Miracle-dz/UniFAR-FTUs huggingface dataset:
Adversarial Machine Learning Attacks and Defense Methods in the Cyber Security Domain

In recent years, machine learning algorithms, and more specifically deep learning algorithms, have been widely used in many fields, including cyber security. However, machine learning systems are vulnerable to adversarial attacks, and this limits the application of machine learning, especially in non-stationary, adversarial environments, such as the cyber security domain, where actual adversaries (e.g., malware developers) exist. This article comprehensively summarizes the latest research on adversarial attacks against security solutions based on machine learning techniques and illuminates the risks they pose. First, the adversarial attack methods are characterized based on their stage of occurrence, and the attacker’ s goals and capabilities. Then, we categorize the applications of adversarial attack and defense methods in the cyber security domain. Finally, we highlight some characteristics identified in recent research and discuss the impact of recent advancements in other adversarial learning domains on future research directions in the cyber security domain. To the best of our knowledge, this work is the first to discuss the unique challenges of implementing end-to-end adversarial attacks in the cyber security domain, map them in a unified taxonomy, and use the taxonomy to highlight future research directions.
Neuroprotective effects and mechanisms of ischemic/hypoxic preconditioning on neurological diseases

As the organ with the highest demand for oxygen, the brain has a poor tolerance to ischemia and hypoxia. Despite severe ischemia/hypoxia induces the occurrence and development of various central nervous system (CNS) diseases, sublethal insult may induce strong protection against subsequent fatal injuries by improving tolerance. Searching for potential measures to improve brain ischemic/hypoxic is of great significance for treatment of ischemia/hypoxia related CNS diseases. Ischemic/hypoxic preconditioning (I/HPC) refers to the approach to give the body a short period of mild ischemic/hypoxic stimulus which can significantly improve the body's tolerance to subsequent more severe ischemia/hypoxia event. It has been extensively studied and been considered as an effective therapeutic strategy in CNS diseases. Its protective mechanisms involved multiple processes, such as activation of hypoxia signaling pathways, anti‐inflammation, antioxidant stress, and autophagy induction, etc. As a strategy to induce endogenous neuroprotection, I/HPC has attracted extensive attention and become one of the research frontiers and hotspots in the field of neurotherapy. In this review, we discuss the basic and clinical research progress of I/HPC on CNS diseases, and summarize its mechanisms. Furthermore, we highlight the limitations and challenges of their translation from basic research to clinical application.
Reply

We reviewed with interest the letter by Thevenot and colleagues,(1) and we appreciate their comments regarding the novelty of the study findings and the need for additional data to further the knowledge about cirrhotic cardiomyopathy (CCM). In response to their inquiry, the echocardiographic studies, in our study, were obtained for liver transplantation (LT) evaluation, and the median time between those studies and LT was 107 days. (2) Although we appreciate the concern about nonselective βblockers (NSBB) potentially affecting myocardial reserve and possibly LT waitlist outcomes if used outside the therapeutic window, it should be noted that βblockers are the standard of care for treatment of other cardiomyopathies (ischemic and nonischemic) especially when the ejection fraction is reduced. (3) Studies addressing the impact of NSBB on waitlist outcomes in patients with CCM are certainly warranted. In our study, the focus was posttransplant outcomes, and therefore waitlist outcomes in relation to CCM and NSBB were not assessed. Although data have been emerging about the potential for reversibility versus progression of CCM after transplant, clear evidence supporting either direction is lacking. (4) The significant association of CCM with cardiovascular events after transplant in our study does not support the postulation that CCM universally reverses after LT. This is supported by the small subgroup analysis of 22 patients with CCM and postLT echocardiography in our study in whom only 6 had normalization of diastolic dysfunction. We agree that the study by Kim et al.(5) provides important insight into the postLT changes in myocardial extracellular volume, which can reflect myocardial fibrosis and/or myocardial edema, although the small sample size, limited availability of T2based data, inclusion of only 1 patient with diastolic dysfunction and 1 patient with late gadolinium enhancement, and lack of patients with reduced contractile function preclude drawing conclusions about CCM reversibility. It is noteworthy that the multifactorial increased cardiometabolic risk after LT and its sequelae make it challenging to draw definitive conclusions about CCM evolution after transplant. We wholeheartedly agree that prospective studies are needed to investigate the natural course of the newly defined CCM after transplant while accounting for confounding risk factors.
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores

Understanding transcriptomes requires documenting the structures, modifications, and abundances of RNAs as well as their proximity to other molecules. The methods that make this possible depend critically on enzymes (including mutant derivatives) that act on nucleic acids for capturing and sequencing RNA. We tested two 3’ nucleotidyl transferases, S. cerevisiae poly(A) polymerase and C. elegans Cid1, for the ability to add base and sugar modified rNTPs to free RNA 3’ ends, eventually focusing on Cid1. Although unable to polymerize ΨTP or 1meΨTP, Cid1 can use 5meUTP and 4thioUTP. Surprisingly, Cid1 can use inosine triphosphate to add poly(I) to the 3’ ends of a wide variety of RNA molecules. Most poly(A) mRNAs efficiently acquire a uniform tract of about 50 inosine residues from Cid1, whereas non-poly(A) RNAs acquire longer, more heterogeneous tails. Here we test these activities for use in direct RNA sequencing on nanopores, and find that Cid1-mediated poly(I)-tailing permits detection and quantification of both mRNAs and non-poly(A) RNAs simultaneously, as well as enabling the analysis of nascent RNAs associated with RNA polymerase II. Poly(I) produces a different current trace than poly(A), enabling recognition of native RNA 3’ end sequence lost by in vitro poly(A) addition. Addition of poly(I) by Cid1 offers a broadly useful alternative to poly(A) capture for direct RNA sequencing on nanopores.
ZomB is essential for chemotaxis of Vibrio alginolyticus by the rotational direction control of the polar flagellar motor

Bacteria exhibit chemotaxis by controlling flagellar rotation to move toward preferred places or away from non-preferred places. The change in rotation is triggered by the binding of the chemotaxis signaling protein CheY to the C-ring in the flagellar motor. Some specific bacteria, including Vibrio spp. and Shewanella spp. have a single transmembrane protein called ZomB. ZomB is essential for controlling the flagellar rotational direction in Shewanella putrefaciens and Vibrio parahaemolyticus. In this study, we confirmed that the zomB deletion results only in the counterclockwise (CCW) rotation of the motor in Vibrio alginolyticus as previously reported in other bacteria. We found that ZomB is not required for the clockwise (CW) rotation-fixing phenotype caused by mutations in fliG and fliM, and that ZomB is essential for CW rotation induced by overproduction of CheY. Purified ZomB proteins form multimers, indicating that ZomB functions as a complex. ZomB may interact with a protein involved in the flagellar rotation, stator proteins or rotor proteins. We found that ZomB is a new player in chemotaxis and is required for the rotational control in addition to CheY in Vibrio alginolyticus. Importance Bacterial chemotaxis is performed by the control of the flagellar rotation. CheY and ZomB control the rotational direction of the flagellar motor in Vibrio spp. and Shewanella spp. In this study, we characterized ZomB in Vibrio alginolyticus, which is essential for the clockwise rotation of the motor.
mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans

Advances in high-throughput single-cell mRNA sequencing (scRNA-seq) have been limited till date by technical challenges like tough cell walls and low RNA quantity that prevented transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity. These experiments are among the first high throughput single cell RNA-seq on different yeast species and demonstrate mDrop-seq as an affordable, easily implementable, and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to better understanding of genetic variation in yeasts in response to stimuli and find immediate applications in investigating drug resistance and infection outcome.
Identification of Single Nucleotide Polymorphism in TaSBEIII and Development of KASP Marker Associated With Grain Weight in Wheat

Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A, which formed the allelic marker allele-T. Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat.
Feasibility of a Sheep Welfare Assessment Tool in the Pre-export Phase of Australian Live Export Industry

Sheep are exposed to numerous stressors and environments during the pre-export phase of the live export industry. Establishing how animal behavior, health and demeanor reflect their experiences prior to sea transport is the first step toward testing the suitability and practicality of animal welfare measures. A total of 240 merino wethers originating from four farms were assessed at four locations in the live export chain: on farm, upon arrival to the registered export feedlot (Fe1), prior to departing the feedlot (Fe2) and 30 min post loading onto a live export vessel. Each of these locations and time points represent relevant assessment points as part of the commercial live export process. Pen-side behavioral and health measures were collected. Video footage was collected and edited to provide 48 30–45 s duration clips that were then scored by 12 assessors against 10 demeanor terms using a Qualitative Behavioral Assessment (QBA) methodology; data were analyzed using Principal Components (PC) analysis. Repeated Measures ANOVAs tested for variation in each dependent measure across each location and time point. There were low levels of health issues recorded overall; however, seven health and behavior measures significantly varied across the locations and time points. Most vocalizing was recorded on farm; most drinking, eating and resting behaviors were recorded at Fe1 and ruminating at Fe2; while the highest percentage of wethers with ocular discharge and lameness was on the vessel. For QBA, PC1 explained 30.5% of the variability, with agitated and nervous loaded to one end of the axis and calm and relaxed loaded to the opposing end. PC2 explained 24.5% of the variability, with interested, alert and sociable loaded to one end of the axis and lethargic loaded to the opposing end. Spearman's rank correlations between behavior, health and PC scores indicated that wethers eating, ruminating and resting were scored as more calm/relaxed, while those scored as more agitated/nervous or/ lethargic were also likely to vocalize. Determining how wethers respond to the different environments in the immediate pre-export phase of the journey informs on their welfare and the practicality of using a behavior tool to assess animal welfare.
Systematic vs. Narrative Reviews in Sport and Exercise Psychology: Is Either Approach Superior to the Other?

With the explosion of published primary research there has been a parallel increase of secondary literature. Literature reviews substantially reduce the burden of readership, as readers are not only given a shortcut to the most important citations without having to review the wider literature pool on a certain topic but are also given an intelligent synthesis from the perspective of an expert. Although there are many publishedmethodological guidelines (e.g., Grant and Booth, 2009; Higgins et al., 2019; Snyder, 2019) on how to conduct literature reviews, the interdisciplinary nature and broad scope of topics that are covered by the umbrella term of sport psychology calls for a critical discussion of how to adopt methodological guidelines developed in other fields. This paper addresses the increasing opinion (Mulrow et al., 1988; Higgins et al., 2019) that systematic reviews are the state of the art and superior to other forms of reviews as they have explicit and reproducible methodology and are assumed to be less biased than other reviews (Faggion et al., 2017). We have made the experience and heard increasing reports in which editors and reviewers reject articles on the simple grounds of being “not systematic. ” It is arguably more difficult and arduous to evaluate narrative reviews compared to systematic reviews given the precise methodological guidelines available for systematic reviews. However, this does not mean that systematic reviews are always the superior form of literature review, particularly in a diverse, interdisciplinary research field like sport and exercise psychology. Similar to Abraham Maslow’s 1966 law of instrument (. . . “it is tempting, if the only tool you have is a hammer, to treat everything as if it were a nail.” p. 15) we will argue that different forms of literature review have different goals, are better suited for different questions or bodies of literature, cannot be ranked hierarchically, should be viewed as complementary, and need to be reviewed and evaluated differently.
Hydroethanolic Extract of A. officinarum Hance Ameliorates Hypertension and Causes Diuresis in Obesogenic Feed-Fed Rat Model

Alpinia officinarum Hance (Zingiberaceae) has been used widely in traditional Chinese and Ayurvedic medicines. Its folkloric uses include relieving stomach ache, treating cold, improving the circulatory system, and reducing swelling. Its effectiveness and mechanism of antihypertension in obesity-induced hypertensive rats have not been studied yet as per our knowledge. This study has been designed to provide evidence of underlying mechanisms to the medicinal use of A. officinarum as a cardiotonic using an obesity-induced hypertension model in rats. Chronic administration of A. officinarum caused a marked reduction in the body weight gain and Lee index of rats compared to the obesogenic diet-fed rats. Its administration also caused attenuation in blood pressure (systolic, diastolic, and mean), serum total cholesterol, triglyceride, and leptin, while an increase in serum HDL and adiponectin levels was noticed. The catalase and superoxide dismutase enzymatic activities were found to be remarkable in the serum of A. officinarum-treated animal groups. A. officinarum showed mild to moderate diuretic, hepatoprotective, and reno-protective effects. The A. officinarum-treated group showed less mRNA expression of 3-hydroxy-3-methylglutaryl-CoA reductase while the mRNA expression of peroxisome proliferator-activated receptor and mRNA expression of cholesterol 7 alpha-hydroxylase were raised in comparison to the hypertensive group of rats evaluated by quantitative real-time polymerase chain reaction. These findings show that A. officinarum possesses antihypertensive and diuretic activities, thus providing a rationale to the medicinal use of A. officinarum in cardiovascular ailments.
Protein Surface Interactions—Theoretical and Experimental Studies

In this review, we briefly describe a theoretical discussion of protein folding, presenting the relative contribution of the hydrophobic effect versus the stabilization of proteins via direct surface forces that sometimes may be overlooked. We present NMR-based studies showing the stability of proteins lacking a hydrophobic core which in turn present hydrophobic surface clusters, such as plant defensins. Protein dynamics measurements by NMR are the key feature to understand these dynamic surface clusters. We contextualize the measurement of protein dynamics by nuclear relaxation and the information available at protein surfaces and water cavities. We also discuss the presence of hydrophobic surface clusters in multidomain proteins and their participation in transient interactions which may regulate the function of these proteins. In the end, we discuss how surface interaction regulates the reactivity of certain protein post-translational modifications, such as S-nitrosation.
Application of Double-Strand RNAs Targeting Chitin Synthase, Glucan Synthase, and Protein Kinase Reduces Fusarium graminearum Spreading in Wheat

Controlling the devastating fungal pathogen Fusarium graminearum (Fg) is a challenge due to inadequate resistance in nature. Here, we report on the identification of RNAi molecules and their applications for controlling Fg in wheat through silencing chitin synthase 7 (Chs7), glucan synthase (Gls) and protein kinase C (Pkc). From transgenic Fg strains four RNAi constructs from Chs7 (Chs7RNAi−1, −2, −3, and −4), three RNAi constructs from Gls (GlsRNAi−2, −3, and −6), and one RNAi construct from Pkc (PkcRNAi−5) were identified that displayed effective silencing effects on mycelium growth in medium and pathogenicity in wheat spikes. Transcript levels of Chs7, Gls and Pkc were markedly reduced in those strains. Double-strand RNAs (dsRNAs) of three selected RNAi constructs (Chs7RNAi-4, GlsRNAi-6 and PkcRNA-5) strongly inhibited mycelium growth in vitro. Spray of those dsRNAs on detached wheat leaves significantly reduced lesion sizes; the independent dsRNAs showed comparable effects on lesions with combination of two or three dsRNAs. Expression of three targets Chs7, Gls, and Pkc was substantially down-regulated in Fg-infected wheat leaves. Further application of dsRNAs on wheat spikes in greenhouse significantly reduced infected spikelets. The identified RNAi constructs may be directly used for spray-induced gene silencing and stable expression in plants to control Fusarium pathogens in agriculture.
Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation

The dairy cattle suffer from severe liver dysfunction during the pathogenesis of ketosis. The Ufm1 conjugation system is crucial for liver development and homeostasis. Ufm1 binding protein (Ufbp1) is a putative Ufm1 target and an integral component, but its role in ketosis-induced liver injury is unclear so far. The purpose of this study is to explore the key role of Ufbp1 in liver fibrosis caused by ketosis in vivo and in vitro. Liver tissues were collected from ketotic cows and Ufbp1 conditional knockout (CKO) mice in vivo. However, Ufbp1–/– mouse embryonic fibroblast cells and Hela cells were used for in vitro validation. Subsequently, various assays were performed to reveal the underlying molecular mechanisms of the Ufbp1 protective effect. In this study, hepatic fibrosis, endoplasmic reticulum (ER) stress, and apoptosis were reported in the liver of ketotic cows, fibrotic markers (alpha-smooth muscle actin, Collagen1) and ER stress markers (glucose-regulated protein 78, CEBP homologous protein) were upregulated remarkably, and the apoptosis-related genes (Bcl2, Bax) were in line with expectations. Interestingly, Ufbp1 expression was almost disappeared, and Smad2/Smad3 protein was largely phosphorylated in the liver of ketotic cows, but Ufbp1 deletion caused Smad3 phosphorylation apparently, rather than Smad2, and elevated ER stress was observed in the CKO mice model. At the cellular level, Ufbp1 deficiency led to serious fibrotic and ER stress response, Smad3 was activated by phosphorylation significantly and then was translocated into the nucleus, whereas p-Smad2 was largely unaffected in embryonic fibroblast cells. Ufbp1 overexpression obviously suppressed Smad3 phosphorylation in Hela cells. Ufbp1 was found to be in full combination with Smad3 using endogenous immunoprecipitation. Taken together, our findings suggest that downregulation or ablation of Ufbp1 leads to Smad3 activation, elevated ER stress, and hepatocyte apoptosis, which in turn causes liver fibrosis. Ufbp1 plays a protective role in ketosis-induced liver injury.