Task-Robust Pre-Training for Worst-Case Downstream Adaptation

Pre-training has achieved remarkable success when transferred to downstream tasks. In machine learning, we care about not only the good performance of a model but also its behavior under reasonable shifts of condition. The same philosophy holds when pre-training a foundation model. However, the foundation model may not uniformly behave well for a series of related downstream tasks. This happens, for example, when conducting mask recovery regression where the recovery ability or the training instances diverge like pattern features are extracted dominantly on pre-training, but semantic features are also required on a downstream task. This paper considers pre-training a model that guarantees a uniformly good performance over the downstream tasks. We call this goal as $\textit{downstream-task robustness}$. Our method first separates the upstream task into several representative ones and applies a simple minimax loss for pre-training. We then design an efficient algorithm to solve the minimax loss and prove its convergence in the convex setting. In the experiments, we show both on large-scale natural language processing and computer vision datasets our method increases the metrics on worse-case downstream tasks. Additionally, some theoretical explanations for why our loss is beneficial are provided. Specifically, we show fewer samples are inherently required for the most challenging downstream task in some cases

Combined amino acids modulation with H2O2 stress for glutathione overproduction in Candida utilis

Strategies of amino acids addition coupled with H2O2 stresses were developed for glutathione (GSH) overproduction in high cell density (HCD) cultivation of Candida utilis. Based on the fact that glycine shows two functions of promoting cells growth as well as GSH production, precursor amino acids modulations of feeding glycine at 4 mmol/l/h at exponential phase and adding precursor amino acids (glutamic acid 42 mmol/l, glycine 40 mmol/l, and cysteine 36 mmol/) at stationary phase were conducted. As a result, cell density reached 114.8 g/l at 45 h and glutathione yield of 2136 mg/l was achieved at 60 h, which was 12.5 and 90.2% higher than the control, respectively. Furthermore, the novel strategies of amino acids modulation combined with H2O2 additions (24 mmol/l at 21 h, 26 mmol/l at 29 h, 28 mmol/l at 37 h and 30 mmol/l at 45 h) were adopted to maximize glutathione production. Final glutathione yield reached 2448 mg/l after 60 h cultivation, suggesting the strategies developed as being feasible for GSH overproduction. Keywords: Amino acids, glutathione (GSH), high cell density (HCD) cultivation, Candida utilis, H2O2 stressesAfrican Journal of Biotechnology Vol. 9(33), pp. 5399-5406, 16 August, 201

Cloning and expression of pineapple sucrosephosphate synthase gene during fruit development

A 1132-base pairs (bp) polymerase-chain-reaction product of sucrose-phosphate synthase (SPS) (EC 2.3.1.14) from pineapple (Ananas comosus cv. Comte de paris) fruit was cloned and nominated as Ac- SPS1. The sequence encodes a putative 377 amino acids protein containing two serine conserved features that had been found in other plant SPS genes: the presence of a 14-3-3 protein special binding domain and an activated site of osmosis stress, which can been activated by phosphorylation and dephosphorylation. The Neighbour-joining tree revealed that Ac-SPS1 belonged to the first kind of sucrose phosphate synthase gene. The results indicated that, the Ac-SPS1 expression was low in the earlier period of fruit growth, then, increasing from 20 days after anthesis and gradually a falling on 40 days, reached the peak with the highest value around 70 days. The SPS activity and sucrose content reached their maximum 80 days after anthesis. It proved that the  accumulation of sucrose was correlated with SPS activity and mRNA content and it maximally occurred at 10 d after SPS mRNA and activity had reached its maxima. These results indicated that Ac-SPS1 gene played a key role in sucrose accumulation during the pineapple fruit development and transcriptional activation with increase in Ac- SPS1 expression might be important regulatory events of sugar during pineapple fruit maturation.Key words: Pineapple fruit, sucrose phosphate synthase, gene cloning, expression

LPI-IBNRA: Long Non-coding RNA-Protein Interaction Prediction Based on Improved Bipartite Network Recommender Algorithm

According to the latest research, lncRNAs (long non-coding RNAs) play a broad and important role in various biological processes by interacting with proteins. However, identifying whether proteins interact with a specific lncRNA through biological experimental methods is difficult, costly, and time-consuming. Thus, many bioinformatics computational methods have been proposed to predict lncRNA-protein interactions. In this paper, we proposed a novel approach called Long non-coding RNA-Protein Interaction Prediction based on Improved Bipartite Network Recommender Algorithm (LPI-IBNRA). In the proposed method, we implemented a two-round resource allocation and eliminated the second-order correlations appropriately on the bipartite network. Experimental results illustrate that LPI-IBNRA outperforms five previous methods, with the AUC values of 0.8932 in leave-one-out cross validation (LOOCV) and 0.8819 ± 0.0052 in 10-fold cross validation, respectively. In addition, case studies on four lncRNAs were carried out to show the predictive power of LPI-IBNRA

Diagnostic accuracy of perfusion-weighted phase-resolved functional lung magnetic resonance imaging in patients with chronic pulmonary embolism

PurposeThis study aimed to evaluate the diagnostic performance of perfusion-weighted phase-resolved functional lung (PW-PREFUL) magnetic resonance imaging (MRI) in patients with chronic pulmonary embolism (CPE).Materials and methodsThis study included 86 patients with suspected chronic thromboembolic pulmonary hypertension (CTEPH), who underwent PREFUL MRI and ventilation/perfusion (V/Q) single-photon emission computed tomography/computed tomography (SPECT/CT). PREFUL MRI was performed at 1.5 T using a balanced steady-state free precession sequence during free breathing. Color-coded PW images and quantitative parameters were obtained by postprocessing. Meanwhile, V/Q SPECT/CT imaging was performed as a reference standard. Hypoperfused areas in the lungs were scored for each lobe and segment using V/Q SPECT/CT images and PW-PREFUL MR images, respectively. Normalized perfusion (QN) and perfusion defect percentage (QDP) were calculated for all slices. For intra- and interobserver variability, the MRI images were analyzed 2 months after the first analysis by the same radiologist and another radiologist (11 years of lung MRI experience) blinded to the results of the first reader.ResultsOf the 86 enrolled patients, 77 met the inclusion criteria (36 diagnosed with CPE using V/Q SPECT/CT and 41 diagnosed with non-CPE etiology). For the PW-PREFUL MRI, the sensitivity, specificity, accuracy, and positive and negative predictive values for the diagnosis of CPE were 97, 95, 96, 95, and 98% at the patient level; 91, 94, 93, 91, and 94% at the lobe level, and 85, 94, 92, 88, and 94% at the segment level, respectively. The detection of segmental and subsegmental hypoperfusion using PW-PREFUL MRI revealed a moderate agreement with V/Q SPECT/CT (κ = 0.65; 95% confidence interval: 0.61–0.68). The quantitative results indicated that the QN was lower in the CPE group than in the non-CPE group [median score (interquartile range, IQR) 6.3 (2.8–9.2) vs. 13.0 (8.8–16.7), p < 0.001], and the QDP was higher [median score (IQR) 33.8 (15.7–51.7) vs. 2.2 (1.4–2.9), p < 0.001].ConclusionPREFUL MRI could be an alternative test to detect CPE without requiring breath-hold, contrast agents, or ionizing radiation

Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars

MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4

Changes in some chemical components and in the physiology of rambutan fruit (

Introduction. Rambutan (Nephelium lappaceum L.) is a kind of tropical fruit with high commercial value in international trade. However, harvested rambutan fruits suffer from a short shelf life and show rapid postharvest deterioration problems due to spintern browning and flesh decay. Materials and methods. Rambutan fruit (cv. ‘Baoyan 5’) were harvested in 2009 and 2010. Changes in some chemical components and the physiology of fruits were investigated at different storage temperatures (25 °C and 10 °C) and with different packing materials (regular low-density polyethylene and anti-moisture polyethylene bags). Results and discussion. Changes in the development of the browning index, and contents of total soluble solids, titratable acidity and vitamin C greatly decreased during low temperature storage (10 °C); moreover, low temperature storage (10 °C) could maintain a significantly higher level of superoxide dismutase activity and lower values of malondialdehyde and cell membrane permeability. The effects of packing material were different according to the different storage temperatures. At 10 °C, the beneficial effects of anti-moisture polyethylene bags on fruit quality and physiology were observed. However, at 25 °C, fruit packed with regular low-density polyethylene proved to be of better quality than those packed with anti-moisture polyethylene bags. Conclusion. The overall results suggest that packing with anti-moisture polyethylene bags and storage at 10 °C were the most suitable conditions to maintain quality and to extend the storage life of rambutan fruit