Automating Object Transformations for Dynamic Software Updating via Online Execution Synthesis

Dynamic software updating (DSU) is a technique to upgrade a running software system on the fly without stopping the system. During updating, the runtime state of the modified components of the system needs to be properly transformed into a new state, so that the modified components can still correctly interact with the rest of the system. However, the transformation is non-trivial to realize due to the gap between the low-level implementations of two versions of a program. This paper presents AOTES, a novel approach to automating object transformations for dynamic updating of Java programs. AOTES bridges the gap by abstracting the old state of an object to a history of method invocations, and re-invoking the new version of all methods in the history to get the desired new state. AOTES requires no instrumentation to record any data and thus has no overhead during normal execution. We propose and implement a novel technique that can synthesize an equivalent history of method invocations based on the current object state only. We evaluated AOTES on software updates taken from Apache Commons Collections, Tomcat, FTP Server and SSHD Server. Experimental results show that AOTES successfully handled 51 of 61 object transformations of 21 updated classes, while two state-of-the-art approaches only handled 11 and 6 of 61, respectively

A study of two bispectral features from envelope signals for bearing fault diagnosis

: To accurately detect and diagnose bearing faults, bispectral analysis has received more attention recently because of its unique property of noise reduction and nonlinearity extraction. Particularly this study investigates two typical bispectra: conventional bispectrum (CB) and modulation signal bispectrum (MSB) for suppressing noise influences in envelope signals and hence obtaining more accurate diagnostic features. The first component from the diagonal slice of CB results and that of the subdiagonal slices of MSB results are taken as the diagnostic features considering effective inclusion of information and easy of computations. Simulative and experimental studies show that both MSB and CB features result in good diagnostic performances but MSB may outperform CB slightly in that it shows smaller variance in attaining the feature and more sensitive to weak fault signatures. This merit of MSB may be due to that the MSB feature has more diagnostic information as it is the combination of first three harmonics, whereas the CB feature is combined from just the first two harmonics

Submission of Evidence on Online Violence Against Women to the UN Special Rapporteur on Violence Against Women, its Causes and Consequences, Dr Dubravka Šimonović

Figure S1. B3GALNT2 levels determined by W.B. and ROC curve. a–c Relative mRNA expression of B3GALNT2 in HCC tumor tissues and normal liver tissues obtained from GSE76427, GSE36376, and TCGA-LIHC datasets. d Western blot analysis of B3GALNT2 levels in 24 pairs of HCC tissues. T HCC tumor tissue, N adjacent non-tumor tissue. e ROC curve analysis of the sensitivity and specificity for the predictive value of TNM model, B3GALNT2 expression, and the combination model. (TIFF 546 kb

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement

Phosphorylation of plant virus proteins: Analysis methods and biological functions

Phosphorylation is one of the most extensively investigated post-translational modifications that orchestrate a variety of cellular signal transduction processes. The phosphorylation of virus-encoded proteins plays an important regulatory role in the infection cycle of such viruses in plants. In recent years, molecular mechanisms underlying the phosphorylation of plant viral proteins have been widely studied. Based on recent publications, our study summarizes the phosphorylation analyses of plant viral proteins and categorizes their effects on biological functions according to the viral life cycle. This review provides a theoretical basis for elucidating the molecular mechanisms of viral infection. Furthermore, it deepens our understanding of the biological functions of phosphorylation in the interactions between plants and viruses

Multi-tissue integrative analysis of personal epigenomes

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics

CARE: cache guided deterministic replay for concurrent Java programs

Deterministic replay tools help programmers debug concurrent pro-grams. However, for long-running programs, a replay tool may generate huge log of shared memory access dependences. In this paper, we present CARE, an application-level deterministic record and replay technique to reduce the log size. The key idea of CARE is logging read-write dependences only at per-thread value predic-tion cache misses. This strategy records only a subset of all exact read-write dependences, and reduces synchronizations protecting memory reads in the instrumented code. Realizing that such record strategy provides only value-deterministic replay, CARE also adopts variable grouping and action prioritization heuristics to synthesize sequentially consistent executions at replay in linear time. We implemented CARE in Java and experimentally evaluated it with recognized benchmarks. Results showed that CARE successfully resolved all missing read-write dependences, producing sequentially consistent replay for all benchmarks. CARE exhibited 1.7–40× (median 3.4×) smaller runtime overhead, and 1.1–309 × (median 7.0×) smaller log size against state-of-the-art technique LEAP

Sugarcane Streak Mosaic Virus P1 Attenuates Plant Antiviral Immunity and Enhances Potato Virus X Infection in <i>Nicotiana benthamiana</i>

The sugarcane streak mosaic virus (SCSMV) is the most important disease in sugarcane produced in southern China. The SCSMV encoded protein 1 (P1SCSMV) is important in disease development, but little is known about its detailed functions in plant–virus interactions. Here, the differential accumulated proteins (DAPs) were identified in the heterologous expression of P1SCSMV via a potato virus X (PVX)-based expression system, using a newly developed four-dimensional proteomics approach. The data were evaluated for credibility and reliability using qRT-RCR and Western blot analyses. The physiological response caused by host factors that directly interacted with the PVX-encoded proteins was more pronounced for enhancing the PVX accumulation and pathogenesis in Nicotiana benthamiana. P1SCSMV reduced photosynthesis by damaging the photosystem II (PSII). Overall, P1SCSMV promotes changes in the physiological status of its host by up- or downregulating the expression of host factors that directly interact with the viral proteins. This creates optimal conditions for PVX replication and movement, thereby enhancing its accumulation levels and pathogenesis. Our investigation is the first to supply detailed evidence of the pathogenesis-enhancing role of P1SCSMV, which provides a deeper understanding of the mechanisms behind virus–host interactions