Miracle-dz/UniFAR-FTUs huggingface dataset:
The clinical value of circulating tumor DNA detection in advanced non-small cell lung cancer

Background Circulating tumor DNA (ctDNA) is a kind of cell-free DNA which comes from tumor cells and effectively reflects the molecular characteristics of tumors, which providing us a novel method to explore its clinical therapeutic value in advanced lung cancer. Methods A total of 36 patients with advanced non-small cell lung cancer (NSCLC) were enrolled in this study, including 28 cases of adenocarcinoma and 8 cases of squamous cell carcinoma. Next-generation sequencing based ctDNA detection, tissue DNA (tDNA) detection, corresponding survival analysis, and retrospective statistics were performed to explore the feasibility of clinical practice directed by molecular characteristics in NSCLC. Results Epidermal growth factor receptor mutation (EGFR mutation) took over the highest mutation frequency (36.11%) in 36 samples, and the subsequent genes were PIK3CA, BRAF, KRAS, NRAS, MAP2K1, and GNAQ; 11 patients were detected with multiple gene mutations, including 8 cases with double gene mutations, 1 case with three gene mutations, and 2 cases with four gene mutations, and the subsequent 12-month survival observation revealed that patients with less mutations also had a longer OS (10.37±0.74 vs. 7.08±1.43 months, P=0.034). Twenty-one patients with EGFR mutation and subsequently treated with EGFR-tyrosine kinase inhibitor (TKI) combined chemotherapy, had significantly longer PFS than those with EGFR wild type and treated with chemotherapy in next 5-year monitoring test (18.00±4.41 vs. 7.33±1.58 months, P=0.024). Conclusions Gene mutation in advanced lung cancer is complex, and ctDNA detection has important guiding significance in clinical treatment of advanced NSCLC.
Reliability Analysis of Flow Meters with Multiple Failure Modes in the Process Industry

Reliability analysis of flow meters is an important issue for process industry companies because of the need to ensure the production quality and operational safety. In practice, field data for flow meters failure process can have complicated structure due to multiple failure modes arising from different electromechanical parts. Besides, incomplete records generally exist. For example, the installation date is usually not available, making the failure data left-truncated. There also exist right-censored cases since many units are still in service when the data are analyzed. In this paper, we use a nonhomogeneous Poisson process model with power-law intensity functions to address multiple failure modes for field data with both left-truncated and right-censored cases. We apply the maximum likelihood method to estimate the model parameters. In order to address the statistical uncertainty, random weighted likelihood bootstrap procedure is used to estimate the standard errors and confidence intervals of the parameters. Real-world flow meters failure data from a process industry company are used in the case study. Estimated intensity functions and estimation of mean time to failure are obtained and show that the parametric model can reasonably fit the failure data well.
Digestibility of canola protein products derived from the physical, enzymatic and chemical processing of commercial canola meal in rainbow trout Oncorhynchus mykiss (Walbaum) held in fresh water

This study was undertaken to assess the relative importance of nutrient composition and levels of antinutritional factors present in various canola protein products derived from the processing of commercial canola meal (CCM) on digestibility in rainbow trout held in 9.9-11 degrees C fresh water. Laboratory sieving of CCM (SCM) reduced levels of crude fibre, cellulose and hemicellulose by 31.6%, 16.6% and 56.4%, respectively. Aqueous methanol-ammonia washing of sieved canola meal (ACM) increased neutral detergent fibre (NDF, insoluble dietary fibre) and phytate, and dramatically decreased levels of total glucosinolates (> 88%) and phenolic compounds (approximately equal to 59%) relative to CCM. Further treatment of ACM with phytase in acidified (pH 5.0) aqueous media (PCM), followed by filtration, increased levels of crude protein, crude fibre and NDF, and decreased levels of phytate (33%), phenolic compounds (81%) and glucosinolates (below detection limit) relative to CCM. Additional treatment of PCM with carbohydrase enzymes (SP-249 and/or Alpha Gal, an oligosaccharide-degrading enzyme) further elevated levels of NDF, cellulose, protein (SP-249 only) and indispensable amino acids (SP-249/Alpha Gal), and concurrently decreased levels of phytate relative to PCM. An industrial source of canola protein isolate (CPI), produced by first extracting CCM with aqueous salt solution and then recovering the protein fraction, had the best nutrient composition and lowest levels of the antinutritional factors mentioned above. The processing protocols had slight or marked negative effects (ACM and SP-249/Alpha Gal) on apparent dry matter digestibility. Protein digestibility coefficients were unaltered in the laboratory-processed products, except for the products treated with SP-249 and SP-249/Alpha-Gal. In these cases, the protein digestibility coefficients (77.4% and 79.5%) were significantly below that found for CCM (88.1%). With two of the treatments, ACM and SP-249/Alpha-Gal, processing depressed DE. In contrast, the DE level in CPI (20.6 MJ kg(-1)) and the digestibility coefficients for dry matter (77.1%) and protein (97.6%) were high. We conclude that high levels of fibre, either alone or together with phytate, have the greatest adverse effects on the digestibility of canola protein products for rainbow trout. The high digestibility of CPI and its low content of antinutritional factors may also enable this protein product to be an excellent substitute for premium quality fish meal in diets for salmonids.
Temperature effect on fructan oligomer contents and fructan-related enzyme activities in stems of wheat (Triticum aestivum L.) during grain filling

SUMMARY Two 2 m2 stands of wheat were grown under controlled conditions from 2 d after anthesis until harvest. Day and night temperature were 18 and 10 °C respectively in crop 1, whereas they were shifted to 28 and 20 °C 5 d after anthesis in crop 2. CO2 exchange rates of the canopies were continuously measured. Samples of 20 plants were collected from each crop two or three times a week. Grain filling was monitored as were various carbohydrates and enzyme activities in stems. Sugar reserves were highly correlated with the difference between cumulative photosynthesis and dry matter stored in grains. Fructan accumulated up to 150 mg culm−1 2 wk after anthesis in crop 1; but it ceased to accumulate in crop 2 as soon as high temperature was applied, because the increased metabolic rates resulted in higher carbon requirement for grain filling. The fructan was mostly phlein or highly 2–6 linked oligomers with a degree of polymerization up to 15. 6-Kestose was the most abundant, reaching 70 mg culm−1 in crop 1. 1-Kestose content never exceeded 25 mg culm−1 and it remained roughly constant from anthesis to harvest. No temperature-related difference in amount of 1-Kestose was noticed. Four kestotetraoses were quantified, 6,6- followed by l&6-kestotetraose were the most abundant of them. The (2–1) linkages in bulk kestotetraose decreased from 40 % of total at anthesis to 10 % at maximum grain fresh weight. This chemical shift of the fructan reserves in the two crops was accelerated but not enhanced by elevated temperature. (2-l)-Fructan exohydrolase increased as soon as temperature was enhanced. However, in both crops its activity peaked at maximum grain dry weight only. Sucrose-sucrose fructosyl transferase was constant at 01 nkat culm−1 in crop 1, whereas its activity decreased in crop 2 when temperature increased. Little change in invertase activity can be reported in both crops later than 1 wk after anthesis.
A New Stator Winding Inter-Turn Short Circuit Fault Detection Method For Brushless Doubly Fed Induction Machine

The brushless Doubly Fed Induction Machine (BDFIM) with high reliability and robust structure demonstrates technical and commercial advantages both as a generator and motor for variable speed drive applications. As a generator it is particularly attractive to be used in offshore wind turbines where reliability improvement and maintenance cost reduction are the key factors in wind power market growth. As a motor it can be utilized in application requiring adjustable speed operation. Inter-turn short circuit fault is one of the most frequent electrical faults in electric machines, which can also be the cause of other stator winding faults in the machine, hence its early detection can significantly reduce the maintenance cost and improve reliability. In this paper a novel fault detection method for inter-turn short circuit fault is proposed for the BDFIM based on the discrete wavelet transform of the stator winding currents. The analytical winding function method as well as the finite element analysis of an experimental D180 BDFIM is used in order to verify the proposed fault detection method.
BER Comparison of Coding Schemes in LowPower Regime

This paper investigates the application of advanced forward error correction techniques mainly: Turbo code, Low-Density Parity Checks (LDPC) code, and Raptor code for wireless communication systems in the low power regime (LPR). These codes are under consideration for many recent technologies. Different code parameters such as code rate and several decoding iterations are used to show their effect on the performance of digital systems. Simulation results showed that the Raptor code is performed better than Turbo code and LDPC code over binary input additive white Gaussian noise (BI_AWGN), for the same coding rate and the number of decoding iterations. Considering bit error rate (BER) performance, Raptor code with rate1/2 and 1/3 provided better performance than Turbo and LDPC for the SNR up to -5dB for the AWGN channel. Finally, in comparison with Turbo and LDPC, Raptor code shows better performance for a large number of decoding iterations and low coding rates.
Olfactory Malformations in Mendelian Disorders of the Epigenetic Machinery

Usually overlooked by physicians, olfactory abnormalities are not uncommon. Olfactory malformations have recently been reported in an emerging group of genetic disorders called Mendelian Disorders of the Epigenetic Machinery (MDEM). This study aims to determine the prevalence of olfactory malformations in a heterogeneous group of subjects with MDEM. We reviewed the clinical data of 35 patients, 20 females and 15 males, with a mean age of 9.52 years (SD 4.99). All patients had a MDEM and an already available high-resolution brain MRI scan. Two experienced neuroradiologists reviewed the MR images, noting abnormalities and classifying olfactory malformations. Main findings included Corpus Callosum, Cerebellar vermis, and olfactory defects. The latter were found in 11/35 cases (31.4%), of which 7/11 had Rubinstein-Taybi syndrome (RSTS), 2/11 had CHARGE syndrome, 1/11 had Kleefstra syndrome (KLFS), and 1/11 had Weaver syndrome (WVS). The irregularities mainly concerned the olfactory bulbs and were bilateral in 9/11 patients. With over 30% of our sample having an olfactory malformation, this study reveals a possible new diagnostic marker for MDEM and links the epigenetic machinery to the development of the olfactory bulbs.
Community Assembly Rules, Morphological Dispersion, and the Coexistence of Plant Species

In order to find and define any assembly rules for communities, we must first investigate the patterns among species assemblages. We used a series of null models to test for patterns in wetland plant composition at the level of species, functional guilds, and traits. At the species level, we found significant checkerboard and nestedness patterns. Three functional guilds had some tendency to contribute a constant percentage to species richness, but after Bonferroni correction there was no significant pattern. Coexisting plant species showed no consistent overall pattern of morphological dispersion. However, when we considered each of 11 traits in turn, we found that 4 traits were overdispersed and 3 were underdispersed. Thus there are morphological assembly rules that constrain wetland plant community composition. These results reconcile contrasting views of community assembly. Communities can be simultaneously structured by a tension between two forces: abiotic external forces that constrain certain traits within limits and biotic internal forces that tend to keep coexisting species from being too similar. Because our sites vary along a fertility/disturbance gradient, we also investigated how trait dispersion varies in space. Trait dispersion increases with soil fertility; soil phosphorus explains about 36% of the variance in mean nearest neighbor distance. Species richness tends to decline with mean nearest neighbor distance, which contrasts with the general pattern for animal assemblages.
Identification of a Novel Mutation in SASH1 Gene in a Chinese Family With Dyschromatosis Universalis Hereditaria and Genotype-Phenotype Correlation Analysis

Dyschromatosis universalis hereditaria (DUH) is a rare genodermatosis characterized by mottled hyperpigmented and hypopigmented macules. SASH1 and ABCB6 have been identified as the causative genes for this disorder. We performed whole exome sequencing on a Chinese family with DUH and genotype-phenotype correlation analysis in DUH and lentiginous phenotype patients. A novel heterozygous missense mutation p.Q518P in SASH1 gene was detected in this family. A majority of patients with SASH1 mutations presented as a distinct clinical phenotype clearly different from that in patients with ABCB6 mutations. Our findings further enrich the reservoir of SASH1 mutations in DUH. The clinical phenotypic difference between SASH1 and ABCB6 variants is suggestive of a close phenotype-genotype link in DUH.
Low Expression of Claudin-7 as Potential Predictor of Distant Metastases in High-Grade Serous Ovarian Carcinoma Patients

High-grade serous ovarian carcinoma (HGSOC) usually spreads directly into the peritoneal cavity following a transcoelomic dissemination route, although distant hematogenous metastasis exist and have been reported. However, no tumor markers can currently predict the risk of distant metastases in HGSOC. Claudins, belonging to tight-junction proteins, are dysregulated in HGSOC and functionally related to cancer progression. Here we analyzed claudin-3, -4, and -7 expression as potential markers of distant metastases. Using quantitative RT-PCR and immunohistochemistry we assessed the expression of claudins in primary HGSOC tissues, normal ovarian, and normal fallopian tube epithelia and correlated it with clinicopathological features, including the site of metastasis and the route of dissemination. Gene set enrichment analysis was performed on microarray-generated gene expression data to investigate key pathways in patients with distant metastases. We found the overall expression level of claudin-3, -4, and -7 mRNA decreased in HGSOC compared to normal tubal epithelium, currently considered the potential site of origin of many HGSOC. The reduced expression of claudin-7 is significantly associated with the development of distant metastases (p = 0.016), mainly by hematogenous route (p = 0.025). In patients with diminished expression of claudin-7, immunohistochemical staining revealed a heterogeneous pattern of membranous staining with discontinuous expression of claudin-7 along the cell border, indicative of a dischoesive architecture. The estimated reduction in the probability of distant disease is of 39% per unit increase in the level of claudin-7 (p = 0.03). Genes involved in epithelial to mesenchymal transition, hypoxia, and angiogenesis processes resulted strongly associated to hematogenous recurrence. Our data suggest a potential role of claudin-7 in discriminating distant metastatic events in HGSOC patients. The quantification of its expression levels could be a useful tool to identify patient deserving a personalized follow-up in terms of clinical and radiological assessment.
EFFECTS OF FALLOW DURATION ON SOIL PHOSPHORUS FRACTIONS AND CROP P UPTAKE UNDER NATURAL REGROWTH AND PLANTED PUERARIA PHASEOLOIDES FALLOW SYSTEMS IN SOUTHWESTERN NIGERIA

Soil phosphorus fractions, maize and cassava P uptakes in natural regrowth fallow and Pueraria phaseoloides fallow systems, as affected by the duration (1–3 years) of fallow, were assessed in 1998 and 1999 in a long-term fallow management trial, established in 1989 at the International Institute of Tropical Agriculture, Ibadan, Nigeria. After one and three years fallow respectively, the mean P accumulation in fallow vegetation was 4.2 and 9.4 kg ha−1 in 1998, and 8.9 and 12.1 kg ha−1 in 1999 for natural fallow. For Pueraria, the corresponding values were 6.3 and 7.4 kg ha−1 in 1998 and 6.1 and 13.5 kg ha−1 in 1999. The positive effects of fallow lengths on dry matter and P accumulation were not as pronounced under Pueraria. Continuous cropping reduced soil pH and depleted Olsen P more than crop-fallow rotations under both fallow systems. An increase in fallow duration enhanced the availability of resin P, NaHCO3-, and NaOH- extractable P fractions, especially under natural fallow. Continuous cropping in a natural fallow system resulted in lower resin inorganic P (Pi) and NaHCO3-extractable inorganic and organic P (Po) fractions, and higher refractory P fractions (concentrated HCl-extractable Pi and Po and residual P) as compared to crop-fallow rotations. Although continuous cropping in the Pueraria system resulted in higher refractory P fractions than the crop-fallow rotations, the effects of fallow length on P fractions were not consistent or pronounced. Maize and cassava P uptakes increased with fallow duration. Phosphorous in maize grain was positively correlated with fallow vegetation P accumulation. Total P uptake by maize was positively but weakly correlated with NaHCO3-Po, Olsen P and fallow vegetation P accumulation.
Phytoplankton composition in the coastal Magnetic Island lagoon, Western Pacific Ocean (Australia)

1 - Coastal lagoons have traditionally been considered as transitional systems between continental and marine domains. The phytoplankton plays a key role in these aquatic environments, forming the base of the food web and having a substantial function in nutrient dynamics and in the carbon biogeochemical cycle. 2 - Due to their short life cycle, planktonic algae respond quickly to environmental changes and they are thus a valuable indicator of water quality. It is essential to investigate the development of phytoplankton populations to understand the biological functioning and to detect changes in aquatic systems. 3 - Phytoplankton studies in the Australian estuaries and lagoons are relatively scarce. This study has provided a broad perspective and preliminary information on taxonomic structure of phytoplankton guilds for the Magnetic Island Lagoon (Queensland, Australia). This work may provide valuable information of interest to later ecological studies. 4 - In the whole sampling a total of 143 taxa were identified. In terms of species richness, diatoms (Bacillariophyceae, Coscinodiscophyceae, Fragilariophyceae) and dinoflagellates (Dinophyceae) were the most important groups. In taxonomic terms, diatoms were the major contributor to the phytoplankton composition (~ 70%) whereas Dinophyceae were moderately abundant (~23%). Diatoms are a very important component in estuarine and shallow coastal wetlands and they are increasingly being utilized as indicators of environmental change.
BAG5 Promotes Alpha-Synuclein Oligomer Formation and Functionally Interacts With the Autophagy Adaptor Protein p62

Molecular chaperones are critical to maintaining intracellular proteostasis and have been shown to have a protective role against alpha-synuclein-mediated toxicity. Co-chaperone proteins regulate the activity of molecular chaperones and connect the chaperone network to protein degradation and cell death pathways. Bcl-2 associated athanogene 5 (BAG5) is a co-chaperone that modulates proteostasis by inhibiting the activity of Heat shock protein 70 (Hsp70) and several E3 ubiquitin ligases, resulting in enhanced neurodegeneration in models of Parkinson’s disease (PD). Here we identify a novel interaction between BAG5 and p62/sequestosome-1 (SQSTM1), suggesting that BAG5 may bridge the chaperone network to autophagy-mediated protein degradation. We found that BAG5 enhanced the formation of pathogenic alpha-synuclein oligomers and regulated the levels and subcellular distribution of p62. These results extend the role of BAG5 in alpha-synuclein processing and intracellular proteostasis.
Collapsin Response Mediator Protein 2 and Endophilin2 Coordinate Regulation of AMPA Receptor GluA1 Subunit Recycling

The dynamic trafficking of AMPA receptors (AMPARs), which enables the endocytosis, recycling, and exocytosis of AMPARs, is crucial for synaptic plasticity. Endophilin2, which directly interacts with the GluA1 subunit of AMPARs, plays an important role in AMPAR endocytosis. Collapsin response mediator protein 2 (CRMP2) promotes the maturation of the dendritic spine and can transfer AMPARs to the membrane. Although the mechanisms of AMPAR endocytosis and exocytosis are well known, the exact molecular mechanisms underlying AMPAR recycling remain unclear. Here, we report a unique interaction between CRMP2 and endophilin2. Our results showed that overexpression of CRMP2 and endophilin2 increased the amplitude and frequency of miniature excitatory synaptic currents (mEPSCs) and modestly enhanced AMPAR levels in hippocampal neurons. Furthermore, the CRMP2 and endophilin2 overexpression phenotype failed to occur when the interaction between these two proteins was inhibited. Further analysis revealed that this interaction was regulated by CRMP2 phosphorylation. The phosphorylation of CRMP2 inhibited its interaction with endophilin2; this was mainly affected by the phosphorylation of Thr514 and Ser518 by glycogen synthase kinase (GSK) 3β. CRMP2 phosphorylation increased degradation and inhibited the surface expression of AMPAR GluA1 subunits in cultured hippocampal neurons. However, the dephosphorylation of CRMP2 inhibited degradation and promoted the surface expression of AMPAR GluA1 subunits in cultured hippocampal neurons. Taken together, our data demonstrated that the interaction between CRMP2 and endophilin2 was conductive to the recycling of AMPA receptor GluA1 subunits in hippocampal neurons.