FInCH: FIJI plugin for automated and scalable whole-image analysis of protein expression and cell morphology.

Study of morphogenesis and its regulation requires analytical tools that enable simultaneous assessment of processes operating at cellular level, such as synthesis of transcription factors (TF), with their effects at the tissue scale. Most current studies conduct histological, cellular and immunochemical (IHC) analyses in separate steps, introducing inevitable biases in finding and alignment of areas of interest at vastly distinct scales of organization, as well as image distortion associated with image repositioning or file modifications. These problems are particularly severe for longitudinal analyses of growing structures that change size and shape. Here we introduce a python-based application for automated and complete whole-slide measurement of expression of multiple TFs and associated cellular morphology. The plugin collects data at customizable scale from the cell-level to the entire structure, records each data point with positional information, accounts for ontogenetic transformation of structures and variation in slide positioning with scalable grid, and includes a customizable file manager that outputs collected data in association with full details of image classification (e.g., ontogenetic stage, population, IHC assay). We demonstrate the utility and accuracy of this application by automated measurement of morphology and associated expression of eight TFs for more than six million cells recorded with full positional information in beak tissues across 12 developmental stages and 25 study populations of a wild passerine bird. Our script is freely available as an open-source Fiji plugin and can be applied to IHC slides from any imaging platforms and transcriptional factors.

Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.

The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g., Interior Alaska and St. Lawrence River have on average 181K and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 kbp and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g., amhby).

Palmar Fibromatosis, Updated Review With Relationship to the A1 Pulley, Trigger Finger, and Presence of the Sonographic Comb Sign.

OBJECTIVES: Updated retrospective review of the sonographic appearance of palmar fibromatosis (PF) with evaluation of the utility of the Comb Sign previously described in plantar fibromas. Additional evaluation was conducted on the location relative to the flexor tendon, anatomic proximity of palmar fibromas to the A1 pulley and evaluate any potential association with trigger finger. METHODS: Medical record and imaging review was performed from 2017 to 2023, for patients with a new onset ultrasound or clinical diagnosis of PF. Clinical associations and imaging morphology were reviewed including presence of the Comb Sign, fibroma association with the A1 pulley, and fibroma association with trigger finger. RESULTS: Exactly 87 total fibromas in 53 patients were evaluated. The Comb Sign was present in 39% of fibromas, usually seen in transverse plane, more prevalent in multifocal disease and larger fibromas. Most (72%) palmar fibromas were within 1 cm of, contacted, or covered the A1 pulley (P < .001). Lateral extension beyond the flexor tendon axis can be seen (44%). Trigger finger and tenosynovitis were rare. However, volume and SI dimension of fibromas were associated with tenosynovitis (P < .0001) and all nine patients with concomitant trigger finger had fibromas within 1 cm from the A1 pulley. CONCLUSIONS: The Comb Sign can aid in sonographic diagnosis of PF. Lateral extension of fibromas can occur. Most palmar fibromas have a significant intimate association with the A1 pulley, and presence of trigger finger with adjacent palmar fibroma can exist and is important for hand surgeons to know preoperatively.

Improving Coccidioidomycosis Testing for Emergency Department Patients With Suspect Community-Acquired Pneumonia: Analysis of Provider Attitudes and the Effect of a Targeted Intervention.

Coccidioidomycosis is a common cause of community-acquired pneumonia in endemic regions. Approximately 20 000 cases of coccidioidomycosis occur annually; however, this statistic is limited by a widespread lack of testing. Here, we analyze emergency medicine provider attitudes toward coccidioidal testing and assess the effect of an intervention to improve testing rates.

A double-blind trial of decoded neurofeedback intervention for specific phobias.

Aim: A new closed-loop fMRI method called multi-voxel neuro-reinforcement has the potential to alleviate the subjective aversiveness of exposure-based interventions by directly inducing phobic representations in the brain, outside of conscious awareness. The current study seeks to test this method as an intervention for specific phobia. Methods: In a randomized, double-blind, controlled single-university trial, individuals diagnosed with at least two (1 target, 1 control) animal subtype specific phobias were randomly assigned (1:1:1) to receive 1, 3, or 5 sessions of multi-voxel neuro-reinforcement in which they were rewarded for implicit activation of a target animal representation. Amygdala response to phobic stimuli was assessed by study staff blind to target and control animal assignments. Pre-treatment to post-treatment differences were analyzed with a 2-way repeated-measures ANOVA. Results: A total of 23 participants (69.6% female) were randomized to receive 1 (n=8), 3 (n=7), or 5 (n=7) sessions of multi-voxel neuro-reinforcement. Eighteen (n=6 each group) participants were analyzed for our primary outcome. After neuro-reinforcement, we observed an interaction indicating a significant decrease in amygdala response for the target phobia but not the control phobia. No adverse events or dropouts were reported as a result of the intervention. Conclusion: Results suggest multi-voxel neuro-reinforcement can specifically reduce threat signatures in specific phobia. Consequently, this intervention may complement conventional psychotherapy approaches with a non-distressing experience for patients seeking treatment. This trial sets the stage for a larger randomized clinical trial to replicate these results and examine the effects on real-life exposure. Clinical Trial Registration: The now-closed trial was prospectively registered at ClinicalTrials.gov with ID NCT03655262.

Magnesium Oxide Reduces Anxiety-like Behavior in Mice by Inhibiting Sulfate-Reducing Bacteria.

The gut microbiota-brain axis allows for bidirectional communication between the microbes in our gastrointestinal (GI) tract and the central nervous system. Psychological stress has been known to disrupt the gut microbiome (dysbiosis) leading to anxiety-like behavior. Pathogens administered into the gut have been reported to cause anxiety. Whether commensal bacteria affect the gut-brain axis is not well understood. In this study, we examined the impact of a commensal sulfate-reducing bacteria (SRB) and its metabolite, hydrogen sulfide (H2S), on anxiety-like behavior. We found that mice gavaged with SRB had increased anxiety-like behavior as measured by the open field test. We also tested the effects of magnesium oxide (MgO) on SRB growth both in vitro and in vivo using a water avoidance stress (WAS) model. We found that MgO inhibited SRB growth and H2S production in a dose-dependent fashion. Mice that underwent psychological stress using the WAS model were observed to have an overgrowth (bloom) of SRB (Deferribacterota) and increased anxiety-like behavior. However, WAS-induced overgrowth of SRB and anxiety-like behavioral effects were attenuated in animals fed a MgO-enriched diet. These findings supported a potential MgO-reversible relationship between WAS-induced SRB blooms and anxiety-like behavior.

Rabies Vaccine for Prophylaxis and Treatment of Rabies: A Narrative Review.

Rabies, a millennia-old viral infection transmitted through animal bites, poses a lethal threat to humans, with a historic fatality rate of 100% if left untreated. Louis Pasteur's introduction of the rabies vaccine in 1885 marked a turning point in the battle against rabies, preventing numerous cases. The purpose of this paper is to review the historical development, current challenges, and future prospects of rabies vaccination and treatment, with emphasis on the importance of continued research and collaborative efforts in the quest to eradicate this deadly infection. Historical vaccine development progressed from inactivated to live-attenuated forms, with modern recombinant techniques showing promise. The preventive measures at present primarily involve vaccination, but challenges persist, such as differing safety profiles and immunogenicity among vaccine types. Pre-exposure prophylaxis with a three-dose vaccine series is crucial, especially in high-risk scenarios. Post-exposure prophylaxis combines human rabies immunoglobulin and inactivated rabies virus vaccine. The quest for the next generation of vaccines explores genetically modified and viral vector-based approaches; emerging treatments include gene therapy, virus-like particles, and monoclonal antibodies, offering hope for improved outcomes. Economic barriers to post-exposure prophylaxis, limited education, and awareness challenge rabies control. Cost-effective solutions and comprehensive awareness campaigns are vital for the successful eradication of rabies. More research and collaborative endeavors remain pivotal in the ongoing journey to eradicate rabies, one of the deadliest infectious diseases known to humans, if not met with prophylactic measures.

Interaction between the prefrontal and visual cortices supports subjective fear.

It has been reported that threatening and non-threatening visual stimuli can be distinguished based on the multi-voxel patterns of haemodynamic activity in the human ventral visual stream. Do these findings mean that there may be evolutionarily hardwired mechanisms within early perception, for the fast and automatic detection of threat, and maybe even for the generation of the subjective experience of fear? In this human neuroimaging study, we presented participants ('fear' group: N = 30; 'no fear' group: N = 30) with 2700 images of animals that could trigger subjective fear or not as a function of the individual's idiosyncratic 'fear profiles' (i.e. fear ratings of animals reported by a given participant). We provide evidence that the ventral visual stream may represent affectively neutral visual features that are statistically associated with fear ratings of participants, without representing the subjective experience of fear itself. More specifically, we show that patterns of haemodynamic activity predictive of a specific 'fear profile' can be observed in the ventral visual stream whether a participant reports being afraid of the stimuli or not. Further, we found that the multivariate information synchronization between ventral visual areas and prefrontal regions distinguished participants who reported being subjectively afraid of the stimuli from those who did not. Together, these findings support the view that the subjective experience of fear may depend on the relevant visual information triggering implicit metacognitive mechanisms in the prefrontal cortex. This article is part of the theme issue 'Sensing and feeling: an integrative approach to sensory processing and emotional experience'.

n-3 PUFA ameliorate functional outcomes following repetitive mTBI in the fat-1 mouse model.

Purpose: Repeated mild traumatic brain injuries (mTBI) are a continuing healthcare concern worldwide, given its potential for enduring adverse neurodegenerative conditions. Past research suggests a potential protective effect of n-3 polyunsaturated fatty acids (PUFA) in experimental models of mTBI. The aim of this study was to investigate whether the neuroprotective benefits of n-3 PUFA persist following repetitive weight drop injury (WDI). Methods: Male fat-1 mice (n = 12), able to endogenously convert n-6 PUFA to n-3 PUFA, and their wild type (WT) counterparts (n = 12) were maintained on a 10% w/w safflower diet. At 9-10 weeks of age, both groups received one mild low-impact WDI on the closed cranium daily, for three consecutive days. Following each WDI, time to righting reflex and seeking behaviour were measured. Neurological recovery, cognitive, motor, and neurobehavioural outcomes were assessed using the Neurological Severity Score (NSS) over 7 days (168 h) post-last WDI. Brains were assessed for cerebral microhemorrhages by Prussian blue and cellular damage by glial fibrillary acidic protein (GFAP) staining. Results: Fat-1 mice exhibited significantly faster righting reflex and seeking behaviour time, and lower mean NSS scores and at all post-WDI time points (p ≤ 0.05) compared to WT mice. Immunohistochemistry showed no significant difference in presence of cerebral microhemorrhage however, fat-1 mice had significantly lower GFAP staining in comparison to WT mice (p ≤ 0.05). Conclusion: n-3 PUFA is effective in restoring cognitive, motor, and behavioural function after repetitive WDI, which may be mediated through reduced cellular damage of the brain.

Synaptic plasticity in human thalamocortical assembloids.

Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids. Single-nucleus RNA sequencing revealed that >80% of cells in thalamic organoids were glutamatergic neurons. When fused to form thalamocortical assembloids, thalamic and cortical organoids formed reciprocal long-range axonal projections and reciprocal synapses detectable by light and electron microscopy, respectively. Using whole-cell patch-clamp electrophysiology and two-photon imaging, we characterized glutamatergic synaptic transmission. Thalamocortical and corticothalamic synapses displayed short-term plasticity analogous to that in animal models. LTP and LTD were reliably induced at both synapses; however, their mechanisms differed from those previously described in rodents. Thus, thalamocortical assembloids provide a model system for exploring synaptic plasticity in human circuits.

Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement.

Protein homeostasis is a tightly conserved process that is regulated through the ubiquitin proteasome system (UPS) in a ubiquitin-independent or ubiquitin-dependent manner. Over the past two decades, the proteasome has become an excellent therapeutic target through inhibition of the catalytic core particle, inhibition of subunits responsible for recognizing and binding ubiquitinated proteins, and more recently, through targeted protein degradation using proteolysis targeting chimeras (PROTACs). The majority of the developed inhibitors of the proteasome's core particle rely on gaining selectivity through binding interactions within the unprimed substrate channel. Although this has allowed for selective inhibitors and chemical probes to be generated for the different proteasome isoforms, much remains unknown about the interactions that could be harnessed within the primed substrate channel to increase potency or selectivity. Herein, we discuss small molecules that interact with the primed substrate pocket and how their differences may give rise to altered activity. Taking advantage of additional interactions with the primed substrate pocket of the proteasome could allow for the generation of improved chemical tools for perturbing or monitoring proteasome activity.

Deep Sternal Wound Infection Caused by Rhizopus Species After Coronary Artery Bypass Graft.

Deep sternal wound infection is a rare complication of cardiac surgery that is typically caused by skin resident flora, such as species of Staphylococcus and Streptococcus. Infections caused by fungi are less common and are generally caused by Candida species. Regardless of etiology, these infections are associated with significant morbidity and mortality. We present a case of postoperative mediastinitis that occurred following a 5-vessel coronary artery bypass graft and was caused by a filamentous fungus of the Rhizopus genus. The patient was treated with serial debridement, liposomal amphotericin B, and isavuconazonium and was discharged from the hospital in stable condition. Fungal mediastinitis is a rare entity, and clinicians must maintain a high level of suspicion to make the diagnosis. A fungal cause of postoperative mediastinitis should be considered in patients with negative bacterial cultures, uncontrolled diabetes, or current immunosuppression or those who present weeks after surgery with a subacute onset of symptoms.

Metacognition as a window into subjective affective experience.

When patients seek professional help for mental disorders, they often do so because of troubling subjective affective experiences. While these subjective states are at the center of the patient's symptomatology, scientific tools for studying them and their cognitive antecedents are limited. Here, we explore the use of concepts and analytic tools from the science of consciousness, a field of research that has faced similar challenges in having to develop robust empirical methods for addressing a phenomenon that has been considered difficult to pin down experimentally. One important strand is the operationalization of some relevant processes in terms of metacognition and confidence ratings, which can be rigorously studied in both humans and animals. By assessing subjective experience with similar approaches, we hope to develop new scientific approaches for studying affective processes and promoting psychological resilience in the face of debilitating emotional experiences.

A systematic review and meta-analysis of pediatric integrated primary care for the prevention and treatment of physical and behavioral health conditions.

OBJECTIVE: To evaluate the effects of behavioral health interventions delivered within pediatric integrated primary care models on clinical outcomes. METHODS: We searched Medline, EMBASE, CENTRAL, PsycINFO, and SCOPUS for studies published from January 1, 1998, to September 20, 2023. We included studies that evaluated onsite behavioral health integration in pediatric primary care using a comparator condition (usual, enhanced usual care, or waitlist). Outcome data on symptom change, impairment/quality of life, health indicator, and behavior change were extracted using Covidence software. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guideline was followed Risk of bias analysis was conducted using the Cochrane Risk of Bias tool. We used multilevel meta-analysis to synthesize multiple outcomes nested within studies. Open Science Foundation pre-registration: #10.17605/OSF.IO/WV7XP. RESULTS: In total, 33 papers representing 27 studies involving 6,879 children and caregivers were included. Twenty-four studies were randomized controlled trials and three were quasi-experimental designs. Seventeen papers reported on treatment trials and 16 reported on prevention trials. We found a small overall effect size (SMD = 0.19, 95% confidence interval [0.11, 0.27]) supporting the superiority of integrated primary care to usual or enhanced usual care. Moderator analyses suggested similar effectiveness between co-located and integrated models and no statistically significant differences were found between treatment and prevention trials. CONCLUSIONS: Results suggest that integrated primary care is superior to usual and enhanced usual care at improving behavior, quality of life, and symptoms. Integrated primary care research needs improved standards for reporting to promote better synthesis and understanding of the literature.

Race and socioeconomic disparities persist in treatment and outcomes of patients with cervical spinal cord injuries: An analysis of the national inpatient sample from 2016 - 2020.

Objective: Previous literature has described race and socioeconomic disparities in both treatment and outcomes following cervical spinal cord injuries (SCI). The goal of this study is to investigate the current state of parity in management and outcomes following SCI. Methods: We surveyed the National Inpatient Sample database (NIS) for patients admitted with primary diagnosis of cervical SCI. 49,320 patients were identified. Univariate and multivariate analyses were performed to evaluate racial and socioeconomic differences in SCI care and outcomes. Results: Compared to white patients, minority race was associated with a longer time from presentation to operative intervention (p < 0.001) and longer length of stay following admission for cervical SCI (16 vs 13 days, p < 0.001). Minority patients were more likely to have an unfavorable discharge (skilled nursing facility, against medical advice, death) status than white patients (p < 0.001). Patients in the bottom quartile of median household income were associated with more unfavorable discharges than the top two quartiles (p < 0.001). Patients with the lowest median household income quartile also had higher total costs than those in the top quartiles ($221,654 vs 191,723, p < 0.001). Black, Hispanic, and Asian/Pacific Islander incurred higher treatment costs than White patients. Conclusion: Minority and lower socioeconomic status are independently associated with unfavorable discharge and LOS in cervical SCI. Furthermore, racial and economically disadvantaged groups have longer wait times from admission to surgical intervention. These disparities persist despite being highlighted by previous publications and increased societal awareness of healthcare inequities, necessitating further work to reach parity.

Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma.

ABSTRACT: Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR repertoire from healthy individuals using RNA-seq data. An average of 52 somatic mutations per patient (range, 2-172) were identified, and ≥2 (median, 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all 4 patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field. This trial was registered at www.ClinicalTrials.gov as #NCT03121677.

A child with unilateral abducens nerve palsy and neurovascular compression in Chiari malformation type 1 resolved with posterior fossa decompression: illustrative case.

BACKGROUND: Unilateral cranial nerve (CN) VI, or abducens nerve, palsy is rare in children and has not been reported in association with Chiari malformation type 1 (CM1) in the absence of other classic CM1 symptoms. OBSERVATIONS: A 3-year-old male presented with acute incomitant esotropia consistent with a unilateral, left CN VI palsy and no additional neurological symptoms. Imaging demonstrated CM1 without hydrocephalus or papilledema, as well as an anterior inferior cerebellar artery (AICA) vessel loop in the immediate vicinity of the left abducens nerve. Given the high risk of a skull base approach for direct microvascular decompression of the abducens nerve and the absence of other classic Chiari symptoms, the patient was initially observed. However, as his palsy progressed, he underwent posterior fossa decompression with duraplasty (PFDD), with the aim of restoring global cerebrospinal fluid dynamics and decreasing possible AICA compression of the left abducens nerve. Postoperatively, his symptoms completely resolved. LESSONS: In this first reported case of CM1 presenting as a unilateral abducens palsy in a young child, possibly caused by neurovascular compression, the patient's symptoms resolved after indirect surgical decompression via PFDD.

Synchrony between midbrain gene transcription and dopamine terminal regulation is modulated by chronic alcohol drinking.

Alcohol use disorder is marked by disrupted behavioral and emotional states which persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. Here, 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired direct sub-second dopamine monitoring via ex vivo voltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. We found persistent augmentation of dopamine transporter function, kappa opioid receptor sensitivity, and dynorphin release - all inhibitory regulators which act to decrease extracellular dopamine. Surprisingly, though transcript expression was not altered, the relationship between gene expression and functional readouts of these encoded proteins was highly dynamic and altered by drinking history. These results outline the long-lasting synaptic impact of alcohol use and suggest that assessment of transcript-function relationships is critical for the rational design of precision therapeutics.

A Biomechanical Comparison of the Back Squat and Hexagonal Barbell Deadlift.

ABSTRACT: Stahl, CA, Regni, G, Tanguay, J, McElfresh, M, Trihy, E, Diggin, D, and King, DL. A biomechanical comparison of the back squat and hexagonal barbell deadlift. J Strength Cond Res 38(5): 815-824, 2024-Coaches often use different exercises to encourage similar strength adaptations and limit monotony. Anecdotally, the hexagonal barbell deadlift (HBD) exhibits similarities to the back squat (BS). To date, research has not examined the empirical differences between these exercises. This study examined kinematic and kinetic differences between the BS and the HBD across different loads. Sixteen resistance-trained individuals (6 men and 10 women) volunteered to participate. Subjects performed 1-repetition maximum (1RM) testing under BS and HBD conditions. Kinematic and kinetic data were collected during performance of both exercises at submaximal (warm-up sets) and maximal (1RM) loads using a 3D motion capture and force-plate system. Results showed that subjects lifted greater 1RM loads in the HBD relative to the BS (p < 0.05; d = -1.75). Kinematic data indicated that subjects exhibited greater maximum forward lean of the trunk and decreased maximum knee flexion while performing the HBD compared with the BS. The BS resulted in higher maximum extension moments at the hip joint than the HBD. Maximum extension moments at the knee joint showed no difference between the exercises. Data suggest that bar design and position facilitate balanced moment arm length at hip and knee joints during performance of the HBD. By contrast, bar position during performance of the BS increases moment arm length at the hip joint, making it a hip-dominant exercise. The present data have implications for the programming of both exercises. Future research should examine differences in muscle-activation strategies between the 2 exercises.