Normal tissue samples are often employed as a control for understanding disease mechanisms, however, collecting matched normal tissues from patients is difficult in many instances. In cancer ...research, for example, the open cancer resources such as TCGA and TARGET do not provide matched tissue samples for every cancer or cancer subtype. The recent GTEx project has profiled samples from healthy individuals, providing an excellent resource for this field, yet the feasibility of using GTEx samples as the reference remains unanswered.
We analyze RNA-Seq data processed from the same computational pipeline and systematically evaluate GTEx as a potential reference resource. We use those cancers that have adjacent normal tissues in TCGA as a benchmark for the evaluation. To correlate tumor samples and normal samples, we explore top varying genes, reduced features from principal component analysis, and encoded features from an autoencoder neural network. We first evaluate whether these methods can identify the correct tissue of origin from GTEx for a given cancer and then seek to answer whether disease expression signatures are consistent between those derived from TCGA and from GTEx.
Among 32 TCGA cancers, 18 cancers have less than 10 matched adjacent normal tissue samples. Among three methods, autoencoder performed the best in predicting tissue of origin, with 12 of 14 cancers correctly predicted. The reason for misclassification of two cancers is that none of normal samples from GTEx correlate well with any tumor samples in these cancers. This suggests that GTEx has matched tissues for the majority cancers, but not all. While using autoencoder to select proper normal samples for disease signature creation, we found that disease signatures derived from normal samples selected via an autoencoder from GTEx are consistent with those derived from adjacent samples from TCGA in many cases. Interestingly, choosing top 50 mostly correlated samples regardless of tissue type performed reasonably well or even better in some cancers.
Our findings demonstrate that samples from GTEx can serve as reference normal samples for cancers, especially those do not have available adjacent tissue samples. A deep-learning based approach holds promise to select proper normal samples.
The use of pediatric donor liver for pediatric liver transplantation (LT) remains controversial and few studies have focused on pediatric deceased donors. To address this issue, we decided to perform ...a retrospective research, trying to compare the clinical effects between deceased donor LTs (DDLTs) and living donor LTs (LDLTs).
A retrospective review of pediatric LTs using grafts from deceased donors and living donors from June 2013 to August 2016 was performed. The children were divided into a DDLT group and a LDLT group based on their donor styles. The incidence of early vascular complications (VC), biliary complications, and graft and patient survival rates were observed between the 2 groups.
There were 217 cases of pediatric LTs performed in our hospital from June 2013 to August 2016 (83 DDLTs and 134 LDLTs). The 1-year cumulative survival rates of grafts and recipients were 89.16% and 91.57% in DDLTs, and 95.47% and 95.52% in LDLTs, respectively (P > .05). The incidence of early VC was lower in LDLTs than that in DDLTs (3.7% vs 19.3%, P < .001). The incidence of HAT in children aged less than 1 year was significantly higher in the DDLT group (P < .001) and can be up to 31.82%. The incidence of biliary complications was similar in the 2 groups (8.4% vs 13.5%, P = .285).
Pediatric DDLTs have similar graft and patient survival rates with LDLT. The incidence of early VC was higher in DDLTs, and children aged less than 1 year are at a higher risk of developing HAT.
•Along with considerable development of organ donation after death of people in China, pediatric donation has become an important supplement to the graft pool, which has an important role in decreasing mortality among patients on the waiting list.•This study evaluated the efficacy of pediatric liver transplantation (LT) using deceased donor whole liver and living donor liver, and compares the outcomes.•There were 217 cases of pediatric LTs performed in our hospital from June 2013 to August 2016 (83 DDLTs and 134 LDLTs).•The 1-year cumulative survival rates of grafts and recipients were 89.16%, 91.57% in DDLT, and 95.47%, 95.52% in LDLT, respectively (P > .05). The ratio of early VC was lower in LDLTs than that in DDLTs (3.73% vs 19.28%, P < .001).•The incidence of HAT in children aged less than 1 year was significantly higher among the DDLT group (P < .001), and the ratio can be up to 31.82%.•Our study showed that pediatric DDLT have a similar graft and patient survival rates with LDLT. The incidence of VC was higher in DDLT, and children aged less than 1 year are at higher risk of developing HAT.
We present a new software ray tracing solution that efficiently computes visibilities in dynamic scenes. We first introduce a novel scene representation: ray‐aligned occupancy map array (ROMA) that ...is generated by rasterizing the dynamic scene once per frame. Our key contribution is a fast and low‐divergence tracing method computing visibilities in constant time, without constructing and traversing the traditional intersection acceleration data structures such as BVH. To further improve accuracy and alleviate aliasing, we use a spatiotemporal scheme to stochastically distribute the candidate ray samples. We demonstrate the practicality of our method by integrating it into a modern real‐time renderer and showing better performance compared to existing techniques based on distance fields (DFs). Our method is free of the typical artifacts caused by incomplete scene information, and is about 2.5×–10× faster than generating and tracing DFs at the same resolution and equal storage.
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Effects of alloying additions on deformation texture in Mg sheet alloys are still controversial. In this study, a quasi-in-situ electron backscatter diffraction method is used for the ...first time to monitor the texture evolution during the cold rolling process of Mg–Zn–Ca and Mg–Zn alloys. It is found that the Ca addition does not cause any texture weakening effect — it only delays the development of a strong basal texture by reducing the growth of deformation twins.
The Fukushima Nuclear Accident (FNA) resulted in a large amount of radionuclides released into the atmosphere and dispersed globally, which has greatly raised public concerns. The state of the art ...for source terms of 19 kinds of radionuclides derived from the FNA was comprehensively collected and compared with levels of the global fallout and the Chernobyl Nuclear Accident (CNA). The atmospheric impacts of the FNA were evaluated from three aspects including radioactive baseline of the atmosphere, the concentration limits in standards and radiological protection. The FNA should not impose significant radiological risk on the public members in the countries excluding Japan. A conceptual scheme of Fukushima-derived radionuclides with physical and physicochemical insights on different temporal–spatial timescales was discussed and illustrated to understand their fates in the atmosphere.
•The radioactive source terms from the FNA were comprehensively collected.•Natural atmospheric radionuclides with total activity of 1–100 Bq/m3 were discussed.•The peak activity from the FNA was less than 1‰ of that in national standards.•The effective dose from the FNA for public excluding Japanese was about 71 nSv.•A conceptual scheme of atmospheric radionuclides from the FNA was illustrated.
CD1 represents a third lineage of antigen-presenting molecules that are distantly related to major histocompatibility complex (MHC) molecules in the immune system. The crystal structure of mouse ...CD1d1, corresponding to human CD1d, at 2.8 Å resolution shows that CD1 adopts an MHC fold that is more closely related to that of MHC class I than to that of MHC class II. The binding groove, although significantly narrower, is substantially larger because of increased depth and it has only two major pockets that are almost completely hydrophobic. The extreme hydrophobicity and shape of the binding site are consistent with observations that human CD1b and CD1c can present mycobacterial cell wall antigens, such as mycolic acid and lipoarabinomannans. However, mouse CD1d1 can present very hydrophobic peptides, but must do so in a very different way from MHC class la and class II molecules.
NiTi shape memory alloy joints were obtained using ultrasonic spot welding and the effect of this manufacturing process on the mechanical behaviour was investigated. Comparing to the as-received ...NiTi, the welded material presented increasing austenite transformation temperatures and decreasing martensite finish transformation temperatures. No detrimental intermetallic compounds were found at the weld interface due to the advantages of this solid-state welding technology. A typical interfacial fracture mode was observed at the fracture surface with numerous cleavage planes and micro cracks. Additionally, plastically deformed regions were observed in the weld spot. Ultrasonic welding can be used to effectively join NiTi shape memory alloys.
AbstractThe rheological behavior of soil–water mixtures can affect the flow dynamics of natural processes such as flow-type landslides and sediment transport. In this study, an experimental ...investigation was carried out on soil–water mixtures containing particles up to 0.425 mm with volumetric solid concentrations of 0.05≤CV≤0.35 using a wide-gap rotational viscometer, and the contributions of particle–fluid, collisional, and colloidal interactions to their rheological behavior were evaluated thoroughly. The torque-scaling method was applied to identify the flow regime and extract the effective rheological parameters from turbulent flows. A transition between dilute and concentrated mixtures can be identified based on their sediment type, CV, and the predominance of particle–fluid and interparticle interactions. For dilute mixtures (CV<0.25–0.28) the particle-fluid interaction is dominant. The colloidal interactions induce another force scale that is independent of the shear rate. Thus, the Bingham model can be applied to such mixtures (debris or mud flood). For concentrated mixtures (CV>0.25–0.28), the shear-thickening rheology can be applied for granular mixtures (debris flows), because the collisional interactions are dominant, whereas shear-thinning rheology can be applied for fine-grained mixtures (mudflows), because colloidal interactions are dominant.
Previously, we used secondary electrospray ionization-mass spectrometry (SESI-MS) to investigate the diurnal patterns and signal intensities of exhaled (EX) volatile fatty acids (VFA) of dairy cows. ...The current study aimed to validate the potential of an exhalomics approach for evaluating rumen fermentation. The experiment was conducted in a switchback design, with 3 periods of 9 d each, including 7 d for adaptation and 2 d for sampling. Four rumen-cannulated original Swiss Brown (Braunvieh) cows were randomly assigned to 1 of 2 diet sequences (ABA or BAB): (A) low starch (LS; 6.31% starch on a dry matter basis) and (B) high starch (HS; 16.2% starch on a dry matter basis). Feeding was once per day at 0830 h. Exhalome (with the GreenFeed System), and rumen samples were collected 8 times to represent every 3 h of a day, and EX-VFA and ruminal (RM)-VFA were analyzed using SESI-MS and HPLC, respectively. Furthermore, the VFA concentration in the gas phase (HR-VFA) was predicted based on RM-VFA and Henry's Law (HR) constants. No interactions were identified between the types of diets (HS vs. LS) and the measurement methods on daily average VFA profiles (RM vs. EX or HR vs. EX), suggesting a consistent performance among the methods. Additionally, when the 3-h interval VFA data from HS and LS diets were analyzed separately, no interactions were observed between methods and time of day, indicating that the relative daily pattern of VFA molar proportions was similar regardless of the VFA measurement method used. The results revealed that the levels of acetate sharply increased immediately after feeding, trailed by an increase in the acetate:propionate ratio and a steady increase for propionate (2 h after feeding the HS diet, 4 h for LS), and butyrate. This change was more pronounced for the HS diet than the LS diet. However, there was no overall diet effect on the VFA molar proportions, although the measurement methods affected the molar proportions. Furthermore, we observed a strong positive correlation between the levels of RM and EX acetate for both diets (HS: r = 0.84; LS: r = 0.85), RM and EX propionate (r = 0.74), and RM and EX acetate:propionate ratio (r = 0.80). Both EX-VFA and RM-VFA exhibited similar responses to feeding and dietary treatments, suggesting that EX-VFA could serve as a useful proxy for characterizing RM-VFA molar proportions to evaluate rumen fermentation. Similar relationships were observed between RM-VFA and HR-VFA. In conclusion, this study underscores the potential of exhalomics as a reliable approach for assessing rumen fermentation. Moving forward, research should further explore the depth of exhalomics in ruminant studies to provide a comprehensive insight into rumen fermentation metabolites, especially across diverse dietary conditions.
This paper presents a fast method to compute large‐scale problems in real‐time finite element simulations in the presence of contact and friction. The approach uses a precondition‐based contact ...resolution that performs a Cholesky decomposition at low frequency. On exploiting the sparsity in assembled matrices, we propose a reduced and parallel computation scheme to address the expensive computation of the Schur‐complement arisen by detailed mesh and accurate contact response. An efficient GPU‐based solver is developed to parallelise the computation, making it possible to provide real‐time simulations in the presence of coupled constraints for contact and friction response. In addition, the pre‐conditioner is updated at low frequency, implying reuse of the factorised system. To benefit a further speedup, we propose a strategy to share the resolution information between consecutive time steps. We evaluate the performance of our method in different contact applications and compare it with typical approaches on CPU and GPU.
This paper presents a fast method to compute large‐scale problems in real‐time finite element simulations in the presence of contact and friction.
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