Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioaugmentation of Bacillus amyloliquefaciens-Bacillus kochii co-cultivation to improve sensory qualities of flue-cured tobacco

Flue-cured tobacco (FCT) with irritating and undesirable flavor must be treated with aging process. However, the spontaneous aging usually takes a very long time for the low efficiency. Bioaugmentation with functional strains is a promising method to improve FCT quality with high aging efficiency. To ease the adverse effect of excessive starch or protein content on the FCT quality, we screened B. amyloliquefaciens LB with high alpha-amylase and B. kochii SC with high neutral protease from the FCT microflora with the flow cytometry. The mono, co-culture of strains was subjected to solid-state fermentation with FCT. B. amyloliquefaciens monoculture at 2 days and B. kochii monoculture at 2.5 days achieved the optimum quality. B. amyloliquefaciens-B. kochii co-culture at a ratio of 3:1 fermenting for 2 days demonstrated a more comprehensive quality enhancement and higher functional enzyme activity than mono-cultivation. With the analysis of OPLS-DA model, there were 38 differential compounds between bioaugmentation samples. In co-cultivation, most of Maillard reaction products and terpenoid metabolites were at a higher level than other samples, which promoted an increase in aroma, softness and a decrease in irritation. This result was in line with our design about the quality enhancement of FCT with co-cultivation. In our study, we presented a promising bioaugmentation technique for changing the quality attributes of FCT in a short aging time.
NgAgo possesses guided DNA nicking activity

Abstract Prokaryotic Argonautes (pAgos) have been proposed as more flexible tools for gene-editing as they do not require sequence motifs adjacent to their targets for function, unlike popular CRISPR/Cas systems. One promising pAgo candidate, from the halophilic archaeon Natronobacterium gregoryi (NgAgo), has been the subject of debate regarding its potential in eukaryotic systems. Here, we revisit this enzyme and characterize its function in prokaryotes. NgAgo expresses poorly in non-halophilic hosts with most of the protein being insoluble and inactive even after refolding. However, we report that the soluble fraction does indeed act as a nicking DNA endonuclease. NgAgo shares canonical domains with other catalytically active pAgos but also contains a previously unrecognized single-stranded DNA binding domain (repA). Both repA and the canonical PIWI domains participate in DNA cleavage activities of NgAgo. NgAgo can be programmed with guides to nick targeted DNA in Escherichia coli and in vitro 1 nt outside the 3′ end of the guide sequence. We also found that these endonuclease activities are essential for enhanced NgAgo-guided homologous recombination, or gene-editing, in E. coli. Collectively, our results demonstrate the potential of NgAgo for gene-editing and provide new insight into seemingly contradictory reports.
Apollo 15 regolith breccia provides first natural evidence for olivine 1 incongruent melting – REVISION 1 2 3

Apollo 15 regolith breccia provides first natural evidence for olivine 1 incongruent melting – REVISION 1 2 3 Niccolò Satta1, 2, *, Masaaki Miyahara3, Shin Ozawa4, Hauke Marquardt2, Masahiko 4 Nishijima5, Tomoko Arai6 and Eiji Ohtani4 5 6 1Bayerisches Geoinstitut, Universität Bayreuth, Bayreuth 95440, Germany 7 8 2Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, United Kingdom 9 10 3Department of Earth and Planetary Systems Science, Graduate School of Science, Hiroshima 11 University, Higashi-Hiroshima 739-8526, Japan 12 13 4Department of Earth Science, Graduate School of Science, Tohoku University, Sendai 98014 8578, Japan 15 16 5Laboratory for Protein Crystallography and Laboratory for Electron Structural Biology 17 Institute for Protein Research, Osaka University, Suita-shi Osaka 565-0871, Japan 18 19 6Planetary Exploration Research Center, Chiba Institute of Technology, Chiba 275-0016, Japan 20 21 Corresponding author: Niccolò Satta (niccolo.satta@earth.ox.ac.uk) 22 23
Disorganized resting‐state functional connectivity between the dorsal attention network and intrinsic networks in Parkinson's disease with freezing of gait

Freezing of gait (FOG) is a common and complex manifestation of Parkinson's disease (PD) and is associated with impairment of attention. The purpose of this study was to evaluate the functional network connectivity (FNc) changes between the dorsal attention network (DAN) and the other seven intrinsic networks relevant to attention, visual–spatial, executive and motor functions in PD with or without FOG. Forty‐three idiopathic PD patients (21 with FOG [FOG+] versus 22 without FOG [FOG−]) and 18 healthy controls (HC) were recruited in this study. The data‐driven independent component analysis (ICA) method was used to extract and analyze the above‐mentioned resting‐state networks (RSNs). Compared with FOG−, FOG+ displayed decreased positive connectivity between the DAN and medial visual network (mVN) and sensory‐motor network (SMN) and increased negative connectivity between the DAN and default mode network (DMN). The within‐network connectivity in the SMN and visual networks were decreased, whereas the connectivity within DMN was increased significantly in FOG+. Correlation analysis showed that the clock drawing test (CDT) scores were positively correlated with the functional connectivity of mVN (r = 0.573, p = 0.008) and lateral visual network (lVN) (r = 0.510, p = 0.022), the Timed Up and Go Test (TUG) duration were negatively correlated with the connectivity of SMN (r = −0.629, p = 0.003), and the Frontal Assessment Battery (FAB) scores were negatively correlated with the connectivity of DMN in FOG+. Functional connectivity was changed in multiple intra‐networks in patients with FOG. Inordinate inter‐network connectivity between the DAN and other intrinsic networks may partly contribute to the mechanism of freezing.
On the microstructural origin of brain white matter hydraulic permeability

Significance Unveiling the mechanisms that drive mass transport in brain tissue is fundamental, not only to plan accurate surgical procedures, but also to shed light on the way solutes move in the extracellular space during the physiological or pathological state. The relation between the white matter (WM) spatial organization and relevant parameters such as permeability is still an unsolved question. Here, we simulate the interstitial flow between the axons of two WM areas reconstructed through three-dimensional electron microscopy imaging. We show that the permeability computed parallel to the axons is significantly higher than the one calculated perpendicularly and that corpus callosum exhibits a higher permeability than fornix, hence demonstrating the importance of the anisotropic and heterogeneous behavior of WM. Brain microstructure plays a key role in driving the transport of drug molecules directly administered to the brain tissue, as in Convection-Enhanced Delivery procedures. The proposed research analyzes the hydraulic permeability of two white matter (WM) areas (corpus callosum and fornix) whose three-dimensional microstructure was reconstructed starting from the acquisition of electron microscopy images. We cut the two volumes with 20 equally spaced planes distributed along two perpendicular directions, and, on each plane, we computed the corresponding permeability vector. Then, we considered that the WM structure is mainly composed of elongated and parallel axons, and, using a principal component analysis, we defined two principal directions, parallel and perpendicular, with respect to the axons’ main direction. The latter were used to define a reference frame onto which the permeability vectors were projected to finally obtain the permeability along the parallel and perpendicular directions. The results show a statistically significant difference between parallel and perpendicular permeability, with a ratio of about two in both the WM structures analyzed, thus demonstrating their anisotropic behavior. Moreover, we find a significant difference between permeability in corpus callosum and fornix, which suggests that the WM heterogeneity should also be considered when modeling drug transport in the brain. Our findings, which demonstrate and quantify the anisotropic and heterogeneous character of the WM, represent a fundamental contribution not only for drug-delivery modeling, but also for shedding light on the interstitial transport mechanisms in the extracellular space.
C-reactive protein and hypertension among Ghanaian migrants and their homeland counterparts: the Research on Obesity and Diabetes among African Migrants study

Supplemental Digital Content is available in the text Background: Hypertension (HTN) is a growing public health problem in sub-Saharan Africa (SSA) and SSA migrants in Europe. Elevated levels of inflammatory marker C-reactive protein (CRP) have been linked to HTN but the relationship of CRP and HTN among SSA populations has not been studied. To address this knowledge gap, we studied the association between CRP and HTN in migrant and nonmigrant SSA populations residing in different settings. Methods: Cross-sectional data from the multicentre Research on Obesity and Diabetes among African Migrants (RODAM) study were analysed including 5683 Ghanaians aged at least 18 years, residing in rural and urban Ghana, and Europe. Multivariate logistic regression analyses were used to assess the association between high levels of CRP (≥3 mg/l) and HTN (SBP ≥140 mmHg and/or DBP ≥90 mmHg and/or use of antihypertensive medication) per geographical site and sex. Results: The association between CRP levels and HTN varied by sex and geographical location. In age-adjusted models, there was an association between high CRP levels and HTN in urban-Ghanaian women (odds ratio 1.50, 95% confidence interval 1.10–2.03), and European-Ghanaian men (1.68, 1.16–2.43) and women (1.63, 1.28–2.07). However, these associations were attenuated after adjustment for conventional risk factors, especially BMI. No association was found in rural-Ghanaians or urban-Ghanaian men. Conclusion: Our findings show an association between CRP and HTN among Ghanaian migrants and urban-Ghanaian women, however, this was largely explained by conventional risk factors. Thus, prevention of conventional risk factors, in particular obesity, may help to reduce the potentially low-grade inflammatory mechanism underlying HTN.
Prenatal overexpression of platelet‐derived growth factor receptor A results in central nervous system hypomyelination

Platelet‐derived growth factor (PDGF) signaling, through the ligand PDGF‐A and its receptor PDGFRA, is important for the growth and maintenance of oligodendrocyte progenitor cells (OPCs) in the central nervous system (CNS). PDGFRA signaling is downregulated prior to OPC differentiation into mature myelinating oligodendrocytes. By contrast, PDGFRA is often genetically amplified or mutated in many types of gliomas, including diffuse midline glioma (DMG) where OPCs are considered the most likely cell‐of‐origin. The cellular and molecular changes that occur in OPCs in response to unregulated PDGFRA expression, however, are not known.
Nonlinear Causal Discovery for High-Dimensional Deterministic Data

Nonlinear causal discovery with high-dimensional data where each variable is multidimensional plays a significant role in many scientific disciplines, such as social network analysis. Previous work majorly focuses on exploiting asymmetry in the causal and anticausal directions between two high-dimensional variables (a cause–effect pair). Although there exist some works that concentrate on the causal order identification between multiple variables, i.e., more than two high-dimensional variables, they do not validate the consistency of methods through theoretical analysis on multiple-variable data. In particular, based on the asymmetry for the cause–effect pair, if model assumptions for any pair of the data are violated, the asymmetry condition will not hold, resulting in the deduction of incorrect order identification. Thus, in this article, we propose a causal functional model, namely high-dimensional deterministic model (HDDM), to identify the causal orderings among multiple high-dimensional variables. We derive two candidates’ selection rules to alleviate the inconvenient effects resulted from the violated-assumption pairs. The corresponding theoretical justification is provided as well. With these theoretical results, we develop a method to infer causal orderings for nonlinear multiple-variable data. Simulations on synthetic data and real-world data are conducted to verify the efficacy of our proposed method. Since we focus on deterministic relations in our method, we also verify the robustness of the noises in simulations.
A Maximum Divergence Approach to Optimal Policy in Deep Reinforcement Learning

Model-free reinforcement learning algorithms based on entropy regularized have achieved good performance in control tasks. Those algorithms consider using the entropy-regularized term for the policy to learn a stochastic policy. This work provides a new perspective that aims to explicitly learn a representation of intrinsic information in state transition to obtain a multimodal stochastic policy, for dealing with the tradeoff between exploration and exploitation. We study a class of Markov decision processes (MDPs) with divergence maximization, called divergence MDPs. The goal of the divergence MDPs is to find an optimal stochastic policy that maximizes the sum of both the expected discounted total rewards and a divergence term, where the divergence function learns the implicit information of state transition. Thus, it can provide better-off stochastic policies to improve both in robustness and performance in a high-dimension continuous setting. Under this framework, the optimality equations can be obtained, and then a divergence actor–critic algorithm is developed based on the divergence policy iteration method to address large-scale continuous problems. The experimental results, compared to other methods, show that our approach achieved better performance and robustness in the complex environment particularly. The code of DivAC can be found in https://github.com/yzyvl/DivAC.
Task‐dependent neural representations of visual object categories

What do we perceive in a glance of an object? If we are questioned about it, will our perception be affected? How does the task demand influence visual processing in the brain and, consequently, our behaviour? To address these questions, we conducted an object categorisation experiment with three tasks, one at the superordinate level (‘animate/inanimate’) and two at the basic levels (‘face/body’ and ‘animal/human face’) along with a passive task in which participants were not required to categorise objects. To control bottom‐up information and eliminate the effect of sensory‐driven dissimilarity, we used a particular set of animal face images as the identical target stimuli across all tasks. We then investigated the impact of top‐down task demands on behaviour and brain representations. Behavioural results demonstrated a superordinate advantage in the reaction time, while the accuracy was similar for all categorisation levels. The event‐related potentials (ERPs) for all categorisation levels were highly similar except for about 170 ms and after 300 ms from stimulus onset. In these time windows, the animal/human face categorisation, which required fine‐scale discrimination, elicited a differential ERP response. Similarly, decoding analysis over all electrodes showed the highest peak value of task decoding around 170 ms, followed by a few significant timepoints, generally after 300 ms. Moreover, brain responses revealed task‐related neural modulation during categorisation tasks compared with the passive task. Overall, these findings demonstrate different task‐related effects on the behavioural response and brain representations. The early and late components of neural modulation could be linked to perceptual and top‐down processing of object categories, respectively.
Automated Segmentation of Fetal Ultrasound Images Using Feature Attention Supervised Network

Abstract Segmentation of anatomical structures from ultrasound images requires the expertise of an experienced clinician, but developing a machine automated segmentation process is complicated because of the existence of characteristic artifacts. In this article, we present a novel end-to-end network that enables automated measurements of the fetal head circumference (HC) and fetal abdomen circumference (AC) to be made from 2-dimensional (2D) ultrasound images during each pregnancy trimester. These measurements are necessary, because the HC and AC are used to predict gestational age and to monitor fetal growth. Automated HC and AC assessments are valuable for providing independent and objective results and are particularly useful for application in developing countries where trained sonographers are in short supply. We propose a scale attention expanding network that builds a feature pyramid inside the network, and the intermediate result of each scale is then concatenated to the feature with a fusion scheme for the next layer. Furthermore, a scale attention module is proposed for selecting the most useful scale and for reducing scale noise. To optimize the network, a deep supervision method based on boundary attention is employed. Results of experiments show that the scale attention expanding network obtained an absolute difference, Hausdorff distance, and dice similarity coefficient of 1.81 ± 1.69%, 1.22 ± 0.77%, and 97.94%, respectively, which were top results in the HC18 data set, and respective results on the abdomen set were 2.23 ± 2.38%, 0.42 ± 0.56%, and 98.04%. The experiments conducted demonstrate that our method provides a superior performance to existing fetal ultrasound segmentation methods.
Fluid Properties at Gas Turbine Inlet due to Fogging Considering Evaporation and Condensation Phenomena as Well as Icing Risk

This study reports on numerically calculated thermophysical properties of air entering a gas turbine compressor after passing through an intake duct affected by different cooling techniques. Case of reference is unaffected ambient air (referenced to as unaffected) passing the intake duct. Furthermore ambient air cooled down to wet bulb temperature by (overspray) fogging (referenced to as wet) was considered. The third case shows air cooled down to the same temperature as it was reached in the wet case but by using chillers (referenced to as chilled). Equilibrium and non-equilibrium properties according to the occurring evaporation and condensation phenomena were compared. Equilibrium conditions seems to have a reduced inlet icing risk for the wet case compared to the chilled case. However comparing the wet case to the unaffected case showed a higher icing risk for the wet case at low ambient relative humidity. In contrast to equilibrium conditions a consideration of non-equilibrium conditions resulted in an increased icing risk due to almost negligible condensation rates.Copyright © 2014 by ASME
Resistance to a nonselective 4‐hydroxyphenylpyruvate dioxygenase‐inhibiting herbicide via novel reduction–dehydration–glutathione conjugation in Amaranthus tuberculatus

Summary Metabolic resistance to 4‐hydroxyphenylpyruvate dioxygenase (HPPD)‐inhibiting herbicides is a threat in controlling waterhemp (Amaranthus tuberculatus) in the USA. We investigated resistance mechanisms to syncarpic acid‐3 (SA3), a nonselective, noncommercial HPPD‐inhibiting herbicide metabolically robust to Phase I oxidation, in multiple‐herbicide‐resistant (MHR) waterhemp populations (SIR and NEB) and HPPD inhibitor‐sensitive populations (ACR and SEN). Dose–response experiments with SA3 provided ED50‐based resistant : sensitive ratios of at least 18‐fold. Metabolism experiments quantifying parent SA3 remaining in excised leaves during a time course indicated MHR populations displayed faster rates of SA3 metabolism compared to HPPD inhibitor‐sensitive populations. SA3 metabolites were identified via LC‐MS‐based untargeted metabolomics in whole plants. A Phase I metabolite, likely generated by cytochrome P450‐mediated alkyl hydroxylation, was detected but was not associated with resistance. A Phase I metabolite consistent with ketone reduction followed by water elimination was detected, creating a putative α,β‐unsaturated carbonyl resembling a Michael acceptor site. A Phase II glutathione–SA3 conjugate was associated with resistance. Our results revealed a novel reduction–dehydration–GSH conjugation detoxification mechanism. SA3 metabolism in MHR waterhemp is thus atypical compared to commercial HPPD‐inhibiting herbicides. This previously uncharacterized detoxification mechanism presents a unique opportunity for future biorational design by blocking known sites of herbicide metabolism in weeds.
Changes in maternal risk factors and their association with changes in cesarean sections in Norway between 1999 and 2016: A descriptive population-based registry study

Background Increases in the proportion of the population with increased likelihood of cesarean section (CS) have been postulated as a driving force behind the rise in CS rates worldwide. The aim of the study was to assess if changes in selected maternal risk factors for CS are associated with changes in CS births from 1999 to 2016 in Norway. Methods and findings This national population-based registry study utilizes data from 1,055,006 births registered in the Norwegian Medical Birth Registry from 1999 to 2016. The following maternal risk factors for CS were included: nulliparous/≥35 years, multiparous/≥35 years, pregestational diabetes, gestational diabetes, hypertensive disorders, previous CS, assisted reproductive technology, and multiple births. The proportion of CS births in 1999 was used to predict the number of CS births in 2016. The observed and predicted numbers of CS births were compared to determine the number of excess CS births, before and after considering the selected risk factors, for all births, and for births stratified by 0, 1, or >1 of the selected risk factors. The proportion of CS births increased from 12.9% to 16.1% (+24.8%) during the study period. The proportion of births with 1 selected risk factor increased from 21.3% to 26.3% (+23.5%), while the proportion with >1 risk factor increased from 4.5% to 8.8% (+95.6%). Stratification by the presence of selected risk factors reduced the number of excess CS births observed in 2016 compared to 1999 by 67.9%. Study limitations include lack of access to other important maternal risk factors and only comparing the first and the last year of the study period. Conclusions In this study, we observed that after an initial increase, proportions of CS births remained stable from 2005 to 2016. Instead, both the size of the risk population and the mean number of risk factors per birth continued to increase. We observed a possible association between the increase in size of risk population and the additional CS births observed in 2016 compared to 1999. The increase in size of risk population and the stable CS rate from 2005 and onward may indicate consistent adherence to obstetric evidence-based practice in Norway.