bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Using a Stress Ball During Endoscopy on Pain, Anxiety, and Satisfaction
Authors: Karatas Tugba Caner , Gezginci Elif
Published: May 2023

A stress ball is a simple and effective distraction method during painful procedures. The aim of this study was to evaluate the effect of using a stress ball during endoscopy on patients' pain, anxiety, and satisfaction levels. The randomized controlled study included 60 patients who underwent endoscopy in a training and research hospital in Istanbul. Patients were randomly assigned to the stress ball group or the control group. Patients in the stress ball group (n = 30) squeezed a stress ball during endoscopy, whereas the control group (n = 30) received no intervention during endoscopy. Data were collected using a sociodemographic form, a postendoscopy questionnaire, the Visual Analog Scale to assess pain and satisfaction, and the State-Trait Anxiety Inventory. Pain scores did not differ significantly between the groups before (p = .925) or during (p = .149) the endoscopy procedure but were significantly lower in the stress ball group after the procedure (p = .008). Similarly, preprocedure anxiety scores were comparable (p = .743), whereas postprocedure anxiety scores were significantly lower in the stress ball group (p < .001). The satisfaction score after endoscopy was higher in the stress ball group, but the difference was not statistically significant (p = .166). This study suggests that use of a stress ball during endoscopy reduces patients' pain and anxiety levels.
Injury Trends aboard U.S. Navy Vessels: A 50-year analysis of Mishaps at Sea
Authors: Benham Derek A. , Vasquez Matthew C. , Kerns Jakob , Checchi Kyle D. , Mullinax Ross , Edson Theodore D. , Tadlock Matthew D.
Published: May 2023

Background

Maritime activities have been associated with unique dangers to civilian and military sailors. We performed a retrospective cohort study analyzing injury mechanisms and clinical outcomes of casualties onboard U.S. Naval ships to determine common injury mechanisms, trends, and outcomes. We hypothesized there would be a downward trend of injuries and fatalities on U.S. Naval ships during the study period via a retrospective cohort study.

Methods

All mishaps recorded by the Naval Safety Command aboard active service U.S. Naval ships from 1970 through 2020 were reviewed. Only mishaps resulting in injury or fatality were included. Over time, injury mechanisms and casualty incidence rates were trended and compared based on medical capabilities. Ships without surgical capabilities were categorized as Role 1, and those with surgical capabilities as Role 2.

Results

3127 total casualties were identified and analyzed, with 1048 fatalities and 2079 injuries. The injury mechanisms associated with the highest mortality included electrocution, blunt head trauma, fall from height, man overboard and explosion. There was a decrease in the trend of mishaps resulting in casualties, fatalities, and injuries over the 50-year study period. The mortality rate for select severe injury mechanisms was higher on Role 1 capable platforms, compared to Role 2 (0.334 vs 0.250, p < .05).

Conclusions

Casualty incidences decreased over 50 years. However, mortality still remains high for certain mechanisms no matter the operational platform. Furthermore, Role 1 capable vessels have a higher overall mortality rate for severe injuries compared to Role 2. The authors propose training, process improvement, and technology-related solutions to improve outcomes on Role 1 capable naval vessels.

Level of Evidence

Prognostic and Epidemiological; Level III
Thermocaproicibacter melissae gen. nov., sp. nov., a thermophilic chain-elongating bacterium, producing n-caproate from polymeric carbohydrates
Authors: Nguyen Tinh Van , Viver Tomeu , Smets Ilse , Bernaerts Kristel , Faust Karoline , Lavigne Rob , Poughon Laurent , Dussap Claude-Gilles , Springael Dirk
Published: May 2023

Strain MDTJ8T is a chain-elongating thermophilic bacterium isolated from a thermophilic acidogenic anaerobic digestor treating human waste while producing the high commodity chemical n-caproate. The strain grows and produces formate, acetate, n-butyrate, n-caproate and lactate from mono-, di- and polymeric saccharides at 37–60 °C (optimum, 50–55 °C) and at pH 5.0–7.0 (optimum, pH 6.5). The organism is an obligate anaerobe, is motile and its cells form rods (0.3–0.5×1.0–3.0 µm) that stain Gram-positive and occur primarily as chains. Phylogenetic analysis of both the 16S rRNA gene and full genome sequence shows that strain MDTJ8T belongs to a group that consists of mesophylic chain-elongating bacteria within the family

Oscillospiraceae

, being nearest to

Caproicibacter fermentans

EA1T (94.8 %) and

Caproiciproducens galactitolivorans

BS-1T (93.7 %). Its genome (1.96 Mbp) with a G+C content of 49.6 mol% is remarkably smaller than those of other chain-elongating bacteria of the family

Oscillospiraceae

. Pairwise average nucleotide identity and DNA–DNA hybridization values between strain MDJT8T and its mesophilic family members are less than 70 and 35 %, respectively, while pairwise average amino acid identity values are less than 68 %. In addition, strain MDJT8T uses far less carbohydrate and non-carbohydrate substrates compared to its nearest family members. The predominant cellular fatty acids of strain MDTJ8T are C14 : 0, C14 : 0 DMA (dimethyl acetal) and C16 : 0, while its polar lipid profile shows three unidentified glycophospholipids, 11 glycolipids, 13 phospholipids and six unidentified lipids. No respiratory quinones and polyamines are detected. Based on its phylogenetic, genotypic, morphological, physiological, biochemical and chemotaxonomic characteristics, strain MDTJ8T represents a novel species and novel genus of the family

Oscillospiraceae

and Thermocaproicibacter melissae gen. nov., sp. nov. is proposed as its name. The type strain is MDTJ8T (=DSM 114174T=LMG 32615T=NCCB 100883T).
Anti-oxidation, anti-inflammation, anti-wrinkle, and pore-tightening effects of phenolic compounds from Aeonium sedifolium leaves
Authors: Kim Jung-In , Kim Min-Jae , Jo Ha-Gyeong , Jeong Da-Eun , Park Hye-Jin , Cho Young-je
Published: May 2023

The succulent plant Aeonium sedifolium leaves contain several compounds that are of interest for their cosmetic uses on the skin. This study measured the inhibitory effects of enzyme production and antioxidant, astringent effects and skin wrinkles using Aeonium sedifolium leaves (ASL). The total phenolics compounds (TPC) content of ASL under optimal extraction conditions was 34.49 mg/g for hot water extract (ASLW) and 61.64 mg/g for 50% ethanol extract (ASLE). The ASLW and ASLE extracts were freeze-dried, powdered, and used as solids. TPC content, 2,2-diphenyl-1-picrylhydrazy (DPPH) radical scavenging activity, and 2,2’-azinobis (3-ethylben-zothiazoline 6-sulfonate) (ABTS) radical inhibition of the ASL phenolics were tested. The DPPH radical scavenging activities of ASLW and ASLE were tested at a TPC of 100 μg/mL. ABTS radical inhibition showed antioxidant activity of 100.00% in ASLW and ASLE, and the antioxidant protection factor of ASLW and ASLE was 1.07 and 1.22, respectively. The thiobarbituric acid-reactive substance (TBARS) inhibitory activity of ASLW and ASLE was 77.00%. The elastase inhibitory activity of ASLE was 69.03%, and collagenase inhibition activity for ASLW and ASLE was 29.82% and 54.76%, respectively. The astringent effect of ASLE was 89.82% at a TPC of 200 μg/mL. Thus, we concluded that ASL has the potential as a functional cosmetic ingredient with anti-aging effects on the skin.
Comprehensive Analysis of Molecular Characteristics, Clinical Signifificance, and Cancer Immune Interactions of Patients by Anoikis-Related Genes in LUAD Combined with Single-cell Data
Authors: Yu Weijie , Miao Zhoulin , Ainiwaer Julaiti , Qiao Bingzhang , Jumai Kawuli , Sheyhidin Ilyar
Published: May 2023

Background

Lung adenocarcinoma(LUAD) is the most prevalent subtype of lung cancer today. There is a close relationship between Anoikis related genes(ARGs) and tumor prognosis, drug susceptibility, and tumor microenvironment(TME).

Method

We calculated differential expression genes using downloaded Anoikis genes and selected genes of prognostic value. Consensus clustering analysis was used and characterized between different clusters. Differences between the different groups were also explored. Risk scores and Nomogram with predictive prognostic functions were established. Immune status and drug sensitivity were also assessed between different risk groups. Single-cell data were downloaded to compare the expression profiles of selected genes, and immunohistochemical results of selected genes were also downloaded to corroborate the reliability of the manuscript.

Result

Two clusters were identified on the basis of related gene expression. We analyzed the survival time, functional enrichment between the two groups and found significant differences between the two clusters. Significant relationships were found between the different clusters and clinical variables. group B had a significantly lower KM curve than group A, as well as a significant enrichment in multiple tumor functions. A risk score with prognostic value was established. The risk score was found to have a high predictive value for prognosis and was an independent prognostic factor. Combined with clinical variables, a Nomogram was established and found to be an accurate predictor of patient prognosis. There were significant differences in immune status between the different risk groups. Patients in the low-risk group were significantly better treated than those in the high-risk group. Finally single cell data confirmed the expression of the selected genes. Also, the immunohistochemical results helped us to confirm the selected genes have increased expression in tumor tissue.

Conclusion

In conclusion, this paper reveals the role of ARGs and immune status, drug susceptibility, and prediction of prognosis in LUAD. Also, an accurate prognostic prediction model was established based on genetic.
Controlled expression of avian migratory fattening influences innate immune responses
Authors: Tobolka Marcin , Zielińska Zuzanna , Fusani Leonida , Huber Nikolaus , Maggini Ivan , Pola Gianni , Marasco Valeria
Published: May 2023

While immunity is frequently suppressed when birds engage in strenuous migratory flights, whether and how immunity changes during the rapid accumulation of energy stores in preparation for migration remains largely unknown. Here, we induced pre-migratory fattening through controlled changes of daylight in common quailsCoturnix coturnixand regularly assessed changes in a marker of constitutive innate immunity (Leukocyte Coping Capacity or LCC) and measures of body composition (lean and fat mass). LCC responses were highest in the mid-fattening phase and lowest when fattening was completed. At mid-fattening, we also found that the birds that kept a higher proportion of lean mass (i.e. accumulated less fat) had the highest LCC peaks. Our results indicate that migratory birds undergo rapid immunological changes as they accumulate energy stores for migration and propose that this could be due to competing or trade-off processes between metabolic remodelling and innate immune system function.

Summary statement

Immunity is vital when migrating to new environments. It is costly and competivite to other physiological processes. Here we bring new evidence on this process in migratory birds.
Stanniocalcin 2 (STC2) is a potent biomarker of hepatocellular carcinoma with its expression being augmented in Nrf1α-deficient cells, but diminished in Nrf2-deficient cells
Authors: Bu Qiqi , Deng Yangxu , Wang Qing , Deng Rongzhen , Hu Shaofan , Pei Zhigang , Zhang Yiguo
Published: May 2023

For insights into the fact that liver-specific knockout of Nrf1 leads to development of non-alcoholic steatohepatitis and spontaneous hepatoma, we previously found that loss of Nrf1α (i.e., a full-length isoform encoded byNfe2l1) promotes HepG2-derived tumor growth in xenograft mice, but malgrowth of the xenograft tumor is significantly suppressed by knockout of Nrf2 (encoded byNfe2l2). The mechanism underlying such marked distinctions in their pathologic phenotypes remains elusive, however, to date. Herein, we mined the transcriptome data of liver cancer from the TCGA database to establish a prognostic model of liver cancer and then calculated the predicted risk score of each cell line. The results indicated that knockout of Nrf1α significantly increased the risk score in HepG2 cells, whereas the risk score was reduced by knockout of Nrf2. Of note, stanniocalcin 2 (STC2, a biomarker of liver cancer, that is up-expressed in hepatocellular carcinoma (HCC) tissues with a reduction in the overall survival ratio of those patients) was augmented inNrf1αNrf2α-/-cells, but diminished in Nrf2-/-cells. Thereby, it is inferable that STC2 is likely involved in mediating the distinction betweenNrf1αNrf2α-/-and Nrf2-/-. Further investigation revealed that HIF1A is an upstream regulator of STC2 in caNrf2ΔN, rather thanNrf1αNrf2α-/-, cells, and regulation of STC2 and HIF1A inNrf1αNrf2α-/-is determined by Nrf2, but the regulation of STC2 by Nrf2 may be independent on HIF1A. In turn, STC2 can regulate Nrf2 via the putative calcium-mediated Keap1-p62 signaling so to form a feedback regulatory loop. Such potential function of STC2 was further corroborated by a series of experiments combined with transcriptomic sequencing. The results unraveled that STC2 manifests as a dominant tumor-promoter, because the STC2-leading increases in clonogenicity of hepatoma cells and malgrowth of relevant xenograft tumor were almost completely abolished inSTC2-/-cells. Together, these demonstrate that STC2 could be paved as a novel potent therapeutic target, albeit as a diagnostic marker, for hepatocellular carcinoma.
The fate of intracoelomic acoustic transmitters in Atlantic Salmon (Salmo salar)post-smolts and wider considerations for casual factors driving tag retention and mortality in fishes
Authors: Lawrence M.J. , Wilson B.M. , Reid G.M. , Hawthorn C. , English G. , Black M. , Leadbeater S. , McKindsey C.W. , Trudel M.
Published: May 2023

Acoustic telemetry is a widely used method in assaying behavioural dynamics in fishes. Telemetry tags are often surgically implanted in the coelom of the animal and are assumed to have minimal rates of post-release mortality and tag shedding. However, fish are capable expelling tags and mortalities do occur following release, with the mechanism(s) underlying these effects not well understood. The purpose of this research was to address causal factors underlying tagging mortality and tag expulsion in fishes. We conducted an empirical assessment of tag retention and post-surgical mortality rates in post-smolt Atlantic salmon (Salmo salar) fitted with a dummy acoustic tag over a 92 day monitoring period. This was complimented with a meta-analysis of factors affecting tag retention and post-surgical mortality rates in the wider literature. Post-smolt salmon exhibited low rates of mortality following tag implantation (≤ 5.1%) but had high rates of tag expulsion (54.8%) and impaired growth and a foreign body response was evident. The meta-analysis showed that mortality was generally low across all studies (12.4%) and was largely unaffected by model cofactors. Tag retention rates were high among the studies investigated here (86.7%) and had a weak negative relationship with tag:body mass ratios. Our results suggest that while mortality is often low among tagging studies, including this one, caution must be exercised in assessing stationary tags as they may represent an expelled tag rather than a mortality event. Our results also indicate that tag dimensions are not nearly important as the tag:body mass ratio.
Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds
Authors: Smith Francesca , Sengar Aditya , Stan Guy‐Bart V. , Ouldridge Thomas E. , Stevens Molly , Goertz John , Bae Wooli
Published: May 2023

Dynamic DNA nanotechnology involves the use of DNA strands to create programmable reaction networks and nanodevices. The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, which is achieved through three-way and four-way DNA exchange reactions. While both of these reactions have been widely used to build reaction circuits, the four-way exchange reaction has traditionally been slower and less efficient than the three-way reaction. In this paper, we describe a new mechanism to optimise the kinetics of the four-way DNA exchange reaction by adding bulges to the toeholds of the four-way DNA complexes involved in the reaction. These bulges facilitate an alternative branch migration mechanism and destabilise the four-way DNA junction, increasing the branch migration rate and unbinding rate of the four-way exchange reaction, bringing it closer to the kinetics of the three-way reaction. This new mechanism has the potential to expand the field of dynamic DNA nanotechnology by enabling efficient four-way DNA exchange reactions for in vivo applications.
ERG activates a stem-like proliferation-differentiation program in prostate epithelial cells with mixed basal-luminal identity
Authors: Feng Weiran , Ladewig Erik , Salsabeel Nazifa , Zhao Huiyong , Lee Young Sun , Gopalan Anuradha , Lange Matthew , Luo Hanzhi , Kang Wenfei , Fan Ning , Rosiek Eric , De Stanchina Elisa , Chen Yu , Carver Brett S. , Leslie Christina S , Sawyers Charles
Published: May 2023

To gain insight into how ERG translocations cause prostate cancer, we performed single cell transcriptional profiling of an autochthonous mouse model at an early stage of disease initiation. Despite broad expression of ERG in all prostate epithelial cells, proliferation was enriched in a small, stem-like population with mixed-luminal basal identity (called intermediate cells). Through a series of lineage tracing and primary prostate tissue transplantation experiments, we find that tumor initiating activity resides in a subpopulation of basal cells that co-express the luminal genes Tmprss2 and Nkx3.1 (called BasalLum) but not in the larger population of classical Krt8+ luminal cells. Upon ERG activation, BasalLum cells give rise to the highly proliferative intermediate state, which subsequently transitions to the larger population of Krt8+ luminal cells characteristic of ERG-positive human cancers. Furthermore, this proliferative population is characterized by an ERG-specific chromatin state enriched for NFkB, AP-1, STAT and NFAT binding, with implications for TF cooperativity. The fact that the proliferative potential of ERG is enriched in a small stem-like population implicates the chromatin context of these cells as a critical variable for unmasking its oncogenic activity.
Repetitive Sulfur Dioxide Exposure in Mice Models Post-Deployment Respiratory Syndrome
Authors: Gutor Sergey S. , Salinas Rodrigo I. , Nichols David S. , Bazzano Julia M. R. , Han Wei , Gokey Jason J. , Vasiukov Georgii , West James D. , Newcomb Dawn C. , Dikalova Anna E. , Richmond Bradley W. , Dikalov Sergey I. , Blackwell Timothy S. , Polosukhin Vasiliy V.
Published: May 2023

Soldiers deployed to Iraq and Afghanistan have a higher prevalence of respiratory symptoms than non-deployed military personnel and some have been shown to have a constellation of findings on lung biopsy termed post-deployment respiratory syndrome (PDRS). Since many of the deployers in this cohort reported exposure to sulfur dioxide (SO2), we developed a model of repetitive exposure to SO2in mice that phenocopies many aspects of PDRS, including adaptive immune activation, airway wall remodeling, and pulmonary vascular disease (PVD). Although abnormalities in small airways were not sufficient to alter lung mechanics, PVD was associated with the development of pulmonary hypertension and reduced exercise tolerance in SO2exposed mice. Further, we used pharmacologic and genetic approaches to demonstrate a critical role for oxidative stress and isolevuglandins in mediating PVD in this model. In summary, our results indicate that repetitive SO2exposure recapitulates many aspects of PDRS and that oxidative stress may mediate PVD in this model, which may be helpful for future mechanistic studies examining the relationship between inhaled irritants, PVD, and PDRS.
Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila
Authors: Datta Ishwaree , Bangi Erdem
Published: May 2023

Cellular senescence is a conserved biological process essential for embryonic development, tissue remodeling, repair, and a key regulator of aging. Senescence also plays a crucial role in cancer, though this role can be tumor-suppressive or tumor-promoting, depending on the genetic context and the microenvironment. The highly heterogeneous, dynamic, and context-dependent nature of senescence-associated features and the relatively small numbers of senescent cells in tissues makesin vivomechanistic studies of senescence challenging. As a result, which senescence-associated features are observed in which disease contexts and how they contribute to disease phenotypes remain largely unknown. Similarly, the specific mechanisms by which various senescence-inducing signals are integratedin vivoto induce senescence and why some cells become senescent while their immediate neighbors do not are unclear. Here, we identify a small number of cells that exhibit multiple features of senescence in a genetically complex model of intestinal transformation we recently established in the developing Drosophila larval hindgut epithelium. We demonstrate that these cells emerge in response to concurrent activation of AKT, JNK, and DNA damage response pathways within transformed tissue. Eliminating senescent cells, genetically or by treatment with senolytic compounds, reduces overgrowth and improves survival. We find that this tumor-promoting role is mediated by Drosophila macrophages recruited to the transformed tissue by senescent cells, which results in non-autonomous activation of JNK signaling within the transformed epithelium. These findings emphasize complex cell-cell interactions underlying epithelial transformation and identify senescent cell-macrophage interactions as a potential druggable node in cancer.

One sentence summary:Interactions between transformed senescent cells and macrophages drive tumorigenesis.
The Role of the Eyes: Investigating Face Cognition Mechanisms Using Machine Learning and Partial Face Stimuli
Authors: Chanpornpakdi Ingon , Tanaka Toshihisa
Published: May 2023

Face cognition plays a significant role in social interaction. The typical stimulus used to study face cognition mechanisms is a rapid serial visual presentation (RSVP). During the RSVP task, the brain response called event-related potential (ERP) is evoked when a person recognizes a target image. Many trials are required to average and obtain a clean ERP to interpret the cognitive mechanism behind the ERP response. However, increasing the trial number can cause fatigue and affect evoked ERP amplitude. This paper adopts a different perspective; machine learning might extract a meaningful cognitive result that reveals the face cognition mechanism without directly focusing on the characteristic of the ERP. We implemented an xDAWN covariance matrix method to enhance the data quality and a support vector machine classification model to predict the participant’s event of interest using ERP components evoked in the partial face cognition task. The effect of face components and the physical response was also investigated to explore the role of each component and find the possibility of reducing fatigue caused during the experiment. We found that the eyes were the most effective component. Similar statistical results were obtained from full face and partial face with eyes visible in both behavioral response and classification performance. From these results, the eye component could be the most crucial in face cognition. So, there could be some similarities in the face cognition mechanism of the full face and the partial face with eyes visible, which should be further investigated using ERP characteristics.
On the results of causal optogenetic engram manipulations
Authors: Jou Claudia , Hurtado José R. , Carrillo-Segura Simon , Park Eun Hye , Fenton André A.
Published: May 2023

Cellular-resolution manipulation technologies like optogenetics enable so-called causal engram-cell experiments in which learning-activated neurons are tagged with a light-responsive protein (opsin) such that subsequent photostimulation elicits memory behavior. The opsin-tagged neurons are considered key neural circuit elements with photostimulation demonstrating their sufficiency for memory expression. Can the sufficiency interpretation be correct if the brain is a complex dynamical system with adaptive, non-linear, and homeostatic interactions? We find that during photostimulation of place avoidance memory-tagged neurons, mouse CA1 hippocampus activity maintains intrinsic ensemble discharge relationships and the low-dimensional manifold organization of the population dynamics. Although the photostimulation causes spatially-precise conditioned avoidance, such manipulations, are better interpreted as eliciting the endogenous population dynamics of a complex system, rather than the causal demonstration of neural circuit function.
Interruption of the Intratumor CD8:Treg Crosstalk Improves the Efficacy of PD-1 Immunotherapy
Authors: Geels Shannon N , Moshensky Alexander , Sousa Rachel S , Walker Benjamin L , Singh Rima , Gutierrez Giselle , Hwang Michael , Mempel Thorsten R , Nie Qing , Othy Shivashankar , Marangoni Francesco
Published: May 2023

PD-1 blockade unleashes the potent antitumor activity of CD8 cells but can also promote immunosuppressive T regulatory (Treg) cells, which may worsen response to immunotherapy. Tumor Treg inhibition is a promising strategy to overcome therapeutic resistance; however, the mechanisms supporting tumor Tregs during PD-1 immunotherapy are largely unexplored. Here, we report that PD-1 blockade increases tumor Tregs in mouse models of immunogenic tumors, including melanoma, and metastatic melanoma patients. Unexpectedly, Treg accumulation was not caused by Treg-intrinsic inhibition of PD-1 signaling but instead depended on an indirect effect of activated CD8 cells. CD8 cells colocalized with Tregs within tumors and produced IL-2, especially after PD-1 immunotherapy. IL-2 upregulated the anti-apoptotic protein ICOS on tumor Tregs, causing their accumulation. ICOS signaling inhibition before PD-1 immunotherapy resulted in increased control of immunogenic melanoma. Thus, interrupting the intratumor CD8:Treg crosstalk is a novel strategy that may enhance the efficacy of immunotherapy in patients.
Monitoring and maturation of cardiomyocyte differentiated from human induced pluripotent stem cells using a multi-functional tissue engineering platform
Authors: Kim A-Ri , Shrivastava Sajal , Lee Han-Byeol , Lee Nae-Eung
Published: May 2023

Background

The use of human induced pluripotent stem cells (hiPSCs) is attracting attention as a potential personalized therapy for damaged myocardium, as they are accessible and compatible with the human body. The hiPSCs can be effectively differentiated into cardiomyocytes (CMs), which are essential for myocardial regeneration. However, current approaches have been unable to fully replicate the electro-mechanical functions of natural CMs.

Methods

Although several methods have been used to stimulate hiPSC-CMs for maturation, the ability to integrate multiple stimuli that influence myocardial cell function has been limited. To address this challenge, we have developed a multi-functional tissue engineering system for CMs that is based on a stretchable multielectrode array (SMEA). The SMEA is housed in a mini-incubator and is stretchable, durable and autoclavable.

Results

The system can independently control co-stimulation parameters of electrical and mechanical stimuli simultaneously. Furthermore, the system can monitor the status of the cells throughout their proliferation and differentiation of hiPSCs, as well as the stimulation of hiPSC-CMs, through electrochemical cell impedance spectroscopy. By applying co-stimulation, we have observed the enhanced maturation of hiPSC-CMs.

Conclusions

Our innovative system holds great potential as a tool for improving the culture and engineering of electrogenic cells with enhanced maturity.
Why Na+ has higher propensity than K+ to condense DNA in a crowded environment
Authors: Kolesnikov Egor S. , Gushchin Ivan Yu. , Zhilyaev Peter A. , Onufriev Alexey V.
Published: May 2023

Experimentally, in the presence of crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here we have used molecular dynamics simulations and the “ion binding shells model” of DNA condensation to provide an atomic level picture that explains the observed variations in condensation of short (25 base pairs) DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. In general, there are two major modes (shells) of ion binding to DNA, internal and external, distinguished by the proximity of bound ions to the helical axis. Externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, as well as for a single DNA duplex, the number of externally bound Na+ions is larger than the number of K+ions over a wide range of NaCl and KCl concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation in the presence of different ions: the aggregation free energy is at least 0.2kBTper base pair more favorable in solution with NaCl than with KCl, at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+depends on the DNA sequence noticeably: we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. The sequence dependence of the DNA aggregation propensity is nearly absent for K+. Counter-intuitively, the addition of a small amount of crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.
Unexpected Death of a Duchenne Muscular Dystrophy Patient in an N-of-1 Trial of rAAV9-delivered CRISPR-transactivator
Authors: Lek Angela , Wong Brenda , Keeler Allison , Blackwood Meghan , Ma Kaiyue , Huang Shushu , Sylvia Katelyn , Batista Ana Rita , Artinian Rebecca , Kokoski Danielle , Parajuli Shestruma , Putra Juan , Carreon Chrystalle Katte , Lidov Hart , Woodman Keryn , Pajusalu Sander , Spinazzola Janelle , Gallagher Thomas , LaRovere Joan , Baulderson Diane , Black Lauren , Sutton Keith , Horgan Richard , Lek Monkol , Flotte Terence
Published: May 2023

An N-of-1 trial was developed to deliver a dCas9-VP64 transgene designed to upregulate the cortical dystrophin as a custom therapy for a Duchenne muscular dystrophy (DMD) patient. After showing signs of mild cardiac dysfunction and pericardial effusion, the patient acutely decompensated and sustained cardiac arrest six-days after dosing and succumbed two-days later. Post-mortem examination revealed severe acute-respiratory distress syndrome with diffuse alveolar damage. Vector biodistribution data was obtained and revealed minimal expression of transgene in liver. There was no evidence of AAV9 antibodies nor of effector T cell reactivity. These findings demonstrate innate immune signaling with capillary leak as a form of toxicity in an advanced DMD case treated with high-dose rAAV gene therapy.
Health system intervention packages on improving coverage of kangaroo mother care for preterm or LBW infants: a mixed-methods systematic review
Authors: Bergman Nils , Talej Megan , Smith Emily R. , Rao Suman PN , Gupta Shuchita
Published: May 2023

Introduction

Global coverage of Kangaroo mother care (KMC) remains low and health system intervention strategies that may improve coverage are not known.

Methods

We conducted a systematic review of studies evaluating the effect of health system intervention strategies for KMC implementation compared to no or different interventions, on KMC coverage in preterm or LBW infants. KMC coverage achieved by various studies was summarized. All included studies were classified as those that achieved increased KMC coverage (defined as ≥25% increase from baseline, with final coverage ≥50%) or low KMC coverage (defined as <25% increase from baseline or final coverage <50%). Studies that achieved increased KMC coverage were further classified based on the mean duration of skin-to-skin contact (SSC; hours per day) achieved. Health system interventions in different categories were summarized by WHO health system building blocks to understand factors linked to increased KMC coverage.

Findings

We identified 16 studies evaluating 15 health system intervention packages for KMC implementation that applied interventions in one or more health system building blocks that reported KMC coverage. All three studies that applied interventions across 5-6 building blocks (100%), two of the four studies that applied interventions across 3-4 building blocks (50%), and three of the nine studies that applied interventions across 1-2 building blocks (33%), achieved increased KMC coverage. Studies that did not achieve increased coverage had interventions primarily targeting health workforce and service delivery and were weak on leadership and governance, financing, and health information systems. All three studies that achieved increased KMC coverage with mean SSC ≥8h/d (100%), three of the five studies that achieved increased KMC coverage with mean SSC <8h/d (60%), and three of the eight studies with low KMC coverage (38%) had high-intensity interventions in at least one health system building blocks. High-level leadership engagement, KMC supportive policies, staff licensing, and facility standards regulations, strengthened numbers and capacity of nursing staff, government funding and expanded health insurance, wards with conducive environment, and recording KMC-specific indicators in clinical registers were key factors among studies that achieved increased KMC coverage.

Conclusion

High-intensity interventions across multiple health system building blocks should be used for equitable scale-up of KMC.
RealSeq2: a software integrated with UMI identification, error correction, and methylation modifications storing
Authors: Wang Ke , Song Mengmeng , Li Min , Cui Tianyu , Liu Zhentian , Yu Enjie , Fang Huan , Gao Xuan , Xia Xuefeng , Wang Jiayin , Guan Yanfang , Liu Tao , Yi Xin
Published: May 2023

High-throughput UMI technology sequencing is widely used in early tumor screening, detection, recurrence monitoring, etc. Detecting extremely low-frequency mutations is especially important for monitoring tumor recurrence, so high-precision data, as well as high-quality data, are required. We developedRealSeq2, a new integrated data-preprocessing software based on fastp and gencore, to achieve adapter removal, quality control, UMI identification, and generate consensus reads by clustering and error correction using multithreading in high-throughput next-generation sequencing background.RealSeq2also supports methylation data of 5-methylcytosine bisulfite-free sequencing.RealSeq2defined a new tag in SAM for storing methylation information, which is beneficial for co-identifying methylation sites and mutation sites for downstream analysis.RealSeq2includes three submodules: ReadsProfiler, ReadsCleaner, and ReadsRecycler. In addition, the output format file (BAM or SAM) is universal for downstream analyses.

RealSeq2is the preferred upstream analysis software for the co-detection of ultra-low frequency mutations and bisulfite-free methylation data. The error profile provides data support for downstream analysis. Additionally, XM tags will become a standard protocol for recording methylation signals.
A central helical hairpin in SPD-5 enables centrosome strength and assembly
Authors: Rios Manolo U. , Ryder Bryan D. , Familiari Nicole , Joachimiak Łukasz A. , Woodruff Jeffrey B.
Published: May 2023

Centrosomes organize microtubules for mitotic spindle assembly and positioning. Forces mediated by these microtubules create tensile stresses on pericentriolar material (PCM), the outermost layer of centrosomes. How PCM resists these stresses is unclear at the molecular level. Here, we use cross-linking mass spectrometry (XL-MS) to map interactions underlying multimerization of SPD-5, an essential PCM scaffold component inC. elegans. We identified an interaction hotspot in an alpha helical hairpin motif in SPD-5 (a.a. 541-677). XL-MS data,ab initiostructural predictions, and mass photometry suggest that this region dimerizes to form a tetrameric coiled-coil. Mutating a helical section (a.a. 610-640) or a single residue (R592) inhibited PCM assembly in embryos. This phenotype was rescued by eliminating microtubule pulling forces, revealing that PCM assembly and material strength are interrelated. We propose that interactions mediated by the helical hairpin strongly bond SPD-5 molecules to each other, thus enabling PCM to assemble fully and withstand stresses generated by microtubules.
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
Authors: Kille Bryce , Garrison Erik , Treangen Todd J , Phillippy Adam M
Published: May 2023

1

Abstracts

Motivation

The Jaccard similarity onk-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.

Results

To address this, we propose theminmerwinnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampledk-mers per window. We show both theoretically and empirically that minmers yield an unbiased estimator of local Jaccard similarity, and we implement this scheme in an updated version of MashMap. The minmer-based implementation is over 10 times faster than the minimizer-based version under the default ANI threshold, making it well-suited for large-scale comparative genomics applications.

Availability

MashMap3 is available athttps://github.com/marbl/MashMap

Contact

blk6@rice.edu,adam.phillippy@nih.gov
Measuring sub-nanometer fluctuations at microsecond temporal resolution with metal-and graphene-induced energy transfer spectroscopy
Authors: Chen Tao , Karedla Narain , Enderlein Jörg
Published: May 2023

Out-of-plane fluctuations, also known as stochastic displacements, of biological membranes play a crucial role in regulating many essential life processes within cells and organelles. Despite the availability of various methods for quantifying membrane dynamics, accurately quantifying complex membrane systems with rapid and tiny fluctuations, such as mitochondria, remains a challenge. In this work, we present a novel methodology that combines metal/graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to quantify out-of-plane fluctuations of membranes with simultaneous spatiotem-poral resolution of approximately one nanometer and one microsecond that is unprecedented.

To validate the technique and spatiotemporal resolution, we measured bending undulations of model membranes. Furthermore, we demonstrate the versatility and applicability of MIET/GIET-FCS for studying diverse membrane systems, including the widely studied fluctuating membrane system of human red blood cells, as well as two unexplored membrane systems with tiny fluctuations, a pore-spanning membrane, and mitochondrial inner/outer membranes.
Apical-driven cell sorting optimised for tissue geometry ensures robust patterning
Authors: Moghe Prachiti , Belousov Roman , Ichikawa Takafumi , Iwatani Chizuru , Tsukiyama Tomoyuki , Graner François , Erzberger Anna , Hiiragi Takashi
Published: May 2023

Tissue patterning coordinates morphogenesis, cell dynamics and fate specification. Understanding how these processes are coupled to achieve precision despite their inherent variability remains a challenge. Here, we investigate how salt-and-pepper epiblast and primitive endoderm (PrE) cells sort and robustly pattern the inner cell mass (ICM) of mammalian blastocysts. Quantifying cellular dynamics and mechanics together with simulations show a key role for the autonomously acquired apical polarity of mouse PrE cells in coupling cell fate and dynamics in tissue contexts. Specifically, apical polarity forms actin protrusions and is required for Rac1-dependent migration towards the ICM surface, where PrE cells are trapped due to decreased tension at their apical domain, while depositing an extracellular matrix gradient, breaking the tissue-level symmetry and collectively guiding their own migration. Tissue size perturbations and comparison with monkey blastocysts further demonstrate that the fixed proportion of PrE/epiblast cells is optimal and robust to variability in embryo size.
A chromosome-level reference genome for the common octopus,Octopus vulgaris(Cuvier, 1797)
Authors: Destanović Dalila , Schultz Darrin T. , Styfhals Ruth , Cruz Fernando , Gómez-Garrido Jèssica , Gut Marta , Gut Ivo , Fiorito Graziano , Simakov Oleg , Alioto Tyler S. , Ponte Giovanna , Seuntjens Eve
Published: May 2023

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio.Octopus vulgarishas been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly is available forO. vulgaristo aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus,O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n=30 chromosomes. Comparisons with other octopus species’ genomes show a conserved octopus karyotype, and a pattern of local genome rearrangements between species. This new chromosome-scale genome ofO. vulgariswill further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.
Effect of AT1 receptor blockade on cardiovascular outcome after cardiorespiratory arrest: an experimental study in rats
Authors: Araújo Filho EAF , Carmona MJC , Otsuki DA , Maia DRR , Lima LGCA , Vane MF
Published: May 2023

Background

AT1 angiotensin II receptor (ATI) antagonists are beneficial in focal ischemia/reperfusion (I/R) cases. However, in cases of global I/R, such as cardiorespiratory arrest (CRA), ATI blocker’s effects are still unknown.

Methods

Rats were allocated into four groups: Sham group (SG) – animals submitted to surgical interventions, without CRA; Control group (CG) – animals submitted to CRA and ventricular fibrillation; Group AT1 (GAT1) – like CG, plus 0.2 mg/kg of Candesartan; Vehicle Group (VG): animals equally induced to CRA, and administration of 0.2 ml/kg of dimethyl sulfoxide. The rate of return of spontaneous circulation (ROSC), survival, hemodynamic variables, histopathology, and markers of tissue injury were analyzed.

Results

Compared to CG, the GAT1 group had a higher rate of ROSC (62.5% vs. 42.1%, p<0.0001), survival (100% vs. 62.5%, CI: 0.014-0.034; p = 0.027), lower incidence of arrhythmia after 10 minutes of ROSC, (10% vs. 62.5%, p=0.000) and lower neuronal and cardiac injury scores (p=0.025 and p=0.021, respectively). The groups did not differ regarding CRA duration, number of adrenaline doses, or number of defibrillations.

Conclusion

ATI receptor blockade was responsible for higher rates of ROSC and survival, in addition to demonstrating neuronal and myocardial protection.

Highlights

AT1 receptor block was responsible per higher rates of ROSC and survival in intervention group.

The AT1 receptor block can be neuroprotector in ischemic injury caused by CPR.

The candesartan administration during CPR can contribute with reduction of ventricular arrythmias.
Vagus nerve stimulation rescues persistent pain following orthopedic surgery in adult mice
Authors: Wu Pau Yen , Caceres Ana Isabel , Chen Jiegen , Sokoloff Jamie , Huang Mingjian , Baht Gurpreet Singh , Nackley Andrea G , Jordt Sven-Eric , Terrando Niccolò
Published: May 2023

Postoperative pain is a major clinical problem imposing a significant burden on our patients and society. Up to 57% of patients experience persistent postoperative pain 2 years after orthopedic surgery [49]. Although many studies have contributed to the neurobiological foundation of surgery-induced pain sensitization, we still lack safe and effective therapies to prevent the onset of persistent postoperative pain. We have established a clinically relevant orthopedic trauma model in mice that recapitulates common insults associated with surgery and ensuing complications. Using this model, we have started to characterize how induction of pain signaling contributes to neuropeptides changes in dorsal root ganglia (DRG) and sustained neuroinflammation in the spinal cord [62]. Here we have extended the characterization of pain behaviors for >3 months after surgery, describing a persistent deficit in mechanical allodynia in both male and female C57BL/6J mice after surgery. Notably, we have applied a novel minimally invasive bioelectronic approach to percutaneously stimulate the vagus nerve (termed pVNS) [24] and tested its anti-nociceptive effects in this model. Our results show that surgery induced a strong bilateral hind-paw allodynia with a slight decrease in motor coordination. However, treatment with pVNS for 30-minutes at10 Hz weekly for 3 weeks prevented pain behavior compared to naïve controls. pVNS also improved locomotor coordination and bone healing compared to surgery without treatment. In the DRGs, we observed that vagal stimulation fully rescued activation of GFAP positive satellite cells but did not affect microglial activation. Overall, these data provide novel evidence for the use of pVNS to prevent postoperative pain and may inform translational studies to test anti-nociceptive effects in the clinic.