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Quantum state tomography (QST) via local measurements on reduced density matrices (LQST) is a promising approach but becomes impractical for large systems. To tackle this challenge, we developed an efficient quantum state tomography method inspired by quantum overlapping tomography [Phys. Rev. Lett. 124, 100401 (2020)PRLTAO0031-900710.1103/PhysRevLett.124.100401], which utilizes parallel measurements (PQST). In contrast to LQST, PQST significantly reduces the number of measurements and offers more robustness against shot noise. Experimentally, we demonstrate the feasibility of PQST in a treelike superconducting qubit chip by designing high-efficiency circuits, preparing W states, ground states of Hamiltonians, and random states, and then reconstructing these density matrices using full quantum state tomography (FQST), LQST, and PQST. Our results show that PQST reduces measurement cost, achieving fidelities of 98.68% and 95.07% after measuring 75 and 99 observables for six-qubit and nine-qubit W states, respectively. Furthermore, the reconstruction of the largest density matrix of the 12-qubit W state is achieved with the similarity of 89.23% after just measuring 243 parallel observables, while 3^{12}=531 441 complete observables are needed for FQST. Consequently, PQST will be a useful tool for future tasks such as the reconstruction, characterization, benchmarking, and properties learning of states.

Industrial processes generate huge volumes of oily saline wastewater. Instead of being sent to the drainage system immediately, extracting osmotic energy from these effluents represents a promising means to reuse these wastes and contributes to mitigate the ever-growing energy crisis. Herein, an MOF-decorated PTFE membrane is engineered to extract osmotic energy from oily wastewaters. Copper hydroxide nanowires (CHNs) are intertwined with polystyrenesulfonate sodium (PSS), deposited onto a poly(tetrafluoroethylene) (PTFE) membrane, and thereafter used as metal precursors to in situ generate HKUST-1 doped with negative charges. The resulting HKUST-1 PSS @PTFE hybrid membrane possesses abundant angstrom-scale channels capable of transporting cations efficiently and features a hierarchically structured surface with underwater superoleophobicity. The energy conversion performance of the HKUST-1 PSS3.5 @PTFE membrane can reach an output power density of 6.21 W m -2 at a 50-fold NaCl gradient, which is superior to those of pristine PTFE membranes. Once exposed to oily saline wastewater, the HKUST-1 PSS @PTFE membrane can exhibit an excellent oil-repellent ability, thus contributing to sustain its osmotic energy harvesting. This work may promote the development of antifouling osmotic energy harvesters with a long working life and pave the way to fully exploit oily wastewater effluents as valuable energy sources.

Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNAseq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in the ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterized, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNAseq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasizes the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies., (© 2024 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species., Competing Interests: Declaration of interests A.B. is a scientific advisory board member of Calico. M.P.S. is a co-founder and the scientific advisory board member of Personalis, Qbio, January AI, SensOmics, Filtricine, Protos, Mirvie, Onza, Marble Therapeutics, Iollo, and NextThought AI. He is also on the scientific advisory board of Jupiter, Applied Cognition, Neuvivo, Mitrix, and Enovone. K.C. is currently an AstraZeneca employee., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Extracting osmotic energy from waste organic solutions via reverse electrodialysis represents a promising approach to reuse such industrial wastes and helps to mitigate the ever-growing energy needs. Herein, a molecularly thin membrane of covalent organic frameworks is engineered via interfacial polymerization to investigate its ion transport behavior in organic solutions. Interestingly, a significant deviation from linearity between ion conductance and reciprocal viscosity is observed, attributed to the nanoscale confinement effect on intermolecular interactions. This finding suggests a potential strategy to modulate the influence of apprarent viscosity on transmembrane transport. The osmotic energy harvesting of the ultrathin membrane in organic systems was studied, achieving an unprecedented output power density of over 84.5 W m -2 at a 1000-fold salinity gradient with a benign conversion efficiency and excellent stability. These findings provide a meaningful stepping stone for future studies seeking to fully leverage the potentials of organic systems in energy harvesting applications.

Photoreceptor cells of vertebrates feature ultrastructural membranes interspersed with abundant photosensitive ion pumps to boost signal generation and realize high gain in dim light. In light of this, superstructured optoionic heterojunctions (SSOHs) with cation-selective nanochannels are developed for manipulating photo-driven ion pumping. A template-directed bottom-up strategy is adopted to sequentially assemble graphene oxide (GO) and PEDOT:PSS into heterogeneous membranes with sculptured superstructures, which feature programmable variation in membrane topography and contain a donor-acceptor interface capable of maintaining electron-hole separation upon photoillumination. Such elaborate design endows SSOHs with a much higher magnitude of photo-driven ion flux against a concentration gradient in contrast to conventional optoionic membranes with planar configuration. This can be ascribed to the buildup of an enhanced transmembrane potential owing to the effective separation of photogenerated carriers at the heterojunction interface and the increase of energy input from photoillumination due to a synergistic effect of reflection reduction, broad-angle absorption, and wide-waveband absorption. This work unlocks the significance of membrane topographies in photo-driven transmembrane transportation and proposes such a universal prototype that could be extended to other optoionic membranes to develop high-performance artificial ion pumps for energy conversion and sensing.

Polyelectrolyte complexes (PECs) have emerged as an attractive category of materials for their water processability and some similarities to natural biopolymers. Herein, we employ the intrinsic hydroplasticity of PEC materials to enable the generation of porous structures with the aid of gas foaming. Such foamable materials are fabricated by simply mixing polycation, polyanion, and a UV-initiated chemical foaming agent in an aqueous solution, followed by molding into thin films. The gas foaming of the PEC films can be achieved upon exposure to UV illumination under water, where the films are plasticized and the gaseous products from the photolysis of foaming agents afford the formation, expanding, and merging of numerous bubbles. The porosity and morphology of the resulting porous films can be customized by tuning film composition, foaming conditions, and especially the degree of plasticizing effect, illustrating the high flexibility of this hydroplastic foaming method. Due to the rapid initiation of gas foaming, the present method enables the formation of porous structures via an instant one-step process, much more efficient than those existing strategies for porous PEC materials. More importantly, such a pore-forming mechanism might be extended to other hydroplastic materials (e.g., biopolymers) and help to yield hydroplasticity-based processing strategies.

Superselective adrenal arterial embolization (SAAE) appears to be beneficial in primary aldosteronism (PA) patients with lateralized aldosterone secretion (unilateral PA). As confirmed by adrenal vein sampling (AVS), nearly 40% of PA patients would be PA without lateralized aldosterone secretion (bilateral PA). We aimed to investigate the efficacy and safety of SAAE on bilateral PA. We identified 171 bilateral PA patients from 503 PA patients who completed AVS. Thirty-eight bilateral PA patients received SAAE, and 31 completed a median 12-month clinical follow-up. The blood pressure and biochemical improvements of these patients were carefully analyzed. 34% of patients were identified as bilateral PA. Plasma aldosterone concentration, plasma renin activity, and aldosterone/renin ratio (ARR) were significantly improved 24-h after SAAE. SAAE was associated with 38.7% and 58.6% of complete/partial clinical and biochemical success within a median 12-month follow-up. A significant reduction in left ventricular hypertrophy was shown in patients who obtained complete biochemical success compared with partial/absent biochemical success. SAAE was associated with a more apparent nighttime blood pressure reduction than daytime blood pressure reduction in patients with complete biochemical success. No major adverse safety events related to SAAE were reported during the intraoperative, postoperative, and follow-up periods. SAAE was associated with blood pressure and biochemical improvements in part of bilateral PA and appeared safe. The biochemistry success was accompanied by improved cardiac remodeling and a more prominent decrease in nocturnal blood pressure. This study was part of a trial registered with the Chinese Clinical Trial Registry, number ChiCTR2100047689., (© 2023. The Author(s), under exclusive licence to The Japanese Society of Hypertension.)

Competing Interests: All the authors declare no potential financial and nonfinancial conflicts of interest.

Introduction: Spinal cord injury (SCI) is a devastating neurological disorder with an enormous impact on individual's life and society. A reliable and reproducible animal model of SCI is crucial to have a deeper understanding of SCI. We have developed a large-animal model of spinal cord compression injury (SCI) with integration of multiple prognostic factors that would have applications in humans., Methods: Fourteen human-like sized pigs underwent compression at T8 by implantation of an inflatable balloon catheter. In addition to basic neurophysiological recording of somatosensory and motor evoked potentials, we introduced spine-to-spine evoked spinal cord potentials (SP-EPs) by direct stimulation and measured them just above and below the affected segment. A novel intraspinal pressure monitoring technique was utilized to measure the actual pressure on the cord. The gait and spinal MRI findings were assessed in each animal postoperatively to quantify the severity of injury., Results: We found a strong negative correlation between the intensity of pressure applied to the spinal cord and the functional outcome ( P < 0.0001). SP-EPs showed high sensitivity for real time monitoring of intraoperative cord damage. On MRI, the ratio of the high-intensity area to the cross-sectional of the cord was a good predictor of recovery ( P < 0.0001)., Conclusion: Our balloon compression SCI model is reliable, predictable, and easy to implement. By integrating SP-EPs, cord pressure, and findings on MRI, we can build a real-time warning and prediction system for early detection of impending or iatrogenic SCI and improve outcomes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hu, Chen, Wang, Sun and Wu.)

The African turquoise killifish Nothobranchius furzeri is an emerging research organism known for its short life span and long-term diapause. Diapause is a unique dormant state that suspends embryonic development without tradeoffs in the adulthood life span. Recently, diapause has been gaining increasing interest from the research community. Here, we report our methods for handling the embryos of N. furzeri that go through diapause. We focus on a few key steps: (1) collecting N. furzeri embryos, (2) sorting embryos entering diapause, (3) storing diapause embryos, (4) screening embryos exiting diapause, and (5) hatching post-diapause and fully developed embryos. This method should help the need to obtain a large number of embryos in synchronization with their diapause-entering and -exiting status and satisfy the need for cell biology, genetic, genomic, and biochemistry experiments., (© 2023 Cold Spring Harbor Laboratory Press.)

Critical physical systems with large numbers of molecules can show universal and scaling behaviors. It is of interest to know whether human societies with large numbers of people can show the same behaviors. Here, we use network theory to analyze Chinese history in periods 209 BCE-23 CE and 515-618 CE) related to the Western Han-Xin Dynasty and the late Northern Wei-Sui Dynasty, respectively. Two persons are connected when they appear in the same historical event. We find that the historical networks from two periods separated about 500 years have interesting universal and scaling behaviors, and they are small-world networks; their average cluster coefficients as a function of degree are similar to the network of movie stars. In the historical networks, the persons with larger degrees prefer to connect with persons with a small degree; however, in the network of movie stars, the persons with larger degrees prefer to connect with persons with large degrees. We also find an interesting similar mechanism for the decline or collapse of historical Chinese dynasties. The collapses of the Xin dynasty (9-23 CE) and the Sui dynasty (581-618 CE) were initiated from their arrogant attitude toward neighboring states.

Background: Every year, esophageal cancer is responsible for 509000 deaths and around 572000 new cases worldwide. Although esophageal cancer treatment options have advanced, patients still have a dismal 5-year survival rate., Aim: To investigate the relationship between genes associated to platelets and the prognosis of esophageal cancer., Methods: We searched differentially expressed genes for changes between 151 tumor tissues and 653 normal, healthy tissues using the "limma" package. To develop a prediction model of platelet-related genes, a univariate Cox regression analysis and least absolute shrinkage and selection operator Cox regression analysis were carried out. Based on a median risk score, patients were divided into high-risk and low-risk categories. A nomogram was created to predict the 1-, 2-, and 3-year overall survival (OS) of esophageal cancer patients using four platelet-related gene signatures, TNM stages, and pathological type. Additionally, the concordance index, receiver operating characteristic curve, and calibration curve were used to validate the nomogram., Results: The prognosis of esophageal cancer was associated to APOOL , EP300 , PLA2G6 , and VAMP7 according to univariate Cox regression analysis and least absolute shrinkage and selection operator regression analysis. Patients with esophageal cancer at high risk had substantially shorter OS than those with cancer at low risk, according to a Kaplan-Meier analysis ( P < 0.05). TNM stage (hazard ratio: 2.187, 95% confidence interval: 1.242-3.852, P = 0.007) in both univariate and multivariate Cox regression and risk score were independently correlated with OS (hazard ratio: 2.451, 95% confidence interval: 1.599-3.756, P < 0.001)., Conclusion: A survival risk score model and independent prognostic variables for esophageal cancer have been developed using APOOL , EP300 , PLA2G6 , and VAMP7 . OS for esophageal cancer might be predicted using the nomogram based on TNM stage, pathological type, and risk score. The nomogram demonstrated strong predictive ability, as shown by the concordance index, receiver operating characteristic curve, and calibration curve., Competing Interests: Conflict-of-interest statement: All the authors report having no relevant conflicts of interest for this article., (©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.)

The African turquoise killifish is an exciting new vertebrate model for aging studies. A significant challenge for any model organism is the control over its diet in space and time. To address this challenge, we created an automated and networked fish feeding system. Our automated feeder is designed to be open-source, easily transferable, and built from widely available components. Compared to manual feeding, our automated system is highly precise and flexible. As a proof of concept for the feeding flexibility of these automated feeders, we define a favorable regimen for growth and fertility for the African killifish and a dietary restriction regimen where both feeding time and quantity are reduced. We show that this dietary restriction regimen extends lifespan in males (but not in females) and impacts the transcriptomes of killifish livers in a sex-specific manner. Moreover, combining our automated feeding system with a video camera, we establish a quantitative associative learning assay to provide an integrative measure of cognitive performance for the killifish. The ability to precisely control food delivery in the killifish opens new areas to assess lifespan and cognitive behavior dynamics and to screen for dietary interventions and drugs in a scalable manner previously impossible with traditional vertebrate model organisms., Competing Interests: AM, EC, JC, CH, XC, CB, RK, MT, PP, TW, AB No competing interests declared, (© 2022, McKay, Costa, Chen et al.)

The coexistence of chronic obstructive pulmonary disease (COPD) and cardiovascular disease is common and causes poor prognoses. Hyperlipidemia is the most common risk factor for cardiovascular disease, but the association between hyperlipidemia and COPD remains ambiguous. This study aimed to investigate the risk of COPD development in patients with hyperlipidemia. This retrospective cohort study used information from the National Health Insurance Research Database in Taiwan. We enrolled 21,790 patients with hyperlipidemia and 87,160 control patients without hyperlipidemia for comparison, with a follow-up period of over 10 years. The incidence of new-onset COPD was higher in patients with hyperlipidemia (36.14 per 1000 person-years) than in the controls (22.29 per 1000 person-years). Patients with hyperlipidemia were 1.48 times more likely to develop subsequent COPD than the controls without hyperlipidemia (95% confidence interval 1.44 to 1.53, p < 0.001) following adjustments for age, sex, and comorbidities. In addition, nephropathy, hypertension, congestive heart failure, age, and sex (female) were potential risk factors for developing COPD in patients with hyperlipidemia. Patients with hyperlipidemia may have an increased risk of developing COPD.

Background: Currently, there are many therapeutic methods for lung adenocarcinoma (LUAD), but the 5-year survival rate is still only 15% at later stages. Epithelial- mesenchymal transition (EMT) has been shown to be closely associated with local dissemination and subsequent metastasis of solid tumors. However, the role of EMT in the occurrence and development of LUAD remains unclear., Aim: To further elucidate the value of EMT-related genes in LUAD prognosis., Methods: Univariate, least absolute shrinkage and selection operator, and multivariate Cox regression analyses were applied to establish and validate a new EMT-related gene signature for predicting LUAD prognosis. The risk model was evaluated by Kaplan-Meier survival analysis, principal component analysis, and functional enrichment analysis and was used for nomogram construction. The potential structures of drugs to which LUAD is sensitive were discussed with respect to EMT-related genes in this model., Results: Thirty-three differentially expressed genes related to EMT were found to be highly associated with overall survival (OS) by using univariate Cox regression analysis (log2FC ≥ 1, false discovery rate < 0.001). A prognostic signature of 7 EMT-associated genes was developed to divide patients into two risk groups by high or low risk scores. Kaplan-Meier survival analysis showed that the OS of patients in the high-risk group was significantly poorer than that of patients in the low-risk group ( P < 0.05). Multivariate Cox regression analysis showed that the risk score was an independent risk factor for OS (HR > 1, P < 0.05). The results of receiver operator characteristic curve analysis suggested that the 7-gene signature had a perfect ability to predict prognosis (all area under the curves > 0.5)., Conclusion: The EMT-associated gene signature classifier could be used as a feasible indicator for predicting OS., Competing Interests: Conflict-of-interest statement: The authors declare no conflicts of interest., (©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.)

Background: Studies have shown that percutaneous coronary intervention (PCI) is considered as the essential therapeutic strategy for the patients with ST-segment elevation myocardial infarction (STEMI). However; no-reflow could still occur in a few patients after PCI. Studies have reported that biomarkers related to no-reflow pathogenetic components could play a prognostic role in the prediction phenomenon. Hence, this study explored the establishment of nomogram model for predicting the occurrence of no-reflow phenomenon after PCI using the lncRNA TUG1 /miR-30e/ NPPB biomarkers in patients with STEMI after PCI., Methods: In this observational study, a total of 76 STEMI patients who underwent emergency PCI between January 2018 and December 2021were included. The patients after PCI, were divided into reflow (n=44) and no-reflow groups (n=32). The demographic, environmental and clinical risk factors were assessed and analysed between the groups. Quantitative RT-PCR was used to detect TUG1 , miR-30e, and NPPB messenger RNA (mRNA) expression levels in the plasma of patients after PCI. Bioinformatic methods were used to predict the interaction of the plasma TUG1 /miR-30e/ NPPB axis. The risk factors in the no-reflow group were screened using a logistic-regression analysis, and a nomogram prediction model was constructed and validated. Subsequently, a gene set enrichment analysis revealed the function of lncRNA TUG1 ., Results: Plasma lncRNA TUG1 and NPPB were more highly expressed and miR-30e was more lowly expressed in the no-reflow group than the normal-reflow group (P<0.001). A negative correlation was observed between lncRNA TUG1 and miR-30e, and between miR-30e and NPPB . However, a positive correlation was observed between lncRNA TUG1 and NPPB mRNA. The bioinformatics analysis predicted multiple binding sites on the lncRNA TUG1 and miR-30e. LncRNA TUG1 [odds ratio (OR): 0.163, 95% confidence interval (CI): 0.021-0.944] and hs-CRP (OR: 2.151, 95% CI: 1.536-3.974) found to be as independent predictors. The C-index of this prediction model was 0.982 (95% CI: 0.956-1.000)., Conclusions: TUG1 could function as an effective biomarker for no-reflow among patients with STEMI after PCT and the proposed nomogram may provide information for individualized treatment in patients with STEMI., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://jtd.amegroups.com/article/view/10.21037/jtd-22-481/coif). The authors have no conflicts of interest to declare., (2022 Journal of Thoracic Disease. All rights reserved.)

Broadband modulation of magnetic circular dichroism (MCD) using a relatively low magnetic field or by producing a field-free magnetoplasmonic effect in the remnant magnetic state was achieved by the integration of the noble metals (NMs) Au and Ag and the perpendicular magnetic anisotropy of Co with ZnO nanowires (NWs) used as the template. The samples containing NMs revealed MCD sign reversals and enhancements when compared with the original Co/ZnO NWs. The magnetoplasmonic effect of Au close to the visible light spectrum could induce the CD change in the visible region. Notably, the ultraviolet (UV) CD in Ag/Co/ZnO NWs is 12.5 times larger under a magnetic field (∼0.2 T) and 10 times greater in the remnant state (field-free) than those of the original Co/ZnO NWs because of the magnetoplasmonic effect of Ag in the UV spectrum. These results are attributable to the coupling of the remnant magnetic state of Co magnetization, the magnetoplasmons of the NMs, and the excitons of the ZnO NWs. The findings are potentially applicable in magneto-optical recording, biosensing, and energy contexts involving magnetoplasmonic functionalization.

How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits, and some behaviors, is linked to cis-regulatory changes in gene expression. Given this, we compare brain gene expression of two interfertile sister species of Peromyscus mice that show large and heritable differences in burrowing behavior. Species-level differential expression and allele-specific expression in F 1 hybrids indicate a preponderance of cis-regulatory divergence, including many genes whose cis-regulation is affected by burrowing behavior. Genes related to locomotor coordination show the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. Furthermore, genetic markers closest to these candidate genes associate with variation in burrow shape in a genetic cross, suggesting an enrichment for loci affecting burrowing behavior near these candidate locomotor genes. Our results provide insight into how cis-regulated gene expression can depend on behavioral context and how this dynamic regulatory divergence between species may contribute to behavioral evolution., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Most long-term care facilities can offer residents' with sufficiently material and physical care, but psychological support may not be always provided due to the tight financial budget or labor resources. Residents' isolation and loneliness then become a big issue, especially for the residents. Social network systems (SNS) have been proved to be a more effective information transmission channel for thoughts, perspectives, and information sharing than traditional channels such as microblogging, e-mails, or telephones. This study conducted a quasi-experiment to identify factors that influence residents' intention of using SNS and the impacts of SNS on them in a long-term care facility. The results showed that residents' attached motivation of personal interacting is a significant factor that influences their intention to use the social network platform. Meanwhile, both the loneliness and depression scales of the participants were decreased significantly.

In recent decades, biologist have focused on the spatiotemporal regulation and function of genes to understand embryogenesis. It is clear that maternal diet impacts fetal development but how nutrients, like lipids and vitamins, modify developmental programs is not completely understood. Fish are useful research organisms for such investigations. Most species of fish produce eggs that develop outside the mother, dependent on a finite amount of yolk to form and grow. The developing embryo is a closed system that can be readily biochemically analyzed, easily visualized, and manipulated to understand the role of nutrients in tissue specification, organogenesis, and growth. Natural variation in yolk composition observed across fish species may be related to unique developmental strategies. In this review, we discuss the reasons that teleost fishes are powerful models to understand nutritional control of development and highlight three species that are particularly valuable for future investigations: the zebrafish, Danio rerio, the African Killifish, Nothobranchius furzeri, and the Mexican tetra, Astyanax mexicanus. This review is a part of a special issue on nutritional, hormonal, and metabolic drivers of development., (Copyright © 2021. Published by Elsevier Inc.)

The limb-girdle muscular dystrophies (LGMD) are a collection of genetic diseases united in their phenotypical expression of pelvic and shoulder area weakness and wasting. More than 30 subtypes have been identified, five dominant and 26 recessive. The increase in the characterization of new genotypes in the family of LGMDs further adds to the heterogeneity of the disease. Meanwhile, better understanding of the phenotype led to the reconsideration of the disease definition, which resulted in eight old subtypes to be no longer recognized officially as LGMD and five new diseases to be added to the LGMD family. The unique variabilities of LGMD stem from genetic mutations, which then lead to protein and ultimately muscle dysfunction. Herein, we review the LGMD pathway, starting with the genetic mutations that encode proteins involved in muscle maintenance and repair, and including the genotype-phenotype relationship of the disease, the epidemiology, disease progression, burden of illness, and emerging treatments., (© 2021. The Author(s).)

Fourteen current-use pesticides (CUPs) in the surface seawaters of the typical Liaoning sea areas were analyzed using HPLC-MS/MS. The concentrations, distribution, and ecological risks were studied, as well as their source appointments using principal component analysis (PCA). The results revealed that seven types of CUPs were detected in the surface seawaters of the typical Liaoning sea areas. The total concentrations of these CUPs ranged from 16.7 ng·L -1 to 176.1 ng·L -1 . The samples with high concentrations were collected mostly from the estuary, and the concentrations of CUPs in the western Liaodong Bay were generally higher than those in the northeastern Yellow Sea. Atrazine and triadimenol were the predominant CUPs, and their contribution rates accounted for 56.0% and 34.5%, respectively. The PCA results indicated that six types of CUPs might be caused by the runoff from farmlands and the wastewater discharge from the chemical pesticide factory, and fruit planting could be a substantial contributor to the single component acetochlor. Atrazine and acetochlor posed medium-high ecological risks to the microalgae, while all the seven types of CUPs showed relatively lower risks to invertebrates and fish.

Background: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and it is unclear how available assays compare., Methods: For the Abbott RealTime SARS-CoV-2 assay (m2000; Abbott Molecular), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from 8538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of 2 other assays with more rapid turnaround times [Cepheid Xpert Xpress (GeneXpert; Cepheid); n = 27] and a laboratory developed test on the Luminex ARIES system [ARIES LDT (Luminex); n = 50] as a function of virus concentrations, from which we projected their false-negative rates in our patient population., Results: SARS-CoV-2 was detected in 27% (95% CI: 26%-28%) of all specimens. Estimated viral concentrations were widely distributed, and 17% (95% CI: 16%-19%) of positive individuals had viral concentrations <845 copies/mL. Positive percent agreement was strongly related to viral concentration, and reliable detection (i.e., ≥95%) was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false-negative rates of 4% (95% CI: 0%-21%) and 27% (95% CI: 11%-46%), respectively., Conclusions: Substantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with less analytic sensitivity., (© American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection, leading to high morbidity and mortality. Currently, bronchoalveolar lavage (BAL) is used in hospitals for VAP diagnosis and guiding treatment options. Although BAL collection procedures are invasive, alternatives such as endotracheal aspirates (ETA) may be of diagnostic value, however, their use has not been thoroughly explored. Longitudinal ETA and BAL were collected from 16 intubated patients up to 15 days, of which 11 developed VAP. We conducted a comprehensive LC-MS/MS based proteome and metabolome characterization of longitudinal ETA and BAL to detect host and pathogen responses to VAP infection. We discovered a diverse ETA proteome of the upper airways reflective of a rich and dynamic host-microbe interface. Prior to VAP diagnosis by microbial cultures from BAL, patient ETA presented characteristic signatures of reactive oxygen species and neutrophil degranulation, indicative of neutrophil mediated pathogen processing as a key host response to the VAP infection. Along with an increase in amino acids, this is suggestive of extracellular membrane degradation resulting from proteolytic activity of neutrophil proteases. The metaproteome approach successfully allowed simultaneous detection of pathogen peptides in patients' ETA, which may have potential use in diagnosis. Our findings suggest that ETA may facilitate early mechanistic insights into host-pathogen interactions associated with VAP infection and therefore provide its diagnosis and treatment., Competing Interests: Conflict of interest—Authors declare no competing interests., (© 2020 Pathak et al.)

Background: The progressive neurodegenerative disorder Parkinson disease (PD) is well-established as the second most common neurodegenerative disease. Associations between the sequential risk of PD and gout have been addressed in other studies, but findings have been inconclusive. Accordingly, we executed the present study with the purpose of assessing PD risk in patients with gout., Methods: From Taiwan's National Health Insurance Research Database, we identified the data of patients newly diagnosed as having gout between January 1, 2000 and December 1, 2000. A cohort of patients without gout, matched for sex and age, was constructed for comparison. Hazard ratios (HRs) and the incidence rate of subsequent PD were calculated for both cohorts and separately for male and female groups. The gout and comparison cohorts consisted of 7900 patients each., Results: The HR for PD was not significantly higher in the gout cohort compared with the control cohort (HR 1.01, 95% confidence interval [CI], 0.93-1.31, P = .268), even after adjustment for age, urbanization, monthly income, sex, and comorbidities. We did not observe gender differences in the gout-PD association (male: HR 1.01, 95% CI, 0.88-1.36, P = .400; female: HR 1.11, 95% CI, 0.84-1.46, P = .466)., Conclusions: Our study identified that there was no protective effect of gout for the risk of PD in the Taiwanese population.

Vertebrates vary in their ability to regenerate, and the genetic mechanisms underlying such disparity remain elusive. Comparative epigenomic profiling and single-cell sequencing of two related teleost fish uncovered species-specific and evolutionarily conserved genomic responses to regeneration. The conserved response revealed several regeneration-responsive enhancers (RREs), including an element upstream to inhibin beta A ( inhba ), a known effector of vertebrate regeneration. This element activated expression in regenerating transgenic fish, and its genomic deletion perturbed caudal fin regeneration and abrogated cardiac regeneration altogether. The enhancer is present in mammals, shares functionally essential activator protein 1 (AP-1)-binding motifs, and responds to injury, but it cannot rescue regeneration in fish. This work suggests that changes in AP-1-enriched RREs are likely a crucial source of loss of regenerative capacities in vertebrates., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish ( Nothobranchius furzeri ), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation., (Copyright © 2020, American Association for the Advancement of Science.)

Selection in a time-periodic environment is modeled via the continuous-time two-player replicator dynamics, which for symmetric payoffs reduces to the Fisher equation of mathematical genetics. For a sufficiently rapid and cyclic (fine-grained) environment, the time-averaged population frequencies are shown to obey a replicator dynamics with a nonlinear fitness that is induced by environmental changes. The nonlinear terms in the fitness emerge due to populations tracking their time-dependent environment. These terms can induce a stable polymorphism, though they do not spoil the polymorphism that exists already without them. In this sense polymorphic populations are more robust with respect to their time-dependent environments. The overall fitness of the problem is still given by its time-averaged value, but the emergence of polymorphism during genetic selection can be accompanied by decreasing mean fitness of the population. The impact of the uncovered polymorphism scenario on the models of diversity is exemplified via the rock-paper-scissors dynamics, and also via the prisoner's dilemma in a time-periodic environment.

Validity conditions for the adiabatic approximation are useful tools to understand and predict the quantum dynamics. Remarkably, the resonance phenomenon in oscillating quantum systems has challenged the adiabatic theorem. In this scenario, inconsistencies in the application of quantitative adiabatic conditions have led to a sequence of new approaches for adiabaticity. Here, by adopting a different strategy, we introduce a validation mechanism for the adiabatic approximation by driving the quantum system to a non-inertial reference frame. More specifically, we begin by considering several relevant adiabatic approximation conditions previously derived and show that all of them fail by introducing a suitable oscillating Hamiltonian for a single quantum bit (qubit). Then, by evaluating the adiabatic condition in a rotated non-inertial frame, we show that all of these conditions, including the standard adiabatic condition, can correctly describe the adiabatic dynamics in the original frame, either far from resonance or at a resonant point. Moreover, we prove that this validation mechanism can be extended for general multi-particle quantum systems, establishing the conditions for the equivalence of the adiabatic behavior as described in inertial or non-inertial frames. In order to experimentally investigate our method, we consider a hyperfine qubit through a single trapped Ytterbium ion 171 Yb + , where the ion hyperfine energy levels are used as degrees of freedom of a two-level system. By monitoring the quantum evolution, we explicitly show the consistency of the adiabatic conditions in the non-inertial frame.

There are three possible classifications of the dimer weights on the bonds of the checkerboard lattice and they are denoted as checkerboard A, B, and C lattices [Phys. Rev. E 91, 062139 (2015)PLEEE81539-375510.1103/PhysRevE.91.062139]. The dimer model on the checkerboard B and C lattices has much richer critical behavior compared to the dimer model on the checkerboard A lattice. In this paper we study in full detail the dimer model on the checkerboard B lattice. The dimer model on the checkerboard B lattice has two types of critical behavior. In one limit this model is the anisotropic dimer model on rectangular lattice with algebraic decay of correlators and in another limit it is the anisotropic generalized Kasteleyn model with radically different critical behavior. We analyze the partition function of the dimer model on a 2M×2N checkerboard B lattice wrapped on a torus. We find very unusual behavior of the partition function zeros and the specific heat of the dimer model. Remarkably, the partition function zeros of finite-size systems can have very interesting structures, made of rings, concentric circles, radial line segments, or even arabesque structures. We find out that the number of the specific heat peaks and the number of circles of the partition function zeros increases with the system size. The lattice anisotropy of the model has strong effects on the behavior of the specific heat, dominating the relation between the correlation length exponent ν and the shift exponent λ, and λ is generally unequal to 1/ν (λ≠1/ν).

We have probed small molecule compound CID 9998128 as a potential multitarget drug for the Alzheimer's disease (AD) using in silico and in vitro experiments. By all-atom simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, we have demonstrated that this compound strongly binds to both amyloid β42 (Aβ 42 ) fibrils and β-secretase, and the van der Waals interaction dominates over the electrostatic interaction in binding affinity. A detailed analysis at the atomic level revealed that indazole in CID 99998128 structure made a major contribution to instability of all studied complexes. In vitro experiments have shown that CID 9998128 inhibits the Aβ 42 amyloid fibrillization and is capable to clear Aβ 42 fibrils. Moreover, the compound dose-dependently decreases β-site amyloid precursor protein cleaving enzyme (BACE-1) activity with EC 50 value in micromolar range. Thus, our study has revealed that CID 9998128 is a good candidate for AD treatment through preventing production of Aβ peptides and degrading their aggregates. For drug design, we predict that the chemical structure of potent AD multitarget inhibitors should not contain indazole.

It is known that high intensity fields are usually required to implement shortcuts to adiabaticity via transitionless quantum driving (TQD). Here, we show that this requirement can be relaxed by exploiting the gauge freedom of generalized TQD, which is expressed in terms of an arbitrary phase when mimicking the adiabatic evolution. We experimentally investigate the performance of generalized TQD in comparison to both traditional TQD and adiabatic dynamics. By using a Yb + 171 trapped ion hyperfine qubit, we implement a Landau-Zener adiabatic Hamiltonian and its (traditional and generalized) TQD counterparts. We show that the generalized theory provides energy-optimal Hamiltonians for TQD, with no additional fields required. In addition, the optimal TQD Hamiltonian for the Landau-Zener model is investigated under dephasing. Even using less intense fields, optimal TQD exhibits fidelities that are more robust against a decohering environment, with performance superior to that provided by the adiabatic dynamics.

To model the dependence of extreme events on locations, we consider extreme events of Brownian particles in a potential. We find that barring the exception of very large potentials and/or very small regions, in general, the probability of extreme events increases with the potential. Our approach is general and can be useful for studying several complex systems.

The African turquoise killifish has recently gained significant traction as a new research organism in the aging field. Our understanding of aging has strongly benefited from canonical research organisms-yeast, C. elegans, Drosophila, zebrafish, and mice. Many characteristics that are essential to understand aging-for example, the adaptive immune system or the hypothalamo-pituitary axis-are only present in vertebrates (zebrafish and mice). However, zebrafish and mice live more than 3 years and their relatively long lifespans are not compatible with high-throughput studies. Therefore, the turquoise killifish, a vertebrate with a naturally compressed lifespan of only 4-6 months, fills an essential gap to understand aging. With a recently developed genomic and genetic toolkit, the turquoise killifish not only provides practical advantages for lifespan and longitudinal experiments, but also allows more systematic characterizations of the interplay between genetics and environment during vertebrate aging. Interestingly, the turquoise killifish can also enter a long-term dormant state during development called diapause. Killifish embryos in diapause already have some organs and tissues, and they can last in this state for years, exhibiting exceptional resistance to stress and to damages due to the passage of time. Understanding the diapause state could give new insights into strategies to prevent the damage caused by aging and to better preserve organs, tissues, and cells. Thus, the African turquoise killifish brings two interesting aspects to the aging field-a compressed lifespan and a long-term resistant diapause state, both of which should spark new discoveries in the field., (© 2018 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.)

Local interneurons (LNs) in the Drosophila olfactory system exhibit neuronal diversity and variability, yet it is still unknown how these features impact information encoding capacity and reliability in a complex LN network. We employed two strategies to construct a diverse excitatory-inhibitory neural network beginning with a ring network structure and then introduced distinct types of inhibitory interneurons and circuit variability to the simulated network. The continuity of activity within the node ensemble (oscillation pattern) was used as a readout to describe the temporal dynamics of network activity. We found that inhibitory interneurons enhance the encoding capacity by protecting the network from extremely short activation periods when the network wiring complexity is very high. In addition, distinct types of interneurons have differential effects on encoding capacity and reliability. Circuit variability may enhance the encoding reliability, with or without compromising encoding capacity. Therefore, we have described how circuit variability of interneurons may interact with excitatory-inhibitory diversity to enhance the encoding capacity and distinguishability of neural networks. In this work, we evaluate the effects of different types and degrees of connection diversity on a ring model, which may simulate interneuron networks in the Drosophila olfactory system or other biological systems.

[This corrects the article on p. 63 in vol. 9, PMID: 29545774.].

Background: Bipolar disorder is a severe mental disorder associated with functional and cognitive impairment. Numerous studies have investigated associations between sexually transmitted infections (STIs) and psychiatric illnesses. However, the results of these studies are controversial., Objective: We explored the association between bipolar disorder and the subsequent development of STIs, including human immunodeficiency virus infection; primary, secondary, and latent syphilis; genital warts; gonorrhea; chlamydial infection; and trichomoniasis., Results: The bipolar cohort consisted of 1293 patients, and the comparison cohort consisted of 5172 matched control subjects without bipolar disorder. The incidence of subsequent STIs (hazard ratio (HR) = 2.23, 95% confidence interval (CI) 1.68-2.96) was higher among the patients with bipolar disorder than in the comparison cohort. Furthermore, female gender is a risk factor for acquisition of STIs (HR = 2.36, 95% CI 1.73-4.89) among patients with bipolar disorder. For individual STIs, the results indicated that the patients with bipolar disorder exhibited a markedly higher risk for subsequently contracting syphilis, genital warts, and trichomoniasis., Conclusions: Bipolar disorder might increase the risk of subsequent newly diagnosed STIs, including syphilis, genital warts, and trichomoniasis. Clinicians should pay particular attention to STIs in patients with bipolar disorder. Patients with bipolar disorder, especially those with a history of high-risk sexual behaviors, should be routinely screened for STIs., Methods: We identified patients who were diagnosed with bipolar disorder in the Taiwan National Health Insurance Research Database. A comparison cohort was constructed of patients without bipolar disorder who were matched with the bipolar cohort according to age and gender. The occurrence of subsequent new-onset STIs was evaluated in both cohorts., Competing Interests: CONFLICTS OF INTEREST The authors declare that they have no conflicts of interest.

The successful completion of cytokinesis requires the coordinated activities of diverse cellular components including membranes, cytoskeletal elements and chromosomes that together form partly redundant pathways, depending on the cell type. The biochemical analysis of this process is challenging due to its dynamic and rapid nature. Here, we systematically compared monopolar and bipolar cytokinesis and demonstrated that monopolar cytokinesis is a good surrogate for cytokinesis and it is a well-suited system for global biochemical analysis in mammalian cells. Based on this, we established a phosphoproteomic signature of cytokinesis. More than 10,000 phosphorylation sites were systematically monitored; around 800 of those were up-regulated during cytokinesis. Reconstructing the kinase-substrate interaction network revealed 31 potentially active kinases during cytokinesis. The kinase-substrate network connects proteins between cytoskeleton, membrane and cell cycle machinery. We also found consensus motifs of phosphorylation sites that can serve as biochemical markers specific to cytokinesis. Beyond the kinase-substrate network, our reconstructed signaling network suggests that combination of sumoylation and phosphorylation may regulate monopolar cytokinesis specific signaling pathways. Our analysis provides a systematic approach to the comparison of different cytokinesis types to reveal alternative ways and a global overview, in which conserved genes work together and organize chromatin and cytoplasm during cytokinesis.

Studying gene regulation networks in a single cell is an important, interesting, and hot research topic of molecular biology. Such process can be described by chemical master equations (CMEs). We propose a Hamilton-Jacobi equation method with finite-size corrections to solve such CMEs accurately at the intermediate region of switching, where switching rate is comparable to fast protein production rate. We applied this approach to a model of self-regulating proteins [H. Ge et al., Phys. Rev. Lett. 114, 078101 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.078101] and found that as a parameter related to inducer concentration increases the probability of protein production changes from unimodal to bimodal, then to unimodal, consistent with phenotype switching observed in a single cell.

Many experiments demonstrate that regions with higher GC-content in natural DNAs unwind at higher temperatures adsorbing more heat than equivalently sized regions with lower GC-content. This simple observation implies that normalized calorimetric melting profiles (calorimetric cDMCs) will not be equivalent differential melting curves (DMCs). We propose simple expressions for long natural and random DNA sequences to reciprocally convert DMCs and corresponding calorimetric cDMCs. The expressions are confirmed by the Poland-Fixman-Freire method and an approach based upon mixtures of homopolymeric duplexes. Using these expressions and experimental calorimetric data, we demonstrate that the average relative deviation between DMC and cDMC is proportional to the temperature melting range of the helix-coil transition ΔT. Corresponding difference between melting temperatures is proportional to ΔT 2 . In general, sequence and ionic conditions influence the deviation through their effect on ΔT. On the basis of the developed approach, we propose a method to determine the thermodynamic melting temperature (ratio of calorimetric enthalpy and entropy of the helix-coil transition) for natural DNAs from optical DMCs without calorimetric experiments., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.

Many human or animal diseases are related to aggregation of proteins. A viable biological organism should maintain in non-equilibrium states. How protein aggregate and why biological organisms can maintain in non-equilibrium states are not well understood. As a first step to understand such complex systems problems, we consider simple model systems containing polymer chains and solvent particles. The strength of the spring to connect two neighboring monomers in a polymer chain is controlled by a parameter s with s → ∞ for rigid-bond. The strengths of bending and torsion angle dependent interactions are controlled by a parameter s A with s A  → -∞ corresponding to no bending and torsion angle dependent interactions. We find that for very small s A , polymer chains tend to aggregate spontaneously and the trend is independent of the strength of spring. For strong springs, the speed distribution of monomers in the parallel (along the direction of the spring to connect two neighboring monomers) and perpendicular directions have different effective temperatures and such systems are in non-equilibrium states.

We consider the Wright-Fisher model of the finite population evolution on a fitness landscape defined in the sequence space by a path of nearly neutral mutations. We study a specific structure of the fitness landscape: One of the intermediate mutations on the mutation path results in either a large fitness value (climbing up a fitness hill) or a low fitness value (crossing a fitness canyon), the rest of the mutations besides the last one are neutral, and the last sequence has much higher fitness than any intermediate sequence. We derive analytical formulas for the first arrival time of the mutant with two point mutations. For the first arrival problem for the further mutants in the case of canyon crossing, we analytically deduce how the mean first arrival time scales with the population size and fitness difference. The location of the canyon on the path of sequences has a crucial role. If the canyon is at the beginning of the path, then it significantly prolongs the first arrival time; otherwise it just slightly changes it. Furthermore, the fitness hill at the beginning of the path strongly prolongs the arrival time period; however, the hill located near the end of the path shortens it. We optimize the first arrival time by applying a nonzero selection to the intermediate sequences. We extend our results and provide a scaling for the valley crossing time via the depth of the canyon and population size in the case of a fitness canyon at the first position. Our approach is useful for understanding some complex evolution systems, e.g., the evolution of cancer.