bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges and Efficacy of Astrocyte-to-Neuron Reprogramming in Spinal Cord Injury: In Vitro Insights and In Vivo Outcomes
Authors: NICEFORO ALESSIA , Zholudeva Lyandysha V , Fernandes Silvia , Shah Yashvi , Lane Michael A , Qiang Liang
Published: March 2024

Traumatic spinal cord injury (SCI) leads to the disruption of neural pathways, causing loss of neural cells, with subsequent reactive gliosis and tissue scarring that limit endogenous repair. One potential therapeutic strategy to address this is to target reactive scar-forming astrocytes with direct cellular reprogramming to convert them into neurons, by overexpression of neurogenic transcription factors. Here we used lentiviral constructs to overexpress Ascl1 or a combination of microRNAs (miRs) miR124, miR9/9*and NeuroD1 transfected into cultured and in vivo astrocytes. In vitro experiments revealed cortically-derived astrocytes display a higher efficiency (70%) of reprogramming to neurons than spinal cord-derived astrocytes. In a rat cervical SCI model, the same strategy induced only limited reprogramming of astrocytes. Delivery of reprogramming factors did not significantly affect patterns of breathing under baseline and hypoxic conditions, but significant differences in average diaphragm amplitude were seen in the reprogrammed groups during eupneic breathing, hypoxic, and hypercapnic challenges. These results show that while cellular reprogramming can be readily achieved in carefully controlled in vitro conditions, achieving a similar degree of successful reprogramming in vivo is challenging and may require additional steps.
Regenerative human liver organoids (HLOs) in a pillar/perfusion plate for hepatotoxicity assays
Authors: Shrestha Sunil , Acharya Prabha , Kang Soo-Yeon , Vanga Manav Goud , Reddy Lekkala Vinod Kumar , Liu Jiafeng , Yang Yong , Joshi Pranav , Lee Moo-Yeal
Published: March 2024

Human liver organoids (HLOs) differentiated from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and adult stem cells (ASCs) can recapitulate the structure and function of human fetal liver tissues, thus being considered as a promising tissue model for liver diseases and predictive compound screening. However, the adoption of HLOs in drug discovery faces several technical challenges, which include the lengthy differentiation process with multiple culture media leading to batch-to-batch variation, short-term maintenance of hepatic functions post-maturation, low assay throughput due to Matrigel dissociation and HLO transfer to a microtiter well plate, and insufficient maturity levels compared to primary hepatocytes. To address these issues, expandable HLOs (Exp-HLOs) derived from human iPSCs were generated by optimizing differentiation protocols, which were rapidly printed on a 144-pillar plate with sidewalls and slits (144PillarPlate) and dynamically cultured for up to 20 days into differentiated HLOs (Diff-HLOs) in a 144-perfusion plate with perfusion wells and reservoirs (144PerfusionPlate) forin situorganoid culture and analysis. The dynamically cultured Diff-HLOs exhibited greater maturity and reproducibility than those cultured statically, especially after a 10-day differentiation period. In addition, Diff-HLOs in the pillar/perfusion plate were tested with acetaminophen and troglitazone for 3 days to assess drug-induced liver injury (DILI) and then incubated in an expansion medium for 10 days to evaluate liver recovery from DILI. The assessment of liver regeneration post-injury is critical to understanding the mechanism of recovery and determining the threshold drug concentration beyond which there will be a sharp decrease in the liver’s regenerative capacity. We envision that bioprinted Diff-HLOs in the pillar/perfusion plate could be used for high-throughput screening (HTS) of hepatotoxic compounds due to the short-term differentiation of passage-able Exp-HLOs, stable hepatic function post-maturation, high reproducibility, and high throughput with capability ofin situorganoid culture, testing, staining, imaging, and analysis.

Graphical abstract

The overall process of dynamic liver organoid culture andin situanalysis in the 144PillarPlate/144PerfusionPlate for high-throughput hepatotoxicity assays.
Functional-based parcellation of the mouse prefrontal cortex for network perturbation analysis
Authors: Savvateev Iurii , Grimm Christina , Markicevic Marija , Grandjean Joanes , Wenderoth Nicole , Polania Rafael , Zerbi Valerio
Published: March 2024

The prefrontal cortex (PFC) is a region of the brain involved in higher-order cognitive processes such as attention, emotional regulation, and social behavior, making it a hotspot for an ongoing clinical and fundamental research. Importantly, its functionality is intricately interconnected within a wide array of functional networks encompassing multiple other brain areas. However, the delineation of distinct subdivisions within the mouse PFC and their contributions to the broader brain network function remain topics of ongoing debate. In the current study, we used resting-state functional magnetic resonance imaging (rsfMRI) from a large cohort of wildtype animals to derive the functional-connectivity (FC) based parcellation of the mouse PFC with voxel resolution. Our findings indicate the presence of FC-based clusters that deviate from the established anatomical subdivisions within the cingulate and prelimbic areas, while they align in infralimbic and orbital cortices. To further underscore the association of these FC-based clusters with distinct functional networks, we performed network-specific perturbations using chemogenetics in the identified clusters in dorsal PFC and monitor the elicited effects with fMRI (chemo-fMRI). Our recordings revealed that FC perturbations were observed only within the functional networks linked to the targeted clusters and did not spread to neighbouring anatomical areas or functional clusters. We propose that FC-based parcellation is a valuable approach for tracking the impact of external activations and confirming the precise site of activation.

Abstract Figure
Integrating Optogenetic Stimulation of Olfactory Bulb Glomeruli with Foot Shock Fear Conditioning: A Robust Method for Investigating Olfactory-based Fear Conditioning
Authors: Kuruppath Praveen
Published: March 2024

The integration of optogenetic techniques with traditional behavioral paradigms has provided novel insights into the neural mechanisms underlying olfactory-based fear conditioning. Olfactory cues are potent triggers for fear responses, and understanding the intricate neural dynamics involved in olfactory fear learning is crucial for unraveling the complexities of aversive memory formation. In this study, a robust method is presented that combines optogenetic stimulation of olfactory bulb glomeruli with foot shock fear conditioning to investigate olfactory-based fear learning in mice. By merging optogenetic manipulation with behavioral assays, a comprehensive framework for studying the mechanisms of olfactory fear conditioning is provided. This method offers new avenues for exploring the neural dynamics of adaptive responses to olfactory threats and may have implications for understanding fear-related disorders.
Comparative framework and adaptation of ACME HS approach to single cell isolation from fresh-frozen endocrine tissues
Authors: Utkina Marina , Shcherbakova Anastasia , Deviatiiarov Ruslan , Ryabova Alina , Loguinova Marina , Trofimov Valentin , Kuznetsova Anna , Petropavlovskiy Mikhail , Salimkhanov Rustam , Maksimov Denis , Albert Eugene , Golubeva Alexandra , Asaad Walaa , Urusova Lilia , Bondarenko Ekaterina , Lapshina Anastasia , Shutova Alexandra , Beltsevich Dmitry , Gusev Oleg , Dzeranova Larisa , Melnichenko Galina , Minniakhmetov Ildar , Dedov Ivan , Mokrysheva Natalya , Popov Sergey
Published: March 2024

Current scRNA-seq studies of solid tissues mostly rely on enzymatic dissociation of fresh samples or the fallback on nuclei isolation from frozen or partially fixed samples. However, due to the complex tissue organization or cell fragility, it could be challenging to apply these approaches to the sensitive endocrine tissues. That is, dissociating intact cells from such problematic fresh-frozen samples routinely collected by biobanks remains challenging.

In this study, we adapted the acetic-methanol dissociation method – ACME High Salt (ACME HS) to effectively isolate intact single cells from fresh-frozen endocrine tumor samples, including adrenal gland neoplasms, thyroid carcinomas, and pituitary neuroendocrine tumors. We compared the ability of enzymatic, ACME HS, and nuclear isolation methods to preserve the integrity of major cell types and gene expression across 41 tissue samples of different origins. We demonstrated that ACME HS simultaneously dissociates and fixes cells, thus preserving morphology and a high RNA integrity number in problematic cell types. This finding renders the ACME HS dissociation method a valuable alternative in scRNA-seq protocols for challenging tissues where obtaining live cell suspension is difficult or impossible.
Volume Electron Microscopy Analysis of Synapses in Associative and Primary Regions of the Human Cerebral Cortex
Authors: Cano-Astorga Nicolás , Plaza-Alonso Sergio , DeFelipe Javier , Alonso-Nanclares Lidia
Published: March 2024

Functional and structural studies investigating macroscopic connectivity in the human cerebral cortex suggest that high-order associative regions exhibit greater connectivity compared to primary ones. However, the synaptic organization of these brain regions remains unexplored due to the difficulties involved in studying the human brain at the nanoscopic level. In the present work, we conducted volume electron microscopy to investigate the synaptic organization of the human brain obtained at autopsy. Specifically, we examined layer III of Brodmann areas 17, 3b, and 4, as representative areas of primary visual, somatosensorial, and motor cortex. Additionally, we conducted comparative analyses with our previous synaptic datasets of layer III from temporopolar and anterior cingulate associative cortical regions (Brodmann areas 24, 38, and 21). 9,690 synaptic junctions were 3D reconstructed, showing that certain synaptic characteristics appeared to be specific to particular cortical regions. The number of synapses per volume, the proportion of the postsynaptic targets, and the synaptic size may distinguish one region from another, regardless of whether they are associative or primary cortex. By contrast, other synaptic characteristics were common to all analyzed regions, such as the proportion of excitatory and inhibitory synapses, their shapes, their spatial distribution, and a higher proportion of synapses located on dendritic spines. These observations may be included within the general rules of synaptic organization of the human cerebral cortex. The present results on nanoscopic characteristics of synapses provide further insights into the structural design of the human cerebral cortex.

Significance statement

Structural and functional studies investigating macroscopic connectivity in the human cerebral cortex have suggested that high-order associative regions exhibit greater connectivity compared to primary ones. However, the synaptic organization of these brain regions remains unexplored. Here, thousands of synaptic junctions were 3D reconstructed in associative and primary cortical regions. We found that certain synaptic characteristics appeared to be specific to particular cortical regions —regardless of whether they are associative or primary cortex— whereas others were common to all analyzed regions. The present results provide further insights into the structural design of the human cerebral cortex.
Anabolic lipid metabolism regulates adipose type 2 innate lymphoid cell differentiation to maintain metabolic health
Authors: Theodorou Maria Rafailia , Yu Jiangyan , Nikolka Fabian , Zurkovic Jelena , Wientjens Chantal , Weiss Patricia , Rombo Roman , Karagiannis Fotios , Thiele Christoph , Hasenauer Jan , Hiller Karsten , Wilhelm Christoph
Published: March 2024

Group 2 innate lymphoid cells (ILC2) residing in the adipose tissue play an important role in maintaining the metabolic health and energy balance of the organisms. In obesity ILC2 numbers are reduced and their function is impaired, leading to the progression of metabolic inflammation. However, which events impact on ILC2 biology in the adipose tissue in obesity remains unresolved. Here, we find that high fat diet (HFD)-induced obesity in mice results in the metabolic reprogramming of adipose ILC2, impairing mitochondrial function and the expression of the enzyme Acetyl-CoA carboxylase 1 (ACC1). Investigating a possible connection between ACC1 and obesity-induced changes in ILC2, we show that fatty acids directly reduce the expression of ACC1, while pharmacological inhibition of ACC1 diminishes mitochondrial function and ILC2 metabolism. Furthermore, deletion of ACC1 in ILC2 phenocopies the overall reduction and functional impairment of ILC2 observed in obesity, which ultimately leads to increased triglycerides in circulation, adipose tissue hypertrophy and inflammation, even in the absence of HFD. Through single-cell RNA sequencing analysis we uncover that HFD-feeding or deletion of ACC1 results in the accumulation of undifferentiated ILC2 and ILC progenitors in the adipose tissue, suggesting that ACC1 may primarily regulate the maturation of ILC2. Together, these results reveal that obesity could predominately impair adipose ILC2 differentiation and activation by impacting on the expression of ACC1, rather than inducing cell death through lipid overload and lipotoxicity.
Plasma cell heterogeneity is driven by type of immune challenge
Authors: Khamyath Mélanie , Lereclus Emilie , Gourhand Vanessa , Debureaux Pierre-Edouard , Moulin Clémentine , Gary Hélène , Bachelerie Françoise , Balabanian Karl , Espéli Marion , Bonaud Amélie
Published: March 2024

Plasma cells play an essential role in humoral immunity, but many questions remain regarding the heterogeneity of this population, both in terms of ontogeny and involvement in the immune response. In this work, we have identified 5 subsets of plasma cells in human and mouse lymphoid tissues. These subpopulations were distinguished by differential expression of CD62L, CXCR4, FcγRIIb and CD93. The antigenic context as well as the B cell of origin directed plasma cell differentiation towards specific subtypes that display distinct migratory and survival abilitiesin vivo. Altogether, ours results unveil that plasma cell phenotypic and functional heterogeneity relies on intrinsic imprinting during B cell activation.
Model-based frequency-and-phase correction of1H MRS data with 2D linear-combination modeling
Authors: Simicic Dunja , Zöllner Helge J. , Davies-Jenkins Christopher W. , Hupfeld Kathleen E. , Edden Richard A. E. , Oeltzschner Georg
Published: March 2024

Purpose

Retrospective frequency-and-phase correction (FPC) methods attempt to remove frequency- and-phase variations between transients to improve the quality of the averaged MR spectrum. However, traditional FPC methods like spectral registration struggle at low SNR. Here, we propose a method that directly integrates FPC into a two-dimensional linear-combination model (2D-LCM) of individual transients (‘model-based FPC’). We investigated how model-based FPC performs compared to the traditional approach, i.e., spectral registration followed by 1D-LCM in estimating frequency-and-phase drifts and, consequentially, metabolite level estimates.

Methods

We created synthetic in-vivo-like 64-transient short-TE sLASER datasets with 100 noise realizations at 5 SNR levels and added randomly sampled frequency and phase variations. We then used this synthetic dataset to compare the performance of 2D-LCM with the traditional approach (spectral registration, averaging, then 1D-LCM). Outcome measures were the frequency/phase/amplitude errors, the standard deviation of those ground-truth errors, and amplitude Cramér Rao Lower Bounds (CRLBs). We further tested the proposed method on publicly available in-vivo short-TE PRESS data.

Results

2D-LCM estimates (and accounts for) frequency-and-phase variations directly from uncorrected data with equivalent or better fidelity than the conventional approach. Furthermore, 2D-LCM metabolite amplitude estimates were at least as accurate, precise, and certain as the conventionally derived estimates. 2D-LCM estimation of frequency and phase correction and amplitudes performed substantially better at low-to-very-low SNR.

Conclusion

Model-based FPC with 2D linear-combination modeling is feasible and has great potential to improve metabolite level estimation for conventional and dynamic MRS data, especially for low-SNR conditions, e.g., long TEs or strong diffusion weighting.
Real-time transcriptomic profiling in distinct experimental conditions
Authors: Butto Tamer , Pastore Stefan , Müller Max , Iyer Kaushik Viswanathan , Mündnich Stefan , Wierczeiko Anna , Friedland Kristina , Helm Mark , Winz Marie-Luise , Gerber Susanne
Published: March 2024

Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis in rapid quality control for long-read RNA-seq. We illustrate its utility through three experimental setups: 1) transcriptome profiling of distinct human cellular populations, 2) identification of experimentally enriched transcripts, and 3) identification of experimentally manipulated genes (knockout and overexpression) in several yeast strains. We show how to perform multiple layers of quality control as soon as sequencing has started, addressing both the quality of the experimental and sequencing traits. Real-time quality control measures assess sample/condition variability and determine the number of identified genes per sample/condition. Furthermore, real-time differential gene/transcript expression analysis can be conducted at various time points post-sequencing initiation (PSI), revealing dynamic changes in gene/transcript expression between two conditions. Using real-time analysis, which occurs in parallel to the sequencing run, we identified differentially expressed genes/transcripts as early as 1-hour PSI. These changes were consistently observed throughout the entire sequencing process. We discuss the new possibilities offered by real-time data analysis, which have the potential to serve as a valuable tool for rapid and cost-effective quality checks in specific experimental settings and can be potentially integrated into clinical applications in the future.
Junctional Adhesion Molecule (JAM)-C recruitment of Pard3 and drebrin to cell contacts initiates neuron-glia recognition and layer-specific cell sorting in developing cerebella
Authors: Hallada Liam P. , Shirinifard Abbas , Solecki David J
Published: March 2024

Sorting maturing neurons into distinct layers is critical for brain development, with disruptions leading to neurological disorders and pediatric cancers. Lamination coordinates where, when, and how cells interact, facilitating events that direct migrating neurons to their destined positions within emerging neural networks and control the wiring of connections in functional circuits. While the role of adhesion molecule expression and presentation in driving adhesive recognition during neuronal migration along glial fibers is recognized, the mechanisms by which the spatial arrangement of these molecules on the cell surface dictates adhesive specificity and translates contact-based external cues into intracellular responses like polarization and cytoskeletal organization remain largely unexplored. We used the cerebellar granule neuron (CGN) system to demonstrate that JAM-C receptor cis-binding on the same cell and trans-binding to neighboring cells controls the recruitment of the Pard3 polarity protein and drebrin microtubule-actin crosslinker at CGN to glial adhesion sites, complementing previous studies that showed Pard3 controls JAM-C exocytic surface presentation. Leveraging advanced imaging techniques, specific probes for cell recognition, and analytical methods to dissect adhesion dynamics, our findings reveal: 1) JAM-C cis or trans mutants result in reduced adhesion formation between CGNs and cerebellar glia, 2) these mutants exhibit delayed recruitment of Pard3 at the adhesion sites, and 3) CGNs with JAM-C mutations experience postponed sorting and entry into the cerebellar molecular layer (ML). By developing a conditional system to image adhesion components from two different cells simultaneously, we made it possible to investigate the dynamics of cell recognition on both sides of neuron-glial contacts and the subsequent recruitment of proteins required for CGN migration. This system and an approach that calculates local correlation based on convolution kernels at the cell adhesions site revealed that CGN to CGN JAM recognition preferentially recruits higher levels of Pard3 and drebrin than CGN to glia JAM recognition. The long latency time of CGNs in the inner external germinal layer (EGL) can be attributed to the combined strength of CGN-CGN contacts and the less efficient Pard3 recruitment by CGN-BG contacts, acting as gatekeepers to ML entry. As CGNs eventually transition to glia binding for radial migration, our research demonstrates that establishing permissive JAM-recognition sites on glia via cis and trans interactions of CGN JAM-C serves as a critical temporal checkpoint for sorting at the EGL to ML boundary. This mechanism integrates intrinsic and extrinsic cellular signals, facilitating heterotypic cell sorting into the ML and dictating the precise spatial organization within the cerebellar architecture.

Graphical Abstract
Maternal characteristics and their relation to early mother-child interaction and cognitive development in toddlers
Authors: Preiß Jasmin , Lang Adelheid , Hauser Theresa , Angerer Monika , Schernhardt Peter , Schabus Manuel
Published: March 2024

Early mother-infant interaction is believed to have a significant impact on the social, cognitive, and emotional development of children. These interactions are not only influenced by child and contextual factors but also by the mother’s personality traits and strain. In this study, we investigated the relation between maternal factors such as personality, depressive symptoms, or experiencing of emotions, with (i) children’s early cognitive development and (ii) interaction patterns in a sample of 116 mother-child dyads (mean child age = 18.63 months ± 6.42). Maternal factors were assessed using standardized questionnaires, children’s cognitive development was measured using the Bayley Scales of Infant and Toddler Development, and interaction patterns were evaluated using the CARE-Index. The study found that children of mothers who scored higher in agreeableness performed better in cognitive assessments. Additionally, our analysis revealed statistical trends indicating that mothers with higher levels of conscientiousness tended to be less unresponsive in the interaction with their infants, while those with higher levels of neuroticism were more likely to exhibit compulsive behavior in their toddlers. Additionally, there was a trend indicating that maternal depression was associated with increased maternal controlling behavior towards toddlers. Finally, mothers who placed significant importance on their bodily signals to assess their overall well-being had higher scores in the quality of interaction with their child. Overall, these findings show the intricate relation between maternal behavior and state with dyadic interaction quality. This should underline that optimal infant development is only possible if mothers are well supported especially if in need due to various burdens such as depressive symptoms.
Harnessing the Power of Large Language Models (LLMs) to Unravel the Influence of Genes and Medication on Biological Processes of Wound Healing*
Authors: Jui Jayati H. , Hauskrecht Milos
Published: March 2024

Recent advancements in Large Language Models (LLMs) have ushered in a new era for knowledge extraction in the domains of biological and clinical natural language processing (NLP). In this research, we present a novel approach to understanding the regulatory effects of genes and medications on biological processes central to wound healing. Utilizing the capabilities of Generative Pre-trained Transformer (GPT) models by OpenAI, specifically GPT-3.5 and GPT-4, we developed a comprehensive pipeline for the identification and grounding of biological processes and the extraction of such regulatory relations. The performances of both GPTs were rigorously evaluated against a manually annotated corpus of 104 PubMed titles, focusing on their ability to accurately identify and ground biological process concepts and extract relevant regulatory relationships from the text. Our findings demonstrate that GPT-4, in particular, exhibits superior performance in all the tasks, showcasing its potential to facilitate significant advancements in biomedical research without requiring model fine-tuning.
Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity
Authors: Fanari Oleksandra , Tavakoli Sepideh , Qiu Yuchen , Makhamreh Amr , Nian Keqing , Akeson Stuart , Meseonznik Michele , McCormick Caroline A. , Bloch Dylan , Gamper Howard , Jain Miten , Hou Ya-Ming , Wanunu Meni , Rouhanifard Sara H.
Published: March 2024

Chemical modifications in mRNAs, such as pseudouridine (psi), can control gene expression. Yet, we know little about how they are regulated, especially in neurons. We applied nanopore direct RNA sequencing to investigate psi dynamics in SH-SY5Y cells in response to two perturbations that model a natural and unnatural cellular state: retinoic-acid-mediated differentiation (healthy) and exposure to the neurotoxicant, lead (unhealthy). We discovered that the expression of some psi writers change significantly in response to physiological conditions. We also found that globally, lead-treated cells have more psi sites but lower relative occupancy than untreated cells and differentiated cells. Interestingly, examples of highly plastic sites were accompanied by constant expression for psi writers, suggesting trans-regulation. Many positions were static throughout all three cellular states, suggestive of a “housekeeping” function. This study enables investigations into mechanisms that control psi modifications in neurons and its possible protective effects in response to cellular stress.
Differential Non-Coding RNA Profiles for Lung Cancer Early Detection in African and White Americans
Authors: Gao Lu , Dhilipkannah Pushpa , Holden Van K , Deepak Janaki , Sachdeva Ashutosh , Todd Nevins W , Stass Sanford A , Jiang Feng
Published: March 2024

Introduction

Lung cancer leads in cancer-related deaths. Disparities are observed in lung cancer rates, with African Americans (AAs) experiencing disproportionately higher incidence and mortality compared to other ethnic groups. Non-coding RNAs (ncRNAs) play crucial roles in lung tumorigenesis. Our objective was to identify ncRNA biomarkers associated with the racial disparity in lung cancer.

Methods

Using droplet digital PCR, we examined 93 lung-cancer-associated ncRNAs in the plasma and sputum samples from AA and White American (WA) participants, which included 118 patients and 92 cancer-free smokers. Subsequently, we validated our results with a separate cohort comprising 56 cases and 72 controls.

Results

In the AA population, plasma showed differential expression of ten ncRNAs, while sputum revealed four ncRNAs when comparing lung cancer patients to the control group. In the WA population, the plasma displayed eleven ncRNAs, and the sputum had five ncRNAs showing differential expression between the lung cancer patients and the control group. For AAs, we identified a three-ncRNA panel (plasma miRs-147b, 324-3p, 422a) diagnosing lung cancer in AAs with 86% sensitivity and 89% specificity. For WAs, a four-ncRNA panel was developed, comprising sputum miR-34a-5p and plasma miRs-103-3p, 126-3p, 205-5p, achieving 88% sensitivity and 87% specificity. These panels remained effective across different stages and histological types of lung tumors and were validated in the independent cohort.

Conclusions

The ethnicity-related ncRNA signatures have promise as biomarkers to address the racial disparity in lung cancer.
Early high-sensitivity troponin elevation in predicting short-term mortality in sepsis: A protocol for a systematic review with meta-analysis
Authors: Ferrière-Steinert Santiago , Jiménez Joaquín Valenzuela , Araya Sebastián Heskia , Carvajal Thomas Kouyoumdjian , Ramos-Rojas José , Gajardo Abraham I. J.
Published: March 2024

Background

Sepsis is a common admission diagnosis in the intensive care unit (ICU). The Sepsis-3 consensus associates sepsis diagnosis with acute organ dysfunction. In these patients troponin elevation is a well-established phenomenon, but its clinical significance is not settled, as no systematic review has addressed the prognostic significance of the increasingly prevalent high-sensitivity troponin assays in acute organ dysfunction setting.

This study aims to clarify the association between early serum troponin levels in high-sensitivity assays with short-term mortality risk in septic patients with acute organ dysfunction.

Methods

We will systematically search PubMed, Scopus and Embase for original articles; additionally, a manual search will be carried out through relevant literature. Generally, studies will be deemed eligible for inclusion if they evaluate the association between high-sensitivity troponin in the first 24 hours of admission and ICU, 30-days, or In-hospital mortality; in patients with septic shock or sepsis related to acute organ dysfunction. Two reviewers will independently select studies and extract the data. A meta-analysis for mortality outcome will be performed for comparative data regarding two effect measures: Odd ratios and Standardized Mean differences.

Discussion

This study will provide further evidence about the role of high-sensitivity troponin assays in predicting mortality in septic patients; potentially helping to guide further research and yielding valuable information for patient assessment.

Conclusion about the certainty of evidence will be presented in a ‘Summary of finding’ table.

PROSPERO registration:(CRD42024468883)
Evaluating Magnetic Stimulation as an Innovative Approach for Treating Dry Eye Syndrome: Safety and Efficacy Initial study
Authors: Ben-Eli Hadas , Perelman Shimon , Wajnsztajn Denise , Solomon Abraham
Published: March 2024

Objective

The objective of this study was to assess the safety and preliminary efficacy of repetitive magnetic stimulation (RMS) as an intervention for dry eye syndrome, focusing on symptom reduction.

Methodology

This investigation involved 22 adult participants diagnosed with moderate to severe dry eye syndrome. These individuals were subjected to RMS treatment targeting one or both eyes using the VIVEYE - Ocular Magnetic Neurostimulation System Ver 1.0 (Epitech-Mag LTD; NIH clinical trials registry #NCT03012698). A placebo-controlled group was also included for comparative analysis, with all subjects being monitored over a three-month period. The evaluation of safety encompassed monitoring changes in best corrected visual acuity, ocular pathology, and reporting of adverse events. Participant tolerance was gauged through questionnaires, measurements of intraocular pressure (IOP), Schirmer’s test, and vital signs. The efficacy of the treatment was assessed by comparing pre- and post-treatment scores on fluorescein staining (according to the National Eye Institute (NEI) grading) and patient-reported outcomes.

Results

The study found no significant changes in visual acuity, IOP, or Schirmer’s test results between the RMS-treated and control groups (p<0.05), indicating RMS does not adversely affect these ocular functions. However, RMS treatment was associated with improved tear film stability (p=0.198 vs. p=0.045) and corneal health (p=0.52 vs. p=0.004), with no improvements in the control group. Initial symptom improvement was observed in both RMS-treated and placebo groups (p=0.007 vs p=0.008), suggesting RMS’s potential for treating ocular surface conditions.

Conclusion

The findings of this study introduce repetitive magnetic stimulation (RMS) as a promising therapeutic option for dry eye syndrome, demonstrating its capability to promote corneal epithelium repair, enhance tear film stability, and improve subjective symptom evaluations without adversely affecting intraocular pressure, visual acuity, or tear production. This confirms the safety and suggests the efficacy of RMS therapy for dry eye conditions.
Distinct Motor Map Characteristics for Biceps and Triceps Muscles in Persons with Chronic Tetraplegia: Implications for Arm Function
Authors: Liu Jia , O’laughlin Kyle , Forrest Gail F. , Arora Tarun , Nemunaitis Gregory , Cunningham David , Kirshblum Steven , Pundik Svetlana , Baker Kelsey , Bryden Anne , Kilgore Kevin , Bethoux Francois , Wang Xiaofeng , Henzel M. Kristi , Brihmat Nabila , Bayram Mehmed Bugrahan , Plow Ela B.
Published: March 2024

Following spinal cord injury (SCI), intact neural resources undergo widespread reorganization within the brain. Animal models reveal motor cortical representations devoted to spared muscles above injury expand at the expense of territories occupied by weaker muscles. In this study, we investigated whether motor representations are similarly reorganized between a relatively spared biceps muscle and a weakened triceps muscle in persons with chronic tetraplegia following traumatic cervical SCI in association with upper limb motor function. Twenty-four adults with cervical SCI and 15 able-bodied participants underwent motor mapping using transcranial magnetic stimulation. We determined following map characteristics: area, amplitude (maximal motor evoked potential and volume), and center of gravity. Maximal voluntary contraction (MVC) and motor function (Capabilities of the Upper Extremity Test or CUE-T) were also assessed. Findings reveal that participants with SCI had hyper-excitable biceps maps than triceps, and hyper-excitable biceps maps also compared to biceps maps in able-bodied participants. Higher amplitude of biceps and triceps maps was associated with better motor function (higher CUE-T) and more distal injury (i.e., more spared segments) in persons with SCI. Amplitudes of biceps but not the triceps maps were associated with higher muscle MVCs. In conclusion, over-excitable biceps than triceps map in SCI may represent deafferentation plasticity. For the first time, we demonstrate how map reorganization of spared and weaker muscles in persons with chronic cervical SCI is associated with upper limb motor status. Use-dependent mechanisms may shift neural balance in favor of spared muscles, supporting potential use as response biomarkers in rehabilitation studies.

New & Noteworthy

Our study reports evidence in humans with cervical SCI that motor representation for the relatively spared muscle becomes hyper-excitable compared to that for the weaker muscle to the extent that hyper-excitability is even higher compared to biceps maps in uninjured individuals. Use-dependent mechanisms likely favor such heightened excitability of spared maps. For the first time, we demonstrate clinical relevance of map excitability in humans with SCI, supporting potential use as a biomarker of recovery.
The Role of Morphological Adaptability inVibrio cholerae’s Motility and Pathogenicity
Authors: Xu Jun , Abe Keigo , Kodama Toshio , Sultana Marzia , Chac Denise , Markiewicz Susan M. , Kuba Erika , Tsunoda Shiyu , Alam Munirul , Weil Ana A. , Nakamura Shuichi , Yamashiro Tetsu
Published: March 2024

Vibrio cholerae, the etiological agent of cholera, exhibits remarkable adaptability to different environmental conditions by undergoing morphological changes that significantly contribute to its pathogenicity and impact the epidemiology of the disease globally. This study investigates the morphological adaptability of the clinically isolatedV. choleraeO1 strain, specifically focusing on the motility and pathogenicity differences between the filamentous and original comma-shaped forms within diverse viscosity conditions. Utilizing the El Tor strain ofV. choleraeO1, we induced the transformation into the filamentous form and performed a comparative analysis with the canonical comma-shaped morphology. Our approach involved assessing motility patterns, swimming speeds, rotation rates, kinematics, and reversal frequencies through dark-field microscopy and high-speed imaging techniques. The findings reveal that filamentousV. choleraecell retains enhanced motility in viscous environments. This suggests an evolutionary adaptation enabling survival across a range of habitats, notably the human gastrointestinal tract. Filamentous forms demonstrated increased reversal behavior at mucin interfaces, hinting at an advantage in penetrating the mucus layer. Rabbit intestinal loop assays further showed that both morphological forms exhibit similar fluid accumulation ratios, thus indicating comparable pathogenic potentials. These results underscore the significance ofV. cholerae’s morphological flexibility in adapting to environmental viscosity changes, shedding light on the bacterium’s intricate survival and infection strategies. Our study provides critical insights into the dynamics of cholera, underlining the importance of considering bacterial morphology in developing effective cholera control strategies.
Inhibitory KIRs decrease HLA class II-mediated protection in Type 1 Diabetes
Authors: Bitria Laura Mora , Debebe Bisrat J. , Miners Kelly , Ladell Kristin , Kaur Charandeep , Traherne James A. , Jiang Wei , Hadcocks Linda , McQuibban Nicholas A.R. , Trowsdale John , Wong F Susan , Pontikos Nikolas , Niederalt Christoph , Asquith Becca
Published: March 2024

Inhibitory killer cell immunoglobulin-like receptors (iKIRs) are a family of inhibitory receptors that are expressed by natural killer cells and late-stage differentiated T cells. There is accumulating evidence that iKIRs regulate T cell-mediated immunity. Recently, we reported that T cell-mediated control was enhanced by iKIRs in chronic viral infections. We hypothesized that in the context of autoimmunity, where an enhanced T cell response might be considered detrimental, iKIRs would have an opposite effect. We studied Type 1 diabetes (T1D) as a paradigmatic example of autoimmunity. In T1D, variation in the Human Leucocyte Antigen (HLA) genes explains up to 50% of the genetic risk, indicating that T cells have a major role in T1D etiopathogenesis. To investigate if iKIRs affect this T cell response we asked whether HLA associations were modified by iKIR genes. We conducted an immunogenetic analysis of a case-control T1D dataset (N= 11,961) and found that iKIR genes, in the presence of genes encoding their ligands, have a consistent and significant effect on protective HLA class II genetic associations. Our results were validated in an independent data set. We conclude that iKIRs significantly decrease HLA class II protective associations and suggest that iKIRs regulate CD4+ T cell responses in T1D.
Role of the NOS-cGMP pathways in time-dependent sensitization of behavioral responses in zebrafish
Authors: de Sousa Eveline Bezerra , Heymbeeck João Alphonse Apóstolo , Feitosa Leonardo Miranda , Xavier Amanda Gabriele Oliveira , Campos Kimberly dos Santos , dos Santos Rodrigues Lais do Socorro , de Freitas Larissa Mota , do Carmo Silva Rhayra Xavier , Ikeda Saulo Rivera , Silva Suellen de Nazaré dos Santos , Rocha Sueslene Prado , do Nascimento Wilker Leite , Moraes Edinaldo Rogério da Silva , Leão Luana Ketlen Reis , Herculano Anderson Manoel , Maximino Caio , Pereira Antonio , Lima-Maximino Monica
Published: March 2024

Nitric oxide (NO) is a molecule involved in plasticity across levels and systems. The role of NOergic pathways in time-dependent sensitization, a behavioral model of translational relevance to trauma and stress-related disorders, was assessed in adult zebrafish. In this model, adult zebrafish acutely exposed to a fear-inducing conspecific alarm substance (CAS) and left undisturbed for an incubation period show increased anxiety-like behavior 24 h after exposure. CAS increased forebrain glutamate immediately after stress and 30 min after stress, an effect that was accompanied by increased nitrite levels immediately after stress, 30 min after stress, 90 min after stress, and 24 h after stress. CAS also increased nitrite levels in the head kidney, where cortisol is produced in zebrafish. CAS-elicited nitrite responses in the forebrain 90 min (but not 30 min) after stress were prevented by a NOS-2 blocker. Blocking NOS-1 30 min after stress prevents TDS; blocking NOS-2 90 min after stress also prevents TDS, as does blocking calcium-activated potassium channels in this latter time window. TDS is also prevented by blocking guanylate cyclase activation in both time windows, and cGMP-dependent channel activation in the second time window. These results suggest that different NO-related pathways converge at different time windows of the incubation period to induce TDS.
Navigating Human Astrocyte Differentiation: Direct and Rapid one-step Differentiation of Induced Pluripotent Stem Cells to Functional Astrocytes Supporting Neuronal Network development
Authors: Schuurmans Imke M.E. , Mordelt Annika , Linda Katrin , Puvogel Sofia , Duineveld Denise , Hommersom Marina P. , Rahm Lisa , Dyke Emma , Scholten Gijs-Jan , Knorz Caroline , Oudakker Astrid , van Bokhoven Hans , de Witte Lot D. , van Karnebeek Clara D.M. , Garanto Alejandro , Kasri Nael Nadif
Published: March 2024

Astrocytes play a pivotal role in neuronal network development. Despite the well-known role of astrocytes in the pathophysiology of neurologic disorders, the utilization of human induced pluripotent stem cell (hiPSC)-derived astrocytes in neuronal networks remains limited. Here, we present a streamlined one-step protocol for the differentiation of hiPSCs directly into functional astrocytes without the need for ectopic gene expression or neural progenitor cell generation. We found that culturing hiPSCs directly in commercial astrocyte medium, was sufficient to differentiate hiPSCs into functional astrocytes within five weeks. Validation to varying extents across thirty hiPSC-lines demonstrated consistent astrocyte differentiation with minimal batch-to-batch variability. We confirmed astrocyte identity and functionality of the hiPSC-astrocyte monocultures by immunofluorescence, flowcytometry, RNA sequencing, glutamate uptake assays and calcium signaling recordings. Optimization of the protocol enabled co-culture of hiPSC-astrocytes with Ngn2 hiPSC-derived neurons (iNeurons), promoting neuronal differentiation and synapse formation. Lastly, we used single-cell electrophysiology and multi-electrode arrays to confirm robust neuronal network development in 5-week-old hiPSC-astrocyte and iNeuron co-cultures. This protocol offers a rapid and efficient method to establish all-human astrocyte-neuron co-cultures, facilitating the investigation of cell-type-specific contributions to disease pathogenesis. While validated across multiple hiPSC lines, we actively encourage researchers to test and provide feedback on this protocol to enhance its validation for future iterations.
Mitogenomics, phylogenetic position, and updated distribution ofErgasilus kandti, an ergasilid copepod parasitizing African cichlid fishes
Authors: Jansen Dries , Vanhove Maarten P. M. , Makasa Lawrence , Vorel Jiří , Kmentová Nikol , Cruz-Laufer Armando J.
Published: March 2024

Ergasilidae are a family of globally distributed copepods parasitizing freshwater fish. Despite their widespread occurrence, their phylogeographic patterns are poorly understood, specifically in the African Great Lakes. Here, we aim to provide an update on distribution ofErgasilus kandti,a copepod species infectingTylochromis polylepis,an endemic cichlid fish species in Lake Tanganyika, and the phylogenetic relationship of African ergasilids. We present the first record ofE. kandtiparasitizing the gills ofT. polylepisin Lake Tanganyika proper, identified through light microcopy and, for the first time for any ergasilid, confocal laser scanning microscopy. We suggest that this technique adds spatial context to characters and are hardly visible while using light microscopy. Phylogenetic analyses based on ribosomal DNA fragments suggest two monophyletic groups of African ergasilids. However, the phylogenetic relationships ofErgasilusremain unresolved, possibly because of the insufficient resolution of these widely used phylogenetic markers and low taxonomic coverage. A comparison of ergasilid mitochondrial genomes highlights traits found in other parasite lineages including genome shrinkage and low evolutionary rates of thecox1gene. This study presents the most extensive molecular characterization of any ergasilid species to date.
Independent size regulation of bones and appendages in zebrafish
Authors: Aramaki Toshihiro , Kondo Shigeru
Published: March 2024

Vertebrate appendages vary in length among species, despite a low divergence in bone configuration. In this study, we assessed whether the total sizes of anatomical features are constrained by the lengths of individual bones during development. We examined size control by expressing mutant genes related to allometric growth in zebrafish fins under cell type-specific promoters. Hyperactive potassium channel (kcnk5bW169L) or dominant-negative gap junction protein connexin (Cx43T154A) expression in epidermal cells increased or decreased fin size, respectively, but did not influence the lengths of fin bone segments. Osteoblast expression of these mutant genes altered fin bone segment length but not total fin size. The combination of kcnk5bW169Lin epidermal cells and Cx43T154Ain osteoblasts resulted in transgenic fish with large fins and short bone segments, and vice versa. These results clearly indicate that fin size and bone segment length are determined separately by independent regulatory systems, despite the use of the same genes. These findings shed new light on the evolution of allometric traits.