Miracle-dz/UniFAR-FTUs huggingface dataset:
From biology to behavior: a cross‐disciplinary seminar series surrounding added sugar and low‐calorie sweetener consumption

This report presents a synopsis of a three‐part, cross‐sector, seminar series held at the George Washington University (GWU) in Washington, DC from February–April, 2018. The overarching goal of the seminar series was to provide a neutral forum for diverse stakeholders to discuss and critically evaluate approaches to address added sugar intake, with a key focus on the role of low‐calorie sweeteners (LCS).
6-Phosphogluconate Dehydrogenase Links Cytosolic Carbohydrate Metabolism to Protein Secretion

The proteinaceous extracellular matrix (ECM) is vital for cancer cell survival, proliferation, migration, and differentiation. However, little is known regarding metabolic pathways required in the ECM secretion process. By using an unbiased computational approach, we searched for enzymes whose suppression may lead to disruptions in protein secretion. Here, we show that 6-phosphogluconate dehydrogenase (PGD), a cytosolic enzyme involved in carbohydrate metabolism, is required for endoplasmic reticulum (ER) structural integrity and protein secretion. Chemical inhibition or genetic suppression of its activity led to cell stress accompanied by significantly expanded ER volume and can be rescued by compensating glutathione supplies. Our results also suggest that this characteristic ER-dilation phenotype may be a general marker indicating increased ECM protein congestion inside cells and decreased secretion. Thus, PGD exemplifies a nexus of cytosolic carbohydrate metabolism and protein secretion.
Nanoporous Boron Nitride for High Efficient Water Desalination

Membrane filtration processes for water desalination have been greatly improved thanks to rapid development of nanoporous 2-dimentional (2D) materials. Nanoporous graphene and molybdenum disulfide have proved to show promising properties for desalination. In this study, we detailly investigated the desalination performance of a different nanoporous 2D material, nanoporous boron nitride (BN), by Molecular Dynamics simulation. Our calculations demonstrated that nanoporous BN allows for rapid water permeability with effective salt rejection. The permeability is not only two orders of magnitude higher than existing commercial techniques but also much higher than nanoporous graphene and molybdenum disulfide membranes. We further showed that the pores with B-h edges or with N-h edges present different desalination efficiency. Compared to N-h pores, B-h pores have better desalination performance in term of higher water flux. To the best of our knowledge, nanoporous BN is the 2D material having the highest water permeability thus far while maintaining high salt rejection. Overall, our results shed light on the potential
The idiosyncratic drivers of correlated evolution

The ultimate causes of correlated evolution among sites in a genome remain difficult to tease apart. To address this problem directly, we performed a high-throughput search for correlated evolution among sites associated with resistance to a fluoroquinolone antibiotic using whole genome data from clinical strains of Pseudomonas aeruginosa, before validating our computational predictions experimentally. We show that for at least two sites, this correlation is underlain by epistasis. Our analysis also revealed eight additional pairs of synonymous substitutions displaying correlated evolution underlain by physical linkage, rather than selection associated with antibiotic resistance. Our results provide direct evidence that both epistasis and physical linkage among sites can drive the correlated evolution identified by high throughput computational tools. In other words, the observation of correlated evolution is not by itself sufficient evidence to guarantee that the sites in question are epistatic; such a claim requires additional evidence, ideally coming from direct estimates of epistasis, based on experimental evidence. Author summary As we shift focus from the detection of independent, strong drivers of evolution, and consider the interacting effects (e.g. epistasis) of multiple factors, we see a growth of high-throughput computational approaches but a dearth of empirical validation. As the breadth and depth of sequencing data continues to grow, it has become important to ensure our growing repertoire of approaches is sufficiently validated prior to widespread usage. In this study, we apply a computational approach recently described to predict correlated evolution within whole-genome sequence data from Pseudomonas aeruginosa in the context of fluoroquinolone antibiotic selection. We then performed direct experimental analyses to identify the causes of correlated evolution. We find that very little of the most strongly correlated evolution is actually epistatic, and that instead, most correlated evolution relates to physical linkage likely driven by horizontal gene transfer.
RESPONSE OF WHEAT PRODUCTIVITY TO IRRIGATION REGIMES AND NITROGEN FERTILIZATION LEVELS

Wheat is the main cereal crop in Egypt. The gap between production and consumption is about 60%. Research efforts are needed to reduce this gap, therefore; the objective of this work was to study the effect of three water regimes as irrigation at 45%, 60% and 70% depletion of the available soil moisture, and three nitrogen fertilization levels on two wheat varieties (Giza 168 and Giza 171). The field experiments were carried out at Bahry El-Methaq region, Alexandria Governorate, Egypt during the two successive winter seasons of 2015/2016 and 2016/2017. The experimental design of the study followed split split plot design (SSPD) with three replicates, keeping two bread wheat cultivars {Giza 168 and Giza 171 } as the main plots, irrigation regimes (irrigation at 45%, 60% and 70% depletion of the available soil moisture) as subplot, and the three fertilization levels as 100%, 80% and 60% from recommended fertilizer rates of nitrogen fertilization common applied as sub-subplot. The results showed that seasonal ET0 was 665.9 mm for the first season and 624.8 for the second season. Wheat crop transpiration was 600.28 mm at 2015-2016 growing season and 572.95 mm for the next season. The seasonal applied irrigation water in total was 2702.2 m3, 2792.6 m3 and 2879.1 m3 at 45%, 60% and 70% depletion treatments for 2015-2016 growing season, respectively. The corresponding values for the next growing season were changed to 2802.5 m3, 2687.4 m3 and 2716.4 m3. Based on the irrigation regimes and water balance by the budget technique, the irrigation events of wheat at 45%, 60% and 70% depletion treatments were 29, 23 and 21, which required irrigating for 23.17, 23.94 and 24.69 hours in the first season, respectively. The second season results changed to 28, 23 and 20 irrigations, which required irrigating for 24.4, 22.96 and 23.29 hours. The results indicated that the maximum grain yield and water use efficiency of wheat regardless of the variety under investigation could be obtained with irrigation at 60% depletion of the available soil moisture and 100% of the recommended nitrogen fertilization. The yield and water use efficiency of Giza 168 under these conditions were 2.78 ton/fed and 1.02 kg/m3. While for Giza 171, 3.4 ton/fed and 1.24 kg/ m3 were obtained with 22.3% and 21.6% increase in yield and water use efficiency, respectively.The results indicated a significant effect of crop cultivars and nitrogen fertilization levels on biological yield, straw yield, grain yield, WUE of grain yield and WUE of straw yield. Meanwhile, irrigation regimes showed insignificant effect on the previous parameters. The interaction of wheat cultivars, nitrogen fertilization levels and irrigation water regime levels showed insignificant effect on biological yield, straw yield, grain yield, WUE of grain yield and WUE of straw yield.
Use of field margins managed under an agri-environment scheme by foraging Barn Swallows Hirundo rustica

ABSTRACT Capsule: Barn Swallows Hirundo rustica were more likely to forage along arable field margins that were enhanced with wildflowers or legumes than control grass margins. Aims: To determine if foraging Barn Swallows displayed preferences for specific arable field boundary habitats (grass margins versus floristically enhanced margins) that were managed as part of an agri-environment scheme. We also aim to determine how Barn Swallow food abundance related to these habitats. Methods: Two foraging activity surveys took place on all grass and floristically enhanced margins (n = 56) present within the 600 m foraging range of seven Barn Swallow colonies during June and July 2016. Margin habitat use was measured by recording the presence/absence of foraging individuals during surveys, the total number of individuals and by calculating an index of foraging activity. Habitat information relating to adjacent boundary type, transect crop type and neighbouring crop type were also recorded. Results: Foraging Barn Swallows were significantly more likely to be recorded when survey transects included a floristically enhanced margin, but there was no significant impact of floristically enhanced margins on the total number of individuals recorded or on the index of foraging activity. Foraging activity was higher along grass verges and hedgerows when compared to treelines and was positively related to length weighted Diptera abundance (a measure of food biomass). Conclusion: Our results suggest that there may be a role for floristically enhanced margins in the conservation of Barn Swallows on arable farmland. More research, however, is needed to determine whether invertebrate-rich agri-environment scheme habitats can influence colony size or improve the breeding success of this species.
An Efficient Framework for Hand Gesture Recognition based on Histogram of Oriented Gradients and Support Vector Machine

— This paper focuses on an empirical hand gesture recognition system in the domain of image processing and machine learning. The hand gesture is probably the most intuitive and frequently used mode of nonverbal communication in human society. The paper analyzes the efficiency of the Histogram of Oriented Gradients (HOG) as the feature descriptor and Support Vector Machine (SVM) as the classification model in case of gesture recognition. There are three stages of the recognition procedure namely image binarization, feature extraction, and classification. The findings of the paper show that the model classifies hand gestures for the given dataset with satisfactory efficiency. The outcome of this work can be further utilized in practical fields of real-world applications dealing with non-verbal communication.
AKTIVITAS ANTIJAMUR EKSTRAK DAUN KELOR (Moringa oleifera Lamck.) DAN DAUN KIRINYUH (Chromolaena odorata L.) TERHADAP Candida albicans DAN Aspergillus flavus

Penelitian ini bertujuan mengetahui pengaruh pemberian ekstrak daun kelor (Moringa oleifera Lamck.) dan kirinyuh (Chromolaena odorata L.) terhadap Candida albicans dan Aspergilus flavus serta untuk mengetahui konsentrasi ekstrak daun kelor (M. oleifera Lamck.) dan kirinyuh (C. odorata L.) yang terbaik untuk menghambat pertumbuhan C. albicans dan A. flavus. Metode penelitian eksperimen menggunakan desain Rancangan Acak Kelompok. Pengujian aktivitas antijamur dilakukan dengan metode difusi sumur (well difusion). Variabel bebas (X) adalah ekstrak daun kelor (M. oleifera Lamck.) dan ekstrak daun kirinyuh (C. odorata L.) konsentrasi 25%, 50% dan 75%, total perlakuan dalam penelitian ini sebanyak 3 perlakuan sehingga total keseluruhan perlakuan jamur indikator adalah 36 unit percobaan. Variabel terikat (Y) yaitu aktivitas antijamur. Teknik analisis data yang digunakan adalah analisis deskriptif dan analisis inferensial berupa ANAVA dan uji lanjut menggunakan uji Beda Jarak Nyata Duncan (BJND) pada taraf kepercayaan 95%. Hasil penelitian menunjukkan bahwa (1) Ekstrak daun kelor (M. oleifera Lamck.) tidak memiliki aktivitas antijamur terhadap pertumbuhan C. albicans dan A. flavus. Sementara, ekstrak daun kirinyuh (C. odorata) memiliki aktivitas antijamur terhadap pertumbuhan A. flavus dan tidak memberikan pengaruh terhadap pertumbuhan C. albicans (2) Ada pengaruh konsentrasi ekstrak daun kirinyuh (C. odorata) terhadap pertumbuhan A. flavus dengan konsentrasi terbaik yaitu ekstrak 75%. Kata Kunci : antijamur, Moringa oleifera Lamck, Chromolaena odorata L,
Development and maintenance of genetic diversity in Scots pine, Pinus sylvestris (L.)

Forests are among the most important repositories of terrestrial biodiversity and provide a broad range of ecosystem services. During millennia, forests have changed, adapted and evolved under changing conditions. However, in the present century, forests are facing environmental changes at rates with no precedents. A major concern is the risk of declining forest genetic diversity, since genetic variation as the raw material underpinning adaptation is key in maintaining the resilience of forest ecosystems against environmental changes. Understanding the different processes responsible for developing and maintaining the genetic diversity of tree species is essential to better predict tree responses under new conditions. Therefore, this thesis aimed to determine how different forces interact to shape and maintain within and among population genetic diversity of Scots pine and what the implications are for conservation and management under forthcoming environmental conditions. From local to continental scales, we followed a multilevel approach, and found that (i) historic climate changes and geographical barriers have played an important role in shaping the extent and spatial distribution of current genetic diversity of Scots pine. Despite contemporary habitat reduction and fragmentation we found that (ii) high levels of neutral genetic diversity remain in the Scottish populations of Scots pine, with gene flow and specifically wind-driven gene flow dominating over genetic drift and preventing differentiation among the Scottish populations. However, (iii) considerable impacts in the spatial distribution of genetic variation have occurred as a consequence of intensive historical forest management practices. Furthermore, we found that (iv) substantial levels of adaptive genetic variation are present in the Scottish populations of Scots pine, likely a result of selective processes resulting from the different environments they live in, with highly heritable traits, although similar capacity for response through phenotypic plasticity to warming. Our results help to further disentangle the forces maintaining genetic diversity in one of most widespread conifers in the world, and improving predictions of likely range shifts and adaptation of the species in response to contemporary changes. We provide some recommendations to conservation and management practices.
Growing environment characteristics and vegetation structure of Vaccinium Oldhamii Miq. native habitats in Korea

Abstract In the present study was surveyed the flora, vegetation structure, growing environment, and soil characteristics in the wild habitats of Vaccinium oldhamii and offered basic information for habitat conservation and restoration. Most of the wild habitats of V. oldhamii were located at altitudes between 5 and 1095 m with inclinations of 2–33°, Dense populations were found around the climbing routes of the north-facing mountain slopes and dry rocky areas along mountain ridges. Vascular plants identified in the surveyed V. oldhamii habitats (28 quadrats in 12 habitat areas) included 129 taxa (50 families, 94 genera, 115 species, 9 varieties, 2 subspecies and 3 forms), of which woody plants accounted for 31.1%. The flora identified in the habitat areas were classified into four community types: Community I (Pinus densiflora – Quercus mongolica), Community II (Pinus thunbergii), Community III (Pinus rigida), and Community IV (Castanea crenata). The differences among communities within V. oldhamii habitats were more dependent on the occurrence of species with high importance percentages than on the population sizes of the species observed. The soil characteristics of V. oldhamii habitats were as follows: mostly silty loams; well-drained; shallow available-soil depth; high acidity (pH 3.93–5.07, mean = 4.63, lower than mean Korean forest soil pH of 5.5); and mean available phosphate (=9.485 mg/kg, lower than the mean Korean forest soil available phosphate of 26 mg/kg). Mean species diversity, evenness and dominance were calculated as 1.216, 0.954 and 0.046, respectively.
Assessment of genetic structure among Australian east coast populations of snapper Chrysophrys auratus (Sparidae)

Snapper Chrysophrys auratus is a high-value food fish in Australia targeted by both commercial and recreational fisheries. Along the east coast of Australia, fisheries are managed under four state jurisdictions (Queensland, Qld; New South Wales, NSW; Victoria, Vic.; and Tasmania, Tas.), each applying different regulations, although it is thought that the fisheries target the same biological stock. An allozyme-based study in the mid-1990s identified a weak genetic disjunction north of Sydney (NSW) questioning the single-stock hypothesis. This study, focused on east-coast C. auratus, used nine microsatellite markers to assess the validity of the allozyme break and investigated whether genetic structure exists further south. Nine locations were sampled spanning four states and over 2000km, including sites north and south of the proposed allozyme disjunction. Analyses confirmed the presence of two distinct biological stocks along the east coast, with a region of genetic overlap around Eden in southern NSW, ~400km south of the allozyme disjunction. The findings indicate that C. auratus off Vic. and Tas. are distinct from those in Qld and NSW. For the purpose of stock assessment and management, the results indicate that Qld and NSW fisheries are targeting a single biological stock.A
Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools

Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
Sparking “The BBC Four Pandemic”: Leveraging citizen science and mobile phones to model the spread of disease

The nexus of mobile technology, mass media, and public engagement is opening new opportunities for research into the human behaviours relevant to the spread of disease. On 22 March 2018, the British Broadcasting Corporation (BBC) released the documentary “Contagion! The BBC Four Pandemic” to describe the science behind pandemic preparedness in the UK. The authors of this article were responsible for producing a mathematical simulation of how a highly contagious respiratory pathogen might spread across the UK. According to the documentary narrative, the ‘outbreak’ begins in the town of Haslemere, England. To ground the simulation in true human interaction patterns, a three-day citizen science experiment was conducted during which the pairwise distances between 469 volunteers in Haslemere were tracked continuously using a mobile phone app. Here, we offer a scientific companion to the documentary in which we describe the methods behind our simulation and release the pairwise distance dataset. We discuss salient features of the dataset, including daily patterns in the clustering and volatility of interpersonal interactions. We also discuss new scientific opportunities opened by the ‘Haslemere dataset’, such as the ability to compare rival methods for empirically estimating the basic reproduction number and the opportunity to develop optimal vaccination strategies. We believe that the Haslemere dataset will productively challenge current strategies for incorporating population structure into disease transmission models, and hope that it will inspire the collection and analysis of other similar datasets in the future.
Learning-Based Probabilistic LTL Motion Planning With Environment and Motion Uncertainties

This article considers control synthesis of an autonomous agent with linear temporal logic (LTL) specifications subject to environment and motion uncertainties. Specifically, the probabilistic motion of the agent is modeled by a Markov decision process (MDP) with unknown transition probabilities. The operating environment is assumed to be partially known, where the desired LTL specifications might be partially infeasible. A relaxed product MDP is constructed that allows the agent to revise its motion plan without strictly following the desired LTL constraints. A utility function composed of violation cost and state rewards is developed. Rigorous analysis shows that, if there almost surely (i.e., with probability 1) exists a policy that satisfies the relaxed product MDP, any algorithm that optimizes the expected utility is guaranteed to find such a policy. A reinforcement learning-based approach is then developed to generate policies that fulfill the desired LTL specifications as much as possible by optimizing the expected discount utility of the relaxed product MDP.
AffectiveNet: Affective-Motion Feature Learning for Microexpression Recognition

Microexpressions are hard to spot due to fleeting and involuntary moments of facial muscles. Interpretation of microemotions from video clips is a challenging task. In this article, we propose an affective-motion imaging that cumulates rapid and short-lived variational information of microexpressions into a single response. Moreover, we have proposed an AffectiveNet: Affective-motion feature learning network that can perceive subtle changes and learns the most discriminative dynamic features to describe the emotion classes. The AffectiveNet holds two blocks: MICRoFeat and MFL block. MICRoFeat block conserves the scale-invariant features, which allows network to capture both coarse and tiny edge variations. Whereas, the MFL block learns microlevel dynamic variations from two different intermediate convolutional layers. Effectiveness of the proposed network is tested over four datasets by using two experimental setups: person independent and cross dataset validation. The experimental results of the proposed network outperform the state-of-the-art approaches with significant margin for MER approaches.