Miracle-dz/UniFAR-FTUs huggingface dataset:
The pan-genome effector-triggered immunity landscape of a host-pathogen interaction

A plant pan-genome immunity landscape Plant pathogens elicit an immune response through effector proteins. In turn, plant genomes encode genes that determine species-specific recognition of these effectors by a process known collectively as effector-triggered immunity (ETI). By examining a range of strains of the pathogen Pseudomonas syringae that infect the model plant Arabidopsis thaliana, Laflamme et al. generated a P. syringae Type III Effector Compendium (PsyTEC) and in turn identified the genes responsible for ETI in Arabidopsis. This pan-genome analysis revealed that relatively few A. thaliana genes are responsible for recognizing the majority of P. syringae effectors. These results provide insight into why most pathogenic microbes only infect specific plant species. Science, this issue p. 763 Effector-triggered immunity in plants contributes to broad-spectrum pathogen resistance in the model plant Arabidopsis thaliana. Effector-triggered immunity (ETI), induced by host immune receptors in response to microbial effectors, protects plants against virulent pathogens. However, a systematic study of ETI prevalence against species-wide pathogen diversity is lacking. We constructed the Pseudomonas syringae Type III Effector Compendium (PsyTEC) to reduce the pan-genome complexity of 5127 unique effector proteins, distributed among 70 families from 494 strains, to 529 representative alleles. We screened PsyTEC on the model plant Arabidopsis thaliana and identified 59 ETI-eliciting alleles (11.2%) from 19 families (27.1%), with orthologs distributed among 96.8% of P. syringae strains. We also identified two previously undescribed host immune receptors, including CAR1, which recognizes the conserved effectors AvrE and HopAA1, and found that 94.7% of strains harbor alleles predicted to be recognized by either CAR1 or ZAR1.
Major role of particle fragmentation in regulating biological sequestration of CO2 by the oceans

Breaking up is easy to do Sinking particles transport carbon to the seafloor, where they are buried in sediments and either provide food for benthic organisms or sequester the carbon they contain. However, only ∼30% of the maximum flux reaches depths of a kilometer. This loss cannot be fully accounted for by current measurements. Briggs et al. used data collected by robotic Biogeochemical-Argo floats to quantify total mesopelagic fragmentation and found that this process accounts for roughly half of the observed flux loss (see the Perspective by Nayak and Twardowski). Fragmentation is thus perhaps the most important process controlling the remineralization of sinking organic carbon. Science, this issue p. 791; see also p. 738 Robotic measurements show that fragmentation of sinking particles exerts a major control on ocean CO2 storage. A critical driver of the ocean carbon cycle is the downward flux of sinking organic particles, which acts to lower the atmospheric carbon dioxide concentration. This downward flux is reduced by more than 70% in the mesopelagic zone (100 to 1000 meters of depth), but this loss cannot be fully accounted for by current measurements. For decades, it has been hypothesized that the missing loss could be explained by the fragmentation of large aggregates into small particles, although data to test this hypothesis have been lacking. In this work, using robotic observations, we quantified total mesopelagic fragmentation during 34 high-flux events across multiple ocean regions and found that fragmentation accounted for 49 ± 22% of the observed flux loss. Therefore, fragmentation may be the primary process controlling the sequestration of sinking organic carbon.
THE EFFECTIVENESS OFICT-ASSISTED PROJECT- BASED LEARNING IN ENHANCING STUDENTS’ STATISTICAL COMMUNICATION ABILITY

This study aims to describe the effectiveness of ICT-assistedproject-based learning (ICT-assisted PBL)to enhance students’ statisticalcommunication ability. This study is quasi experiment, with pretest-posttest control group design. The number of sample are 51 students who were selected in purposive sampling from 102 students. In collecting data, statistical communication ability test, observation, and interview were used. Data obtained was analyzed by using Mann-Whitney U test. The result of this study shows that the application of ICTassisted PBL is effective that can enhance students’ statistic ability; (1) Statistical communication ability achievement and enhancement of students who got ICTassistedPBL is significantly higher than students who got conventional learning, (2) students’ activity is categorized good, and (3)in classical competence, 76,92% of students who achieve individual competence. ICT assited project based learning can be used to improve student’ statical comminication ability in introductory statistics learning.
The crowding dynamics of the motor protein kinesin-II

Intraflagellar transport (IFT) in C. elegans chemosensory cilia is an example of functional coordination and cooperation of two motor proteins with distinct motility properties operating together in large groups to transport cargoes: a fast and processive homodimeric kinesin-2, OSM-3, and a slow and less processive heterotrimeric kinesin-2, kinesin-II. To study the mechanism of the collective dynamics of kinesin-II of C. elegans cilia in an in vitro system, we used Total Internal Reflection Fluorescence microscopy to image the motility of truncated, heterodimeric kinesin-II constructs at high motor densities. Using an analysis technique based on correlation of the fluorescence intensities, we extracted quantitative motor parameters, such as motor density, velocity and average run length, from the image. Our experiments and analyses show that kinesin-II motility parameters are far less affected by (self) crowding than OSM-3. Our observations are supported by numerical calculations based on the TASEP-LK model (Totally Asymmetric Simple Exclusion Process-Langmuir Kinetics). From a comparison of data and modelling of OSM-3 and kinesin-II, a general picture emerges of the collective dynamics of the kinesin motors driving IFT in C. elegans chemosensory cilia and the way the motors deal with crowding.
The dynamic relationship between daily caffeine intake and sleep duration in middle‐aged and older adults

The effect of caffeine on sleep has been well documented. However, most studies examined this relationship in laboratories or used a cross‐sectional design analysing between‐person differences. This study investigated the within‐person relationship between caffeine intake and sleep duration at home. In a national database, 377 participants (aged 35–85 years) completed a 7‐day diary study. Sleep duration was measured by Actigraphy and caffeine intake was self‐reported in sleep logs. Three analytic strategies were used. The average sleep duration and the average caffeine intake were not significantly correlated. Multilevel regressions using daytime caffeine intake to predict night‐time sleep, and using night‐time sleep to predict next day caffeine intake, also did not detect any significant effect. Then dynamical systems analysis was performed, where the daily change rate and change tendency of caffeine and sleep were estimated, and the relationship among these momentums was examined. Results revealed a significant effect of sleep duration on the change tendency of caffeine use: a shorter sleep duration predicted a stronger tendency to consume caffeine, and this phenomenon was only found in middle‐aged adults (aged 35–55 years) not in older adults (aged 55+). This study did not detect any effect of daily caffeine intake on sleep duration, implying that habitual use of caffeine in real life may not coincide with laboratory findings, and that using caffeine to compensate for sleep loss is the habit of middle‐aged adults, not the elderly. The advantage of using a dynamic approach to analyse interrelated processes with uncertain time lags is also highlighted.
Additive effect of contrast and velocity suggests the role of strong excitatory drive in suppression of visual gamma response

It is commonly acknowledged that gamma-band oscillations arise from interplay between neural excitation and inhibition; however, the neural mechanisms controlling the power of stimulus-induced gamma responses (GR) in the human brain remain poorly understood. A moderate increase in velocity of drifting gratings results in GR power enhancement, while increasing the velocity beyond some ‘transition point’ leads to GR power attenuation. We tested two alternative explanations for this nonlinear input-output dependency in the GR power. First, the GR power can be maximal at the preferable velocity/temporal frequency of motion-sensitive V1 neurons. This ‘velocity tuning’ hypothesis predicts that lowering contrast either will not affect the transition point or shift it to a lower velocity. Second, the GR power attenuation at high velocities of visual motion can be caused by changes in excitation/inhibition balance with increasing excitatory drive. Since contrast and velocity both add to excitatory drive, this ‘excitatory drive’ hypothesis predicts that the ‘transition point’ for low-contrast gratings would be reached at a higher velocity, as compared to high-contrast gratings. To test these alternatives, we recorded magnetoencephalography during presentation of low (50%) and high (100%) contrast gratings drifting at four velocities. We found that lowering contrast led to a highly reliable shift of the GR suppression transition point to higher velocities, thus supporting the excitatory drive hypothesis. No effects of contrast or velocity were found in the alpha-beta range. The results have implications for understanding the mechanisms of gamma oscillations and developing gamma-based biomarkers of disturbed excitation/inhibition balance in brain disorders.
Dietary Sodium Intake and Food Sources among Chinese Adults: Data from the CNNHS 2010–2012

The present study was done to examine the status of dietary sodium intake and dietary sources of sodium among Chinese adults. Data were obtained from China National Nutrition and Health Surveillance (CNNHS) 2010–2012. All adults recruited in this study provided complete dietary data on three-day consecutive 24-h dietary recalls combining with the household weighing method. Sodium intake was adjusted for energy to 2000 kcal/day using the residual method. Average sodium intake was 5013 (95% Confidence Interval, CI: 4858, 5168) mg/day, and 92.6% of adults’ sodium intake exceeded the standard in the Chinese proposed intake for preventing non-communicable chronic diseases (PI-NCD). The salt added to food was the main contributor to daily sodium intake, representing 69.2% of the total sodium consumption. The proportion of sodium from salt was different in some subgroups. The contribution ranged from 64.8% for those who came from urban areas aged 18–49 years old to 74.7% for those who came from rural areas with education levels of primary school or less, and sodium from soy sauce was the next highest contributor (8.2%). The proportion of the subjects with sodium intake contributed by flour products was higher in the north with 7.1% than the south with 1.4%. The average consumption of sodium among Chinese was more than the recommended amount, and salt was the main source of sodium.
Effect of Feed Supplemented with Selenium-Enriched Olive Leaves on Plasma Oxidative Status, Mineral Profile, and Leukocyte DNA Damage in Growing Rabbits

Simple Summary Olive trees (Olea europaea L., Oleaceae) are among the most extensively cultivated crops in the Mediterranean countries (98% of the world’s olive production) and are used for oil extraction or table olives, whereas the residues from pruning (olive leaves and wood) and extraction process (olive pomace) are considered waste or by-products. Furthermore, many agronomic practices, such as foliar spray administration of selenium used to reduce the water stress damage of olive trees, could further improve the nutritional value of these “wastes”. The use of by-products as part of the rabbit diet can be a very effective example of recovery of healthy molecules while at the same time a way of developing a more sustainable production system. Accordingly, the idea of the present research is to administer the by-product “olive leaves” to growing rabbits to improve their health status and partially solve the problem of waste disposal of olive trees. Abstract This study investigated the effect of a dietary combination of selenium and olive leaves on rabbit health status in order to evaluate the potential use of these combinations as functional ingredients in feed and food. Sixty weaning rabbits were fed with three diets: control feed (C), control feed + 10% normal olive leaves (OL), or olive leaves enriched in Se (2.17 mg Se/kg d.m.; SeOL). The plasma mineral profile, antioxidant status, and leukocyte DNA damage were determined. Inorganic Se was the most abundant form in the OL diet, while the organic one was higher in SeOL than C and OL. A similar trend was found in the plasma. Protein oxidation showed higher values in both supplemented groups; in addition, dietary Se led to a significant improvement (+40%) in ferric reducing ability of plasma (FRAP). A marked reduction in DNA damage (9-fold) was observed in the SeOL group compared to C. The combination of selenium and olive leaves in the diet of growing rabbits increased plasma SeMet and FRAP and reduced leukocyte DNA damage.
Psychometric Properties of the Child Attachment Interview in Italian Context: A Focus on Normative and Specific Clinical Groups in School-Aged Children

While attachment assessments developed for infancy and adulthood are well established, no such gold standard measure exists for school years, where measures are not yet sufficiently robust. Nevertheless, the last decade has witnessed some progress in this field with the development of the Child Attachment Interview (CAI), a semistructured interview designed to access children’s mental representations of their attachment relationships. This study aimed to test the validity and reliability of the CAI for an Italian population, using a normative group and a clinical group of disruptive behavior disorder and somatic symptom disorder patients. A total sample of 311 Italian children (213 normative and 98 clinical) aged 8 to 15 years completed a battery of measures assessing attachment, verbal IQ, and symptomatology. The psychometric properties of the CAI alongside other children (Kerns Security Scale, Inventory of Parent and Peer Attachment) and parents (Adult Attachment Interview) attachment measures in normative sample, as well as the distribution of attachment patterns in normative and clinical samples, were examined. The results revealed the CAI to have adequate interrater and test–retest reliability, as well as discriminant, and convergent validity. Significant differences in the CAI’s distribution of attachment patterns for normative and specific clinical groups were found. Taken together, the findings show that the CAI Italian version is a reliable and valid measure for assessing attachment in school years and beyond.
Maternal Larp6 controls oocyte development, chorion formation and elevation

ABSTRACT La-related protein 6 (Larp6) is a conserved RNA-binding protein found across eukaryotes that has been suggested to regulate collagen biogenesis, muscle development, ciliogenesis, and various aspects of cell proliferation and migration. Zebrafish have two Larp6 family genes: larp6a and larp6b. Viable and fertile single and double homozygous larp6a and larp6b zygotic mutants revealed no defects in muscle structure, and were indistinguishable from heterozygous or wild-type siblings. However, larp6a mutant females produced eggs with chorions that failed to elevate fully and were fragile. Eggs from larp6b single mutant females showed minor chorion defects, but chorions from eggs laid by larp6a;larp6b double mutant females were more defective than those from larp6a single mutants. Electron microscopy revealed defective chorionogenesis during oocyte development. Despite this, maternal zygotic single and double mutants were viable and fertile. Mass spectrometry analysis provided a description of chorion protein composition and revealed significant reductions in a subset of zona pellucida and lectin-type proteins between wild-type and mutant chorions that paralleled the severity of the phenotype. We conclude that Larp6 proteins are required for normal oocyte development, chorion formation and egg activation. Summary: Genome-edited larp6a and larp6b double-knockout zebrafish appear morphologically and behaviourally wild type and are fertile. Larp6 proteins are, however, required maternally for normal oocyte development and chorion formation and elevation.
Phenotypic and molecular characterisation of a novel species, Mycobacterium hubeiense sp., isolated from the sputum of a patient with secondary tuberculosis in Hubei of China

Abstract A new fast-growing mycobacterium, designated strain QGD101T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101T could not be identified to a species level. Mycobacterium moriokaense ATCC43059T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101T = CCTCCAA 2017003T = KCTC39927T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.
Older Adults’ Perceptions of the Usefulness of Technologies for Engaging in Physical Activity: Using Focus Groups to Explore Physical Literacy

Insufficient physical activity (PA) levels observed among older adults remain extremely high and pose a danger to developing and maintaining their physical literacy (PL). Each person’s level of PL partly depends on their physical and cognitive skills, confidence level, and degree of motivation to practice PA daily. New technologies, such as exergames and wearable fitness trackers, may enable older adults to increase their PL, stimulating uptake and ongoing PA participation. Objective: This focus group study aims to describe older adults’ perceptions of the use of technologies to engage in physical exercise programs. Methods: Fifteen participants were randomly selected from a sample of 40 older adults who completed a randomized controlled trial that investigated the benefits of using technology in the context of group-based exercise programs. Separate post-intervention focus groups were performed with an exergaming group, a conventional physical training group, and a no training group (control). Data were mapped onto constructs from the four domains of PL: affective, physical, cognitive, and behavioral. Results: Generally, participants expressed positive perceptions about the benefits of using technology to engage in PA. These positive feelings outweighed the costs and the lack of familiarization with technology. Common themes for the three groups emerged from the discussions and included familiarization with technology, using fitness tracker to monitor PA, previous exposure to technology, and interaction with peers, staff members, and relatives. In particular, participants from the exergaming group explored the ideas of training their cognitive skills while using the exergame accessories, exercising in an alternative way, competitive versus cooperative play, changes in sense of humor, skill transferability from game to real environment, progressions of the exercise intensities, and the potential use of exergames for rehabilitation. Conclusions: Participants in this study reported positive perceptions about implementing technology into exercise. Emphasizing the benefits of using technology in group-based exercise programs may increase older adults’ PL levels and their future technology adoption. The potential implementation of technology into conventional exercise programs should focus on older adults’ lifelong values, biopsychosocial conditions, and the possibility of reducing age-related risk of injuries and chronic diseases.
Combined effect of n-3 fatty acids and phytosterol esters on alleviating hepatic steatosis in non-alcoholic fatty liver disease subjects: a double-blind placebo-controlled clinical trial

Abstract The aim of this study was to investigate the combined effect of n-3 fatty acids (EPA and DHA, at an EPA:DHA ratio of 150:500) and phytosterol esters (PS) on non-alcoholic fatty liver disease (NAFLD) patients. We conducted a randomised, double-blind, placebo-controlled trial. Ninety-six NAFLD subjects were randomly assigned to the following groups: the PS group (receiving 3·3 g/d PS); the FO group (receiving 450 mg EPA + 1500 mg DHA/d); the PS + FO combination group (receiving 3·3 g/d PS and 450 mg EPA + 1500 mg DHA/d) and the PO group (a placebo group). The baseline clinical characteristics of the four groups were similar. The primary outcome was liver:spleen attenuation ratio (L:S ratio). The percentage increase in liver–spleen attenuation (≤1) in the PS + FO group was 36 % (P = 0·083), higher than those in the other three groups (PS group, 11 %, P = 0·519; FO group, 18 %, P = 0·071; PO group, 15 %, P = 0·436). Compared with baseline, transforming growth factor-β (TGF-β) was significantly decreased in the three study groups at the end of the trial (PS, P = 0·000; FO, P = 0·002; PS + FO, P = 0·001) and TNF-α was significantly decreased in the FO group (P = 0·036), PS + FO group (P = 0·005) and PO group (P = 0·032) at the end of the intervention. Notably, TGF-β was reduced significantly more in the PS + FO group than in the PO group (P = 0·032). The TAG and total cholesterol levels of the PS + FO group were reduced by 11·57 and 9·55 %, respectively. In conclusion, co-supplementation of PS and EPA + DHA could increase the effectiveness of treatment for hepatic steatosis.
Impact of Vancomycin‐Induced Changes in the Intestinal Microbiota on the Pharmacokinetics of Simvastatin

The pharmacokinetic (PK) properties of drugs are affected in several ways by interactions with microbiota. The aim of this study was to investigate the effects of oral vancomycin on the gut microbiota and, consequently, on the PKs of simvastatin. An open‐label, single arm, sequential crossover study was conducted in six healthy Korean male subjects. After 6 days on a control diet, simvastatin 40 mg was orally administered to the subjects before and after 1 week of oral vancomycin treatment. Blood samples for PK analysis and fecal samples for metagenomic and metabolomic analyses were collected. After vancomycin treatment, the richness of microbiota considerably decreased, and the composition was altered. In particular, the relative abundance of Bacteroidetes decreased, whereas that of proteobacteria increased. In addition, changes in fecal metabolites, including D‐glucuronic acid, were observed. However, systemic exposure of simvastatin was not changed whereas that of hydroxysimvastatin showed a tendency to increase. The relationship between the change of PKs of simvastatin and the change of gut microbiota and fecal metabolites were not clearly observed.