Complex systems

T lymphocytes are indispensable for the host systems of defense against pathogens, tumors, and environmental threats. The therapeutic potential of harnessing the cytotoxic properties of T lymphocytes for antigen-specific cell elimination is both evident and efficacious. Genetically engineered T-cells, such as those employed in CAR-T and TCR-T cell therapies, have demonstrated significant clinical benefits in treating cancer and autoimmune disorders. However, the current landscape of T-cell genetic engineering is dominated by strategies that necessitate in vitro T-cell isolation and modification, which introduce complexity and prolong the development timeline of T-cell based immunotherapies...

Clinical diagnostics of infectious diseases via nucleic acid amplification tests (NAATs) depend on a separate step of isolation of nucleic acids from cells/viruses embedded in complex biological matrices. The most recent example has been reverse transcription polymerase chain reaction (RT-PCR) for amplification and detection of SARS-CoV-2 RNA for COVID-19 diagnostics. Kits for RNA extraction and purification are commercially available; however, their integration with amplification systems is generally lacking, resulting in two separate steps, i...

Self-powered microfluidics presents a revolutionary approach to address the challenges of healthcare in decentralized and point-of-care settings where limited access to resources and infrastructure prevails or rapid clinical decision-making is critical. These microfluidic systems exploit physical and chemical phenomena, such as capillary forces and surface tension, to manipulate tiny volumes of fluids without the need for external power sources, making them cost-effective and highly portable. Recent technological advancements have demonstrated the ability to preprogram complex multistep liquid operations within the microfluidic circuit of these standalone systems, which enabled the integration of sensitive detection and readout principles...

PURPOSE: Preoperative imaging plays a pivotal role in sinus surgery where CTs offer patient-specific insights of complex anatomy, enabling real-time intraoperative navigation to complement endoscopy imaging. However, surgery elicits anatomical changes not represented in the preoperative model, generating an inaccurate basis for navigation during surgery progression. METHODS: We propose a first vision-based approach to update the preoperative 3D anatomical model leveraging intraoperative endoscopic video for navigated sinus surgery where relative camera poses are known...

Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression...

The recombinant human proteoglycan aggrecan-G1 domain (rhG1)-induced arthritis (GIA) mouse model is a complex model of rheumatoid arthritis (RA). In GIA, autoimmune arthritis is induced by repeated intraperitoneal immunization of genetically susceptible BALB/c mice with the rhG1 antigen emulsified in the adjuvant dimethyldioctadecylammonium (DDA). This article describes the steps for producing and purifying the rhG1 antigen, the immunization protocol, methods for following the clinical picture of arthritis, and the evaluation of relevant laboratory parameters...

ABSTRACT An alternative transcription start site (ATSS) is a major driving force for increasing the complexity of transcripts in human tissues. As a transcriptional regulatory mechanism, ATSS has biological significance. Many studies have confirmed that ATSS plays an important role in diseases and cell development and differentiation. However, exploration of its dynamic mechanisms remains insufficient. Identifying ATSS change points during cell differentiation is critical for elucidating potential dynamic mechanisms...

The shape of flexible endoscopic surgical robot should be obtained to increase control accuracy and prevent unwanted tissue damage. To estimate the shape of flexible manipulator, space efficiency, cost-effectiveness, system complexity, and ease of calibration should be considered to integrate sensors into the manipulator. In this article, we propose a real-time method to estimate the shape of a hyper-redundant manipulator having embedded coiled fiber sensors. The main advantage of this method is guaranteeing shape recognition even when the manipulator is subjected to an external load...

Molecular Dynamics (MD) simulations are essential in analyzing the physical movement of molecules, with GROMACS being a widely recognized open-source package for this purpose. However, conducting analyses individually in GROMACS can take excessive time and effort. Addressing this challenge, we introduce ASGARD, an innovative workflow designed to streamline and automate the analysis of MD simulation of protein or protein-ligand complex. Unlike the traditional, manual approach, ASGARD enables researchers to generate comprehensive analyses with a single command line, significantly accelerating the research process and avoiding the laborious task of manual report generation...

UNLABELLED: A dysfunction of human host genes and proteins in coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key factor impacting clinical symptoms and outcomes. Yet, a detailed understanding of human host immune responses is still incomplete. Here, we applied RNA sequencing to 94 samples of COVID-19 patients with and without hematological tumors as well as COVID-19 uninfected non-tumor individuals to obtain a comprehensive transcriptome landscape of both hematological tumor patients and non-tumor individuals...

Neisseria meningitidis serogroup B (NmB) strains have diverse antigens, necessitating methods for predicting meningococcal serogroup B (MenB) vaccine strain coverage. The genetic Meningococcal Antigen Typing System (gMATS), a correlate of MATS estimates, predicts strain coverage by the 4-component MenB (4CMenB) vaccine in cultivable and non-cultivable NmB isolates. In Taiwan, 134 invasive, disease-causing NmB isolates were collected in 2003-2020 (23.1%, 4.5%, 5.2%, 29.8%, and 37.3% from individuals aged ≤11 months, 12-23 months, 2-4 years, 5-29 years, and ≥30 years, respectively)...

Understanding wear, a critical factor impacting the reliability of mechanical systems, is vital for nano-, meso-, and macroscale applications. Due to the complex nature of nanoscale wear, the behavior of nanomaterials such as two-dimensional materials under cyclic wear and their surface damage mechanism is yet unexplored. In this study, we used atomic force microscopy coupled with molecular dynamic simulations to statistically examine the cyclic wear behavior of monolayer graphene, MoS2 , and WSe2 . We show that graphene displays exceptional durability and lasts over 3000 cycles at 85% of the applied critical normal load before failure, while MoS2 and WSe2 last only 500 cycles on average...

BACKGROUND: Robotic ventral hernia repair has been increasing globally, with comparable outcomes to laparoscopic repair and lower rates of conversion to open surgery. Robotic surgery is increasing in popularity, and there is a number of new robotic systems entering the marketing. We report the first case of a Roboic eTEP using the Versius robotic system in a patient with an incisional hernia. METHODS: Surgery was performed using the Versius system from CMR surgical which consists of bedside units for each instrument and a console...

Metallo-supramolecular polymer networks (MSPNs) are fabricated from the crosslinking of polymers by discrete supramolecular coordination complexes. Due to the availability of various coordination complexes, e.g., 2D macrocycles and 3D nanocages, the MSPNs have been recently developed with broadly tuned visco-elasticity and enriched functions inherited from the coordination complexes. The coordination complexes possess enriched topologies and unique structural relaxation dynamics, rendering them the capability to break the traditional tradeoffs of polymer systems for the design of materials with enhanced mechanical performance...

Ion hydration plays a crucial role in numerous fundamental processes. Various spectroscopic methods are employed to investigate the slowing down of hydration bond dynamics in the proximity of both anions and cations. To date, most of these studies have primarily focused on the properties of binary systems. However, in comparison to ion-water binary systems, ternary systems that involve ions, water, and organic matter are more prevalent in nature and provide more realistic insights into biological processes...

Chemical phenomena involving near-degenerate electronic states, such as conical intersections or avoided crossing, can be properly described using quasi-degenerate perturbation theory. This study proposed a highly scalable quasi-degenerate second-order N-electron valence state perturbation theory (QD-NEVPT2) using the local pair-natural orbital (PNO) method. Our recent study showed an efficient implementation of the PNO-based state-specific NEVPT2 method using orthonormal localized virtual molecular orbitals (LVMOs) as an intermediate local basis...

Diabetic foot ulcers (DFU) are chronic, refractory wounds caused by diabetic neuropathy, vascular disease, and bacterial infection, and have become one of the most serious and persistent complications of diabetes mellitus because of their high incidence and difficulty in healing. Its malignancy results from a complex microenvironment that includes a series of unfriendly physiological states secondary to hyperglycemia, such as recurrent infections, excessive oxidative stress, persistent inflammation, and ischemia and hypoxia...

BACKGROUND: Cardiomyocyte differentiation involves a stepwise clearance of repressors and fate-restricting regulators through the modulation of BMP (bone morphogenic protein)/Wnt-signaling pathways. However, the mechanisms and how regulatory roadblocks are removed with specific developmental signaling pathways remain unclear. METHODS: We conducted a genome-wide CRISPR screen to uncover essential regulators of cardiomyocyte specification in human embryonic stem cells using a myosin heavy chain 6 ( MYH6 )-GFP (green fluorescence protein) reporter system...

'Biological motion' refers to the distinctive kinematics observed in many living organisms, where visually-observable points on the animal move at fixed distances from each other. Across the animal kingdom, many species have developed specialized visual circuitry to recognize such biological motion and to discriminate it from other patterns. Recently, this ability has been observed in the distributed visual system of jumping spiders. These eight-eyed animals usesix eyes to perceive motion, while the remaining two (the principal anterior-medial eyes) are shifted across the visual scene to further inspect detected objects...

Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by persistent activation of immune cells and overproduction of autoantibodies. The accumulation of senescent T and B cells has been observed in SLE and other immune-mediated diseases. However, the exact mechanistic pathways contributing to this process in SLE remain incompletely understood. In this study, we found that in SLE patients: (1) the frequency of CD4+ CD57+ senescent T cells was significantly elevated and positively correlated with disease activity; (2) the expression levels of B-lymphoma-2 (BCL-2) family and interferon-induced genes (ISGs) were significantly upregulated; and (3) in vitro, the cytokine IL-15 stimulation increased the frequency of senescent CD4+ T cells and upregulated the expression of BCL-2 family and ISGs...