Miracle-dz/UniFAR-FTUs huggingface dataset:
Mendelian randomization analysis reveals causal effects of plasma proteome on body composition traits.

BACKGROUND Observational studies have demonstrated associations between plasma proteins and obesity, but evidence of causal relationship remains to be studied. METHODS To evaluate the causal relationship between plasma proteins and body composition, we conducted a two-sample Mendelian randomization (MR) analysis based on the genome-wide association study (GWAS) summary statistics of 23 body composition traits and 2,656 plasma proteins. We then performed hierarchical cluster analysis to evaluate the structure and pattern of the identified causal associations, and performed gene ontology enrichment analysis to explore the functional relevance of the identified proteins. RESULTS We identified 430 putatively causal effects of 96 plasma proteins on 22 body composition traits (except obesity status) with strong MR evidence (P < 2.53 × 10 -6, at a Bonferroni-corrected threshold). The top 3 causal associations are FST (follistatin) on trunk fat-free mass (Beta = -0.63, SE = 0.04, P = 2.00 × 10 -63), IGFBP1 (insulin-like growth factor-binding protein 1) on trunk fat-free mass (Beta = -0.54, SE = 0.03, P = 1.79 × 10 -57) and RSPO3 (r-spondin-3) on WHR (waist circumference/hip circumference) (Beta = 0.01, SE= 4.47 × 10 -4, P = 5.45 × 10 -60), respectively. Further clustering analysis and pathway analysis demonstrated that the pattern of causal effect to fat mass and fat-free mass may be different. CONCLUSION Our findings may provide evidence for causal relationships from plasma proteins to various body composition traits and provide basis for further targeted functional studies.
Mechanism and Bias Considerations for Design of a Bi-Directional Artificial Muscle Actuator

Pneumatic artificial muscles (PAMs), or McKibben actuators, have received considerable attention for robotic manipulators and in aerospace applications due to their similarity to natural muscles. Like natural muscles, PAMs are a purely contractile actuator, so that, in order to produce bi-directional or rotational motion, they must be arranged in an agonist/antagonist pair, which inherently limits the deflection of the system due to the high parasitic stiffness of the antagonistic PAM. This study presents two methods for increasing the performance of an antagonistic PAM system by decreasing the passive parasitic torque, rather than increasing the active torque. The first involves selection of the kinematic mechanism geometry, and the second involves the introduction of bias into the system, both in terms of PAM contraction and passive (antagonistic) PAM pressure. It was found with the proper selection of design parameters, including mechanism geometry, PAM geometry, and bias conditions, that an ideal actuator configuration can be chosen that maximizes deflection for a given arbitrary loading. When comparing a baseline design to an improved design for a simplified case, a nearly 50% increase in maximum deflection was predicted simply by optimizing mechanism geometry and bias contraction. These results were experimentally verified with quasi-static testing that showed a 300% increase in actuator deflection over the baseline design.
MnFtz-f1 Is Required for Molting and Ovulation of the Oriental River Prawn Macrobrachium nipponense

Molting and ovulation are the basic processes responsible for the growth and reproduction of Macrobrachium nipponense; however, the molecular mechanisms of molting and ovulation in M. nipponense are poorly understood. The present study aimed to use MnFtz-f1 as the starting point to study the molting and ovulation phenomena in M. nipponense at the molecular level. The full-length MnFtz-f1 cDNA sequence was 2,198 base pairs (bp) in length with an open reading frame of 1,899 bp encoding 632 amino acids. Quantitative real-time PCR analysis showed that MnFtz-f1 was highly expressed in the ovary at the cleavage stage and on the fifth day after hatching. In vivo administration of 20-hydroxyecdysone (20E) showed that 20E effectively inhibited the expression of the MnFtz-f1 gene, and the silencing of the MnFtz-f1 gene reduced the content of 20E in the ovary. In situ hybridization (ISH) analysis revealed the localization of MnFtz-f1 in the ovary. Silencing of MnFtz-f1 by RNA interference (RNAi) resulted in significant inhibition of the expression of the vitellogenin (Vg), Spook, and Phantom genes, thus confirming that MnFtz-f1 had a mutual regulatory relationship with Vg, Spook, and Phantom. After RNAi, the molting frequency and ovulation number of M. nipponense decreased significantly, which demonstrated that MnFtz-f1 played a pivotal role in the process of molting and ovulation.
Identification and Validation of a Potent Multi-lncRNA Molecular Model for Predicting Gastric Cancer Prognosis

Gastric cancer (GC) remains the third deadliest malignancy in China. Despite the current understanding that the long noncoding RNAs (lncRNAs) play a pivotal function in the growth and progression of cancer, their prognostic value in GC remains unclear. Therefore, we aimed to construct a polymolecular prediction model by employing a competing endogenous RNA (ceRNA) network signature obtained by integrated bioinformatics analysis to evaluate patient prognosis in GC. Overall, 1,464 mRNAs, 14,376 lncRNAs, and 73 microRNAs (miRNAs) were found to be differentially expressed in GC. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these differentially expressed RNAs were mostly enriched in neuroactive ligand–receptor interaction, chemical carcinogenesis, epidermis development, and digestion, which were correlated with GC. A ceRNA network consisting of four lncRNAs, 21 miRNAs, and 12 mRNAs were constructed. We identified four lncRNAs (lnc00473, H19, AC079160.1, and AC093866.1) as prognostic biomarkers, and their levels were quantified by qRT-PCR in cancer and adjacent noncancerous tissue specimens. Univariable and multivariable Cox regression analyses suggested statistically significant differences in age, stage, radiotherapy, and risk score groups, which were independent predictors of prognosis. A risk prediction model was created to test whether lncRNAs could be used as an independent risk predictor of GC or not. These novel lncRNAs’ signature independently predicted overall survival in GC (p < 0.001). Taken together, this study identified a ceRNA and protein–protein interaction networks that significantly affect GC, which could be valuable for GC diagnosis and therapy.
Dynamic Interpretation of Falling Weight Deflectometer Test Results: Spectral Element Method

The use of spectral analysis as a means of analyzing the dynamic impact of falling weight deflectometer (FWD) load pulses on pavements is covered. The spectral element technique is utilized. Only forward analyses of pavement dynamics are presented, with the emphasis on the suitability of the method for solving inverse problems. LAMDA (layered media dynamic analysis), a newly developed spectral element program, is utilized for the simulation of the interaction between the FWD load pulse and the pavement structure. In LAMDA, the formulation of the wave propagation, reflection, and refraction in a layer is done in a closed form. The assembling of the elements (in the multilayer system) is carried out in a manner similar to that in the finite element method. Consequently, the size of the mesh of a pavement structure is as large as the number of the layers involved. This reduces the computational requirements substantially and hence enables utilization of LAMDA in iterative algorithms for backcalculation purposes.
Evaluating the Genetic Capacity of Mycoplasmas for Coenzyme A Biosynthesis in a Search for New Anti-mycoplasma Targets

Mycoplasmas are responsible for a wide range of disease states in both humans and animals, in which their parasitic lifestyle has allowed them to reduce their genome sizes and curtail their biosynthetic capabilities. The subsequent dependence on their host offers a unique opportunity to explore pathways for obtaining and producing cofactors – such as coenzyme A (CoA) – as possible targets for the development of new anti-mycoplasma agents. CoA plays an essential role in energy and fatty acid metabolism and is required for membrane synthesis. However, our current lack of knowledge of the relevance and importance of the CoA biosynthesis pathway in mycoplasmas, and whether it could be bypassed within their pathogenic context, prevents further exploration of the potential of this pathway. In the universal, canonical CoA biosynthesis pathway, five enzymes are responsible for the production of CoA. Given the inconsistent presence of the genes that code for these enzymes across Mycoplasma genomes, this study set out to establish the genetic capacity of mycoplasmas to synthesize their own CoA de novo. Existing functional annotations and sequence, family, motif, and domain analysis of protein products were used to determine the existence of relevant genes in Mycoplasma genomes. We found that most Mycoplasma species do have the genetic capacity to synthesize CoA, but there was a differentiated prevalence of these genes across species. Phylogenetic analysis indicated that the phylogenetic position of a species could not be used to predict its enzyme-encoding gene combinations. Despite this, the final enzyme in the biosynthesis pathway – dephospho-coenzyme A kinase (DPCK) – was found to be the most common among the studied species, suggesting that it has the most potential as a target in the search for new broad-spectrum anti-mycoplasma agents.
SlpB Protein Enhances the Probiotic Potential of L. lactis NCDO 2118 in Colitis Mice Model

Bacteria used in the production of fermented food products have been investigated for their potential role as modulators of inflammation in gastrointestinal tract disorders such as inflammatory bowel diseases (IBD) that cause irreversible changes in the structure and function of gut tissues. Ulcerative colitis (UC) is the most prevalent IBD in the population of Western countries, and it is marked by symptoms such as weight loss, rectal bleeding, diarrhea, shortening of the colon, and destruction of the epithelial layer. The strain Propionibacterium freudenreichii CIRM-BIA 129 recently revealed promising immunomodulatory properties that greatly rely on surface-layer proteins (Slp), notably SlpB. We, thus, cloned the sequence encoding the SlpB protein into the pXIES-SEC expression and secretion vector, and expressed the propionibacterial protein in the lactic acid bacterium Lactococcus lactis NCDO 2118. The probiotic potential of L. lactis NCDO 2118 harboring pXIES-SEC:slpB (L. lactis-SlpB) was evaluated in a UC-mice model induced by Dextran Sulfate Sodium (DSS). During colitis induction, mice receiving L. lactis-SlpB exhibited reduced severity of colitis, with lower weight loss, lower disease activity index, limited shortening of the colon length, and reduced histopathological score, with significant differences, compared with the DSS group and the group treated with L. lactis NCDO 2118 wild-type strain. Moreover, L. lactis-SlpB administration increased the expression of genes encoding tight junction proteins zo-1, cln-1, cln-5, ocln, and muc-2 in the colon, increased IL-10 and TGF-β, and decreased IL-17, TNF-α, and IL-12 cytokines in the colon. Therefore, this work demonstrates that SlpB recombinant protein is able to increase the probiotic potential of the L. lactis strain to alleviate DSS-induced colitis in mice. This opens perspectives for the development of new approaches to enhance the probiotic potential of strains by the addition of SlpB protein.
Micro-Expression Recognition Based on Pixel Residual Sum and Cropped Gaussian Pyramid

Facial micro-expression(ME) recognition has great significance for the progress of human society and could find a person's true feelings. Meanwhile, ME recognition faces a huge challenge, since it is difficult to detect and easy to be disturbed by the environment. In this article, we propose two novel preprocessing methods based on Pixel Residual Sum. These methods can preprocess video clips according to the unit pixel displacement of images, resist environmental interference, and be easy to extract subtle facial features. Furthermore, we propose a Cropped Gaussian Pyramid with Overlapping(CGPO) module, which divides images of different resolutions through Gaussian pyramids and crops different resolutions images into multiple overlapping subplots. Then, we use a convolutional neural networks of progressively increasing channels based on the depthwise convolution to extract preliminary features. Finally, we fuse preliminary features and make position embedding to get the last features. Our experiments show that the proposed methods and model have better performance than the well-known methods.
Climate Change Impact Assessment and Adaptation Strategies for Rainfed Wheat in Contrasting Climatic Regions of Iran

This is the first large-scale study to assess the climate change impact on the grain yield of rainfed wheat for three provinces of contrasting climatic conditions (temperate, cold semi-arid, and hot arid) in Iran. Five integrative climate change scenarios including +0.5°C temperature plus−5% precipitation, +1°C plus−10%, +1.5°C plus−15%, +2°C plus−20%, and +2.5°C plus−25% were used and evaluated. Nitrogen fertilizer and shifting planting dates were tested for their suitability as adaptive strategies for rainfed wheat against the changing climate. The climate change scenarios reduced the grain yield by −6.9 to −44.8% in the temperate province Mazandaran and by −7.3 to −54.4% in the hot arid province Khuzestan but increased it by +16.7% in the cold semi-arid province Eastern Azarbaijan. The additional application of +15, +30, +45, and +60 kg ha−1 nitrogen fertilizer as urea at sowing could not, in most cases, compensate for the grain yield reductions under the climate change scenarios. Instead, late planting dates in November, December, and January enhanced the grain yield by +6 to +70.6% in Mazandaran under all climate change scenarios and by +94 to +271% in Khuzestan under all climate change scenarios except under the scenario +2.5°C temperature plus−25% precipitation which led to a grain yield reduction of −85.5%. It is concluded that rainfed wheat production in regions with cold climates can benefit from the climate change, but it can be impaired in temperate regions and especially in vulnerable hot regions like Khuzestan. Shifting planting date can be regarded as an efficient yield-compensating and environmentally friendly adaptive strategy of rainfed wheat against the climate change in temperate and hot arid regions.
Comparative Analysis of Two Surgical Treatment Options for Giant Cell Tumor of the Proximal Femur: Extended Curettage and Segmental Resection

Aim As a locally destructive intermediate bone tumor with low incidence, high recurrence rate, and difficulty in reconstruction, giant cell tumor of bone (GCTB) in the proximal femur has no unified surgical treatment standard. This study aimed to compare the differences in local recurrence, reconstruction durability, and postoperative function after treatment with either extended curettage (EC) or segmental resection (SR) for GCTB in the proximal femur so as to provide constructive suggestions for the rational selection of EC or SR operation scheme. Patients and Methods 29 patients (15 men and 14 women) were included in this retrospective study, with a mean age of 32.1 years. According to the division method of proximal femur of International Society Of Limb Salvage (ISOLS), there was 1 case in the H1 area, 17 cases in the H2 area, 10 cases in the H1+H2 area, and 1 case in the H1+H2+H3 area. Among them were 11 cases of Campanacci grade II GCTB, 18 cases of Campanacci grade III GCTB, and 7 cases with pathological fractures. All patients underwent either EC or SR surgery. The Musculoskeletal Tumor Society (MSTS) score was used for patient evaluation. The operation effectiveness was analyzed according to the Mankin evaluation standard. Regular follow-up was performed to evaluate the recurrence rate, limb function, and long-term complications of the two surgical methods. Results All patients were followed up for a mean of 60.4 months. Local recurrence occurred in one of 19 patients treated with EC (5.3%) and one of 10 patients treated with SR (10%). The MSTS score of lower limb function in patients in the EC group was better compared to patients in the SR group (P = 0.002). Complications occurred in 2 cases (10.5%) and 5 cases (50%) in the EC group (osteoarthritis, osteonecrosis) and SR group (joint stiffness, infection, prosthesis loosening), respectively, with significant differences between the two groups (P = 0.03). The operation effectiveness was analyzed according to the Mankin evaluation standard. The EC group showed an optimal rate of 94.7% (18/19) as opposed to 80% (8/10) in the SR group. Conclusions For GCTB in the proximal femur, when the tumor does not extensively involves the surrounding soft tissues, the articular surface was not damaged, and there is no pathological fracture with apparent displacement, EC surgery should be fully considered.
Lifetime Estimation of IGBTs in a Grid-connected STATCOM

Lifetime estimation of power semiconductor devices, and IGBT devices in particular, used in the power electronics integrated with power systems has gained technical importance in recent times with increased scope of distributed generation, renewable energy systems and FACTS. Since most of the common failures (wire bond and solder fatigue) are caused by thermo-mechanical stresses, the methodology of lifetime estimation starts with temperature estimation, cycle counting based on rainflow algorithm, and finally degradation calculation based on linear accumulation model. Different number of RC cells for each packaging layer in the module for the thermal model, including the influence of encapsulant is proposed for temperature estimation of IGBTs in power modules. A modified rainflow algorithm with faster execution time and time dependent temperature calculation is introduced for cycle counting. Finally, the lifetime of the IGBT is estimated during STATCOM operation using real-time load profiles for power factor variation. For a power factor variation data for a building, the lifetime is estimated to be about 3 years. Similarly, a month long arc furnace load data is considered to compare the equivalent temperature based calculation to conventional tests. 4% more degradation is observed in the equivalent temperature based calculation than compared with conventional rainflow algorithm. A simulation study on the operation parameter dependence on the stresses in a wire is considered to estimate lifetime from Finite Element Analysis (FEA) in COMSOL. Power cycling tests are conducted on two different modules (600 V, 50 A H-bridge module and a 1200 V, 150 A phase leg module) to validate the lifetime model for four months. The low power module was tested without any protection circuits and hence failed catastrophically. Wire melt-off or fusing failure was dominantly observed, following by dielectric based short circuit failure. The high power module was tested with protection circuits to prevent catastrophic damage for a maximum of 4 months. A maximum of 20% degradation in static characteristics, with decreased on state resistance was observed in the modules. The degradation is attributed to increased junction temperature as the thermal resistance increases owing to solder fatigue.
HMGB3 is Associated With an Unfavorable Prognosis of Neuroblastoma and Promotes Tumor Progression by Mediating TPX2

Neuroblastoma (NB) is the most common solid tumor apart from central nervous system malignancies in children aged 0–14 years, and the outcomes of high-risk patients are dismal. High mobility group box 3 (HMGB3) plays an oncogenic role in many cancers; however, its biological role in NB is still unclear. Using data mining, we found that HMGB3 expression was markedly elevated in NB patients with unfavorable prognoses. When HMGB3 expression in NB cell lines was inhibited, cell proliferation, migration, and invasion were suppressed, and HMGB3 knockdown inhibited NB tumor development in mice. RT−PCR was employed to detect mRNA expression of nine coexpressed genes in response to HMGB3 knockdown, and TPX2 was identified. Furthermore, overexpression of TPX2 reversed the cell proliferation effect of HMGB3 silencing. Multivariate Cox regression analysis indicated that HMGB3 and TPX2 might be independent prognostic factors for overall survival and event-free survival, which showed the highest significance (p < 0.001). According to the nomogram predictor constructed, the integration of gene expression and clinicopathological features exhibited better prognostic prediction power. Furthermore, the random forest algorithm and receiver operating characteristic curves also showed that HMGB3 and TPX2 played important roles in discriminating the vital status (alive/dead) of patients in the NB datasets. Our informatics analysis and biological experiments suggested that HMGB3 is correlated with the unfavorable clinical outcomes of NB, and plays an important role in promoting cell growth, proliferation, and invasion in NB, potentially representing a new therapeutic target for tumor progression.
Fuzzy Time-Dependent Reliability Analysis of RC Beams Subject to Pitting Corrosion

Steel bars pitting corrosion is an electrochemical process that could seriously jeopardize the reliability of reinforced concrete structures. Even if detailed models exist to predict the lifetime of the concrete element when it is subject to this environmental attack, their applications present serious limitations that undergo, to the noteworthy sources of, uncertainty of many problem parameters. This restriction could produce erroneous solutions, especially when analysis deals with existing buildings or little information about problem parameters are accessible. In detail this takes place when real environmental conditions, mechanical properties as well as load conditions, could only be estimated and not known with enough accuracy. To overcome this problem, some methodologies have been developed, assuming that uncertainty variables can be suitably modeled in a probabilistic way, and therefore traditional theories for reliability assessment can be used. Nonetheless, in the analysis of this problem, there are other parameters that cannot be treated opportunely in a probabilistic way. The main purpose of this paper is to develop an efficient alternative approach for time-dependent reliability analysis regarding reinforced concrete beams subject to pitting corrosion, when probabilistic and nonprobabilistic parameters occur at the same time. With this new approach, it is possible to obtain a versatile tool to support the decision maker in planning maintenance interventions.