bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of ζ-deficient CARs into theCD3-zetagene conveys potent cytotoxicity in T and NK cells
Authors: Kath Jonas , Franke Clemens , Drosdek Vanessa , Du Weijie , Glaser Viktor , Fuster-Garcia Carla , Stein Maik , Zittel Tatiana , Schulenberg Sarah , Porter Caroline E. , Andersch Lena , Künkele Annette , Alcaniz Joshua , Hoffmann Jens , Abken Hinrich , Abou-el-Enein Mohamed , Pruß Axel , Suzuki Masataka , Cathomen Toni , Stripecke Renata , Volk Hans-Dieter , Reinke Petra , Schmueck-Henneresse Michael , Wagner Dimitrios L.
Published: November 2023

I.

Chimeric antigen receptor (CAR)-reprogrammed immune cells hold significant therapeutic potential for oncology, autoimmune diseases, transplant medicine, and infections. All approved CAR-T therapies rely on personalized manufacturing using undirected viral gene transfer, which results in non-physiological regulation of CAR-signaling and limits their accessibility due to logistical challenges, high costs and biosafety requirements. Here, we propose a novel approach utilizing CRISPR-Cas gene editing to redirect T cells and natural killer (NK) cells with CARs. By transferring shorter, truncated CAR-transgenes lacking a main activation domain into the humanCD3ζ(CD247)gene, functional CAR fusion-genes are generated that exploit the endogenousCD3ζ gene as the CAR’s activation domain. Repurposing this T/NK-cell lineage gene facilitated physiological regulation of CAR-expression and reprogramming of various immune cell types, including conventional T cells, TCRγ/δ T cells, regulatory T cells, and NK cells. In T cells,CD3ζ in-frame fusion eliminated TCR surface expression, reducing the risk of graft-versus-host disease in allogeneic off-the-shelf settings.CD3ζ-CD19-CAR-T cells exhibited comparable leukemia control toT cell receptor alpha constant(TRAC)-replaced and lentivirus-transduced CAR-T cellsin vivo. Tuning ofCD3ζ-CAR-expression levels significantly improved thein vivoefficacy. Compared toTRAC-edited CAR-T cells, integration of a Her2-CAR intoCD3ζ conveyed similarin vitrotumor lysis but reduced susceptibility to activation-induced cell death and differentiation, presumably due to lower CAR-expression levels. Notably,CD3ζ gene editing enabled reprogramming of NK cells without impairing their canonical functions. Thus,CD3ζ gene editing is a promising platform for the development of allogeneic off-the-shelf cell therapies using redirected killer lymphocytes.

Key points

Integration of ζ-deficient CARs intoCD3ζ gene allows generation of functional TCR-ablated CAR-T cells for allogeneic off-the-shelf use

CD3ζ-editing platform allows CAR reprogramming of NK cells without affecting their canonical functions
An agent based model (ABM) to reproduce the boolean logic behaviour of neuronal self organized communities through pulse delay modulation and generation of logic gates
Authors: Irastorza-Valera Luis , Benitez José María , Montáns Francisco J. , Saucedo-Mora Luis
Published: November 2023

The human brain is arguably the most complex “machine” to ever exist. Its detailed functioning is yet to be fully understood, let alone modeled. Neurological processes have logical signal-processing aspects and biophysical aspects, and both affect the brain structure, functioning and adaptation. Mathematical approaches based on both information and graph theory have been extensively used in an attempt to approximate its biological functioning, along with Artificial Intelligence approaches inspired by its logical functioning. In this article, we present an approach to model some aspects of the brain learning and signal processing, mimicking the metastability and backpropagation found in the real brain while also accounting for neuroplasticity. Several simulations are carried out with this model, to demonstrate how dynamic neuroplasticity, neural inhibition and neurons migration can remodel the brain logical connectivity to syncronize signal processing and obtain target latencies. This work demonstrates the importance of dynamic logical and biophysical remodelling in brain plasticity.
Characterization of a Novel Mouse Platelet Transfusion Model
Authors: Gordy Dominique , Swayne Theresa , Berry Gregory J. , Thomas Tiffany A. , Hudson Krystalyn E. , Stone Elizabeth F.
Published: November 2023

BACKGROUND

Platelet transfusions are increasing with advances in medical care. Based on FDA criteria, platelet units are assessed byin vitromeasures; however, it is not known how platelet processing and storage duration affect functionin vivo. To address this, we developed a novel platelet transfusion model that meets FDA criteria adapted to mice, and transfused fresh and stored platelets are detected in clotsin vivo.

STUDY DESIGN AND METHODS

Platelet units stored in mouse plasma were prepared using a modified platelet rich plasma collection protocol. Characteristics of fresh and stored units, including pH, cell count, in vitro measures of activity, including activation and aggregation, and post-transfusion recovery (PTR), were determined. Lastly, a tail transection assay was conducted using mice transfused with fresh or stored units, and transfused platelets were identified by confocal imaging.

RESULTS

Platelet units had acceptable platelet and white cell counts and were negative for bacterial contamination. Fresh and 1-day stored units had acceptable pH; the platelets were activatable by thrombin and ADP, aggregable with thrombin, had acceptable PTR, and were presentin vivoin clots of recipients after tail transection. In contrast, 2-day stored units had clinically unacceptable quality.

DISCUSSION

We developed mouse platelets for transfusion analogous to human platelet units using a modified platelet rich plasma collection protocol with maximum storage of 1 day for an “old” unit. This provides a powerful tool to test how process modifications and storage conditions affect transfused platelet functionin vivo.
Nucleoporin93 (Nup93) Limits Yap Activity to Prevent Endothelial Cell Senescence
Authors: Nguyen Tung D. , Rao Mihir K. , Dhyani Shaiva P. , Banks Justin M. , Winek Michael A. , Michalkiewicz Julka , Lee Monica Y.
Published: November 2023

Endothelial cells (ECs) form the innermost lining of the vasculature and serve a pivotal role in preventing age-related vascular disease. Endothelial health relies on the proper nucleocytoplasmic shuttling of transcription factors via nuclear pore complexes (NPCs). Emerging studies report NPC degradation with natural aging, suggesting impaired nucleocytoplasmic transport in age-related EC dysfunction. We herein identify nucleoporin93 (Nup93), a crucial structural NPC protein, as an indispensable player for vascular protection. Endothelial Nup93 protein levels are significantly reduced in the vasculature of aged mice, paralleling observations of Nup93 loss when usingin vitromodels of endothelial aging. Mechanistically, we find that loss of Nup93 impairs NPC transport, leading to the nuclear accumulation of Yap and downstream inflammation. Collectively, our findings indicate maintenance of endothelial Nup93 as a key determinant of EC health, where aging targets endothelial Nup93 levels to impair NPC function as a novel mechanism for EC senescence and vascular aging.
Impact of central carbon metabolism bypasses on the production of beta-carotene inYarrowia lipolytica
Authors: Markuš Tadej , Soldat Mladen , Magdevska Vasilka , Horvat Jaka , Kavšček Martin , Kosec Gregor , Fujs Štefan , Petrovič Uroš
Published: November 2023

Yarrowia lipolyticais an oleaginous yeast with ever growing popularity in the metabolic engineering circles. It is well known for its ability to accommodate a high carbon flux through acetyl-CoA and is being extensively studied for production of chemicals derived from it.

We investigated the effects of modifying the upstream metabolism leading to acetyl-CoA on beta-carotene production, including its titer, yield, and content. We examined the pyruvate and the phosphoketolase bypass, both of which are stoichiometrically favorable for the production of acetyl-CoA and beta-carotene. Additionally, we examined a set of genes involved in the carnitine shuttle. We constructed a set of parental strains derived from theY. lipolyticaYB-392 wild-type strain, each with a different capacity for beta-carotene production, and introduced genes for the metabolic bypasses in each of the constructed parental strains. Subsequently, we subjected these constructed strains to a series of fermentation experiments.

We discovered that altering the upstream metabolism in most cases led to a decrease in performance for production of beta-carotene. Most notably, a set of genes used for the pyruvate bypass (YlPDC2,YlALD5, andYlACS1) and the phosphoketolase bypass (LmXPKandCkPTA) resulted in the reduction of more than 30%.

Our findings contribute to our understanding ofY. lipolytica’s metabolic capacity and suggest that production of beta-carotene is most likely not limited solely by the acetyl-CoA supply. We also highlight a complex nature of engineeringY. lipolytica, as most of the results from studies using a different strain background did not align with our findings.
Flexible Perception of Tactile Motion in Multiple Reference Frames
Authors: Ahuja Himanshu , Shivkumar Sabyasachi K. , Feistritzer Catalina , Haefner Ralf , DeAngelis Gregory C. , Gomez-Ramirez Manuel
Published: November 2023

Perceptual representations of tactile motion are thought to emerge from computations that integrate cutaneous cues such as direction, speed, and saliency of the object moving on the skin. However, this knowledge was accrued from studies that presented stimuli with the hand in a fixed proprioceptive state. We studied how perception of tactile motion is modulated by proprioception, and how interactions between proprioceptive and tactile motion inputs are controlled by the reference frame of motion judgements. Participants judged the direction of motion of stimuli presented to their index finger in two reference frames (relative to the hand or their sternum) while the stimulated hand was placed in different positions. Our data show that tactile motion can be flexibly perceived in different reference frames, with proprioceptive modulations occurring only for motion judgements made in a Sternum-centric reference frame. We developed a Bayesian model that robustly accounts for participants’ perceptual decisions. Taken together, our data highlight the flexibility of the brain to represent tactile motion information in different coordinate systems. Our study also provides a computational framework for how task-dependent reference frame signals regulate the integration of proprioceptive and tactile inputs to generate flexible perception of tactile motion.
Speeding up iterative applications of the Build supertree algorithm
Authors: Redelings Benjamin D. , Holder Mark T.
Published: November 2023

The Open Tree of Life (OToL) project produces a supertree that summarizes phylogenetic knowledge from tree estimates published in the primary literature. The supetree construction algorithm iteratively calls Aho’s Build algorithm thousands of times in order to assess the compatability of different phylogenetic groupings. We describe an incrementalized version of the Build algorithm that is able to share work between successive calls to Build. We provide details that allow a programmer to implement the incremental algorithm BuildInc, including pseudo-code and a description of data structures. We assess the effect of BuildIncon our supertree algorithm by analyzing simulated data and by analyzing a supertree problem taken from the OToL 13.4 synthesis tree. We find that BuildIncprovides up to 550-fold speedup for our supertree algorithm.
A Spatio-temporal Investigation of Dynamics of a Two-dimensional Multi-scale Fitz-Hugh Nagumo Neuronal Network
Authors: Gharahi Alireza , Mohajerani Majid
Published: November 2023

The multi scale architecture by Breakspear and Stam [2] introduces a framework to consider the dynamical processes specific to a nested hierarchy of spatial scales, from neuronal masses to cortical columns and functional brain regions. They hypothesize that the neural dynamics is a function of the structural properties of the neural system at a certain scale as well as the emergent behaviour of the smaller scale activities. In this paper, we adopt the multi scale framework to investigate a generalized version of the stochastic Fitz-Hugh Nagumo (FHN) neuronal system within the small scale process and their emergent large scale synchronization effects leading to the formation of travelling waves in the large scale system. We extend the multi scale framework to incorporate the nonlinear biological synaptic connectivity at the neuronal mass scale. The modified multi scale scheme utilizes the two-dimensional wavelet decomposition in the plane of dynamical interconnected neurons. In addition, we consider the large-scale spatio-temporal system of FHN reaction-diffusion partial differential equations and evaluate the formation of travelling waves in the simplified context of a cellular neural network (CNN) model. Numerical examples are given to illustrate the response and the isolated influence of the strength of neural connectivity on the travelling wave formation modes.
Complexity Measures of Psychotic Brain Activity in the Fmri Signal
Authors: Li Qiang , Seraji Masoud , Calhoun Vince D , Iraji Armin
Published: November 2023

When viewing the brain as a sophisticated, nonlinear dynamic system, employing complexity measures offers a valuable way to measure the intricate and dynamic aspects of spontaneous psychotic brain activity. These measures can help us identify irregularities and patterns in complex systems. In our study, we utilized fuzzy recurrence plots and sample entropy to evaluate the dynamic characteristics of psychiatric disorders. This assessment focused on understanding the temporal and spatial neural activity patterns, and more specifically, we applied complexity measures to investigate the functional connectivity within the psychotic brain. This involves understanding how different brain regions synchronize their activity, and complexity measures can reveal the patterns of these connections. It provides a means to understand how different brain regions interact and communicate under resting-state abnormal conditions. This study offers evidence demonstrating that fuzzy recurrence plots can serve as descriptors for functional connectivity and discusses their relevance to sample entropy in the context of the psychotic brain. In summary, complexity measures offer valuable insights that enrich our comprehension of atypical brain activity and the complexities present in the psychotic brain1.
Therapeutic targeting of immunometabolism in Alzheimer’s disease reveals a critical reliance on Hexokinase 2 dosage on microglial activation and disease progression
Authors: Codocedo Juan F. , Mera-Reina Claudia , Lin Peter Bor-Chian , Puntambekar Shweta S. , Casali Brad T. , Jury Nur , Martinez Pablo , Lasagna-Reeves Cristian A. , Landreth Gary E.
Published: November 2023

Microgliosis and neuroinflammation are prominent features of Alzheimer’s disease (AD). Disease-responsive microglia meet their increased energy demand by reprogramming metabolism, specifically, switching to favor glycolysis over oxidative phosphorylation. Thus, targeting of microglial immunometabolism might be of therapeutic benefit for treating AD, providing novel and often well understood immune pathways and their newly recognized actions in AD. We report that in the brains of 5xFAD mice and postmortem brains of AD patients, we found a significant increase in the levels of Hexokinase 2 (HK2), an enzyme that supports inflammatory responses by rapidly increasing glycolysis. Moreover, binding of HK2 to mitochondria has been reported to regulate inflammation by preventing mitochondrial dysfunction and NLRP3 inflammasome activation, suggesting that its inflammatory role extends beyond its glycolytic activity. Here we report, that HK2 antagonism selectively affects microglial phenotypes and disease progression in a gene-dose dependent manner. Paradoxically, complete loss of HK2 fails to improve AD progression by exacerbating inflammasome activity while its haploinsufficiency results in reduced pathology and improved cognition in the 5XFAD mice. We propose that the partial antagonism of HK2, is effective in slowed disease progression and inflammation through a non-metabolic mechanism associated with the modulation of NFKβ signaling, through its cytosolic target IKBα. The complete loss of HK2 affects additional inflammatory mechanisms associated to mitochondrial dysfunction.

Highlights

Hexokinase 2, the first and rate-limiting enzyme of glycolysis, is specifically upregulated in plaque-associated microglia of AD mice models and in the postmortem cortex of human AD patients.

Microglia haploinsufficient in HK2 exhibit reduced amyloid burden and inflammation as well as improved cognition in a mouse model of AD. Paradoxically, the complete loss of HK2 results in opposite effects, by exacerbating inflammation.

Lonidamine, an anticancer drug that inhibits HK2, mimics the salutary effects of HK2 haploinsufficiency in the 5xFAD mice, but only in males during the early stages of disease.

HK2 deletion induced mitochondrial dysfunction associated to increased expression of inflammasome elements and IL-1β.

HK2 partial antagonism exerts beneficial effects independent of its energetic or mitochondrial role, likely through cytosolic stabilization of IκBα and inhibition of the NF-κB pathway, leading to reduced proinflammatory gene expression.
Loss of TMEM106B exacerbates Tau pathology and neurodegeneration in PS19 mice
Authors: Feng Tuancheng , Du Huan , Hu Fenghua
Published: November 2023

TMEM106B, a gene encoding a lysosome membrane protein, is tightly associated with brain aging, hypomyelinating leukodystrophy, and multiple neurodegenerative diseases, including frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Recently,TMEM106Bpolymorphisms have been associated with tauopathy in chronic traumatic encephalopathy (CTE) and FTLD-TDP patients. However, how TMEM106B influences Tau pathology and its associated neurodegeneration, is unclear. Here we show that loss of TMEM106B enhances the accumulation of pathological Tau, especially in the neuronal soma in the hippocampus, resulting in severe neuronal loss in the PS19 Tau transgenic mice. Moreover,Tmem106b-/-PS19 mice develop significantly increased disruption of the neuronal cytoskeleton, autophagy-lysosomal function, and lysosomal trafficking along the axon as well as enhanced gliosis compared with PS19 andTmem106b-/-mice. Together, our findings demonstrate that loss of TMEM106B drastically exacerbates Tau pathology and its associated disease phenotypes, and provide new insights into the roles of TMEM106B in neurodegenerative diseases.
Genome assembly and genomic architecture of a prominent cold-resistant rapeseed germplasm
Authors: Wu Zefeng , Zheng Guoqiang , Sun Yali , Dong Xiaoyun , Wang Ying , Li Hui , Wei Jiaping , Cui Junmei , Fang Yan , Niu Yinin , Huang Zhen , Hu Jihong , Liu Zigang
Published: November 2023

Graphical Abstract

The genomic landscape of cold-tolerant winter rapeseed (Brassica napus, L) has been poorly characterized. We assembled a high-quality reference genome of a prominent cold-tolerant winter rapeseed cultivar, NTS57, and performed phylogenetic and pan-genomic analyses by integrating other reportedBrassica napusaccessions. The transcriptome analysis revealed that microtubule-associated biological pathways were much more active in NTS57 under cold stress than in the cold-sensitive variety. Whole genome methylation data analysis revealed that DNA demethylation on protein-coding genes and repetitive elements, especially at CHH sites, is essential for cold response in winter rapeseed.
Dual therapy with corticosteroid ablates the beneficial effect of DP2 antagonism in chronic experimental asthma
Authors: Ullah Md Ashik , Rittchen Sonja , Li Jia , Curren Bodie F. , Rahman Muhammed Mahfuzur , Sikder Md Al Amin , Rashid Ridwan B. , Collinson Natasha , Lor Mary , Smythe Mark L. , Phipps Simon
Published: November 2023

Background

Prostaglandin D2 (PGD2) signals via the DP1 and DP2 receptors. In Phase II trials, DP2 antagonism decreased airway inflammation and airway smooth muscle (ASM) area in patients with moderate-to-severe asthma, but in the Phase III clinical trials, DP2 antagonism failed to significantly lower the rate of exacerbations. Here, we hypothesised that DP2 antagonism resolves established ASM remodeling via endogenous PGD2/DP1 activation and that this beneficial effect is ablated by dual corticosteroid therapy.

Methods

Neonatal mice were co-exposed to pneumonia virus of mice (PVM) and cockroach extract in early life to induce severe bronchiolitis, then re-infected with PVM and challenged to cockroach extract in adulthood to progress disease to chronic experimental asthma (CEA). The efficacy of DP2 antagonism monotherapy or various dual therapies was assessed in the setting of a rhinovirus (RV)-induced exacerbation.

Results

RV inoculation increased PGD2 release, mucus production, collagen deposition, transforming growth factor (TGF)-β1 expression and type-2 inflammation. Treatment with a DP2 antagonist or DP1 agonist ablated the aforementioned phenotypes, increased type-1 immunity, and decreased ASM area. Dual DP1-DP2 antagonism or dual corticosteroid/DP2 antagonism, which attenuated endogenous PGD2 levels, prevented the resolution of ASM area induced by DP2 antagonism alone. The resolution of ASM remodelling following DP2 antagonism was mediated by IFN-γ and associated with decreased TGF-β1 expression.

Conclusion

DP2 antagonism resolved ASM remodelling via PGD2/DP1-mediated upregulation of interferon-γ expression. Dual DP2 antagonism/corticosteroid therapy, as occurred in many of the human trials, suppressed PGD2 and IFN-γ production, impairing the efficacy of DP2 antagonism.
Self-supervised contrastive learning improves machine learning discrimination of full thickness macular holes from epiretinal membranes in retinal OCT scans
Authors: Wheeler Tim , Hunter Kaitlyn , Garcia Patricia , Li Henry , Thomson Andrew , Hunter Allan , Mehanian Courosh
Published: November 2023

There is a growing interest in using computer-assisted models for the detection of macular conditions using optical coherence tomography (OCT) data. As the quantity of clinical scan data of specific conditions is limited, these models are typically developed by fine-tuning a generalized network to classify specific macular conditions of interest. Full thickness macular holes (FTMH) present a condition requiring timely surgical intervention to prevent permanent vision loss. Other works on automated FTMH classification have tended to use supervised ImageNet pre-trained networks with good results but leave room for improvement. In this paper, we develop a model for FTMH classification using OCT slices around the central foveal region to pre-train a naïve network using contrastive self-supervised learning. We found that self-supervised pre-trained networks outperform ImageNet pre-trained networks despite a small training set size (284 eyes total, 51 FTMH+ eyes, 3 slices from each eye). 3D spatial contrast pre-training yields a model with an F1-score of 1.0 on holdout data (50 eyes total, 10 FTMH+), compared ImageNet pre-trained models, respectively. These results demonstrate that even limited data may be applied toward self-supervised pre-training to substantially improve performance for FTMH classification, indicating applicability toward other OCT-based problems.

Author Summary

Full thickness macular holes (FTMH) are a sight-threatening condition that involves the fovea, the area of the eye involved in central vision. Timely diagnosis is paramount because of the risk of permanent vision loss. In clinical practice, full thickness macular holes are commonly diagnosed with the aid of optical coherence tomography (OCT) images of the fovea. However, certain conditions such as pseudoholes and epiretinal membranes may complicate the diagnosis of full thickness macular holes on imaging. Here, we employ the use of artificial intelligence and present a machine-learning model for full thickness macular hole classification and distinction from conditions that may present similarly upon image review. Despite training our model with a smaller data set, it outperformed traditional models previously seen in other works. We provide a strong framework for a self-supervised pre-trained model that can accurately distinguish full thickness macular holes from epiretinal membranes and pseudoholes. Overall, our study provides evidence of the benefit and efficacy with the introduction of artificial intelligence for image classification.
The Cognitive Connectome in Dementia with Lewy Bodies
Authors: Yánez-Pérez Roraima , García-Cabello Eloy , Habich Annegret , Cedres Nira , Diaz-Galvan Patricia , Abdelnour Carla , Toledo Jon B. , Barroso José , Ferreira Daniel
Published: November 2023

Objectives

Cognition plays a central role for diagnosing and characterizing dementia with Lewy bodies (DLB). However, the complex associations among cognitive functions are largely unknown in DLB. To fill this gap, we compared the cognitive connectome of DLB patients, healthy controls (HC) and patients with Alzheimer’s disease (AD).

Methods

We obtained data from the National Alzheimer’s Coordinating Center (NIA/NIH Grant U24-AG072122). We built separate cognitive connectomes for DLB (n=104), HC (n= 3703), and AD (n=1985) groups using pairwise correlations between 24 cognitive variables mapping multiple cognitive functions. The cognitive connectomes in DLB, HC, and AD groups were compared using standard global and nodal graph measures of centrality, integration, and segregation.

Results

In global connectome measures, DLB patients showed a higher global efficiency (integration) and lower transitivity (segregation) than HCs and AD. Nodal connectome measures showed a higher global efficiency in most cognitive functions in DLB compared to HCs. Additionally, we found a lower local efficiency (segregation) and nodal strength (centrality) in memory variables and a higher participation coefficient in executive variables (centrality) in DLB compared with both HCs and AD.

Conclusions

The cognitive connectome in DLB showed a signature dedifferentiation pattern of aberrant correlations. Executive, processing speed and attention functions played a central role in the cognitive connectome of DLB patients. Furthermore, the role of executive and memory functions in the cognitive connectome distinguished DLB and AD patients. These findings may help advance our understanding of the clinical phenotype in DLB, and continue to improve the challenging differential diagnosis between DLB and AD.
Improving Interprofessional Collaboration: Building Confidence Using A Novel HIV Curriculum For Healthcare Workers Across Sub-Saharan Africa
Authors: Khanyola Judy , Reid Mike , Dadasovich Rand , Derbew Miliard , Couper Ian , Dassah Edward T. , Forster Maeve , Gachuno Onesmus , Haruzivishe Clara , Kazembe Abigail , Martin Shayanne , Moltwantwa Mmoloki , Motlhatlhedi Keneilwe , Mteta Kien Alfred , Nadesan-Reddy Nisha , Suleman Fatima , Ngoma Catherine , Odaibo Georgina N. , Mubuuke Roy , von Zinkernagel Deborah , Kiguli-Malwadde Elsie , Sears David
Published: November 2023

The 21st century presents significant global health challenges that necessitate an integrated health workforce capable of delivering person-centered and integrated healthcare services. Interprofessional collaboration (IPC) plays a vital role in achieving integration and training an IPC-capable workforce in Sub-Saharan Africa (SSA) has become imperative. This study aimed to assess changes in IPC confidence among learners participating in a team-based, case-based HIV training program across diverse settings in SSA. Additionally, it sought to examine the impact of different course formats (in-person, synchronous virtual, or blended learning) on IPC confidence. Data from 20 institutions across 18 SSA countries were collected between May 1, 2021, and December 31, 2021. Logistic regression analysis was conducted to estimate associations between variables of interest and the gain in IPC confidence. The analysis included 3,842 learners; nurses comprised 37.9% (n=1,172) and physicians 26.7% (n=825). The majority of learners (67.2%, n=2,072) were pre-service learners, while 13.0% (n=401) had graduated within the past year. Factors significantly associated with increased IPC confidence included female gender, physician cadre, completion of graduate training over 12 months ago, and participation in virtual or in-person synchronous workshops (p<0.05). The insights gained from this analysis can inform future curriculum development to strengthen interprofessional healthcare delivery across SSA.
Protocol for the systematic review of thePneumocystis jirovecii-associated pneumonia in non-HIV immunocompromised patients
Authors: Orozco-Ugarriza Mauricio Ernesto , Rodger-Cervantes Yuranis E. , Olivo-Martínez Yenifer
Published: November 2023

Introduction

Pneumocystis jiroveciipneumonia (PJP) is a well-known and frequent opportunistic infection in HIV patients. However, there has been an increase in the number of reports of PJP in other immunosuppressed patients with autoimmune inflammatory disorders or because of chemotherapy and high doses of steroids, especially when used in combination as part of immunosuppressive therapy.

Objective

Despite the increasing importance of PJP in non-HIV patients, there is a lack of comprehensive and updated information on the epidemiology, pathogenesis, diagnosis, microbiology, treatments, and prophylaxis of this infection in this population. Therefore, the objective of this systematic review is to synthesize information on these aspects, from a perspective of evidence-based medicine.

Methods

The protocol is prepared following the preferred reporting items for systematic reviews and meta-analyses (PRISMA-P) guidelines. We will perform a systematic review from 2010 to 2022 in PubMed, Google Scholar, ScienceDirect, and Web of Science. In addition, manual searches will be carried out through related articles, and references to included articles. The main findings and clinical outcomes were extracted from all the eligible studies with a standardized instrument. Two authors will independently screen titles and abstracts, review full texts, and collect data. Disagreements will be resolved by discussion, and a third reviewer will decide if there is no consensus. We will synthesize the results using a narrative or a meta-analytic approach, depending on the heterogeneity of the studies.

Expected results

It is expected that this systematic review will provide a comprehensive and up-to-date overview of the state-of-the-art of PJP in non-HIV patients. Furthermore, the study will highlight possible gaps in knowledge that should be addressed through new research.

Conclusions

Here, we present the protocol for a systematic review which will consider all existing evidence from peer-reviewed publication sources relevant to the primary and secondary outcomes related to diagnosing and managing PJP in non-HIV patients.

Systematic review registry

This study was registered at the International Prospective Registry for Systematic Reviews (PROSPERO registration number:CRD42023429112)
Hao-Fountain Syndrome: 32 novel patients reveal new insights into the clinical spectrum
Authors: Wimmer Moritz Claudius , Brennenstuhl Heiko , Hirsch Steffen , Dötsch Laura , Unser Samy , Caro Pilar , Schaaf Christian Patrick
Published: November 2023

Hao-Fountain syndrome (HAFOUS, OMIM: #616863) is a neurodevelopmental disorder caused by pathogenic variants in the geneUSP7coding for USP7, a protein involved in several crucial cellular homeostatic mechanisms and the recently described MUST complex. The phenotype of HAFOUS is insufficiently understood, yet there is a great need to better understand the spectrum of disease, genotype-phenotype correlations, and disease trajectories.

We now present a larger cohort of 32 additional individuals and provide further clinical information about six previously reported individuals. A questionnaire-based study was performed to characterize the phenotype of Hao-Fountain syndrome more clearly, to highlight new traits, and to better distinguish the disease from related neurodevelopmental disorders. In addition to confirming previously described features, we report hyperphagia and increased body weight in a subset of individuals. HAFOUS patients present an increased rate of birth complications, congenital anomalies, and abnormal pain thresholds. Speech impairment emerges as a potential hallmark of Hao-Fountain syndrome. Cognitive testing reports reveal borderline intellectual functioning on average, although some individuals score in the range of intellectual disability.

Finally, we created a syndrome-specific severity score. This score neither indicates a sex-nor age-specific difference of clinical severity, yet highlights a more severe outcome when amino acid changes colocalize to the catalytic domain of the USP7 protein.
Prediction of plant complex traits via integration of multi-omics data
Authors: Wang Peipei , Lehti-Shiu Melissa D. , Lotreck Serena , Abá Kenia Segura , Krysan Patrick J. , Shiu Shin-Han
Published: November 2023

The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigated whether integrating different omics data could improve trait prediction. We built prediction models using genomic, transcriptomic, and methylomic data from the Arabidopsis 1001 Genomes Project for six Arabidopsis traits, and found that transcriptome- and methylome-based models had performances comparable to those of genome-based models. However, when comparing models for flowering time prediction, we found that models built using different omics data identified different benchmark genes. Nine novel genes identified as important for flowering time from our models were experimentally validated as regulating flowering. In addition, we found that gene contributions to flowering time prediction are accession-dependent and that distinct genes contribute to trait prediction in different genetic backgrounds. Models integrating multi-omics data performed best and revealed known and novel gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.
GCN2 mediates access to stored amino acids for somatic maintenance duringDrosophilaageing
Authors: Johnstone Joshua N. , Mirth Christen K. , Johnson Travis K. , Schittenhelm Ralf B. , Piper Matthew D.W.
Published: November 2023

Many mechanistic theories of ageing argue that a progressive failure of somatic maintenance, the use of energy and resources to prevent and repair damage to the cell, underpins ageing. To sustain somatic maintenance an organism must acquire dozens of essential nutrients from the diet, including essential amino acids (EAAs), which are physiologically limiting for many animals. InDrosophila, adulthood deprivation of each individual EAA yields vastly different lifespan trajectories, and adulthood deprivation of one EAA, phenylalanine (Phe), has no associated lifespan cost; this is despite each EAA being strictly required for growth and reproduction. Moreover, survival under any EAA deprivation depends entirely on the conserved AA sensor GCN2, a component of the integrated stress response (ISR), suggesting that a novel ISR-mediated mechanism sustains lifelong somatic maintenance during EAA deprivation. Here we investigated this mechanism, finding that flies chronically deprived of dietary Phe continue to incorporate Phe into new proteins, and that challenging flies to increase the somatic requirement for Phe shortens lifespan under Phe deprivation. Further, we show that autophagy is required for full lifespan under Phe deprivation, and that activation of the ISR can partially rescue the shortened lifespan ofGCN2-nulls under Phe deprivation. We therefore propose a mechanism by which GCN2, via the ISR, activates autophagy during EAA deprivation, breaking down a larvally-acquired store of EAAs to support somatic maintenance. These data refine our understanding of the strategies by which flies sustain lifelong somatic maintenance, which determines length of life in response to changes in the nutritional environment.
Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome
Authors: Chan Jennifer C , Alenina Natalia , Cunningham Ashley M , Ramakrishnan Aarthi , Shen Li , Bader Michael , Maze Ian
Published: November 2023

Brain development requires appropriate regulation of serotonin (5-HT) signaling from distinct tissue sources across embryogenesis. At the maternal-fetal interface, the placenta is thought to be an important contributor of offspring brain 5-HT and is critical to overall fetal health. Yet, how placental 5-HT is acquired, and the mechanisms through which 5-HT influences placental functions, are not well understood. Recently, our group identified a novel epigenetic role for 5-HT, in which 5-HT can be added to histone proteins to regulate transcription, a process called H3 serotonylation. Here, we show that H3 serotonylation undergoes dynamic regulation during placental development, corresponding to gene expression changes that are known to influence key metabolic processes. Using transgenic mice, we demonstrate that placental H3 serotonylation largely depends on 5-HT uptake by the serotonin transporter (SERT/SLC6A4). SERT deletion robustly reduces enrichment of H3 serotonylation across the placental genome, and disrupts neurodevelopmental gene networks in early embryonic brain tissues. Thus, these findings suggest a novel role for H3 serotonylation in coordinating placental transcription at the intersection of maternal physiology and offspring brain development.
DNA Origami – Lipid Membrane Interactions Defined at Single-Molecular Resolution
Authors: Georgiou Elena , Cabello-Garcia Javier , Xing Yongzheng , Howorka Stefan
Published: November 2023

Rigid DNA nanostructures that bind to floppy bilayer membranes are of fundamental interest as they replicate biological cytoskeletons for synthetic biology, biosensing, and biological research. Here, we establish principles underpinning the controlled interaction of DNA structures and lipid bilayers. As membrane anchors mediate interaction, more than 20 versions of a core DNA nanostructure are built each carrying up to five individual cholesterol anchors of different steric accessibility within the 3D geometry. The structures’ binding to membrane vesicles of tunable curvature is determined with ensemble methods and by single-molecule localization microscopy. This screen yields quantitative and unexpected insight on which steric anchor points cause efficient binding. Strikingly, defined nanostructures with a single molecular anchor discriminate effectively between vesicles of different nanoscale curvatures which may be exploited to discern diagnostically relevant membrane vesicles based on size. Furthermore, we reveal anchor-mediated bilayer interaction to be co-controlled by non-lipidated DNA regions and localized membrane curvatures stemming from heterogenous lipid composition, which modifies existing biophysical models. Our study extends DNA nanotechnology to control interactions with bilayer membranes and thereby facilitate the design of nanodevices for vesicle-based diagnostics, biosensing, and protocells.
Strong sequence dependence in RNA/DNA hybrid strand displacement kinetics
Authors: Smith Francesca G. , Goertz John P. , Stevens Molly M. , Ouldridge Thomas E.
Published: November 2023

Strand displacement reactions underlie dynamic nucleic acid nanotechnology. The kinetic and thermodynamic features of DNA-based displacement reactions are well understood and well predicted by current computational models. By contrast, understanding of RNA/DNA hybrid strand displacement kinetics is limited, restricting the design of increasingly complex RNA/DNA hybrid reaction networks with more tightly regulated dynamics. Given the importance of RNA as a diagnostic biomarker, and its critical role in intracellular processes, this shortfall is particularly limiting for the development of strand displacement-based therapeutics and diagnostics. Herein, we characterise 22 RNA/DNA hybrid strand displacement systems, systematically varying several common design parameters including toehold length and branch migration domain length. We observe the differences in stability between RNA-DNA hybrids and DNA-DNA duplexes have large effects on strand displacement rates, with rates for equivalent sequences differing by up to 3 orders of magnitude. Crucially, however, this effect is strongly sequence-dependent, with RNA invaders strongly favoured in a system with RNA strands of high purine content, and disfavoured in a system when the RNA strands have low purine content. These results lay the groundwork for more general design principles, allowing for creation ofde novoreaction networks with novel complexity while maintaining predictable reaction kinetics.
FeLIX is a restriction factor for mammalian retrovirus infection
Authors: Pramono Didik , Takeuchi Dai , Katsuki Masato , AbuEed Loai , Abdillah Dimas , Kimura Toru , Kawasaki Junna , Miyake Ariko , Nishigaki Kazuo
Published: November 2023

Endogenous retroviruses (ERVs) are remnants of ancestral viral infections. Feline leukemia virus (FeLV) is an exogenous and endogenous retrovirus in domestic cats. It is classified into several subgroups (A, B, C, D, E, and T) based on viral receptor interference properties or receptor usage. ERV-derived molecules benefit animals, conferring resistance to infectious diseases. However, the soluble protein encoded by the defective envelope (env) gene of endogenous FeLV (enFeLV) functions as a co-factor in FeLV subgroup T infections. Thus, whether the gene emerged to facilitate viral infection is unclear. Based on the properties of ERV-derived molecules, we hypothesized that the defectiveenvgenes possess antiviral activity that would be advantageous to the host because FeLV subgroup B (FeLV-B), a recombinant virus derived from enFeLVenv, is restricted to viral transmission among domestic cats. When soluble truncated Env proteins from enFeLV were tested for their inhibitory effects against enFeLV and FeLV- B, they inhibited viral infection. Notably, this antiviral machinery was extended to infection with the Gibbon ape leukemia virus, Koala retrovirus-A, and Hervey pteropid gammaretrovirus. Although these viruses used feline phosphate transporter1 (fePit1) or fePit1 and phosphate transporter2 (fePit2) as receptors, the inhibitory mechanism involved competitive receptor binding in a fePit1-dependent manner. The shift of receptor usage may have occurred to avoid the inhibitory effect. Overall, these findings highlight the possible emergence of soluble truncated Env proteins from enFeLV as a restriction factor against retroviral infection, and might help in the control of retroviral spread for host immunity and antiviral defense.

Importance

Retroviruses are unique in using reverse transcriptase to convert RNA genomes into DNA, infecting germ cells, and transmitting to offspring. A large amount of ancient retroviral sequences are known as endogenous retroviruses (ERVs). Soluble Env protein derived from ERVs have been identified to function as a co-factor that assists in FeLV-T infection. However, herein, we show that the soluble Env protein exhibits antiviral activity and provides resistance to mammalian retrovirus infection through competitive receptor binding. In particular, this finding may explain why FeLV-B transmission is not observed among domestic cats. ERV-derived molecules can benefit animals in an evolutionary arm race, highlighting the double-edged sword nature of ERVs.
Rapid Adeno-Associated Virus Genome Quantification with Amplification-Free CRISPR-Cas12a
Authors: Hetzler Zach , Marinakos Stella M. , Lott Noah , Mohammad Noor , Lass-Napiorkowska Agnieszka , Kolbe Jenna , Turrentine Lauren , Fields Delaney , Overton Laurie , Marie Helena , Hucknall Angus , Rammo Oliver , George Henry , Wei Qingshan
Published: November 2023

Efficient manufacturing of recombinant Adeno-Associated Viral (rAAV) vectors to meet rising clinical demand remains a major hurdle. One of the most significant challenges is the generation of large amounts of empty capsids without the therapeutic genome. There is no standardized analytical method to accurately quantify the viral genes, and subsequently the empty-to-full ratio, making the manufacturing challenges even more complex. We propose the use of CRISPR diagnostics (CRISPR-Dx) as a robust and rapid approach to determine AAV genome titers. We designed and developed the CRISPR-AAV Evaluation (CRAAVE) assay to maximize sensitivity, minimize time-to-result, and provide a potentially universal design for quantifying multiple transgene constructs encapsidated within different AAV serotypes. We also demonstrate an on-chip CRAAVE assay with lyophilized reagents to minimize end user assay input. The CRAAVE assay was able to detect AAV titers as low as 7e7 vg/mL with high precision (<3% error) in quantifying unknown AAV titers when compared with conventional quantitative PCR (qPCR) method. The assay only requires 30 minutes of assay time, shortening the analytical workflow drastically. Our results suggest CRISPR-Dx could be a promising tool for efficient rAAV genome titer quantification and has the potential to revolutionize biomanufacturing process analytical technology (PAT).

Graphical Abstract
Factors influencing the outcomes of non-pharmacological interventions for managing fatigue across the lifespan of people living with musculoskeletal (MSK) conditions: a scoping review protocol
Authors: Fishpool Katie , Young George , Ciurtin Coziana , Cramp Fiona , Erhieyovwe Emmanuel , Farisogullari Bayram , Macfarlane Gary , Machado Pedro M. , Pearson Jen , Santos Eduardo , Dures Emma
Published: November 2023

Introduction

Fatigue is an important and distressing symptom for many people living with chronic musculoskeletal (MSK) conditions. Many non-pharmacological interventions have been investigated in recent years and some have been demonstrated to be effective in reducing fatigue and fatigue impact, however there is limited guidance for clinicians to follow regarding the most appropriate management options. The objective of this scoping review is to understand and map the extent of evidence in relation to the impact of non-pharmacological interventions on MSK condition-related fatigue across the lifespan.

Methods and analysis

This scoping review will include evidence relating to people of all ages living with chronic MSK conditions who have been offered a non-pharmacological intervention with either the intention or effect of reducing fatigue and its impact. Databases including AMED, PsycINFO, CINAHLPlus, MEDLINE, EMBASE and Scopus will be searched for peer reviewed primary research studies published after 1stJanuary 2007 in English language. These findings will be used to identify factors associated with successful interventions and to map gaps in knowledge.

Ethics and dissemination

Ethical approval was not required for this review. Findings will be disseminated by journal publication, conference presentation and by communicating with relevant healthcare and charity organisations.

Article Summary

Strengths and limitations of this study

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Patient and Public Involvement and Engagement (PPIE) workshops at key time points will ensure that the protocol, review findings and subsequent discussion are relevant to stakeholders and reflect lived experience of MSK-fatigue

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All studies will be reviewed, and data extraction checked by a minimum of two researchers

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The effectiveness of specific interventions and methodological quality of included studies is not covered in this scoping review

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Only evidence available in English will be reviewed