bluuebunny/crossref_metadata_2025 huggingface dataset:
Are We in Control of Our Demons?
Authors: Kong Kar Yee Catrin , Ganapathy Sashikumar
Published: February 2022

Background

The medical profession, with its remarkable physical and emotional demands, predisposes physicians to compassion fatigue (CF) and burnout (BO). Although these conditions have been studied individually, little attention has been paid to how pediatric emergency physicians experience these conditions in the context of an Asian emergency setting especially during a global pandemic In our study, we aim to understand the experiences of individual physicians and describe the potential triggers or protective factors of compassion satisfaction, BO, and compassion satisfaction among physicians in an Asian pediatric emergency department during a pandemic.

Methods

A qualitative, individual interview methodology was used. From March to April 2020, we enrolled 20 physicians involved in frontline care during the coronavirus disease 2019 (COVID-19) pandemic in the pediatric emergency department to participate. Semistructured interviews were conducted, audiotaped, and transcribed in verbatim, with identifiers removed. Themes were identified, and data were analyzed using qualitative data analysis and iterative data analysis.

Results

We recruited 20 physicians. Three themes emerged from data analysis. First, we showed how workplace conditions are protective, including work morale, leadership and management, and social support received. Second, workload affected participants emotionally and in terms of its heavier quantity and longer hours. Finally, intrinsic factors that were protective in developing CF or BO include having professional autonomy, experience, work-life balance, and having emotional resilience to develop self-care. Cultural influences affect emotional regulation and can lead to negative coping with negative peer pressure. In general, participants quantified their levels of satisfaction at work as average to above average. However, they highlighted experiencing greater stress during COVID-19 with the underlying fear of contagion and infection.

Conclusions

Being a pediatric emergency physician puts one at greater risk of experiencing CF and BO because of work and nonwork stressors, especially during a global pandemic, influenced by sociocultural factors. A positive and supportive work environment should be created while providing culturally adapted strategies to improve individual physician resilience to maintain their well-being.
“Code Green Active” Curriculum
Authors: Kusulas Matthew P. , Drenis Anastasios , Cooper Alison , Fishbein Joanna , Crevi Diana , Stein Etess Melanie , Bullaro Francesca
Published: February 2022

Background

There has been an increase in violent acts against hospital employees, including active shooter events. Emergency department (ED) staff must be able to respond to these events efficiently to ensure the safest possible outcome. However, few in our ED were aware of our hospital's active shooter protocol. We aimed to increase staff knowledge of and confidence in these guidelines.

Methods

We developed and implemented a 7-week spiral curriculum using the Kern model of curriculum development. Each week, a segment of the hospital active shooter protocol was featured. Multimodal instructional methods including posters, instruction at daily team huddles, descriptions in the weekly division newsletter, and email summaries were used.

A 10-question assessment was administered to ED staff both before and after the implementation of our curriculum. During both assessments, staff were asked to rate their confidence in both knowledge of and ability to follow hospital active shooter guidelines.

Results

There were 95 and 102 participants in the preintervention and postintervention periods, respectively.

The median proportion of correct answers on the knowledge assessment increased when comparing preintervention with postintervention performances (P < 0.05).

Staff confidence in both knowledge of and ability to follow active shooter protocols increased after the implementation of our curriculum (P < 0.05).

Conclusions

Our 7-week curriculum resulted in improved knowledge of and confidence in hospital active shooter protocols among ED staff. Given that our sample was an unpaired convenience sample, inferences from our analysis were limited. Tabletop simulations are currently underway to further reinforce and clarify concepts.
Oil Cyst Formation after Lower Blepharoplasty with Fat Grafts
Authors: Huang Chih-Wei , Yen Yu-Hsiu , Lu Shiuh-Yen , Pu Chi-Ming
Published: February 2022

Background

Fat grafting is increasingly used as an adjuvant surgery to blepharoplasty to refill the volume loss of an aged face and promote cellular regeneration. Complications, such as hematoma, infection, seroma, and palpable mass, may occur. We collected the patients that underwent lower blepharoplasty combined with fat graft to evaluate the incidence of oil cyst formation in the lower eyelid and to identify risk factors.

Material and Methods

A retrospective review was performed of all patients who underwent lower or total blepharoplasty combined with fat graft at the authors' institution between January 2018 and June 2020. Complication rates were observed, and associations between preoperative variables and outcomes were assessed.

Results

A total of 119 patients were included in the series (all bilateral, 238 eyelids). The average patient age was 54.88 ± 11.94 years, and the average grafted fat was 1.88 ± 1.0 mL. On a per-eyelid basis for all patients, the complication rate of oil cyst formation was 6.72% (16 of 238 eyelids). The occurrence of oil cyst formation was associated with hypertension (P = 0.012; adjusted odds ratio, 9.27; 95% confidence interval, 1.62–52.99) and diabetes mellitus (P = 0.005; adjusted odds ratio, 14.02; 95% confidence interval, 2.22–88.45), but not associated with anticoagulants use (P = 0.931), age (P = 0.784), sex (P = 0.317), or fat volume (P = 0.215). The mean interval between the fat graft procedure and oil cyst noted was 236.5 ± 118.9 days.

Conclusions

Oil cyst in lower eyelid can be defined as a palpable, firm, and persistent subcutaneous cystic lesion found postoperatively in any size during physical examination. The complication rate of oil cyst formation occurring after lower blepharoplasty with autologous fat grafting is 6.72%. Hypertension and diabetes mellitus maybe are risk factors of oil cyst formation. Steroid injection, needle capsulotomy, liposuction, and excision are safe and effective treatments. Reduce surgical trauma by diminishing anterior lamina trauma and capsulopalpebral fascia repair might decrease the complication rate of oil cyst formation.

Transconjunctival lower blepharoplasty with fat graft or 2-stage surgery may be a choice to prevent oil cyst formation.
An In Vitro Study of the Effects of Mechanical and Enzymatic Isolation of Stromal Vascular Fraction on Wound Healing
Authors: Dai Lien-Guo , Huang Nien-Chi , Kang Lan-Ya , Fu Keng-Yen , Hsieh Pai-Shan , Dai Niann-Tzyy
Published: February 2022

The adipose-derived stromal vascular fraction (SVF) is considered to be an attractive source of stem cells in cell therapy. Besides stem cells, it also contains functional cells, such as macrophages, precursor cells, somatic stem cells, and pericytes. Collagenase digestion is the most frequently used method to isolate SVF, but it is time-consuming and costly and has some problems, such as infectious agents and immune reactions. In this research, we compared the yield, cell population ratios, and cell viability when isolating SVF by the ultrasonic physics (U-SVF) method and traditional enzymatic method (E-SVF). Then, we isolated exosomes from U-SVF and E-SVF, respectively, and cocultured them with fibroblasts to investigate the potential of applying this cell secretion in wound repair. The results showed that there was no significant difference between the ultrasonic method and enzymatic method in terms of cell viability, cell numbers, or the expression of CD markers of stem cells. However, exosome analysis identified a greater number and smaller size of exosome particles obtained by U-SVF. In terms of cell proliferation efficiency, although the proliferation efficiency of U-SVF was lower than that of E-SVF. Trilineage differentiation experiments revealed that both E-SVF and U-SVF had good differentiation ability, owing to high stem cell content. Finally, E-SVF and U-SVF exosomes were cocultured with fibroblasts. The efficiency of fibroblast migration increased in the SVF exosome treated groups, and the expression of related genes (integrin α5β1) was slightly upregulated; however, the expression of FAK, AKT, ERK, and RhoA was significantly upregulated at 24 hours. From the abovementioned experiments, we found that there was no significant difference in stem cell-related characteristics between SVF isolated by ultrasonic cavitation and SVF isolated by the enzymatic method. In addition, exosomes secreted by SVF may have excellent therapeutic effect on skin injuries, which provides a new viewpoint and therapeutic strategy for soft tissue repair.
The Effect of Biological Scaffold (Biodesign) in Postmastectomy Direct-to-Implant Breast Reconstruction
Authors: Sou Weng-Kit , Perng Cherng-Kang , Ma Hsu , Tseng Ling-Ming , Tsai Yi-Fang , Lin Yen-Shu , Lien Pei-Ju , Hsiao Fu-Yin , Feng Chin-Jung
Published: February 2022

Background

Direct-to-implant (DTI) breast reconstruction is one of the immediate implant-based breast reconstruction methods. If the amount of soft tissue (eg, muscle or fascia) is insufficient to completely cover the implant, biological scaffold or acellular dermal matrix can be safely used for implant coverage. In this study, we used an acellular porcine small intestinal submucosa (SIS) mesh (Biodesign; Cook Medical Inc, Bloomington, IN) for DTI reconstruction to explore the impact of its use on breast reconstruction results.

Methods

We retrospectively assessed cases involving DTI reconstruction at Taipei Veterans General Hospital from 2015 to 2019. Women, 18 years or older, who underwent immediate DTI reconstruction after mastectomy were included in the study. Mastectomy may have been performed because of therapeutic or prophylactic reasons. Patients who did and did not use SIS mesh for reconstruction were studied separately, and the 2 groups were compared in terms of clinical outcomes and complications. The validated, self-administered BREAST-Q Reconstruction Module version 2.0 survey was used to evaluate health-related quality of life and satisfaction among patients who underwent breast reconstruction.

Results

A total of 30 DTI breast reconstructions were enrolled. The mean age was 49.2 years, and the mean body mass index was 22.3 kg/m2. The mean postoperative follow-up duration was 17.1 months. Nipple-sparing mastectomy was performed for 26 cases (86.7%), and DTI breast reconstructions using SIS mesh for implant coverage were done in 14 cases (46.7%). The overall complication rate was 53.3% in 30 reconstructions, with nipple complications being the most common complication. The non-SIS and SIS-using groups had a similar overall complication rate postoperatively. As for the quality-of-life assessment, the SIS group obtained a higher score on BREAST-Q than those for whom SIS was not used.

Conclusions

Porcine SIS mesh might be a safe and effective alternative to biological scaffolds in immediate 1-stage implant-based breast reconstruction to improve the quality of life after surgery.
Long-Term Complications and Patient-Reported Outcomes After Alloplastic Breast Reconstruction
Authors: Lee Chia-Chun , Perng Cherng-Kang , Ma Hsu , Wu Szu-Hsien , Hsiao Fu-Yin , Tseng Ling-Ming , Tsai Yi-Fang , Lin Yen-Shu , Lien Pei-Ju , Feng Chin-Jung
Published: February 2022

Background

The most widely used method for breast reconstruction in Taiwan is alloplastic breast reconstruction, and traditionally, it can be categorized into immediate or delayed, single-stage or 2-stage procedures. We evaluated clinical outcomes and analyzed patients' self-reported satisfaction and quality of life after alloplastic breast reconstruction based on a previous preliminary study.

Patient and Methods

The patients who underwent primary alloplastic breast reconstruction after mastectomy were recruited in 2006 to 2020 at a single institute in Taiwan. The assessment of clinical outcomes was conducted by retrospective chart review and risk analysis. The patients also completed the BREAST-Q, a condition-specific patient-reported outcome measure, at least 6 months after treatment.

Results

A total of 237 patients with 247 reconstructed breasts were enrolled in this study. The demographics showed that 205 (83%) were reconstructed using a 2-stage tissue expander-based procedure and 42 (17%) were 1-stage direct-to-implant reconstructions. The mean follow-up time was 79.5 months. The clinical assessment revealed that the overall complication rate was 34%, with infection being the most common (21 patients; 8%). According to risk analysis, smoking (odds ratio, 7.626; 95% confidence interval, 1.56–37.30; P = 0.012), and nipple-sparing mastectomy (odds ratio, 3.281; 95% confidence interval, 1.54–6.99; P = 0.002) were significant risk factors for overall complications. The questionnaire response rate was 38% (94 of 247), at least 6 months after treatment. The total mean score was 69.78.

Conclusions

At a single institute in Taiwan from 2006 to 2020, alloplastic breast reconstruction, either single- or 2-stage, have acceptable complication rate and good postoperative satisfaction based on patient-reported outcomes. Both patient- and surgery-related factors presented as significant risk factors. Precise patient selection and comprehensive discussion between the patient and physician may play the important role to achieve optimal aesthetic outcomes.
A new perspective on ancient Mitis group streptococcal genetics
Authors: Belman Sophie , Chaguza Chrispin , Kumar Narender , Lo Stephanie , Bentley Stephen D.
Published: February 2022

Mitis group

Streptococcus

are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in

S. pneumoniae

, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group

Streptococcus

.
Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values
Authors: Flight Robert M , Bhatt Praneeth S , Moseley Hunter NB
Published: February 2022

Almost all correlation measures currently available are unable to directly handle missing values. Typically, missing values are either ignored completely by removing them or are imputed and used in the calculation of the correlation coefficient. In both cases, the correlation value will be impacted based on a perspective that missing data represents no useful information. However, missing values occur in real data sets for a variety of reasons. In omics data sets that are derived from analytical measurements, the primary reason for missing values is that a specific measurable phenomenon falls below the detection limits of the analytical instrumentation. These missing data are not missing at random, but represent some information by virtue of their “missingness”. Therefore, we propose the information-content-informed Kendall-tau (ICI-Kt) correlation coefficient that allows missing values to carry explicit information in the determination of concordant and discordant pairs. With both simulated and real data sets from RNA-seq, metabolomics, and lipidomics experiments, we demonstrate that the ICI-Kt allows for the inclusion of missing data values as interpretable information, enabling both improved determination of outlier samples and improved feature-feature network construction, without explicitly using imputation. Moreover, our implementation of ICI-Kt uses a mergesort-like algorithm that provides O(nlog(n)) computational performance, a significant improvement over the Kendall-tau correlation available in base R.

The ICI-Kt correlation calculation is available in an R package and Python module on GitHub athttps://github.com/moseleyBioinformaticsLab/ICIKendallTauandhttps://github.com/moseleyBioinformaticsLab/icikt, respectively.
Conserved neuropeptidergic regulation of intestinal integrity in invertebrate models of aging
Authors: Singh Anupama , Kaduskar Bhagyashree , Reddy Kirthi C , Kumsta Caroline , Bier Ethan , Hansen Malene , Chalasani Sreekanth H
Published: February 2022

Age-related decline in intestinal barrier function impacts survival across species, but the underlying cell intrinsic and extrinsic factors remain unclear. Here, we demonstrate a role for neuropeptides in regulating aging-associated increases in intestinal leakiness. Adult-specific knockdown of insulin-like peptides daf-28 or ins-7 in C. elegans neurons or dilp3 in D. melanogaster neurons improves intestinal integrity and lifespan of these animals, respectively. Neuropeptide knockdowns activate intestinal DAF-16/FOXO transcription factor that likely increases expression of epithelial barrier components. Furthermore, age-associated changes in neuronal DAF-28 peptide secretion mirrors C. elegans reproductive span and overexpression of this peptide suppresses the improved intestinal health in long-lived germline-less animals. Collectively, we show that intestinal integrity is subject to neuronal regulation, and this neuropeptidergic axis may be modulated by the animal’s germline.
Fish as model systems to study epigenetic drivers in human self-domestication and neurodevelopmental cognitive disorders
Authors: Anastasiadi Dafni , Piferrer Francesc , Wellenreuther Maren , Burraco Antonio Benítez
Published: February 2022

Modern humans exhibit phenotypic traits that are shared across independent domestication events, suggesting the human self-domestication hypothesis. Epigenetic changes may facilitate early self-domestication in humans, since they can be the first layer of response to a novel environment. Here, we argue that fish provide model systems to study epigenetic drivers in human self-domestication. To do this, we compare genes that carry epigenetic changes in early domesticates of European sea bass with 1) anatomically modern humans and 2) neurodevelopmental cognitive disorders with abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome and autism spectrum disorders. We found that genes with epigenetic changes in fish and in modern vs ancient humans were shared and were involved in processes like limb morphogenesis and phenotypes like abnormal snout morphology and hypopigmentation. Moreover, early domestication in fish and neurodevelopmental cognitive impairment in humans affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. We conclude that parallel epigenetic changes may occur at the initial steps of domestication in absence of deliberate selection in phylogenetically distant vertebrates. These findings pave the way for future studies using fish as models to investigate epigenetic changes as drivers of human-self domestication and as triggers of cognitive disorders.
Improving ascertainment of suicidal ideation and suicide attempt with natural language processing
Authors: Bejan Cosmin A. , Ripperger Michael , Wilimitis Drew , Ahmed Ryan , Kang JooEun , Robinson Katelyn , Morley Theodore J. , Ruderfer Douglas M. , Walsh Colin G.
Published: February 2022

Methods relying on diagnostic codes to identify suicidal ideation and suicide attempt in Electronic Health Records (EHRs) at scale are suboptimal because these phenotypes are heavily under-coded. We propose to improve the ascertainment of suicide phenotypes using natural language processing (NLP). We developed information retrieval methodologies to search over 200 million notes from the Vanderbilt EHR. Suicide query terms were extracted using word2vec. A weakly supervised approach was designed to label cases of suicidal outcomes. The NLP validation of the top 200 retrieved patients showed high performance for suicidal ideation (area under the receiver operator curve [AUROC]: 98.6, 95% confidence interval [CI]: 97.1−99.5) and suicide attempt (AUROC: 97.3, 95% CI: 95.2−98.7). Case extraction produced the best performance when combining NLP and diagnostic codes and when accounting for negated suicide expressions in notes. Overall, we demonstrated that scalable and accurate NLP methods can be developed to identify suicide phenotypes in EHRs to enhance prevention efforts, predictive models, and precision medicine.
Functional Plasticity in Chromosome-Microtubule Coupling on the Evolutionary Time Scale
Authors: Sankaranarayanan Sundar Ram , Polisetty Satya Dev , Das Kuladeep , Dumbrepatil Arti , Medina-Pritchard Bethan , Singleton Martin , Jeyaprakash A. Arockia , Sanyal Kaustuv
Published: February 2022

The Dam1 complex is essential for mitotic progression across evolutionarily divergent fungi. Upon analyzing amino acid (aa) sequences of Dad2, a Dam1 complex subunit, we identified a conserved 10-aa-long Dad2 signature sequence (DSS). An arginine residue (R126) in the DSS is essential for viability inSaccharomyces cerevisiaethat possesses point centromeres. The corresponding arginine residues are functionally important but not essential for viability inCandida albicansandCryptococcus neoformans,both carry several kilobases long regional centromeres. The purified recombinant Dam1 complex containing either Dad2ΔDSSor Dad2R126Afailed to bind microtubules (MTs) or form any visible rings like the wild-type complex. Intriguingly, functional analysis revealed that the requirement of the conserved arginine residue for chromosome biorientation and mitotic progression reduced with increasing centromere length. We propose that plasticity of the invariant arginine of Dad2 in organisms with regional centromeres is achieved by conditional elevation of the kinetochore protein(s) to enable multiple kinetochore MTs (kMTs) to bind to each chromosome. The capacity of a chromosome to bind multiple kMTs may mask deleterious effects of such lethal mutations.
Metagenomic binning with assembly graph embeddings
Authors: Lamurias Andre , Sereika Mantas , Albertsen Mads , Hose Katja , Nielsen Thomas Dyhre
Published: February 2022

Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning.

We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared to state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning. GraphMB is available fromhttps://github.com/MicrobialDarkMatter/GraphMB.
Biogeographical history shapes evolution of reproduction in a global warming scenario
Authors: Santos Marta A. , Antunes Marta A. , Grandela Afonso , Carromeu-Santos Ana , Quina Ana S. , Santos Mauro , Matos Margarida , Simões Pedro
Published: February 2022

Adaptive evolution might be critical for animal populations to thrive on the fast-changing natural environments. Ectotherms are particularly vulnerable to global warming and, although their limited coping ability has been suggested, few real-time evolution experiments have directly accessed their evolutionary potential. Here, we report a long-term experimental evolution study addressing the evolution of thermal reaction norms, after ∼30 generations under different thermal environments. We analyzed the evolutionary dynamics ofDrosophila subobscurapopulations as a function of the thermally variable environments in which they evolved and their distinct biogeographical background. Our results showed clear differences between the historically differentiated populations: while the northernD. subobscurapopulations showed a temporal increase in performance at higher temperatures, their southern counterparts presented the opposite pattern. This suggests that the northern populations might be better equipped to cope with the current rising temperatures. Remarkably, no effect of thermal selection was found. The lack of a clear long-term adaptive response at higher temperatures after evolution under a global warming scenario raises concerns about the evolutionary potential of ectotherms. Our results highlight the complex nature of thermal responses in face of environmental heterogeneity and emphasize the importance of considering intra-specific variation in thermal evolution studies.
Opioid Antagonism in Humans: A Primer on Optimal Dose and Timing for Central Mu-Opioid Receptor Blockade
Authors: Trøstheim Martin , Eikemo Marie , Haaker Jan , Frost J. James , Leknes Siri
Published: February 2022

Non-human animal studies outline precise mechanisms of central mu-opioid regulation of pain, stress, affiliation and reward processing. In humans, pharmacological blockade with non-selective opioid antagonists such as naloxone and naltrexone is typically used to assess involvement of the mu-opioid system in such processing. However, robust estimates of the opioid receptor blockade achieved by opioid antagonists are missing. Dose and timing schedules are highly variable and often based on single studies. Here, we provide a detailed analysis of central opioid receptor blockade after opioid antagonism based on existing positron emission tomography data. We also create models for estimating opioid receptor blockade with intravenous naloxone and oral naltrexone. We find that common doses of intravenous naloxone (0.10-0.15 mg/kg) and oral naltrexone (50 mg) are more than sufficient to produce full blockade of central MOR (>90% receptor occupancy) for the duration of a typical experimental session (∼60 minutes), presumably due to initial super saturation of receptors. Simulations indicate that these doses also produce high KOR blockade (78-100%) and some DOR blockade (10% with naltrexone and 48-74% with naloxone). Lower doses (e.g., 0.01 mg/kg intravenous naloxone) are estimated to produce less DOR and KOR blockade while still achieving a high level of MOR blockade for ∼30 minutes. The models and simulations form the basis of two novel web applications for detailed planning and evaluation of experiments with opioid antagonists. These tools and recommendations enable selection of appropriate antagonists, doses and assessment time points, and determination of the achieved receptor blockade in previous studies.
Meaningful Local Signaling in Sinoatrial Node Identified by Random Matrix Theory
Authors: Norris Chloe F. , Maltsev Anna V
Published: February 2022

Abstract

The sinoatrial node (SAN) is the pacemaker of the heart. Recently calcium signals, believed to be crucially important in rhythm generation, have been imaged in intact SAN and shown to be heterogeneous in various regions of the SAN and shown to be heterogeneous in various regions of the SAN with a lot of analysis relying on visual inspection rather than mathematical tools. Here we apply methods of random matrix theory (RMT) developed for financial data and various biological data sets including β-cell collectives and EEGs to analyse correlations in SAN calcium signals using eigenvalues and eigenvectors of the correlation matrix. We use principal component analysis (PCA) to locate signalling modules corresponding to localization properties the eigenvectors corresponding to high eigenvalues. We find that the top eigenvector captures the common response of the SAN to action potential. In some cases, the eigenvector corresponding to the second highest eigenvalue yields a pacemaker region whose calcium signals predict the action potential. Furthermore, using new analytic methods, we study the relationship between covariance coefficients and distance, and find that even inside the central zone, there are non-trivial long range correlations, indicating intercellular interactions in most cases. Lastly, we perform an analysis of nearest-neighbor eigenvalue distances and find that it coincides with universal Wigner surmise under all available experimental conditions, while the number variance, which captures eigenvalue correlations, is sensitive to experimental conditions. Thus RMT application to SAN allows to remove noise and the global effects of the action potential and thereby isolate the local and meaningful correlations in calcium signalling.
Oropouche orthobunyavirus infection is mediated by the cellular host factor Lrp1
Authors: Schwarz Madeline M. , Price David A. , Ganaie Safder S. , Feng Annie , Mishra Nawneet , Hoehl Ryan M. , Fatma Farheen , Stubbs Sarah H. , Whelan Sean P.J. , Cui Xiaoxia , Egawa Takeshi , Leung Daisy W. , Amarasinghe Gaya K. , Hartman Amy L.
Published: February 2022

Oropouche orthobunyavirus (OROV; Peribunyaviridae) is a mosquito-transmitted virus that causes widespread cases of human febrile illness in South America, with occasional progression to neurologic effects. Host entry factors mediating cellular entry of OROV are undefined. Here, we show that OROV requires the host protein low density lipoprotein-related protein 1 (Lrp1) for cellular infection. Cells from evolutionarily distinct species lacking Lrp1 were less permissive to OROV infection than cells with Lrp1. Treatment of cells with either the high-affinity Lrp1 ligand receptor-associated protein (RAP) or recombinant ectodomain truncations of Lrp1 significantly reduced OROV infection. Thus, Lrp1 is an important host factor required for infection of cells by OROV. Taken together with our results showing that Lrp1 is a newly identified receptor for Rift Valley fever virus (RVFV), Lrp1 may play a broader role in cellular infection by bunyaviruses than previously appreciated.
Hypoxia promotes osteogenesis via regulation of the mito-nuclear communication
Authors: Pouikli Andromachi , Maleszewska Monika , Parekh Swati , Nikopoulou Chrysa , Bonfiglio Juan-Jose , Mylonas Constantine , Sandoval Tonantzi , Schumacher Anna-Lena , Hinze Yvonne , Matic Ivan , Tessarz Peter
Published: February 2022

Bone marrow mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. Several studies have highlighted the critical role of hypoxia (low oxygen concentration) in the regulation of stem cell function, reporting differentiation defects following a switch to normoxia (high oxygen concentration). However, the molecular events triggering changes in stem cell fate decisions in response to high oxygen remain elusive. Here, we study the impact of normoxia in the mito-nuclear communication, with regards to stem cell differentiation. We show that normoxia-cultured MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces rewiring of metabolism, resulting in high acetyl-CoA levels, histone hypo-acetylation occurs due to trapping of acetyl-CoA inside mitochondria, likely due to lower CiC activity. Strikingly, restoring the cytosolic acetyl-CoA pool via acetate supplementation remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is heavily perturbed in response to high oxygen and identify CiC as a novel, oxygen-sensitive regulator of MSC function.
Microbes are potential key players in the evolution of life histories and aging inCaenorhabditis elegans
Authors: Santos Josiane , Matos Margarida , Flatt Thomas , Chelo Ivo M
Published: February 2022

Microbes can have profound effects on host fitness and health and the appearance of late-onset diseases. Host-microbe interactions thus represent a major environmental context for healthy aging of the host and might also mediate trade-offs between life-history traits in the evolution of host senescence. Here, we have used the nematodeCaenorhabditis elegansto study how host-microbe interactions may modulate the evolution of life histories and aging. We first characterized the effects of two non-pathogenic and one pathogenicEscherichia colistrains, together with the pathogenicSerratia marcescensDB11 strain, on population growth rates and survival ofC. elegansfrom five different genetic backgrounds. We then focused on an outbredC. eleganspopulation, to understand if microbe-specific effects on the reproductive schedule and in traits such as developmental rate and survival were also expressed in the presence of males and standing genetic variation, which could be relevant for the evolution ofC. elegansand other nematode species in nature. Our results show that host-microbe interactions have a substantial host-genotype-dependent impact on the reproductive aging and survival of the nematode host. Although both pathogenic bacteria reduced host survival in comparison with benign strains, they differed in how they affected other host traits. Host fertility and population growth rate were affected byS. marcescensDB11 only during early adulthood, whereas this occurred at later ages with the pathogenicE. coliIAI1. In both cases, these effects were largely dependent on the host genotypes. Given such microbe-specific genotypic differences in host life history, we predict that the evolution of reproductive schedules and senescence might be critically contingent on host-microbe interactions in nature.
Multicenter international assessment of a SARS-CoV-2 RT-LAMP test for point of care clinical application
Authors: Lu Suying , Duplat David , Benitez-Bolivar Paula , León Cielo , Villota Stephany D , Veloz-Villavicencio Eliana , Arévalo Valentina , Jaenes Katariina , Guo Yuxiu , Cicek Seray , Robinson Lucas , Peidis Philippos , Pearson Joel D , Woodgett Jim , Mazzulli Tony , Ponce Patricio , Restrepo Silvia , González John M , Bernal Adriana , Guevara-Suarez Marcela , Pardee Keith , Cevallos Varsovia E , González Camila , Bremner Rod
Published: February 2022

Continued waves, new variants, and limited vaccine deployment mean that SARS-CoV-2 tests remain vital to constrain the COVID-19 pandemic. Affordable, point-of-care (PoC) tests allow rapid screening in non-medical settings. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is an appealing approach. A crucial step is to optimize testing in low/medium resource settings. Here, we optimized RT-LAMP for SARS-CoV-2 and human β-actin, and tested clinical samples in multiple countries. “TTTT” linker primers did not improve performance, and while guanidine hydrochloride, betaine and/or Igepal-CA-630 enhanced detection of synthetic RNA, only the latter two improved direct assays on nasopharygeal samples. With extracted clinical RNA, a 20 min RT-LAMP assay was essentially as sensitive as RT-PCR. With raw Canadian nasopharygeal samples, sensitivity was 100% (95% CI: 67.6% - 100%) for those with RT-qPCR Ct values ≤ 25, and 80% (95% CI: 58.4% - 91.9%) for those with 25 < Ct ≤ 27.2. Highly infectious, high titer cases were also detected in Colombian and Ecuadorian labs. We further demonstrate the utility of replacing thermocyclers with a portable PoC device (FluoroPLUM). These combined PoC molecular and hardware tools may help to limit community transmission of SARS-CoV-2.
Cryo-EM structures of Doravirine and Rilpivirine with HIV-1 Reverse Transcriptase/DNA Aptamer – Nonnucleoside Inhibitor Resistance by E138K and M184I Mutations
Authors: Singh Abhimanyu K. , De Wijngaert Brent , Bijnens Marc , Uyttersprot Kris , Nguyen Hoai , Martinez Sergio E. , Schols Dominique , Herdewijn Piet , Pannecouque Christophe , Arnold Eddy , Das Kalyan
Published: February 2022

Structures trapping a verity of functional and conformational states of HIV-1 reverse transcriptase (RT) have been determined by X-ray crystallography. These structures have played important roles in understanding the mechanisms of catalysis, inhibition and drug resistance, and in driving drug design. However, structures of several desired complexes of RT could not be obtained even after many crystallization or crystal soaking experiments. The ternary complexes of doravirine and rilpivirine with RT/DNA are such examples.

Structural study of HIV-1 RT by single-particle cryo-EM has been challenging due to the enzyme’s relatively smaller size and higher flexibility. We optimized a protocol for rapid structure determination of RT complexes by cryo-EM and determined six structures of wild-type and E138K/M184I mutant RT/DNA in complexes with the nonnucleoside inhibitors rilpivirine, doravirine, and nevirapine. RT/DNA/rilpivirine and RT/DNA/doravirine complexes have structural differences between them and from the representative conformation of RT/DNA/nevirapine (or efavirenz); the primer grip in the RT/DNA/doravirine and the YMDD motif in the RT/DNA/rilpivirine complexes have large shifts. The DNA primer 3’-end in the doravirine-bound structure is positioned at the active site, but the complex is in a non-productive state. In the mutant RT/DNA/rilpivirine structure, I184 is stacked with the DNA such that their relative positioning can influence rilpivirine in the pocket. Simultaneously, E138K mutation widens the NNRTI-binding pocket entrance, potentially contributing to a faster rate of rilpivirine dissociation by E138K/M184I mutant RT, as reported by earlier kinetic studies. These structural differences have implications for drug design and for understanding molecular mechanisms of drug resistance.
Interrogating Metabolic Interactions Between Skeletal Muscle and Liver Circadian Clocks In Vivo
Authors: Smith Jacob G. , Koronowski Kevin B. , Sato Tomoki , Greco Carolina , Petrus Paul , Verlande Amandine , Chen Siwei , Samad Muntaha , Deyneka Ekaterina , Mathur Lavina , Blazev Ronnie , Molendijk Jeffrey , Mortimer Thomas , Kumar Arun , Deryagin Oleg , Vaca-Dempere Mireia , Liu Peng , Orlando Valerio , Parker Benjamin L. , Baldi Pierre , Welz Patrick-Simon , Jang Cholsoon , Masri Selma , Benitah Salvador Aznar , Muñoz-Cánoves Pura , Sassone-Corsi Paolo
Published: February 2022

Expressed throughout the body, the circadian clock system achieves daily metabolic homeostasis at every level of physiology, with clock disruption associated with metabolic disease (1, 2). Molecular clocks present in the brain, liver, adipose, pancreas and skeletal muscle each contribute to glucose homeostasis (3). However, it is unclear; 1) which organ clocks provide the most essential contributions, and 2) if these contributions depend on inter-organ communication. We recently showed that the liver clock alone is insufficient for most aspects of daily liver glucose handling and requires connections with other clocks (4). Considering the pathways that link glucose metabolism between liver and skeletal muscle, we sought to test whether a clock connection along this axis is important. Using our previous published methodology for tissue-specific rescue of Bmal1 in vivo (4, 5), we now show that in the absence of feeding-fasting cycles, liver and muscle clocks are not sufficient for systemic glucose metabolism, nor do they form a functional connection influencing local glucose handling or daily transcriptional rhythms in each tissue. However, the introduction of a daily feeding-fasting rhythm enables a synergistic state between liver and muscle clocks that leads to restoration of systemic glucose tolerance. These findings reveal limited autonomous capabilities of liver and muscle clocks and highlight the need for inter-organ clock communication for glucose homeostasis which involves at least two peripheral metabolic organs.
Telomerase deficiency in humans is associated with systemic age-related changes in energy metabolism
Authors: James Emma Naomi , Sagi-Kiss Virag , Bennett Mark , Mycielska Maria , Peng Karen-Ng Lee , Roberts Terry , Matta Sheila , Dokal Inderjeet , Bundy Jacob Guy , Parkinson Eric Kenneth
Published: February 2022

Underlying mechanisms of plasma metabolite signatures of human ageing and age-related diseases are not clear but telomere attrition and dysfunction are central to both. Dyskeratosis Congenita (DC) is associated with mutations in the telomerase enzyme complex (TERT,TERC,DKC1) and progressive telomere attrition. We show extracellular citrate is repressed by canonical telomerase functionin vitroand associated with DC leukocyte telomere attritionin vivo;leading to the hypothesis that altered citrate metabolism detects telomere dysfunction. However, citrate and senescence factors only weakly distinguished DC patients from controls, whereas other tricarboxylic acid cycle metabolites, lactate and especially pyruvate distinguished them with high significance, consistent with further metabolism of citrate and lactate in the liver and kidneys. Citrate uptake in certain organs modulates age-related disease in mice and our data has similarities with age-related disease signatures in humans. Our results have implications for the early diagnosis of telomere dysfunction and anti-senescence therapeutics.

Highlights

Extracellular citrate is regulated by telomere functionin vitro and in vivo.

Dyskeratosis Congenita (DC) is a human disease characterized by systemic telomere attrition, which showed an age-related plasma energetic profile, distinct from age-related disease and that of centenarians.

The DC profile strikingly out-performed senescence factors in discriminating DC from controls, and pyruvate associated with a low lactate:pyruvate ratio is potentially a useful and cheap minimally invasive diagnostic aid for DC and telomere dysfunction.

Mechanistically DC systemic metabolism is indicative of a shift to reduced pyruvate dehydrogenase activity, glycolysis and/or increased citrate and lactate production followed by further metabolism in the kidneys and liver.
Combined effects of inlet airflow temperature and upper expansion angle on the performance of scramjet nozzle
Authors: Sun Yifang , Duan Chunxu , Li Renfu , Li Chenghu
Published: February 2022

Purpose

The purpose of this paper is to study the combined effects of inlet airflow temperature and the expansion angle of the upper expansion surface (upper expansion angle) on the performance of the scramjet nozzle.

Design/methodology/approach

The Spalart-Allmaras turbulence two-dimensional model of the nozzle is established for the study. The influence of inlet airflow temperature on the performance of the nozzle is analyzed by detecting the change of the wall pressure of the nozzle. The three angles are chosen for the upper expansion angle (βb) in the model: 8°, 12° and 16°. The temperature of inlet airflow is 600–1,800 K.

Findings

The study results show that when the βb is 8° and 16°, the wall pressure of the nozzle has a complicated and large fluctuation with the inlet airflow temperature, while the wall pressure has little change as βb is 12°; the thrust coefficient, pitching moment coefficient and lift coefficient of the nozzle fluctuate greatly with the increase of the inlet airflow temperature when βb is 8° and 16°, while the thrust coefficient, pitching moment coefficient and lift coefficient have little fluctuation as βb is 12°.

Originality/value

The study of the combined effects of the inlet airflow temperature and upper expansion angle on the performance of the scramjet nozzle can provide guidance for the design of scramjet nozzles.
Optimization of triage time and sample delivery path in health infrastructure to combat COVID-19
Authors: Zhou Cheng , Li Rao , Xiong Xiaoju , Li Jie , Gao Yuyue
Published: February 2022

Purpose

This study presented the experience of improving the nucleic acid sample collection and transportation service in response to the epidemic. The main purpose is that through intelligent path planning, combined with the time scheduling of sample points, the process of obtaining results to determine the state of COVID-19 patients could be speeding up.

Design/methodology/approach

The research optimized the process, including finding an optimal path to traverse all sample points in the hospital area via intelligent path planning method and standardizing the operation through the time sequence scheduling of each round of support staff to collect and send samples in the hospital area, so as to ensure the shortest time in each round. And the study examines these real-time experiments through retrospective examination.

Findings

The real-time experiments' data showed that the proposed path planning and scheduling model could provide a reliable reference for improving the efficiency of hospital logistics. Testing is a very important part of diagnosis and prompt results are essential. It shows the possibility of applying the shortest-path algorithms to optimize sample collection processes in the hospital and presents the case study that gives the expected outcomes of such a process.

Originality/value

The value of the study lies in the abstraction of a very practical and urgent problem into a TSP. Combining the ant colony algorithm with the genetic algorithm (ACAGA), the performance of path planning is improved. Under the intervention and guidance, the efficiency of hospital regional logistics planning was greatly improved, which may be of greater benefit to critical patients who must go through fever clinic during the epidemic. By detailing how to more rapidly obtain results through engineering method, the paper contributes ideas and plans for practitioners to use. The experience and lessons learned from Tongji Hospital are expected to provide guidance for supporting service measures in national public health infrastructure management and valuable reference for the development of hospitals in other countries or regions.