Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis

Currently, RNA-seq as a high throughput technology is being widely applied to various species to elucidate the complexity of the transcriptome and to discover large number of novel genes. However, the technology has had poor success in elucidating the transcriptome of tropical palms, as it is difficult to isolate high quality RNA from tropical palm tissues due to their high polysaccharide and polyphenol content. Here, we developed an RNA-isolation protocol for tropical palms, the MRIP method (Methods for RNA Isolation from Palms). The integrity of the RNA molecules extracted using this protocol was determined to be of high quality by means of gel electrophoresis and Agilent 2100 Bioanalyzer microfluidic electrophoresis chip examination with a RIN (RNA Integrity Number) value of more than 9, indicating that the mRNAs were of good integrity. Subsequently the isolated RNA was used for transcription analysis without further purification. With Illumina sequencing, we obtained 54.9 million short reads and then conducted de novo assembly to gain 57,304 unigenes with an average length of 752 base pairs. Moreover, the RNA isolated with this protocol was also successfully used for real-time RT-PCR. These results suggested that the RNA isolated was suitable for Illumina RNA sequencing and quantitative real-time RT-PCR. Furthermore, this method was also successful in isolating total RNA from the leaves of various Palmaceae species

The emission positions of kHz QPOs and Kerr spacetime influence

Based the Alfven wave oscillation model (AWOM) and relativistic precession model (RPM) for twin kHz QPOs, we estimate the emission positions of most detected kHz QPOs to be at r=18+-3 km (R/15km) except Cir X-1 at r = 30\+-5 km (R/15km). For the proposed Keplerian frequency as an upper limit to kHz QPO, the spin effects in Kerr Spacetime are discussed, which have about a 5% (2%) modification for that of the Schwarzchild case for the spin frequency of 1000 (400) Hz.The application to the four typical QPO sources, Cir X-1, Sco X-1, SAX J1808.4-3658 and XTE 1807-294, is mentioned.Comment: Science China, Physics, Mechanics & Astronomy, 2010, 53, NO.

Common and Specific Functional Activity Features in Schizophrenia, Major Depressive Disorder, and Bipolar Disorder

Objectives: Schizophrenia (SZ), major depressive disorder (MDD), and bipolar disorder (BD) are serious mental disorders with distinct diagnostic criteria. They share common clinical and biological features. However, there are still only few studies on the common and specific brain imaging changes associated with the three mental disorders. Therefore, the aim of this study was to identify the common and specific functional activity and connectivity changes in SZ, MDD, and BD.Methods: A total of 271 individuals underwent functional magnetic resonance imaging: SZ (n = 64), MDD (n = 73), BD (n = 41), and healthy controls (n = 93). The symptoms of SZ patients were evaluated by the Positive and Negative Syndrome Scale. The Beck Depression Inventory (BDI), and Beck Anxiety Inventory (BAI) were used to evaluate the symptoms of MDD patients. The BDI, BAI, and Young Mania Rating Scale were used to evaluate the symptoms of MDD and BD patients. In addition, we compared the fALFF and functional connectivity between the three mental disorders and healthy controls using two sample t-tests.Results: Significantly decreased functional activity was found in the right superior frontal gyrus, middle cingulate gyrus, left middle frontal gyrus, and decreased functional connectivity (FC) of the insula was found in SZ, MDD, and BD. Specific fALFF changes, mainly in the ventral lateral pre-frontal cortex, striatum, and thalamus were found for SZ, in the left motor cortex and parietal lobe for MDD, and the dorsal lateral pre-frontal cortex, orbitofrontal cortex, and posterior cingulate cortex in BD.Conclusion: Our findings of common abnormalities in SZ, MDD, and BD provide evidence that salience network abnormality may play a critical role in the pathogenesis of these three mental disorders. Meanwhile, our findings also indicate that specific alterations in SZ, MDD, and BD provide neuroimaging evidence for the differential diagnosis of the three mental disorders

Acidification oxidation reagent system optimization on coal seams and stimulation effect evaluation

China has abundant coalbed methane (CBM) resources, and most of them are low-permeability and tight reservoirs, with generally low production rate and small recovery factor. Existing technologies face great challenges to meet the demand on CBM in China. It is desirable to develop new methods to improve the production rate and enhance recovery factor. In addition to physical stimulation methods such as hydraulic fracturing and open-hole cave completion, the use of chemical methods to improve physical properties of coal reservoirs has also been a hot research topic in recent years. Coal reservoir acidification and oxidation technology can promote desorption of gas and enlarge permeability of reservoir. But for different coal rank coal reservoirs, the acidification and oxidation agents need to be optimized and their performance evaluated. Laboratory experiments are conducted to compare and analyze the physical properties coal samples from Baode, Mu’ai, and Xinjiang blocks, including coal rank, texture, macroscopic characteristics, quality, porosity, permeability, element, and mineral composition. The optimal concentration of hydrochloric acid is determined through pre-dissolution experiment of coal powder in acid solution. Then a five-factor and three-level orthogonal experiment for acid solution optimization is designed and performed by using Design-Expert software, which identifies the sensitive factors affecting the dissolution. For the coal samples in Baode, Mu’ai, and Xinjiang blocks, the oxidant types and the corresponding acidification and oxidation agent systems are optimized. Applying these acidification and oxidation agent systems to coal samples from Baode, Mu’ai, and Xinjiang blocks, the change of porosity, permeability, and wettability are compared and analyzed. Finally, through numerical simulation, the gas production is predicted for acidification and oxidation in typical well group in Block Mu’ai. Results show that the acid solution has the best dissolution at a concentration of hydrochloric acid of 3 mol/L to 4 mol/L; Top factors played in the experiment are soaking time, acid type, soaking temperature, coal sample type, and acid concentration, in descending order of importance; The optimal oxidant is a hydrogen peroxide solution with a concentration of 3%; the mixed acidification oxidant formula in Baode block is 10% HCl + 2% CH3COOH + 2% HF + 3% H2O2; The optimal mixed acidification oxidant formula in Mu’ai block is 8% HCl + 2% CH3COOH + 4% HF + 3% H2O2; the optimal mixed acidification oxidant formula in Xinjiang block is 12% HCl + 1% CH3COOH + 1% HF + 3% H2O2; The higher the coal rank, the greater the HF content in the optimal acidification oxidant system. Both acidification and oxidation improve the porosity and permeability of coal samples to some extent, and the improvement in low-rank coal is more significant than that in high-rank coal. Acidification and oxidation have different effects on the wettability of coal: Acidification increases the hydrophilicity of coal, whereas oxidation reduce the hydrophilicity of coal; and the hydrophilicity of coal samples treated by the optimized acidification and oxidation system is weakened. Reservoir simulation results show that acidification and oxidation lead to a recovery factor of 64.64% after 10 years of production, which is 19.72% higher than that without acidification and oxidation. The advantage of acidification and oxidation is 0.97% after 18 years of production. However, the acidification and oxidation saved 8 years of production time to achieve a close final recovery factor, which greatly reduces the operating costs. The optimized acidizing oxidation agent systems for CBM reservoirs with low, medium, and high ranks improved the desorption and permeability of the target reservoirs, and increase well production and recovery factor. This research provides technical support for stimulation practices of CBM reservoirs in the aforementioned blocks in China, as well as similar coal reservoirs in the world

From GPT-4 to Gemini and Beyond: Assessing the Landscape of MLLMs on Generalizability, Trustworthiness and Causality through Four Modalities

Multi-modal Large Language Models (MLLMs) have shown impressive abilities in generating reasonable responses with respect to multi-modal contents. However, there is still a wide gap between the performance of recent MLLM-based applications and the expectation of the broad public, even though the most powerful OpenAI's GPT-4 and Google's Gemini have been deployed. This paper strives to enhance understanding of the gap through the lens of a qualitative study on the generalizability, trustworthiness, and causal reasoning capabilities of recent proprietary and open-source MLLMs across four modalities: ie, text, code, image, and video, ultimately aiming to improve the transparency of MLLMs. We believe these properties are several representative factors that define the reliability of MLLMs, in supporting various downstream applications. To be specific, we evaluate the closed-source GPT-4 and Gemini and 6 open-source LLMs and MLLMs. Overall we evaluate 230 manually designed cases, where the qualitative results are then summarized into 12 scores (ie, 4 modalities times 3 properties). In total, we uncover 14 empirical findings that are useful to understand the capabilities and limitations of both proprietary and open-source MLLMs, towards more reliable downstream multi-modal applications

Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward

Research of a Novel Non-Axisymmetric Side-Compressed Variable Polarity Plasma Arc and Its Pressure Distribution Characteristics

In the keyhole variable polarity plasma arc weldng (VPPAW) process at horizontal position, the metal driven by gravity gathered on one side of the molten pool, and the weld formation is difficult, especially for thick workpiece welding. A specially designed experiment to analyze the influence of gravity on weld formation and a novel nozzle structure with side holes was proposed to generate a novel non-axisymmetric side-compressed plasma arc and redistribute arc pressure. The arc shape and pressure distribution were studied, and the ratio of difference for arc pressure in different directions Rp was introduced to evaluate the effects of non-axisymmetric side compression for the plasma arc. The results indicate that the non-axisymmetric distributed side holes reshape the plasma arc both in the EN and EP phases. The pressure of the non-axisymmetric side-compressed plasma arc decreases relatively strongly in one direction (direction b) and relatively weakly in the other direction (direction a). Rp is significant at 1 mm to 5 mm from the arc center, with a relatively large Rp within this range. The compression effect is enhanced with an increase in welding current or plasma gas flow rate, and Rp increases from 24% to 49% as the plasma gas flow rate increases from 2 L/min to 4.5 L/min. Specially designed validation experiments confirm that the new plasma arc significantly affects the weld formation in keyhole VPPAW process. An aluminum alloy workpiece with 8 mm thickness and no groove preparation was welded by the novel plasma arc in a horizontal welding position, and the weld is well formed

Image Processing for Laser Imaging Using Adaptive Homomorphic Filtering and Total Variation

Laser active imaging technology has important practical value and broad application prospects in military fields such as target detection, radar reconnaissance, and precise guidance. However, factors such as uneven laser illuminance, atmospheric backscatter, and the imaging system itself will introduce noise, which will affect the quality of the laser active imaging image, resulting in image contrast decline and blurring image edges and details. Therefore, an image denoising algorithm based on homomorphic filtering and total variation cascade is proposed in this paper, which strives to reduce the noise while retaining the edge features of the image to the maximum extent. Firstly, the image type is determined according to the characteristics of the laser image, and then the speckle noise in the low-frequency region is suppressed by adaptive homomorphic filtering. Finally, the image denoising method of minimizing the total variation is adopted for the impulse noise and Gaussian noise. Experimental results show that compared with separate homomorphic filtering, total variation filtering, and median filtering, the proposed algorithm significantly improves the contrast, retains edge details, achieves the expected effect. It can better adjust the image brightness and is beneficial for subsequent processing