bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuropathologic Features in Chronic Methamphetamine Use
Authors: Persons Jane E. , Conway Kyle S.
Published: February 2023

Methamphetamine is a psychostimulant that exerts its euphoric and stimulant effects by increasing cytosolic monoamine concentration at the nerve terminal. In addition to its known systemic cardiovascular effects, there is compelling evidence to suggest a direct neurotoxic effect of methamphetamine; however, the existing body of literature includes very few human tissue studies. This exploratory analysis used postmortem human brain specimens to examine histologic and immunohistochemical features associated with chronic methamphetamine use. This retrospective cohort study included 60 decedents who were autopsied at the University of Iowa Hospitals and Clinics between the years 2015 and 2021. Logistic regression models demonstrated no definite pathologic changes in the hippocampi of individuals with a history of chronic methamphetamine use. Decedents with a history of methamphetamine use had a marginally increased odds of basal ganglia arteriosclerosis, which did not reach statistical significance (odds ratio, 3.33; 95% confidence interval, 0.6–19.2; P = 0.17), which may be independent of the systemic hypertensive effects of methamphetamine. Future studies that include targeted examination of brain regions of interest, such as the basal ganglia and specifically the striatum, may prove revealing.
The Impact of Alar Flare Reduction Goes Beyond Just the Ala
Authors: Gordon Alexandra R. , Patel Anmol , Schreiber Jillian E. , Layke John C. , Tepper Oren M.
Published: February 2023

Introduction:

Alar flare reduction (AFR) is a widely utilized technique in rhinoplasty. While the impact of AFR on the alar base has been well studied, its effect on the surrounding tissues is largely unknown. This study aims to elucidate the potential effect of AFR on the overall nasal and peri-nasal anatomy.

Methods:

AFR was performed on cadavers (n=7) with sequential crescent shaped alar excisions of 2, 4 and 6mm. 2D and 3D-photographs were obtained at baseline and subsequent intervals. Analysis was performed with Adobe Photoshop and Vectra. Standardized landmarks were placed at the nasal tip point (NTP) and alar base point (ABP) to quantify NTP vector distances, NTP surface distances, and alar crease angle.

Results:

The surface and vector distances between the NTP and ABP decreased for increasing AFR intervals. AFR created a surface decrease of 1.90±1.60, 3.54±1.85, and 4.91±1.89mm respectively. AFR created a vector decrease of 1.50±1.14, 2.83±1.37, and 3.97±1.38mm respectively. NTP projection decreased by 0.54±0.31mm for 6mm excision. AFR led to cheek elevation of 0.87±0.70, 1.25±0.60, and 1.96±0.48mm respectively. This alar crease elevation blunted the transition between the cheek and upper lip skin at the level of the alar rim with the angle of this transition increasing 26.62±12.78 degrees from baseline to 6mm.

Conclusions:

3D-analysis demonstrates the influence of AFR on the alar base and surrounding peri-nasal contour. AFR results in nasal tip de-projection, alar crease elevation, and alar flare width narrowing. Further investigation into the impact of modifying the alar base on surrounding structures is warranted.
’Implant-based and DIEP flap breast reconstruction: a comparison of breast sensation and quality of life within a singular patient sample’’
Authors: van Rooij Joep A.F. , Bijkerk Ennie , van der Hulst René R.J.W. , van Kuijk Sander M.J. , Tuinder Stefania M.H.
Published: February 2023

Background:

In this cohort study we compared breast sensation and quality of life (QoL) after replacement of an implant-based breast reconstruction (IBBR) with a deep inferior epigastric perforator (DIEP) flap reconstruction in a singular sample of women.

Method:

Women with IBBR prior to their DIEP flap were included. Women formed their own control. Breast sensation was measured using Semmes-Weinstein monofilaments (SWM). QoL was evaluated using BREAST-Q questionnaires. Preoperative (T0) sensation and QoL was compared to postoperative at 6 (T1), 12 months (T2) and maximum follow-up (Tmax, sensation only). A linear mixed effects regression was used for SWM measurements, a paired samples t-test for BREAST-Q scores. Most women chose replacement of their implant by a DIEP flap due to implant-related complaints.

Results:

Postoperative sensation decreased significantly compared to preoperative sensation after T1 (mean 5·1 months), T2 (mean 14·6), and Tmax (mean 17·6) for the total breast but recovers to preoperative levels for the native skin after an average of 1.5 years. Nerve coaptation positively influenced recovery of sensation. BREAST-Q scores increased significantly after 6 and 12 months over the domains satisfaction with breast, psychosocial wellbeing, physical wellbeing of the chest, and sexual wellbeing. Scores decreased significantly in physical wellbeing of the abdomen after 6 months.

Conclusions:

Replacing an implant with a DIEP flap initially causes a decrease in overall breast sensation, gradually recovering to preoperative levels for native skin, and can significantly increase QoL with the right indication. Superior recovery of sensation and QoL may be obtained by accompanying the DIEP flap with nerve coaptation.
Autologous Breast Reconstruction in Massive Weight Loss Patients: Understanding Risks in a Growing Population
Authors: Sinik Lauren M , Elver Ashlie A , Egan Katie G , Johnson Braden M , Cullom Melissa E , Limpiado MarcArthur , Nazir Niaman , Lai Eric C , Butterworth James A
Published: February 2023

Background:

Massive weight loss (MWL) may have suboptimal effects on tissues used for autologous reconstruction. With the rise of obesity and bariatric surgery, more MWL patients will be presenting for breast reconstruction. We hypothesize that autologous breast reconstruction in patients with a history of MWL will have more complications and require more revisions compared to patients without a history of MWL.

Methods:

A retrospective review was performed on patients who underwent autologous breast reconstruction by five microsurgeons at an academic institution from 2009 to 2020. Patients with a history of bariatric surgery or >50-pound weight loss were identified and compared to non MWL patients. Analysis compared demographics, operative details, complications, revision rates, and BREAST-Q scores.

Results:

Of 916 patients who underwent 1465 flaps, 39 MWL patients (4.3%) underwent 68 flaps (4.6%) and 877 non MWL patients underwent 1397 flaps. MWL patients were more likely to require blood transfusions postoperatively (p=.005). MWL patients experienced more surgical site infections (p=.02), wound healing complications of flap (p=.007) and donor sites (p=.03), and late partial flap losses (p=.03). More revisional surgeries for flap (p=.009) and donor sites (p=.01) were required. BREAST-Q scores were not statistically different for satisfaction with breasts or surgeon but were lower in MWL patients for psychosocial (p=.01) and sexual well-being (p=.04).

Conclusion:

Reconstructive surgeons should expect increased postoperative complications when performing autologous breast reconstruction in MWL patients. These patients should be counseled on the possibility of more postoperative complications and need for revisional surgeries.
Does the Type of Reconstruction Matter? A Propensity Score Matched Analysis of Immediate Post-mastectomy Implant and Flap Reconstruction
Authors: Jung Wooram F. , Pollie Meridith P. , Ho Kaylee K. , Mauer Elizabeth A. , Newman Lisa A. , Otterburn David M.
Published: February 2023

Background:

No randomized controlled trials have compared implant and flap reconstruction. Recently, worse longitudinal outcomes have been suggested for flap reconstruction. We compared long-term oncologic outcomes of post-mastectomy breast reconstruction using propensity score matching.

Methods:

A retrospective study of post-mastectomy reconstruction was achieved using the Weill Cornell Breast Cancer Registry between 1998 and 2019. Patients were matched using propensity scores based on demographic, clinical, and surgical characteristics. Kaplan-Meier estimates, Cox-regression models, and restricted mean survival times (RMST) were used to evaluate patient outcomes.

Results:

Before matching, 1395 implant and 586 flap patients were analyzed. No difference in overall survival and recurrence were observed. Multivariable models showed decreased survival for Medicare/Medicaid (HR: 3.09; 95% CI: 1.63, 5.87; P <.001), pathological stage II (HR: 2.98; 95% CI: 1.12, 7.90; P = .028), stage III (HR: 4.88; 95% CI: 1.54, 15.5; P = .007), 11 to 20 lymph nodes positive (HR: 3.66; 95% CI: 1.31, 10.2; P = .013), >20 lymph nodes positive (HR: 6.41; 95% CI: 1.49, 27.6; P = .013). RMST at 10 years post-flap reconstruction showed 2 months of decreased survival time compared to implants (9.56 vs 9.74 years; 95% CI: -.339, -.024; P = .024). After matching, 563 implant and 563 flap patients were compared. Reconstruction was not associated with overall survival and recurrence. RMST between implant and flap reconstruction showed no difference in each 5-year interval over 20 years.

Conclusions:

Post-mastectomy breast reconstruction was not associated with a difference in long-term oncologic outcomes over a twenty-year period.
Artificial Contrast
Authors: Haase Robert , Pinetz Thomas , Kobler Erich , Paech Daniel , Effland Alexander , Radbruch Alexander , Deike-Hofmann Katerina
Published: February 2023

Deep learning approaches are playing an ever-increasing role throughout diagnostic medicine, especially in neuroradiology, to solve a wide range of problems such as segmentation, synthesis of missing sequences, and image quality improvement. Of particular interest is their application in the reduction of gadolinium-based contrast agents, the administration of which has been under cautious reevaluation in recent years because of concerns about gadolinium deposition and its unclear long-term consequences. A growing number of studies are investigating the reduction (low-dose approach) or even complete substitution (zero-dose approach) of gadolinium-based contrast agents in diverse patient populations using a variety of deep learning methods. This work aims to highlight selected research and discusses the advantages and limitations of recent deep learning approaches, the challenges of assessing its output, and the progress toward clinical applicability distinguishing between the low-dose and zero-dose approach.
Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Authors: Hanafy Radwa A. , Wang Yan , Stajich Jason E. , Pratt Carrie J. , Youssef Noha H. , Elshahed Mostafa S.
Published: February 2023

The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as ‘genera incertae sedis’ in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.
A unique cytotoxic CD4+T cells signature defines critical COVID-19
Authors: Baird Sarah , Ashley Caroline L. , Marsh-Wakefield Felix , Alca Sibel , Ashhurst Thomas M. , Ferguson Angela L. , Lukeman Hannah , Counoupas Claudio , Post Jeffrey J. , Konecny Pamela , Bartlett Adam , Martinello Marianne , Bull Rowena A. , Lloyd Andrew , Grey Alice , Hutchings Owen , Palendira Umaimainthan , Britton Warwick J. , Steain Megan , Triccas James A.
Published: February 2023

Background and objectives

SARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T cell response to the resolution or progression of disease is still unclear. Optimal protective immunity may require activation of distinct immune pathways. As such, defining the contribution of individual T cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. To address this, we performed immunophenotyping of T cell responses in unvaccinated individuals, representing the full spectrum of COVID-19 clinical presentation.

Methods

Spectral cytometry was performed on peripheral blood mononuclear cell samples from patients with PCR-confirmed SARS-CoV-2 infection. Computational and manual analyses were used to identify T cell populations associated with distinct disease states through unbiased clustering, principal component analysis and discriminant analysis.

Results

Critical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+(CTL) cells of a T follicular helper (TFH) or effector memory re-expressing CD45RA (TEMRA) phenotype. These CD4+CTLs were largely absent in those with less severe disease. In contrast, those with asymptomatic or mild disease were associated with high proportions of naïve T cells and reduced expression of activation markers.

Conclusion

Highly activated and cytotoxic CD4+T cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Potential for induction of these detrimental T cell responses should be considered when developing and implementing effective COVID-19 control strategies.
Relationship between Serum Leptin, Lipid Metabolism, HbA1c, and Renal Function in Individuals with Type 2 Diabetes Mellitus and Obesity and in Individuals with Type 2 Diabetes Mellitus without Obesity
Authors: Akinjinmi A. A. , Amballi A.A. , Opeyemi Abdulrahman Abdulbasit , Nicholas Aderinto , Ayokunle Adeniyi Akinbobola , Akindele I. A. , Muili AbdulBasit Opeyemi
Published: February 2023

Background

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterised by hyperglycaemia, impaired lipid metabolism, and insulin resistance. In addition to the traditional risk factors, recent studies have suggested that adipose tissue-derived hormones such as Leptin play a crucial role in the pathogenesis of T2DM and its related complications. However, the exact mechanism underlying the relationship between serum leptin levels and these comorbidities remains unclear.

Methods and Materials

The study included 222 individuals, with 74 having T2DM and obesity, and 74 having T2DM without obesity and 74 control group. Serum levels of leptin, total cholesterol, triglycerides, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and HbA1c were measured, and the glomerular filtration rate (GFR) was used as a measure of renal function.

Results

Serum leptin levels were significantly higher in individuals with T2DM and obesity compared to those without obesity (p<0.05). Additionally, total cholesterol, triglycerides, and LDL were significantly higher in individuals with T2DM and obesity compared to those without obesity (p<0.05). Serum leptin levels were positively correlated with total cholesterol, triglycerides, and LDL (p<0.05) and negatively correlated with HDL (p<0.01). The GFR was not significant when both groups were compared.

Conclusion

Obesity has a negative impact on lipid profile and glycemic control in type 2 diabetes patients and highlights the significance of considering the effect of obesity on the relationship between leptin and lipid profile in diabetic patients. These findings suggest that targeting obesity and leptin levels may be an effective strategy for improving lipid profile and glycemic control in type 2 diabetes.
ANALYSIS OF RIFAMPICIN INDETERMINATE RESULTS USING SHEWHART CONTROL CHARTS: IMPLICATIONS FOR PATIENTS AND TUBERCULOSIS CONTROL PROGRAMMES
Authors: Abaate Taagbara Jolly , Alali Aloni Adolphus
Published: February 2023

Background

Antimicrobial resistance is a growing global public health concern, and multidrug-resistant tuberculosis is responsible for roughly one-quarter of all antimicrobial-resistant infection-related deaths worldwide. GeneXpert is a rapid, automated molecular test that detects multi-drug-resistant tuberculosis using rifampicin as a predictor. It was recommended by the World Health Organization (WHO) in 2010 for national tuberculosis programs in developing countries; however, it has limitations. Indeterminate results for Mycobacterium tuberculosis indicate that the test was unable to determine whether the bacteria were resistant to rifampicin. This study used Shewhart Control Chart, which has action limits, to investigate the causes of indeterminate results.

Methods

The control limits on the Shewhart chart are central, upper, and lower. GeneXpert indeterminate results obtained between January 2017 and December 2020 in a tertiary hospital in a low and middle-income country were plotted. Points above the upper control limit were used to determine whether or not the process was under control.

Result

The proportion of GeneXpert results that were indeterminate varied, with 58% exceeding the upper limit. Only 42% were within the control limit, in comparison.

The majority of the laboratory results revealed an out-of-control signal by displaying points outside the control limits or non-random patterns of points known as special-cause variation, according to this study.

Conclusions

GeneXpert indeterminate results have an impact on patient management by preventing accurate diagnosis and delaying the start of anti-tuberculosis medication. Machine malfunctions, insufficient bacterial load, poor quality samples, operator errors, or faulty laboratory materials could all be to blame. Regular equipment checks by laboratory personnel, program sponsors, or leadership will be extremely beneficial in achieving the desired results and initiating appropriate treatment. Statistical process control is widely used in hospital performance monitoring and improvement, and it is becoming more popular in public health surveillance.
In Vivo CRISPR Gene Editing in Patients with Herpes Stromal Keratitis
Authors: Wei Anji , Yin Di , Zhai Zimeng , Ling Sikai , Le Huangying , Tian Lijia , Xu Jianjiang , Paludan Soren R , Cai Yujia , Hong Jiaxu
Published: February 2023

In vivo CRISPR gene therapy holds large clinical potential, but the safety and efficacy remain largely unknown. Here, we injected a single dose of HSV-1-targeting CRISPR formulation in the cornea of three patients with severe refractory herpes stromal keratitis (HSK) during corneal transplantation. Our study is an investigated initiated, open-label, single-arm, non-randomized interventional trial at a single center (NCT04560790). We found neither detectable CRISPR-induced off-target cleavages by GUIDE-seq nor systemic adverse events for 18 months on average in all three patients. The HSV-1 remained undetectable during the study. Our preliminary clinical results suggest that in vivo gene editing targeting the HSV-1 genome holds acceptable safety as a potential therapy for HSK.

One-Sentence Summary

Our study is the first in vivo CRISPR therapy for treating infectious disease and the first virus-like particle (VLP)-delivered gene therapy, reporting clinical follow-up to 21 months in HSK patients without seeing virus relapse, HSK recurrence, and CRISPR-associated side effects.
Machine Diagnosis of Chronic Obstructive Pulmonary Disease using a Novel Fast-Response Capnometer
Authors: Talker Leeran , Neville Daniel , Wiffen Laura , Selim Ahmed B , Haines Matthew , Carter Julian C , Broomfield Henry , Lim Rui Hen , Lambert Gabriel ,   BRS study team, Weiss Scott T , Hayward Gail , Brown Thomas , Chauhan Anoop , Patel Ameera X
Published: February 2023

Background

Although currently most widely used in mechanical ventilation and cardiopulmonary resuscitation, features of the carbon dioxide waveform produced through capnometry have been shown to correlate with V/Q mismatch, dead space volume, type of breathing pattern, and small airway obstruction. This study applied feature engineering and machine learning techniques to capnography data collected by the N-Tidal™ device across four clinical studies to build a classifier that could distinguish CO2recordings (capnograms) of patients with COPD from those without COPD.

Methods

Capnography data from four longitudinal observational studies (CBRS, GBRS, CBRS2 and ABRS) was analysed from 295 patients, generating a total of 88,186 capnograms. CO2sensor data was processed using Cambridge Respiratory Innovations’ regulated cloud platform, performing real-time geometric analysis on CO2waveforms to generate 82 physiologic features per capnogram. These features were used to train machine learning classifiers to discriminate COPD from ‘non-COPD’ (a group that included healthy participants and those with other cardiorespiratory conditions); model performance was validated on independent test sets.

Results

The best machine learning model (XGBoost) performance provided a class-balanced AUROC of 0·968 ± 0·017 and a positive predictive value (PPV) of 0·911 ± 0·028 for a diagnosis of COPD. The waveform features that are most important for driving classification are related to the alpha angle and expiratory plateau regions. These features correlated with spirometry readings, supporting their proposed properties as markers of COPD.

Conclusion

The N-Tidal device can be used to accurately diagnose COPD in near-real-time, lending support to future use in a clinical setting.

Funding

NIHR (i4i grant), Innovate UK, SBRI Healthcare and Pfizer OpenAir.
Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes
Authors:   Epi25 Collaborative, Chen Siwei , Neale Benjamin M , Berkovic Samuel F
Published: February 2023

Identifying genetic risk factors for highly heterogeneous disorders like epilepsy remains challenging. Here, we present the largest whole-exome sequencing study of epilepsy to date, with >54,000 human exomes, comprising 20,979 deeply phenotyped patients from multiple genetic ancestry groups with diverse epilepsy subtypes and 33,444 controls, to investigate rare variants that confer disease risk. These analyses implicate seven individual genes, three gene sets, and four copy number variants at exome-wide significance. Genes encoding ion channels show strong association with multiple epilepsy subtypes, including epileptic encephalopathies, generalized and focal epilepsies, while most other gene discoveries are subtype-specific, highlighting distinct genetic contributions to different epilepsies. Combining results from rare single nucleotide/short indel-, copy number-, and common variants, we offer an expanded view of the genetic architecture of epilepsy, with growing evidence of convergence among different genetic risk loci on the same genes. Top candidate genes are enriched for roles in synaptic transmission and neuronal excitability, particularly postnatally and in the neocortex. We also identify shared rare variant risk between epilepsy and other neurodevelopmental disorders. Our data can be accessed via an interactive browser, hopefully facilitating diagnostic efforts and accelerating the development of follow-up studies.
DNA damage signaling inDrosophilamacrophages modulates systemic cytokine levels in response to oxidative stress
Authors: Hersperger Fabian , Meyring Tim , Weber Pia , Chhatbar Chintan , Monaco Gianni , Dionne Marc S. , Paeschke Katrin , Prinz Marco , Groß Olaf , Classen Anne-Kathrin , Kierdorf Katrin
Published: February 2023

Environmental factors, infection, or injury can cause oxidative stress in diverse tissues and loss of tissue homeostasis. Effective stress response cascades, conserved from invertebrates to mammals, ensure reestablishment of homeostasis and tissue repair. Hemocytes, theDrosophilablood-like cells, rapidly respond to oxidative stress by immune activation. However, the precise signals how they sense oxidative stress and integrate these signals to modulate and balance the response to oxidative stress in the adult fly are ill-defined. Furthermore, hemocyte diversification was not explored yet on oxidative stress. Here, we employed high throughput single nuclei RNA-sequencing to explore hemocytes and other cell types, such as fat body, during oxidative stress in the adult fly. We identified distinct cellular responder states in plasmatocytes, theDrosophilamacrophages, associated with immune response and metabolic activation upon oxidative stress. We further define oxidative stress-induced DNA damage signaling as a key sensor and a rate-limiting step in immune-activated plasmatocytes controlling JNK-mediated release of the pro-inflammatory cytokineunpaired-3. We subsequently tested the role of this specific immune activated cell stage during oxidative stress and found that inhibition of DNA damage signaling in plasmatocytes, as well as JNK or upd3 overactivation, result in a higher susceptibility to oxidative stress. Our findings uncover that a balanced composition and response of hemocyte subclusters is essential for the survival of adultDrosophilaon oxidative stress by regulating systemic cytokine levels and cross-talk to other organs, such as the fat body, to control energy mobilization.
Seizure Semiology and Response to Treatment in a Pediatric Cohort withSCN2AVariants: A Parent Report
Authors: O’Connor John B. , Kirschenblatt Emily B. , Laux Linda , Berg Anne T. , Misra Sunita N. , Millichap John J.
Published: February 2023

We examined seizure semiology and response to medications in 28 children (9 female, 19 male) with likely pathogenic and pathogenicSCN2A-related epilepsy. Parents reported seizure onset, seizure semiology, genetic variants, therapies used for seizures, and response to treatment. 27 children experienced defined seizures and 1 reported no seizure history. The most common initial seizures were focal or hemi-convulsions (n=8). Tonic seizures were the most common reported seizure type while febrile and atonic or drop seizures were the least common. Most patients experienced multiple seizures daily or were entirely seizure-free, with no difference based on age at seizure onset. The proportion of effective trials of the 8 most commonly reported medications ranged from 4 of 26 trials (levetiracetam) to 5 of 10 trials (valproic acid). Phenytoin was the most commonly reported effective treatment (N=4). Topiramate was reported to be the most effective treatment in combination with another treatment (N=6). We found a wide phenotypic spectrum ofSCN2A-related disorders and a possible correlation between genotype and seizure onset, semiology, and treatment response. Gain-of-function mutations in early-onsetSCN2Aepilepsies responded well to sodium channel blockers. Further exploration ofSCN2Apathogenic variants are needed to identify mediation mechanisms of action inSCN2A-related epilepsy.
Disseminating sleep education to graduate psychology programs online: A knowledge translation study to improve the management of insomnia
Authors: Meaklim Hailey , Meltzer Lisa J. , Rehm Imogen C. , Junge Moira F. , Monfries Melissa , Kennedy Gerard A. , Bucks Romola S. , Graco Marnie , Jackson Melinda L.
Published: February 2023

Study objectives

Despite the negative impact of poor sleep on mental health, evidence-based insomnia management guidelines have not been translated into routine mental healthcare. Here, we evaluate a state-wide knowledge translation effort to disseminate sleep and insomnia education to graduate psychology programs online using the RE-AIM (Reach, Effectiveness, Adoption, Implementation, and Maintenance) evaluation framework.

Methods

Using a non-randomized waitlist control design, graduate psychology students attended a validated six-hour online sleep education workshop delivered as part of their graduate psychology program in Victoria, Australia. Sleep knowledge, attitudes, and practice assessments were conducted pre- and post-program, with long-term feedback collected at 12 months.

Results

Seven out of ten graduate psychology programs adopted the workshop (adoption rate = 70%). The workshop reached 313 graduate students, with a research participation rate of 81%. The workshop was effective at improving students’ sleep knowledge and self-efficacy to manage sleep disturbances using Cognitive Behavioral Therapy for Insomnia (CBT-I), compared to the waitlist control with medium-to-large effect sizes (allp<.001). Implementation feedback was positive, with 96% of students rating the workshop as very good-to-excellent. Twelve-month maintenance data demonstrated that 83% of students had used the sleep knowledge/skills learned in the workshop in their clinical practice. However, more practical training is required to achieve CBT-I competency.

Conclusion

Online sleep education workshops can be scaled to deliver cost-effective foundational sleep training to graduate psychology students. This workshop will accelerate the translation of insomnia management guidelines into psychology practice to improve sleep and mental health outcomes nationwide.
Structural basis of histone H2A lysine 119 deubiquitination by Polycomb Repressive Deubiquitinase BAP1/ASXL1
Authors: Thomas Jonathan F. , Valencia-Sánchez Marco Igor , Tamburri Simone , Gloor Susan L. , Rustichelli Samantha , Godínez-López Victoria , De Ioannes Pablo , Lee Rachel , Abini-Agbomson Stephen , Gretarsson Kristjan , Burg Jonathan M. , Hickman Allison R. , Sun Lu , Gopinath Saarang , Taylor Hailey , Meiners Matthew J. , Cheek Marcus A. , Rice William , Nudler Evgeny , Lu Chao , Keogh Michael-Christopher , Pasini Diego , Armache Karim-Jean
Published: February 2023

The maintenance of gene expression patterns during metazoan development is achieved by the actions of Polycomb group (PcG) complexes. An essential modification marking silenced genes is monoubiquitination of histone H2A lysine 119 (H2AK119Ub) deposited by the E3 ubiquitin ligase activity of the non-canonical Polycomb Repressive Complex 1. The Polycomb Repressive Deubiquitinase (PR-DUB) complex cleaves monoubiquitin from histone H2A lysine 119 (H2AK119Ub) to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. BAP1 and ASXL1, subunits that form active PR-DUB, are among the most frequently mutated epigenetic factors in human cancers, underscoring their biological importance. How PR-DUB achieves specificity for H2AK119Ub to regulate Polycomb silencing is unknown, and the mechanisms of most of the mutations in BAP1 and ASXL1 found in cancer have not been established. Here we determine a cryo-EM structure of human BAP1 bound to the ASXL1 DEUBAD domain in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for remodeling the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing new insight into understanding cancer etiology.

One Sentence Summary

We reveal the molecular mechanism of nucleosomal H2AK119Ub deubiquitination by human BAP1/ASXL1.
Cortical interneurons: fit for function and fit to function? Evidence from development and evolution
Authors: Keijser Joram , Sprekeler Henning
Published: February 2023

Cortical inhibitory interneurons form a broad spectrum of subtypes. This diversity suggests a division of labour, in which each cell type supports a distinct function. In the present era of optimisation-based algorithms, it is tempting to speculate that these functions were the evolutionary or developmental driving force for the spectrum of interneurons we see in the mature mammalian brain. In this study, we evaluated this hypothesis using the two most common interneuron types, parvalbumin (PV) and somatostatin (SST) expressing cells, as examples. PV and SST interneurons control the activity in the cell bodies and the apical dendrites of excitatory pyramidal cells, respectively, due to a combination of anatomical and synaptic properties. But was this compartment-specific inhibition indeed the function for which PV and SST cells originally evolved? Does the compartmental structure of pyramidal cells shape the diversification of PV and SST interneurons over development? To address these questions, we reviewed and reanalysed publicly available data on the development and evolution of PV and SST interneurons on one hand, and pyramidal cell morphology on the other. These data speak against the idea that the compartment structure of pyramidal cells drove the diversification into PV and SST interneurons. In particular, pyramidal cells mature late, while interneurons are likely committed to a particular fate (PV vs. SST) during early development. Moreover, comparative anatomy and single cell RNA-sequencing data indicate that PV and SST cells, but not the compartment structure of pyramidal cells, existed in the last common ancestor of mammals and reptiles. Specifically, turtle and songbird SST cells also express theElfn1andCbln4genes that are thought to play a role in compartment-specific inhibition in mammals. PV and SST cells therefore evolved and developed the properties that allow them to provide compartment-specific inhibition before there was selective pressure for this function. This suggest that interneuron diversity originally resulted from a different evolutionary driving force and was only later co-opted for the compartment-specific inhibition it seems to serve in mammals today. Future experiments could further test this idea using our computational reconstruction of ancestral Elfn1 protein sequences.
The structural basis of the Talin-KANK1 interaction that coordinates the actin and microtubule cytoskeletons at focal adhesions
Authors: Li X , Goult B.T , Ballestrem C , Zacharchenko T
Published: February 2023

Adhesion between cells and the extracellular matrix (ECM) is mediated by heterodimeric (αβ) integrin receptors that are intracellularly linked to the contractile actomyosin machinery. One of the proteins that control this link is talin, which organises cytosolic signalling proteins into discrete complexes on β-integrin tails referred to as focal adhesions (FAs). The adapter protein KANK1 binds to talin in the region of FAs known as the adhesion belt. Here, we developed a novel crystallographic method to resolve the talin-KANK1 complex. This structure revealed that the talin binding KN motif of KANK1 has a novel fold, where a β-turn stabilises the α-helical region, explaining its specific interaction with talin R7 and high affinity. Single point mutants in KANK1 identified from the structure abolished the interaction and enabled us to examine KANK1 enrichment in the adhesion belt. Strikingly, in cells expressing a constitutively active form of vinculin that keeps the FA structure intact even in the presence of myosin inhibitors, KANK1 localises throughout the entire FA structure even when actomyosin tension is released. We propose a model whereby actomyosin forces on talin eliminate KANK1 from talin binding in the centre of FAs while retaining it at the adhesion periphery.
Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to Cold Water Disease
Authors: Lee Bo-Hyung , Quillet Edwige , Rigaudeau Dimitri , Dechamp Nicolas , Duchaud Eric , Bernardet Jean-François , Boudinot Pierre , Rochat Tatiana
Published: February 2023

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused byFlavobacterium psychrophilumrepresents a major threat for freshwater salmonid farming worldwide. A collection of rainbow trout (Oncorhynchus mykiss) isogenic lines was previously produced from a French domestic population. Here, we compared BCWD resistance phenotypes using a subset of isogenic lines chosen for their contrasted susceptibilities toF. psychrophilum. We applied individual monitoring to document the infection process, including time-course quantification of bacteremia and innate immune response. Strikingly, BCWD resistance was correlated with a lower bacterial growth rate in blood. Several immune genes were expressed at higher levels in resistant fish regardless of infection: the Type II arginase (arg2), a marker for M2 macrophages involved in anti-inflammatory responses and tissue repair, and two Toll-like receptors (tlr2/tlr7), responsible for pathogen detection and inflammatory responses. This study highlights the importance of innate and intrinsic defense mechanisms in determining the outcome ofF. psychrophiluminfections, and illustrates that non-lethal time-course blood sampling for individual monitoring of bacteremia is a powerful tool to resolve within-host pathogen behavior in bacterial fish diseases.
Sensitivity to outcome devaluation in operant tasks is better predicted by food restriction level than reinforcement training schedule in mice
Authors: Chevée Maxime , Kim Courtney J. , Crow Nevin , Follman Emma G. , Calipari Erin S.
Published: February 2023

Behavioral strategies are often classified based on whether reinforcement is controlled by the value of the reinforcer. Value-sensitive behaviors, in which animals update their actions when reinforcer value is changed, are classified as goal-directed; conversely, value-insensitive actions, where behavior remains consistent when the reinforcer is removed or devalued, are considered habitual. Understanding the features of operant training that bias behavioral control toward either strategy is essential to understanding the cognitive and neuronal processes on which they rely. Using basic reinforcement principles, behavior can be biased toward relying on either process: random ratio (RR) schedules are thought to promote the formation of goal-directed behaviors while random intervals (RI) promote habitual control. However, how the schedule-specific features of these task structures relate to external factors to influence behavior is not well understood. Using male and female mice on distinct food restriction levels, we trained each group on RR schedules with responses-per-reinforcer rates matched to their RI counterparts to control for differences in reinforcement rate. We determined that food restriction level has a stronger effect on the behavior of mice following RR schedules than mice following RI schedules and that food restriction better predicted sensitivity to outcome devaluation than training schedule. Our results support the idea the relationships between RR or RI schedules with goal-directed or habitual behaviors, respectively, are more nuanced than previously appreciated and suggest that an animal’s engagement in a task must be accounted for, together with the structure of reinforcement schedules, to appropriately interpret the cognitive underpinnings of behavior.

Significance statement

Understanding the basic learning principles that control behavior is essential to developing therapies for psychiatric disorders such as addiction or obsessive-compulsive disorder. Reinforcement schedules are thought to control the reliance on habitual versus goal-directed control during adaptive behaviors. However, external factors that are independent of training schedule also influence behavior, for example by modulating motivation or energy balance. In this study, we find that food restriction levels are at least equally important as reinforcement schedules in shaping adaptive behavior. Our results add to the growing body of work showing the distinction between habitual and goal-directed control is nuanced.
Duplex Sequencing Provides Detailed Characterization of Mutation Frequencies and Spectra in the Bone Marrow of MutaMouse Males Exposed to Procarbazine Hydrochloride
Authors: Dodge Annette E. , LeBlanc Danielle P.M. , Zhou Gu , Williams Andrew , Meier Matthew J. , Van Phu , Lo Fang Yin , Valentine Charles C. , Salk Jesse J. , Yauk Carole L. , Marchetti Francesco
Published: February 2023

Mutagenicity testing is an essential component of health safety assessment. Duplex Sequencing (DS), an emerging high-accuracy DNA sequencing technology, may provide substantial advantages over conventional mutagenicity assays. DS could be used to eliminate reliance on standalone reporter assays and provide mechanistic information alongside mutation frequency (MF) data. However, the performance of DS must be thoroughly assessed before it can be routinely implemented for standard testing. We used DS to study spontaneous and procarbazine (PRC)-induced mutations in the bone marrow (BM) of MutaMouse males across a panel of 20 diverse genomic targets. Mice were exposed to 0, 6.25, 12.5, or 25 mg/kg-bw/day for 28 days by oral gavage and BM sampled 42 days post-exposure. Results were compared with those obtained using the conventionallacZviral plaque assay on the same samples. DS detected significant increases in mutation frequencies and changes to mutation spectra at all PRC doses. Low intra-group variability within DS samples allowed for detection of increases at lower doses than thelacZassay. While thelacZassay initially yielded a higher fold-change in mutant frequency than DS, inclusion of clonal mutations in DS mutation frequencies reduced this discrepancy. Power analyses suggested that three animals per dose group and 500 million duplex base pairs per sample is sufficient to detect a 1.5-fold increase in mutations with >80% power. Overall, we demonstrate several advantages of DS over classical mutagenicity assays and provide data to support efforts to identify optimal study designs for the application of DS as a regulatory test.
FTSH3 facilitates complex I degradation through a direct interaction with the complex I subunit PSST
Authors: Ghifari Abi S. , Ivanova Aneta , Berkowitz Oliver , Whelan James , Murcha Monika W.
Published: February 2023

Complex I (NADH dehydrogenase), the largest complex involved in mitochondrial oxidative phosphorylation is composed of nuclear and mitochondrial encoded subunits. Its assembly requires sequential addition of subdomains and modules. As it is prone to oxidative damage, complex I subunits continually undergo proteolysis and turnover. We describe the mechanism by which complex I abundance is regulated in a complex I deficient mutant. Using a forward genetic approach we have identified that the complex I Q-module domain subunit PSST, interacts with FTSH3 (Filamentous Temperature Sensitive H3) to mediate the disassembly of the matrix arm domain module for proteolysis and turnover as a means of protein quality control. We show the direct interaction of FTSH3 with PSST and identify the amino acid residues required for this interaction. It is the ATPase function of FTSH3 that is required for the interaction, as the mutation can be compensated by a proteolytically inactive form of FTSH3. Furthermore, it cannot be compensated by FTSH10 that is also located in mitochondria, as the latter does not interact with PSST. This study reveals the mechanistic process at the resolution of the residues involved of how FTSH3 recognises complex I for degradation.
A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters
Authors: Gronniger Jessica L. , Gray Patrick C. , Niebergall Alexandria K. , Johnson Zackary I. , Hunt Dana E.
Published: February 2023

Abstract

Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyllaalong with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lowerTrichodesmiumand higherProchlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 clades) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception; additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.
Self-association of a nucleoid-binding protein increases with macromolecular crowding inEscherichia coli
Authors: Pittas Theodoros , Boersma Arnold J.
Published: February 2023

Many proteins self-associate to achieve function. Macromolecular crowding enhances protein self-assembly in buffer experiments with added crowders, and crowding could therefore regulate protein function and organization in cells. In eukaryotic cells, protein condensation has been shown to increase with crowding. However, it is unclear what the effect of crowding is on native protein self-assembly in the highly crowdedEscherichia colicell. To determine the role of crowding in the self-assembly of a native protein, we study here the nucleoid-binding H-NS inE. coliand alter macromolecular crowding using a set of perturbations. We followed H-NS self-assembly using a FRET-based method for determining intermolecular interactions with a single genetic intervention. In dilute cell lysate, we see that H-NS self-assembly increases with salts, macromolecular crowding, and its own concentration. InE. coli, the oligomerization increases with crowding. We see that the response of H-NS oligomerization to a sudden crowding change is not immediate but requires time to adapt. Our findings implicate that in-cell crowding affects intracellular organization by promoting self-assembly.