Mildly Constrained Evaluation Policy for Offline Reinforcement Learning

Offline reinforcement learning (RL) methodologies enforce constraints on the policy to adhere closely to the behavior policy, thereby stabilizing value learning and mitigating the selection of out-of-distribution (OOD) actions during test time. Conventional approaches apply identical constraints for both value learning and test time inference. However, our findings indicate that the constraints suitable for value estimation may in fact be excessively restrictive for action selection during test time. To address this issue, we propose a Mildly Constrained Evaluation Policy (MCEP) for test time inference with a more constrained target policy for value estimation. Since the target policy has been adopted in various prior approaches, MCEP can be seamlessly integrated with them as a plug-in. We instantiate MCEP based on TD3-BC [Fujimoto and Gu, 2021] and AWAC [Nair et al., 2020] algorithms. The empirical results on MuJoCo locomotion tasks show that the MCEP significantly outperforms the target policy and achieves competitive results to state-of-the-art offline RL methods. The codes are open-sourced at https://github.com/egg-west/MCEP.git

Treatment Effects of the Second-Generation Tyrosine Kinase Inhibitor Dasatinib on Autoimmune Arthritis

Rheumatoid arthritis (RA) is a multifactorial autoimmune disease that primarily manifests as persistent synovitis and progressive joint destruction. Imatinib exhibited a therapeutic effect in murine collagen-induced arthritis (CIA) via selective inhibition tyrosine kinases. The second-generation tyrosine kinase inhibitor dasatinib exhibits more durable hematological and cytogenetic effects and more potency compared to imatinib. However, the effect of dasatinib on CIA is poorly understood. The present study investigated the treatment effect of dasatinib on autoimmune arthritis. We demonstrated that dasatinib alleviated arthritis symptoms and histopathological destruction in CIA mice. Dasatinib treatment inhibited the production of proinflammatory cytokines including IL-1β, TNF-α, and IL-6, and promoted the production of the anti-inflammatory cytokine IL-10. Dasatinib treatment also suppressed the expression of anti-mouse CII antibodies including total IgG, IgG1, IgG2, and IgG2b, in CIA mice. We further demonstrated that dasatinib inhibited the migration and proliferation of fibroblast-like synoviocytes (FLS) from RA patients and promoted FLS apoptosis. The mRNA expression of MMP13, VEGF, FGF, and DKK1 was down-regulated in FLS treated with dasatinib. Our findings suggest that dasatinib exhibited treatment effects on CIA mice and that FLS are an important target cell of dasatinib treatment in autoimmune arthritis

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Advancing DNA Language Models through Motif-Oriented Pre-Training with MoDNA

Acquiring meaningful representations of gene expression is essential for the accurate prediction of downstream regulatory tasks, such as identifying promoters and transcription factor binding sites. However, the current dependency on supervised learning, constrained by the limited availability of labeled genomic data, impedes the ability to develop robust predictive models with broad generalization capabilities. In response, recent advancements have pivoted towards the application of self-supervised training for DNA sequence modeling, enabling the adaptation of pre-trained genomic representations to a variety of downstream tasks. Departing from the straightforward application of masked language learning techniques to DNA sequences, approaches such as MoDNA enrich genome language modeling with prior biological knowledge. In this study, we advance DNA language models by utilizing the Motif-oriented DNA (MoDNA) pre-training framework, which is established for self-supervised learning at the pre-training stage and is flexible enough for application across different downstream tasks. MoDNA distinguishes itself by efficiently learning semantic-level genomic representations from an extensive corpus of unlabeled genome data, offering a significant improvement in computational efficiency over previous approaches. The framework is pre-trained on a comprehensive human genome dataset and fine-tuned for targeted downstream tasks. Our enhanced analysis and evaluation in promoter prediction and transcription factor binding site prediction have further validated MoDNA’s exceptional capabilities, emphasizing its contribution to advancements in genomic predictive modeling

Solute cluster evolution during deformation and high strain hardening capability in naturally aged Al–Zn–Mg alloy

International audienc

Rational Metabolic Engineering Combined with Biosensor-Mediated Adaptive Laboratory Evolution for <span style="font-variant: small-caps">l</span>-Cysteine Overproduction from Glycerol in <i>Escherichia coli</i>

l-Cysteine is an important sulfur-containing amino acid with numerous applications in the pharmaceutical and cosmetic industries. The microbial production of l-cysteine has received substantial attention, and the supply of the precursor l-serine is important in l-cysteine biosynthesis. In this study, to achieve l-cysteine overproduction, we first increased l-serine production by deleting genes involved in the pathway of l-serine degradation to glycine (serine hydroxymethyl transferase, SHMT, encoded by glyA genes) in strain 4W (with l-serine titer of 1.1 g/L), thus resulting in strain 4WG with l-serine titer of 2.01 g/L. Second, the serine-biosensor based on the transcriptional regulator NCgl0581 of C. glutamicum was constructed in E. coli, and the validity and sensitivity of the biosensor were demonstrated in E. coli. Then 4WG was further evolved through adaptive laboratory evolution (ALE) combined with serine-biosensor, thus yielding the strain 4WGX with 4.13 g/L l-serine production. Moreover, the whole genome of the evolved strain 4WGX was sequenced, and ten non-synonymous mutations were found in the genome of strain 4WGX compared with strain 4W. Finally, 4WGX was used as the starting strain, and deletion of the l-cysteine desulfhydrases (encoded by tnaA), overexpression of serine acetyltransferase (encoded by cysE) and the key enzyme of transport pathway (encoded by ydeD) were performed in strain 4WGX. The recombinant strain 4WGX-∆tnaA-cysE-ydeD can produce 313.4 mg/L of l-cysteine using glycerol as the carbon source. This work provides an efficient method for the biosynthesis of value-added commodity products associated with glycerol conversion

Highly stable coherent nanoprecipitates via diffusion-dominated solute uptake and interstitial ordering

Lightweight design strategies and advanced energy applications call for highstrength Al alloys that can serve at 300-400 °C temperature range. However, the present commercial high-strength Al alloys are limited to low-temperature applications < ~150 °C, because the antagonism between high thermal stability (preferentially associated with slowdiffusing solutes) and large volume fraction (mostly derived from high-solubility and fastdiffusing solutes) innate to coherent nanoprecipitates remains unsolved. Here we demonstrate an interstitial solute stabilizing strategy to produce highly-stable coherent nanoprecipitates (termed V phase) in Sc-added Al-Cu-Mg-Ag alloys that have a strong coarsening-resistance up to ~ 400 ºC and simultaneously a volume fraction of ~ 1.8 vol.%. The assembling of slowdiffusing Sc and fast-diffusing Cu atoms into coherent V is triggered by a coherent ledgeaided in-situ phase transformation from early-formed Cu-rich nanoprecipitates, with diffusion-dominated Sc uptake and self-organization into interstitially ordering. Stable V nanoprecipitates, with an inherited high density, enable the Al alloys to reach an unprecedent creep resistance as well as exceptional tensile strength (~ 100 MPa) at 400 ºC. We envisage that the ledge-mediated interaction between slow-and fast-diffusing atoms may pave the way for the stabilization of coherent nanoprecipitates toward advanced 400 ºC-level light alloys, which could be readily adapted to large-scale industrial production

CEPC Conceptual Design Report: Volume 2 - Physics & Detector

The Circular Electron Positron Collider (CEPC) is a large international scientific facility proposed by the Chinese particle physics community to explore the Higgs boson and provide critical tests of the underlying fundamental physics principles of the Standard Model that might reveal new physics. The CEPC, to be hosted in China in a circular underground tunnel of approximately 100 km in circumference, is designed to operate as a Higgs factory producing electron-positron collisions with a center-of-mass energy of 240 GeV. The collider will also operate at around 91.2 GeV, as a Z factory, and at the WW production threshold (around 160 GeV). The CEPC will produce close to one trillion Z bosons, 100 million W bosons and over one million Higgs bosons. The vast amount of bottom quarks, charm quarks and tau-leptons produced in the decays of the Z bosons also makes the CEPC an effective B-factory and tau-charm factory. The CEPC will have two interaction points where two large detectors will be located. This document is the second volume of the CEPC Conceptual Design Report (CDR). It presents the physics case for the CEPC, describes conceptual designs of possible detectors and their technological options, highlights the expected detector and physics performance, and discusses future plans for detector R&D and physics investigations. The final CEPC detectors will be proposed and built by international collaborations but they are likely to be composed of the detector technologies included in the conceptual designs described in this document. A separate volume, Volume I, recently released, describes the design of the CEPC accelerator complex, its associated civil engineering, and strategic alternative scenarios

CEPC Conceptual Design Report: Volume 2 - Physics & Detector

The Circular Electron Positron Collider (CEPC) is a large international scientific facility proposed by the Chinese particle physics community to explore the Higgs boson and provide critical tests of the underlying fundamental physics principles of the Standard Model that might reveal new physics. The CEPC, to be hosted in China in a circular underground tunnel of approximately 100 km in circumference, is designed to operate as a Higgs factory producing electron-positron collisions with a center-of-mass energy of 240 GeV. The collider will also operate at around 91.2 GeV, as a Z factory, and at the WW production threshold (around 160 GeV). The CEPC will produce close to one trillion Z bosons, 100 million W bosons and over one million Higgs bosons. The vast amount of bottom quarks, charm quarks and tau-leptons produced in the decays of the Z bosons also makes the CEPC an effective B-factory and tau-charm factory. The CEPC will have two interaction points where two large detectors will be located. This document is the second volume of the CEPC Conceptual Design Report (CDR). It presents the physics case for the CEPC, describes conceptual designs of possible detectors and their technological options, highlights the expected detector and physics performance, and discusses future plans for detector R&D and physics investigations. The final CEPC detectors will be proposed and built by international collaborations but they are likely to be composed of the detector technologies included in the conceptual designs described in this document. A separate volume, Volume I, recently released, describes the design of the CEPC accelerator complex, its associated civil engineering, and strategic alternative scenarios