Human branch point consensus sequence is yUnAy

Yeast carries a strictly conserved branch point sequence (BPS) of UACUAAC, whereas the human BPS is degenerative and is less well characterized. The human consensus BPS has never been extensively explored in vitro to date. Here, we sequenced 367 clones of lariat RT-PCR products arising from 52 introns of 20 human housekeeping genes. Among the 367 clones, a misincorporated nucleotide at the branch point was observed in 181 clones, for which we can precisely pinpoint the branch point. The branch points were comprised of 92.3% A, 3.3% C, 1.7% G and 2.8% U. Our analysis revealed that the human consensus BPS is simply yUnAy, where the underlined is the branch point at position zero and the lowercase pyrimidines (‘y’) are not as well conserved as the uppercase U and A. We found that the branch points are located 21–34 nucleotides upstream of the 3′ end of an intron in 83% clones. We also found that the polypyrimidine tract spans 4–24 nucleotides downstream of the branch point. Our analysis demonstrates that the human BPSs are more degenerative than we have expected and that the human BPSs are likely to be recognized in combination with the polypyrimidine tract and/or the other splicing cis-elements

Visual Framing of Science Conspiracy Videos: Integrating Machine Learning with Communication Theories to Study the Use of Color and Brightness

Recent years have witnessed an explosion of science conspiracy videos on the Internet, challenging science epistemology and public understanding of science. Scholars have started to examine the persuasion techniques used in conspiracy messages such as uncertainty and fear yet, little is understood about the visual narratives, especially how visual narratives differ in videos that debunk conspiracies versus those that propagate conspiracies. This paper addresses this gap in understanding visual framing in conspiracy videos through analyzing millions of frames from conspiracy and counter-conspiracy YouTube videos using computational methods. We found that conspiracy videos tended to use lower color variance and brightness, especially in thumbnails and earlier parts of the videos. This paper also demonstrates how researchers can integrate textual and visual features in machine learning models to study conspiracies on social media and discusses the implications of computational modeling for scholars interested in studying visual manipulation in the digital era. The analysis of visual and textual features presented in this paper could be useful for future studies focused on designing systems to identify conspiracy content on the Internet

A New Method for Optimal Regularization Parameter Determination in the Inverse Problem of Load Identification

According to the regularization method in the inverse problem of load identification, a new method for determining the optimal regularization parameter is proposed. Firstly, quotient function (QF) is defined by utilizing the regularization parameter as a variable based on the least squares solution of the minimization problem. Secondly, the quotient function method (QFM) is proposed to select the optimal regularization parameter based on the quadratic programming theory. For employing the QFM, the characteristics of the values of QF with respect to the different regularization parameters are taken into consideration. Finally, numerical and experimental examples are utilized to validate the performance of the QFM. Furthermore, the Generalized Cross-Validation (GCV) method and the L-curve method are taken as the comparison methods. The results indicate that the proposed QFM is adaptive to different measuring points, noise levels, and types of dynamic load

doi:10.1093/nar/gkn073 Human branch point consensus sequence is yUnAy

Yeast carries a strictly conserved branch point sequence (BPS) of UACUAAC, whereas the human BPS is degenerative and is less well characterized. The human consensus BPS has never been extensively explored in vitro to date. Here, we sequenced 367 clones of lariat RT-PCR products arising from 52 introns of 20 human housekeeping genes. Among the 367 clones, a misincorporated nucleotide at the branch point was observed in 181 clones, for which we can precisely pinpoint the branch point. The branch points were comprised of 92.3 % A, 3.3 % C, 1.7 % G and 2.8 % U. Our analysis revealed that the human consensus BPS is simply yUnAy, where the underlined is the branch point at position zero and the lowercase pyrimidines (‘y’) are not as well conserved as the uppercase U and A. We found that the branch points are located 21–34 nucleotides upstream of the 3 ’ end of an intron in 83 % clones. We also found that the polypyrimidine tract spans 4–24 nucleotides downstream of the branch point. Our analysis demonstrates that the human BPSs are more degenerative than we have expected and that the human BPSs are likely to be recognized in combination with the polypyrimidine tract and/or the other splicing cis-elements

Long-term outcomes of macrovascular diseases and metabolic indicators of bariatric surgery for severe obesity type 2 diabetes patients with a meta-analysis.

There is currently no detailed evidence for the long-term effects of bariatric surgery on severely obese with type 2 diabetes, such as the risk of myocardial infarction and stroke. In order to provide evidence on the risks of macrovascular diseases and metabolic indicators of bariatric surgery follow-up for more than five years, we searched in the Cochrane library, Pubmed, and EMBASE databases from the earliest studies to January 31, 2019. Randomized clinical trials or cohort studies compared bariatric surgery and conventional medical therapy for long-term incidence of macrovascular events and metabolic outcomes in severely obese patients with T2DM. Fixed-effects and random-effects meta-analyses were performed to pool the relative risks (RRs), hazard ratios (HRs) and weighted mean difference (WMD). Publication bias and heterogeneity were examined. Four RCTs and six cohort studies were finally involved in this review. Patients in the bariatric surgery group as compared to the conventional treatment group had lower incidence of macrovascular complications (RR = 0.43, 95%CI = 0.27~0.70), cardiovascular events (CVEs) (HR = 0.52, 95%CI = 0.39~0.71), and myocardial infarction (MI) (RR = 0.40, 95%CI = 0.26~0.61). At the same time, the results demonstrate that bariatric surgery is associated with better weight and better glycemic control over the long-term than non-surgical therapies, and reveal that different surgical methods have different effects on various metabolic indicators. Bariatric surgery significantly decreases macrovascular complications over the long term and is associated with greater weight loss and better intermediate glucose outcomes among T2DM patients with severe obesity as compared to patients receiving only conservative medical measures

Research Update on the Impact of Lactic Acid Bacteria on the Substance Metabolism, Flavor, and Quality Characteristics of Fermented Meat Products

This paper reviews the effects of domestic and foreign influences on the substance metabolism pathways and the flavor and flora of LAB in fermented meat products to provide a new theoretical basis for developing new products for the industrial application of lactic acid bacteria (LAB) in fermented meat products. LAB are extensively used among commonly fermented ingredients, such as fermented meat products and yogurt. As fermenting agents, LAB metabolize proteins, lipids, and glycogen in meat products through their enzyme system, which affects the tricarboxylic acid cycle, fatty acid metabolism, amino acid decomposition, and other metabolic processes, and decompose biological macromolecules into small molecules, adding a special flavor with a certain functionality to the final product. Metabolites of LAB in the fermentation process also exert nitrite degradation, as well as antibacterial and antioxidant functions, which improve the physical and chemical qualities of fermented meat products. While fermenting meat products, LAB not only add unique flavor substances to the products, but also improve the safety profile of fermented foods

Research Progress on Water–Fertilizer Coupling and Crop Quality Improvement and Its Implication for the Karst Rock Desertification Control

An important problem currently faced by karst rocky desertification management is the degradation of vegetation fruits, which encourages the search for a solution for the sustainable growth of vegetation. Water and fertilizer are key factors affecting crop quality (the formation of soluble solids, protein, amino acids, soluble sugar content, etc.). A comprehensive review of research related to water–fertilizer coupling and crop quality improvement may be beneficial for rocky desertification control. This study analyzed 427 related papers, and the results showed that: (1) the number of published papers showed an “S” curve growth trend over time, indicating that research in the field of water–fertilizer coupling has entered a mature stage after rapid growth, yet it is still in the initial stage in karst areas; (2) the research was mainly theoretical, but also included technology research and development, model construction, demonstration and extension, and monitoring and evaluation; (3) except for research related to greenhouse facilities, the research areas are mainly located in arid and semi-arid regions. The study further revealed (4) the frontier theory of water–fertilizer coupling and crop quality research. Finally, it was found that the theoretical and technical studies related to water–fertilizer coupling and crop quality improvement in karst areas are insufficient. Whether the existing theories and techniques are applicable to karst areas needs further verification. In addition to the areas of selecting germplasm with high water/fertilizer utilization efficiency and tolerance to rocky desertification, further improvement in the dynamic model of water–fertilizer coupling and the construction of a more applicable water–fertilizer coupling model could also be future research hotspots

The Changes Occurring in Proteins during Processing and Storage of Fermented Meat Products and Their Regulation by Lactic Acid Bacteria

Protein, which is the main component of meat, is degraded and oxidized during meat fermentation. During fermentation, macromolecular proteins are degraded into small peptides and free amino acids, and oxidation leads to amino acid side chain modification, molecular crosslinking polymerization, and peptide chain cleavage. At different metabolic levels, these reactions may affect the protein structure and the color, tenderness, flavor, and edible value of fermented meat products. Lactic acid bacteria are currently a research hotspot for application in the fermented meat industry. Its growth metabolism and derivative metabolites formed during the fermentation of meat products regulate protein degradation and oxidation to a certain extent and improve product quality. Therefore, this paper mainly reviews the changes occurring in proteins in fermented meat products and their effects on the quality of the products. Referring to studies on the effects of lactic acid bacteria on protein degradation and oxidation from all over the world, this review aims to provide a relevant reference for improving the quality of fermented meat products

Research Progress on Water–Fertilizer Coupling and Crop Quality Improvement and Its Implication for the Karst Rock Desertification Control

An important problem currently faced by karst rocky desertification management is the degradation of vegetation fruits, which encourages the search for a solution for the sustainable growth of vegetation. Water and fertilizer are key factors affecting crop quality (the formation of soluble solids, protein, amino acids, soluble sugar content, etc.). A comprehensive review of research related to water–fertilizer coupling and crop quality improvement may be beneficial for rocky desertification control. This study analyzed 427 related papers, and the results showed that: (1) the number of published papers showed an “S” curve growth trend over time, indicating that research in the field of water–fertilizer coupling has entered a mature stage after rapid growth, yet it is still in the initial stage in karst areas; (2) the research was mainly theoretical, but also included technology research and development, model construction, demonstration and extension, and monitoring and evaluation; (3) except for research related to greenhouse facilities, the research areas are mainly located in arid and semi-arid regions. The study further revealed (4) the frontier theory of water–fertilizer coupling and crop quality research. Finally, it was found that the theoretical and technical studies related to water–fertilizer coupling and crop quality improvement in karst areas are insufficient. Whether the existing theories and techniques are applicable to karst areas needs further verification. In addition to the areas of selecting germplasm with high water/fertilizer utilization efficiency and tolerance to rocky desertification, further improvement in the dynamic model of water–fertilizer coupling and the construction of a more applicable water–fertilizer coupling model could also be future research hotspots