bluuebunny/crossref_metadata_2025 huggingface dataset:
Intraoperative Frontal Electroencephalogram Alpha Power Is Associated with Postoperative Mortality and Other Adverse Outcomes
Authors: Mather Rory Vu , Nipp Ryan , Balanza Gustavo , Stone Tom A. D. , Gutierrez Rodrigo , Raje Praachi , Higuchi Masaya , Liu Ran , Santa Cruz Mercado Laura A. , Bittner Edward A. , Kunitake Hiroko , Purdon Patrick L.
Published: November 2024

Background:

With estimated global postoperative mortality rates at 1% to 4% leading to approximately 3 million to 12 million deaths per year, an urgent need exists for reliable measures of perioperative risk. Existing approaches suffer from poor performance, place a high burden on clinicians to gather data, or do not incorporate intraoperative data. Previous work demonstrated that intraoperative anesthetics induce prefrontal electroencephalogram (EEG) oscillations in the alpha band (8 to 12 Hz) that correlate with postoperative cognitive outcomes.

Methods:

The authors analyzed a retrospective cohort of 1,081 patients undergoing surgery with general anesthesia at Massachusetts General Hospital (Boston, Massachusetts) with intraoperative EEG recordings. The association between EEG alpha power and adverse outcomes was characterized using statistical models that were fitted on propensity weighted data. The primary outcome was postoperative mortality, measured from date of surgery to date of death or last follow-up. Secondary outcomes included mortality within prespecified time windows (30 days, 90 days, 180 days, and 1 yr), hospital and postanesthesia care unit lengths of stay, discharge to long-term care, and 30-day hospital readmission.

Results:

Alpha power was associated with mortality risk (hazard ratio, 0.92; 95% CI, 0.85 to 0.99; P = 0.039). Within specified time windows, alpha power was associated with 30-day mortality (odds ratio, 0.81; 95% CI, 0.66 to 0.95; P = 0.010), 90-day mortality (odds ratio, 0.68; 95% CI, 0.55 to 0.79; P < 0.001), 180-day mortality (odds ratio, 0.75; 95% CI, 0.66 to 0.83; P < 0.001), and 1-yr mortality (odds ratio, 0.85; 95% CI, 0.79 to 0.91; P < 0.001). Additionally, alpha power was associated with discharge to long-term care (odds ratio, 0.91; 95% CI, 0.86 to 0.96; P < 0.001). We did not find significant associations among alpha power and 30-day readmission and hospital or postanesthesia care unit lengths of stay.

Conclusions:

Intraoperative EEG alpha power is independently associated with postoperative mortality and adverse outcomes, suggesting it could represent a broad measure of postoperative physical resilience and provide clinicians with a low-burden, personalized measure of postoperative risk.
Is Reconstructive Plastic Surgery Appropriately Valued? Comparison of Reimbursement per Unit Time for Reconstructive versus Aesthetic Procedures
Authors: De la Fuente Hagopian Alexa , Farhat Souha , Reddy Narainsai K. , Guadarrama-Sistos Vazquez Sebastian , Padilla Pablo L. , Echo Anthony
Published: November 2024

Background:

The work relative value units (wRVUs) system was established as a quantifier of physician labor, technical skill, medical decision-making, and training time required to complete a surgical procedure; hence, more challenging operations should theoretically result in higher reimbursement or compensation. Our purpose was to highlight the discrepancies between insurance-based reconstructive and fee-for-service aesthetic procedures based upon dollar/unit time.

Methods:

We analyzed national data from the American College of Surgeons National Surgical Quality Improvement Program, Aesthetic Surgery Databank, and Centers for Medicare and Medicaid Services to compare reimbursement for 8 reconstructive microsurgery and 3 aesthetic procedures and assessed operative times and reimbursement rates, then calculated “relative value unit per unit time” to measure compensation efficiency.

Results:

This difference in remuneration translates to a 4.7× difference, with an overwhelming gap of $25.26 per minute between microsurgical reconstructive and aesthetic cases. These findings suggest that aesthetic cases are more profitable considering the compensation per unit time. Based on national rates of reimbursement, there is a large discrepancy between reimbursement in microsurgical reconstructive procedures and aesthetic procedures.

Conclusions:

We demonstrated that complexity and time are not directly related to compensation.
Findings Consistent with a Breast Implant–associated Somatic System Disorder (BIA-SSD) Among Patients Self-reporting Breast Implant Illness
Authors: Bresnick Stephen D. , Morris Susie , Lagman Carlito
Published: November 2024

Background:

Self-reported breast implant illness (BII) has been found to be associated with anxiety as well as medically diagnosed anxiety and depression. Somatic symptom disorder (SSD) is a relatively common mental health condition that includes anxiety and somatic symptoms, often without a clear cause.

Methods:

We evaluated patients with BII symptoms, with or without a history of an anxiety disorder, for findings consistent with SSD. A total of 120 women were evaluated in 2 cohorts, 60 women with somatic symptoms and breast implants desiring explantation as well as 60 women desiring explantation without BII symptoms. Patient demographics, a patient survey, and validated anxiety scale and somatic symptom scale measurements were obtained.

Results:

Patients with a history of an anxiety disorder and BII symptoms had very high levels of anxiety and highly elevated somatic symptom scores. Patients with a combined diagnosis of anxiety and BII symptoms demonstrated an SSD prevalence of 70.2%, with the difference between the BII/anxiety group and other groups statistically significant (P < 0.01). Other patients with BII symptoms and no history of anxiety had a lower SSD prevalence (21.7%). Patients without a history of BII had little to no SSD inclusion.

Conclusions:

Our data suggest that a significant subset of patients with somatic symptoms have findings consistent with a breast implant–associated somatic symptom disorder. Patients with persistent or excessive thoughts about somatic symptoms will benefit from counseling and referral to an SSD specialist if they wish to maintain breast implants.
Impact of Shifting From Office Work to Telework on Workers’ Physical Health
Authors: Hoshi Rena , Kikuchi Hiroyuki , Machida Masaki , Nakanishi Yutaka , Inoue Shigeru
Published: November 2024

Objective

The aim of the study is to clarify the longitudinal association between teleworking and physical health changes of Japanese workers before and during the COVID-19 pandemic.

Methods

Participants were in a certain company who received mandatory health examinations in 2019 and 2020. In June 2020, the participants were asked about frequency of teleworking, which was introduced owing to the COVID-19. Whether physical health differed by the frequency of teleworking was analyzed.

Results

The participants were 3689 workers. Frequency of teleworking were associated with more deleterious changes in diastolic blood pressure, antilipidemic drug use, low-density lipoprotein (LDL) cholesterol, Glutamic Oxaloacetic Transaminase(GOT), Glutamic Pyruvic Transaminase(GPT), metabolic syndrome, and insufficient walking time among men. In contrast, no significant changes were observed in women.

Conclusions

Male workers who teleworked more frequently were more likely to experience a deterioration in their physical health within 1-year compared with those who worked at the office.
The OCCHLTH Mnemonic—Construction and Content of a Tool for Increasing Awareness of Occupational Illness and Injury
Authors: Pandalai Sudha P.
Published: November 2024

Introduction

Unidentified or nonmitigated occupational illnesses and injuries can complicate disease management. The “occupational health” (OCCHLTH) mnemonic aims to raise awareness of work-related exposures and associated illnesses and injuries.

Methods

Occupational safety and health history-taking elements were combined with peer-reviewed information [from the PubMed database (first review January 1, 2000, to February 8, 2016; updated to February 8, 2021)] about workplace exposure-outcome associations to create the mnemonic.

Results

Seven components constitute the OCCHLTH mnemonic. Literature results support its categories and subcategories. Three components represent symptom onset and health conditions. Four represent occupational exposures. Evaluating published occupational illness cases explored mnemonic applicability.

Conclusions

Awareness of occupational risk factors can affect clinical decision-making. The OCCHLTH mnemonic encourages consideration of occupational causes of illness and injury to optimize patient care. Further evaluation of the utility of the OCCHLTH mnemonic is needed.
Elucidation of the Cranial Arterial Anatomy Using the Transorbital Endoscopic Approach
Authors: Ikizoglu Ersin , Akdag Beyza Alkis , Kaya Ismail , Kizmazoglu Ceren , Kiray Amac , Kalemci Orhan
Published: November 2024

New surgical techniques that access the orbit and intracranial cavity have been developed in recent years called transorbital neuroendoscopic surgery. The superior eyelid route, as a transorbital corridor, is a clinically feasible route to access selected anterior and middle skull base pathologies. However, studies regarding the suitability of this approach in vascular surgery are lacking. In this study, transorbital endoscopic dissections were performed bilaterally in 4 cadavers through the superior eyelid approach. The authors aimed to define the arterial vascular structures that can be accessed through this approach. In this study, the M1 and M2 segments of the middle cerebral artery and the branches originating from it were accessible with a 0 degree endoscope after an appropriate dissection. Thus, the endoscopic superior eyelid approach may be a novel alternative approach for some cranial pathologies.
Orbital Inflammatory Manifestations in a Patient With VEXAS (Vacuoles, E1 Enzyme, X-Linked, Autoinflammatory, Somatic) Syndrome
Authors: Colman Blake D. , Smolyansky Eliot D. , Parmar Hemant A. , Puvanakumar Pratheepan , Fraser Rogan G. , Ramachandran Prashanth , Sheth Shivanand , Shuey Neil , Raviskanthan Subahari
Published: November 2024

An 84-year-old man with a genetically confirmed diagnosis of VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome treated with tocilizumab reported with a 3-day history of left eye pain, conjunctival chemosis and injection, and horizontal binocular diplopia. Examination revealed restriction of left eye ductions in all directions with mild unilateral proptosis. MRI of his brain and orbits demonstrated abnormal enhancement of the left posterior sclera and intraorbital optic nerve sheath, without involvement of the extraocular muscles, cavernous sinus, or optic nerve parenchyma. B-scan ultrasonography heralded a positive “T-sign.” Empiric treatment with high-dose intravenous methylprednisolone led to rapid clinical improvement. Workup for alternative causes was unremarkable. Oral prednisone dose and tocilizumab ultimately resulted in complete resolution after 4 weeks. The final diagnosis was consistent with orbital inflammatory manifestations of VEXAS syndrome.
Upper bill bending as an adaptation for nectar feeding in hummingbirds
Authors: Rico-Guevara Alejandro , Sustaita Diego , Hurme Kristiina J. , Hanna Jenny E. , Jung Sunghwan , Field Daniel J.
Published: November 2024

Observations of maxillary (upper bill) bending in hummingbirds have been considered an optical illusion, yet a recent description of out-of-phase opening and closing between their bill base and tip suggests a genuine capacity for bill bending. We investigate bill kinematics during nectar feeding in six species of hummingbirds. We employed geometric morphometrics to identify bending zones and combined these data with measurements of bill flexural rigidity from micro-computed tomography scans to better understand the flexing mechanism. We found that the mandible remains in place throughout the licking cycle, while the maxilla undergoes significant shape deformation, such that the distal portion of the upper bill bends upwards. We propose that bill bending is a key component of the drinking mechanism in hummingbirds, allowing the coordination of bill function (distal wringing and basal expansion) and tongue function (raking/squeegeeing) during intra-oral transport. We present a fluid analysis that reveals a combination of pressure-driven (Poiseuille) and boundary-driven (Couette) flows, which have previously been thought to represent alternative drinking mechanisms. Bill bending allows for separation of the bill tips while maintaining a tightly closed middle section of the bill, enabling nectar exploitation in long and narrow flowers that can exclude less efficient pollinators.
DyNDG: Identifying Leukemia-Related Genes based on the Time-Series Dynamical Network by Integrating Differential Genes
Authors: Jin A , Xiang Ju , Meng Xiangmao , Sheng Yue , Peng Hongling , Li Min
Published: November 2024

Leukemia is a malignant disease of progressive accumulation characterized by high morbidity and mortality rates, and investigating its disease genes is crucial for understanding its etiology and pathogenesis. Network propagation methods have emerged and been widely employed in disease gene prediction, but most of them focus on static biological networks, which hinders their applicability and effectiveness in the study of progressive diseases. Moreover, there is currently a lack of special algorithms for the identification of leukemia disease genes. Here, we proposed DyNDG, a novel Dynamic Network-based model, which integrates Differentially Expressed Genes to identify leukemia-related genes. Initially, we constructed a time-series dynamic network to model the development trajectory of leukemia. Then, we built a background-temporal multilayer network by integrating both the dynamic network and the static background network, which was initialized with differentially expressed genes at each stage. To quantify the associations between genes and leukemia, we extended a random walk process to the background-temporal multilayer network. The experimental results demonstrate that DyNDG achieves superior accuracy compared to several state-of-the-art methods. Moreover, after excluding housekeeping genes, DyNDG yields a set of promising candidate genes associated with leukemia progression or potential biomarkers, indicating the value of dynamic network information in identifying leukemia-related genes. The implementation of DyNDG is available athttps://github.com/CSUBioGroup/DyNDG.
Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs
Authors: Rizzo Nicola , Cáceres Manuel , Mäkinen Veli
Published: November 2024

Sequence-to-graph alignment is a central challenge of computational pangenomics. To overcome the theoretical hardness of the problem, state-of-the-art tools useseed-and-extendorseed-chain-extendheuristics to alignment, therefore reducing the computational resources required for the task. However, two main problems still remain: on the one hand, the daunting amount of sequencing data requires us to trade alignment accuracy with computational resources; on the other hand, current graph representations of pangenomes introduce an excessive amount of spurious recombinations.

In this paper, we implement a complete seed-chain-extend alignment workflow based onindexable elastic founder graphs(iEFGs), a class of graphs built from aligned sequences and supporting fast pattern matching while reducing the number of artificial recombinations. We show how to construct iEFGs from the variations to a linear reference, find high-quality seeds, and extend them usingGraphAligner, at the scale of a telomere-to-telomere assembled human chromosome.

The main ingredient of our workflow is the use and the efficient computation ofsemi-repeat-free seeds(srf), a novel class of iEFG-based seeds introduced in this work. The amount of srf seeds is two orders of magnitude less than that of minimizers at the human chromosome level while maintaining comparable speed. Thanks to the uniqueness properties of iEFGs, we show that srf-based seeds suffice to maintain high accuracy while leveraging the speed of our tool. To further stress our point, we also implement chaining of seeds on the elastic degenerate string relaxation of the iEFG and show that only chained seeds suffice to achieve high accuracy alignments.

Our sequence-to-graph alignment tool and the scripts to replicate our experiments are available inhttps://github.com/algbio/SRFAligner.
Immune organization in sentinel lymph nodes of melanoma patients is prognostic of distant metastases
Authors: Amitay Yael , Milo Idan , Keidar Haran Tal , Deis Saif , Truzman Guy , Elhanani Ofer , Salame Tomer-Meir , Azimov Michal , Stein Ilan , Cohen Jonathan E. , Lotem Michal , Pikarsky Eli , Keren Leeat
Published: November 2024

Sentinel lymph node (sLN) biopsy is part of melanoma staging, as involved LNs indicate a higher risk of recurrence. However, how the sLN is shaped by the tumor and reciprocally affects metastatic progression is poorly understood. Here, we mapped immune organization in involved and non-involved sLNs of 69 melanoma patients using high-resolution spatial proteomics, spatial transcriptomics and deep learning, leveraging the data for prognostic evaluation. In patients with involved LNs, a robust T cell response correlated with absence of recurrence. In non-involved LNs, protection from metastases was linked to expanded sinuses colocalized with plasmablasts whereas CCR7+ cells and Tregs correlated with future development of distant metastases. We trained a model that predicts development of distant metastases with 79% and 93% AUC for non-metastatic and metastatic LNs, respectively. Our findings reveal conserved immune patterns in sLNs that prospectively identify patients at risk for metastatic disease and may aid in therapeutic decisions.
Promoting Polarization and Differentiation of Primary Human Salivary Gland Stem/Progenitor Cells in Protease-Degradable Hydrogels via ROCK Inhibition
Authors: Metkari Apoorva S. , Witt Robert L. , Cognetti David M. , Dhong Charles , Jia Xinqiao
Published: November 2024

Towards the goal ofin vitroengineering of functional salivary gland tissues, we cultured primary human salivary stem/progenitor cells (hS/PCs) in hyaluronic acid-based matrices with varying percentages of proteolytically degradable crosslinks in the presence of Rho kinase (ROCK) inhibitor. Single cells encapsulated in the hydrogel grew into organized multicellular structures by day 15, and over 60% of the structures developed in the non-degradable and 50% degradable hydrogels contained a central lumen. Importantly, ROCK inhibition led to the establishment of multicellular structures that were correctly polarized, as evidenced by apical localization of a Golgi marker GM130, apical/lateral localization of tight junction protein zonula occludens-1 (ZO-1), and basal localization of integrin β1 and basement membrane proteins laminin α1 and collagen IV. Cultures maintained in 50% degradable gels with ROCK inhibition exhibited an increased expression of acinar markersAQP5andSLC12A2(at the transcript level) and AQP5 and NKCC1 (at the protein level) as compared to those without ROCK inhibition. Upon stimulation with isoproterenol, α-amylase secretion into the lumen was observed. Particle-tracking microrheology was employed to analyze the stiffness of cells using mitochondria as the passive tracer particles. Our results indicated that cells grown in 100% degradable gels were stiffer than those maintained in non-degradable gels, and cells cultured with the ROCK inhibitor were softer than those maintained without the inhibitor. We conclude that reducing cellular contractility via ROCK inhibition while retaining some degree of matrix confinement promotes the establishment of multicellular structures containing pro-acinar cells with correct apicobasal polarization.
HIV Pre-Exposure Prophylaxis Scale-Up in Mozambique from October 2021 to December 2023
Authors: Maibaze Gonçalves , Gaspar Nuno , Seleme Jessica , Swor Meghan , Couto Aleny , Malimane Inacio , Canda Marcos , Simbine Ana Paula , Troger Mark , Namburete Evangelina
Published: November 2024

In 2021, The Mozambique Ministry of Health began offering HIV pre-exposure prophylaxis (PrEP) in all provinces. The number of new clients increased more than three-fold within two years. Among 51,848 new people receiving PrEP by December 2023, the largest groups were females and adolescent young adults.
Processing negative words in pun-humor: dynamic representation of mixed feelings blending amusement and negativity
Authors: Sun Yingying , Jiang Zhufang , Yin Xinyue , Li Xiaoqing , Chang Ruohan
Published: November 2024

This study aims to investigate whether amusement and negativity counteract each other or are jointly intensified during the online processing of negative keywords in pun-humor sentences, and how mixed feelings blending these two emotional states are dynamically experienced over time. Participants read three types of sentences that included the same negative words as keywords: pun-humor (negative words can generate humorous effects by resonating with the context), non-humor (negative words seamlessly align with the context), and nonsensical (negative words cannot be integrated with the context) sentences. The behavioral ratings revealed that compared with non-humor and nonsensical sentences, pun-humor sentences evoked stronger amusement and intensified negative feelings, indicating that pun-humor sentences containing negative keywords can effectively elicit mixed feelings that encompass conflicting emotional states. The ERP results showed that the N400 (300-500 ms) elicited by negative words in pun-humor sentences was comparable to that in non-humor sentences, suggesting that negative words were connected contextually in both sentence types. Besides, negative words elicited greater LPC (600-800 ms) in pun-humor sentences than in non-humor and nonsensical sentences, suggesting that pun-humor sentences require additional semantic processing and more elaborate emotional processing. Moreover, the representational similarity analysis (RSA) results revealed that in pun-humor sentences, the representation of negativity persisted for a longer duration, and it occurred and peaked earlier than that of amusement. This implies that within the dynamic representation of mixed feelings, negativity was experienced first, whereas amusement was subsequently felt within a brief period, during which negativity was not offset but rather continued to be represented over a longer time span, resulting in the simultaneous presence of both amused and negative feelings. Taken together, these findings show that mixed feelings elicited during the online processing of negative keywords in pun-humor sentences can be dynamically experienced in a way that aligns with the highly simultaneous pattern and that negativity can be experienced before amusement during the dynamic representation of mixed feelings.
SPACE: STRING proteins as complementary embeddings
Authors: Hu Dewei , Szklarczyk Damian , von Mering Christian , Jensen Lars Juhl
Published: November 2024

Representation learning has revolutionized sequence-based prediction of protein function and subcellular localization. Protein networks are an important source of information complementary to sequences, but the use of protein networks has proven to be challenging in the context of machine learning, especially in a cross-species setting. To address this, we leveraged the STRING database of protein networks and orthology relations for 1,322 eukaryotes to generate network-based cross-species protein embeddings. We did this by first creating species-specific network embeddings and subsequently aligning them based on orthology relations to facilitate direct cross-species comparisons. We show that these aligned network embeddings ensure consistency across species without sacrificing quality compared to species-specific network embeddings. We also show that the aligned network embeddings are complementary to sequence embedding techniques, despite the use of seqeuence-based orthology relations in the alignment process. Finally, we demonstrate the utility and quality of the embeddings by using them for two well-established tasks: subcellular localization prediction and protein function prediction. Training logistic regression classifiers on aligned network embeddings and sequence embeddings improved the accuracy over using sequence alone, reaching performance numbers close to state-of-the-art deep-learning methods. A set of precomputed cross-species network embeddings and ProtT5 embeddings for all eukaryotic proteins have been included in STRING version 12.0.
Quantum Spin Resonance in Engineered Magneto-Sensitive Fluorescent Proteins Enables Multi-Modal Sensing in Living Cells
Authors: Abrahams Gabriel , Spreng Vincent , Štuhec Ana , Kempf Idris , James Jessica , Sechkar Kirill , Stacey Scott , Trelles-Fernandez Vicente , Antill Lewis M. , Ingaramo Maria , York Andrew , Tetienne Jean-Philippe , Timmel Christiane R. , Steel Harrison
Published: November 2024

Quantum mechanical phenomena have been identified as fundamentally significant to an increasing number of biological processes. Simultaneously, quantum sensing is emerging as a cutting-edge technology for precision biosensing. However, biological based candidates for quantum-sensors have thus far been limited toin vitrosystems, are prone to light induced degradation, and require sophisticated experimental setups making high-throughput studies prohibitively complex. We recently created a new class of magneto-sensitive fluorescent proteins (MFPs) [1], which we now show overcome these challenges and represent the first biological quantum-based sensor that functions at physiological conditions and in living cells. Through directed evolution, we demonstrate the possibility of engineering these proteins to alter properties of their response to magnetic fields and radio frequencies. These effects are explained in terms of the spin correlated radical pair (SCRP) mechanism, involving the protein backbone and a bound flavin cofactor. Using this engineered system we demonstrate the first observation of a fluorescent protein exhibiting Optically Detected Magnetic Resonance (ODMR) in living bacterial cells at room temperature, at sufficiently high signal-to-noise to be detected in a single cell, paving the way for development of a new class ofin vivobiosensors. Magnetic resonance measurements using fluorescent proteins enable unprecedented technologies, for instance 3D spatial localisation of the fluorescence using gradient fields (i.e. Magnetic Resonance Imaging but using an endogenous probe). We further demonstrate the use of multiple variants of MFPs for multiplexing or lock-in amplification of fluorescence signals, opening a new approach to combining or extracting multiple signals from a biological measurement. Taken together, our results represent a new intersection of imaging and perhaps actuation modalities for engineered biological systems, based on and designed around understanding the quantum mechanical properties of MFPs.
Tissue-dependent nature of plant susceptibility: a comparative pathogenicity study of the systemic phytopathogenRalstonia pseudosolanacearumin eggplant and tomato seedlings through root and leaf
Authors: Bhuyan Shuvam , Jain Monika , Boruah Lakhyajit , Tara Tana Sun , Begum Shuhada , Dutta Lukapriya , Giri Shubhra Jyoti , Phukan Tarinee , Kabyashree Kristi , Mandal Manabendra , Ray Suvendra Kumar
Published: November 2024

Ralstonia pseudosolanacearumcauses a lethal bacterial wilt disease in many plant species, posing significant economic challenges. Although tomato has been a primary model host for investigating the pathogenicity and systemic infection of this bacterium, this manuscript presents a comparative pathogenicity study between two closely related solanaceous hosts, tomato and eggplant, revealing differential host responses to the same pathogen, specifically through leaves and roots. Interestingly, eggplant seedlings exhibited a significantly higher susceptibility to cotyledon leaf inoculation than tomato seedlings. In the case of tomato, a few seedlings escaped wilting (called escapees), which was usual at a high pathogen load, unlike the case of eggplant seedlings where escapees could not be observed even at a 100-fold lower pathogen concentration. The greater susceptibility of eggplant was further demonstrated by performing both single- and double-leaf inoculations in the seedlings. Surprisingly, root inoculations resulted in a significantly lower mortality for eggplant than for tomato seedlings. The contrasting susceptibility between the two hosts regarding root and leaf regions indicates the tissue-dependent nature of susceptibility. The study underscores the value of employing multiple host species to uncover new insights into pathogen behaviour and host-pathogen interactions.
CD47 predominates over CD24 as a macrophage immune checkpoint in cancer
Authors: Allen Juliet , Meglan Anna , Vaccaro Kyle , Velarde José , Chen Victor , Ribeiro Juliano , Blandin Jasmine , Gupta Sumeet , Mishra Ranjan , Ho Raymond , Love Jennifer , Reinhardt Ferenc , Bell George W. , Chen Jin , Weinberg Robert , Yang Dian , Weissman Jonathan , Weiskopf Kipp
Published: November 2024

Macrophages hold tremendous promise as effectors of cancer immunotherapy, but the best strategies to provoke these cells to attack tumors remain unknown. Here, we evaluated the therapeutic potential of targeting two distinct macrophage immune checkpoints: CD47 and CD24. We found that antibodies targeting these antigens could elicit maximal levels of phagocytosis when combined together in vitro. However, to our surprise, via unbiased genome-wide CRISPR screens, we found that CD24 primarily acts as a target of opsonization rather than an immune checkpoint. In a series of in vitro and in vivo genetic validation studies, we found that CD24 was neither necessary nor sufficient to protect cancer cells from macrophage phagocytosis in most mouse and human tumor models. Instead, anti-CD24 antibodies exhibit robust Fc-dependent activity, and as a consequence, they cause significant on-target hematologic toxicity in mice. To overcome these challenges and leverage our findings for therapeutic purposes, we engineered a collection of 77 novel bispecific antibodies that bind to a tumor antigen with one arm and engage macrophages with the second arm. We discovered multiple novel bispecifics that maximally activate macrophage-mediated cytotoxicity and reduce binding to healthy blood cells, including bispecifics targeting macrophage immune checkpoint molecules in combination with EGFR, TROP2, and CD71. Overall, our findings indicate that CD47 predominates over CD24 as a macrophage immune checkpoint in cancer, and that the novel bispecifics we created may be optimal immunotherapies to direct myeloid cells to eradicate solid tumors.
In silicotarget discovery for aromatic amino acid production inEscherichia coli
Authors: Fonseca André , Avendãno Leslie , Ferreira Sofia , Rocha Isabel
Published: November 2024

Aromatic amino acids (AAA) and derived compounds are rising on global market demand, which leads to the need of better production means. These compounds are usually produced by means of microbial cell factories. However, bacterial metabolism is complex and highly regulated, which complicates the discovery of new higher yield strains, optimized for the production of these compounds. Dynamic modelling has the capability to solve this problem by predicting metabolic behavior and helping to find targets for strain design. In this paper, a newEscherichia colidynamic model is presented. Evolutionary algorithm processes were used in order to find targets for metabolic engineering strategies for AAA increased production. The solutions obtained are compatible with strategies found in literature, while at the same time presenting new possible targets, not yet reported in literature.
Elevational and Oceanic Barriers Shape the Distribution, Dispersal and Diversity of Aotearoa’s Kapokapowai (Uropetala) Dragonflies
Authors: Tolman Ethan R. , Beatty Chris D. , Goodman Aaron , Ramchand Priscilla , McAllister Tara , Reyes Kelly , Zahara Akifa , Taveras Kassandra , Wade Vincent , Abbott John , Bybee Seth , Frandsen Paul B. , Guralnick Robert , Kohli Manpreet K. , Ware Jessica , Suvorov Anton
Published: November 2024

Mountains and islands provide an opportunity for studying the biogeography of diversification and population fragmentation. Aotearoa (New Zealand) is an excellent location to investigate both phenomena due to alpine emergence and oceanic separation. While it would be expected that separation across oceanic and elevation gradients are major barriers to gene flow in animals, including aquatic insects, such hypotheses have not been thoroughly tested in these taxa. Here, we show that mountains and oceanic separation function as semi-permeable barriers for Kapokapowai (Uropetala) dragonflies. Although Te Moana o Raukawa (Cook Strait), is likely responsible for some of the genetic structure observed, speciation has not yet occurred in populations separated by the strait. We find no evidence that they are an impervious barrier, but Kā Tiritiri-o-te-Moana (the Southern Alps) significantly restrict gene flow between named species. Our data support the hypothesis of an active colonization of Kā Tiritiri-o-te-Moana by the ancestral population of Kapokapowai, followed by a recolonization of the lowlands. These findings suggest that aquatic insects could be an exciting new frontier in the study of the biogeography and population fragmentation in the landscape of Aotearoa.
Neutrophil-chemoattractant CXCL5 induces lung barrier permeability in acute lung injury
Authors: Berger Sarah , Goekeri Cengiz , Pennitz Peter , Gutbier Birgitt , Michalick Laura , Hoffmann Karen , Lopez-Rodriguez Elena , Gluhovic Vladimir , Wienhold Sandra-Maria , Behrendt Ulrike , Taylor Alexander , Dietert Kristina , Kirsten Holger , Kunder Sandra , Mueller Kristina , Weigel Markus , Hain Torsten , Volkers Sarah M. , Weis Sebastian , Gruber Achim D. , Sander Leif E. , Kuebler Wolfgang M. ,   CAPSyS study group, Witzenrath Martin , Nouailles Geraldine
Published: November 2024

Rationale

Acute lung injury is frequently caused by pneumonia, and severity correlates with inflammatory cell recruitment and lung barrier failure. Deciphering drug-targetable pathways is of clinical importance.

Objectives

Investigation of paracrine and autocrine effects of epithelial-derived chemokine CXCL5 in acute lung injury.

Methods

We assessed the role of CXCL5 and related chemokines in patients with severe pneumonia and primary cells or cell lines challenged withStreptococcus pneumoniaeor exposed to mechanical stretch. Furthermore, we evaluated the role of CXCL5 inin vivomodels of acute lung injury through use ofCxcl5-deficient mice andin vitrohuman lung barrier models.

Results

Pneumococcal infection and mechanical ventilation were associated with CXCL5 production in human subjects and in mice. CXCL5 was produced by bronchial and alveolar epithelial cells. The alveolar-epithelial barrier was protected in acute lung injury models inCxcl5-deficient mice, independent of alveolar neutrophil recruitment. Single-cell transcriptomics revealed enhanced cell junctional transcripts in epithelial, but not endothelial cells inCxcl5-deficient mice. Accordingly, CXCL5 exposure disrupted the barrier function of TNF-primed human primary alveolar epithelial cells, but not pulmonary microvascular endothelial cells.

Conclusions

We describe a novel function of CXCL5 in acute lung injury. Besides its recognized role in recruiting highly inflammatory cells such as neutrophils, CXCL5 increases alveolar-epithelial barrier permeability. Thus, in severe bacterial pneumonia, targeting of CXCL5 as adjunctive therapy to antibiotics may aid in reducing overshooting inflammation as well as stabilizing lung barrier function.
Mechanism of MCUB-dependent inhibition of mitochondrial calcium uptake
Authors: Rai Neeraj K. , Balynas Anthony M. , MacEwen Melissa JS , Bratt Ashley R. , Sancak Yasemin , Chaudhuri Dipayan
Published: November 2024

Mitochondrial Ca2+levels are regulated to balance stimulating respiration against the harm of Ca2+overload. Contributing to this balance, the main channel transporting Ca2+into the matrix, the mitochondrial Ca2+uniporter, can incorporate a dominant-negative subunit (MCUB). MCUB is homologous to the pore-forming subunit MCU, but when present in the pore-lining tetramer, inhibits Ca2+transport. Here, using cell lines deleted of both MCU and MCUB, we identify three factors that contribute to MCUB-dependent inhibition. First, MCUB protein requires MCU to express. The effect is mediated via the N-terminal domain (NTD) of MCUB. Replacement of the MCUB NTD with the MCU NTD recovers autonomous expression but fails to rescue Ca2+uptake. Surprisingly, mutations to MCUB that affect interactions with accessory subunits or the conduction pore all failed to rescue Ca2+uptake, suggesting the mechanism of inhibition may involve global rearrangements. Second, using concatemeric tetramers with varying MCU:MCUB ratios, we find that MCUB incorporation does not abolish conduction, but rather inhibits Ca2+influx proportional to the amount of MCUB present in the channel. Reducing rather than abolishing Ca2+transport is consistent with MCUB retaining the highly-conserved selectivity filter DIME sequence. Finally, we apply live-cell Förster resonance energy transfer to establish that the endogenous stoichiometry is 2:2 MCU:MCUB. Taken together, our results suggest MCUB preferentially incorporates into nascent uniporters, and the amount of MCUB protein present linearly correlates with the degree of inhibition of Ca2+transport, creating a precise, tunable mechanism for cells to regulate mitochondrial Ca2+uptake.
Insights into the causes and consequences of DNA repeat expansions from 700,000 biobank participants
Authors: Hujoel Margaux L.A. , Handsaker Robert E. , Kamitaki Nolan , Mukamel Ronen E. , Rubinacci Simone , Palamara Pier F. , McCarroll Steven A. , Loh Po-Ru
Published: November 2024

Expansions and contractions of tandem DNA repeats are a source of genetic variation in human populations and in human tissues: some expanded repeats cause inherited disorders, and some are also somatically unstable. We analyzed DNA sequence data, derived from the blood cells of >700,000 participants in UK Biobank and theAll of UsResearch Program, and developed new computational approaches to recognize, measure and learn from DNA-repeat instability at 15 highly polymorphic CAG-repeat loci. We found that expansion and contraction rates varied widely across these 15 loci, even for alleles of the same length; repeats at different loci also exhibited widely variable relative propensities to mutate in the germline versus the blood. The high somatic instability ofTCF4repeats enabled a genome-wide association analysis that identified seven loci at which inherited variants modulateTCF4repeat instability in blood cells. Three of the implicated loci contained genes (MSH3,FAN1, andPMS2) that also modulate Huntington’s disease age-at-onset as well as somatic instability of theHTTrepeat in blood; however, the specific genetic variants and their effects (instability-increasing or-decreasing) appeared to be tissue-specific and repeat-specific, suggesting that somatic mutation in different tissues—or of different repeats in the same tissue—proceeds independently and under the control of substantially different genetic variation. Additional modifier loci included DNA damage response genesATAD5andGADD45A. Analyzing DNA repeat expansions together with clinical data showed that inherited repeats in the 5’ UTR of the glutaminase (GLS)gene are associated with stage 5 chronic kidney disease (OR=14.0 [5.7–34.3]) and liver diseases (OR=3.0 [1.5–5.9]). These and other results point to the dynamics of DNA repeats in human populations and across the human lifespan.
Platelet Factor 4 (PF4) Regulates Hematopoietic Stem Cell Aging
Authors: Zhang Sen , Ayemoba Charles E. , Di Staulo Anna M. , Joves Kenneth , Patel Chandani M. , Leung Eva Hin Wa , Ong Sang-Ging , Nerlov Claus , Maryanovich Maria , Chronis Constantinos , Pinho Sandra
Published: November 2024

Hematopoietic stem cells (HSCs) responsible for blood cell production and their bone marrow regulatory niches undergo age-related changes, impacting immune responses and predisposing individuals to hematologic malignancies. Here, we show that the age-related alterations of the megakaryocytic niche and associated downregulation of Platelet Factor 4 (PF4) are pivotal mechanisms driving HSC aging. PF4-deficient mice display several phenotypes reminiscent of accelerated HSC aging, including lymphopenia, increased myeloid output, and DNA damage, mimicking physiologically aged HSCs. Remarkably, recombinant PF4 administration restored old HSCs to youthful functional phenotypes characterized by improved cell polarity, reduced DNA damage, enhancedin vivoreconstitution capacity, and balanced lineage output. Mechanistically, we identified LDLR and CXCR3 as the HSC receptors transmitting the PF4 signal, with double knockout mice showing exacerbated HSC aging phenotypes similar to PF4-deficient mice. Furthermore, human HSCs across various age groups also respond to the youthful PF4 signaling, highlighting its potential for rejuvenating aged hematopoietic systems. These findings pave the way for targeted therapies aimed at reversing age-related HSC decline with potential implications in the prevention or improvement of the course of age-related hematopoietic diseases.

Key Points

Age-related attrition of the megakaryocytic niche and associated PF4 downregulation is a central mechanism in HSC aging.

PF4 supplementation, acting on LDLR and CXCR3 receptors, rejuvenates the function of aged HSCs.
Visualization of a multi-turnover Cas9 after product release
Authors: Kiernan Kaitlyn A. , Taylor David W.
Published: November 2024

While the most widely used CRISPR-Cas enzyme is theS. pyogenesCas9 endonuclease (Cas9), it exhibits single-turnover enzyme kinetics which leads to long residence times on product DNA. This blocks access to DNA repair machinery and acts as a major bottleneck during CRISPR-Cas9 gene editing. Although Cas9 can eventually be forcibly removed by extrinsic factors (translocating polymerases, helicases, chromatin modifying complexes, etc), the mechanisms contributing to Cas9 dissociation following cleavage remain poorly understood. Interestingly, it’s been shown that Cas9 can be more easily dislodged when complexes collide with the PAM-distal region of the Cas9 complex or when the strength of Cas9 interactions in this region are weakened. Here, we employ truncated guide RNAs as a strategy to weaken PAM-distal nucleic acid interactions and still support Cas9 activity. We find that guide truncation promotes much faster Cas9 turnover and used this to capture previously uncharacterized Cas9 reaction states. Kinetics-guided cryo-EM enabled us to enrich for rare, transient states that are often difficult to capture in standard workflows. From a single dataset, we examine the entire conformational landscape of a multi-turnover Cas9, including the first detailed snapshots of Cas9 dissociating from product DNA. We discovered that while the PAM-distal product dissociates from Cas9 following cleavage, tight binding of the PAM-proximal product directly inhibits re-binding of new targets. Our work provides direct evidence as to why Cas9 acts as a single-turnover enzyme and will guide future Cas9 engineering efforts.
Risk of evolution driven population-wide emergence of mpox: the paradoxic effect of moderate interventions
Authors: Nedényi F. , Benke J. M. , Szalai M. , Röst G.
Published: November 2024

The global mpox outbreak has recently been declared a public health emergency of international concern. In this paper, we investigate the spread of mpox primarily evolving and propagating within a core population before affecting the general population. A main public health concern is that through evolution, mpox gains the ability to widely spread in the entire population. We examine how effective various intervention strategies are in preventing this from happening. These non-pharmaceutical inter-ventions include reducing disease transmission in the core population, in the general population, or in both. Our analysis encompasses the optimal timing for these interventions, considering the effects of early versus late intervention and the potential impact of different mutation patterns on disease spread. Our findings highlight that effective early intervention can be achieved with lower intensity, while delayed intervention requires stronger measures. Notably, our results reveal an intriguing phenomenon where moderate intervention could lead to worse outcome than no intervention. This counterintuitive outcome arises because moderate restrictions may prolong transmission chains within the core group, leading to more opportunities for the pathogen to acquire mutations resulting in higher transmission potential in the general population. Consequently, a comprehensive understanding of the role of the core group in disease dynamics and the mutation patterns is crucial for developing tailored and effective public health strategies.
Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision
Authors: Han Jane , Chauhan Vassiki , Philip Rebecca , Taylor Morgan K. , Jung Heejung , Halchenko Yaroslav O. , Gobbini M. Ida , Haxby James V. , Nastase Samuel A.
Published: November 2024

We effortlessly extract behaviorally relevant information from dynamic visual input in order to understand the actions of others. In the current study, we develop and test a number of models to better understand the neural representational geometries supporting action understanding. Using fMRI, we measured brain activity as participants viewed a diverse set of 90 different video clips depicting social and nonsocial actions in real-world contexts. We developed five behavioral models using arrangement tasks: two models reflecting behavioral judgments of the purpose (transitivity) and the social content (sociality) of the actions depicted in the video stimuli; and three models reflecting behavioral judgments of the visual content (people, objects, and scene) depicted in still frames of the stimuli. We evaluated how well these models predict neural representational geometry and tested them against semantic models based on verb and nonverb embeddings and visual models based on gaze and motion energy. Our results revealed that behavioral judgments of similarity better reflect neural representational geometry than semantic or visual models throughout much of cortex. The sociality and transitivity models in particular captured a large portion of unique variance throughout the action observation network, extending into regions not typically associated with action perception, like ventral temporal cortex. Overall, our findings expand the action observation network and indicate that the social content and purpose of observed actions are predominant in cortical representation.