PNBACE: an ensemble algorithm to predict the effects of mutations on protein-nucleic acid binding affinity.

BACKGROUND: Mutations occurring in nucleic acids or proteins may affect the binding affinities of protein-nucleic acid interactions. Although many efforts have been devoted to the impact of protein mutations, few computational studies have addressed the effect of nucleic acid mutations and explored whether the identical methodology could be applied to the prediction of binding affinity changes caused by these two mutation types. RESULTS: Here, we developed a generalized algorithm named PNBACE for both DNA and protein mutations. We first demonstrated that DNA mutations could induce varying degrees of changes in binding affinity from multiple perspectives. We then designed a group of energy-based topological features based on different energy networks, which were combined with our previous partition-based energy features to construct individual prediction models through feature selections. Furthermore, we created an ensemble model by integrating the outputs of individual models using a differential evolution algorithm. In addition to predicting the impact of single-point mutations, PNBACE could predict the influence of multiple-point mutations and identify mutations significantly reducing binding affinities. Extensive comparisons indicated that PNBACE largely performed better than existing methods on both regression and classification tasks. CONCLUSIONS: PNBACE is an effective method for estimating the binding affinity changes of protein-nucleic acid complexes induced by DNA or protein mutations, therefore improving our understanding of the interactions between proteins and DNA/RNA.

Numerical simulation and in vitro experimental study of the hemodynamic performance of vena cava filters with helical forms.

Inferior vena cava filter (IVCF) implantation is a common method of thrombus capture. By implanting a filter in the inferior vena cava (IVC), microemboli can be effectively blocked from entering the pulmonary circulation, thereby avoiding acute pulmonary embolism (PE). Inspired by the helical flow effect in the human arterial system, we propose a helical retrievable IVCF, which, due to the presence of a helical structure inducing a helical flow pattern of blood in the region near the IVCF, can effectively avoid the deposition of microemboli in the vicinity of the IVCF while promoting the cleavage of the captured thrombus clot. It also reduces the risk of IVCF dislodging and slipping in the vessel because its shape expands in the radial direction, allowing its distal end to fit closely to the IVC wall, and because its contact structure with the inner IVC wall is curved, increasing the contact area and reducing the risk of the vessel wall being punctured by the IVCF support structure. We used ANSYS 2023 software to conduct unidirectional fluid-structure coupling simulation of four different forms of IVCF, combined with microthrombus capture experiments in vitro, to explore the impact of these four forms of IVCF on blood flow patterns and to evaluate the risk of IVCF perforation and IVCF dislocation. It can be seen from the numerical simulation results that the helical structure does have the function of inducing blood flow to undergo helical flow dynamics, and the increase in wall shear stress (WSS) brought about by this function can improve the situation of thrombosis accumulation to a certain extent. Meanwhile, the placement of IVCF will change the flow state of blood flow and lead to the deformation of blood vessels. In in vitro experiments, we found that the density of the helical support rod is a key factor affecting the thrombus trapping efficiency, and in addition, the contact area between the IVCF and the vessel wall has a major influence on the risk of IVCF displacement.

Flavour Profile of Traditional Dry Sausage Prepared with Partial Substitution of NaCl with KCl.

The effects of partial substitution of NaCl with 0%, 20%, 30% and 40% KCl on the physical characteristics, bacterial community and flavour profile of traditional dry sausage were investigated in this study. With the increase in KCl substitution ratio, the moisture content, astringency, bitterness and umami increased significantly, and the saltiness gradually decreased (p < 0.05). The high-throughput sequencing results showed that the dry sausages with KCl substitution had relatively high abundances of Staphylococcus. For volatile compounds, increasing the KCl substitution ratio reduced the formation of aldehydes, ketones and some alcohols, but promoted the formation of acids and esters (p < 0.05). Sensory evaluation and partial least square regression analysis showed that the dry sausages with 20% and 30% KCl were similar in overall physical and microbial properties, flavour profiles and sensory attributes, and the sausages with 40% KCl were characterized by taste defects. Overall, partial substitution of NaCl with 30% KCl could ensure the acceptable flavour and sensory attributes of dry sausages.

Changes of brain function in patients with type 2 diabetes mellitus measured by different analysis methods: A new coordinate-based meta-analysis of neuroimaging.

Objective: Neuroimaging meta-analysis identified abnormal neural activity alterations in patients with type 2 diabetes mellitus (T2DM), but there was no consistency or heterogeneity analysis between different brain imaging processing strategies. The aim of this meta-analysis was to determine consistent changes of regional brain functions in T2DM via the indicators obtained by using different post-processing methods. Methods: Since the indicators obtained using varied post-processing methods reflect different neurophysiological and pathological characteristics, we further conducted a coordinate-based meta-analysis (CBMA) of the two categories of neuroimaging literature, which were grouped according to similar data processing methods: one group included regional homogeneity (ReHo), independent component analysis (ICA), and degree centrality (DC) studies, while the other group summarized the literature on amplitude of low-frequency fluctuation (ALFF) and cerebral blood flow (CBF). Results: The final meta-analysis included 23 eligible trials with 27 data sets. Compared with the healthy control group, when neuroimaging studies were combined with ReHo, ICA, and DC measurements, the brain activity of the right Rolandic operculum, right supramarginal gyrus, and right superior temporal gyrus in T2DM patients decreased significantly. When neuroimaging studies were combined with ALFF and CBF measurements, there was no clear evidence of differences in the brain function between T2DM and HCs. Conclusion: T2DM patients have a series of spontaneous abnormal brain activities, mainly involving brain regions related to learning, memory, and emotion, which provide early biomarkers for clarifying the mechanism of cognitive impairment and neuropsychiatric disorders in diabetes. Systematic review registration: https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=247071, PROSPERO [CRD42021247071].

Gray Matter Abnormalities in Patients with Complex Regional Pain Syndrome: A Systematic Review and Meta-Analysis of Voxel-Based Morphometry Studies.

Current findings on brain structural alterations in complex regional pain syndrome (CRPS) are heterogenous and controversial. This study aimed to perform a systematic review and meta-analysis to explore the significant gray matter volume (GMV) abnormalities between patients with CRPS and healthy controls (HCs). A systematic search of the PubMed, Web of Science, and MEDLINE databases was performed, updated through 27 January 2022. A total of five studies (93 CRPS patients and 106 HCs) were included. Peak coordinates and effect sizes were extracted and meta-analyzed by anisotropic effect size-signed differential mapping (AES-SDM). Heterogeneity, sensitivity, and publication bias of the main results were checked by the Q test, jackknife analysis, and the Egger test, respectively. Meta-regression analysis was performed to explore the potential impact of risk factors on GMV alterations in patients with CRPS. The main analysis exhibited that patients with CRPS had increased GMV in the left medial superior frontal gyrus (SFGmedial.L), left striatum, and an undefined area (2, 0, -8) that may be in hypothalamus, as well as decreased GMV in the corpus callosum (CC) (extending to right supplementary motor area (SMA.R), right median cingulate/paracingulate gyri (MCC.R)), and an undefined area (extending to the right caudate nucleus (CAU.R), and right thalamus (THA.R)). Meta-regression analysis showed a negative relationship between increased GMV in the SFGmedial.L and disease duration, and the percentage of female patients with CRPS. Brain structure abnormalities in the sensorimotor regions (e.g., SFGmedial.L, SMA.R, CAU.R, MCC.R, and THA.R) may be susceptible in patients with CRPS. Additionally, sex differences and disease duration may have a negative effect on the increased GMV in SFGmedial.L.

Gray and white matter abnormality in patients with T2DM-related cognitive dysfunction: a systemic review and meta-analysis.

AIMS/HYPOTHESIS: Brain structure abnormality in patients with type 2 diabetes mellitus (T2DM)-related cognitive dysfunction (T2DM-CD) has been reported for decades in magnetic resonance imaging (MRI) studies. However, the reliable results were still unclear. This study aimed to make a systemic review and meta-analysis to find the significant and consistent gray matter (GM) and white matter (WM) alterations in patients with T2DM-CD by comparing with the healthy controls (HCs). METHODS: Published studies were systemically searched from PubMed, MEDLINE, Cochrane Library and Web of Science databases updated to November 14, 2021. Studies reporting abnormal GM or WM between patients with T2DM-CD and HCs were selected, and their significant peak coordinates (x, y, z) and effect sizes (z-score or t-value) were extracted to perform a voxel-based meta-analysis by anisotropic effect size-signed differential mapping (AES-SDM) 5.15 software. RESULTS: Total 15 studies and 16 datasets (1550 participants) from 7531 results were involved in this study. Compared to HCs, patients with T2DM-CD showed significant and consistent decreased GM in right superior frontal gyrus, medial orbital (PFCventmed. R, BA 11), left superior temporal gyrus (STG. L, BA 48), and right calcarine fissure / surrounding cortex (CAL. R, BA 17), as well as decreased fractional anisotropy (FA) in right inferior network, inferior fronto-occipital fasciculus (IFOF. R), right inferior network, longitudinal fasciculus (ILF. R), and undefined area (32, -60, -42) of cerebellum. Meta-regression showed the positive relationship between decreased GM in PFCventmed.R and MoCA score, the positive relationship between decreased GM in STG.L and BMI, as well as the positive relationship between the decreased FA in IFOF.R and age or BMI. CONCLUSIONS/INTERPRETATION: T2DM impairs the cognitive function by affecting the specific brain structures. GM atrophy in PFCventmed. R (BA 11), STG. L (BA 48), and CAL. R (BA 17), as well as WM injury in IFOF. R, ILF. R, and undefined area (32, -60, -42) of cerebellum. And those brain regions may be valuable targets for future researches. Age, BMI, and MoCA score have a potential influence on the altered GM or WM in T2DM-CD.

Optimizing the radiomics-machine-learning model based on non-contrast enhanced CT for the simplified risk categorization of thymic epithelial tumors: A large cohort retrospective study.

PURPOSE: This study aimed to establish and compare the radiomics machine learning (ML) models based on non-contrast enhanced computed tomography (NECT) and clinical features for predicting the simplified risk categorization of thymic epithelial tumors (TETs). EXPERIMENTAL DESIGN: A total of 509 patients with pathologically confirmed TETs from January 2009 to May 2018 were retrospectively enrolled, consisting of 238 low-risk thymoma (LRT), 232 high-risk thymoma (HRT), and 39 thymic carcinoma (TC), and were divided into training (n = 433) and testing cohorts (n = 76) according to the admission time. Volumes of interest (VOIs) covering the whole tumor were manually segmented on preoperative NECT images. A total of 1218 radiomic features were extracted from the VOIs, and 4 clinical variables were collected from the hospital database. Fourteen ML models, along with varied feature selection strategies, were used to establish triple-classification models using the radiomic features (radiomic models), while clinical-radiomic models were built after combining with the clinical variables. The diagnostic accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC) of radiologist assessment, the radiomic and clinical-radiomic models were evaluated on the testing cohort. RESULTS: The Support Vector Machine (SVM) clinical-radiomic model demonstrated the highest AUC of 0.841 (95% CI 0.820 to 0.861) on the cross-validation result and reached an AUC of 0.844 (95% CI 0.793 to 0.894) in the testing cohort. For the one-vs-rest question of LRT vs HRT + TC, the sensitivity, specificity, and accuracy reached 80.00%, 63.41%, and 71.05%, respectively. For HRT vs LRT + TC, they reached 60.53%, 78.95%, and 69.74%. For TC vs LRT + HRT they reached 33.33%, 98.63%, and 96.05%, respectively. Compared with the radiomic models, superior diagnostic efficacy was demonstrated for most clinical-radiomics models, and the AUC of the Bernoulli Naive Bayes model was significantly improved. Radiologist2's assessment achieved a higher AUC of 0.813 (95% CI: 0.756-0.8761) than other radiologists, which was slightly lower than the SVM clinical-radiomic model. Combined with other evaluation indicators, SVM, as the best ML model, demonstrated the potential of predicting the simplified risk categorization of TETs with superior predictive performance to that of radiologists' assessment. CONCLUSION: Most of the ML models are promising in predicting the simplified TETs risk categorization with superior efficacy to that of radiologists' assessment, especially the SVM models, demonstrated the integration of ML with NECT may be valuable in aiding the diagnosis and treatment planning.

Achyranthes bidentate saponins protect rat articular chondrocytes against interleukin-1ß-induced inflammation and apoptosis in vitro.

Achyranthes bidentate Blume (Niuxi) is often employed for treatment of arthritis in Traditional Chinese Medicine and possesses anti-inflammatory properties. Phytochemical and pharmacological studies proved the oleanane-type saponins to be the main bioactive principles. In the present study, protective effects of A. bidentata saponins (ABS) on inflammation and apoptosis in interleukine-1ß (IL-1ß)-induced chondrocytes were investigated. Rat chondrocytes were pretreated with ABS at 3 µg/mL, 10 µg/mL, and 30 µg/mL, and subsequently stimulated with IL-1ß (10 ng/mL). Methylthiazolyldiphenyl-tetrazolium bromide assay and annexin V/propidium iodide dual staining demonstrated that ABS could protect IL-1ß-induced chondrocyte injury. ABS suppressed IL-1ß-induced apoptosis by suppressing the activation of caspase-3, inhibiting levels of proapoptotic proteins Bax and Bad, decreasing p53 protein phosphorylation, and promoting the expression of antiapoptotic protein Bcl-xL and proliferating cell nuclear antigen. IL-1ß-induced inflammation and matrix degradation were also alleviated by ABS through the downregulation of the expressions of matrix metalloproteinases 3 and 9 and cyclooxygenase-2. Moreover, ABS inhibited IL-1ß-induced nuclear factor κB activation in rat chondrocytes. We demonstrated, for the first time, the protective effects of ABS on IL-1ß-stimulated chondrocytes and their molecular mechanisms. Thus, it is suggested that ABS might be a potential drug in the treatment of osteoarthritis.

Dosimetric study of different radiotherapy planning approaches for hippocampal avoidance whole-brain radiation therapy (HA-WBRT) based on fused CT and MRI imaging.

The purpose of this study was to compare the dosimetric characteristics for hippocampal avoidance (HA) between the treatment plans based on fused CT and MRI imaging during whole brain radiotherapy (WBRT) pertaining to: (1) 3-dimensional conformal radiotherapy (3D-CRT), (2) dynamic intensity modulated radiation therapy (dIMRT), and (3) RapidArc for patients with brain metastases. In our study, HA was defined as hippocampus beyond 5 mm, and planning target volume (PTV) was obtained subtracting HA volume from the volume of whole brain. There were 10 selected patients diagnosed with brain metastases receiving WBRT. These patients received plans for 3D-CRT (two fields), dIMRT (seven non-coplanar fields) and RapidArc (dual arc). The prescribed dose 30 Gy in 10 fractions was delivered to the whole-brain clinical target volume of patients. On the premise of meeting the clinical requirements, we compared target dose distribution, target coverage (TC), homogeneity index (HI), dose of organs at risk (OARs), monitor units (MU) and treatment time between the above three radiotherapy plans. V90 %, V95 % and TC of PTV for 3D-CRT plan were lowest of the three plans. V90 %, V95 % and HI of PTV in RapidArc plan were superior to the other two plans. TC of PTV in RapidArc plan was similar with dIMRT plan (P > 0.05). 3D-CRT was the optimal plan in the three plans for hippocampal protection. The median dose (Dmedian) and the maximum doses (Dmax) of hippocampus in 3D-CRT were 4.95, 10.87 Gy, which were lowest among the three planning approaches (P < 0.05). Dmedian and Dmax of hippocampus in dIMRT were 10.68, 14.11 Gy. Dmedian and Dmax of hippocampus in RapidArc were 10.30 gGy, 13.92 Gy. These parameters of the last two plans pertain to no significant difference (P > 0.05). When WBRT (30 Gy,10F) was equivalent to single dose 2 Gy,NTDmean of hippocampus in 3D-CRT, dIMRT and RapidArc were reduced to 3.60, 8.47, 8.20 Gy2, respectively. In addition, compared with dIMRT, MU of RapidArc was reduced and the treatment time was shortened by nearly 25 %. All three radiotherapy planning approaches in our study can meet the clinical requirements of HA. Although TC in 3D-CRT was lowest, hippocampus was protected best by this plan. So many radiation fields and the design of non-coplanar fields lead to the complication of dIMRT. TC and HI in RapidArc were superior to the other two plans with the precise of meeting the clinical requirements. The difference in protection for hippocampus between dIMRT and RapidArc was statistically significant. In addition, RapidArc can remarkably reduce MU and the treatment time.

[Comparison of vitrification cryopreservation among different stages of mouse embryos].

The cryopreservation of different embryo stages collected from ICR, C57BL/6 and F1 of DBA*C57BL/6 was carried out by using vitrification method. The morphology, in vitro development and birth rates of these embryos were compared after frozen-thawed. The results showed that more than 75% of the morphology from 2-cell embryos to morula stages from different strains was normal, the normal morphology rates of 8-cell embryos being the highest, while those of blastulas being the lowest. The in vitro development rates became higher as the embryos developed. The morphology of in vivo and in vitro fertilized frozen 2-cell embryos showed no difference, but the development rate of in vivo fertilized frozen 2-cell embryos was significantly higher than that of in vitro ones. Embryos that underwent 3 times frozen-thawing remained normal morphology. The pregnant rate and birth rate of frozen 2-cell embryos after embryo transfer were 64% and 40% respectively, but lower than those of fresh 2-cell embryo transfer.