Improvement of peptide identification with considering the abundance of mRNA and peptide

Scripts used for data analysis in this study. (DOCX 35 kb

From Summary to Action: Enhancing Large Language Models for Complex Tasks with Open World APIs

The distinction between humans and animals lies in the unique ability of humans to use and create tools. Tools empower humans to overcome physiological limitations, fostering the creation of magnificent civilizations. Similarly, enabling foundational models like Large Language Models (LLMs) with the capacity to learn external tool usage may serve as a pivotal step toward realizing artificial general intelligence. Previous studies in this field have predominantly pursued two distinct approaches to augment the tool invocation capabilities of LLMs. The first approach emphasizes the construction of relevant datasets for model fine-tuning. The second approach, in contrast, aims to fully exploit the inherent reasoning abilities of LLMs through in-context learning strategies. In this work, we introduce a novel tool invocation pipeline designed to control massive real-world APIs. This pipeline mirrors the human task-solving process, addressing complicated real-life user queries. At each step, we guide LLMs to summarize the achieved results and determine the next course of action. We term this pipeline `from Summary to action', Sum2Act for short. Empirical evaluations of our Sum2Act pipeline on the ToolBench benchmark show significant performance improvements, outperforming established methods like ReAct and DFSDT. This highlights Sum2Act's effectiveness in enhancing LLMs for complex real-world tasks

Endothelial Cell-Specific Molecule 2 (Ecsm2) Localizes To Cell-Cell Junctions And Modulates Bfgf-Directed Cell Migration Via The Erk-Fak Pathway

Background: Despite its first discovery by in silico cloning of novel endothelial cell-specific genes a decade ago, the biological functions of endothelial cell-specific molecule 2 (ECSM2) have only recently begun to be understood. Limited data suggest its involvement in cell migration and apoptosis. However, the underlying signaling mechanisms and novel functions of ECSM2 remain to be explored. Methodology/Principal Findings: A rabbit anti-ECSM2 monoclonal antibody (RabMAb) was generated and used to characterize the endogenous ECSM2 protein. Immunoblotting, immunoprecipitation, deglycosylation, immunostaining and confocal microscopy validated that endogenous ECSM2 is a plasma membrane glycoprotein preferentially expressed in vascular endothelial cells (ECs). Expression patterns of heterologously expressed and endogenous ECSM2 identified that ECSM2 was particularly concentrated at cell-cell contacts. Cell aggregation and transwell assays showed that ECSM2 promoted cell-cell adhesion and attenuated basic fibroblast growth factor (bFGF)-driven EC migration. Gain or loss of function assays by overexpression or knockdown of ECSM2 in ECs demonstrated that ECSM2 modulated bFGF-directed EC motility via the FGF receptor (FGFR)-extracellular regulated kinase (ERK)-focal adhesion kinase (FAK) pathway. The counterbalance between FAK tyrosine phosphorylation (activation) and ERK-dependent serine phosphorylation of FAK was critically involved. A model of how ECSM2 signals to impact bFGF/FGFR-driven EC migration was proposed. Conclusions/Significance: ECSM2 is likely a novel EC junctional protein. It can promote cell-cell adhesion and inhibit bFGF-mediated cell migration. Mechanistically, ECSM2 attenuates EC motility through the FGFR-ERK-FAK pathway. The findings suggest that ECSM2 could be a key player in coordinating receptor tyrosine kinase (RTK)-, integrin-, and EC junctional component-mediated signaling and may have important implications in disorders related to endothelial dysfunction and impaired EC junction signaling. © 2011 Shi et al

Spectroscopic Evidence for Interfacial Charge Separation and Recombination in Graphene-MoS2 Vertical Heterostructures

Vertical van der Waals (vdW) heterostructures consisting of graphene (Gr) and transition metal dichalcogenides (TMDs) have created a fascinating platform for exploring optical and electronic properties in the two-dimensional limit. Previous study has revealed the ultrafast formation of interfacial excitons and the exciton dynamics in the Gr/MoS2 heterostructure. However, a fully understanding of interfacial charge separation and the subsequent dynamics in graphene-based heterostructures remains elusive. Here, we investigate the carrier dynamics of Gr-MoS2 (including Gr/MoS2 and MoS2/Gr stacking sequences) heterostructures under different photoexcitation energies and stacking sequences by comprehensive ultrafast means, including time-resolved terahertz spectroscopy (TRTS), terahertz emission spectroscopy (TES) and transient absorption spectroscopy (TAS). We demonstrate that the Gr/MoS2 heterostructure generates hot electron injection from graphene into the MoS2 layer with photoexcitation of sub-A-exciton of MoS2, while the interfacial charge separation in the MoS2/Gr could be partially blocked by the electric field of substrate. Charge transfer (CT) occurs in same directions for the Gr-MoS2 heterostructures with opposite stacking order, resulting in the opposite orientations of the interfacial photocurrent, as directly demonstrated by the terahertz (THz) emission. Moreover, we demonstrate that the recombination time of interfacial charges after CT is on a timescale of 18 ps to 1 ns, depending on the density of defect states in MoS2 layer. This work provides a comprehensive and unambiguous picture of the interfacial charge dynamics of graphene-based heterostructures, which is essential for developing Gr/TMDs based optoelectronic devices.Comment: 23 pages, 5 Figure

Three‐channel electrical impedance spectroscopy for field‐scale root phenotyping

AbstractElectrical impedance spectroscopy has long been considered a promising technique for noninvasive, in‐situ root investigation because of its sensitivity to anatomy and physiology. However, the complexity of the root system and its coupling with stem and soil have hindered the signal interpretation and methodological upscaling to field applications. This study addresses these key issues by introducing three‐channel acquisitions and their interpretation through Cole–Cole fitting. This solution could successfully decouple the impedance response of stem, roots, and soil, as well as provide convenient parametrization and comparison of their impedance signals. The methodological solution was tested on 80 wheat (Triticum aestivum L.) and 10 pecan [Carya illinoensis (Wangenh.) K. Koch] plants, the first extensive and field investigation. The investigation provided evidence of (a) proximal current leakage in herbaceous root systems, extending recent laboratory results and previous indirect field studies. (b) Major role of the plant stem, which has been a substantial concern raised in numerous studies. (c) Minor contribution from the soil, addressing the doubts on the comparability of results obtained in different soil conditions. All together, these evidences lead to indirect correlations between impedance signals and root traits. The explored solution is expected to support the adoption of the impedance spectroscopy, in line with the diffusion of multichannel impedance meters and growing interest in root physiology and phenotyping

Seismic Performance and Ice-Induced Vibration Control of Offshore Platform Structures Based on the ISO-PFD-SMA Brace System

Pall-typed frictional damper (PFD) has higher capacity of energy dissipation, whereas shape memory alloy (SMA) has excellent superelastic performance. Therefore, combining PFD and SMA together as a brace system has a great prospect in vibration control of structures. This paper investigates the performance of offshore platform with three structural configurations including the SMA brace system, the ISO-SMA (where ISO stands for isolation) brace system, and the ISO-PFD-SMA brace system, which are subjected to seismic and ice-induced excitations. In this study, PFD-SMA brace system is installed on the isolation layer of jacket platform, which is under earthquake excitations and ice loading. Then, the reduction of vibration is evaluated by using ANSYS program. The results show that the PFD-SMA brace system is useful in reducing the seismic response and ice-induced response of offshore platform structures; meanwhile, it also demonstrates excellent energy dissipation and hysteretic behavior