bluuebunny/crossref_metadata_2025 huggingface dataset:
Current Practices in Dorsal Augmentation Rhinoplasty
Authors: Fisher Mark , Alba Brandon , Ahmad Jamil , Robotti Enrico , Cerkes Nazim , Gruber Ronald P. , Rohrich Rod J. , Bradley James P. , Tanna Neil
Published: March 2022

Background:

Dorsal augmentation rhinoplasty addresses the aesthetic and functional impairments caused by a deficient nasal dorsum. Augmentation rhinoplasty can be performed using a variety of different surgical techniques and grafting materials that all have distinct advantages and disadvantages.

Methods:

Grafting materials have unique characteristics, uses, and safety profiles. A detailed overview of various grafting materials and their uses, risks, and benefits is provided.

Results:

Autologous grafting materials include septal cartilage, auricular cartilage, and costal cartilage. These donor sites can provide various amounts of en bloc or diced cartilage. Alternatively, bone may be used when strong structural stability is required, and soft tissue may be used to fill mild to moderate defects. Homologous grafts (e.g., irradiated and nonirradiated rib) and acellular dermal matrices are alternatives to autologous graft with many similar advantages and no need for an additional surgical site. Lastly, alloplastic implants may be successfully used for dorsal augmentation if both patient and surgeon understand their associated risks.

Conclusion:

To perform successful dorsal augmentation, surgeons should be familiar with the wide variety of operative approaches and augmentation materials that are currently available and understand their risks, benefits, and uses.
YouTube™ as a Source of Information for Patients Regarding Dental Implant Failure: A Content Analysis
Authors: Özkan Enes , Acar Ahmet Hüseyin
Published: March 2022

The aim of this study is to investigate the quality of the information YouTubeTM offers to patients concerning dental implant failure. YouTubeTM was searched systematically using the keyword ‘dental implant failure’. The first 100 videos were viewed by two independent researchers. For each video, its purpose, target audience and source were also recorded. A 10 point content scale (CS) was used to evaluate the video content. The Global Quality Scale (GQS) was also used to determine the quality of videos. Statistical analyses were performed using the Kruskal Wallis and Mann Whitney test and correlation coefficient analyses were performed using Spearman’s Rho. While 92.2% of the videos included in the study were uploaded by dentists/health institutions, only 3.1% were uploaded by laypersons. Of the videos, 40.6% were aimed at informing laypersons and 56.3% targetted professionals. The content which was discussed most (71.9%) was ‘definition of a dental implant’ followed by ‘reasons for failure’ (65.6%). The mean CS and GQS score of the videos were 3.75 ± 2.35 (moderate) and 2.07 ± 1.05 (generally poor), respectively. There was a positive correlation between the CS and GQS score (r = 0.620). The quality of information on YouTubeTM regarding dental implant failure was found inadequate. Thus, the information currently available online needs to be constantly checked and improved by professionals. In addition, clinicians should improve the ways in which they use YouTubeTM to better inform patients about the causes, risks and treatment choices involved with failed dental implants.
A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery
Authors: Eckhoff Austin M. , Connor Ashton A. , Thacker Julie K. M. , Blazer Dan G. , Moore Harvey G. , Scheri Randall P. , Lagoo-Deenadayalan Sandhya A. , Harpole David H. , Seymour Keri A. , Purves J. Todd , Ravindra Kadiyala V. , Southerland Kevin W. , Rocke Daniel J. , Gilner Jennifer B. , Parker Daniel C. , Bain James R. , Muehlbauer Michael J. , Ilkayeva Olga R. , Corcoran David L. , Modliszewski Jennifer L. , Devos Nicolas , Foster Matthew W. , Moseley M. Arthur , Dressman Holly K. , Chan Cliburn , Huebner Janet L. , Chasse Scott , Stempora Linda , Aschenbrenner Mary E. , Joshi Mary-Beth , Hollister Beth , Henao Ricardo , Barfield Richard T. , Ellison Mark A. , Bailey Sean , Woody Stephen , Huang Erich S. , Kirk Allan , Hwang E. Shelley
Published: March 2022

Objective:

To design and establish a prospective biospecimen repository that integrates multi-omics assays with clinical data to study mechanisms of controlled injury and healing.

Background:

Elective surgery is an opportunity to understand both the systemic and focal responses accompanying controlled and well-characterized injury to the human body. The overarching goal of this ongoing project is to define stereotypical responses to surgical injury, with the translational purpose of identifying targetable pathways involved in healing and resilience, and variations indicative of aberrant peri-operative outcomes.

Methods:

Clinical data from the electronic medical record combined with large-scale biological data sets derived from blood, urine, fecal matter, and tissue samples are collected prospectively through the peri-operative period on patients undergoing 14 surgeries chosen to represent a range of injury locations and intensities. Specimens are subjected to genomic, transcriptomic, proteomic, and metabolomic assays to describe their genetic, metabolic, immunologic, and microbiome profiles, providing a multidimensional landscape of the human response to injury.

Results:

The highly multiplexed data generated includes changes in over 28,000 mRNA transcripts, 100 plasma metabolites, 200 urine metabolites, and 400 proteins over the longitudinal course of surgery and recovery. In our initial pilot dataset, we demonstrate the feasibility of collecting high quality multi-omic data at pre- and postoperative time points and are already seeing evidence of physiologic perturbation between timepoints.

Conclusions:

This repository allows for longitudinal, state-of-the-art geno-mic, transcriptomic, proteomic, metabolomic, immunologic, and clinical data collection and provides a rich and stable infrastructure on which to fuel further biomedical discovery.
Increased risk of death compared to other antipsychotics in elderly clozapine users in Poland
Authors: Zagożdzon Paweł , Waszak Przemysław
Published: March 2022

Clozapine can cause severe adverse effects. Few epidemiologic studies have considered the effect of clozapine use in elderly patients. The aim of this study was to assess mortality in elderly patients treated with clozapine in comparison to patients treated with first- or second-generation antipsychotics. We conducted a retrospective cohort study involving 26 639 patients who were 65 years of age or older and were receiving antipsychotic medication between 2008 and 2012. Cox proportional-hazards models were used to compare the risk of death between different groups of antipsychotics after controlling for age, sex, concomitant treatment with cardiovascular or metabolic medications. The use of antipsychotic medications other than clozapine was associated with a lower adjusted risk of death [hazard ratio, 0.89; 95% confidence interval (95% CI), 0.79–0.99]. The use of cardiac and antilipemic but not antidiabetic drugs was associated with a significantly lower risk of death in this population (hazard ratio, 0.88; 95% CI, 0.83–0.93; hazard ratio, 0.66; 95% CI, 0.58–0.75 and hazarad ratio, 1.09; 95% CI, 0.96–1.24, respectively). These results suggest that clozapine is associated with an increased risk of death in the elderly. Although the study was based on administrative records linkage, its results suggest that attention should be paid to patients taking antipsychotics.
Highly efficient protein expression of Plasmodium vivax surface antigen, Pvs25 by silkworm, Bombyx mori, and its biochemical analysis
Authors: Miyata Takeshi , Minamihata Kosuke , Kurihara Koichi , Kamizuru Yui , Gotanda Mari , Obayashi Momoka , Kitagawa Taiki , Sato Keita , Kimura Momoko , Oyama Kosuke , Ikeda Yuta , Tamaki Yukihiro , Lee Jae Man , Sakao Kozue , Hamanaka Daisuke , Kusakabe Takahiro , Tachibana Mayumi , Ibrahim Hisham R.
Published: March 2022

Plasmodium vivax ookinete surface protein, Pvs25 is a transmission-blocking vaccine (TBV) candidate for malaria. Pvs25 has four EGF-like domains containing 22 cysteine residues forming 11 intramolecular disulfide bonds and this structural feature makes recombinant expression of Pvs25 difficult. In this study, we report the high expression of recombinant Pvs25 as a soluble form in silkworm, Bombyx mori. The Pvs25 protein was purified from hemolymphs of larvae and pupae by affinity chromatography. In the Pvs25 expressed by silkworm, no isoform with inappropriate disulfide bonds was found, requiring no further purification step which is necessary in case of Pichia pastoris based expressions systems. The Pvs25 from silkworm were confirmed to be the molecularly uniform by sodium dodecyl sulfate gel electrophoresis analysis and size exclusion chromatography analysis. To examine the immunogenicity, the Pvs25 from B. mori, was administered to BALB/c mice by the subcutaneous (s.c.) route with the oil adjuvant. The Pvs25 produced by silkworm induced potent and robust immune response, and the induced antisera correctly recognized P. vivax ookinetes in vitro, demonstrating the potency of Pvs25 from silkworm as a TBV candidate for malaria. This is the first study that to construct a mass production system for malaria TBV antigens by the silkworm to the best of our knowledge.
Deep learning on reflectance confocal microscopy improves Raman spectral diagnosis of basal cell carcinoma
Authors: Chen Mengkun , Feng Xu , Fox Matthew C. , Reichenberg Jason S. , Lopes Fabiana C.P.S. , Sebastian Katherine R. , Markey Mia K. , Tunnell James W.
Published: March 2022

Significance

Raman spectroscopy may be useful to assist Mohs micrographic surgery for skin cancer diagnosis; however, the specificity of Raman spectroscopy is limited by the high spectral similarity between tumors and normal tissues structures such as epidermis and hair follicles. Reflectance confocal microscopy (RCM) can provide imaging guidance with morphological and cytological details similar to histology. Combining Raman spectroscopy with deep-learning-aided RCM has the potential to improve the diagnostic accuracy of Raman without requiring additional input from the clinician.

Aim

We seek to improve the specificity of Raman for basal cell carcinoma (BCC) by integrating information from RCM images using an Artificial Neural Network.

Approach

A Raman biophysical model was used in prior work to classify BCC tumors from surrounding normal tissue structures. 191 RCM images were collected from the same site as the Raman data and served as inputs to train two ResNet50 networks. The networks selected the hair structure images and epidermis images respectively within all the images corresponding to the positive predictions of the Raman Biophysical Model.

Results

Deep learning on RCM images removes 54% of false positive predictions from the Raman Biophysical Model result and keeps the sensitivity as 100%. The specificity was improved from 84.8% by using Raman spectra alone to 93.0% by integrating Raman spectra with RCM images

Conclusions

Combining Raman spectroscopy with deep-learning-aided RCM imaging is a promising tool to guide tumor resection surgery.
Transcytosis-mediated anterograde transport of TrkA receptors is necessary for sympathetic neuron development and function
Authors: Connor Blaine , Yamashita Naoya , Kuruvilla Rejji
Published: March 2022

In neurons, many membrane proteins, synthesized in cell bodies, must be efficiently delivered to axons to influence neuronal connectivity, synaptic communication, and repair. Previously, we found that axonal targeting of TrkA neurotrophin receptors in sympathetic neurons occurs via an atypical transport mechanism called transcytosis, which relies on TrkA interactions with PTP1B, a protein tyrosine phosphatase. Here, we generated TrkAR685A mice, where TrkA receptor signaling is preserved, but its PTP1B-dependent transcytosis is disrupted, to show that this mode of axonal transport is essential for sympathetic neuron development and autonomic function. TrkAR685A mice have decreased axonal TrkA levels in vivo, developmental loss of sympathetic neurons, and reduced innervation of targets. Postnatal TrkAR685A mice exhibit reduced pupil size and eyelid ptosis, indicative of sympathetic dysfunction. These findings establish the necessity of transcytosis in supplying TrkA receptors to sympathetic axons and highlight the physiological relevance of this axon targeting mechanism in the nervous system.
A new method to estimate the ecological niche throughn-dimensional hypervolumes that combines convex hulls and elliptical envelopes
Authors: Carrasco Jaime , Lisón Fulgencio , Jiménez Laura , Weintraub Andrés
Published: March 2022

Methods that estimate the niche of a species by calculating a convex hull or an elliptical envelope have become popular due to their simplicity and interpretation, given Hutchinson’s conception of the niche as ann-dimensional hypervolume.

It is well known that convex hulls are sensitive to outliers and do not have the ability to differentiate between regions of low and high concentration of presences, while the elliptical envelopes may contain large regions of niche space that are not relevant for the species. Thus, when the goal is to estimate the realized niche of the species, both methods may overestimate the niche.

We present a methodology that combines both the convex hull and the elliptical envelope methods producing ann-dimensional hypervolume that better fits the observed density of species presences, making it a better candidate to model the realized niche. Our method, called the CHE approach, allows defining regions of iso-suitability as a function of the significance levels inherited from the method (Mahalanobis distance model, minimum covariance determinant, or minimum volume ellipsoid) used to fit an initial elliptical envelope from which we then discard regions not relevant for the species by calculating a convex hull.

We applied the CHE approach to a case study of twenty-five species of bats present in the Iberian Peninsula, fitting a hypervolume for each species and comparing them to both the convex hulls and elliptical envelopes obtained with the same data and different values ofn. We show that as the number of variables used to define the niche space increases, both the convex hull and elliptical envelope models produce overly large hypervolumes, while the size of the hypervolume fitted with the CHE approach remains stable. As a consequence, similarity measures that account for the niche overlap among different species may be inflated when using convex hulls or elliptical envelopes to model the niche; something that does not occur under the CHE approach.
A rapid review of the effectiveness of alternative education delivery strategies in medical, dental, nursing and pharmacy education during the COVID-19 pandemic
Authors: Carrier Judith , Edwards Deborah , Tombs Michal , Riley Steve , Lewis Ruth , Gillen Elizabeth , Cooper Alison , Edwards Adrian
Published: March 2022

Background

Education delivery in higher education institutions was severely affected by the COVID-19 pandemic, with emergency remote teaching developed and adapted promptly for the circumstances. This rapid review investigated the effectiveness of alternative education delivery strategies during the pandemic for medical, dental, nursing and pharmacy students, to help plan and adapt further education provision.

Methods

We included 23 primary studies in undergraduate education, all published in 2020-2021, no relevant UK-based or postgraduate studies were found. Included studies comprised 10 single cohort descriptive; 11 comparative descriptive; and two RCTs. There was considerable variability in terms of students, type of distance learning, platforms used and outcome measures.

Results

In medicine (n=14), self-reported competency and confidence, and demonstrable suturing skills were achieved through participating in remote learning. However, lower levels of knowledge were obtained by students who received virtual or blended learning compared to in-person teaching (low-very low confidence). Using bespoke interactive platforms in undergraduate medical training was superior to standard video (low confidence) or ‘textbook’ presentations (very low confidence).

In dentistry (n=2), remote learning led to knowledge gained (low confidence), but self-reported practical and interpersonal skills were lower with remote rather than in-person learning (very low confidence).

In nursing (n=3), remote learning, when compared to in-person, resulted in similar knowledge and self-reported competency levels (very low confidence) pre-COVID, but confidence was higher when learning or assessment was conducted virtually (low confidence).

In pharmacy (n=4), virtual learning was associated with higher skills, but lower knowledge compared to in-person, pre-COVID; self-reported competency and confidence scores were similar between the two groups (very low confidence).

Conclusions

Remote teaching was valued, and learning was achieved, but the comparative effectiveness of virtual versus in-person teaching is less clear. Supplementary alternative or in-person practical sessions may be required post-emergency to address learning needs for some disadvantaged student groups.
Biologically-derived neoproteoglycans for profiling protein-glycosaminoglycan interactions
Authors: Porell Ryan N. , Follmar Julianna L. , Purcell Sean C. , Timm Bryce , Laubach Logan K. , Kozirovskiy David , Thacker Bryan E. , Glass Charles A. , Gordts Philip L. S. M. , Godula Kamil
Published: March 2022

Glycosaminoglycans (GAGs) are a class of highly negatively charged membrane associated and extracellular matrix polysaccharides involved in the regulation of myriad biological functions, including cell adhesion, migration, signaling and differentiation, among others. GAGs are typically attached to core proteins, termed proteoglycans (PGs), and can engage >500 binding proteins, making them prominent relays for sensing external stimuli and transducing cellular responses. However, their unique substructural protein-recognition domains that confer their binding specificity remain elusive. While the emergence of glycan arrays has rapidly enabled the profiling of ligand specificities of a range of glycan-binding proteins, their adaptation for the analysis of GAG-binding proteins has been considerably more challenging. Current GAG-microarrays primarily employ synthetically defined oligosaccharides, which capture only a fraction of the structural diversity of native GAG polysaccharides. Augmenting existing array platforms to include GAG structures purified from tissues or produced in cells with engineered glycan biosynthetic pathways may significantly advance the understanding of structure-activity relationships in GAG-protein interactions. Here, we demonstrate an efficient and tunable strategy to mimic cellular proteoglycan architectures by conjugating biologically-derived GAG chains to a protein scaffold, defined as neoproteoglycans (neoPGs). The use of a reactive fluorogenic linker enabled real-time monitoring of the conjugation reaction efficiency and tuning of the neoPG valency. Immobilization of the reagents on a 96-well array platform allowed for efficient probing of ligand binding and enzyme substrate specificity, including growth factors and the human sulfatase 1. The neoPGs can also be used directly as soluble probes to evaluate GAG-dependent growth factor signaling in cells.

Graphical Abstract
Notch signaling in germ line stem cells controls reproductive aging in C. elegans
Authors: Kocsisova Zuzana , Bagatelas Elena D. , Santiago-Borges Jesus , Lei Hanyue Cecilia , Egan Brian M. , Mosley Matthew C. , Schneider Daniel L. , Schedl Tim , Kornfeld Kerry
Published: March 2022

Reproductive aging in females often occurs early in life, resulting in a substantial post-reproductive lifespan. Despite the medical importance of age-related infertility, relatively little is known about mechanisms that control this age-related decline. C. elegans is a leading system for aging biology due to its short lifespan and powerful experimental tools, and detailed descriptions of molecular and cellular changes in the gonad during reproductive aging were recently reported. Here we show that reproductive aging occurs early in life in multiple species in the genus Caenorhabditis, indicating this is a feature of both female/male and hermaphrodite/male species. In mutants previously established to display delayed reproductive aging (daf-2, eat-2, phm-2), we observed correlations between changes in the distal germline and changes in egg-laying, consistent with the model that distal germline changes are a cause of reproductive aging. By screening for additional mutants that delay reproductive aging, we identified an allele of che-3 with impaired sensory perception that displayed increased progeny production in mid-life, a pattern of reproductive aging distinct from previous mutants. To directly test the role of Notch signaling in the distal germline, we analyzed the effect of ectopic expression of the Notch effector gene SYGL-1. Ectopic expression of SYGL-1 was sufficient to delay reproductive aging, suggesting that an age-related decline in Notch signaling in the distal germline is a root cause of reproductive aging.
A dual-target herbicidal inhibitor of lysine biosynthesis
Authors: Mackie Emily R. R. , Barrow Andrew S. , Christoff Rebecca M. , Abbott Belinda M. , Gendall Anthony R. , Soares da Costa Tatiana P.
Published: March 2022

Herbicides with novel modes of action are urgently needed to safeguard global agricultural industries against the damaging effects of herbicide-resistant weeds. We recently developed the first herbicidal inhibitors of lysine biosynthesis, which provided proof-of-concept for a promising novel herbicide target (Soares da Costa et al., 2021). In this study, we expanded upon our understanding of the mode of action of herbicidal lysine biosynthesis inhibitors. We previously postulated that these inhibitors may act as proherbicides (Soares da Costa et al., 2021). Here we show this is not the case. We report an additional mode of action of these inhibitors, through their inhibition of a second lysine biosynthesis enzyme, and investigate the molecular determinants of inhibition. Furthermore, we extend our herbicidal activity analyses to include a weed species of global significance.
Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth
Authors: Chure Griffin , Banks Rachel A. , Flamholz Avi I. , Sarai Nicholas S. , Kamb Mason , Lopez-Gomez Ignacio , Bar-On Yinon , Milo Ron , Phillips Rob
Published: March 2022

The Human Impacts Database (www.anthroponumbers.org) is a curated searchable resource housing quantitative data relating to the diverse anthropogenic impacts on our planet, with topics ranging from sea level rise, to livestock populations, greenhouse gas emissions, fertilizer use, and beyond. Each entry in the database relates a quantitative value (or a time-series of values) along with clear referencing of the primary source, the method of measurement or estimation, an assessment of uncertainty, links to the underlying data, as well as a permanent identifier called an Human Impacts ID (“HuID”). While there are other databases that house some of these values, they are typically focused on a single topic area like energy usage or greenhouse gas emissions. The Human Impacts Database provides centralized access to quantitative information about the myriad ways in which humans impact the Earth, giving links to more specialized databases for interested readers. Here, we outline the structure of the database and describe our curation procedures. Finally, we use this database to generate a graphical summary of the current state of human impacts on the Earth, illustrating both their numerical values and their dense interconnections.

The Bigger Picture

Over the last 10,000 years, human activities have transformed the Earth through farming, forestry, mining and industry. The complex results of these activities are now observed and quantified as “human impacts” on Earth’s atmosphere, oceans, biosphere and geochemistry. While myriad studies have explored facets of human impacts on the planet, they are necessarily technical and often tightly-focused. Thus, finding reliable quantitative information requires a significant investment of time to assess each quantity, its methods of determination, and associated uncertainty. We present the Human Impacts Database (www.anthroponumbers.org), which houses a diverse array of such quantities. We review a subset of these values and how they help build intuition for understanding the Earth-human system. While collation alone does not tell us how to best ameliorate human impacts, we contend that any future plans should be made in light of a quantitative understanding of the interconnected ways in which humans impact the planet.
Ancestry-specific maps of GRCh38 linkage disequilibrium blocks for human genome research
Authors: MacDonald James W. , Harrison Tabitha A. , Bammler Theo K. , Mancuso Nicholas , Lindström Sara
Published: March 2022

A map of approximately independent linkage disequilibrium (LD) blocks has many uses in statistical genetics. Current publicly available LD block maps are based on sparse recombination maps and are only available for GRCh37 (hg19) and prior genome assemblies. We generated LD blocks in GRCh38 coordinates for African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) ancestry populations. These new maps consist of 1,143 (EAS) - 1,604 (AFR) independent LD blocks across the 22 autosomal chromosomes and can be accessed athttps://github.com/jmacdon/LDblocks_GRCh38.
A Systematic Review and Meta-analysis of Polycystic Ovary Syndrome and Mental Health among Black Asian Minority Ethnic populations
Authors: Delanerolle Gayathri , Ayis Salma , Barzilova Vanya , Phiri Peter , Zeng Yutian , Ranaweera Sandali , Shetty Ashish , Haque Nyla , Kar Debasish , Majumder Kingshuk , Rathod Shanaya , Raymont Vanessa , Shi Jian Qing , Hapangama Dharani K.
Published: March 2022

Background

Polycystic Ovary Syndrome (PCOS) is a chronic and a common gynaecological condition impacting women of reproductive age. Women with PCOS have hormonal, ovulatory and metabolic dysfunction resulting in multiple symptoms. The correlation between hormonal disbalance and the impact on women’s mental health (MH) has been researched for decades. However, the prevalence among different ethnicities has not been fully evaluated.

Methods

A systematic methodology was developed, and a protocol was published in PROSPERO (CRD42020210863) and a systematic review of publications between 1st January 1990-30th January 2021 was conducted. Multiple electronic databases were explored using keywords and MeSH terms. The finalised dataset was analysed using statistical methods such as random-effect models, subgroup analysis and sensitivity analysis.

Findings

We included 30 studies reporting on 3,944 PCOS women. Majority of studies addressed depression anxiety, and common mental health. Studies had fair to poor methodological quality and includes observational studies and Randomised Clinical Trials (RCTs). Overall, 17% (95% CI: 7% to 29%) of women with PCOS have clinical diagnosis of major or severe depression; 33% (95% CI: 26% to 40%) have elevated depressive symptoms or a clinical diagnosis of depression; 41% (95% CI: 28% to 54%) report anxiety symptoms, and 31% (95% CI: 15% to 51%) have a form a common mental health or are takingpsychiatric medication for anxiety and / or depression. The use of various tools to assess mental health symptoms was among the reasons for the substantial heterogeneity across studies.

Interpretation

PCOS is associated with an increased risk of mental health disorders including depressive s, anxiety, and other mental health disorders. While BAME populations account for about 20% of most of the samples studied, stratification by ethnicity was rarely attempted which made it difficult to elucidate the MH impact of PCOS on different communities.

Funding

Not applicable

PROSPERO registration number

CRD42020210863
A guide to examining intramuscular fat formation and its cellular origin in skeletal muscle
Authors: Johnson Connor D. , Zhou Lylybell Y. , Kopinke Daniel
Published: March 2022

Fibro-adipogenic progenitors (FAPs) are mesenchymal stromal cells that play a crucial role during skeletal muscle homeostasis and regeneration. FAPs build and maintain the extracellular matrix that acts as a molecular myofiber scaffold. In addition, FAPs are indispensable for myofiber regeneration as they secrete a multitude of beneficial factors sensed by the muscle stem cells (MuSCs). In diseased states, however, FAPs are the cellular origin of intramuscular fat and fibrotic scar tissue. This fatty fibrosis is a hallmark of sarcopenia and neuromuscular diseases, such as Duchenne Muscular Dystrophy. One significant barrier in determining why and how FAPs differentiate into intramuscular fat is effective preservation of adipocytes, especially in frozen tissue sections. Conventional methods of skeletal muscle tissue processing, such as snap-freezing, do not properly preserve the morphology of individual adipocytes, thereby preventing accurate visualization and quantification. Here, we describe a protocol that provides robust preservation of adipocyte morphology in skeletal muscle sections allowing visualization, imaging, and quantification of intramuscular fat. We also outline how to process a portion of muscle tissue for RT-qPCR, enabling users to confirm observed changes in fat formation by viewing differences in expression of adipogenic genes. Additionally, we will describe how our protocol can be adopted to visualize adipocytes by whole mount immunofluorescence of muscle samples. Finally, we will outline how to combine this protocol with genetic lineage tracing of Pdgfrα-expressing FAPs to study the adipogenic conversion of FAPs. Our protocol consistently yields high-resolution and morphologically accurate immunofluorescent images of adipocytes that, along with confirmation by RT-qPCR, allows for robust, rigorous, and reproducible visualization and quantification of intramuscular fat. Together, our analysis pipeline is the first step to improve our understanding of how FAPs differentiate into intramuscular fat and provides a framework to validate novel interventions to prevent fat formation.
Cell Chromatography: Biocompatible chromatographic separation and interrogation of microbial cells
Authors: Hazu M. , Ahmed A. , Curry E. , Hornby D.P. , Gjerde D.T.
Published: March 2022

The isolation of pure, single colonies lies at the heart of experimental microbiology. However, a microbial colony typically contains around one million cells at all stages of the life cycle. Here we describe a novel, cell chromatography method that facilitates the capture, purification and interrogation of microbial cells from both single and mixed cultures. The method described relies on, but is not limited to, differences in surface charge to separate bacterial strains. The method is fully biocompatible, leading to no significant loss of cell viability,. The chromatographic capture of cells, combined with selective elution methods facilitates a greater level of experimental control over the sample inputs required for downstream high throughput and high sensitivity, analytical methods. The application of the method for interrogating the antibiotic resistance of bacterial strains and for the separation of bacteria from environmental samples is illustrated.
Extraction of individual associative memory related dominant theta frequency for personalized transcranial brain stimulation
Authors: Bjekić Jovana , Paunovic Dunja , Živanović Marko , Stanković Marija , Griškova-Bulanova Inga , Filipović Saša R.
Published: March 2022

Non-invasive brain stimulation (NIBS) has gained increased interest in research and therapy of associative memory (AM) and its impairments. However, the one-size-fits-all approach yields inconsistent findings, thus putting forward the need for the development of personalized frequency-modulated NIBS protocols to increase the focality and the effectiveness of the interventions. There have been only a few attempts to deliver theta frequency-personalized tES. The current study explores the feasibility of determining dominant individual theta-band frequency (ITF) based on AM task evoked EEG activity. In a sample of 42 healthy young adults, we extracted the frequencies (2-15 Hz, in 0.5 Hz steps) with the highest event-related spectral perturbation from the EEG recorded during successful encoding in the AM task. The developed method for extraction of the dominant theta-band frequency based on the AM-evoked EEG changes is able to reliably determine the AM-related ITF and can be used for personalization of the oscillatory NIBS techniques.
Structural analogue-based protein structure domain assembly assisted by deep learning
Authors: Peng Chun-Xiang , Zhou Xiao-Gen , Xia Yu-Hao , Liu Jun , Hou Ming-Hua , Zhang Gui-Jun
Published: March 2022

Motivation

With the breakthrough of AlphaFold2, the protein structure prediction problem has made a remarkable progress through end-to-end deep learning techniques, in which correct folds could be built for nearly all single-domain proteins. However, the full-chain modelling appears to be lower on average accuracy than that for the constituent domains and requires higher demand on computing hardware, indicating the performance of full-chain modelling still needs to be improved. In this study, we investigate whether the predicted accuracy of full-chain model can be further improved by domain assembly assisted by deep learning.

Results

In this article, we developed a structural analogue-based protein structure domain assembly method assisted by deep learning, named SADA. In SADA, a multi-domain protein structure database (MPDB) was constructed for the full-chain analogue detection using individual domain models. Starting from the initial model constructed from the analogue, the domain assembly simulation was performed to generate the full-chain model through a two-stage differential evolution algorithm guided by the physics-based force field and an inter-residue distance potential predicted by deep learning. SADA was compared with the state-of-the-art domain assembly methods on 356 benchmark proteins, and the average TM-score of SADA models is 8.1% and 27.0% higher than that of DEMO and AIDA, respectively. We also assembled full-chain models of 20 human multi-domain proteins using individual domain models independently predicted by AlphaFold2, where the SADA full-chain models obtained a 4.8% higher average TM-score than full-chain models directly predicted by AlphaFold2 and fewer computing resources were required. In addition, we also find that the domains often interact in the similar way in the quaternary orientations if the domains have similar tertiary structures. Furthermore, homologous templates and structural analogues are complementary for multi-domain protein full-chain modelling.

Availability

The SADA web server are freely available at http://zhanglab-bioinf.com/SADA.
Targeting neuronal homeostasis to prevent seizures
Authors: Mulroe Fred , Lin Wei-Hsiang , Scott Connie Mackenzie-Gray , Aourz Najat , Fan Yuen Ngan , Coutts Graham , Parrish R Ryley , Smolders Ilse , Trevelyan Andrew , Wykes Robert , Allan Stuart , Freeman Sally , Baines Richard A.
Published: March 2022

Manipulating neuronal homeostasis, which enables neurons to regulate their intrinsic excitability, offers an attractive opportunity to prevent seizures. However, no anticonvulsant compounds have yet been reported that directly manipulate neuronal homeostasis. Here, we describe a novel class of anticonvulsant compounds, based on 4-tert-butyl-benzaldehyde (4-TBB), with a mode-of-action that includes increased expression of the homeostatic regulator Pumilio (Pum). In Drosophila and mouse we use a pentylenetetrazole (PTZ) induced seizure model, and an electrically induced seizure model for refractory seizures to evaluate anticonvulsant efficacy. The pyrazole analogue (RAB216) demonstrates best efficacy, protecting 50% of mice from PTZ-induced seizure. Knock-down of Pum, in Drosophila, blocks anticonvulsive effects, whilst analysis of validated Pum targets show significant reductions following exposure of mouse brain to 4-TBB. This study provides proof-of-principle that anticonvulsant effects can be achieved through regulation of neuronal homeostasis and identifies a chemical lead compound for future development.
Low memory T cells blood counts and high naïve regulatory T cells percentage at relapsing remitting multiple sclerosis diagnosis
Authors: Canto-Gomes João , Silva Carolina S. , Rb-Silva Rita , Boleixa Daniela , Silva Ana Martins da , Cheynier Rémi , Costa Patrício , González-Suárez Inés , Correia-Neves Margarida , Cerqueira João , Nobrega Claudia
Published: March 2022

Objective

To assess the peripheral immune system of newly diagnosed relapsing remitting multiple sclerosis (RRMS) patients and compare it to healthy controls (HC).

Methods

Cross-sectional study with 30 treatment-naïve newly diagnosed RRMS patients, and 33 sex and age-matched HC. Their peripheral blood mononuclear cells were analysed regarding: i) thymic function surrogates [T cell receptor excision circles (TRECs) and recent thymic emigrants (RTEs)]; ii) naïve and memory CD4+ and CD8+ T cells subsets; iii) T helper (Th) phenotype and chemokine receptors expression on T cells subsets; iv) regulatory T cell (Tregs) phenotype; and vi) expression of activating/inhibitory receptors by natural killer (NK) and NKT cells. Analyses were controlled for age, sex, and human cytomegalovirus (HCMV) IgG seroprevalence.

Results

Newly diagnosed RRMS patients and HC have equivalent thymic function as determined by similar numbers of RTEs, and levels of sjTRECs, DJβTRECs and sj/DJβTREC ratio. In the CD8+ T cells compartment RRMS patients have a higher naïve/memory ratio and lower memory cell counts in blood, specifically of effector memory and TemRA CD8+ T cells. Among CD4+ T cells lower blood counts of effector memory cells are found in patients upon controlling for sex, age and HCMV IgG seroprevalence. RRMS patients have higher percentage of naive Tregs comparing to HC. Percentages of immature CD56bright NK cells expressing the inhibitory receptor KLRG1, and of mature CD56dimCD57+ NK cells expressing NKp30 are higher in patients. No major alterations are observed on NKT cells. MS severity and time from relapse correlate with immune cells alterations.

Conclusion

Characterization of the peripheral immune system of treatment-naïve newly diagnosed RRMS patients unveiled immune features present at clinical onset including lower memory T cells blood counts, particularly among CD8+ T cells, higher percentage of naïve Tregs and altered percentages of NK cells subsets expressing inhibitory or activating receptors. These findings might set the basis to better understand disease pathogenesis.
Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration
Authors: Nguyen Phong Quoc , Huecas Sonia , Asif-Laidin Amna , Plaza-Pegueroles Adrián , Palmic Noé , Acker Joël , Reguera Juan , Lesage Pascale , Fernández-Tornero Carlos
Published: March 2022

The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and Pol III, currently uncharacterized at the atomic level. Here, we report cryo-EM structures of Pol III in complex with IN1, revealing a 16-residue segment at the IN1 C-terminus that contacts Pol III subunits AC40 and AC19, an interaction that we validate byin vivomutational analysis. Unexpectedly, IN1 binding associates with insertion of subunit C11 C-terminal Zn-ribbon into the Pol III funnel, which provides atomic evidence for a two-metal mechanism during RNA cleavage. Moreover, unstructured regions of subunits C53 and C37 reorganize close to C11, likely explaining the connection between the C37/C53 heterodimer and C11 during transcription reinitiation. Our results suggest that IN1 binding induces a Pol III configuration that favors chromatin residence, thus improving the likelihood of Ty1 integration.
Comparative analysis of the Illumina Mouse Methylation BeadChip and Reduced Representation Bisulphite Sequencing for routine DNA methylation analysis of murine samples
Authors: Fennell Lochlan J , Hartel Gunter , McKeone Diane M , Bond Catherine E , Kane Alexandra , Leggett Barbara A , Patch Ann-Marie , Whitehall Vicki LJ
Published: March 2022

Background

Researching the murine epigenome in disease models has been hampered by the lack of an appropriate and cost-effective DNA methylation array. Until recently, investigators have been limited to the relatively expensive and analysis intensive bisulphite sequencing methods. Here, we performed a comprehensive, comparative analysis between the new Mouse Methylation BeadChip (MMB) and reduced representation bisulphite sequencing (RRBS) in two murine models of colorectal carcinogenesis, providing insight into the utility to each platforms in a real world environment.

Results

We captured 1.47×106 CpGs by RRBS and 2.64×105 CpGs by MMB, mapping to 13,778 and 13,365 CpG islands, respectively. RRBS captured significantly more CpGs per island (median 41 for RRBS versus 2 for MMB). We found that 64.4% of intra-island CpG methylation variability can be captured by measuring approximately one quarter of CpG island (CGI) CpGs. MMB was more precise in measuring DNA methylation, especially at sites that had low RRBS coverage. This impacted differential methylation analysis, with more statistically significantly differentially methylated CpG sites identified by MMB in all experimental conditions, however the difference was minute when appropriate thresholding for the magnitude of methylation change (0.2 beta value difference) was applied, providing confidence that both techniques can identify similar differential DNA methylation. Gene ontology enrichment analysis of differentially hypermethylated gene promoters identified similar biological processes and pathways by both RRBS and MMB across two murine model systems.

Conclusion

MMB is an effective tool for profiling the murine methylome that performs comparably to RRBS, identifying similar differentially methylated pathways. Although MMB captures a similar proportion of CpG islands, it does so with fewer CpGs per island. We show that subsampling informative CpGs from CpG islands is an appropriate strategy to capture whole island variation. Choice of technology is experiment dependent and will be predicated on the underlying biology being probed.
Dentate gyrus mossy cells exhibit sparse coding via adaptive spike threshold dynamics
Authors: Trinh Anh-Tuan , Girardi-Schappo Mauricio , Béïque Jean-Claude , Longtin André , Maler Leonard
Published: March 2022

Hilar mossy cells (hMCs) are glutamatergic neurons in the dentate gyrus (DG) that receive inputs primarily from DG granule cells (GCs), CA3 pyramidal cells and local inhibitory interneurons. The hMCs then provide direct excitatory and disynaptic inhibitory feedback input to GCs. Behavioral and in vivo single unit recording experiments have implicated hMCs in pattern separation as well as is in spatial navigation and learning. It has, however, been difficult to mechanistically link the in vivo physiological behavior of hMCs with their intrinsic excitability properties that convert their synaptic inputs into spiking output. Here, we carried out electrophysiological recordings from the main cell types in the DG and found that hMCs displayed a highly adaptive threshold acting over a remarkably protracted time-scale. The hMC spike threshold increased linearly with increasing current stimulation and saturated at high current intensities. This threshold also increased in response to spiking and this effect also decayed over a long timescale, allowing for activity-dependent summation that limited hMC firing rates. This mechanism operates in parallel with a prominent medium after-hyperpolarizing potential (AHP) generated by the small conductance K+ channel. Based on experimentally derived parameters, we developed a phenomenological exponential integrate-and-fire model that closely mimics the hMC adaptive threshold. This lightweight model is amenable to its incorporation into large network models of the DG that will be conducive to deepen our understanding of the neural bases of pattern separation, spatial learning and navigation in the hippocampus.

Statement of significance

Recent studies on hilar mossy cells have revealed that they are implicated in spatial navigation and mnemonic functions. Yet, the basic intrinsic characterization of these hMCs is still too superficial to explain their spiking behavior in vivo. Here, we describe novel biophysical properties of hMCs, including an independent relationship between spike latency and spike threshold as well as a slowly adapting spike threshold. These findings complement several other biophysical and connectivity similarities between hMCs and CA3 pyramidal cells, while emphasizing the contrast with hilar interneurons. Additionally, our results are well captured by a phenomenological model of the hMC which provides a useful framework to study the neural substrate of spatial navigation and learning in the dentate gyrus.
Generation and Maturation of Human iPSC-derived Cardiac Organoids in Long Term Culture
Authors: Ergir Ece , La Cruz Jorge Oliver-De , Fernandes Soraia , Cassani Marco , Niro Francesco , Sousa Daniel , Vrbský Jan , Vinarský Vladimír , Perestrelo Ana Rubina , Debellis Doriana , Cavalieri Francesca , Pagliari Stefania , Redl Heinz , Ertl Peter , Forte Giancarlo
Published: March 2022

Cardiovascular diseases remain the leading cause of death worldwide; hence there is an increasing focus on developing physiologically relevant in vitro cardiovascular tissue models suitable for studying personalized medicine and pre-clinical tests. Despite recent advances, models that reproduce both tissue complexity and maturation are still limited.

We have established a scaffold-free protocol to generate multicellular, beating and self-organized human cardiac organoids (hCO) in vitro from hiPSCs that can be cultured for long term. This is achieved by differentiation of hiPSC in 2D monolayer culture towards cardiovascular lineage, followed by further aggregation on low-attachment culture dishes in 3D. The generated human cardiac organoids (hCOs) containing multiple cell types that physiologically compose the heart, gradually self-organize and beat without external stimuli for more than 50 days. We have shown that 3D hCOs display improved cardiac specification, survival and maturation as compared to standard monolayer cardiac differentiation. We also confirmed the functionality of hCOs by their response to cardioactive drugs in long term culture. Furthermore, we demonstrated that hCOs can be used to study chemotherapy-induced cardiotoxicity.

This study could help to develop more physiologically-relevant cardiac tissue models, and represent a powerful platform for future translational research in cardiovascular biology.