Transcription start site mapping of geminiviruses using the in vitro cap-snatching of a tenuivirus.

Geminiviruses are a family of single-stranded DNA viruses that cause significant yield losses in crop production worldwide. Transcription start site (TSS) mapping is crucial in understanding the gene expression mechanisms of geminiviruses. However, this often requires costly and laborious experiments. Rice stripe virus (RSV) has a mechanism called cap-snatching, whereby it cleaves cellular mRNAs and uses the 5' cleavage product, a capped-RNA leader (CRL), as primers for transcription. Our previous work demonstrated that RSV snatches CRLs from geminiviral mRNAs in co-infected plants, providing a convenient and powerful approach to map the TSSs of geminiviruses. However, co-infections are not always feasible for all geminiviruses. In this study, we evaluated the use of in vitro cap-snatching of RSV for the same purpose, using tomato yellow leaf curl virus (TYLCV) as an example. We incubated RNA extracted from TYLCV-infected plants with purified RSV ribonucleoproteins in a reaction mixture that supports in vitro cap-snatching of RSV. The RSV mRNAs produced in the reaction were deep sequenced. The CRLs snatched by RSV allowed us to locate 28 TSSs in TYLCV. These results provide support for using RSV's in vitro cap-snatching to map geminiviral TSSs.

A Survey on Vision Transformer.

Transformer, first applied to the field of natural language processing, is a type of deep neural network mainly based on the self-attention mechanism. Thanks to its strong representation capabilities, researchers are looking at ways to apply transformer to computer vision tasks. In a variety of visual benchmarks, transformer-based models perform similar to or better than other types of networks such as convolutional and recurrent neural networks. Given its high performance and less need for vision-specific inductive bias, transformer is receiving more and more attention from the computer vision community. In this paper, we review these vision transformer models by categorizing them in different tasks and analyzing their advantages and disadvantages. The main categories we explore include the backbone network, high/mid-level vision, low-level vision, and video processing. We also include efficient transformer methods for pushing transformer into real device-based applications. Furthermore, we also take a brief look at the self-attention mechanism in computer vision, as it is the base component in transformer. Toward the end of this paper, we discuss the challenges and provide several further research directions for vision transformers.

Development and properties of new kojic acid and chitosan composite biodegradable films for active packaging materials.

Chitosan and kojic acid composite films (CHn-KAm) utilizing three chitosan with differing molecular weights and kojic acid in different ratios were investigated. Results showed that chitosan with higher molecular weights presented higher viscosity, mechanical properties and lower water vapor permeability. Furthermore, kojic acid addition further significantly decreased apparent viscosity, water content, water vapor permeability as well as increasing the antibacterial activity of the films. Increasing the kojic acid concentration resulted in increased levels of a*, b*, ΔE*, opacity values and a decreased L* value, as compared to chitosan films. The mechanical properties of CHn-KAm films increased significantly with kojic acid addition into chitosan. FTIR spectral analyses revealed a strong interaction in the film matrix consistent with composite film mechanical and physical properties. The CHn-KAm films showed significant antibacterial effectiveness. The results suggested that the use of chitosan with a higher molecular weight as CHn-KAm films is expected to be a promising material for food packaging.

The Protective Effect of Beraprost Sodium on Diabetic Nephropathy by Inhibiting Inflammation and p38 MAPK Signaling Pathway in High-Fat Diet/Streptozotocin-Induced Diabetic Rats.

Background. p38 mitogen-activated protein kinase (MAPK) plays a crucial role in regulating signaling pathways implicated in inflammatory processes leading to diabetic nephropathy (DN). This study aimed to examine p38 MAPK activation in DN and determine whether beraprost sodium (BPS) ameliorates DN by inhibiting inflammation and p38 MAPK signaling pathway in diabetic rats. Methods. Forty male Sprague Dawley (SD) rats were randomly divided into the normal control group, type 2 diabetic group, and BPS treatment group. At the end of the 8-week experiment, we measured renal pathological changes and the activation of the p38 MAPK signaling pathway and inflammation. Result. After BPS treatment, renal function, 24-hour urine protein, lipid profiles, and blood glucose level were improved significantly; meanwhile, inflammation and the expression of p38 MAPK signaling pathway in the diabetic kidney were attenuated. Conclusions. BPS significantly prevented type 2 diabetes induced kidney injury characterized by renal dysfunction and pathological changes. The protective mechanisms are complicated but may be mainly attributed to the inhibition of the p38 MAPK signaling pathway and inflammation in the diabetic kidney.

The time course of the tonic oculomotor proprioceptive signal in area 3a of somatosensory cortex.

A proprioceptive representation of eye position exists in area 3a of primate somatosensory cortex (Wang X, Zhang M, Cohen IS, Goldberg ME. Nat Neurosci 10: 640-646, 2007). This eye position signal is consistent with a fusimotor response (Taylor A, Durbaba R, Ellaway PH, Rawlinson S. J Physiol 571: 711-723, 2006) and has two components during a visually guided saccade task: a short-latency phasic response followed by a tonic response. While the early phasic response can be excitatory or inhibitory, it does not accurately reflect the eye's orbital position. The late tonic response appears to carry the proprioceptive eye position signal, but it is not clear when this component emerges and whether the onset of this signal is reliable. To test the temporal dynamics of the tonic proprioceptive signal, we used an oculomotor smooth pursuit task in which saccadic eye movements and phasic proprioceptive responses are suppressed. Our results show that the tonic proprioceptive eye position signal consistently lags the actual eye position in the orbit by ~60 ms under a variety of eye movement conditions. To confirm the proprioceptive nature of this signal, we also studied the responses of neurons in a vestibuloocular reflex (VOR) task in which the direction of gaze was held constant; response profiles and delay times were similar in this task, suggesting that this signal does not represent angle of gaze and does not receive visual or vestibular inputs. The length of the delay suggests that the proprioceptive eye position signal is unlikely to be used for online visual processing for action, although it could be used to calibrate an efference copy signal.