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Abstract Factor-dependent termination uses molecular motors to remodel transcription machineries, but the associated mechanisms, especially in eukaryotes, are poorly understood. Here we use single-molecule fluorescence assays to characterize in real time the composition and the catalytic states of Saccharomyces cerevisiae transcription termination complexes remodeled by Sen1 helicase. We confirm that Sen1 takes the RNA transcript as its substrate and translocates along it by hydrolyzing multiple ATPs to form an intermediate with a stalled RNA polymerase II (Pol II) transcription elongation complex (TEC). We show that this intermediate dissociates upon hydrolysis of a single ATP leading to dissociation of Sen1 and RNA, after which Sen1 remains bound to the RNA. We find that Pol II ends up in a variety of states: dissociating from the DNA substrate, which is facilitated by transcription bubble rewinding, being retained to the DNA substrate, or diffusing along the DNA substrate. Our results provide a complete quantitative framework for understanding the mechanism of Sen1-dependent transcription termination in eukaryotes.

Abstract Homotypic membrane fusion of the endoplasmic reticulum (ER) is mediated by dynamin-like GTPase atlastin (ATL). This fundamental process relies on GTP-dependent domain rearrangements in the N-terminal region of ATL (ATLcyto), including the GTPase domain and three-helix bundle (3HB). However, its conformational dynamics during the GTPase cycle remain elusive. Here, we combine single-molecule FRET imaging and molecular dynamics simulations to address this conundrum. Different from the prevailing model, ATLcyto can form a loose crossover dimer upon GTP binding, which is tightened by GTP hydrolysis for membrane fusion. Furthermore, the α-helical motif between the 3HB and transmembrane domain, which is embedded in the surface of the lipid bilayer and self-associates in the crossover dimer, is required for ATL function. To recycle the proteins, Pi release, which disassembles the dimer, activates frequent relative movements between the GTPase domain and 3HB, and subsequent GDP dissociation alters the conformational preference of the ATLcyto monomer for entering the next reaction cycle. Finally, we found that two disease-causing mutations affect human ATL1 activity by destabilizing GTP binding-induced loose crossover dimer formation and the membrane-embedded helix, respectively. These results provide insights into ATL-mediated homotypic membrane fusion and the pathological mechanisms of related disease.

Abstract Modulation of protein function through allosteric regulation is central in biology, but biomacromolecular systems involving multiple subunits and ligands may exhibit complex regulatory mechanisms at different levels, which remain poorly understood. Here, we discover an aldo-keto reductase termed AKRtyl and present its three-level regulatory mechanism. Specifically, by combining steady-state and transient kinetics, X-ray crystallography and molecular dynamics simulation, we demonstrate that AKRtyl exhibits a positive synergy mediated by an unusual Monod-Wyman-Changeux (MWC) paradigm of allosteric regulation at low concentrations of the cofactor NADPH, but an inhibitory effect at high concentrations is observed. While the substrate tylosin binds at a remote allosteric site with positive cooperativity. We further reveal that these regulatory mechanisms are conserved in AKR12D subfamily, and that substrate cooperativity is common in AKRs across three kingdoms of life. This work provides an intriguing example for understanding complex allosteric regulatory networks.

In deep rock engineering, natural cracks in rock mass subjected to thermo-hydro-mechanical-chemical (THMC) loads have tendency to initiate and propagate, and result in potential safety hazards. Current literature on cracking behaviors and mechanism of pre-cracked rock under multi-field loads is focused on single (M), two (TM, HM) or three fields (THM, HMC), less on THMC fields. In this study, a series of self-designed triaxial compressive tests were performed to study different THMC fields influencing on mechanical behaviors and failure patterns of pre-cracked red sandstone specimens. A new THMC fracture criterion, recently proposed by our group team, is used to further analyze the crack initiation mechanism of red sandstone under THMC loads. Research results suggest that the stress-strain curve is greatly influenced by the temperature, confining pressure and acidity and alkalinity of chemical solution, but relatively less by the hydraulic pressure. As the temperature and hydraulic pressure increase, the confining pressure decreases, and the acidity or the alkalinity of chemical solutions becomes strong, both the elastic modulus, crack initiation stress and peak strength of specimen are decreased, and the failure pattern is changed from shear failure to tensile failure. The crack initiation stress and peak strength usually have the largest, middle, smallest values in the shear, tension-shear and tensile failures, respectively, while the peak strain has largest value in the mixed tensile-shear failure. The acid solution has greater weakening effect than the alkaline solution with the same concentration. Theoretical results indicate that the temperature and chemical fields influencing on crack initiation is mainly attributable to its weakening of rock fracture toughness, while seepage and stress fields on crack initiation to its change of the stress state at crack-tips. The THMC mechanism of crack initiation can be well revealed by the new THMC fracture criterion.

Objective This study explored the dynamic functional connective (DFC) alterations in patients with rheumatoid arthritis (RA) and investigated the correlation between the neuropsychiatric symptoms, peripheral inflammation and DFC alterations.Method Using resting-state functional MRI, we investigated the DFC based on spatial independent component analysis and sliding window method for 30 patients with RA and 30 healthy controls (HCs). The Spearman correlation was calculated between aberrant DFC alterations, Montreal Cognitive Assessment (MoCA), Hospital Anxiety and Depression Scale (HAD), C reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Diagnostic efficacy of indicators was assessed using receiver operating characteristic analysis (ROC).Results Three dynamic functional states were identified. Compared with HC, patients with RA showed reduced FC variabilities between sensorimotor network (SMN) and insula, SMN and orbitofrontal cortex, which were the crucial regions of sensory processing network. The above FC variabilities were correlated with the MoCA, HAD, CRP and ESR in patients with RA. Additionally, the CRP and ESR were negatively correlated to MoCA and positively related to HAD in patients with RA. The ROC analysis results showed that MoCA, HAD and FC variabilities of the sensory processing network could distinguish patients with RA from HC and also identify patients with RA with high ESR.Conclusion Our findings demonstrated that abnormal DFC patterns in sensory processing networks in patients with RA were closely associated with peripheral inflammation and neuropsychiatric symptoms. This indicates that the dynamic temporal characteristics of the brain functional network may be potential neuroimaging biomarkers for revealing the pathological mechanism of RA.

Abstract Objective To identify the potential diagnostic biomarkers of rheumatoid arthritis (RA) and assess the relation between visuospatial dysfunction and disease activity in RA patients using mental rotation task (MRT)-based functional magnetic resonance imaging (fMRI). Methods A total of 27 RA patients (11 in remission, 16 in active) and 27 well-matched controls were enrolled. The visuospatial function of the subjects was measured by MRT. Brain activity data were collected using blood oxygen level dependent fMRI technique under MRT. Disease activity score 28 (DAS28) was used to evaluate the disease severity of RA patients. An analysis of the correlations between abnormal visuospatial-related brain regions, MRT performance, and DAS28 was conducted. Results RA patients performed worse on MRT than controls. Compared to the control group, RA patients showed enhanced activation in the left precuneus, left superior frontal gyrus and right cingulate gyrus during the rotation task, with left hemisphere dominance. RA patients in active showed enhanced activation in the left precuneus, left middle frontal gyrus and right cingulate gyrus compared to the patients in remission. The left precuneus activation was negatively correlated with MRT accuracy (r = −0.621, p = 0.01) and positively correlated with DAS28 (r = 0.710, p = 0.002), and MRT accuracy was negatively correlated with DAS28 in RA patients (r = −0.702, p = 0.002). Conclusion Enhanced activation of the left precuneus in RA patients affects visuospatial function and is closely related to disease activity. These changes may provide a valuable diagnostic neuroimaging biomarker of RA.

The recombination of charges and thermal excitation of carriers at the interface between methylammonium lead iodide perovskite (PVK) and the carbon electrode are crucial factors that affect the optoelectronic performance of carbon-based hole transport layer (HTL)-free perovskite photodetectors. In this work, a method was employed to introduce SnS quantum dots (QDs) on the back surface of perovskite, which passivated the defect states on the back surface of perovskite and addressed the energy-level mismatch issue between perovskite and carbon electrode. Performance testing of the QDs and the photodetector revealed that SnS QDs possess energy-level structures that are well matched with perovskite and have high absorption coefficients. The incorporation of these QDs into the interface layer effectively suppresses the dark current of the photodetector and greatly enhances the utilization of incident light. The experimental results demonstrate that the introduction of SnS QDs reduces the dark current by an order of magnitude compared to the pristine device at 0 V bias and increases the responsivity by 10%. The optimized photodetector exhibits a wide spectral response range (350 nm to 750 nm), high responsivity (0.32 A/W at 500 nm), and high specific detectivity (>1 × 1012 Jones).

Amyloid light chain (AL) amyloidosis is a rare plasma cell dyscrasia with dismal prognosis. This study aims to investigate the T-cell immune checkpoint expression patterns in systemic AL amyloidosis and its relationship with clinicobiological traits. We examined the frequencies of V-domain immunoglobulin suppressor of T cell activation+ (VISTA+), programmed cell death 1+ (PD-1+), T cell immunoglobulin and mucin-domain-containing-3+ (Tim-3+), T cell immunoreceptor with Ig and ITIM domains+ (TIGIT+) T cells in peripheral blood (PB) and bone marrow (BM) from 19 patients with newly diagnosed AL amyloidosis. Patients with AL amyloidosis had significantly higher percentages of VISTA+ and PD-1+ T cells in PB than healthy individuals (HIs), with no statistical differences in BM. The percentages of some double-positive T cells in PB were also considerably higher in AL amyloidosis than those in HIs. Additionally, the patients with renal involvement had more PD-1+ and TIGIT+ T cells than the patients without, and PD-1+CD3+%, PD-1+CD4+%, PD-1+Treg% were positively correlated with 24-hour proteinuria levels. Furthermore, the AL amyloidosis patients had higher counts of PD-1+ Treg in PB than multiple myeloma (MM) patients, while the MM patients had higher counts of TIGIT+ T cells than AL amyloidosis patients. Collectively, this is the first report of elevated proportions of VISTA+ and PD-1+ T cells in PB of AL amyloidosis patients, indicating an immunosuppressive milieu, and the increased PD-1+ and TIGIT+ T cells were associated with renal damage. VISTA, PD-1, and TIGIT may be potential targets for reversing T-cell exhaustion in AL amyloidosis.

Background: Cognitive deficits are common in rheumatoid arthritis (RA) patients, but the mechanisms remain unclear. We investigated the effective connectivity and structural alterations of the core brain regions in RA patients with cognitive impairment. Methods: Twenty-four female patients with RA and twenty-four healthy controls were enrolled. We analyzed abnormal brain activity patterns using functional MRI during the Iowa gambling task (IGT) and core regions effective connectivity using dynamic causal model (DCM). Structural alterations of white matter volume (WMV) and gray matter volume (GMV) were detected using voxel-based morphometry (VBM). Results: RA patients showed altered activation patterns of the cortico-thalamo-cortical network, increased coupling strength from the left ventromedial prefrontal gyrus to the anterior cingulate cortex (ACC), the ACC to the right thalamus, and decreased connectivity from the thalamus to left hippocampus. VBM structural analysis showed increased GMV in the bilateral orbital frontal gyrus, bilateral hippocampus and right putamen, and reduced GMV and WMV in the bilateral thalamus in RA patients. Right thalamic GMV and WMV were positively correlated with the right thalamus-to-hippocampus connective strength. Additionally, the bold signal, GMV and WMV of the right thalamus were positively correlated with cognitive performance (IGT score) in RA patients. Conclusion: Results suggest a structural and functional deficiency in the cortico-thalamo-cortical network, which is characterized by increased ACC-to-thalamus strength and reduced thalamus-to-hippocampus coupling in RA patients. The cognitive dysfunction may be the result of compensatory measures against imbalanced cortico-thalamic-cortical coupling.

ABSTRACTWith the success of immune checkpoint inhibitors (ICI), such as anti- programmed death-1 (PD-1) antibody for solid tumors and lymphoma immunotherapy, a number of clinical trials with ICIs have been attempted for acute myeloid leukemia (AML) immunotherapy; however, limited clinical efficacy has been reported. This may be due to the heterogeneity of immune microenvironments and various degrees of T cell exhaustion in patients and may be involved in the IFN-γ pathway. In this study, we first characterized the percentage of PD-1+ and T cell immunoglobulin mucin-domain-containing-3 (Tim-3) +IFN-γ+ T cells in peripheral blood (PB) in AML compared with healthy individuals (HIs) by flow cytometry and further discussed the possibility of the reversal of T cell exhaustion to restore the secretion capacity of cytokines in T cells in AML based on blockade of PD-1 or Tim-3 (anti-PD-1 and anti-Tim-3 antibody) in vitro using a cytokine protein chip. A significantly increased percentage of PD-1+, Tim-3+, and PD-1+Tim-3+ IFN-γ+ T cells was observed in PB from patients with AML in comparison with HIs. Moreover, higher PD-1+IFN-γ+CD3+/CD8+ T cell levels were associated with poor overall survival in AML patients. Regarding leukemia cells, the percentage of Tim-3 in CD117+CD34+ AML cells was positively correlated with PD-1 in IFN-γ+CD4+ T cells. Furthermore, blocking PD-1 and Tim-3 may involve multiple cytokines and helper T cell subsets, mainly Th1 and Treg cells. Blockade of PD-1 or Tim-3 tends to restore cytokine secretion to a certain extent, a synergistic effect shown by the co-blockade of PD-1 and Tim-3. However, we also demonstrated the heterogeneity of secretory cytokines in ICI-treated T cells in AML patients.

Abstract The error caused by pseudo-midpoint effect in the use of the Moody chart was analyzed. The pseudo-midpoint effect appears in the linear interpolation method usually used to read the Moody chart. The maximum of the error is about 4%, which is significantly lower than the 15% accuracy of the chart in the literature.

Abstract Previous studies have shown increased aberrant expression of immune checkpoint (IC) proteins, such as programmed cell death receptor-1 (PD-1) and T cell immunoglobulin mucin-domain-containing-3 (Tim-3) on T cells from patients with multiple myeloma (MM), which result in T cell exhaustion and dysfunction. However, little is known about the mechanism regulating aberrant IC protein expression. In this study, we analyzed the expression of TOX (thymocyte selection-associated HMG BOX), a crucial transcription factor involved in T cell exhaustion, and its co-expression with PD-1, Tim-3, and CD244 in T cell subsets by multi-color fluorescent flow cytometry in peripheral blood (PB) and bone marrow (BM) samples from patients with MM. Significantly, the percentage of TOX + CD3 +/CD4 +/CD8 + T cells was increased, and similarly, higher numbers of TOX co-expression with PD-1, Tim-3, and CD244 on CD3 +/CD4 +/CD8 + T cells were found. Interestingly, the numbers of TOX +, TOX + PD-1 +, and TOX + Tim-3 + regulatory T (Treg) cells also significantly increased in both the PB and BM of MM patients. In summary, we for the first time observed increased TOX expression concurrent with PD-1, Tim-3, and CD244 on T cells, which may contribute to T cell exhaustion and impair their function in MM. Thus, TOX may be considered a potential target for reversing T cell exhaustion and improving T cell function in MM.

V-type immunoglobulin domain-containing suppressor of T cell activation (VISTA) is considered as an immunosuppressive factor and potential therapeutic target for anticancer therapy. However, little is known about VISTA expression and its role in immunosuppression in multiple myeloma (MM). In this study, VISTA expression and co-expression with programmed cell death receptor-1 (PD-1), T cell immunoglobulin mucin-domain-containing-3 (Tim-3), and T cell immunoglobulin and ITIM domain (TIGIT) in CD3+, CD4+, CD8+, and regulatory T (Treg) cells were analyzed in patients with MM by multi-color fluorescent flow cytometry of peripheral blood (PB) and bone marrow (BM) samples from 36 patients with MM and compared to 36 PB samples and 10 BM samples from healthy individuals (HIs), which served as controls. The results demonstrated a significant increased percentage of VISTA co-expression with PD-1, Tim-3, and TIGIT in CD3+, CD4+, CD8+, and Treg cells in PB from MM patients compared with HIs. A similar trend for VISTA+CD8+ T cells was found in BM. Moreover, a trend of a high percentage on VISTA expression and co-expression in PB rather than BM was found. Furthermore, significant positive correlations existed for VISTA expression concurrent with PD-1, Tim-3, and TIGIT in T cell subsets and clinical indicators, including Revised International Staging System (R-ISS) staging of multiple myeloma, Eastern Cooperative Oncology Group (ECOG) score, and beta-2-microglobulin (β2-MG). In conclusion, higher VISTA expression concurrent with PD-1, Tim-3, and TIGIT on T cells, particularly in the PB of patients with MM, may result in T cell exhaustion and dysfunction and be closely associated with disease progression and clinical indicators. Thus, VISTA may be considered a potential target for reversing T cell exhaustion and improving T cell function in MM.

The reliable viscoelastic characterization and prediction of micellar solution is still required in industrial applications of the solution, e.g., in surfactant flooding and pharmaceuticals. Based on the recent theoretical characterization of the viscoelastic properties of a cetyl pyridinium chloride/sodium salicylate (CPyCl/NaSal) wormlike micellar solution with a structuralized constitutive model in the work published in 2022, the present work predicted five groups of transient shear viscoelasticities of the solution experimentally obtained in 2010, which include the first normal stress difference (N1) versus time curve in the start-up experiment, the shear stress (τ12) in the start-up experiment, τ12 in the long-term start-up experiment, the stress relaxation upon cessation of steady shear flow, and the transient N1/τ12 in the step strain experiment. The study findings clearly show an improvement in the predictions of the viscoelastic properties of the micellar solution compared with those predicted previously. For example, the experimental N1/τ12 is 9 at the strain of 9 in the step strain experiment, and the corresponding previous and present predictions are 2.47 and 8.45, respectively.

Thymocyte selection-associated HMG box (TOX) is a transcription factor that belongs to the high mobility group box (HMG-box) superfamily, which includes four subfamily members: TOX, TOX2, TOX3, and TOX4. TOX is related to the formation of multiple malignancies and contributes to CD8+ T cell exhaustion in solid tumors. However, little is known about the role of TOX genes in hematological malignancies. In this study, we explored the prognostic value of TOX genes from 40 patients with de novo acute myeloid leukemia (AML) by quantitative real-time PCR (qRT-PCR) in a training cohort and validated the results using transcriptome data from 167 de novo AML patients from the Cancer Genome Atlas (TCGA) database. In the training cohort, higher expression of TOX and TOX4 was detected in the AML samples, whereas lower TOX3 expression was found. Moreover, both the training and validation results indicated that higher TOX2, TOX3, and TOX4 expression of AML patients (3-year OS: 0% vs. 37%, P = 0.036; 3-year OS: 4% vs. 61%, P < 0.001; 3-year OS: 0% vs. 32%, P = 0.010) and the AML patients with highly co-expressed TOX, TOX2, TOX4 genes (3-year OS: 0% vs. 25% vs. 75%, P = 0.001) were associated with poor overall survival (OS). Interestingly, TOX2 was positively correlated with CTLA-4, PD-1, TIGIT, and PDL-2 (rs = 0.43, P = 0.006; rs = 0.43, P = 0.006; rs = 0.56, P < 0.001; rs = 0.54, P < 0.001). In conclusion, higher expression of TOX genes was associated with poor OS for AML patients, which was related to the up-regulation of immune checkpoint genes. These data might provide novel predictors for AML outcome and direction for further investigation of the possibility of using TOX genes in novel targeted therapies for AML.

Experimental viscoelastic data and the corresponding theoretical analysis of corn starch paste in the past 30 years indicate an evident deficiency of the viscoelastic characterization of the paste. The purposes of the study are to check the capability of a recent model on describing the viscoelasticity of the paste and to improve the viscoelastic analysis. The linear viscoelastic property; the steady shear viscosity and the first normal stress difference (N1) of a cross-linked waxy corn starch paste mixed with sucrose experimentally reported in 2003 were characterized with a structuralized viscoelastic constitutive equation in the present paper. The structuralized parameter f in the equation was obtained using the viscosities in the dynamic and steady shear experiment. Both a power law strain model and a linear strain model were proposed to describe the normal component in the strain matrix. Three kinds of viscoelastic properties of the paste can be described well with the structuralized equation. Both the power law and the linear strain model can yield reasonable calculations of N1. The maximum deviation of N1 calculated by two strain models is about 10%. The theoretical model adopted is available for describing the complex viscoelastic behaviors of corn starch paste usually appearing in the processing of corn starch.

An intelligent land vehicle utilizes onboard sensors to acquire observed states at a disorderly intersection. However, partial observation of the environment occurs due to sensor noise. This causes decision failure easily. A collision relationship-based driving behavior decision-making method via deep recurrent Q network (CR-DRQN) is proposed for intelligent land vehicles. First, the collision relationship between the intelligent land vehicle and surrounding vehicles is designed as the input. The collision relationship is extracted from the observed states with the sensor noise. This avoids a CR-DRQN dimension explosion and speeds up the network training. Then, DRQN is utilized to attenuate the impact of the input noise and achieve driving behavior decision-making. Finally, some comparative experiments are conducted to verify the effectiveness of the proposed method. CR-DRQN maintains a high decision success rate at a disorderly intersection with partially observable states. In addition, the proposed method is outstanding in the aspects of safety, the ability of collision risk prediction, and comfort.

The time-dependent viscoelastic behaviors of a low-density polyethylene melt (LDPE) in a triangular- and trapezoidal-loop shear experiment reported previously are described here by an integral-type Rivlin–Sawyers (RS) constitutive equation. The linear viscoelasticity of the melt was obtained through a dynamic frequency sweep experiment at a small strain and fitted by a relaxation spectrum. The nonlinear viscoelasticity was characterized by viscosity. All the experimental viscoelastic behaviors of the melt can be divided into two types in terms of the predictions of the RS model: (1) predictable time-dependent viscoelastic behaviors at low shear rates or during short-term shear, and (2) unpredictable shear weakening behavior occurring at the high shear rate of 3–5 s−1 during long-term shear with the characteristic time interval of about 40–100 s. The influence of experimental error caused possibly by inhomogeneous samples on the viscoelasticity of the melt was analyzed, and the large relative error in the experiment is about 10–30%.