Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Variability, Character Association and Path Analysis in Boro Rice (Oryza sativa L.) Germplasm from Bangladesh

The success of varietal development programmme largely depends on the nature and magnitude of genetic variability, heritability and characters association of the crop. The objective of the present study was to estimate the extent of genetic variability and relation between yield and related characters of rice. Forty Boro rice germplasm were evaluated in a randomised complete block design with three replications. Analysis of variance indicated significant differences among the genotypes for 14 quantitative characters. The presence of slightly higher phenotypic coefficient of variation than genotypic coefficient of variation indicated the negligible influence of environment on the expression of yield and its component traits. Leaf length, days to flowering, days to maturity and 1000 grain weight showed highly positive significant correlation present with yield hill-1. High heritability had been observed for yield contributing traits during the study, suggested that these traits would respond to selection owing to their high genetic variability and transmissibility. Therefore, a thorough understanding of the inheritance of traits, their heritability and relationship with other important characteristics is important for the choice of breeding and selection methods for crop improvement. Bangladesh Rice j. 2018, 22(1): 35-43
Harvest effects on density and biomass of Neopicrorhiza scrophulariiflora vary along environmental gradients in the Nepalese Himalayas

Abstract A surprisingly large number of species potentially threatened by human harvest lack quantitative ecological studies incorporating harvest effects, especially clonal species in the alpine Himalayas. We studied density and biomass variation of a threatened medicinal herb, Neopicrorhiza scrophulariiflora, to examine the effect of harvest on plant performance. The study covered two regions with contrasting harvest situations—one with open‐access and another protected from commercial harvesting. Four populations from each region were compared along an elevation gradient (3,800–4,800 m). Also, we conducted in situ interviews with 165 and 38 medicinal and aromatic plant users in open‐access and protected regions, respectively, to assess the collection and use patterns of the target species. The quantity harvested per household for traditional healthcare use was similar in both regions. We found no evidence of trade‐driven collection in the protected region but in the open‐access region a trade‐based annual collection of 35–465 kg dried rhizomes per household had a strong negative effect on both density and biomass. In the protected region, the effect of harvest intensity on plant density was positive for vegetative and negative for reproductive individuals, whereas in the open‐access region, the effect was negative for both vegetative and reproductive individuals. The results indicated that a low harvest intensity had no adverse impact on N. scrophulariiflora populations; however, quantification of the optimum level of harvest remains to be explored. Shrub vegetation appeared to buffer the harvest impact on plant density, possibly through the retention of additional moisture. To maintain population viability, we suggest regulating harvest, for example, by introducing rotational harvest systems, ensuring that a sufficient number of reproductive individuals are left as a source of propagules in each harvested population and that populations are given time to recover between harvests.
MSX1 and PAX9 genetic alteration in malaysian families with hypodontia

Hypodontia is characterized by the absence of one to six teeth. Malaysia has a high prevalence of hypodontia (2.8%). This study aimed to investigate the MSX1 mutation with clinical variability in Malaysian hypodontia families and to correlate the findings a previous study of the PAX9 mutation. Materials and methods: We re-examined seven individuals from two families of the previous PAX9 study. Orthophantomogram (OPG) and intraoral photos were re-assessed. Saliva was collected for genetic analysis. Direct sequencing was done on exons 1 and 2 of MSX1 and exons 2 and 3 of PAX9. Results: In family 1, three out of five members are affected. The mother has posterior hypodontia, while the daughters have anterior hypodontia. Point mutations on exon 1 of MSX1 (c.599C>T, c.732G>A) and on exon 3 of PAX9 (c.477delG, c.480delT) were identified on 1B (mother) and 1D (second daughter). Her carrier-son (1E) exhibited c.597C>T, c.730G>A on exon 1 of MSX1 and c.273T>G on exon3 of PAX9. In family 2, the daughter has a missing lower premolar with a point mutation on exon 1 of MSX1 (c.730G>A). A similar point mutation in her nonhypodontia father on exon 2 of PAX9 (c.628C>T) was observed. Conclusion: Mutation of MSX1 is observed in familial hypodontia; both genes MSX1 and PAX9 are needed to manifest hypodontia whereby PAX9 is the predominant gene mutation.
Automatically Assessing the Quality of Wikipedia Articles

Since its inception in 2001, Wikipedia has fast become one of the Internet's most dominant sources of information. Dubbed "the free encyclopedia", Wikipedia contains millions of articles that are written, edited, and maintained by volunteers. Due in part to the open, collaborative process by which content is generated, many have questioned the reliability of these articles. The high variance in quality between articles is a potential source of confusion that likely leaves many visitors unable to distinguish between good articles and bad. In this work, we describe how a very simple metric – word count – can be used to as a proxy for article quality, and discuss the implications of this result for Wikipedia in particular, and quality assessment in general.
A genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics

Biomechanical cues dynamically control major cellular processes but whether genetic variants actively participate in mechano-sensing mechanisms remains unexplored. Vascular homeostasis is tightly regulated by hemodynamics. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constitutive activation of vascular endothelium contributing to atherosclerosis, the major cause of coronary artery disease (CAD) and ischemic stroke (IS). Conversely, unidirectional flow promotes quiescent endothelium. Genome-wide association studies have identified chromosome 1p32.2 as one of the most strongly associated loci with CAD/IS; however, the causal mechanism related to this locus remains unknown. Employing statistical analyses, ATAC-seq, and H3K27ac/H3K4me2 ChIP-Seq in human aortic endothelium (HAEC), our results demonstrate that rs17114036, a common noncoding polymorphism at the 1p32.2, is located in an endothelial enhancer dynamically regulated by hemodynamics. CRISPR/Cas9-based genome editing shows that rs17114036-containing region promotes endothelial quiescence under unidirectional flow by regulating phospholipid phosphatase 3 (PLPP3). Chromatin accessibility quantitative trait locus mapping using HAECs from 56 donors, allelic imbalance assay from 7 donors, and luciferase assays further demonstrate that CAD/IS protective allele at rs17114036 in PLPP3 intron 5 confers an increased endothelial enhancer activity. ChIPPCR and luciferase assays show that CAD/IS protective allele at rs17114036 creates a binding site for transcription factor Krüppel-like factor 2, which increases the enhancer activity under unidirectional flow. These results demonstrate for the first time that a human single-nucleotide polymorphism contributes to critical endothelial mechanotransduction mechanisms and suggest that human haplotypes and related cisregulatory elements provide a previously unappreciated layer of regulatory control in cellular mechano-sensing mechanisms. Significance Statement Biomechanical stimuli control major cellular functions and play critical roles in the pathogenesis of diverse human diseases. Although recent studies have implicated genetic variation in regulating key biological processes, whether human genetic variants contribute to the cellular mechano-sensing mechanisms remains unclear. This study provides the first line of evidence supporting an underappreciated role of genetic predisposition in cellular mechanotransduction mechanisms. Employing epigenomic profiling, genome-editing, and latest human genetics approaches, our data demonstrate that rs17114036, a common noncoding polymorphism implicated in coronary artery disease and ischemic stroke by genome-wide association studies, dynamically regulates endothelial responses to blood flow (hemodynamics) related to atherosclerosis via regulation of an intronic enhancer. The results provide new molecular insights linking disease-associated genetic variants to cellular mechanobiology.
Decoding of human hand actions to handle missing limbs in

13 classifier, PPCA, activities of daily living, finger movement. 14 15 Abstract 16 The only way we can interact with the world is through movements, and our primary interactions are 17 via the hands, thus any loss of hand function has immediate impact on our quality of life. However, 18
6-OHDA-induced dopaminergic neurodegeneration in C. elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33

Oxidative stress is linked to many pathological conditions including the loss of dopaminergic neurons in Parkinson’s disease. The vast majority of disease cases appear to be caused by a combination of genetic mutations and environmental factors. We screened for genes protecting Caenorhabditis elegans dopaminergic neurons from oxidative stress induced by the neurotoxin 6-hydroxydopamine (6-OHDA) and identified the transthyretin-related gene ttr-33. The only described C. elegans transthyretin-related protein to date, TTR-52, has been shown to mediate corpse engulfment as well as axon repair. We demonstrate that TTR-52 and TTR-33 have distinct roles. TTR-33 is likely produced in the posterior arcade cells in the head of C. elegans larvae and is predicted to be a secreted protein. TTR-33 protects C. elegans from oxidative stress induced by paraquat or H2O2 at an organismal level. The increased oxidative stress sensitivity of ttr-33 mutants is alleviated by mutations affecting the KGB-1 MAPK kinase pathway, whereas it is enhanced by mutation of the JNK-1 MAPK kinase. Finally, we provide genetic evidence that the C. elegans cell corpse engulfment pathway is required for the degeneration of dopaminergic neurons after exposure to 6-OHDA. In summary, we describe a new neuroprotective mechanism and demonstrate that TTR-33 normally functions to protect dopaminergic neurons from oxidative stress-induced degeneration, potentially by acting as a secreted sensor or scavenger of oxidative stress. Author summary Animals employ multiple mechanisms to prevent their cells from damage by reactive oxygen species, chemically reactive molecules containing oxygen. Oxidative stress, caused by the overabundance of reactive oxygen species or a decreased cellular defence against these chemicals, is linked to a variety of neurodegenerative conditions, including the loss of dopaminergic neurons in Parkinson’s disease. In this study, we discovered a novel protective molecule that functions to prevent dopaminergic neurodegeneration caused by oxidative stress induced by the neurotoxin 6-hydroxydopamine (6-OHDA). We used the nematode C. elegans, a well-characterised model in which mechanisms can be studied on an organismal level. When C. elegans is exposed to 6-OHDA, its dopaminergic neurons gradually die. Our major findings include (i) mutations of the transthyretin-related gene ttr-33 causes highly increased dopaminergic neurodegeneration after 6-OHDA exposure; (ii) TTR-33 is likely produced and secreted by several cells in the head of the animal; (iii) TTR-33 protects against oxidative stress induced by other compounds; (iv) mutations in the KGB-1 MAP kinase stress pathway alleviate dopaminergic neuron loss in the ttr-33 mutant; and (v) the cell corpse engulfment pathway is required for dopaminergic neurodegeneration. We hypothesise that TTR-33 protects dopaminergic neurons against 6-OHDA-induced oxidative stress by acting as an oxygen sensor or scavenger.
Mechanical properties of plasma membrane vesicles correlate with lipid order and viscosity and depend on cell density

Plasma membranes dynamically respond to external cues and changing environment. Quantitative measurements of these adaptations can elucidate the mechanism that cells exploit to survive, adapt and function. However, cell-based assays are affected by active processes while measurements on synthetic models suffer from compositional limitations. Here, as a model system we employ giant plasma membrane vesicles (GPMVs), which largely preserve the plasma membrane lipidome and proteome. From analysis of fluorescence emission and lifetime of environment-sensitive dyes, and membrane shape fluctuations, we investigate how plasma membrane order, viscosity and bending rigidity are affected by different stimuli such as cell seeding density in three different cell models. Our studies reveal that bending rigidity of plasma membranes vary with lipid order and microviscosity in a highly correlated fashion. Thus, readouts from polarity- and viscosity-sensitive probes represent a promising indicator of membrane mechanical properties. Quantitative analysis of the data allows for comparison to synthetic lipid membranes as plasma membrane mimetics.
Unraveling the relation between EEG-correlates of attentional orienting and sound localization performance: a diffusion model approach

Understanding the contribution of cognitive processes and their underlying neurophysiological signals to behavioral phenomena has been a key objective in recent neuroscience research. Using a diffusion-model framework, we investigated to what extent well-established correlates of spatial attention in the electro-encephalogram contribute to behavioral performance in an auditory free-field sound-localization task. Younger and older participants were instructed to indicate the horizontal position of a pre-defined target among three simultaneously presented distractors. The central question of interest was whether posterior alpha lateralization and amplitudes of the anterior contralateral N2 subcomponent (N2ac) predict sound localization performance (accuracy, mean reaction time) and/or diffusion model parameters (drift rate, boundary separation, non-decision time). Two age groups were compared to explore whether in older adults, who struggle with multi-speaker environments, the brain-behavior relationship would differ from younger adults. Regression analyses revealed that N2ac amplitudes predicted drift rate and accuracy, whereas alpha lateralization was not related to behavioral or diffusion modeling parameters. This was true irrespective of age. The results indicate that a more efficient attentional filtering and selection of information within an auditory scene, reflected by increased N2ac amplitudes, was associated with a higher speed of information uptake (drift rate) and better localization performance (accuracy), while the underlying response criteria (threshold separation), mean reaction times, and non-decisional processes remained unaffected. The lack of a behavioral correlate of post-stimulus alpha power lateralization constrast the well-established notion that pre-stimulus alpha power reflects a functionally relevant attentional mechanism. This highlights the importance of distinguishing anticipatory from post-stimulus alpha power modulations.
Incidental Vocabulary Acquisition from Pleasure Reading

This study investigated whether pleasure reading of two graded readers over a three-week period contributes to learning unknown words contained in the texts. The 52 participants in this study were divided into two groups. The experimental group consisted of 27 English as foreign language (EFL) learners who read the texts, and the control group consisted of 25 EFL learners who did not read the texts. Three tests were administered to measure three receptive aspects of word knowledge. Statistical analyses revealed no significant gains occurred on the post-tests, but two aspects of word knowledge showed significant increase on the delayed post-tests. Moreover, the results suggest that words that occurred less frequently were learned more than words that occurred more frequently, and that nouns were learned slightly more than verbs. This study investigated the relationship between pleasure r eading a nd i ncidental vocabulary acquisition. The term pleasure reading is employed to d istinguish it f rom extensive r eading. T he term extensive reading implies that readers read pleasurable and easy texts. Since it is extremely difficult to demonstrate that the participants in this study were able to comprehend 98-99% of the vocabulary items contained in the reading materials, but their enjoyment of the texts can be verified, the term pleasure reading appears to capture the actual reading conditions. This s tudy a sked t he following r esearch questions: 1. Does pleasure reading lead to incidental learning of three receptive aspects of word knowledge: recognition of word-form, recognition of formmeaning and recall of form-meaning? 2. Are the vocabulary gains retained 2.5 weeks after reading?
Spatial distribution of epibionts on olive ridley sea turtles at Playa Ostional, Costa Rica

There is a wealth of published information on the epibiont communities of sea turtles, yet many of these studies have exclusively sampled epibionts found only on the carapace. Considering that epibionts may be found on almost all body-surfaces and that it is highly plausible to expect different regions of the body to host distinct epibiont taxa, there is a need for quantitative comparative studies to investigate spatial variation in the epibiont communities of turtles. To achieve this, we measured how total epibiont abundance and biomass on olive ridley turtles Lepidochelys olivacea varies among four body-areas of the hosts (n = 30). We show that epibiont loads on olive ridleys are higher, both in terms of number and biomass, on the skin than they are on the carapace or plastron. This contrasts with previous findings for other hard-shelled sea turtles, where epibionts are usually more abundant on the carapace. Moreover, the arguably most ubiquitous epibiont taxon for other hard-shelled sea turtles, the barnacle Chelonibia spp. , only occurs in relatively low numbers on olive ridleys, while the barnacles Stomatolepas elegans and Platylepas hexastylos are far more abundant. We postulate that these differences between the epibiont communities of different sea turtle taxa could indicate that the carapaces of olive ridley turtles provide a more challenging substratum for epibionts than do the hard shells of other sea turtles. In addition, we conclude that it is important to conduct full body surveys when attempting to produce a holistic qualitative or quantitative characterization of the epibiont communities of sea turtles.
Impact of different intensities of intermittent theta burst stimulation on the cortical properties during TMS-EEG and working memory performance

Introduction Intermittent theta burst stimulation (iTBS) is a non-invasive brain stimulation technique capable of increasing cortical excitability beyond the stimulation period. Due to the rapid induction of modulatory effects compared to conventional repetitive transcranial magnetic stimulation (rTMS) paradigms, prefrontal application of iTBS is gaining popularity as a therapeutic tool for psychiatric disorders such as depression. In an attempt to increase efficacy, higher than conventional intensities are currently being applied. The assumption that this increases neuromodulatory effect is well established for the standard rTMS paradigms but may be mechanistically false for iTBS. This study examined the influence of intensity on the neurophysiological and behavioural effects of iTBS in the prefrontal cortex. Methods 16 healthy participants received iTBS over prefrontal cortex (F1 electrode) at either 50, 75 or 100% resting motor threshold (rMT) in separate sessions. Single-pulse TMS and concurrent electroencephalography (EEG) was used to assess changes in cortical reactivity measured as TMS-evoked potentials (TEPs) and TMS-evoked oscillations. The n-back task (2-back and 3-back) were used to assess changes in working memory (accuracy and reaction time). Results The data can be summarised as an inverse U-shape relationship between intensity and iTBS plastic effects, where 75% iTBS resulted in the largest neurophysiological changes both in TMS-EEG and working memory. Even though 75% iTBS showed significantly decreased reaction time in the 3-back task, between condition comparisons revealed no significant differences. Conclusions The assumption that higher intensity results in greater neuromodulatory effects is false, at least in healthy individuals, and should be carefully considered for clinical populations. Neurophysiological changes associated with working memory following iTBS suggest functional relevance. However, the effects of different intensities on behavioural performance remain elusive in the present healthy sample. Highlights Effects of prefrontal iTBS at 50, 75 and 100% rMT were investigated Inverse U-shape relationship between intensity and neurophysiological effects Effects on the behavioural performance remain elusive in healthy individuals Disclosures and conflict of interests SWC was supported by a Monash Graduate Scholarship. NCR is supported by a NHMRC Early Career Fellowship (1072057). KEH is supported by a NHMRC Career Development Fellowship (1082894). PBF is supported by a NHMRC Practitioner Fellowship (1078567). PBF has received equipment for research from MagVenture A/S, Medtronic Ltd, Cervel Neurotech and Brainsway Ltd and funding for research from Neuronetics and Cervel Neurotech. He is on the scientific advisory board for Bionomics Ltd. There are no other conflicts.
Syllabic Length Effect in Visual Word Recognition by SLA Learners

Studies on visual word recognition have resulted in different and sometimes contradictory proposals as Multi-Trace Memory Model (MTM), Dual-Route Cascaded Model (DRC), and Parallel Distribution Processing Model (PDP). The role of the number of syllables in word recognition was examined by the use of five groups of English words and nonwords. The reaction time of the participants to these words was measured using reaction time measuring software. The results indicated that there was syllabic effect on recognition of both high and low frequency words. The pattern was incremental in terms of syllable number. This pattern prevailed in high and low frequency words and non-words except in one syllable words. In general, the results are in line with the PDP model which claims that a single processing mechanism is used in both words and non-words recognition. In other words, the findings suggest that lexical items are mainly processed via a lexical route. A pedagogical implication of the findings would be that reading in English as a foreign language involves analytical processing of the syllable of the words.