 h. AniolGdeletion mutant, which encodes an inositol dehydrogenase, was unable to grow onmyo-inositol. Within theiolclusters were an MFS-type (iolT1)and an ABC-type (iolXYZ)transporter and analyses showed that both transportedmyo-inositol. IolG and IolA phylogeny amongVibrionaceaespecies showed different evolutionary histories indicating multiple acquisition events. Outside ofVibrionaceae, IolG was most closely related to IolG from a small group ofAeromonasfish and human pathogens andProvidenciaspecies. However, IolG from hypervirulentA. hydrophilastrains clustered with IolG fromEnterobacter,and divergently fromPectobacterium, Brenneria,andDickeyaplant pathogens. Theiolcluster was also present withinAliiroseovarius, Burkholderia, Endozoicomonas, Halomonas, Labrenzia, Marinomonas, Marinobacterium, Cobetia, Pantoea,andPseudomonas,of which many species were associated with marine flora and fauna.

IMPORTANCE

Host associated bacteria such asV. coralliilyticusencounter competition for nutrients and have evolved metabolic strategies to better compete for food. Emerging studies show thatmyo-inositol is exchanged in the coral-algae symbiosis, is likely involved in signaling, but is also an osmolyte in algae. The bacterial consumption ofmyo-inositol could contribute to a breakdown of the coral-algae symbiosis during thermal stress or disrupt the coral microbiome. Phylogenetic analyses showed that the evolutionary history ofmyo-inositol metabolism is complex, acquired multiple times inVibrio,but acquired once in many bacterial plant pathogens. Further analysis also showed that a conservediolcluster is prevalent among many marine species (commensals, mutualists, and pathogens) associated with marine flora and fauna, algae, sponges, corals, molluscs, crustaceans, and fish.