A structural atlas of death domain fold proteins reveals their versatile roles in biology and function.

Death domain fold (DDF) superfamily proteins are critically important players in pathways of cell death and inflammation. DDFs are often essential scaffolding domains in receptors, adaptors, or effectors of these pathways by mediating homo- and hetero-oligomerization including helical filament assembly. At the downstream ends of these pathways, effector oligomerization by DDFs brings the enzyme domains into proximity for their dimerization and activation.

Refinement and curation of homologous groups facilitated by structure prediction.

Domain classification of protein predictions released in the AlphaFold Database (AFDB) has been a recent focus of the Evolutionary Classification of protein Domains (ECOD). Although a primary focus of our recent work has been the partition and assignment of domains from these predictions, we here show how these diverse predictions can be used to examine the reference domain set more closely. Using results from DPAM, our AlphaFold-specific domain parsing algorithm, we examine hierarchical groupings that share significant levels of homologous links, both between groups that were not previously assessed to be definitively homologous and between groups that were not previously observed to share significant homologous links.

Emergency Admission Plasma D-Dimer and Prothrombin Activity: Novel Predictors for Clinical Outcomes After Thrombectomy in Acute Ischemic Stroke With Large Artery Occlusion.

Background: The coagulation system is intrinsically linked to pathological mechanisms and progression of ischemic stroke. However, the role of preoperative coagulation function in determining the functional outcomes of acute ischemic stroke patients following large artery occlusion (AIS-LVO) has not been extensively evaluated in peer-reviewed literature.

Methods: We utilized logistic regression analyses, complemented by the construction of receiver operating characteristic (ROC) curves, to identify significant predictive factors for poor prognosis following endovascular thrombectomy (EVT).

A new prognostic model based on serum apolipoprotein AI in patients with HBV-ACLF and acutely decompensated liver cirrhosis.

Background/aim: To investigate the prognostic value of circulating apolipoprotein AI (apoAI) levels and develop a new prognostic model in individuals with acute-on-chronic liver failure (ACLF) and acute decompensation (AD) of liver cirrhosis caused by hepatitis B virus (HBV) infection.

Methods: Baseline levels of serum lipids were measured, and data concerning the presence of complications were collected from 561 HBV-ACLF and AD patients. Survival analysis was conducted by log-rank test.

New taxa of butterflies supported by genomic analysis.

Continuing with the genomic analysis of butterflies, we present a taxonomic update. As a result of this work, 3 genera, 6 subgenera, 16 species, and 2 subspecies are described as new. New genera and subgenera are (type species in parenthesis): Grishin, ( W.

Genomic analysis reveals hidden species diversity in Fabricius (Lepidoptera: Riodinidae).

Genomic analysis of [Fabricius], 1807 (Lepidoptera: Riodinidae Grote, 1895) reveals species richness higher than anticipated. As a result, one subgenus, 22 species, and one subspecies are proposed as new (type species or type localities in parenthesis): Grishin, ( Prittwitz, 1865), () Grishin, (Peru: Rio Pachitea, Monte Alegre), () Grishin, (Guyana: Cuyuni-Mazaruni), () Grishin, (Brazil: Santa Catarina), () Grishin, (Panama: Darién), () Grishin, (Ecuador: Santo Domingo), () Grishin, (Peru: Cuzco), () Grishin, (Panama: Chiriquí), () Grishin, (Mexico: Tamaulipas), () Grishin, (Mexico: Nuevo León), () Grishin, (Argentina: Salta), () Grishin, (Peru: Piura), () Grishin, (Bolivia: La Paz), () Grishin, (Mexico: Sonora), () Grishin, (Peru: Madre de Dios), () Grishin, (Bolivia: La Paz), () Grishin, (Mexico: Chiapas), () Grishin, (Panama: Darién), () Grishin, (Panama: Darién), () Grishin, (Panama: Darién), () Grishin, (Panama: Panamá), () Grishin, (Peru: Cuzco), () Grishin, (Brazil: São Paulo), and () Grishin, (Brazil: Paraná). The following five taxa are (not subspecies): () Schaus, 1928, (not () (Linnaeus, 1767)), () Stichel, 1910, (not () Westwood, 1851), () Stichel, 1929, (not () Godman and Salvin, 1886), () R.

Chemo-Mechanical Due-Biomimetic Approach for Ultra-Stable Adsorption Across Multiple Scenarios.

The unique adhesion capabilities of soft-bodied creatures such as leeches and octopuses have provided considerable inspiration for the development of artificial adhesive materials. However, previous studies have either focused on the design of sucker structures or concentrated on the synthesis of adhesive materials, with the combination of these two aspects not yet having been deeply investigated. In this study, inspired from leech's unique adsorption ability, a biomimetic approach is proposed that combined artificial sucker and mucus, to achieve remarkable adhesion stability on rough surfaces using 5 cm diameter silicone suction cups.

Orthogonalized human protease control of secreted signals.

Synthetic circuits that regulate protein secretion in human cells could support cell-based therapies by enabling control over local environments. Although protein-level circuits enable such potential clinical applications, featuring orthogonality and compactness, their non-human origin poses a potential immunogenic risk. In this study, we developed Humanized Drug Induced Regulation of Engineered CyTokines (hDIRECT) as a platform to control cytokine activity exclusively using human-derived proteins.

DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Motivation: Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering nearly the entire protein universe. Segmenting these models into domains and classifying them into an evolutionary hierarchy hold tremendous potential for unraveling essential insights into protein function.

Results: We introduce DPAM-AI, a Domain Parser for AlphaFold Models based on Artificial Intelligence.

ECOD: integrating classifications of protein domains from experimental and predicted structures.

The evolutionary classification of protein domains (ECOD) classifies protein domains using a combination of sequence and structural data (http://prodata.swmed.edu/ecod).

Orthogonalized human protease control of secreted signals.

Synthetic circuits that regulate protein secretion in human cells could support cell-based therapies by enabling control over local environments. While protein-level circuits enable such potential clinical applications, featuring orthogonality and compactness, their non-human origin poses a potential immunogenic risk. Here, we developed Humanized Drug Induced Regulation of Engineered CyTokines (hDIRECT) as a platform to control cytokine activity exclusively using human-derived proteins.

Bionic Design and Adsorption Performance Analysis of Vacuum Suckers.

This study addresses the problem that the traditional method is not effective in improving the adsorption performance of vacuum suckers. From the perspective of bionics, the adsorption performance of bionic suckers based on the excellent adsorption of the abalone abdominal foot was studied. A bionic sucker was designed by extracting the sealing ring structure of the abdominal foot tentacle.

Protein interactions in human pathogens revealed through deep learning.

Identification of bacterial protein-protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors.

Range-wide population genomic structure of the Karner blue butterfly, () .

The Karner blue butterfly, () , is an endangered North American climate change-vulnerable species that has undergone substantial historical habitat loss and population decline. To better understand the species' genetic status and support Karner blue conservation, we sampled 116 individuals from 22 localities across the species' geographical range in Wisconsin (WI), Michigan (MI), Indiana (IN), and New York (NY). Using genomic analysis, we found that these samples were divided into three major geographic groups, NY, WI, and MI-IN, with populations in WI and MI-IN each further divided into three subgroups.

Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models.

Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool.

[Effects of Straw and Fertilizer Managements on Nitrogen Loss in Rice Cultivation in Taihu Lake Basin].

Nitrogen loss from rice systems is an important source of agricultural non-point source pollution. Many studies revolve around reducing the rate of nitrogen fertilizer application. However, studies examining the characteristics of nitrogen loss in multiple loss paths （runoff, leaching, and lateral seepage） under different straw and fertilizer managements are lacking.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands.

Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs).

Design of Bionic Foot Inspired by the Anti-Slip Cushioning Mechanism of Yak Feet.

In recent years, legged robots have been more and more widely used on non-structured terrain, and their foot structure has an important impact on the robot's motion performance and stability. The structural characteristics of the yak foot sole with a high outer edge and low middle, which has excellent soil fixation ability and is an excellent bionic prototype, can improve the friction between the foot and the ground. At the same time, the foot hooves can effectively alleviate the larger impact load when contacting with the ground, which is an excellent anti-slip buffer mechanism.

Computational analysis of propeptide-containing proteins and prediction of their post-cleavage conformation changes.

A propeptide is removed from a precursor protein to generate its active or mature form. Propeptides play essential roles in protein folding, transportation, and activation and are present in about 2.3% of reviewed proteins in the UniProt database.

Experimental Study on the Adhesion of Abalone to Surfaces with Different Morphologies.

To date, research on abalone adhesion has primarily analyzed the organism's adhesion to smooth surfaces, with few studies on adhesion to non-smooth surfaces. The present study examined the surface morphology of the abalone's abdominal foot, followed by measuring the adhesive force of the abalone on a smooth force measuring plate and five force measuring plates with different surface morphologies. Next, the adhesion mechanism of the abdominal foot was analyzed.

Essential and virulence-related protein interactions of pathogens revealed through deep learning.

Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors.

Intraventricular haemorrhage treated by extra ventricular drainage with catheter mistakenly penetrating the cisterna ambiens: A case report.

Intraventricular haemorrhage (IVH) is a severe and acute type of stroke with a complex pathophysiology and is a therapeutic challenge. This case report described a man in his early 50's diagnosed with IVH by computed tomography (CT). Although bilateral extraventricular drainage (EVD) was undertaken, a postoperative CT scan showed that while the left catheter was correctly positioned, the right catheter had been wrongly inserted into the cisterna ambiens.

'An eye for an eye' therapeutic strategy for cavernous sinus dural arteriovenous fistula: a single-center experience.

Background: In cavernous sinus dural arteriovenous fistulas (CS-DAVF), ophthalmological symptoms are usually the main clinical presentation, caused by abnormal drainage of the superior ophthalmic vein (SOV). Early opacification of the SOV during cerebral angiography inevitably signifies the fistula's shunt point at the confluence of the SOV and CS. We aimed to leverage this anatomical feature to achieve precise embolization, thereby enhancing the embolization success rate and preventing CS-related symptoms and complications resulting from overpacking.