Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Biosynthetic Pathway of the C50 Carotenoid Bacterioruberin from Lycopene in the Extremely Halophilic Archaeon Haloarcula japonica

ABSTRACT Haloarcula japonica, an extremely halophilic archaeon that requires high concentrations of NaCl for growth, accumulates the C50 carotenoid bacterioruberin (BR). By homology analysis, a gene cluster, including c0507, c0506, and c0505, was found and predicted to be involved in the synthesis of bacterioruberin. To elucidate the function of the encoded enzymes, we constructed Ha. japonica mutants of these genes and analyzed carotenoids produced by the mutants. Our research showed that c0507, c0506, and c0505 encoded a carotenoid 3,4-desaturase (CrtD), a bifunctional lycopene elongase and 1,2-hydratase (LyeJ), and a C50 carotenoid 2″,3″-hydratase (CruF), respectively. The above three carotenoid biosynthetic enzymes catalyze the reactions that convert lycopene to bacterioruberin in Ha. japonica. This is the first identification of functional CrtD and CruF in archaea and elucidation of the complete biosynthetic pathway of bacterioruberin from lycopene. IMPORTANCE Haloarcula japonica, an extremely halophilic archaeon, accumulates the C50 carotenoid bacterioruberin (BR). In this study, we have identified three BR biosynthetic enzymes and have elucidated their functions. Among them, two enzymes were found in an archaeon for the first time. Our results revealed the biosynthetic pathway responsible for production of BR in Ha. japonica and provide a basis for investigating carotenoid biosynthetic pathways in other extremely halophilic archaea. Elucidation of the carotenoid biosynthetic pathway in Ha. japonica may also prove useful for producing the C50 carotenoid BR efficiently by employing genetically modified haloarchaeal strains.
Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu

ABSTRACT “Daqu” is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota. IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.
Underwater Mine Classification with Imperfect Labels

A new algorithm for performing classification with imperfectly labeled data is presented. The proposed approach is motivated by the insight that the average prediction of a group of sufficiently informed people is often more accurate than the prediction of any one supposed expert. This idea that the "wisdom of crowds" can outperform a single expert is implemented by drawing sets of labels as samples from a Bernoulli distribution with a specified labeling error rate. Additionally, ideas from multiple imputation are exploited to provide a principled way for determining an appropriate number of label sampling rounds to consider. The approach is demonstrated in the context of an underwater mine classification application on real synthetic aperture sonar data collected at sea, with promising results.
Denoising realization based on wavelet transform modulus maximum

Based on different properties of signals and noise with wavelet transform, the wavelet transform modulus maximum is introduced to eliminate the noise. It includes Mallat alternative projection algorithm and denoising algorithm based on modulus maximum in wavelet field. The first method is introduced to remove the modulus maximum that decreases with increasing scale and reserve those to the contrary, and then, the remainder are reconstructed to the original signal so as to denoise. The wavelet field modulus maximum is realized by obtaining modulus maximum according to adhoc algorithm and compute its definition to get the wavelet coefficients; Finally, the singularity is reconstructed through inverse wavelet transform. Experiment result shows that two methods suppress the noise effectively.
A Survey of Smart Parking Solutions

Considering the increase of urban population and traffic congestion, smart parking is always a strategic issue to work on, not only in the research field, but also from economic interests. Thanks to information and communication technology evolution, drivers can more efficiently find satisfying parking spaces with smart parking services. The existing and ongoing works on smart parking are complicated and transdisciplinary. While deploying a smart parking system, cities, as well as urban engineers, need to spend a very long time to survey and inspect all the possibilities. Moreover, many varied works involve multiple disciplines, which are closely linked and inseparable. To give a clear overview, we introduce a smart parking ecosystem and propose a comprehensive and thoughtful classification by identifying their functionalities and problematic focuses. We go through the literature over the period of 2000–2016 on parking solutions as they were applied to smart parking development and evolution, and propose three macro-themes: information collection, system deployment, and service dissemination. In each macro-theme, we explain and synthesize the main methodologies used in the existing works and summarize their common goals and visions to solve current parking difficulties. Finally, we give our engineering insights and show some challenges and open issues. Our survey gives an exhaustive study and a prospect in a multidisciplinary approach. Besides, the main findings of the current state-of-the-art throw out recommendations for future research on smart cities and the Internet architecture.
Pre-Coding Based Compressed Sensing UWB Communication System for Bursty Applications

A pre-coding based compressed sensing (CS) ultra-wideband (UWB) communication system is proposed in this paper. Our major contribution is that we attempt to achieve effective signal measurement required in CS by applying a digital random pre-coding block at the transmitter instead of analog schemes. By exploiting pulse modulation and UWB channel as parts of CS measurement process, signal model from transmitter to receiver is established. Signal reconstruction is discussed and UWB channel estimation is study based on CS theory. Simulation results in IEEE 802.15. 3a CM1 channel model show that the proposed system is feasible to detect UWB signals without a very high-frequency analog-to-digital converter (ADC). Moreover, it can operate in a regime of heavy inter-symbol interference (ISI).
Monoclonal antibody 57B stains tumor tissues that express gene MAGE‐A4

Monoclonal antibody (Mab) 57B, which was raised against a recombinant MAGE‐A3 protein, was tested for its ability to stain cells expressing various members of the MAGE‐A gene family. COS‐7 cells transfected with cDNAs encoding MAGE‐A1, A2, A3, A4, A6, or A12 were stained, whereas those transfected with MAGE‐A8, A9, A10, or A11 cDNAs were not. However, in tissue sections, we observed a different pattern of staining: the antibody effectively stained the tumors that expressed MAGE‐A4 and only these tumors, regardless of the expression of the other MAGE‐A genes. It seems, therefore, that at the level of MAGE gene expression found in tumors, a level clearly lower than that observed in transfected COS cells, only the MAGE‐A4 protein can be reliably detected. We conclude that the 57B Mab should be useful for tumor diagnosis related to therapeutic vaccination involving MAGE‐A4. Int. J. Cancer 86:835–841, 2000. © 2000 Wiley‐Liss, Inc.
Rethinking Reusable Resources

We address the common and recurring problem of data reuse, focusing on the following topics: (i) the current state of affairs (in particular, problems with data); (ii) requirements for change; (iii) the proposed solution (its problems and advantages, as well as related work in this area), including the canonical-, I/O-, and data transformation models; (iv) maintenance issues; (v) implementation and deployment aspects; (vi) conclusions and future directions, including results from work done so far and aspects that merit future work.
Spectral Decomposition Modeling Method and Its Application to EM Scattering Calculation of Large Rough Surface With SSA Method

The small slope approximation (SSA) method is a practical method to calculate the electromagnetic (EM) scattering from rough surfaces. However, the SSA method requires that the interval for sampling surfaces must be small enough, such as less than one-tenth of incident wavelength. This constraint condition will cause the problem of huge memory consumption and insufficient memory when the EM scattering of large rough surfaces is calculated. Although the hard disk has large space to keep data and can solve the insufficient memory problem, its read/write speed is still too slow. In addition, massive data transmission will reduce the computational efficiency for the compute unified device architecture (CUDA) parallel computation under some conditions. In this paper, the main idea of the spectral decomposition modeling method is that the whole spectrum of rough surface is divided into several parts and these parts can be used to generate different-scale rough surfaces. Then, by analyzing the different-scale rough surfaces, the large rough surface can be achieved and applied to the calculation of EM scattering with the SSA method. Due to the small memory consumption of different-scale rough surfaces, it takes less time to translate data for the different-scale rough surfaces than that for the standard large surface. Thus, the spectral decomposition modeling method could readily be applied to CUDA parallel computation.
Utility of C-arm CT in overcoming challenges in patients undergoing Transarterial chemoembolization for hepatocellular carcinoma

Abstract Transarterial chemoembolization (TACE) is the well-known treatment for hepatocellular carcinoma. Multiple digital subtraction angiography (DSA) acquisitions in different projections are required to identify difficult arterial feeders. Moreover, the tell-tale tumor blush can be obscured by proximity to lung base, small size of lesion, and breathing artifacts. C-arm CT is a revolutionary advancement in the intervention radiology suite that allows acquisition of data which can be reformatted in multiple planes and volume rendered incorporating both soft tissue and vascular information like multidetector computed tomography (MDCT). These images acquired during the TACE procedure can provide critical inputs for achieving a safe and effective therapy. This case series aims to illustrate the utility of C-arm CT in solving specific problems encountered while performing TACE.
Mycobacterium avium Complex Extracellular Vesicles Attenuate Inflammation via Inducing IL-10

Mycobacterium avium complex (MAC) is an ubiquitous acid-fast bacterium. MAC cell wall and membrane release extracellular vesicles (EVs) into different media. The immunogenic effects of EVs isolated from MAC remain unknown. The aim of this study was to determine the EVs effect on macrophage cytokine production. MAC EVs were extracted and purified using differential centrifuges also known as Claassen’s method, with some modifications. After protein analysis of EVs, and scanning electron microscopy (SEM), the EVs were injected into BALB/c mice for in vivo experiments. The concentration of interferon gamma (IFN-γ) and interleukin 10 (IL-10) in the spleen immune cell culture was measured by sandwich ELISA. We for the first time showed that MAC can naturally produce EVs. The extraction method was technically-feasible, efficient and affordable. The SEM analysis showed that EVs diameter was similar to other studies on mycobacteria, and EVs maintained their spatial characterization. The results of the cytokine assays indicated that EV-treated cells secreted IL-10 (P = 0.034) but not IFN-γ (P = 0.037). Our findings suggest that EVs of M. avium could have anti-inflammatory effects. They can be used as a suppressor or regulator of inflammation via IL-10. The replication of the anti-inflammatory response of MAC EVs in future studies may indicate a new therapeutic agent for inflammation.
The duration of the PhD at Spain from a stochastic frontier perspective: Is it really a trick-or-treat issue?

The duration of the PhD is a relevant factor which influences the career prospects of the student during the rest of his life. It is also important because there are different resources, such as public expenditure or the reputation of the research centre or university where it has been done, which depends on this question. This paper examines the effect of different characteristics of Spanish PhD students on the duration of their PhD thesis. Previous evidence has found that individual characteristics as much as public funding and the existence of a supervisor affects the duration of the studies but also the prospective career of the PhD student. We assume that the duration of the PhD depends on an efficiency issue which could be analyzed from a new methodological point of view. To that aim, this paper proposes a stochastic frontier model to measure the lost of efficiency of some students due to different factors and which could be the cause that contributes to increase their PhD duration at Spain. We estimate the frontier model for the years 2006 and 2009, which also let us to analyze if the economic crisis has affected the influence of the variables on the PhD duration.
Social Categorization, Self-Esteem, and the Estimated Musical Preferences of Male Adolescents

Abstract The authors investigated the intergroup processes of male adolescents within the context of social identity theory (SIT; H. Tajfel, 1978; H. Tajfel & J. C. Turner, 1979). The participants were English male adolescents (age = 14–15 years). They estimated in-group and out-group musical preferences and evaluated the in-group and out-group along a series of scales. The results showed in-group favoritism effects along the musical preference and evaluative dimensions. The participants reported greater liking for the in-group. Compared with the out-group, they associated the in-group more with positively stereotyped music and less with negatively stereotyped music. Compared with the out-group, they rated the in-group as more fun, more masculine, more sporty, less boring, less snobbish, and less weird. The participants with lower levels of self-esteem showed greater differentiation between groups and greater derogation of the out-group. The results supported the predictions of SIT and demonstrated the applicability of SIT for the study of adolescent behavior.
Detection and localization of chemokine gene expression in autoimmune thyroid disease

objective Autoimmune thyroid disease (Hashimoto's thyroiditis and Graves’ disease) is characterized by lymphocytic infiltration of the thyroid gland. Chemokines are cytokines with chemoattractant properties for a range of immune effector cells and might therefore play a significant role in the initiation and maintenance of the autoimmune process. The aim of this study was to analyse chemokine gene expression in autoimmune thyroid tissue and in cultured thyroid follicular cells (TFC).
Structural Symmetries of the Lifted Representation of Classical Planning Tasks

We transfer the notion of structural symmetries to lifted planning task representations, based on a generalizing concept of abstract structures we use to model planning tasks. We show that symmetries are preserved by common grounding methods and shed some light on the relation to previous symmetry concepts. An analysis of common planning benchmarks reveals that symmetries occur in the lifted representation of many domains. Our concept prepares the ground for exploiting symmetries beyond their current scope, such as for faster grounding and mutex generation, as well as for state space transformations and state space reductions.
Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis

MicroRNAs (miRNAs) are endogenous small RNAs which play important negative regulatory roles at both the transcriptional and post-transcriptional levels in plants. Wheat is the most commonly cultivated plant species worldwide. In this study, RNA-seq analysis was used to examine the expression profiles of miRNA in the spikelets of photo-thermosenisitive genic male sterile (PTGMS) wheat line BS366 during male fertility transition. Through mapping on their corresponding precursors, 917–7,762 novel miRNAs were found in six libraries. Six novel miRNAs were selected for examination of their secondary structures and confirmation by stem-loop RT-PCR. In a differential expression analysis, 20, 22, and 58 known miRNAs exhibited significant differential expression between developmental stages 1 (secondary sporogenous cells had formed), 2 (all cells layers were present and mitosis had ceased), and 3 (meiotic division stage), respectively, of fertile and sterile plants. Some of these differential expressed miRNAs, such as tae-miR156, tae-miR164, tae-miR171, and tae-miR172, were shown to be associated with their targets. These targets were previously reported to be related to pollen development and/or male sterility, indicating that these miRNAs and their targets may be involved in the regulation of male fertility transition in the PTGMS wheat line BS366. Furthermore, target genes of miRNA cleavage sites were validated by degradome sequencing. In this study, a possible signal model for the miRNA-mediated signaling pathway during the process of male fertility transition in the PTGMS wheat line BS366 was developed. This study provides a new perspective for understanding the roles of miRNAs in male fertility in PTGMS lines of wheat.
A meta-analysis of nutritional supplementation for management of hospitalized alcoholic hepatitis.

BACKGROUND Alcoholic liver disease (ALD) is associated with a high risk of morbidity and mortality. Malnutrition accompanies this condition and may be both a consequence of and contributor to the pathology. Many trials have investigated the benefits of providing supplemental nutrition in the management of patients with ALD. The present study is a meta-analysis of the available evidence. METHOD A meta-analysis of randomized controlled studies comparing nutritional supplementation plus a normal hospital diet versus diet alone. RESULTS Seven randomized controlled studies including 262 patients with ALD were identified. Pooled analysis revealed no statistical difference in mortality between groups given special nutritional therapy versus a normal balanced diet (OR 0.80 [95% CI 0.42 to 1.52]). In addition, nutrition did not significantly improve ascites (OR 1.29 [95% CI 0.52 to 3.20]) or any biochemical parameters. However, encephalopathy showed a significant improvement or resolution (OR 0.24 [95% CI 0.06 to 0.93]). CONCLUSION Nutritional supplementation provided no mortality benefit in patients with ALD, and neither ascites nor biochemical parameters significantly improved. However, encephalopathy was significantly ameliorated and, therefore, nutritional supplementation should be encouraged in that setting.
The role of nitric oxide in the cardiovascular response to chronic and acute hypoxia in White Leghorn chicken (Gallus domesticus)

Prenatal hypoxia due to placental insufficiency results in deleterious phenotypes and compensatory mechanisms including increased sympathetic tone. Utilizing the embryonic chicken model, we investigated (i) changes in nitric oxide (NO)‐mediated tone in response to chronic hypoxic development and (ii) the in vivo role of NO‐mediated tone during acute hypoxic exposure, which has not been previously studied. We hypothesized that NO tone on the cardiovascular system would be unaffected by chronic hypoxic incubation in White Leghorn chicken (Gallus domesticus) embryos.
The Creativity-Centric Model of the Organization

The paper describes a model of organization in dynamic environment and improves performance of the organization. It is assumed that there is a creative part of the organization which determine innovative type of organization. The key players of creativity centric organization are creative stakeholders: internal – creative employees, external – creative followers and creative managers. There are number of factors/conditions which influence the process of creativity:· Cooperative networks – the creative stakeholders have to work in communities as it is provide better creativity. · High ethics and Morality – lighten the cooperation among creative stakeholders through trust and fairness. · Personal goals and Vision of the organization – have to be in complementarity, correspond to each other as provide base for intrinsic motivation.The paper overviews the previous theories, models and describes typology of stakeholders.