bluuebunny/crossref_metadata_2025 huggingface dataset:
The Lay Public's Knowledge of the Most Common Acute Coronary Syndrome Symptoms Experienced by Women and Men
Authors: Blakeman John R. , Eckhardt Ann L. , Kim MyoungJin
Published: July 2022

Background

Although extensive research and public education for the last 2 decades has focused on symptom differences experienced by men and women, little is known about what acute coronary syndrome symptoms the lay public associates with men, with women, and with both men and women.

Objective

The aim of this study was to describe what acute coronary syndrome symptoms the lay public associates with men, with women, and with both men and women and to explore whether differences in participant gender affect how these symptoms are associated.

Methods

A descriptive, cross-sectional survey design was used, using an online survey. We recruited women (n = 209) and men (n = 208) living in the United States from the crowdsourcing platform Mechanical Turk in April and May 2021.

Results

Most participants (78.4%) selected a chest symptom as the most common acute coronary syndrome symptom experienced by men, compared with only 49.4% who selected a chest symptom as the most common for women. Almost half (46.9%) of women indicated that they believe men and women have “fairly different” or “very different” acute coronary syndrome symptoms, compared with 17.3% of men.

Conclusions

Whereas most participants associated symptoms with both men and women's experiences of acute coronary syndrome symptoms, some associated symptoms in ways that are not reflected in the literature. Additional research is needed to further understand the impact of messaging on acute coronary syndrome symptom differences between men and women and the lay public's interpretation of these messages.
Differences in the management of thyroid nodules in children and adolescents as compared to adults
Authors: Goldfarb Melanie , Dinauer Catherine
Published: July 2022

Purpose of review

To describe recent advances in the diagnosis and management of thyroid nodules in both children and adults, highlighting differences between the two groups.

Recent findings

Thyroid nodules are less common in children than adults but the risk of malignancy is higher. Screening recommendations for patients with certain genetic syndromes or specific risk factors for thyroid nodules and cancer continue to evolve ultrasound is the most appropriate imaging modality for evaluating thyroid nodules in all patients, but radiographic risk stratification systems validated in adults have not been extensively studied in children. Criteria for proceeding to fine needle aspiration (FNA) biopsy differ some between children and adults, with nodule size being less of a consideration in young patients. Molecular testing continues to improve the diagnostic capabilities of FNA for all age groups, but options for pediatric thyroid nodules are currently limited. In children, only oncogene panels are validated and their exact utility, along with miRNA classifiers, is an evolving area of study. For adults, data support selection of a specific molecular test based on ultrasound characteristics and pretest probability of malignancy. Multiple series have shown that fusion mutations are more common in pediatric thyroid nodules, while point mutations are seen more often in adult thyroid nodules. Molecular data help guide management recommendations regarding the need for surgery when FNA is indeterminate, but clinical use is still being refined. Radiofrequency ablation is a nonoperative approach that has gained significant traction for the treatment of symptomatic benign nodules in adults, but data are currently extremely limited in children.

There are difference in the diagnosis and treatment of thyroid nodules in adults and children, the nuances of which are important for clinical management.
7 T Musculoskeletal MRI
Authors: Pazahr Shila , Nanz Daniel , Sutter Reto
Published: July 2022

This review summarizes the current state-of-the-art of musculoskeletal 7 T magnetic resonance imaging (MRI), the associated technological challenges, and gives an overview of current and future clinical applications of 1H-based 7 T MRI. The higher signal-to-noise ratio at 7 T is predominantly used for increased spatial resolution and thus the visualization of anatomical details or subtle lesions rather than to accelerate the sequences. For musculoskeletal MRI, turbo spin echo pulse sequences are particularly useful, but with altered relaxation times, B1 inhomogeneity, and increased artifacts at 7 T; specific absorption rate limitation issues quickly arise for turbo spin echo pulse sequences. The development of dedicated pulse sequence techniques in the last 2 decades and the increasing availability of specialized coils now facilitate several clinical musculoskeletal applications. 7 T MRI is performed in vivo in a wide range of applications for the knee joint and other anatomical areas, such as ultra-high-resolution nerve imaging or bone trabecular microarchitecture imaging. So far, however, it has not been shown systematically whether the higher field strength compared with the established 3 T MRI systems translates into clinical advantages, such as an early-stage identification of tissue damage allowing for preventive therapy or an influence on treatment decisions and patient outcome. At the moment, results tend to suggest that 7 T MRI will be reserved for answering specific, targeted musculoskeletal questions rather than for a broad application, as is the case for 3 T MRI. Future data regarding the implementation of clinical use cases are expected to clarify if 7 T musculoskeletal MRI applications with higher diagnostic accuracy result in patient benefits compared with MRI at lower field strengths.
Low-Dose CT Imaging of the Pelvis in Follow-up Examinations—Significant Dose Reduction and Impact of Tin Filtration
Authors: Schüle Simone , Gärtner Klaus , Halt Daniel , Beer Meinrad , Hackenbroch Carsten
Published: July 2022

Objectives

Low-dose (LD) computed tomography (CT) is still rarely used in musculoskeletal (MSK) radiology. This study evaluates the potentials of LD CT for follow-up pelvic imaging with special focus on tin filtration (Sn) technology for normal and obese patients with and without metal implants.

Materials and Methods

In a phantom study, 5 different LD and normal-dose (ND) CT protocols with and without tin filtration were tested using a normal and an obese phantom. Iterative reconstruction (IR) and filtered back projection (FBP) were used for CT image reconstruction. In a subsequent retrospective patient study, ND CT images of 45 patients were compared with follow-up tin-filtered LD CT images with a 90% dose reduction. Sixty-four percent of patients contained metal implants at the follow-up examination. Computed tomography images were objectively (image noise, contrast-to-noise ratio [CNR], dose-normalized contrast-to-noise ratio [CNRD]) and subjectively, using a 6-point Likert score, evaluated. In addition, the figure of merit was calculated. For group comparisons, paired t tests, Wilcoxon signed rank test, analysis of variance, or Kruskal-Wallis tests were used, where applicable.

Results

The LD Sn protocol with 67% dose reduction resulted in equal values in qualitative (Likert score) and quantitative image analysis (image noise) compared with the ND protocol in the phantom study. For follow-up examinations, dose could be reduced up to 90% by using Sn LD CT scans without impairment in the clinical study. However, metal implants resulted in a mild impairment of Sn LD as well as ND CT images. Cancellous bone (P < 0.001) was assessed worse and cortical bone (P = 0.063) equally in Sn LD CT images compared with ND CT images. Figure of merit values were significant (P ≤ 0.02) lower and hence better in Sn LD as in ND protocols. Obese patients benefited in particular from tin filtration in LD MSK imaging in terms of image noise and CNR (P ≤ 0.05).

Conclusions

Low-dose CT scans with tin filtration allow maximum dose reduction while maintaining high image quality for certain clinical purposes, for example, follow-up examinations, especially metal implant position, material loosening, and consolidation controls. Overweight patients benefit particularly from tin filter technology. Although metal implants decrease image quality in ND as well as in Sn LD CT images, this is not a relevant limitation for assessability.
Developing and leading a sustainable organization for early career acute care surgeons: Lessons from the inaugural American Association for the Surgery of Trauma Associate Member Council
Authors: Dumas Ryan P. , Bankhead Brittany K. , Coleman Julia R. , Dhillon Navpreet K. , Meizoso Jonathan P. , Bessoff Kovi , Butler William J. , Strickland Matt , Dultz Linda A. , Davis Kimberly , Bulger Eileen M. , Reilly Patrick M. , Croce Martin A. , Spain David A. , Livingston David H. , Brasel Karen J. , Coimbra Raul , Knowlton Lisa M.
Published: July 2022

The associate membership of the American Association for the Surgery of Trauma (AAST) was established in 2019 to create a defined but incorporated entity within the larger AAST for the next generation of acute care surgeons. The Associate Member Council (AMC) was subsequently established in 2020 to provide the new AM with an elected group of leaders who would represent them within the AAST. In its inaugural year, this cohort of junior faculty and surgical trainees had developed for the AM a set of bylaws, a mission statement, a strategic vision, and a succession plan. The experience of the AAST AMC is exemplary of what can be accomplished with collaboration, mentorship, innovation, and tenacity. It has the potential to serve as a template for the creation and vitalization of future professional groups. In this piece, the AMC proposes a blueprint for the successful conception of a new organization.
Pain-Related Vertex Evoked Potentials. Comparison of Surface Electrical to Heat Stimulation
Authors: Guiloff Roberto J. , Campero Mario , Barraza Gonzalo R. , Treede Rolf-Detlef , Matamala Jose M. , Castillo Jose L.
Published: July 2022

Introduction:

Demonstration of nociceptive fiber abnormality is important for diagnosing neuropathic pain and small fiber neuropathies. This is usually assessed by brief heat pulses using lasers, contact heat, or special electrodes. We hypothesized that pain-related evoked potentials to conventional surface electrical stimulation (PREPse) can index Aδ afferences despite tactile Aß fibers coactivation. PREPse may be more readily used clinically than contact heat evoked potentials (CHEPS).

Methods:

Twenty-eight healthy subjects. Vertex (Cz-A1/A2) recordings. Electrical stimulation of middle finger and second toe with conventional ring, and forearm/leg skin with cup, electrodes. Contact heat stimulation to forearm and leg. Compression ischemic nerve blockade.

Results:

PREPse peripheral velocities were within the midrange of Aδ fibers. N1-P1 amplitude increased with pain numerical rating scale graded (0–10) electrical stimulation (n = 25) and decreased with increasing stimulation frequency. Amplitudes were unchanged by different presentation orders of four stimulation intensities. PREPse N1 (∼130 milliseconds) and N2 (∼345 milliseconds) peaks were approximately 40 milliseconds earlier than that with CHEPS. PREPse and CHEPS N1-N2 interpeak latency (∼207 milliseconds) were similar. PREPse became unrecordable with nerve blockade of Aδ fibers.

Conclusions:

PREPse earlier N1 and N2 peaks, and similar interpeak N1-N2 latencies and central conduction velocities, or synaptic delays, to CHEPS are consistent with direct stimulation of Aδ fibers. The relation of vertex PREPse amplitude and pain, or the differential effects of frequency stimulation, is similar to pain-related evoked potential to laser, special electrodes, or contact heat stimulation. The relationship to Aδ was validated by conduction velocity and nerve block. Clinical utility of PREPse compared with CHEPS needs validation in somatosensory pathways lesions.
Palidis: fast discovery of novel insertion sequences
Authors: Carr Victoria R. , Pissis Solon P. , Mullany Peter , Shoaie Saeed , Gomez-Cabrero David , Moyes David L.
Published: July 2022

The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognises insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterised. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.

Data Summary

Palidis is available here: github.com/blue-moon22/palidis

The Insertion Sequence Catalogue is available to download here:https://github.com/blue-moon22/ISC

The raw reads from the Human Microbiome Project can be retrieved using the download links provided in Supplementary Data 1

The analysis for this paper is available here: github.com/blue-moon22/palidis_paper_analysis

The output of Palidis that was run on these reads is available in Supplementary Data 2

Impact Statement

Insertion sequences are a class of transposable element that play an important role in the dissemination of antimicrobial resistance genes. However, it is challenging to completely characterise the transmission dynamics of insertion sequences and their precise contribution to the spread of antimicrobial resistance. The main reasons for this are that it is impossible to identify all insertion sequences based on limited reference databases and thatde novocomputational methods are ill-equipped to make fast or accurate predictions based on incomplete genomic assemblies. Palidis generates a larger, more comprehensive catalogue of insertion sequences based on a fast algorithm harnessing genomic diversity in mixed microbial communities. This catalogue will enable genomic epidemiologists and researchers to annotate genomes for insertion sequences more extensively and advance knowledge of how insertion sequences contribute to bacterial evolution in general and antimicrobial resistance spread across microbial lineages in particular. This will be useful for genomic surveillance, and for development of microbiome engineering strategies targeting inactivation or removal of important transposable elements carrying antimicrobial resistance genes.
Neural correlates of changing food choices while bypassing values
Authors: Zahedi Anoushiravan , Artigas Sergio Oroz , Swaboda Nora , Wiers Corinde E. , Görgen Kai , Park Soyoung Q.
Published: July 2022

Current theories suggest that altering choices requires value modification. To investigate this, normal-weight participants’ food choices and values were tested before and after an approach-avoidance training (AAT), while neural activity was recorded during the choice task using functional magnetic resonance imaging (fMRI). During AAT, participants consistently approached low-while avoiding high-calorie food cues. AAT facilitated low-calorie food choices, leaving food values unchanged. Instead, we observed a shift in indifference points, indicating the decreased contribution of food values in food choices. Training-induced choice shifts were associated with increased activity in the posterior cingulate cortex (PCC). In contrast, the medial PFC activity was not changed. Additionally, PCC grey matter density predicted individual differences in training-induced functional changes, suggesting anatomic predispositions to training impact. Our findings demonstrate neural mechanisms underlying choice modulation independent of valuation-related processes, with substantial theoretical significance for decision-making frameworks and translational implications for health-related decisions resilient to value shifts.
Mice lacking dopamine production in neurotensin receptor 1 neurons voluntarily undergo time-restricted feeding of high fat diet and resist obesity
Authors: Farahmand Firozeh , Sidikpramana Michael , Yousef Bara , Sharif Sarah , Shao Kieana , Tang Qijun , Leinninger Gina M. , Güler Ali D. , Steele Andrew D.
Published: July 2022

The introduction of processed foods high in fat and sugars has caused a dramatic increase in obesity in humans. Diet-induced obesity (DIO) can be modeled in laboratory mice by increasing the fat content of their diet. Previously, it was determined that mice lacking dopamine receptor 1 (Drd1) are completely resistant to DIO and do not eat as much food during the day as control mice. Surprisingly, when Drd1 is restored to the suprachiasmatic nucleus (SCN), which is the central regulator of circadian rhythms, these mice increase day-eating and become obese. The source of dopamine in the SCN is the ventral tegmental area (VTA), but the genetic identity of the dopamine neurons is unknown. Here we create conditional deletion mutants for tyrosine hydroxylase (TH) using neurotensin receptor 1 (Ntsr1) Cre and other Cre drivers and measure feeding and body weight homeostasis on standard and high fat diets. Control mice were susceptible to DIO and overate during the day whereas Ntsr1-Cre conditional knockouts for TH mice did not increase day-eating, nor did they gain much weight on HFD. We used an adeno-associated virus to selectively restore TH to the VTA Ntsr1 neurons and observed an increase in body weight and increased day-eating of HFD. These results implicate VTA Ntsr1 dopamine neurons as promoting out-of-phase feeding behavior on a high fat diet that could be an important contributor to diet-induced obesity.
Correspondence of Newcomb-Benford Number Law with Ecological Processes
Authors: Davic Robert D.
Published: July 2022

The Newcomb-Benford number law has been applied in the natural sciences for decades, with little ecological attention. Empirical data transformed into significant digits reveal statistical correspondence between the discrete Benford probability distribution and physical systems in dynamic equilibrium along a continuum of stability. Analytic methods are presented to detect this mathematical representation across multiple levels of ecological organization and spatial scale. Case studies demonstrate novel application to help identify bidirectional regime changes to alternative states of dynamic equilibrium. Widespread documentation of the surprising phenomenon is anticipated as ecologists revisit historic sets of random measurement data and design future sampling protocols. Controlled experiments with measurement variables that span multiple orders of magnitude would be well suited for future empirical and theoretical inquiry.
Variations in microbial diversity affect the stability and function of dark fermentation bioreactors
Authors: Navarro-Díaz Marcelo , Aparicio-Trejo Valeria , Valdez-Vazquez Idania , Carrillo-Reyes Julián , Avitia Morena , Escalante Ana E.
Published: July 2022

The relationship between the taxonomic diversity and the function of microbial communities is complex. Specifically, the ecological mechanisms that drive the dynamics of microbial populations and the consequences of these dynamics on functional traits have remained elusive. Among the simplest but natural microbial communities are dark fermentation consortia, a subset of the more diverse and complex microbial communities, anaerobic digestion communities. Dark fermentation consortia have been of interest as they produce biofuels such as hydrogen and different alcohols that can be used as fossil fuels alternatives. However, these hydrogen-producing communities have unresolved instability and low yield issues. We have previously proposed that instability and low yields in dark fermentation communities could be due to reduced diversity that results from aggressive pretreatments of original anaerobic digestion communities. In this work, we used dark fermentation communities to examine experimentally the effect of diversity reduction in functional traits, including stability and microbial interactions. We established two types of treatment, (i) maintaining strict culture conditions that are known to induce hydrogen production and ii) applying a heat-shock treatment known for selecting hydrogen-producing bacteria, which resulted in two types of communities, high and low diversity. Each treatment consisted of 12 replicates that were transferred to fresh medium daily (during 28 days for the non-treated bioreactors and 61 days for the heat-shock treated bioreactors). Microbial communities of the two treatments were characterized in their function as well as resistance to invasion. Microbial composition was characterized by culture-independent 16S rRNA gene amplicon sequencing. We analyzed microbial community composition and function through time, establishing statistical relationships between bacterial groups and metabolite production. Also, we inferred the potential ecological interactions that might have been established. Results show that the replicate bioreactors for each treatment predictably shifted to a similar composition and increased and stable biogas production. The non-treated bioreactors showed less susceptibility to the invasion (with the invasive bacteria establishing only in one replicate in the non-treated bioreactors vs 6 invaded replicates of the heat-shock treated bioreactors). However, the effect observed in the non-treated bioreactor replicate where the invader bacteria established was more drastic since the invasive bacteria managed to become dominant.
Analysis of Alzheimer’s disease Polygenic Risk Scores using RNA-sequencing provides further novel biological pathways
Authors: Crawford K. , Leonenko G. , Baker E. , Grozeva D. , Lan-Leung B. , Holmans P. , Williams J. , O’Donovan M. C. , Escott-Price V. , Ivanov DK.
Published: July 2022

Polygenic risk scores (PRS) have been widely adopted as a tool for measuring common variant liability and it has been shown to predict lifetime risk of Alzheimer’s disease (AD) development. However, the relationship between PRS and AD pathogenesis is largely unknown. We aimed to address some of the knowledge gaps with respect to the downstream molecular consequences associated with PRS. We also make a direct comparison of the disrupted biological mechanisms in a case/control classification and in response to PRS in the same individuals.

We performed an integrative computational analysis of the transcriptome of the largest human brain-derived cohort sample (288 individuals; cerebellum and temporal cortex; MayoRNAseq; AMP-AD) with matched AD genetic and gene-expression data (WGS; bulk-brain RNA-seq). There was little overlap in terms of differentially expressed genes in case/control and PRS analyses, but a consensus of commonly disrupted biological mechanisms. Genes implicated by previous AD GWAS were found to be significantly enriched with respect to PRS in temporal cortex only. We identified mechanisms that were previously implicated in AD, including immune/stress response, lipid/cholesterol/fatty acid metabolism, endosome, death/apoptosis, neuronal processes, ageing and the involvement of glial cells. We also provide novel evidence for the significant involvement in AD of cellular structures, including the Golgi apparatus and endoplasmic reticulum as well as mitochondrial function.

The largely common biological mechanisms between a case/control classification and in association with PRS suggests that PRS stratification can be used for studies where suitable case/control samples are not available or the selection of individuals with high and low PRS in clinical trials.
Automatic Bolus Tracking in Abdominal CT scans with Convolutional Neural Networks
Authors: Li Angela , Noël Peter B. , Shapira Nadav
Published: July 2022

Background

Bolus tracking can optimize the time delay between contrast injection and diagnostic scan initiation in contrast-enhanced computed tomography (CT), yet the procedure is time-consuming and subject to inter- and intra-operator variances which affect the enhancement levels in diagnostic scans. The objective of the current study is to use artificial intelligence algorithms to fully automate the bolus tracking procedure in contrast-enhanced abdominal CT exams for improved standardization and diagnostic accuracy while providing a simplified imaging workflow.

Methods

This retrospective study used abdominal CT exams collected under a dedicated IRB. Input data consisted of CT topograms and images with high heterogeneity in terms of anatomy, sex, cancer pathologies, and imaging artifacts acquired with four different CT scanner models. Our method consisted of two sequential steps: (i) automatic locator scan positioning on topograms, and (ii) automatic ROI positioning within the aorta on locator scans. The task of locator scan positioning is formulated as a regression problem, where the limited amount of annotated data is circumvented using transfer learning. The task of ROI positioning is formulated as a segmentation problem.

Results

Our locator scan positioning network offered improved positional consistency compared to a high degree of variance in manual slice positionings, verifying inter-operator variance as a significant source of error. When trained using expert-user ground truth labels, the locator scan positioning network achieved a sub-centimeter error (9.76 ± 6.78 mm) on a test dataset. The ROI segmentation network achieved a sub-millimeter absolute error (0.99 ± 0.66 mm) on a test dataset.

Conclusions

Locator scan positioning networks offer improved positional consistency compared to manual slice positionings and verified inter-operator variance as an important source of error. By significantly reducing operator-related decisions, this method opens opportunities to standardize and simplify the workflow of bolus tracking procedures for contrast-enhanced CT.
Disruption of lactate metabolism in the peripheral nervous system leads to motor-selective deficits
Authors: Bloom A. Joseph , Hackett Amber R. , Strickland Amy , Yamada Yurie , Ippolito Joseph , Schmidt Robert E. , Sasaki Yo , DiAntonio Aaron , Milbrandt Jeffrey
Published: July 2022

Schwann cells (SCs) myelinate and provide trophic support to axons in the peripheral nervous system (PNS) and disruption of SC cellular metabolism leads to demyelination and axon degeneration, both symptoms of peripheral neuropathies. The lactate shuttle hypothesis proposes that glycolytic support cells supply lactate to adjacent axons to sustain their high metabolic demands, a process that requires the interconversion of lactate and pyruvate via lactate dehydrogenase (LDH) in both SCs and neurons. To test this hypothesis in the PNS, we selectively knocked out the genes for both LDH enzymes, LDHA and LDHB, in motor neurons (MNs), sensory neurons (SNs), or SCs. Interestingly, motor axons and their synapses progressively degenerate when LDH is deleted from either MNs or SCs; however, defects in sensory axons or their terminals were not observed when LDH was excised from either SNs or SCs. Deletion of LDH in SCs also leads to a decrease in total ATP levels in peripheral nerves despite a marked accumulation of pyruvate and glycolytic intermediates, consistent with the failure of pyruvate to lactate conversion in SCs leading to energetic deficits in axons. These results support a model in which motor axons are more dependent on SC-derived lactate than are sensory axons, a specific dependency that suggests LDH and lactate shuttling influence the course of motor-dominated neuropathies such as ALS.
Revealing allostery in PTPN11 SH2 domains from MD simulations
Authors: Anselmi Massimiliano , Hub Jochen S.
Published: July 2022

Src-homology 2 (SH2) domains are protein interaction domains that bind to specific peptide motifs containing phosphotyrosine. SHP2, a tyrosine phosphatase encoded by PTPN11 gene, which has been emerged as positive or negative modulator in multiple signaling pathways, contains two SH2 domains, respectively called N-SH2 and C-SH2. These domains play a relevant role in regulating SHP2 activity, either by recognizing its binding partners or by blocking its catalytic site. Considering the multiple functions that these domains carry out in SHP2, N-SH2 and C-SH2 represent an interesting case of study. Here, we present a methodology that permits, by means of the principal component analysis (PCA), to study and to rationalize the structures adopted by the SH2 domains, in terms of the conformations of their binding sites. The structures can be distinguished, grouped, classified and reported in a diagram. This approach permits to identify the accessible conformations of the SH2 domains in different binding conditions and to eventually reveal allosteric interactions. The method further reveals that the conformation dynamics of N-SH2 and C- SH2 strongly differ, which likely reflects their distinct functional roles.
From Molecular Dynamics to Supramolecular Organization: The Role of PIM Lipids in the Originality of theMycobacterialPlasma Membrane
Authors: Brown Chelsea M. , Corey Robin A. , Gao Ya , Choi Yeol Kyo , Gilleron Martine , Destainville Nicolas , Fullam Elizabeth , Im Wonpil , Stansfeld Phillip J. , Chavent Matthieu
Published: July 2022

Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis, a disease that claims ~1.5 million lives annually. The current treatment regime is long and expensive, and missed doses contribute to drug resistance. There is much to be understood about theMtbcell envelope, a complicated barrier that antibiotics need to negotiate to enter the cell. Within this envelope, the plasma membrane is the ultimate obstacle and is proposed to be comprised of over 50% mannosylated phosphatidylinositol lipids (phosphatidyl-myoinositol mannosides, PIMs), whose role in the membrane structure remains elusive. Here we used multiscale molecular dynamics (MD) simulations to understand the structure-function relationship of the PIM lipid family and decipher how they self-organize to drive biophysical properties of theMycobacterialplasma membrane. To validate the model, we tested known anti-tubercular drugs and replicated previous experimental results. Our results shed new light into the organization of theMycobacterialplasma membrane and provides a working model of this complex membrane to use forin silicostudies. This opens the door for new methods to probe potential antibiotic targets and further understand membrane protein function.

Abstract Figure
Development of esterase-resistant and highly active ghrelin analogs via thiol-ene click chemistry
Authors: Li Hao-Zheng , Shao Xiao-Xia , Shou Li-Li , Li Ning , Liu Ya-Li , Xu Zeng-Guang , Guo Zhan-Yun
Published: July 2022

The orexigenic peptide ghrelin exerts important functions in energy metabolism and cellular homeostasis by activating the growth hormone secretagogue receptor type 1a (GHSR1a), and thus has therapeutic potential to treat certain diseases. Native ghrelin carries an essentialO-fatty acyl moiety at the side-chain of its third Ser residue; however, this posttranslational modification is susceptible to hydrolysis by certain esterases in circulation, representing a major route ofin vivoinactivation of ghrelin. In the present study, we developed a novel approach to prepare various esterase-resistant ghrelin analogs via photo-induced thiol-ene click chemistry. A recombinant unacylated human ghrelin mutant carrying a unique Cys residue at the third position was reacted with commercially available end alkenes, thus various alkyl moieties were introduced to the side-chain of its unique Cys residue via a thioether bond. Among elevenS-alkylated ghrelin analogs, analog11, generated by reacting with 2-methyl-1-octene, not only acquired much higher stability in human serum and fetal bovine serum, but also acquired moderately higher activity compared with native human ghrelin. Thus, the present study not only provided an efficient approach to prepare various esterase-resistant ghrelin analogs, but also produced a novel highly stable and highly active ghrelin analog with therapeutic potential.
Avian and Human Influenza Viruses Exhibit Distinct Glycoconjugate Receptor Specificities in Human Lung Cells
Authors: Liang Chieh-Yu , Huang Iris , Han Julianna , Manivasagam Senthamizharasi , Plung Jesse , Strutz Miranda , Yu Yolanda , Kandasamy Matheswaran , Gourronc Francoise A. , Klingelhutz Aloysius J. , Choudhury Biswa , Rong Lijun , Perez Jasmine T. , Neelamegham Sriram , Manicassamy Balaji
Published: July 2022

IAV utilize sialic acid (Sia) containing cell surface glycoconjugates for host cell infection, and IAV strains from different host species show preferences for structurally distinct Sia at the termini of glycoconjugates. Various types of cell surface glycoconjugates (N-glycans, O-glycans, glycolipids) display significant diversity in both structure and carbohydrate composition. To define the types of glycoconjugates that facilitate IAV infection, we utilized the CRISPR/Cas9 technique to truncate different types of glycoconjugates, either individually or in combination, by targeting glycosyltransferases essential to glycan biosynthesis in a human lung epithelial cell line. Our studies show that both human and avian IAV strains do not display strict preferences for a specific type of glycoconjugate. Interestingly, truncation of all three types of glycoconjugates significantly decreased the replication of human IAV strains, yet did not impact the replication of avian IAV strains. Taken together, our studies demonstrate that avian IAV strains utilize a broader repertoire of glycoconjugates for host cell infection as compared to human IAV strains.

Author Summary

It is well known that influenza A viruses (IAV) initiate host cell infection by binding to sialic acid, a sugar molecule present at the ends of various sugar chains called glycoconjugates. These glycoconjugates can vary in chain length, structure, and composition. However, it remains unknown if IAV strains preferentially bind to sialic acid on specific glycoconjugates for host cell infection. Here, we utilized CRISPR gene editing to abolish sialic acid on different glycoconjugate types in human lung cells, and evaluated human versus avian IAV infections. Our studies show that both human and avian IAV strains can infect human lung cells by utilizing any of the three major sialic acid-containing glycoconjugate types, specifically N-glycans, O-glycans, and glycolipids. Interestingly, simultaneous elimination of sialic acid on all three glycoconjugate types in human lung cells dramatically decreased human IAV infection, yet had little effect on avian IAV infection. Our studies indicate that avian IAV strains can utilize a wide variety of glycoconjugates for infection, whereas human IAV strains display restrictions in glycoconjugate type usage. These novel studies show distinct differences in host glycoconjugate preferences between human and avian IAV strains.
Influenza and pneumococcal vaccination and the risk of COVID-19: A systematic review and meta-analysis
Authors: Kapoula Georgia G. , Vennou Konstantina E. , Bagos Pantelis G.
Published: July 2022

A number of studies have investigated the potential non-specific effects of some routinely administered vaccines (e.g. influenza, pneumococcal) on COVID-19 related outcomes, with contrasting results. In order to elucidate this discrepancy, we conducted a systematic review and meta-analysis to assess the association between seasonal influenza vaccination and pneumococcal vaccination with SARS-CoV-2 infection and its clinical outcomes. PubMed and medRxiv databases were searched, up until November 2021. Random effects model was used in the meta-analysis to pool odds ratio (OR) and adjusted estimates with their 95% confidence intervals (CIs). Heterogeneity was quantitatively assessed using the Cohran’sQand theI2index. Sub-group analysis, sensitivity analysis and assessment of publication bias were performed for all outcomes. In total 38 observational studies were included in the meta-analysis and there was substantial heterogeneity. Influenza and pneumococcal vaccination were associated with lower risk of SARS-Cov-2 infection (OR: 0.80, 95% CI: 0.75-0.86 and OR: 0.70, 95% CI: 0.57-0.88, respectively). Regarding influenza vaccination, it seems that the majority of studies did not properly adjust for all potential confounders, so when the analysis was limited to studies that adjusted for age, sex, comorbidities and socioeconomic indices, the association diminished. This is not the case regarding the pneumococcal vaccination, for which even after adjustment for such factors the association persisted. Regarding harder endpoints such as ICU admission and death, current data do not support the association. Possible explanations are discussed, including trained immunity, inadequate matching for socioeconomic indices and possible coinfection.
Scanning ion-conductance microscopy for studying β-amyloid aggregate formation on living cell surface
Authors: Kolmogorov Vasilii S. , Erofeev Alexander S. , Barykin Evgeny P. , Timoshenko Roman V. , Lopatukhina Elena V. , Kozin Sergey A. , Salikhov Sergey V. , Klyachko Natalia L. , Mitkevich Vladimir A. , Edwards Christopher R.W. , Korchev Yuri E. , Makarov Alexander A. , Gorelkin Petr V.
Published: July 2022

Alzheimer’s disease (AD) is the most common form of dementia, a progressive neurological disorder characterized by short and long-term memory loss, including cognitive and functional impairment, which is refractory to current therapy. It is suggested that the aggregation of β-amyloid (Aβ) peptide on neuronal cell surface leads to various deviations of its vital function due to myriad pathways defined by internalization of calcium ions, apoptosis promotion, reduction of membrane potential, synaptic activity loss etc. These are associated with structural reorganizations and pathologies of the cell cytoskeleton mainly involving actin filaments and microtubules, and consequently – alterations of cell mechanical properties. Thus, the effect of amyloid oligomers on cells’ Young’s modulus has been observed in a variety of studies. However, the precise connection between the formation of amyloid aggregates on cell membranes and their effects on local mechanical properties of living cells is still unresolved. In this work, we have used correlative scanning ion-conductance microscopy (SICM) to study cell topography, Young’s modulus mapping and confocal imaging of Aβ aggregates formation on living cell surfaces with subsequent assessment of the reactive oxygen species levels inside single cells using platinum nanoelectrodes. We showed that correlative SICM technique, in conjunction with topography mapping and confocal imaging, can be used for Patch-Clamp recordings from living cells with evidently formed FAM-labeled Aβ aggregates on its surface. As we demonstrated, SICM can be successfully applied to studying cytotoxicity mechanisms of Aβ aggregates on living cell surface.
High resolution studies of DNA lesion bypass by human DNA polymerase δ holoenzymes
Authors: Dannenberg Rachel L. , Cardina Joseph A. , Pytko Kara G. , Hedglin Mark
Published: July 2022

During DNA replication, DNA lesions present in lagging strand templates are initially encountered by DNA polymerase δ (pol δ). The historical view for what transpires from these encounters is that replication of the afflicted lagging strand template abruptly stops, activating DNA damage tolerance (DDT) pathways that replicate the offending lesion and adjacent DNA sequence, allowing pol δ to resume downstream. However, qualitative studies observed that human pol δ is capable of replicating various DNA lesions, albeit to unknown extents, which raises issues regarding the roles of pol δ and DDT in the replication of DNA lesions. To address these issues, we re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with DNA lesions. The results indicate that pol δ holoenzymes support stable dNTP incorporation opposite and beyond multiple lesions and the extent of these activities depends on the lesion and pol δ proofreading. Furthermore, after encountering a given DNA lesion, subsequent dissociation of pol δ is distributed around the lesion and a portion of pol δ does not dissociate at all. The distributions of these events are dependent on the lesion and pol δ proofreading. These results challenge our understanding of DNA lesion replication and DDT.
Small CD4 mimetics sensitize HIV-1-infected macrophages to antibody-dependent cellular cytotoxicity
Authors: Laumaea Annemarie , Marchitto Lorie , Beaudoin-Bussières Guillaume , Ding Shilei , Gasser Romain , Chatterjee Debashree , Gendron-Lepage Gabrielle , Medjahed Halima , Chen Hung-Ching , Smith Amos B , Ding Haitao , Kappes John C. , Hahn Beatrice H. , Kirchhoff Frank , Richard Jonathan , Duerr Ralf , Finzi Andrés
Published: July 2022

HIV-1 Envelope (Env) conformation determines the susceptibility of infected CD4+T cells to Antibody Dependent Cellular Cytotoxicity (ADCC). Upon interaction with CD4, Env adopts more “open” conformations, exposing ADCC epitopes. HIV-1 limits Env-CD4 interaction and protects infected cells against ADCC by downregulating CD4 via Nef, Vpu and Env. Limited data exists however of the role of these proteins in downmodulating CD4 on infected macrophages and how this impacts Env conformation. While Nef, Vpu and Env are all required to efficiently downregulate CD4 on infected CD4+T cells, we show here that any one of these proteins is sufficient to downmodulate most CD4 from the surface of infected macrophages. Consistent with this finding, Nef and Vpu have a lesser impact on Env conformation and ADCC sensitivity in infected macrophages compared to CD4+T cells. However, treatment of infected macrophages with small CD4-mimetics expose vulnerable CD4-induced Env epitopes and sensitize them to ADCC.
Wnt7a Suppresses Adipogenesis of Skeletal Muscle Mesenchymal Stem Cells and Fatty Infiltration Through the Alternative Wnt-Rho-YAP/TAZ Signaling Axis
Authors: Fu Chengcheng , Guzmán-Seda Mariana , Laudier Damien , Han Woojin M.
Published: July 2022

Intramuscular fatty infiltration in muscle injuries and diseases, caused by aberrant adipogenesis of fibro-adipogenic progenitors, negatively impacts function. Intramuscular delivery of Wnt7a offers a promising strategy to stimulate muscle regeneration but its effects on adipogenic conversion of fibro-adipogenic progenitors remain unknown. Here we show that Wnt7a inhibits adipogenesis of FAPs through the alternative Wnt-Rho-YAP/TAZ signaling that subsequently upregulates the canonical Wnt pathway. Furthermore, intramuscular injection of Wnt7a in vivo effectively suppresses fatty infiltration in mice. Our results collectively suggest Wnt7a as a potential protein-based therapeutic for inhibiting adipogenesis of FAPs and intramuscular fatty infiltration in pathological muscle injuries or diseases.
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae
Authors: Foster-Nyarko Ebenezer , Cottingham Hugh , Wick Ryan R. , Judd Louise M. , Lam Margaret M. C. , Wyres Kelly L. , Stanton Thomas D. , Tsang Kara K. , David Sophia , Aanensen David M. , Brisse Sylvain , Holt Kathryn E.
Published: July 2022

Background

Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs.

Methods

We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique Klebsiella pneumoniae isolates. ONT reads generated via MinION with R9.4 flowcells were basecalled using three alternative models (Fast, High-accuracy (HAC) and Super-accuracy (SUP), available within ONT’s Guppy software), assembled with Flye and polished using Medaka. Accuracy of typing using ONT-only assemblies was compared with that of Illumina-only and hybrid ONT+Illumina assemblies, constructed from the same isolates as reference standards.

Results

The most resource-intensive ONT-assembly approach (SUP basecalling, with or without Medaka polishing) performed best, yielding reliable capsule (K) type calls for all strains (100% exact or best matching locus), reliable multi-locus sequence type (MLST) assignment (98.3% exact match or single-locus variants), and good detection of acquired AMR genes and mutations (88% – 100% correct identification across the various drug classes). Distance-based trees generated from SUP+Medaka assemblies accurately reflected overall genetic relationships between isolates; however, the definition of outbreak clusters from ONT-only assemblies was problematic. HAC basecalling + Medaka polishing performed similarly to SUP basecalling without polishing, and polishing introduced errors into HAC- or Fast-basecalled assemblies. Therefore, we recommend investing compute resources into basecalling (SUP model) over polishing, where compute resources and/or time are limiting.

Conclusions

Overall, our results show that MLST, K type and AMR determinants can be reliably identified with ONT-only data. However, cluster detection remains challenging with this technology.
Elastic properties and shape of the Piezo dome underlying its mechanosensory function
Authors: Haselwandter Christoph A. , Guo Yusong R. , Fu Ziao , MacKinnon Roderick
Published: July 2022

In a companion paper we show that the free membrane shape of lipid bilayer vesicles containing the mechanosensitive ion channel Piezo can be predicted, with no free parameters, from membrane elasticity theory together with measurements of the protein geometry and vesicle size (accompanying paper). Here we use these results to determine the force that Piezo exerts on the free membrane and, hence, that the free membrane exerts on Piezo, for a range of vesicle sizes. From vesicle shape measurements alone, we thus obtain a force-distortion relationship for Piezo, from which we deduce Piezo’s intrinsic radius of curvature, 42 ± 12 nm, and bending stiffness, 18 ± 2.1 kBT, in free-standing lipid bilayer membranes mimicking cell membranes. Applying these estimates to a spherical cap model of Piezo embedded in a lipid bilayer, we suggest that Piezo’s intrinsic curvature, surrounding membrane footprint, small stiffness, and large area are the key properties of Piezo that give rise to low-threshold, high-sensitivity mechanical gating.