Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species.

The assembly of complete and circularized mitochondrial genomes (mitogenomes) is essential for population genetics, phylogenetics and evolution studies. Recently, Song et al. developed a seed-free tool called MEANGS for de novo mitochondrial assembly from whole genome sequencing (WGS) data in animals, achieving highly accurate and intact assemblies. However, the suitability of this tool for marine fish remains unexplored. Additionally, we have concerns regarding the overlap sequences in their original results, which may impact downstream analyses. In this Letter to the Editor, the effectiveness of MEANGS in assembling mitogenomes of cartilaginous and ray-finned fish species was assessed. Moreover, we also discussed the appropriate utilization of MEANGS in mitogenome assembly, including the implementation of the data-cut function and circular detection module. Our observations indicated that with the utilization of these modules, MEANGS efficiently assembled complete and circularized mitogenomes, even when handling large WGS datasets. Therefore, we strongly recommend users employ the data-cut function and circular detection module when using MEANGS, as the former significantly reduces runtime and the latter aids in the removal of overlapped sequences for improved circularization. Furthermore, our findings suggested that approximately 2× coverage of clean WGS data was sufficient for MEANGS to assemble mitogenomes in marine fish species. Moreover, due to its seed-free nature, MEANGS can be deemed one of the most efficient software tools for assembling mitogenomes from animal WGS data, particularly in studies with limited species or genetic background information.

Biocompatible Electrical and Optical Interfaces for Implantable Sensors and Devices.

Implantable bioelectronics hold tremendous potential in the field of healthcare, yet the performance of these systems heavily relies on the interfaces between artificial machines and living tissues. In this paper, we discuss the recent developments of tethered interfaces, as well as those of non-tethered interfaces. Among them, systems that study neural activity receive significant attention due to their innovative developments and high relevance in contemporary research, but other functional types of interface systems are also explored to provide a comprehensive overview of the field. We also analyze the key considerations, including perforation site selection, fixing strategies, long-term retention, and wireless communication, highlighting the challenges and opportunities with stable, effective, and biocompatible interfaces. Furthermore, we propose a primitive model of biocompatible electrical and optical interfaces for implantable systems, which simultaneously possesses biocompatibility, stability, and convenience. Finally, we point out the future directions of interfacing strategies.

End-to-End Point Cloud Completion Network with Attention Mechanism.

We propose a conceptually simple, general framework and end-to-end approach to point cloud completion, entitled PCA-Net. This approach differs from the existing methods in that it does not require a "simple" network, such as multilayer perceptrons (MLPs), to generate a coarse point cloud and then a "complex" network, such as auto-encoders or transformers, to enhance local details. It can directly learn the mapping between missing and complete points, ensuring that the structure of the input missing point cloud remains unchanged while accurately predicting the complete points. This approach follows the minimalist design of U-Net. In the encoder, we encode the point clouds into point cloud blocks by iterative farthest point sampling (IFPS) and k-nearest neighbors and then extract the depth interaction features between the missing point cloud blocks by the attention mechanism. In the decoder, we introduce a new trilinear interpolation method to recover point cloud details, with the help of the coordinate space and feature space of low-resolution point clouds, and missing point cloud information. This paper also proposes a method to generate multi-view missing point cloud data using a 3D point cloud hidden point removal algorithm, so that each 3D point cloud model generates a missing point cloud through eight uniformly distributed camera poses. Experiments validate the effectiveness and superiority of PCA-Net in several challenging point cloud completion tasks, and PCA-Net also shows great versatility and robustness in real-world missing point cloud completion.

Thermal Probing Techniques for a Single Live Cell.

Temperature is a significant factor in determining and characterizing cellular metabolism and other biochemical activities. In this study, we provide a brief overview of two important technologies used to monitor the local temperatures of individual living cells: fluorescence nano-thermometry and an array of micro-/nano-sized thin-film thermocouples. We explain some key technical issues that must be addressed and optimised for further practical applications, such as in cell biology, drug selection, and novel antitumor therapy. We also offer a method for combining them into a hybrid measuring system.

Three-Dimensional Encoding Approach for Wearable Tactile Communication Devices.

In this work, we presented a novel encoding method for tactile communication. This approach was based on several tactile sensory characteristics of human skin at different body parts, such as the head and neck, where location coordinates in the three-dimensional (3D) space were clearly mapped in the brain cortex, and gentle stimulations of vibrational touching with varied strengths were received instantly and precisely. For certain applications, such as playing cards or navigating walk paths for blinded people, we demonstrated specifically designed code lists with different patterns of tactile points in varied temporal sequences. By optimizing these codes, we achieved excellent efficiency and accuracy in our test experiments. As this method matched well with the natural habits of tactile sensory, it was easy to learn in a short training period. The results of the present work have offered a silent, efficient and accurate communication solution for visually impaired people or other users.

Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1.

The flathead fish Platycephalus sp.1 is an ecologically and commercially important marine fish in the northwestern Pacific with notable sexual differences in growth and development. Yet the genomic data of this species is lacking. In the present study, whole genome sequencing of two individuals (one male and one female) of Platycephalus sp.1 were conducted to provide fundamental genomic information. The genome sizes were estimated to be 674.96 Mb (male) and 684.15 Mb (female) by using k-mer analyses. The heterozygosity and repeat ratios suggested possible male heterogamety of this species. The draft genome sequences were initially assembled and genome-wide microsatellite motifs were identified. Besides, the complete mitochondrial genome sequences were assembled and the phylogenetic analyses genetically supported the validation of Platycephalus sp.1. The reported genomic data and genetic markers in this study could be useful in future comparative genomics and evolutionary biology studies.

Three-Dimensional Reconstruction Method of Rapeseed Plants in the Whole Growth Period Using RGB-D Camera.

The three-dimensional reconstruction method using RGB-D camera has a good balance in hardware cost and point cloud quality. However, due to the limitation of inherent structure and imaging principle, the acquired point cloud has problems such as a lot of noise and difficult registration. This paper proposes a 3D reconstruction method using Azure Kinect to solve these inherent problems. Shoot color images, depth images and near-infrared images of the target from six perspectives by Azure Kinect sensor with black background. Multiply the binarization result of the 8-bit infrared image with the RGB-D image alignment result provided by Microsoft corporation, which can remove ghosting and most of the background noise. A neighborhood extreme filtering method is proposed to filter out the abrupt points in the depth image, by which the floating noise point and most of the outlier noise will be removed before generating the point cloud, and then using the pass-through filter eliminate rest of the outlier noise. An improved method based on the classic iterative closest point (ICP) algorithm is presented to merge multiple-views point clouds. By continuously reducing both the size of the down-sampling grid and the distance threshold between the corresponding points, the point clouds of each view are continuously registered three times, until get the integral color point cloud. Many experiments on rapeseed plants show that the success rate of cloud registration is 92.5% and the point cloud accuracy obtained by this method is 0.789 mm, the time consuming of a integral scanning is 302 s, and with a good color restoration. Compared with a laser scanner, the proposed method has considerable reconstruction accuracy and a significantly ahead of the reconstruction speed, but the hardware cost is much lower when building a automatic scanning system. This research shows a low-cost, high-precision 3D reconstruction technology, which has the potential to be widely used for non-destructive measurement of rapeseed and other crops phenotype.

Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19).

BACKGROUND: The emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. The current method of detection involves a quantitative polymerase chain reaction (qPCR)-based technique, which identifies the viral nucleic acids when present in sufficient quantity. False-negative results can be achieved and failure to quarantine the infected patient would be a major setback in containing the viral transmission. We aim to describe the time kinetics of various antibodies produced against the 2019 novel coronavirus (SARS-CoV-2) and evaluate the potential of antibody testing to diagnose COVID-19. METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. 208 plasma samples were collected from 82 confirmed and 58 probable cases (qPCR negative but with typical manifestation). The diagnostic value of IgM was evaluated in this cohort. RESULTS: The median duration of IgM and IgA antibody detection was 5 (IQR, 3-6) days, while IgG was detected 14 (IQR, 10-18) days after symptom onset, with a positive rate of 85.4%, 92.7%, and 77.9%, respectively. In confirmed and probable cases, the positive rates of IgM antibodies were 75.6% and 93.1%, respectively. The detection efficiency by IgM ELISA is higher than that of qPCR after 5.5 days of symptom onset. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). CONCLUSIONS: The humoral response to SARS-CoV-2 can aid in the diagnosis of COVID-19, including subclinical cases.

Multifunctional Freestanding Microprobes for Potential Biological Applications.

Deep-level sensors for detecting the local temperatures of inner organs and tissues of an animal are rarely reported. In this paper, we present a method to fabricate multifunctional micro-probes with standard cleanroom procedures, using a piece of stainless-steel foil as the substrate. On each of the as-fabricated micro-probes, arrays of thermocouples made of Pd-Cr thin-film stripes with reliable thermal sensing functions were built, together with Pd electrode openings for detecting electrical signals. The as-fabricated sword-shaped freestanding microprobes with length up to 30 mm showed excellent mechanical strength and elastic properties when they were inserted into the brain and muscle tissues of live rats, as well as suitable electrochemical properties and, therefore, are promising for potential biological applications.

Phenomena of synchronized response in biosystems and the possible mechanism.

Phenomena of synchronized response is common among organs, tissues and cells in biosystems. We have analyzed and discussed three examples of synchronization in biosystems, including the direction-changing movement of paramecia, the prey behavior of flytraps, and the simultaneous discharge of electric eels. These phenomena and discussions support an electrical communication mechanism that in biosystems, the electrical signals are mainly soliton-like electromagnetic pulses, which are generated by the transient transmembrane ionic current through the ion channels and propagate along the dielectric membrane-based softmaterial waveguide network to complete synchronized responses. This transmission model implies that a uniform electrical communication mechanism might have been naturally developed in biosystem.

The efficacy of initial ventilation strategy for adult immunocompromised patients with severe acute hypoxemic respiratory failure: study protocol for a multicentre randomized controlled trial (VENIM).

BACKGROUND: Acute respiratory failure (ARF) is still one of the most severe complications in immunocompromised patients. Our previous systematic review showed noninvasive mechanical ventilation (NIV) reduced mortality, length of hospitalization and ICU stay in AIDS/hematological malignancy patients with relatively less severe ARF, compared to invasive mechanical ventilation (IMV). However, this systematic review was based on 13 observational studies and the quality of evidence was low to moderate. The efficacy of NIV in more severe ARF and in patients with other causes of immunodeficiency is still unclear. We aim to determine the efficacy of the initial ventilation strategy in managing ARF in immunocompromised patients stratified by different disease severity and causes of immunodeficiency, and explore predictors for failure of NIV. METHODS AND ANALYSIS: The VENIM is a multicentre randomized controlled trial (RCT) comparing the effects of NIV compared with IMV in adult immunocompromised patients with severe hypoxemic ARF. Patients who meet the indications for both forms of ventilatory support will be included. Primary outcome will be 30-day all-cause mortality. Secondary outcomes will include in-hospital mortality, length of stay in hospital, improvement of oxygenation, nosocomial infections, seven-day organ failure, adverse events of intervention, et al. Subgroups with different disease severity and causes of immunodeficiency will also be analyzed. DISCUSSION: VENIM is the first randomized controlled trial aiming at assessing the efficacy of initial ventilation strategy in treating moderate and severe acute respiratory failure in immunocompromised patients. The result of this RCT may help doctors with their ventilation decisions. TRIAL REGISTRATION: ClinicalTrials.gov NCT02983851 . Registered 2 September 2016.

Geometric Shape Induced Small Change of Seebeck Coefficient in Bulky Metallic Wires.

In this paper, we report the results of slight changes in the thermopower of long W, Mo, Zn, Cu, brass, and Ti wires, that resulted from changes in the wire's diameter or cross-sectional area. The samples used in the tests had a round shape with a diameter that ranged from tens of micron to 2 mm, which was much larger than the corresponding mean free paths of these materials. Nevertheless, a small change in thermopower, at the order of 1-10 nV/K, was repeatedly observed when the wire diameter was changed, or when the cross-sectional area of the wire was altered by mechanical methods, such as grinding or splitting. The results are consistent with previous observations showing that the thermopower in metallic thin film stripes changes with their width, from 100 µm to as little as 70 nm, implying a universal, geometric-boundary-related size effect of thermopower in metal materials, that occurs at the nanometer scale and continuously decreases all the way to the millimeter scale. This effect could be applied in the manufacturing of high-temperature sensors with simple structures.

Mapping Sensory Spots for Moderate Temperatures on the Back of Hand.

Thermosensation with thermoreceptors plays an important role in maintaining body temperature at an optimal state and avoiding potential damage caused by harmful hot or cold environmental temperatures. In this work, the locations of sensory spots for sensing moderate temperatures of 40-50 °C on the back of the hands of young Chinese people were mapped in a blind-test manner with a thermal probe of 1.0 mm spatial resolution. The number of sensory spots increased along with the testing temperature; however, the surface density of sensory spots was remarkably lower than those reported previously. The locations of the spots were irregularly distributed and subject-dependent. Even for the same subject, the number and location of sensory spots were unbalanced and asymmetric between the left and right hands. The results may offer valuable information for designing artificial electronic skin and wearable devices, as well as for clinical applications.

Real-Time Two-Dimensional Mapping of Relative Local Surface Temperatures with a Thin-Film Sensor Array.

Dynamic mapping of an object's local temperature distribution may offer valuable information for failure analysis, system control and improvement. In this letter we present a computerized measurement system which is equipped with a hybrid, low-noise mechanical-electrical multiplexer for real-time two-dimensional (2D) mapping of surface temperatures. We demonstrate the performance of the system on a device embedded with 32 pieces of built-in Cr-Pt thin-film thermocouples arranged in a 4 × 8 matrix. The system can display a continuous 2D mapping movie of relative temperatures with a time interval around 1 s. This technique may find applications in a variety of practical devices and systems.

Nanoscale opening fabrication on Si (111) surface from SiO2 barrier for vertical growth of III-V nanowire arrays.

We reported here a selectively additive process to fabricate nanoscale openings of an Si (111) surface from an SiO2 barrier layer. Such nanoscale openings are made for the growth of vertical III-V nanowires. The Si (111) surface protected by a patterned SiNx layer was thermally oxidized, which resulted in a selectively added SiO2 barrier layer. After removing the SiNx, nanoscale openings of the Si (111) surface were exposed for the nanowire growth. Arrays with patterned nanoholes of varied diameters from 60 nm to 334 nm have been used for position-controlled catalyst-free growth of vertical InAs nanowire arrays by metal-organic chemical vapor deposition. Correlations between the nanohole diameter and the diameter, length and growth yield of as-fabricated nanowire arrays have been investigated, showing a repeatable stability. This technique offers an alternative approach for the fabrication of novel III-V nanowire devices using vertical array configuration. A lateral thermal oxidation effect led to a smaller size of the Si opening than that of the SiNx protection nanoislands; therefore, the technique also offers a controllable way to produce nanoholes with an ultra-small diameter.

A nano-stripe based sensor for temperature measurement at the submicrometer and nano scales.

Submicrometer dual-stripe temperature sensors made from a single piece of metal thin film (e.g., Pd) are developed. With the narrowest sensor being 900 nm in width, they show sensitivity of 1-2 µV/K for the full range of 10-300 K. The results confirm the size effect in Seebeck coefficient previously observed in microstripe sensors of the same device configuration.

The mechanism of human color vision and potential implanted devices for artificial color vision.

Vision plays a major role in perceiving external stimuli and information in our daily lives. The neural mechanism of color vision is complicated, involving the co-ordinated functions of a variety of cells, such as retinal cells and lateral geniculate nucleus cells, as well as multiple levels of the visual cortex. In this work, we reviewed the history of experimental and theoretical studies on this issue, from the fundamental functions of the individual cells of the visual system to the coding in the transmission of neural signals and sophisticated brain processes at different levels. We discuss various hypotheses, models, and theories related to the color vision mechanism and present some suggestions for developing novel implanted devices that may help restore color vision in visually impaired people or introduce artificial color vision to those who need it.

Opportunity for severe and critical COVID-19 pneumonia treatment with corticosteroids: a retrospective cohort study.

Background: The coronavirus disease 2019 (COVID-19) pandemic has been the most significant infectious disease outbreak worldwide in the past 3 years, with the potential to progress to severe pneumonia and trigger systemic inflammatory response, posing a threat to human health and life. This study aims to explore the use of corticosteroids for COVID-19 and provide recommendations on the timing and dosage of the treatment. Methods: We conducted a retrospective cohort study, enrolling 100 with COVID-19 pneumonia between December 2022 and January 2023. The diagnosis of severe and critical COVID-19 pneumonia patients was according to China's Ninth Edition of the Diagnosis and Treatment Plan for COVID-19 Pneumonia. T test and univariate proportional hazard analysis were employed to investigate the opportunity of corticosteroids therapy in relation to patients' prognosis. Results: Compared to COVID-19 pneumonia patients treated with corticosteroids in the early phase, those who received late-phase corticosteroid therapy had a higher proportion of intensive care unit (ICU) admission (P=0.01), longer hospital stay (P=0.006), lower in-hospital survival rate (P=0.03), and slower recovery (P<0.001). A significant difference was also observed in logistic univariate proportional hazard analysis. Conclusions: The early administration of corticosteroid therapy has been shown to significantly improve the prognosis of COVID-19 pneumonia patients, promoting recovery with significant clinical significance. Our recommendation for the administration of corticosteroid therapy is to be applied on the 6th-9th day of persisting unrelieved symptoms of COVID-19 pneumonia.

A novel predictor of unsustained return of spontaneous circulation in cardiac arrest patients through a combination of capnography and pulse oximetry: a multicenter observational study.

BACKGROUND: Unsustained return of spontaneous circulation (ROSC) is a critical barrier to survival in cardiac arrest patients. This study examined whether end-tidal carbon dioxide (ETCO2) and pulse oximetry photoplethysmogram (POP) parameters can be used to identify unsustained ROSC. METHODS: We conducted a multicenter observational prospective cohort study of consecutive patients with cardiac arrest from 2013 to 2014. Patients' general information, ETCO2, and POP parameters were collected and statistically analyzed. RESULTS: The included 105 ROSC episodes (from 80 cardiac arrest patients) comprised 51 sustained ROSC episodes and 54 unsustained ROSC episodes. The 24-hour survival rate was significantly higher in the sustained ROSC group than in the unsustained ROSC group (29.2% vs. 9.4%, P<0.05). The logistic regression analysis showed that the difference between after and before ROSC in ETCO2 (ΔETCO2) and the difference between after and before ROCS in area under the curve of POP (ΔAUCp) were independently associated with sustained ROSC (odds ratio [OR]=0.931, 95% confidence interval [95% CI] 0.881-0.984, P=0.011 and OR=0.998, 95% CI 0.997-0.999, P<0.001). The area under the receiver operating characteristic curve of ΔETCO2, ΔAUCp, and the combination of both to predict unsustained ROSC were 0.752 (95% CI 0.660-0.844), 0.883 (95% CI 0.818-0.948), and 0.902 (95% CI 0.842-0.962), respectively. CONCLUSION: Patients with unsustained ROSC have a poor prognosis. The combination of ΔETCO2 and ΔAUCp showed significant predictive value for unsustained ROSC.

Chinese Society of Cardiology guidelines on the diagnosis and treatment of adult fulminant myocarditis.

Fulminant myocarditis is an acute diffuse inflammatory disease of myocardium. It is characterized by acute onset, rapid progress and high risk of death. Its pathogenesis involves excessive immune activation of the innate immune system and formation of inflammatory storm. According to China's practical experience, the adoption of the "life support-based comprehensive treatment regimen" (with mechanical circulation support and immunomodulation therapy as the core) can significantly improve the survival rate and long-term prognosis. Special emphasis is placed on very early identification,very early diagnosis,very early prediction and very early treatment.