Miracle-dz/UniFAR-FTUs huggingface dataset:
Chinese Wheat Mosaic Virus-Induced Gene Silencing in Monocots and Dicots at Low Temperature

Virus-induced gene silencing (VIGS) is an important tool for functional genomics studies in plants. With this method, it is possible to target most endogenous genes and downregulate the messenger RNA (mRNA) in a sequence-specific manner. Chinese wheat mosaic virus (CWMV) has a bipartite, single-strand positive RNA genome, and can infect both wheat and Nicotiana benthamiana, and the optimal temperature for systemic infection in plants is 17°C. To assess the potential of the virus as a vector for gene silencing at low temperature, a fragment of the N. benthamiana or wheat phytoene desaturase (PDS) gene was expressed from a modified CWMV RNA2 clone and the resulting photo bleaching in infected plants was used as a reporter for silencing. Downregulation of PDS mRNA was also measured by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR). In experiments using fragments of PDS ranging from 500 to 1500 nucleotides, insert length influenced the stability and the efficiency of VIGS. The CWMV induced silencing system was also used to suppress miR165/166 and miR3134a through expression of miRNA target mimics. The relative expression levels of mature miR165/166 and miR3134a decreased whereas the transcript levels of their target genes increased. Interestingly, we also found the CWMV-induced silencing system was more efficient compare with the vector based on Barley stripe mosaic virus (BSMV) or Foxtail mosaic virus (FoMV) in wheat or the vector based on TRV in N. benthamiana at 17°C. In summary, the CWMV vector is effective in silencing endogenous genes and miRNAs at 17°C, thereby providing a powerful tool for gene function analysis in both N. benthamiana and wheat at low temperature.
Swabbing the surface: critical factors in environmental monitoring and a path towards standardization and improvement

Abstract Cross-contamination can be broadly defined as the transfer, direct or indirect, of microorganisms from a contaminated product to a non-contaminated product. Events that may result in cross-contamination include inadequate hygiene practices, contaminated equipment surfaces, contamination via food handling personnel, further product processing, or storage abuse All of these niches require consistent environmental surveillance systems to monitor microbial harborage sites to prevent foodborne illnesses via cross-contamination. Environmental surveillance is achieved through routine surface sampling of the food contact surfaces and surrounding areas. To better understand cross-contamination, the role of environmental surface transmission during outbreaks due to the presence and persistence of pathogenic microorganisms on various food contact surfaces must be investigated. However, studies on environmental sampling techniques are rarely performed in an actual food processing environment but rather under controlled variables within a laboratory-setting. Moreover, results and conclusions of studies differ because of the considerable variability across surface sampling tools due to individual operator dependency, low recovery rates, and low reproducibility. Information is also often lacking on environmental sampling tools used within a processing facility, the characterization of these tools, and the optimization of recovery of microorganisms for surface sampling. Thus, this review aims to: (1) discuss and compare factors impacting the recovery of microorganisms and the standardization of surface sampling methods for optimal recovery of microorganisms and (2) examine how research strategies could focus more towards the development of standard methodologies for surface sampling.
Patient-Controlled Nutrition After Abdominal Surgery: Novel Concept Contrary to Surgical Dogma

Purpose According to surgical dogma, patients who are recovering from general anesthesia after abdominal surgery should begin with a clear liquid diet, progress to a full liquid diet and then to a soft diet before taking regular meals. We propose patient-controlled nutrition (PCN), which is a novel concept in postoperative nutrition after abdominal surgery. Methods A retrospective pilot study was conducted to evaluate the feasibility and effects of PCN. This study was carried out with a total of 179 consecutive patients who underwent a laparoscopic appendectomy between August 2014 and July 2016. In the PCN group, diet was advanced depending on the choice of the patients themselves; in the traditional group, diet was progressively advanced to a full liquid or soft diet and then a regular diet as tolerated. The primary endpoints were time to tolerance of regular diet and postoperative hospital stay. Results Time to tolerance of a regular diet (P < 0.001) and postoperative hospital stay (P < 0.001) showed statistically significant differences between the groups. Multivariate analysis using linear regression showed that the traditional nutrition pattern was the only factor associated with postoperative hospital stay (P < 0.001). Multivariate analysis using logistic regression showed that traditional nutrition was the only risk factor associated with prolonged postoperative hospital stay (≥3 days). Conclusion After abdominal surgery, PCN may be a feasible and effective concept in postoperative nutrition. In our Early Recovery after Surgery program, our PCN concept may reduce the time to tolerance of a regular diet and shorten the postoperative hospital stay.
Roles of mucus adhesion and cohesion in cough clearance

Significance Mucoobstructive lung diseases, including chronic obstructive pulmonary disease, asthma, and cystic fibrosis, are characterized by intrapulmonary accumulations of hyperconcentrated mucus. Ultimately, mucus accumulation in disease reflects the failure of the major rescue mucus clearance pathway, i.e., cough. Studies were performed to understand how abnormal mucus and its interactions with the cell surface produce a failure of cough clearance. These studies identified mucus concentration-dependent cohesive and adhesive properties, governed by mucus viscous energy dissipation, as rate limiting for the efficiency of cough clearance. Parallel studies designed to restore mucus cough clearability identified reduction of mucus concentration (rehydration) and use of mucolytics as additive and promising therapeutic strategies. Clearance of intrapulmonary mucus by the high-velocity airflow generated by cough is the major rescue clearance mechanism in subjects with mucoobstructive diseases and failed cilial-dependent mucus clearance, e.g., subjects with cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD). Previous studies have investigated the mechanical forces generated at airway surfaces by cough but have not considered the effects of mucus biophysical properties on cough efficacy. Theoretically, mucus can be cleared by cough from the lung by an adhesive failure, i.e., breaking mucus-cell surface adhesive bonds and/or by cohesive failure, i.e., directly fracturing mucus. Utilizing peel-testing technologies, mucus-epithelial surface adhesive and mucus cohesive strengths were measured. Because both mucus concentration and pH have been reported to alter mucus biophysical properties in disease, the effects of mucus concentration and pH on adhesion and cohesion were compared. Both adhesive and cohesive strengths depended on mucus concentration, but neither on physiologically relevant changes in pH nor bicarbonate concentration. Mucus from bronchial epithelial cultures and patient sputum samples exhibited similar adhesive and cohesive properties. Notably, the magnitudes of both adhesive and cohesive strength exhibited similar velocity and concentration dependencies, suggesting that viscous dissipation of energy within mucus during cough determines the efficiency of cough clearance of diseased, hyperconcentrated, mucus. Calculations of airflow-induced shear forces on airway mucus related to mucus concentration predicted substantially reduced cough clearance in small versus large airways. Studies designed to improve cough clearance in subjects with mucoobstructive diseases identified reductions of mucus concentration and viscous dissipation as key therapeutic strategies.
Prevalence and Phylogenetic Analyses of Trichuris suis in Pigs in Hunan Province, Subtropical China

Trichuris suis infection in pigs is ubiquitous in intensive and extensive farms, which causes potential threat to human health. The objective of this research was to investigate the prevalence of T. suis in pigs in Hunan province. Total 2,267 fresh fecal samples distributed in 28 pig farms from 7 different administrative regions (Hunan province) were evaluated for the existence of T. suis eggs using saturated NaCl floating method. The average infection rate of T. suis in pigs was 8.91% in Hunan province. To determine genetic variation of the gained T. suis isolates in the present study, the internal transcribed spacer (ITS) regions from nuclear ribosomal DNA (rDNA) of 7 T. suis isolates were cloned and analyzed. Nucleotide diversities were 1.0–3.5% and 0–3.8% for ITS-1 and ITS-2, respectively. Phylogenetic analyses indicated that all isolates collected in the present study and T. suis available in Genbank generated a monophyletic clade. The present investigation revealed high infection rates of T. suis in pigs in Hunan province, which shed light on making effective measures to prevent and control T. suis infection in pigs in Hunan province.
miR-130a and miR-27b Enhance Osteogenesis in Human Bone Marrow Mesenchymal Stem Cells via Specific Down-Regulation of Peroxisome Proliferator-Activated Receptor γ

Mesenchymal stem cell (MSC) is a type of stem cell that is capable of differentiating into osteoblasts and adipocytes. The pathological perturbation of MSC fate determination is well demonstrated by the replacement of bone tissues with fat in those with osteoporosis and osteopenia. Cell fate determination can be regulated by epigenetic and post-transcriptional mechanisms. MicroRNAs (miRNAs) are small endogenous non-coding RNA molecules that mediates the post-transcriptional regulation of genes expression. We hypothesized that miRNA specified to PPARγ, a major transcription factor of adipogenesis, is responsible for the differentiation of MSCs into osteoblasts. Candidate miRNA that is responsible for target gene inhibition was identified from the miRNA database via bioinformatic analyses. In this study, miR-130a and miR-27b were selected for investigation on their role in specifically binding to peroxisome proliferator-activated receptor γ (PPARγ) via in vitro osteogenesis of human MSCs. During osteogenic differentiation of human MSCs, the expression level of miR-130a and miR-27b were found to be upregulated. In the meanwhile, adipogenic marker genes (PPARγ and C/EBPβ) were found to decrease, which is in contrary to the increased expression of osteogenic marker genes (RUNX2 and Osterix). MSCs were transfected with mimics and inhibitors of miR-130a and miR-27b during in vitro osteogenesis followed by evaluation for the presence of osteogenic markers via quantitative gene expression, Western blot analysis and alkaline phosphatase activity assay. The overexpression of miR-130a and miR-27b is shown to enhance osteogenesis by increasing the gene expression of RUNX2 and Osterix, the protein expression of RUNX2, COL1A1, and Osterix as well as the alkaline phosphatase activity. Taken altogether, these results suggested that miR-130a and miR-27b could promote osteogenesis in human MSCs by targeting the PPARγ.
Ethanol‐induced alterations in endocannabinoids and relevant neurotransmitters in the nucleus accumbens of fatty acid amide hydrolase knockout mice

Deletion of fatty acid amide hydrolase (FAAH), enzyme responsible for degrading endocannabinoids, increases alcohol consumption and preference. However, there is a lack of data on neurochemical events in mice exposed to alcohol in the absence of FAAH. Extracellular levels of endocannabinoids and relevant neurotransmitters were measured by in vivo microdialysis in the nucleus accumbens (NAc) of FAAH knockout (KO) and wild‐type (WT) mice during an ethanol (EtOH; 2 g/kg, ip) challenge in EtOH‐naive and repeated (r) EtOH–treated mice. In both genotypes, EtOH treatment caused no changes in baseline endocannabinoid levels, although FAAH KO mice displayed higher baseline N‐arachidonoylethanolamine levels than WT mice. EtOH challenge caused a sustained increase in 2‐arachidonoylglycerol (2‐AG) levels in EtOH‐naive WT mice but not in FAAH KO mice. In contrast, 2‐AG levels were decreased following EtOH challenge in (r)EtOH‐treated mice in both genotypes. Whereas (r)EtOH‐treated mice showed higher baseline dopamine and serotonin levels than EtOH‐naive mice in WT mice, these differences were attenuated in FAAH KO mice. Significant differences in baseline γ‐aminobutyric acid (GABA) and glutamate levels by EtOH history were observed in WT mice but not in FAAH KO mice. Moreover, opposed effects on glutamate response were observed after EtOH challenge in EtOH‐naive and (r)EtOH‐treated FAAH KO mice. Finally, FAAH deletion failed to show EtOH‐induced locomotion sensitivity. These data provide evidence of a potential influence of 2‐AG in the neurochemical response to EtOH exposure in the NAc.
How People Explain Action (and Autonomous Intelligent Systems Should Too)

To make Autonomous Intelligent Systems (AIS), such as virtual agents and embodied robots, “explainable” we need to understand how people respond to such systems and what expectations they have of them. Our thesis is that people will regard most AIS as intentional agents and apply the conceptual framework and psychological mechanisms of human behavior explanation to them. We present a well-supported theory of how people explain human behavior and sketch what it would take to implement the underlying framework of explanation in AIS. The benefits will be considerable: When an AIS is able to explain its behavior in ways that people find comprehensible, people are more likely to form correct mental models of such a system and calibrate their trust in the system.
SSR-Linkage map of interspecific populations derived from Gossypium trilobum and Gossypium thurberi and determination of genes harbored within the segregating distortion regions

Wild cotton species have significant agronomic traits that can be introgressed into elite cultivated varieties. The use of a genetic map is important in exploring, identification and mining genes which carry significant traits. In this study, 188 F2mapping individuals were developed from Gossypium thurberi (female) and Gossypium trilobum (male), and were genotyped by using simple sequence repeat (SSR) markers. A total of 12,560 simple sequence repeat (SSR) markers, developed by Southwest University, thus coded SWU were screened out of which only 994 were found to be polymorphic, and 849 markers were linked in all the 13 chromosomes. The map had a length of 1,012.458 cM with an average marker distance of 1.193 cM. Segregation distortion regions (SDRs) were observed on Chr01, Chr02, Chr06, Chr07 Chr09, Chr10 and Chr11 with a large proportion of the SDR regions segregating towards the heterozygous allele. There was good syntenic block formation that revealed good collinearity between the genetic and physical map of G. raimondii, compared to the Dt_sub genome of the G. hirsutum and G. barbadense. A total of 2,496 genes were mined within the SSR related regions. The proteins encoding the mined genes within the SDR had varied physiochemical properties; their molecular weights ranged from 6.586 to 252.737 kDa, charge range of -39.5 to 52, grand hydropathy value (GRAVY) of -1.177 to 0.936 and isoelectric (pI) value of 4.087 to 12.206. The low GRAVY values detected showed that the proteins encoding these genes were hydrophilic in nature, a property common among the stress responsive genes. The RNA sequence analysis revealed more of the genes were highly upregulated in various stages of fiber development for instance; Gorai.002G241300 was highly up regulated at 5, 10, 20 and 25 day post anthesis (DPA). Validation through RT-qPCR further revealed that these genes mined within the SDR regions might be playing a significant role under fiber development stages, therefore we infer that Gorai.007G347600 (TFCA), Gorai.012G141600 (FOLB1), Gorai.006G024500 (NMD3), Gorai.002G229900 (LST8) and Gorai.002G235200 (NSA2) are significantly important in fiber development and in turn the quality, and further researches needed to be done to elucidate their exact roles in the fiber development process. The construction of the genetic map between the two wild species paves away for the mapping of quantitative trait loci (QTLs) since the average distance between the markers is small, and mining of genes on the SSR regions will provide an insight in identifying key genes that can be introgressed into the cultivated cotton cultivars.
Automatically Generating Malware Analysis Reports Using Sandbox Logs

SUMMARY Analyzing a malware sample requires much more time and cost than creating it. To understand the behavior of a given malware sample, security analysts often make use of API call logs collected by the dynamic malware analysis tools such as a sandbox. As the amount of the log generated for a malware sample could become tremendously large, in-specting the log requires a time-consuming e ﬀ ort. Meanwhile, antivirus vendors usually publish malware analysis reports (vendor reports) on their websites. These malware analysis reports are the results of careful analysis done by security experts. The problem is that even though there are such analyzed examples for malware samples, associating the vendor reports with the sandbox logs is di ﬃ cult. This makes security analysts not able to retrieve useful information described in vendor reports. To address this issue, we developed a system called AMAR-Generator that aims to automate the generation of malware analysis reports based on sandbox logs by making use of existing vendor reports. Aiming at a convenient assistant tool for security analysts, our system employs techniques including template matching, API behavior mapping, and malicious behavior database to produce concise human-readable reports that describe the malicious behaviors of malware programs. Through the performance evaluation, we ﬁrst demonstrate that AMAR-Generator can generate human-readable reports that can be used by a security analyst as the ﬁrst step of the malware analysis. We also demonstrate that AMAR-Generator can identify the malicious behaviors that are conducted by malware from the sandbox logs; the detection rates are up to 96.74%, 100%, and 74.87% on the sandbox logs collected in 2013, 2014, and 2015, respectively. We also present that it can detect
The association between dietary protein intake, energy intake and physical frailty: results from the Rotterdam Study

Abstract Sufficient protein intake has been suggested to be important for preventing physical frailty, but studies show conflicting results which may be explained because not all studies address protein source and intake of other macronutrients and total energy. Therefore, we studied 2504 subjects with data on diet and physical frailty, participating in a large population-based prospective cohort among subjects aged 45+ years (the Rotterdam Study). Dietary intake was assessed with a FFQ. Frailty was defined according to the frailty phenotype as the presence of at least three out of the following five symptoms: weight loss, low physical activity, weakness, slowness and fatigue. We used multinomial logistic regression models to evaluate the independent association between protein intake and frailty using two methods: nutrient residual models and energy decomposition models. With every increase in 10 g total, plant or animal protein per d, the odds to be frail were 1·06 (95 % CI 0·98, 1·15), 0·87 (95 % CI 0·71, 1·07) and 1·07 (95 % CI 0·99, 1·15), respectively, using the nutrient residual method. Using the energy partition model, we observed that the odds to be frail were lower with higher vegetable protein intake (OR per 418·4 kJ (100 kcal): 0·61, 95 % CI 0·39, 0·97), however, results disappeared when adjusting for physical activity. For energy intake from any source we observed that with every 418·4 kJ (100 kcal) increase, the odds to be frail were 5 % lower (OR: 0·95, 95 % CI 0·93, 0·97). Our results suggest that energy intake, but not protein specifically, is associated with less frailty. Considering other macronutrients, physical activity and diet quality seems to be essential for future studies on protein and frailty.
Brain Functional State Analysis of Mindfulness Using Graph Theory and Functional Connectivity

We human beings spend about ﬁfty percent of the time of our waking hours without any awareness what we are doing now. It is said that such a mind wandering affects happiness. To overcome this issue, mindfulness meditation—paying attention to one’s experience in an accepting and nonjudgmental way is getting popular. In spite of its popularity, meditation needs a lot of practice until we can experience its beneﬁt. A key to a good practice of the meditation is quality evaluation and feedback of it. In this paper, we proposed a novel feature extraction method to deﬁne the meditation state. We measured brain activity during a breath-counting meditation using functional magnetic resonance imaging, and the whole-brain functional connectivity and the amplitude of low-frequency ﬂuctuation were derived and utilized as feature vectors. The experimental results showed that resting and meditation states were classiﬁed on the feature space constructed by proposed method.
Comment on “Systematic Review and Meta-Analysis of Diagnostic Accuracy of miRNAs in Patients with Pancreatic Cancer”

Pancreatic cancer is one of the most malignant and aggressive cancers, with poor survival rates and diagnosis being based on nonspecific tumour biomarkers. Due to this, the publication, “Systematic Review and Meta-Analysis of Diagnostic Accuracy of miRNAs in Patients with Pancreatic Cancer”, by Sun et al. has excellent potential for highlighting potential miRNAs as high-accuracy diagnostic markers in pancreatic cancer [1]. However, we believe that despite the comprehensive study conducted by Sun et al., there are a few improvements that could be made to heighten the clinical utility of the paper further. As it stands, we believe that the study has some issues that prevent such applications of Sun et al.’s study.
Mobile Augmented Reality Adaptation through Smartphone Device Based Hybrid Tracking to Support Cultural Heritage Experience

In this paper, we exploit the advent of new technologies present in Smartphone device to implement a Mobile Augmented Reality (MAR) application that uses a hybrid tracking which combines two modes of augmented reality technology namely: image-based and location-based in order to bring the kind of information-rich and adaptive to the real world where the user stands. In spite of the proliferation of MAR available prototypes, the relevant literature still lacks studies combining both modes of AR in one application. In the other hand, visiting Points of Interests (POIs) in cultural heritage is a self-learning experience expecting to promote visitors' interests in heritage sites. This paper aims to shed light on the potential of hybrid AR approach for assisting mobile guidance applications. Herein, we introduce Seraj, a mobile augmented reality tour guide that supports adaptive content provision and navigation features to pilgrims in heritage cultural visit of Al-Madinah sites (Saudi-Arabia). Indeed, with such environment, the visitor is continuously on move. S/he can be in different situations with different contexts such as walking in her/his pathway along a city where s/he needs indications about POIs nearby (Location-based mode is suitable) or in front of a particular POI (Image-based mode is suitable). To the best of the researchers' knowledge, this is the first implementation of MAR application that attempts to address and improve AR adaptation using hybrid tracking in cultural heritage.