bluuebunny/crossref_metadata_2025 huggingface dataset:
The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated byLactobacillus inersregardless of HPV status
Authors: Vargas-Robles Daniela , Romaguera Josefina , Alvarado-Velez Ian , Tosado-Rodríguez Eduardo , Dominicci-Maura Anelisse , Sanchez Maria , Wiggin Kara J. , Gilbert Jack A. , Martinez-Ferrer Magaly , Forney Larry J. , Godoy-Vitorino Filipa
Published: May 2023

Introduction

The cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, non-pregnant and menopausal women living in Puerto Rico with and without Human Papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota associated with variation in cervical cytology. A total of 294 women comprised of reproductive-age non-pregnant (N=196), pregnant (N=37), and menopausal (N=61) women were enrolled. The cervicovaginal bacteria was characterized by 16S rRNA amplicon sequencing, the HPV were genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated byLactobacillus iners. Pregnant women in the 2ndand 3rdtrimesters had decreased diversity and a decreased abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than pre-menopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota women living in Puerto Rican were either dominated byL. inersor diverse microbial communities regardless of a woman’s physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV, increase the risk of cervical lesions of women living in Puerto Rico.
Validation of the in-house designed one-trial inhibitory avoidance test for two strains of adult zebrafish
Authors: Ferreira Jorge M. , Silva Joana , Barros Sofia , Caetano Inês , Fernandes Pedro , Olsson Anna , Valentim Ana M.
Published: May 2023

Open-source validated tools are important for affordable high-quality science. Zebrafish model is often used in behavioral sciences, thus validated tools must be developed for this species. We aimed to implement the memory task one-trial inhibitory avoidance test in our laboratory by creating a custom-built 3D printed apparatus and custom-made hardware and software using microcontrollers; this decreases the costs and increases methodological flexibility. In this task, a mild electric shock (3.3 ± 0.3V and 2A for 5sec) is used as an aversive stimulus for the one-trial inhibitory avoidance task based on classical conditioning. For this study we used 72-adult zebrafish from the AB and TU strain. The aversive stimulus caused a robust and long-lasting memory that was learned in one session. The apparatus consisted in one aquarium with two compartments (white and black) where, during the conditioning session, the shock was delivered in the preferred side (black), followed by 30min of immersion in 20μM MK-801, a compound known for inducing amnesia (amnesic group, n= 20 for AB and 17 for TU), or in clean water (control, n= 20 for AB and 15 for TU). Both the AB and TU strain animals from the control group took more time to enter in the black compartment after conditioning (p≤0.039), indicating avoidance for the black side, while the latency was not altered in the MK-801 group, demonstrating impaired memory. In summary, this open-source apparatus is an affordable and validated option for memory assessment for the two most used strains of zebrafish in research.
The uniqueness of the Brazilian Yellow Fever Virus. Are the vaccines less effective against it?
Authors: Mamidi Prabhudutta , Gaur Mahendra , Mishra Baijayantimala , Subudhi Bharat Bhusan , Rath Sutapa , Mohanty Monalisa
Published: May 2023

The years 2016-2019 witnessed the expansion of Yellow Fever Virus (YFV) circulation area in Brazil. Deforestation and mutations in the nsp genes were presumed responsible for the reemergence of YFV in brazil. However, our data analysis involving 200 clinical isolates worldwide including vaccine strains showed two amino acids substitutions exclusively in the Brazilian strains at critical positions (V318A and I335M) in the ED III domain of E protein. Our molecular dynamics analysis involving reference and mutant structures suggests that the mutations significantly changed the conformational rearrangement and folding of the YFV-EDIII domain as revealed by RMSF, PCA, Porcupine plots and secondary structure analysis. Briefly, the regions 324-330, 339-346 and 347-359 had a higher fluctuation than the wild, while regions 313-318 and 379-384 had a lower fluctuation. As reported earlier that the residues E325 and E380 are part of vaccine epitopes and any mutations in these residues reduced the binding of vaccine generated mabs to the epitopes. Hence, it may be speculated from our porcupine plot data analysis that that the commercial YFV vaccines may not be fully effective against the Brazilian strains in particular owing to the fluctuations of these residues. However, future investigation is required to validate the observations.
SARS-COV-2 Spike Protein Fragment eases Amyloidogenesis of α-Synuclein
Authors: Chesney Andrew D. , Maiti Buddhadev , Hansmann Ulrich H. E.
Published: May 2023

Parkinson’s Disease is accompanied by presence of amyloids in the brain formed of α-synuclein chains. Correlation between COVID-19 and the onset of Parkinson’s disease let to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, shifts preferentially the ensemble of α-synuclein monomer towards rod-like fibril seeding conformations, and at the same time stabilizes differentially this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2.
Quantifying Effects of Dataset Size, Data Variability, and Data Curvature on Modelling of Simulated Age-Related Motor Development Data
Authors: Dobri Stephan C.D. , Scott Stephen H. , Davies T. Claire
Published: May 2023

Motor development in children and youth occurs non-linearly; improvements are rapid at younger ages and decrease as they reach adulthood. There is also evidence that performance variability changes as children and youth age. Accurate models of typical performance are necessary to identify deficits in motor performance and to track the efficacy of therapies. Robotic devices have been used previously to measure motor performance in children and youth, and produce models of typical performance; however, power analyses on these models have not been explored.

An algorithm was created to generate normative models of typical motor performance. The accuracy and repeatability of the algorithm were tested using simulated data that changed the number of data points, and the curvature and variability of the data. Two-hundred and eighty-eight participants who are typically developing (ages 5-18) completed a robotic point-to-point reaching task with the Kinarm Exoskeleton. Exponential curves were fit to reaction time measured by the Kinarm to model typical performance. The results of the simulations were used to generate confidence intervals on the models of typical performance.

The simulations showed that number of datapoints had the largest impact on accuracy and repeatability of the models, and that repeatability was age-dependent. The simulations with the uniform and non-uniform datasets generated different confidence intervals; however, these differences were minimal when the number of datapoints at each age were matched between the two datasets.

To ensure identification of deficits is accurately determined, there is a need to account for differences in repeatability when developing models of typical motor performance in children and youth. The results of our simulations can be used to assess repeatability of non-linear models of motor performance based on dataset size in the future.
The Mechanical Influence of Densification on Initial Epithelial Architecture
Authors: Cammarota Christian , Dawney Nicole S. , Bellomio Phillip M. , Jüng Maren , Fletcher Alexander G. , Finegan Tara M. , Bergstralh Dan T.
Published: May 2023

Epithelial tissues are the most abundant tissue type in animals, lining body cavities and generating compartment barriers. The function of a monolayer epithelium – whether protective, secretory, absorptive, or filtrative –relies on regular tissue architecture with respect to the apical-basal axis. Using an unbiased 3D analysis pipeline developed in our lab, we previously showed that epithelial tissue architectures in culture can be divided into distinct developmental categories, and that these are intimately connected to cell density: at sparse densities, cultured epithelial cell layers have a squamous morphology (Immature); at intermediate densities, these layers develop lateral cell-cell borders and rounded cell apices (Intermediate); cells at the highest densities reach their full height and demonstrate flattened apices (Mature). These observations prompted us to ask whether epithelial architecture emerges from the mechanical constraints of densification, and to what extent a hallmark feature of epithelial cells, namely cell-cell adhesion, contributes. In other words, to what extent is the shape of cells in an epithelial layer a simple matter of sticky, deformable objects squeezing together? We addressed this problem using a combination of computational modeling and experimental manipulations. Our results show that the first morphological transition, from Immature to Intermediate, can be explained simply by cell crowding. Additionally, we identify a new division (and thus transition) within the Intermediate category, and find that this second morphology relies on cell-cell adhesion.
MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing
Authors: Jarva Taiya , Zhang Jialin , Flynt Alex
Published: May 2023

RNA interference (RNAi) is mediated by small (20-30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefited from genetic models where key enzymatic events were identified that lead to stereotypical positioning of small RNAs relative to precursor transcripts. Increasingly there is interest in using RNAi in non-model systems due to ease of generating synthetic small RNA precursors for research and biotechnology. Unfortunately, small RNAs are often rapidly evolving, requiring investigation of a species’ endogenous small RNAs prior to deploying an RNAi approach. This can be accomplished through small non-coding RNA sequencing followed by applying various computational tools; however, the complexity and separately maintained packages lead to significant challenges for annotating global small RNA populations. To address this need, we developed a simple and efficient R package (MiSiPi-Rna) which can be used to characterize pre-selected loci with plots and statistics, aiding researchers understanding RNAi biology specific to their target species. Additionally, MiSiPi-Rna pioneers several computational approaches to identifying Dicer processing to assist annotation of miRNA and siRNA.
Delayed blood pressure recovery after exercise stress test is associated with autonomic dysfunction and pulse pressure in a middle-aged healthy group
Authors: Lee Hancheol , Kim Hyeongsoo , Oh Seungjin , Park Jong-Kwan , Jang Ji-Yong , Chun Kyeong-Hyeon , Yoon Se-Jung
Published: May 2023

Background

Delayed heart rate (HR) and blood pressure recovery after exercise test is known as the reliable indexes of autonomic dysfunction. Here we tried to evaluate the serial changes in various indicators during exercise test and correlations among them in a normotensive healthy middle-aged group.

Methods

A total of 122 patients without hypertension or diabetes was enrolled (mean age, 55.6 ± 11.0; male, 56.6 %; mean blood pressure, 124.8 ± 16.6 / 81.5 ± 9.6 mmHg). Treadmill test was performed for evaluation of chest pain. Patients with coronary artery disease, positive treadmill test result, left ventricular dysfunction or renal failure were excluded. Heart rate recovery was calculated by subtracting the HR in the first or second minute of recovery period from the HR of peak exercise (HRR1 or HRR2). Systolic blood pressure in the 4thminute of recovery stage (SBPR4) was used to show delayed blood pressure recovery.

Results

Metabolic equivalents (METs) and HR in stage 2 to 4 were significantly correlated with both HRR1 and HRR2. Multiple regression analysis of HRR revealed significant correlation of METs and SBPR4. SBPR4 was significantly correlated with both HRR1 and HRR2 (HRR1, r=-0.376, p<0.001; HRR2, r=-0.244, p=0.008). SBPR4 revealed significant correlation with SBP in the baseline to stage 3 and pulse pressure (r=0.406, p<0.001).

Conclusions

Delayed BP recovery after peak exercise test revealed significant association with autonomic dysfunction and pulse pressure in normotensive middle-aged healthy group. It can be a simple and useful marker of autonomic dysfunction and arterial stiffness.
IL-10 constrains sphingolipid metabolism via fatty acid desaturation to limit inflammation
Authors: York Autumn G. , Skadow Mathias H. , Qu Rihao , Oh Joonseok , Mowel Walter K. , Brewer J. Richard , Kaffe Eleanna , Williams Kevin J. , Kluger Yuval , Crawford Jason M. , Smale Stephen T. , Bensinger Steven J. , Flavell Richard A.
Published: May 2023

Unchecked chronic inflammation is the underlying cause of many diseases, ranging from inflammatory bowel disease to obesity and neurodegeneration. Given the deleterious nature of unregulated inflammation, it is not surprising that cells have acquired a diverse arsenal of tactics to limit inflammation. IL-10 is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types; however, the exact mechanism by which IL-10 signaling subdues inflammation remains unclear. Here, we find that IL-10 signaling constrains sphingolipid metabolism. Specifically, we find increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10-deficient macrophages. Genetic deletion of CerS2, the enzyme responsible for VLC ceramide production, limited exacerbated inflammatory gene expression associated with IL-10 deficiency bothin vitroandin vivo, indicating that “metabolic correction” is able to reduce inflammation in the absence of IL-10. Surprisingly, accumulation of saturated VLC ceramides was regulated by flux through thede novomono-unsaturated fatty acid (MUFA) synthesis pathway, where addition of exogenous MUFAs could limit both saturated VLC ceramide production and inflammatory gene expression in the absence of IL-10 signaling. Together, these studies mechanistically define how IL-10 signaling manipulates fatty acid metabolism as part of its molecular anti-inflammatory strategy and could lead to novel and inexpensive approaches to regulate aberrant inflammation.
Polygenic risk of obesity and BMI trajectories over 36 years: a longitudinal study of adult Finnish twins
Authors: Berntzen Bram J. , Palviainen Teemu , Silventoinen Karri , Pietiläinen Kirsi H. , Kaprio Jaakko
Published: May 2023

Objective

We investigated 36-year body mass index (BMI) trajectories in twins whose BMI in young adulthood was below, within, or above their genetically expected BMI, with a focus on twin pairs with large intrapair BMI differences (within-pair ΔBMI ≥ 3 kg/m2).

Methods

Together, 3227 like-sexed twin pairs (34% monozygotic [MZ]) were examined at age ∼30 in 1975 and followed up in 1981, 1990, and 2011. In 1975, the observed BMI of an individual was considered either within (±2.0 kg/m2), below (<-2.0 kg/m2), or above (>+2.0 kg/m2) genetically expected BMI, measured by a polygenic risk score of 996,919 single nucleotide polymorphisms.

Results

In MZ and DZ twin pairs with large intrapair BMI differences, the co-twin with a higher observed BMI in 1975 deviated above expected BMI more frequently (∼2/3rd) than the co-twin with a lower BMI deviated below expectation (∼1/3rd). Individuals below, within, and above expectation in 1975 reached, respectively, normal weight, overweight, and obesity by 2011, with a mean BMI increase of 4.5 (95% confidence interval 4.3 to 4.8) kg/m2.

Conclusion

Categorizing BMI as below, within, or above PRS-predicted BMI helps identifying individuals who have been resistant or susceptible to weight gain. This may provide new insights into determinants and consequences of obesity.
Assessing Contributing and Mediating Factors of Telemedicine on Burnout
Authors: Boksa Valerie , Pennathur Priyadarshini
Published: May 2023

Scientific Abstract

Objective

The prevalence of burnout among healthcare providers has been steadily increasing, with a call to action issued in 2019. Immediately following this call to action, the COVID-19 pandemic drastically changed demand. Use of telemedicine expanded in response to COVID-19 and changed the experience of care delivery for healthcare providers. The impact of telemedicine use during COVID-19 on the provider well-being is less well known. This study aims to assess the prevalence of burnout in providers who used telemedicine and to better understand how specific factors of telemedicine can impact workplace stress.

Methods

Providers in urgent care clinics were invited to participate in a burnout assessment survey using the Maslach Burnout Inventory questionnaire. The prevalence of burnout, burnout profiles, and correlations were analyzed in the resulting data. Follow-up interviews provided further insight on contributing and mediating factors of telemedicine on provider burnout.

Results

The findings from this study provide technology- and organizational-level recommendations to prevent increased risk of burnout among telemedicine providers. The classification of contributing and mediating factors also provides a framework for understanding the risks that this technology can pose to workplace stress. Future research recommendations to better quantify the relationship between burnout and telemedicine use and to effectively design intervention and implementation strategies are discussed.

Public Interest Summary

Considering the high rates of burnout in the healthcare industry prior to the pandemic, the severe demands the COVID-19 pandemic had on healthcare workers, and the drastic changes in workflow due to the widespread adoption of telemedicine, it is important to assess current levels of provider burnout and to collect information from frontline clinicians on how telemedicine impacts workplace stress. A survey was administered to assess burnout in healthcare workers who provided care via telemedicine. The interviews provided additional insight on how telemedicine affected workplace stress. Survey results showed that 25% of the respondents reported one or more manifestations of burnout; and there was a correlation between personal accomplishment scores and reported months of telemedicine use. Findings from the interviews and review of literature identified what design and use characteristics of telemedicine contributed to and/or alleviated burnout. Results address how organizations can best support their employees who administer care via telemedicine and guide researchers with direction for future studies.
Specific Modulation of CRISPR Transcriptional Activators through RNA-Sensing Guide RNAs in Mammalian Cells and Zebrafish Embryos
Authors: Pelea Oana , Mayes Sarah , Ferry Quentin RV. , Fulga Tudor A. , Sauka-Spengler Tatjana
Published: May 2023

Cellular transcripts encode important information regarding cell identity and disease status. The activation of CRISPR in response to RNA biomarkers holds the potential for controlling CRISPR activity with spatiotemporal precision. This would enable the restriction of CRISPR activity to specific cell types expressing RNA biomarkers of interest while preventing unwanted activity in other cells. Here, we present a simple and specific platform for modulating CRISPR activity in response to RNA detection through engineeringStreptococcus pyogenesCas9 single-guide RNAs (sgRNAs). sgRNAs are engineered to fold into complex secondary structures that, in the ground state, inhibit their activity. The engineered sgRNAs become activated upon recognising complementary RNAs, thus enabling Cas9 to perform its function. Our approach enables CRISPR activation in response to RNA detection in both HEK293T cells and zebrafish embryos. Iterative design optimisations allowed the development of computational tools for generating sgRNAs capable of detecting RNA sequences of choice. Mechanistic investigations reveal that engineered sgRNAs are cleaved during RNA detection, and we identify key positions that benefit from chemical modifications to improve the stability of engineered sgRNAsin vivo. Our sensors open up novel opportunities for developing new research and therapeutic applications using CRISPR activation in response to endogenous RNA biomarkers.
CD38 regulates ovarian function and fecundity via NAD+metabolism
Authors: Perrone Rosalba , Ashok Kumaar Prasanna Vadhana , Haky Lauren , Hahn Cosmo , Riley Rebeccah , Balough Julia , Zaza Giuliana , Soygur Bikem , Hung Kaitlyn , Prado Leandro , Kasler Herbert G. , Tiwari Ritesh , Matsui Hiroyuki , Hormazabal Genesis Vega , Duncan Francesca Elizabeth , Verdin Eric
Published: May 2023

Mammalian female reproductive lifespan is typically significantly shorter than life expectancy and is associated with a decrease in ovarian NAD+ levels. However, the mechanisms underlying this loss of ovarian NAD+ are unclear. Here, we show that CD38, a NAD+ consuming enzyme, is expressed in the ovarian extrafollicular space, primarily in immune cells, and its levels increase with reproductive age. Reproductively young mice lacking CD38 exhibit larger primordial follicle pools, elevated ovarian NAD+ levels, and increased fecundity relative to wild type controls. This larger ovarian reserve results from a prolonged window of follicle formation during early development. However, the beneficial effect of CD38 loss on reproductive function is not maintained at advanced age. Our results demonstrate a novel role of CD38 in regulating ovarian NAD+ metabolism and establishing the ovarian reserve, a critical process that dictates a female’s reproductive lifespan.
Prefrontal cortex proteomic alteration after social instability stress in adolescents rats
Authors: Santos Evelyn C. S. , Terceiro Ana Filipa , Vitorino Rui , Lopes Igor , Alves Renata L. , Relvas João B. , Summavielle Teresa , Magalhães Ana
Published: May 2023

Early life stress can have significant effects on the developing brain and lead to changes in the structure and function of brain regions involved in stress regulation, emotion and cognitive control. Here, we used the social instability stress (SIS) protocol to understand the impact of social stress during mild (PND30) and late (PND45) adolescence. Our results revealed that SIS can compromise the dominance-subordination coping strategy but does not affect social recognition and motivation in rats. Moreover, SIS can lead to subtle modifications at the molecular level that hamper normal development of the prefrontal cortex in a sex- and age-dependent manner. Understanding the impact of early life stress on brain organization is crucial for developing effective prevention and intervention strategies. By identifying those who are most vulnerable to the effects of stress and providing targeted support and resources, it may be possible to mitigate the negative consequences of early adversity and promote healthy brain development.
Self-organisation of mortal filaments: the role of FtsZ treadmilling in bacterial division ring formation
Authors: Vanhille-Campos Christian , Whitley Kevin D. , Radler Philipp , Loose Martin , Holden Séamus , Šarić Anđela
Published: May 2023

Protein filaments in the cell commonly treadmill – they grow on one end while shrinking on the other, driven by energy consumption. Treadmilling filaments appear to be moving, even though individual proteins remain static. Here, we investigate the role of treadmilling, implemented as dynamic turnover, in the collective filament self-organisation. On the example of the bacterial FtsZ protein, a highly conserved tubulin homologue, we show, in computer simulations andin vitroexperiments, that treadmilling drives filament nematic ordering by dissolving misaligned filaments. We demonstrate that ordering via local dissolution allows the system to quickly respond to chemical and geometrical biases in the cell, and is necessary for the formation of the FtsZ ring required for bacterial cell division in livingBacillus subtiliscells. We finally use simulations to quantitatively explain the characteristic dynamics of FtsZ ring formationin vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a novel mechanism for nematic ordering via constant birth and death of energy-consuming filaments.
Genome-wide analysis of Respiratory burst oxidase homolog (Rboh) genes inAquilariaspecies and its association with agarwood formation
Authors: Begum Khaleda , Das Ankur , Ahmed Raja , Akhtar Suraiya , Kulkarni Ram , Banu Sofia
Published: May 2023

Respiratory burst oxidase homolog (Rboh), generate reactive oxygen species (ROS) to maintain normal growth and pathogen induced defence responses in plants. InAquilariaplants, wounding and fungal invasion results in the biosynthesis of secondary metabolites as a defence response which with due course develop into agarwood. During pathogen invasion,Aquilariatree accumulate ROS species through the action of Rboh enzymes. Although in agarwood formation role of Rboh gene family has been implicated, an comprehensives study onRbohgene family and information of its role during agarwood formation in missing. In this study, sevenRbohgenes were identified from the genomes of twoAquilariaspecies viz.,Aquilaria agallochaandAquilaria sinensisand phylogenetically classified into five groups.

Stress response, hormone regulation, and development related regulatory elements were identified in the promoter regions. The protein sequences comprised of four conserved domains, an EF-hand domain, and a transmembrane region which they probably utilise for MAPK signaling, plant-pathogen interaction and plant hormone signal transduction pathways. Expression analyses revealed that among the seven members,AaRbohAandAaRhobCwere involved in generation of ROS species, and also probably play role in agarwood formation. These findings provide valuable information regarding the Rboh members ofA. agallochawhich can be further used for functional analyses for in-depth understanding of ROS mediated signalling and regulation of agarwood formation.

Graphical abstract
Application of a1H Brain MRS Benchmark Dataset to Deep Learning for Out-of-Voxel Artifacts
Authors: Gudmundson Aaron T. , Davies-Jenkins Christopher W. , Özdemir İpek , Murali-Manohar Saipavitra , Zöllner Helge J. , Song Yulu , Hupfeld Kathleen E. , Schnitzler Alfons , Oeltzschner Georg , Stark Craig E. L. , Edden Richard A. E.
Published: May 2023

Neural networks are potentially valuable for many of the challenges associated with MRS data. The purpose of this manuscript is to describe the AGNOSTIC dataset, which contains 259,200 synthetic1H MRS examples for training and testing neural networks. AGNOSTIC was created using 270 basis sets that were simulated across 18 field strengths and 15 echo times. The synthetic examples were produced to resemblein vivobrain data with combinations of metabolite, macromolecule, residual water signals, and noise. To demonstrate the utility, we apply AGNOSTIC to train two Convolutional Neural Networks (CNNs) to address out-of-voxel (OOV) echoes. A Detection Network was trained to identify the point-wise presence of OOV echoes, providing proof of concept for real-time detection. A Prediction Network was trained to reconstruct OOV echoes, allowing subtraction during post-processing. Complex OOV signals were mixed into 85% of synthetic examples to train two separate CNNs for the detection and prediction of OOV signals. AGNOSTIC is available through Dryad and all Python 3 code is available through GitHub. The Detection network was shown to perform well, identifying 95% of OOV echoes. Traditional modeling of these detected OOV signals was evaluated and may prove to be an effective method during linear-combination modeling. The Prediction Network greatly reduces OOV echoes within FIDs and achieved a median log10normed-MSE of –1.79, an improvement of almost two orders of magnitude.
Connectome-wide structure-function coupling models implicate polysynaptic alterations in autism
Authors: Park Bo-yong , Benkarim Oualid , Weber Clara F. , Kebets Valeria , Fett Serena , Yoo Seulki , Martino Adriana Di , Milham Michael P. , Misic Bratislav , Hong Seok-Jun , Bernhardt Boris C.
Published: May 2023

Abstract

Autism spectrum disorder (ASD) is one of the most common neurodevelopmental diagnoses. Although incompletely understood, structural and functional network alterations are increasingly recognized to be at the core of the condition. We utilized multimodal imaging and connectivity modeling to study structure-function coupling in ASD, and probed mono- and polysynaptic mechanisms on structurally-governed network function. We examined multimodal magnetic resonance imaging data in 47 ASD and 37 neurotypical controls from the Autism Brain Imaging Data Exchange (ABIDE) II initiative. We predicted intrinsic functional connectivity from structural connectivity data in each participant using a Riemannian optimization procedure that varies the times that simulated signals can unfold along tractography-derived personalized connectomes. In both ASD and neurotypical controls, we observed improved structure-function prediction at longer diffusion time scales, indicating better modeling of brain function when polysynaptic mechanisms are accounted for. Prediction improvements were marked in transmodal association systems, such as the default mode network, in both controls and ASD. Improvements were, however, lower in ASD in a polysynaptic regime at higher simulated diffusion times. Regional differences followed a sensory-to-transmodal cortical hierarchy, with an increased gap between groups in transmodal compared to sensory/motor systems. Multivariate associative techniques revealed that structure-function differences reflected inter-individual differences in autistic symptoms and verbal as well as non-verbal intelligence. Our network modeling approach sheds light on atypical structure-function coupling in autism, and suggests that polysynaptic network mechanisms are implicated in the condition and can help explain its wide range of associated symptoms.
Patterned Metal Grids for Flexible and Transparent Neural Microelectrode Arrays
Authors: Trêpo Ivânia , Pinto Joana V. , Santa Ana , Pereira Maria E. , Calmeiro Tomás , Coelho Beatriz , Henriques Célia , Martins Rodrigo , Fortunato Elvira , Carey Megan R. , Marques Hugo G. , Barquinha Pedro , Neto Joana P.
Published: May 2023

Flexible and transparent microelectrodes can provide large-scale neural recordings with temporal and spatial resolution when used alongside functional calcium imaging. Patterned metal grids defined by direct laser writing (DWL) are a promising approach for these electrodes, as they resort to standard microfabrication processes and materials, allowing the possibility of mass production. For these reasons, a study exploring transparent grid-based electrodes using DWL for measuring electrocorticography signal was performed. Patterned metal grids with 1 μm of linewidth and 22 μm of spacing between lines showed a sheet resistance of 6 Ω/sq and a transmittance of 81% at 550 nm. The grids were transferred to a 5 μm Parylene-C membrane using an optimized procedure that involves an oxygen plasma pre-treatment. This procedure ensures mechanical robustness and stability of the grids. Finally, a flexible and transparent prototype was fabricated with a microelectrode array composed by 16 electrodes with 500 μm of diameter. These microelectrodes shown an impedance of 10 kΩ at 1 kHz in saline solution and they are highly conformal facilitating in vivo implantation and the recording of neural activity in the mouse cerebellum surface. To conclude, patterned metal grids based-electrodes exhibit a promising performance compared to transparent conductive oxides or graphene. Moreover, the introduction of DLW enables easy and fast manipulation of grid shape and dimensions without the need of physical masks, while keeping large scale compatibility, which is important for tools used in neuroscience community.
Monomethylation of Lysine 27 at Histone 3 Confers Lifelong Susceptibility to Stress
Authors: Torres-Berrío Angélica , Estill Molly , Ramakrishnan Aarthi , Kronman Hope , Patel Vishwendra , Minier-Toribio Angélica , Issler Orna , Browne Caleb J. , Parise Eric M. , van der Zee Yentl , Walker Deena , Martínez-Rivera Freddyson J. , Lardner Casey K. , Durand-de Cuttoli Romain , Russo Scott J. , Shen Li , Sidoli Simone , Nestler Eric J.
Published: May 2023

Histone post-translational modifications are critical for mediating persistent alterations in gene expression. By combining unbiased proteomics profiling, and genome-wide approaches, we uncovered a role for mono-methylation of lysine 27 at histone H3 (H3K27me1) in the enduring effects of stress. Specifically, mice exposed to early life stress (ELS) or to chronic social defeat stress (CSDS) in adulthood displayed increased enrichment of H3K27me1, and transient decreases in H3K27me2, in the nucleus accumbens (NAc), a key brain-reward region. Stress induction of H3K27me1 was mediated by the VEFS domain of SUZ12, a core subunit of the polycomb repressive complex-2, which is induced by chronic stress and controls H3K27 methylation patterns. Overexpression of the VEFS domain led to social, emotional, and cognitive abnormalities, and altered excitability of NAc D1 mediums spiny neurons. Together, we describe a novel function of H3K27me1 in brain and demonstrate its role as a “chromatin scar” that mediates lifelong stress susceptibility.
Optogenetic determination of dynamic and cell-type-specific chloride equilibrium potentials
Authors: Burman Richard J. , Diviney Tara , Călin Alexandru , Gothard Gemma , Jouhanneau Jean-Sébastien M. , Poulet James F.A. , Sen Arjune , Akerman Colin J.
Published: May 2023

Optogenetics has revolutionized neurobiological research by providing tools for modulating neuronal activity. As these tools utilise light-activated ion fluxes, they afford new opportunities to examine the nature of transmembrane ion gradients. Traditional investigation into the equilibrium potential for chloride (ECl) has been limited to studying endogenous chloride-permeable receptors. Here we demonstrate the utility of using a light-activated chloride channel, stGtACR2, to probe somatic EClin rodent. This agonist-independent optogenetic strategy is validatedin vitroandin vivo, captures differences in ECldynamics following manipulations of endogenous chloride fluxes, and reveals distinct resting EClacross genetically-defined neuronal subpopulations. Using this approach to challenge chloride homeostasis, we uncover cell-specific ECldynamics that are supported by the differential expression of endogenous handling mechanisms. Our findings establish an optical method for investigating transmembrane chloride gradients and thereby expand the repertoire of optogenetics.
Short- and long-term high-fat diet exposure differentially alters phasic and tonic GABAergic signaling onto lateral orbitofrontal pyramidal neurons
Authors: Seabrook L.T , Peterson C , Noble D , Sobey M , Tayyab T , Kenney T , Judge A.K , Armstrong M , Lin S , Borgland S.L.
Published: May 2023

The chronic consumption of caloric dense high-fat foods is a major contributor to increased body weight, obesity, and other chronic health conditions. The orbitofrontal cortex (OFC) is critical in guiding decisions about food intake and is altered with diet-induced obesity. Obese rodents have altered morphological and synaptic electrophysiological properties in the lateral orbitofrontal cortex (lOFC). Yet the time course by which exposure to a high-fat diet (HFD) induces these changes is poorly understood. Here male mice are exposed to either short- (7 day) or long-term (90 day) HFD. Long-term HFD exposure increases body weight, and glucose signaling compared to short-term HFD or a standard chow control diet (SCD). Both short and long-term HFD exposure increased the excitability of lOFC pyramidal neurons. However, phasic and tonic GABAergic signalling was differentially altered depending on HFD exposure length, such that tonic GABAergic signaling was decreased with early exposure to the HFD and phasic signaling was changed with long-term diet exposure. Furthermore, alterations in the short-term diet exposure were transient, as removal of the diet restored electrophysiological characteristics similar to mice fed SCD whereas long-term HFD electrophysiological changes were persistent and remained after HFD removal. Finally, we demonstrate that changes in reward devaluation occur early with diet exposure. Together, these results suggest that the duration of HFD exposure differentially alters lOFC function and provides mechanistic insights into the susceptibility of the OFC to impairments in outcome devaluation.

Significant statement

This study provides mechanistic insight on the impact of short- and long-term high fat diet (HFD) exposure on GABAergic function in the lateral orbitofrontal cortex (lOFC), a region known to guide decision making. We find short-term HFD exposure induces transient changes in firing and tonic GABA action on lOFC pyramidal neurons, whereas long-term HFD induces obesity and has lasting changes on firing, tonic GABA and inhibitory synaptic transmission onto lOFC neurons. Given that GABAergic signaling in the lOFC can influence decision making around food, these results have important implications in present society as palatable energy dense foods are abundantly available.
Slit-independent guidance of longitudinal axons byDrosophilaRobo3
Authors: Carranza Abigail , Howard LaFreda J. , Brown Haley E. , Ametepe Ayawovi Selom , Evans Timothy A.
Published: May 2023

DrosophilaRobo3 is a member of the evolutionarily conserved Roundabout (Robo) receptor family and one of threeDrosophilaRobo paralogs. During embryonic ventral nerve cord development, Robo3 does not participate in canonical Slit-dependent midline repulsion, but instead regulates the formation of longitudinal axon pathways at specific positions along the medial-lateral axis. Longitudinal axon guidance by Robo3 is hypothesized to be Slit dependent, but this has not been directly tested. Here we create a series of Robo3 variants in which the N-terminal Ig1 domain is deleted or modified, in order to characterize the functional importance of Ig1 and Slit binding for Robo3’s axon guidance activity. We show that Robo3 requires its Ig1 domain for interaction with Slit and for proper axonal localization in embryonic neurons, but deleting Ig1 from Robo3 only partially disrupts longitudinal pathway formation. Robo3 variants with modified Ig1 domains that cannot bind Slit retain proper localization and fully rescue longitudinal axon guidance. Our results indicate that Robo3 guides longitudinal axons independently of Slit, and that sequences both within and outside of Ig1 contribute to this Slit-independent activity.
SGRN: A Cas12a-driven Synthetic Gene Regulatory Network System
Authors: Kang HyunJin , Fitch John C. , Varghese Reeba P. , Thorne Curtis A. , Cusanovich Darren A.
Published: May 2023

Gene regulatory networks, which control gene expression patterns in development and in response to stimuli, use regulatory logic modules to coordinate inputs and outputs. One example of a regulatory logic module is the gene regulatory cascade (GRC), where a series of transcription factor genes turn on in order. Synthetic biologists have derived artificial systems that encode regulatory rules, including GRCs. Furthermore, the development of single-cell approaches has enabled the discovery of gene regulatory modules in a variety of experimental settings. However, the tools available for validating these observations remain limited. Based on a synthetic GRC using DNA cutting-defective Cas9 (dCas9), we designed and implemented an alternative synthetic GRC utilizing DNA cutting-defective Cas12a (dCas12a). Comparing the ability of these two systems to express a fluorescent reporter, the dCas9 system was initially more active, while the dCas12a system was more streamlined. Investigating the influence of individual components of the systems identified nuclear localization as a major driver of differences in activity. Improving nuclear localization for the dCas12a system resulted in 1.5-fold more reporter-positive cells and a 15-fold increase in reporter intensity relative to the dCas9 system. We call this optimized system the “Synthetic Gene Regulatory Network” (SGRN, pronounced “sojourn”).
Remodeling the central metabolism ofEscherichia colienables a universal chassis
Authors: Liu Min , Guo Likun , Huo Meitong , Feng Xinjun , Zhao Zhe , Qi Qingsheng , Xian Mo , Zhao Guang
Published: May 2023

E. coliis the host of choice to produce a wide variety of chemicals and proteins. Overflow metabolism is considered as the widespread and major obstacle in microbial synthesis, and overcoming this common bottleneck may enable a universal chassis. Here, we constructed anE. coliuniversal chassis (ABKS strain) with significantly suppressed overflow metabolism, presenting similar growth rate, decreased glucose consumption, and increased production of desired chemicals and proteins when compared with wild-type BL21(DE3) strain. Furthermore, we demonstrated that metabolic flux of ABKS strain was reprogrammed from TCA cycle to glyoxylate bypass at isocitrate node via the synergistic effect of multi-layer regulation in gene transcription and protein modification. This metabolic reconfiguration alleviates overflow metabolism, avoids CO2release in TCA cycle, finally improving the carbon atom economy in bioprocess. Our chassis has widespread and practical use for elevating the production and yield of multiple desired chemicals and proteins from different carbon source. The metabolic reconfiguration also provides theoretical basis for rational design of efficient bioproduction strains.
Anisotropy factors in small-angle scattering for dilute rigid-rod suspensions
Authors: Rooks Jack , Gilbert Peter H. , Porcar Lionel , Liu Yun , Butler Paul
Published: May 2023

Alignment of anisotropic particles along specific orientations influences the mechanical and rheological properties of a material. Small-angle scattering techniques are widely used to probe this alignment through analysis of anisotropic two-dimensional scattering intensity patterns. The anisotropy factor is the simplest and most common quantitative parameter for describing scattering anisotropy, especially in systems containing rod-like particles, and there are several methods for calculating this factor. However, there has been no systematic study comparing these methods while also evaluating the limitations imposed by non-idealities from instrumentation or polydisperse morphology. Three of the most common methods for calculating an anisotropy factor are examined here and their effectiveness for describing the orientation of a theoretical cylinder is evaluated. It is found that the maximum theoretical value of 1 for the anisotropy factor is only accessible at certain values of scattering vectorq. The analysis details recommendations forq-range selection and data binning, as these influence the calculations. The theoretical results are supported by experimental small-angle neutron scattering data for a wormlike micelle solution undergoing shear, where different calculation methods yield distinct quantifications of anisotropy.
Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis
Authors: Sowerby Kate , Freitag-Pohl Stefanie , Murillo Ana Milena , Silber Ariel Mariano , Pohl Ehmke
Published: May 2023

Chagas disease is a neglected tropical disease (NTD) caused by Trypanosoma cruzi, whilst leishmaniasis, which is caused by over 20 species of Leishmania, represents a group of NTDs endemic to most countries in the tropical and subtropical belt of the planet. These diseases remain a significant health problem both in endemic countries and globally. These parasites and other trypanosomatids, including T. theileri, a bovine pathogen, rely on cysteine biosynthesis for the production of trypanothione, which is essential for parasite survival in hosts. The de novo pathway of cysteine biosynthesis requires the conversion of O-acetyl-L-serine into L-cysteine, which is catalysed by cysteine synthase (CS). These enzymes present potential for drug development against T. cruzi, Leishmania spp. and T. theileri. To enable these possibilities, biochemical and crystallographic studies of CS from T. cruzi (TcCS), L. infantum (LiCS) and T. theileri (TthCS) were conducted. Crystal structures of the three enzymes were determined at resolutions of 1.80 Å for TcCS, 1.75 Å for LiCS and 2.75 Å for TthCS. These three homodimeric structures show the same overall fold and demonstrate that the active-site geometry is conserved, supporting a common reaction mechanism. Detailed structural analysis revealed reaction intermediates of the de novo pathway ranging from an apo structure of LiCS and holo structures of both TcCS and TthCS to the substrate-bound structure of TcCS. These structures will allow exploration of the active site for the design of novel inhibitors. Additionally, unexpected binding sites discovered at the dimer interface represent new potential for the development of protein–protein inhibitors.
Applying means-end to hospitality hosts: a study of winery tasting rooms
Authors: Lease Terry , Goldenberg Marni , Haberland Matt , Wallan Sam
Published: May 2023

Purpose

The paper has a twofold purpose: (1) to test the application of means-end theory to providers of hospitality goods and services, and (2) to explore this question in the context of winery tasting rooms when they had a unique opportunity to restructure their hospitality experience due to government restrictions in response to COVID.

Design/methodology/approach

A qualitative approach was adopted, and a convenience sample was used to conduct semi-structured laddering interviews. Forty interview transcripts were coded as means-end ladders, which were analyzed using a custom computer program to develop the implication matrix and the hierarchical value map.

Findings

This paper demonstrates that means-end is a useful approach to investigate the values and behaviors of the producer, specifically hospitality hosts. It finds that the principal goal of tasting rooms is to generate sales, and offering a compelling guest experience is the characteristic that contributes the most to achieving that goal. The staff and the atmosphere created for the guests are the two factors with the greatest influence on the guest experience.

Originality/value

This is the first paper to use means-end theory to study the hospitality host, or the producer of goods and services in general, and the first to study winery hospitality primarily through the lens of means-end theory. The study also helps fill a gap in research on tasting room sales focused on the winery’s goals.