bluuebunny/crossref_metadata_2025 huggingface dataset:
Management and outcomes of chemotherapy-associated pneumoperitoneum in cancer patients: a scoping review protocol
Authors: Maina Renee M. , Rader Caroline A. , Kypa Jeevan , Jasmin Hilary M. , Asahngwa Constantine , Muenyi Clarisse S. , Foretia Denis A.
Published: September 2023

Introduction:

Pneumoperitoneum – free air within the peritoneal cavity – is often the result of bowel perforation, though other causes include residual postprocedural or postoperative air and barotrauma. In non-cancer patients, operative intervention is often required. Cancer patients, on the other hand, present a unique set of challenges as they usually have elevated risk of pneumoperitoneum from local radiation therapy, frequent endoscopic procedures, and tumor invasion. Factors such as malnutrition, neutropenia, chemotherapy, and steroid use make emergent surgery tenuous in cancer patients. There is a paucity of published literature on the management of pneumoperitoneum in patients actively undergoing chemotherapy. The main objective of this scoping review is to assess the presentation, management, and subsequent outcomes of this unique patient population.

Materials and Methods:

The authors will utilize the framework for performing scoping reviews as outlined by Arksey and O’Malley. They will perform the search for articles in three electronic databases (i.e. SCOPUS, PubMed, Embase) and relevant gray literature. Only articles available in English and published between 1999 and 2022 will be included. Inclusion criteria will be a known diagnosis of cancer, chemotherapy within 6 months of presentation, and imaging confirmation of pneumoperitoneum. Exclusion criteria will be cancer diagnosis at the time of presentation, perforation secondary to cancer itself, and chemotherapy greater than 6 months prior to presentation. A tailored extraction frame to extract relevant information from published articles that meet our inclusion criteria. The data using both descriptive statistics and thematic analysis of the main study questions.

Ethics and Dissemination:

Since the authors will not be collecting primary data, formal ethical approval is not required. They study findings will be disseminated through abstracts, conference presentations, and peer-reviewed publications.
Development of LIBRA-seq for the Guinea Pig Model System as a Tool for the Evaluation of Antibody Responses to Multivalent HIV-1 Vaccines
Authors: Vukovich Matthew J. , Raju Nagarajan , Kgagudi Prudence , Manamela Nelia P. , Abu-Shmais Alexandra A. , Gripenstraw Kathryn R. , Wasdin Perry T. , Shen Shaunna , Dwyer Bridget , Akoad Jumana , Lynch Rebecca M. , Montefiori David C. , Richardson Simone I. , Moore Penny L. , Georgiev Ivelin S.
Published: September 2023

Consistent elicitation of serum antibody responses that neutralize diverse clades of HIV-1 remains a primary goal of HIV-1 vaccine research. Prior work has defined key features of soluble HIV-1 Envelope (Env) immunogen cocktails that influence the neutralization breadth and potency of multivalent vaccine-elicited antibody responses including the number of Env strains in the regimen. We designed immunization groups that consisted of different numbers of Env strains to be used in a cocktail immunization strategy: the smallest cocktail (group 2) consisted of a set of two Env strains, which were a subset of the three Env strains that made up group 3, which in turn were a subset of the six Env strains that made up group 4. Serum neutralizing titers were broadest in guinea pigs that were immunized with a cocktail of three Envs compared to cocktails of two and six, suggesting that multivalent Env immunization provides a benefit but may be detrimental when the cocktail size is too large. We then adapted the LIBRA-seq platform for antibody discovery to be compatible with guinea pigs, and isolated several tier 2 neutralizing monoclonal antibodies. Three antibodies isolated from two separate guinea pigs were similar in their gene usage and CDR3s, establishing evidence for a guinea pig public clonotype elicited through vaccination. Taken together, this work investigated multivalent HIV-1 Env immunization strategies and provides a novel methodology for screening guinea pig B cell receptor antigen specificity at a high throughput level using LIBRA-seq.

IMPORTANCE

Multivalent vaccination with soluble Env immunogens is at the forefront of HIV-1 vaccination strategies, but little is known about the influence of the number of Env strains included in vaccine cocktails. Our results suggest that adding more strains is sometimes beneficial but may be detrimental when the number of strains is too high. Additionally, we adapted the LIBRA-seq platform to be compatible with guinea pig samples and isolated several tier 2 neutralizing monoclonal antibodies, some of which share V and J gene usage and >80% CDR3 identity, thus establishing the existence of public clonotypes in guinea pigs elicited through vaccination.
Poly ADP-ribosylation regulatesArcexpression and promotes adaptive stress-coping
Authors: Dahan Eliyahu , Taub Tze’ela , Pergamenchik Leah , Vovk Arthur , Manier Jade , Avneri Raphael , Lax Elad
Published: September 2023

Rapid adaptation to stressful events is essential for survival and requires acute stress response and stress-coping strategy. Yet, the molecular mechanisms that govern this coping strategy have to be fully discovered. Poly ADP-ribosylation (PARylation) is a post-translational protein modification that plays a vital role in histone modification following neuronal activity and is required for long-term memory formation. Previous studies showed that inhibiting Parp1, the primary enzyme that catalyzes poly ADP-ribose polymers (PAR), impairs long-term memory formation. However, the target genes of Parp1-induced PARylation following acute stress are unknown. Here, we showed that the forced swim test, a well-established acute stress paradigm, induced elevated cortical PARylation and increased the expression of activity-dependent genes in mice. Systemic pharmacological Parp1 inhibition with ABT888 (Veliparib), impaired stress-coping in a second forced swim test done 24 hours later as measured by diminished immobility response. This effect was associated with reduced PARylation of Arc promoter and reduced Arc expression, 1 hour after Parp1 inhibition, suggesting Arc PARylation regulates its expression and hence successful stress-coping behavior.
Afferents to Action: Cortical proprioceptive processing assessed with corticokinematic coherence specifically predicts gross motor skills
Authors: Scott Mongold , Christian Georgiev , Thomas Legrand , Mathieu Bourguignon
Published: September 2023

Voluntary motor control is thought to be predicated on the ability to efficiently integrate and process somatosensory afferent information. However, current approaches in the field of motor control have not factored in objective markers of how the brain actually tracks incoming somatosensory information. Here, we asked whether motor performance relates with such markers obtained with an analysis of the coupling between peripheral kinematics and cortical oscillations during continuous movements, best known as corticokinematic coherence (CKC). Motor performance was evaluated by measuring both gross and fine motor skills using the Box and Blocks Test (BBT) and the Purdue Pegboard Test (PPT), respectively, and with a biomechanics measure of coordination. Sixty-one participants completed the BBT, while equipped with electroencephalography and electromyography, and the PPT. We evaluated CKC, from the signals collected during the BBT, as the coherence between movement rhythmicity and brain activity, and coordination as the cross-correlation between muscle activity. CKC at movements’ first harmonic was positively associated with BBT scores, and showed a relationship with PPT scores, but only in synergy with BBT scores, where participants with lower PPT score had higher CKC than expected based on their BBT score. Coordination was not associated with motor performance and at most, weakly related to CKC. These findings demonstrate that cortical somatosensory processing in the form of strengthened brain-peripheral coupling is specifically associated with better gross motor skills. CKC might be considered as a valuable addition to classical tests of proprioceptive acuity, with important perspectives for future clinical studies and practice.

Significance Statement

Whether standing upright, jogging, or in Olympic competition, our nervous system not only sends out motor commands prompting muscles to contract, but also receives incoming information to fine-tune motor actions. Though the machinery involved in sensing mechanical changes is well-described, the neural processing of this information is not, making its relevance to motor function unresolved. We found that the coupling strength between peripheral kinematics and cortical activity was related to motor function and at most, only weakly related to conventional muscle-only assessments. We present novel behavioral relevance of this coupling and its specific relationship to gross motor skill. Our study paves the way for including novel brain-centered approaches to complement classical assessment sensorimotor functions in health and disease.
Colonic spermidine promotes proliferation and migration of intestinal epithelial cells
Authors: Flory Madison , Gao Angela , Morrow Morgan , Alam Ashfaqul
Published: September 2023

The gut microbiome, comprising trillions of diverse microorganisms, profoundly influences the efficient development and maintenance of the intestinal barrier. While shifts in microbial composition are observed in Inflammatory Bowel Disease (IBD) and Colorectal Cancer (CRC), the causal relationship between these changes and resolution of inflammation remains elusive. Notably, IBD is not only marked by shifts in microbial composition but also by changes in microbial metabolites. Polyamines, produced by both gut bacteria and human cells, have emerged as potential regulators of gut pathology, cancer and mucosal repair. Investigating how elevated polyamine levels influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. To dissect the complex interplay between the gut microbiome, polyamines, and IEC, we focused on the overrepresented bacteriumB. uniformisand its primary metabolite, spermidine. Here, we show thatB. uniformis, a dominant member of gut microbiota, expands during the repair & resolution phase of the chemically induced chronic murine colitis. Furthermore, we found that the abundance of colonic polyamines was also altered, with spermidine being the abundant polyamine. Our RNA sequencing and transcriptomic analysis of cultured colonic epithelial cells demonstrate that spermidine regulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. We also found that spermidine stimulates the proliferation of cultured colonic epithelial cells in vitro. Additionally, our findings indicate that spermidine enhances the migrations of enterocytes. Our study emphasizes the crucial functions of the gut microbiome and polyamines in governing the functions of intestinal epithelial cells. Thus, these microorganisms and their metabolic byproducts hold promise as prospective therapeutic agents.
Cell Typing and Sub-typing Based on Detecting Characteristic Subspaces of Morphological Features Derived from Neuron Images
Authors: Zhao Sujun , Qian Penghao , Liu Lijuan
Published: September 2023

Motivation

Recent advances in reconstructing 3D neuron morphologies at the whole brain level offer exciting opportunities to study single cell genotyping and phenotyping. However, it remains challenging to define cell types and sub-types properly.

Results

As morphological feature spaces are often too complicated to classify neurons, we introduce a method to detect the optimal subspace of features so that neurons can be well clustered. We have applied this method to one of the largest curated databases of morphological reconstructions that contains more than 9,400 mouse neurons of 19 cell types. Our method is able to detect the distinctive feature subspaces for each cell type. Our approach also outperforms prevailing cell typing approaches in terms of its ability to identify key morphological indicators for each neuron type and separate superclasses of these neuron types. the subclasses of neuronal types could supply information for brain connectivity and modeling, also promote other analysis including feature spaces.

Availability

All datasets used in this study are publicly available. All analyses were conducted with python package Scikitlearn 0.23.1 version. Source code used for data processing, analysis and figure generation is available as an open-source Python package, onhttps://github.com/SEU-ALLEN-codebase/ManifoldAnalysis

Contact

ljliu@braintell.org
Deep learning models of RNA base-pairing structures generalize to unseen folds and make accurate zero-shot predictions of base-base interactions of RNA complexes
Authors: lang mei , Litfin Thomas , Chen Ke , Zhan Jian , Zhou Yaoqi
Published: September 2023

The intricate network of RNA-RNA interactions, crucial for orchestrating essential cellular processes like transcriptional and translational regulation, has been unveiling through high-throughput techniques and computational predictions. With the emergence of deep learning methodologies, the question arises: how do these cutting-edge techniques for base-pairing prediction compare to traditional free-energy-based approaches, particularly when applied to the challenging domain of interaction prediction via chain concatenation? In this study, we employ base pairs derived from three-dimensional RNA complex structures as the gold standard benchmark to assess the performance of 23 different methods, including recently developed deep learning models. Our results demonstrate that the deep-learning-based methods, SPOT-RNA can be generalized to make accurate zero-shot predictions of RNA-RNA interactions not only between previously unseen RNA structures but also between RNAs without monomeric structures. The finding underscores the potential of deep learning as a robust tool for advancing our understanding of these complex molecular interactions.
DeepGO-SE: Protein function prediction as Approximate Semantic Entailment
Authors: Kulmanov Maxat , Guzmán-Vega Francisco J. , Roggli Paula Duek , Lane Lydie , Arold Stefan T. , Hoehndorf Robert
Published: September 2023

The Gene Ontology (GO) is one of the most successful ontologies in the biological domain. GO is a formal theory with over 100,000 axioms that describe the molecular functions, biological processes, and cellular locations of proteins in three sub-ontologies. Many methods have been developed to automatically predict protein functions. However, only few of them use the background knowledge provided in the axioms of GO for knowledge-enhanced machine learning, or adjust and evaluate the model for the differences between the sub-ontologies.

We have developed DeepGO-SE, a novel method which predicts GO functions from protein sequences using a pretrained large language model combined with a neuro-symbolic model that exploits GO axioms and performs protein function prediction as a form of approximate semantic entailment. We specifically evaluate DeepGO-SE on proteins that have no significant similarity with training proteins and demonstrate that DeepGO-SE can improve function prediction for those proteins.
Clusterin can mediate apoptosis-induced molecular mechanisms in immune thrombocytopenia
Authors: Stein T. , Bitsina C. , Schmugge M. , Franzoso F.
Published: September 2023

Abnormalities in the apoptosis pathway are possible risk factors for various autoimmune diseases including immune thrombocytopenia (ITP). ITP is an autoimmune bleeding disorder characterized by a low platelet count and mostly mild but in rare occasions life threatening bleeding symptoms. Platelets and megakaryocytes (MKs) may be seen as the major targets of the pathogenic immune responses in ITP. A mechanistic understanding of the ITP pathogenesis is still lacking. Our data indicate that mechanisms associated with impaired clusterin-mediated apoptosis might play a role in ITP platelet pathophysiology and platelet production by MKs.

We could demonstrate by apoptosis proteomic profiling significantly increased expression levels of some apoptotic genes such as clusterin (CLU), pro-caspase 3, catalase, TRAILR1/DR4, Bax, Bad and Bcl-2 compared to healthy controls in platelet-rich plasma (PRP) from 10 ITP patients. We could validate by both RT-qPCR and Western blotting that CLU, a stress-activated chaperone, is significantly increased in both newly diagnosed and chronic ITP. We used the human megakaryoblastic cell line MEG-01, treated for 4h with plasma from acute and chronic ITP patients and healthy controls. We performed chemical treatments in plasma treated MEG-01 by using pan-caspase inhibitors (Z-VAD-FMK), apoptosis inducer ABT-737, Rotenone and Rapamycin. We determined the expression at mRNA levels of apoptosis pathway regulatory genes Bax, caspase-3, -8, -9 as well as CLU, GRP78 and GRP94 by qRT-PCR. We could demonstrate significantly downregulation of mRNA expression levels of these apoptotic markers in ITP plasma treated and CLU siRNA transfected MEG-01 cells. Our results indicate a possible impairment of apoptosis pathway via upregulation of CLU and Bax in platelets and in their producers MKs that can lead to platelet destruction in ITP disease.
Bacteria colonies modify their shear and compressive mechanical properties in response to different growth substrates
Authors: Kochanowski Jakub A. , Carroll Bobby , Asp Merrill E. , Kaputa Emma , Patteson Alison E.
Published: September 2023

Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct multicellular structures in response to different environmental conditions remains incompletely understood. Here, we investigated the connection between bacteria colony mechanics and the colony growth substrate by measuring the oscillatory shear and compressive rheology of bacteria colonies grown on agar substrates. We found that bacteria colonies modify their own mechanical properties in response to shear and uniaxial compression with the increasing agar concentration of their growth substrate. These findings highlight that mechanical interactions between bacteria and their microenvironment are an important element in bacteria colony development, which can aid in developing strategies to disrupt or reduce biofilm growth.
Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord
Authors: Schilling Kurt G , Combes Anna J.E. , Ramadass Karthik , Rheault Francois , Sweeney Grace , Prock Logan , Sriram Subramaniam , Cohen-Adad Julien , Gore John C , Landman Bennett A , Smith Seth A , O’Grady Kristin P.
Published: September 2023

Diffusion MRI of the spinal cord (SC) is susceptible to geometric distortion caused by field inhomogeneities, and prone to misalignment across time series and signal dropout caused by biological motion. Several modifications of image acquisition and image processing techniques have been introduced to overcome these artifacts, but their specific benefits are largely unproven and warrant further investigations. We aim to evaluate two specific aspects of image acquisition and processing that address image quality in diffusion studies of the spinal cord: susceptibility corrections to reduce geometric distortions, and cardiac triggering to minimize motion artifacts. First, we evaluate 4 distortion preprocessing strategies on 7 datasets of the cervical and lumbar SC and find that while distortion correction techniques increase geometric similarity to structural images, they are largely driven by the high-contrast cerebrospinal fluid, and do not consistently improve the geometry within the cord nor improve white-to-gray matter contrast. We recommend at a minimum to perform bulk-motion correction in preprocessing and posit that improvements/adaptations are needed for spinal cord distortion preprocessing algorithms, which are currently optimized and designed for brain imaging. Second, we design experiments to evaluate the impact of removing cardiac triggering. We show that when triggering is foregone, images are qualitatively similar to triggered sequences, do not have increased prevalence of artifacts, and result in similar diffusion tensor indices with similar reproducibility to triggered acquisitions. When triggering is removed, much shorter acquisitions are possible, which are also qualitatively and quantitatively similar to triggered sequences. We suggest that removing cardiac triggering for cervical SC diffusion can be a reasonable option to save time with minimal sacrifice to image quality.
SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants
Authors: An Yaling , Zhou Xuemei , Tao Lifeng , Xie Haitang , Li Dedong , Wang Ruyue , Hu Hua , Xu Zepeng , Dai Lianpan , Xu Kun , Gao George F.
Published: September 2023

The continual emergence and circulation of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused a great challenge for the coronavirus disease 2019 (COVID-19) pandemic control. Recently, Omicron BA.2.86 was identified with more than 30 amino acid changes on the spike (S) protein, compared to Omicron BA.2 or XBB.1.5. The immune evasion potential of BA.2.86 is of great concern. In this study, we evaluated the neutralizing activities of sera collected from participants and mice. Participants were divided into five groups according to their vaccination (inactivated vaccine, protein subunit vaccine ZF2001 or ZF2202-A) and infection (Omicron BF.7/BA.5.2) status. ZF2202-A is ZF2001 vaccine’s next-generation COVID-19 vaccine with updated bivalent Delta-BA.5 RBD-heterodimer immunogen. BALB/c mice were immunized with XBB.1.5 RBD-homodimer, BA.5-BA.2, Delta-XBB.1.5 or BQ.1.1-XBB.1.5 RBD-heterodimers protein vaccine candidates for evaluating the neutralizing responses. We found that Omicron BA.2.86 shows stronger immune evasion than BA.2 due to >30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future.
Sample preparation and data collection for Serial Block Face Scanning Electron Microscopy of Mammalian Cell Monolayers
Authors: Antao Noelle V. , Sall Joseph , Petzold Christopher , Ekiert Damian C. , Bhabha Gira , Liang Feng-Xia
Published: September 2023

Volume electron microscopy encompasses a set of electron microscopy techniques that can be used to examine the ultrastructure of biological tissues and cells in three dimensions. Two block face techniques, focussed ion beam scanning electron microscopy (FIB-SEM) and serial block face scanning electron microscopy (SBF-SEM) have often been used to study biological tissue samples. More recently, these techniques have been adapted toin vitrotissue culture samples. Here we describe detailed protocols for two sample embedding methods forin vitrotissue culture cells intended to be studied using SBF-SEM. The first protocol focuses on cell pellet embedding and the second onen faceembedding.En faceembedding can be combined with light microscopy, and this CLEM workflow can be used to identify specific biological events in a light microscope, which can then be imaged using SBF-SEM. We systematically outline the steps necessary to fix, stain, embed and image adherent tissue culture cell monolayers by SBF-SEM. In addition to sample preparation, we discuss optimization of parameters for data collection. We highlight the challenges and key steps of sample preparation, and the consideration of imaging variables that will facilitate the acquisition of high quality datasets. Users experienced with electron microscopy sample preparation methodology will be able to complete this protocol in 10-11 days from initial seeding of cells in tissue culture to image acquisition.
Contribution of image statistics and semantics in local vs. distributed EEG decoding of rapid serial visual presentation
Authors: Holm Eric Lützow , Slezak Diego Fernández , Tagliazucchi Enzo
Published: September 2023

Spatio-temporal patterns of evoked brain activity contain information that can be used to decode and categorize the semantic content of visual stimuli. This procedure can be biased by statistical regularities which can be independent from the concepts that are represented in the stimuli, prompting the need to dissociate between the contributions of image statistics and semantics to decoding accuracy. We trained machine learning models to distinguish between concepts included in the THINGS-EEG dataset using electroencephalography (EEG) data acquired during a rapid serial visual presentation protocol. After systematic univariate feature selection in the temporal and spatial domains, we constructed simple models based on local signals which superseded the accuracy of more complex classifiers based on distributed patterns of information. Simpler models were characterized by their sensitivity to biases in the statistics of visual stimuli, with some of them preserving their accuracy after random replacement of the training dataset while maintaining the overall statistics of the images. We conclude that model complexity impacts on the sensitivity to confounding factors regardless of performance; therefore, the choice of EEG features for semantic decoding should ideally be informed by the underlying neurobiological mechanisms.
CYP79B2 and CYP79B3 contribute to root branching through production of the auxin precursor indole-3-acetonitrile
Authors: van Zelm Eva , Koevoets Iko T. , Meyer A. Jessica , van der Velde Kyra , de Zeeuw Thijs A. J. , Verstappen Francel , Holmer Rens , Kohlen Wouter , Willemsen Viola , Gommers Charlotte M.M. , Testerink Christa
Published: September 2023

Lateral root placement, outgrowth and density are influenced by environmental changes, including salinity stress. CYP79B2 and B3 are two cytochrome P450 enzymes previously identified as required for root architecture remodeling in salt. They produce iAOx, a metabolite that can be converted into indole glucosinolates (IGs), camalexin and indole-3-acetic acid (IAA), a type of auxin. We report here that lateral root appearance, induced by an auxin maximum in the bending zone after gravistimulation, is delayed in the absence of CYP79B2/B3. This delay traces back to a decrease in early lateral root growth after emergence, taking place before lateral roots are macroscopically visible. We measured gene transcripts and abundance of metabolites in the iAOx pathway in root segments that are forming lateral roots. Genes involved in tryptophane and IG biosynthesis were upregulated incyp79b2/b3mutants, suggesting a transcriptional feedback-loop. Salt stress was found to increase the expression of genes involved in IAN biosynthesis, a precursor of both IAA and camalexin, in the root during lateral root formation. Moreover, salt increases the concentration of IAN in tissue forming lateral roots in a CYP79B2/B3 dependent manner, but these changes in IAN did not coincide with altered IAA levels. Both the reduction in lateral root density under salt and the delayed lateral root appearance incyp79b2/b3knock-out mutants can be complemented by exogenous application of IAN. Our results reveal a role for the iAOx pathway in regulating the timing of lateral root appearance, allowing the modulation of lateral root density under salt stress.
Bed Nucleus of the Stria Terminalis (BNST) neurons containing the serotonin 5HT2creceptor modulate operant alcohol self-administration behavior in mice
Authors: Flanigan Meghan E. , Gianessi Carol , Castle Megan , Dorlean Winifred , Sides Tori , Kash Thomas L.
Published: September 2023

The serotonin 5HT2creceptor has been widely implicated in the pathophysiology of alcohol use disorder (AUD), particularly alcohol seeking and the affective consequences of chronic alcohol consumption. However, little is known about the brain sites in which 5HT2cexerts its effects on specific alcohol-related behaviors, especially in females. Here, we investigated the effects of site-specific manipulation of the 5HT2creceptor system in the BNST on operant alcohol self-administration behaviors in adult mice of both sexes, including the acquisition and maintenance of fixed-ratio responding, motivation for alcohol (progressive ratio), and quinine-adulterated responding for alcohol on a fixed-ratio schedule (punished alcohol seeking). Knockdown of 5HT2cin the BNST did not affect the acquisition or maintenance of operant alcohol self-administration, nor did it affect progressive ratio responding for alcohol. This manipulation had only a subtle effect on responding for quinine alcohol selectively in females. On the other hand, chemogenetic inhibition of BNST 5HT2c-containing neurons (BNST5HT2c) increased operant alcohol self-administration behavior in both sexes on day 2, but not day 9, of testing. It also increased operant responding for 1000 μM quinine-adulterated alcohol selectively in males. Importantly, chemogenetic inhibition of BNST5HT2cdid not alter operant sucrose responding or motivation for sucrose in either sex. We then performed cell-type specific anterograde tracing, which revealed that BNST5HT2cproject to similar regions in males and females, many of which have been previously implicated in AUD. We next used chemogenetics and quantification of the immediate early gene cFos to characterize the functional influence of BNST5HT2cinhibition on vlPAG activity. We show that chemogenetic inhibition of BNST5HT2creduces vlPAG cFos in both sexes, but that this reduction is more robust in males. Together these findings suggest that BNST5HT2cneurons, and to a small extent the BNST 5HT2creceptor, serve to promote aversive responses to alcohol consumption, potentially through sex-dependent disinhibition of vlPAG neurons.
The Use of Electronic Health Record Embedded MRC-ICU as a Metric for Critical Care Pharmacist Workload
Authors: Webb Andrew J , Carver Bayleigh , Rowe Sandra , Sikora Andrea
Published: September 2023

Objective

A lack of pharmacist-specific risk-stratification scores in the electronic health record (EHR) may limit resource optimization. The medication regimen complexity-intensive care unit (MRC-ICU) score was implemented into our center’s EHR for use by clinical pharmacists. The purpose of this evaluation was to evaluate MRC-ICU as a predictor of pharmacist workload and to assess its potential as an additional dimension to traditional workload measures.

Materials

Data were abstracted from the EHR on adult ICU patients, including MRC-ICU scores and two traditional measures of pharmacist workload: numbers of medication orders verified and interventions logged.

Methods

This was a single-center study of an EHR-integrated MRC-ICU tool. The primary outcome was the association of MRC-ICU with institutional metrics of pharmacist workload. Associations were assessed using the initial 24-hour maximum MRC-ICU score’s Pearson’s correlation with overall admission workload and the day-to-day association using generalized linear mixed-effects modeling.

Results

A total of 1,205 patients over 5,083 patient-days were evaluated. Baseline MRC-ICU was correlated with both cumulative order volume (Spearman’s rho 0.41, p < 0.001) and cumulative interventions placed (Spearman’s rho 0.27, p < 0.001). A one-point increase in maximum daily MRC-ICU was associated with 31% increase in order volume (95% CI 24-38%) and 4% increase in interventions (95% CI 2-5%).

Discussion

The MRC-ICU is a validated score that has been previously correlated with important patient-centered outcomes. Here, MRC-ICU was modestly associated with two traditional objective measures of pharmacist workload, including orders verified and interventions placed, which is an important step for its use as a tool for resource utilization needs.

Lay Summary

Measuring critical care clinical pharmacist workload is challenging because currently available metrics, including number of medication orders verified or medication interventions logged, do not capture the full breadth of work critical care pharmacists do. The medication regimen complexity-intensive care unit (MRC-ICU) score is a tool designed to quantify the complexity of an ICU patient’s medication regimen and may serve as an alternative measure of overall critical care pharmacist workload. In this study, we assessed whether MRC-ICU scores from 1,205 ICU patients admitted to a single academic medical center were correlated with traditional metrics used to assess pharmacist workload, including medication orders and documented interventions. MRC-ICU was correlated with both workflow measures and traditional measures of patient acuity and also was predictive of the next day’s workload, suggesting MRC-ICU could be explored as an additional tool to optimize critical care pharmacist resource utilization. Further studies should assess how MRC-ICU can be utilized to optimize critical care pharmacist workload.
Notch signalling plays a critical role in patterning the ventral mesoderm during early embryogenesis inDrosophila melanogaster
Authors: Megaly Marvel , Foran Gregory , Ali Arsala , Turgambayeva Anel , Hallam Ryan D. , Necakov Aleksandar
Published: September 2023

Notch signaling is a critical regulator of multiple developmental processes through its ability to control gene expression, and thereby influence cell fate specification and cell proliferation through direct cell-cell communication. Although Notch signalling has been implicated in myogenesis during late embryogenesis, the role of Notch signalling in early mesoderm development in largely unexplored. Endocytosis of the ligand and receptor extracellular domain is observed in the mesoderm and mesectoderm and therefore indicative of signalling activity. Here we present evidence that critical mesodermal genes require and are responsive to Notch signalling activity. We also developed a novel light-inducible variant of NICD to allow precise control of ectopic activation of Notch signalling. Using a combination of high-resolution fluorescent mRNAin situhybridizations and qPCR, we identified a set of mesodermal genes that are directly regulated by Notch signalling. We also show evidence that Notch signalling indirectly regulates the dorsal-ventral patterning program mediated by the Toll signalling pathway through the Dorsal/ Twist/ Snail network. Our findings in this paper show that Notch signalling regulates mesoderm patterning and boundary formation between it and the ectoderm by regulating the expression of critical genes and providing negative feedback on the upstream patterning network.
Temporal profiling ofSalmonellatranscriptional dynamics during macrophage infection using a comprehensive reporter library
Authors: Nguyen Taylor H. , Diaz Oscar R. , Rajendram Manohary , Butler Daniel S.C. , Wang Benjamin X. , Hinton Jay C. D. , Monack Denise , Huang Kerwyn Casey
Published: September 2023

The transcriptome ofSalmonella entericaserovar Typhimurium (S. Tm) dynamically responds to the rapid environmental shifts intrinsic toS.Tm lifestyle, exemplified by entry into theSalmonella-containing vacuole (SCV) within macrophages. IntracellularS. Tm must respond to the acidity of the SCV, accumulation of reactive oxygen/nitrogen species, and fluctuations in nutrient availability. Despite thorough RNA-seq-based investigations, the precise transcriptional timing of the expression of many secretion systems, metabolic pathways, and virulence effectors involved in infection has yet to be elucidated. Here, we construct a comprehensive library of GFP-reporter strains representing ∼3,000 computationally identifiedS.Tm promoter regions to study the dynamics of transcriptional regulation. We quantified promoter activity duringin vitrogrowth in defined and complex media and throughout the timeline of intracellular infection of RAW 246.7 macrophages. Using bulk measurements and single-cell imaging, we uncovered condition-specific transcriptional regulation and population-level heterogeneity in the activity of virulence-related promoters, including SPI2 genes such asssaRandssaG. We discovered previously unidentified transcriptional activity from 234 genes, including ones with novel activity during infection that are associated with pathogenecity islands and are involved in metabolism and metal homeostasis. Our library and data sets should provide powerful resources for systems-level interrogation ofSalmonellatranscriptional dynamics.
Development of genetically-encoded fluorescent KSR1-based probes to track ceramides during phagocytosis
Authors: Girik Vladimir , van Ek Larissa , Quadri Isabelle Dentand , Azam Maral , Cobo Maria Cruz , Mandavit Marion , Riezman Isabelle , Riezman Howard , Gavin Anne-Claude , Nunes-Hasler Paula
Published: September 2023

Ceramides regulate phagocytosis, however their exact function remains poorly understood. Here we sought 1) to develop genetically encoded fluorescent tools for imaging ceramide, and 2) to use them to examine ceramide dynamics during phagocytosis. Fourteen EGFP fusion constructs based on four known ceramide-binding domains were generated and screened. While most constructs localized to the nucleus or cytosol, three based on the CA3 ceramide-binding domain of KSR1 localized to plasma membrane or endolysosomes. C-terminally-tagged CA3 with a vector-based (C-KSR) or glycine-serine linker (C-KSR-GS) responded sensitively and similarly to ceramide depletion and accumulation using a panel of ceramide modifying drugs, whereas N-terminally tagged CA3 (N-KSR) responded differently to a subset of treatments. Lipidomic and liposome microarray analysis suggested that, instead, N-KSR preferentially binds to glucosyl-ceramide. Additionally, the three probes showed distinct dynamics during phagocytosis. Despite partial lysosomal degradation, C-KSR robustly accumulated at the plasma membrane during phagocytosis, whereas N-KSR becomes cytoplasmic at later timepoints. Moreover, weak recruitment of C-KSR-GS to endoplasmic reticulum and phagosomes was enhanced by overexpression of the endoplasmic reticulum proteins STIM1 and Sec22b, and was more salient in dendritic cells. The data suggest these novel probes can be used to analyze sphingolipid dynamics and function in living cells.
Molecular signatures of heat tolerance and sensitivity in the alpine plantWahlenbergia ceraceaduring moderate warming
Authors: Notarnicola Rocco F. , Arnold Pieter A. , Feng Zhi-Ping , Hamilton Jemimah , Jones Ashley W. , Loke Stella , Schwessinger Benjamin , Nicotra Adrienne B. , Ganguly Diep R.
Published: September 2023

Understanding the molecular basis of plant heat tolerance helps to predict the consequences of climate warming on plant performance, particularly in vulnerable environments. Our current understanding comes primarily from studies inArabidopsis thaliana(Arabidopsis) and select crops exposed to short and intense periods of heat stress. In this study we sought to characterise the transcriptomic responses ofWahlenbergia ceracea(W. ceracea), an Australian alpine herb, to growth under sustained moderate warming. We compared responses of pre-defined tolerant and sensitive lines, based on measures of photosynthetic thermostability, to growth under cool (24/15 °C day/night) or warm (30/20 °C day/night) temperatures to identify the pathways involved in heat tolerance and acclimation. Under warmer growth temperatures,W. ceraceaup-regulated genes involved in RNA metabolism, while down-regulating those involved in photosynthesis and pigment metabolism. In tolerant lines, genes related to photosystem II and light-dependent photosynthetic reactions were more strongly down- regulated. This suggests that the regulation of electron transport and its components may be involved in thermal acclimation. Our results also highlight the importance of hormonal gene networks, particularly those responsive to ethylene, during longer-term moderate warming. In conclusion, our results point to post-transcriptional processes and the stabilisation of the electron transport chain as candidate mechanisms for thermal acclimation in heat-tolerantW. ceracea. The study also revealed many temperature-responsive genes with no detectable ortholog in Arabidopsis, whose characterization may enhance our understanding of physiological acclimation and have relevance for the biotechnological improvement of threatened species and crops.
Oculomotor routines for perceptual judgments
Authors: Aizenman Avi M. , Gegenfurtner Karl R. , Goettker Alexander
Published: September 2023

In everyday life we frequently make simple visual judgments about object properties, e.g., how big or wide is a certain object? Our goal is to test whether there are also task specific oculomotor routines which support perceptual judgments, similar to the well-established exploratory routines for haptic perception. In a first study, observers saw different scenes with two objects presented in a photorealistic virtual reality environment. Observers were asked to judge which of two objects was taller or wider while gaze was tracked. All tasks were performed with the same set of virtual objects in the same scenes, so that we can compare spatial characteristics of exploratory gaze behavior to quantify oculomotor routines for each task. Width judgments showed fixations around the center of the objects with larger horizontal spread. In contrast, for height judgments, gaze was shifted towards the top of the objects with larger vertical spread. These results suggest specific strategies in gaze behavior that presumably are used for perceptual judgments. To test the causal link between oculomotor behavior and perception, in a second study, observers either could freely gaze at the object or we introduced a gaze contingent set up forcing observers to fixate specific positions on the object. Discrimination performance was similar between free gaze and the gaze contingent conditions for width and height judgments. These results suggest that although gaze is adapted for different tasks, performance seems to be based on a perceptual strategy, independent of potential cues that can be provided by the oculomotor system.
Proteolytic activation of fatty acid synthase signals pan-stress resolution
Authors: Wei Hai , Weaver Yi M. , Yang Chendong , Zhang Yuan , Hu Guoli , Karner Courtney M. , DeBerardinis Ralph J. , Weaver Benjamin P.
Published: September 2023

Chronic stress and inflammation are not only outcomes of pathological states but rather major drivers of many human diseases1-4. Ideally, a given stress program is downregulated to basal levels upon restoration of homeostasis. Chronic responsiveness despite stress mitigation suggests a failure to sense the resolution of the initiating stressor. Here we show that a proteolytic cleavage event of fatty acid synthase (FASN) activates a global cue for stress resolution. FASN is well-established as the multifunctional enzyme catalyzingde novobiosynthesis of saturated fatty acid5, 6. Surprisingly, our results demonstrate FASN functioning as a signaling molecule promoting an anti-inflammatory profile apart from fatty acid synthesis. Redox-dependent proteolytic cleavage of FASN by caspase activates a truncated C-terminal enzymatic fragment (FASN-CTF) that is sufficient to down-regulate multiple aspects of stress-responsiveness including gene expression and metabolic programs. Only a fraction of FASN is cleaved allowing for continued fat synthesis. FASN-CTF can signal stress resolution across tissues in a cell non-autonomous manner. Consistent with these findings, FASN processing is also seen in well-fed but not fasted mouse liver. As down-regulation of stress responsiveness is critical to health, our findings provide a potential pathway to control the magnitude for diverse aspects of stress responses.
Engineered Lactiplantibacillus plantarum as a Biosensor Probe for the Lungs
Authors: Brasino Michael , Wagnell Eli , Manalo Elise C , Drennan Samuel , Fischer Jared M , Merritt Justin
Published: September 2023

Lungs are a frequent site for disease but are difficult to image and probe, potentially exacerbating lung disease, delaying diagnoses and impacting survival. Here, we demonstrate a low cost, minimally invasive method to probe the lungs for disease, using genetically engineeredLactiplantibacillus plantarumstrain WCFS1. Genetically modified WCFS1 was delivered specifically to the lungs of mice, where it was shown to remain transcriptionally active for several hours and then be cleared without further colonization. WCFS1 was further modified to secrete nanoluciferase as a synthetic biomarker, which traveled from the bacteria in the lung to the urine where it was easily detected. The administered bacteria also secreted nano-luciferase upon detecting a specific peptide secreted by a mouse lung cancer cell line in vitro or in vivo from syngeneic tumors.
Trait level somatic arousal modulates fMRI neural synchrony to naturalistic stimuli
Authors: Klamer K. , Craig J. , Sullivan K. , Haines C. , Ekstrand C.
Published: September 2023

Somatic arousal refers to the physiological and bodily responses that occur in reaction to different emotional and psychological stimuli and is a crucial component of the fight or flight response. Symptoms associated with higher levels of somatic arousal such as higher heart and respiration rates have been shown to impact the blood oxygenation level dependent (BOLD) signal during functional magnetic resonance imaging (fMRI) studies. Differences in baseline levels of somatic arousal may therefore modulate the brain’s response to incoming stimuli during fMRI. Previous studies typically investigate somatic arousal as a state, rather than as a trait, in which some individuals are more likely to have heightened physiological responses to psychological stimuli, causing the neurological mechanisms behind baseline somatic arousal levels to remain poorly understood. The current study seeks to identify how differing levels of baseline somatic arousal modulate neural synchrony in response to an audiovisual film. We hypothesize that individuals with higher levels of somatic arousal will show overall heightened neural synchrony in response to a complex audiovisual stimulus. We identified that higher levels of somatic arousal are associated with widespread neural synchrony across the brain, including frontal gyri, parietal and temporo-occipital cortices. Taken together, this research suggests that baseline somatic arousal levels should be measured during naturalistic fMRI paradigms, as baseline somatic arousal levels may have a profound influence on synchronous neural activity.