Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation

Gut dysbiosis contributes to the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in development of various diseases. However, emerging evidence has indicated data inconsistency between different studies frequently, but gained very little attention by scientists. There are many factors that can cause data variation and inconsistency during the process of microbiota study, in particular, sample storage conditions and subsequent sequencing process. Here, we systemically evaluated the impacts of six fecal sample storage conditions (including −80 °C, −80 °C with 70% ethanol (ET_-80 °C), 4°C with 70% ethanol (ET_4°C), and three commercial storage reagents including OMNIgene•GUT OMR-200 (GT), MGIEasy (MGIE), and Longsee (LS)), storage periods (1, 2 weeks or 6 months), and sequencing platform on gut microbiome profile using 16S rRNA gene sequencing. Our results suggested that −80°C is acceptable for fecal sample storage, and the addition of 70% ethanol offers some benefits. Meanwhile, we found that samples in ET_4 °Cand GT reagents are comparable, both introduced multi-dimensional variations. The use of MGIE resulted in the least alteration, while the greatest changes were observed in samples stored in LS reagents during the whole experiment. Finally, we also confirmed that variations caused by storage condition were larger than that of storage time and sequencing platform. IMPORTANCE In the current study, we performed a multi-dimensional evaluation on the variations introduced by types of storage conditions, preservation period and sequencing platform on the basis of data acquired from 16S rRNA gene sequencing. The efficacy of preservation methods was comprehensively evaluated by DNA yield and quality, α and β diversity, relative abundance of the dominant bacteria and functional bacteria associated with SCFAs producing and BAs metabolism. Our results confirmed that variations introduced by storage condition were larger than that of storage periods and sequencing platform. Collectively, our study provided a comprehensive view to the impacts of storage conditions, storage times, and sequencing platform on gut microbial profile.
A Heat Balance Method for Measuring Water Flow Rate in Stems of Intact Plants and Its Application to Sugarcane Plants

In recent years, intense interest has been focused on attaining high water-use efficiency while maintaining high productivity, because of increasing competition for water with nonagricultural users and of increasing demand for the expansion of agricultural areas into marginal lands. For this purpose, the relations of transpiration of crops with environmental factors and dry matter production have been actively investigated. One of the· major problems in such investigation is how to estimate the transpiration rate of crops in the natural conditions. The chamber method, in which transpiring plants are covered by a tent or a box made of transparent materials, has been widely used. The direct measuring methods of transpiration stream in a plant stem in the natural condition have been also employed by some researchers. However, each method has important shortcomings. In the · former, microclimate in the chamber differs from out-door conditions, and in the latter, it is difficult to obtain reliable values of water flux in a plant stem.
GWRA: grey wolf based reconstruction algorithm for compressive sensing signals

The recent advances in compressive sensing (CS) based solutions make it a promising technique for signal acquisition, image processing and other types of data compression needs. In CS, the most challenging problem is to design an accurate and efficient algorithm for reconstructing the original data. Greedy-based reconstruction algorithms proved themselves as a good solution to this problem because of their fast implementation and low complex computations. In this paper, we propose a new optimization algorithm called grey wolf reconstruction algorithm (GWRA). GWRA is inspired from the benefits of integrating both the reversible greedy algorithm and the grey wolf optimizer algorithm. The effectiveness of GWRA technique is demonstrated and validated through rigorous simulations. The simulation results show that GWRA significantly exceeds the greedy-based reconstruction algorithms such as sum product, orthogonal matching pursuit, compressive sampling matching pursuit and filtered back projection and swarm based techniques such as BA and PSO in terms of reducing the reconstruction error, the mean absolute percentage error and the average normalized mean squared error.
Sympathetic and parasympathetic involvement in time constrained sequential foraging

Appraising sequential offers relative to an unknown future opportunity and a time cost requires an optimization policy that draws on a learned estimate of an environment’s richness. Converging evidence points to a learning asymmetry, whereby estimates of this richness update with a bias toward integrating positive information. We replicate this bias in a sequential foraging (prey selection) task and probe associated activation within two branches of the autonomic system, sympathetic and parasympathetic branches, using trial-by-trial measures of simultaneously recorded cardiac autonomic physiology. In general, lower value offers were accepted during periods of autonomic drive, both in the sympathetic (shorter pre-ejection period PEP) and parasympathetic (higher HF HRV) branches. In addition, we reveal a unique adaptive role for the sympathetic branch in learning. It was specifically associated with adaptation to a deteriorating environment: it correlated with both the rate of negative information integration in belief estimates and downward changes in moment-to-moment environmental richness, and was predictive of optimal performance on the task. The findings are consistent with a parallel processing framework whereby autonomic function serves both learning and executive demands of prey selection. Significance statement The value of choices (accepting a job) depends on context (richness of the current job market). Learning contexts, therefore, is crucial for optimal decision-making. Humans demonstrate a bias when learning contexts; we learn faster about improvements vs deteriorations. New techniques allow us to cleanly measure fast acting stress responses that might fluctuate with trial-by-trial learning. Using these new methods, we observe here that increased stress – specifically sympathetic (heart contractility) – might help overcome the learning bias (making us faster at learning contextual deterioration) and thereafter guide us toward better context appropriate decisions. For the first time we show that specific building blocks of good decision-making might benefit from short bursts of specific inputs of the stress system.
In vitro antimicrobial combination testing of and evolution of resistance to the first-in-class spiropyrimidinetrione zoliflodacin combined with six therapeutically relevant antimicrobials for Neisseria gonorrhoeae.

OBJECTIVES Resistance in Neisseria gonorrhoeae to all gonorrhoea therapeutic antimicrobials has emerged. Novel therapeutic antimicrobials are imperative and the first-in-class spiropyrimidinetrione zoliflodacin appears promising. Zoliflodacin could be introduced in dual antimicrobial therapies to prevent the emergence and/or spread of resistance. We investigated the in vitro activity of and selection of resistance to zoliflodacin alone and in combination with six gonorrhoea therapeutic antimicrobials against N. gonorrhoeae. METHODS The international gonococcal reference strains WHO F (WT) and WHO O, WHO V and WHO X (strains with different AMR profiles) were examined. Zoliflodacin was evaluated alone or combined with ceftriaxone, cefixime, spectinomycin, gentamicin, tetracycline, cethromycin or sitafloxacin in chequerboard assays, time-kill curve analysis and selection-of-resistance studies. RESULTS Zoliflodacin alone or in combination with all six antimicrobials showed rapid growth inhibition against all examined strains. The time-kill curve analysis indicated that tetracycline or cethromycin combined with zoliflodacin can significantly decrease the zoliflodacin kill rate in vitro. The frequency of selected zoliflodacin-resistance mutations was low when evaluated as a single agent and further reduced for all antimicrobial combinations. All resistant mutants contained the GyrB mutations D429N, K450T or K450N, resulting in zoliflodacin MICs of 0.5-4 mg/L. CONCLUSIONS Zoliflodacin, alone or in combination with sexually transmitted infection therapeutic antimicrobials, rapidly kills gonococci with infrequent resistance emergence. Zoliflodacin remains promising for gonorrhoea oral monotherapy and as part of dual antimicrobial therapy with low resistance emergence potential. A Phase III trial evaluating efficacy and safety of zoliflodacin for uncomplicated gonorrhoea treatment is planned in 2019.
Lymphoedema education needs of clinicians: a national study

Background: Poor knowledge of lymphoedema among clinicians can delay its management, increasing the burden on affected individuals, carers, and services. Aims: To determine the nature of, and means to address, lymphoedema education needs of clinicians within the context of their working lives. Methods: Electronic surveys of lymphoedema specialists and generalist clinicians in Scotland, followed by focus group discussions. Results: Gaps in knowledge and constraints imposed by referral criteria to specialist services contribute to a feeling of professional impotence among both generalists and specialists, as they are unable to provide consistency of care across different care settings. Conclusions: Clinicians have unmet education needs that are profession and healthcare setting specific. Information technology has the potential to improve lymphoedema knowledge, care, and managing patients with lymphoedema. Declaration of interest: The University of Glasgow provides post-registration courses for clinicians to specialise in lymphoedema. A full report of this study is available on request from NHS Education Scotland at: http://tinyurl.com/LymphEducReport
The choreography of human attraction: physiological synchrony in a blind date setting

Humans are social animals whose mental wellbeing is shaped by the ability to attract and connect with each other. In a dating world, in which success can be determined by brief interactions, apart from physical features, there is a whole choreography of movements, physical reactions and subtle expressions that drive humans’ sexual attraction. To determine what drives attraction, we measured nonverbal dynamics between people during real-life interactions outside the laboratory, where dating is most relevant. Participants wore eye-tracking glasses with embedded cameras, and devices to measure physiological signals including heart rate and skin conductance. Crucially, visible signals that can be controlled, such as facial expressions or gaze, did not predict attraction. Instead, attraction was predicted by synchrony in heart rate and skin conductance between partners, which are unconscious and difficult to regulate. Our findings suggest that shared emotionality is vital for mutual attraction. Moreover, physiological synchrony may provide a medium for translating visible expressions into embodied emotions, which can turn into intentions via somatosensory simulation. Significance Statement In our modern world where millions of people meet online without interacting face-to-face, the question “what defines attraction” has become very relevant. In this study, we used modern technologies to lay down a foundation for the processes that drive human attraction during real-life interactions. Contrary to common belief, we found that attraction is not predicted by a frequency of expression or eye fixation duration, nor is linearly related to the participant’s autonomic nervous system activity. Importantly, we found that the more a participant synchronized their heart rate and skin conductance with their partner, the more they felt attracted toward that person. This study reveals a fundamental physiological process that plays a role in the formation of romantic relations.
Behavioural disturbances and underlying neurophysiological mechanisms during ocean acidification and warming in Gadus morhua and Boreogadus saida

Polar cod (Boreogadus saida) inhabiting the Arctic Ocean will experience man-made ocean acidification in the near future and has been shown to be behaviourally sensitive to a mild increase of environmental CO2 which is projected for the end of 21st century. We conducted an in vivo MRI study combined with 31P-NMR spectroscopy on B. saida in order to observe the effect of an acute mild increase of environmental CO2 (1668 ± 250 μatm) on ventilation frequency, vascular blood flow and acid-base status in the head of Polar cod for four days. We observed a significant increase of ventilation frequency, which stabilized after one day under hypercapnic conditions. Arterial and venous blood flow both decreased significantly with the increase of environmental CO2 and were not restored to control values during the observation period. A slight reduction of intracellular pH with the onset of high CO2 conditions remained insignificant. This study indicates that a rise of environmental CO2 might lead to long lasting effects in the cardiovascular system of B. saida, with unclear long-term implications for the fitness of this species in a warmer, more acidified future ocean.
Mitigation of drought stress in maize through inoculation with drought tolerant ACC deaminase containing PGPR under axenic conditions

Drought is one of abiotic factors that hampers the growth and yield of crops via an elevated level of ethylene too, inspite of limited nutrients supply. The ACC deaminase containing PGPR can mitigate drought stress in crops by decreasing the synthesis and accumulation of ethylene. As maize is widely cultivated cereal and fodder crop, a glass jar study was conducted for screening of drought-tolerant ACC deaminase containing PGPR under axenic condition. Under various levels (i.e., 0, 10 and 20%) of polyethylene glycol (PEG) induced drought stress, some of the ACC deaminase containing PGPR significantly enhanced shoot and root length, shoot fresh and dry weight and root fresh and dry weight in maize seedlings. Further, a significant improvement in photosynthetic pigments formation and nutrients concentrations i.e., NPK in maize shoot validated the efficacious functioning of PGPR strains, Pseudomonas aeruginosa, Enterobacter cloacae, Achromobacter xylosoxidans and Leclercia adecarboxylata regarding reduction in ethylene accumulation in maize seedlings under drought. Pseudomonas aeruginosa, Enterobacter cloacae and Achromobacter xylosoxidans are previously documented but Leclercia adecarboxylata is a new drought tolerant ACC deaminase containing PGPR that might have the potential to alleviate drought stress by improving root elongation, NPK uptake and possibility decreasing ethylene in plants.
Seasonal shifts and complementary use of pollen sources by two bees, a lacewing and a ladybeetle species in European agricultural landscapes

Continuous availability of food resources, such as pollen, is vital for many insects that provide pollination and pest control services to agriculture. However, there is a lack of knowledge about the shared or complementary use of floral resources by such species, which hampers more effective landscape management to simultaneously promote them in agroecosystems. Here, we simultaneously quantified pollen use by a bumblebee (Bombus terrestris) and a mason bee (Osmia bicornis), two bee species recognized as important crop pollinators, as well as a lacewing (Chrysoperla carnea) and a ladybeetle species (Harmonia axyridis), both common predators of crop aphids, throughout the season in 23 agricultural landscapes in Germany and Switzerland. Pollen diets were more diverse and similar among C. carnea and H. axyridis compared to the two bee species, but all four species shared key pollen types early in the season such as Acer, Quercus, Salix and Prunus. All species exhibited a pronounced shift in pollen sources from primarily woody plants (mainly trees) in spring to primarily herbaceous plants in summer. The majority of pollen (overall ≥64%) came from non‐agricultural plants even in crop‐dominated landscapes. Synthesis and applications. Our results highlight the importance of trees as pollen sources for many insect species, particularly early in the season. Our findings support incentives that promote heterogeneous agricultural landscapes including both woody and herbaceous semi‐natural habitats, ensuring phenological complementarity of floral resources for insect species that can provide pollination and pest control services to agriculture. The identified key plant species can help to design and optimize agri‐environment schemes to promote these functionally important insects.
Are Sources of EEG and MEG rhythmic activity the same? An analysis based on BC-VARETA

In the resting state (closed or open eyes) the electroencephalogram (EEG) and the magnetoencephalogram (MEG) exibit rhythmic brain activity is typically the 10 Hz alpha rhythm. It has a topographic frequency spectral distribution that is, quite similar for both modalities--something not surprising since both EEG and MEG are generated by the same basic oscillations in thalamocortical circuitry. However, different physical aspects underpin the two types of signals. Does this difference lead to a different distribution of reconstructed sources for EEG and MEG rhythms? This question is important for the transferal of results from one modality to the other but has surprisingly received scant attention till now. We address this issue by comparing eyes open EEG source spectra recorded from 77 subjects from the Cuban Human Brain Mapping project with the MEG of 63 subjects from the Human Connectome Project. Source spectra for each voxel and frequency were obtained via a novel sparse-covariance inverse method (BC-VARETA) based on individualized BEM head models with subject-specific regularization parameters (noise to signal ratio). We circumvent the zero inflated statistical issue arising from sparse estimation by employing a novel dimensionality reduction technique known as Zero-inflated Factor Analysis (ZIFA). Both minimum energy and Hotelling’s T-2 tests showed that ZIFA scores for MEG and EEG sources were significantly different at all frequency bands. These results exclude a simple identification of MEG and EEG sources of resting-state EEG rhythms. Further study is required to determine the relative contribution of instrumental, physical or physiological mechanisms to these differences.
Desenvolvimento de um protocolo pré-clínico para terapia gênica in vivo de Mucopolissacaridose do tipo I

8 Introdução. 9 Objetivos . 20 Nonviral in vivo gene transfer in the mucopolysaccharidosis I murine model . 22 Informações Complementares Aos Resultados. 45 Discussão . 54 Referências Bibliográficas. 58
Contrasting responses of plants and pollinators to woodland disturbance

Preserving species diversity is critical to ensure ecosystem functioning; however, different components of diversity might respond to human disturbance in different ways. Similarly, trophic levels might have uncoupled responses to the same disturbance, thus ameliorating or aggravating the persistence of ecological communities. In this study, we analysed how the density, richness and evenness of flowers and pollinators respond to four levels of woodland thinning intensity (0, 30, 50 and 70% of woodland basal area removed) over 2 years in three contrasting sites. We found a mismatch in the response of flowers and pollinators to thinning. Flower density and richness had disparate responses, depending on the site and year, while evenness did not change with thinning. In contrast, pollinator density and richness, but not evenness, consistently increased with thinning among years and sites. These results suggest that thinning has a great influence on pollinators through changes in abiotic conditions and, perhaps, flower attractiveness rather than through small-scale changes in flower density and richness. At the site where tree flowers were absent, bee pollinator community composition was impoverished, suggesting that trees provide important floral resources to pollinators. Our findings indicate that disturbance may diminish local plant abundance and richness, but pollinator abundance and richness are enhanced after intense thinning at small scales.
The complete mitochondrial genome of Cochliobolus miyabeanus (Dothideomycetes, Pleosporaceae) causing brown spot disease of rice

Abstract Cochliobolus miyabeanus is known as a significant causal agent in relation to brown spot disease of rice and causes significant yield losses. In the present study, the complete mitochondrial genome was determined using next-generation sequencing technology. This complete mitogenome is a circular molecule of 124,887 bp in length. It contains 13 conserved protein-coding genes, 21 transfer RNA genes, 2 ribosomal RNA genes and 9 open reading frames. The overall base composition of C. miyabeanus is 35.4% A, 34.4% T, 14.4% C, 15.8% G, with a CG content of 30.2%. Phylogenetic analysis based on concatenated protein genes from 15 taxa within Pezizomycotina showed that C. miyabeanus is closely related to Bipolaris cookei in the family Pleosporaceae (Dothideomycetes, Pleosporales). This work would facilitate the understanding of systematics and evolutionary biology of phytopathogenic fungi.
Complete chloroplast genome of an orchid species Cymbidium floribundum Lindl

Abstract Cymbidium floribundum Lindl. is an ornamental plant and its native range is south China to north Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. floribundum, which was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome was 153998 bp in length. Its structure contained a large single-copy (LSC) region of 84,725 bp and a small single-copy (SSC) region of 19,009 bp, which were separated by a pair of extremely inverted repeats (IRs) of 25,132 bp each. The phylogenetic analysis indicated that C. floribundum was in the basal of subgenus Jenson.