Miracle-dz/UniFAR-FTUs huggingface dataset:
Diel Rhythm in Photosynthetic Performance of Phytoplankton Assemblages Is Predicted to Be Light-Dependent from in situ and Mesocosm Chlorophyll Fluorescence

ABSTRACT Xu, G. ; Liu, J.H. ; Song, X.Y. ; Tan, M.T. ; Ren, H.W. ; Li, D.N. ; Tan, Y.H. ; Huang, L.M. , and Li, G. , 2020. Diel rhythm in photosynthetic performance of phytoplankton assemblages is predicted to be light-dependent from in situ and mesocosm chlorophyll fluorescence. In: Guido Aldana, P.A. and Kantamaneni, K. (eds.), Advances in Water Resources, Coastal Management, and Marine Science Technology. Journal of Coastal Research, Special Issue No. 104, pp. 445–454. Coconut Creek (Florida), ISSN 0749-0208. Marine physical and chemical changes caused by the ebb-and-flow of tide are well known to influence phytoplankton photophysiology; while it is unclear whether such changes affect the diel rhythm of phytoplankton photosynthesis. The diel changes of photosynthetic performance of phytoplankton assemblages were comparably explored from in situ and from two mesocosms in Daya Bay, northern South China Sea. The in situ Chl a content varied daily from 1.4 to 16.7 µg L-1 during the study period, but with a limited diel variation. The maximum photochemical quantum yield of Photosystem II (FV/FM) decreased from morning to noon, then increased till dusk, and maintained steady all night except for a sudden increase before next sunrise. Diel changes of electron transport efficiency (α) coincided with that of the FV/FM in daytime, but not in nighttime. The absorption cross section for photochemistry of Photosystem II (σPSII) varying from 4.1 to 7.7 nm-2 showed a similar diel change as that of the FV/FM. Diel changes of non-photochemical quenching (NPQ), saturating irradiance (EK) and maximum relative electron transport rate (rETRmax) mirrored the change of solar irradiation, with the highest and lowest values occurred at midday and midnight, respectively. The σPSII in surface and 3.5 m layers showed similar diel change pattern and had insignificant difference between the σPSII values. Moreover, all the photosynthetic parameters (i.e., FV/FM, σPSII, NPQ, α, EK and rETRmax,) from in situ showed the same diel change patterns as those from mesocosms, indicating the influence of tide-induced physical and chemical changes is limited. These results indicate that the diel rhythm in photosynthetic performance of natural phytoplankton assemblages is mainly available-light dependent.
MicroRNA regulation of cardiac development

Author(s): Morton, Sarah | Advisor(s): Srivastava, Deepak | Abstract: microRNAs (miRNAs) are small RNAs known to be necessary for normal development of vertebrates, including development of the heart. miRNAs act primarily through post-transcriptional inhibition of protein expression. Two miRNAs described in this thesis, miR-138 and miR-202*, are shown to be necessary for cardiac development in zebrafish.miR-138 ensures proper patterning of the cardiac chambers by clearing mRNA transcripts from the ventricle, allowing proper maturation of ventricular cardiomyocytes. Reduction in miR-138 results in cardiac dysfunction and lack of maturation in cardiomyocytes located on the outer curvature of the ventricle. Direct inhibition of Raldh2 protein by miR-138 in the ventricle, resulting in reduced expression of retinoic acid (RA), is necessary to restrict expression of proteins such as Versican to the atrioventricular canal. Interestingly, Versican expression in the ventricle is also directly inhibited by miR-138. Thus miR-138 is demonstrated to be the first miRNA involved in cardiac patterning, and achieves inhibition of Versican expression both directly and indirectly via targeting of Raldh2. The targeting of multiple members of a pathway allows for robust clearance of early ventricular mRNAs.miR-202*, in contrast, is necessary for both proper development and function of zebrafish hearts. Inhibition of miR-202* in zebrafish embryos leads to randomization of the left-right patterning of the heart, as well as cardiac conduction abnormalities. In cell culture, miR-202* is able to target Pkd2 protein for inhibition; Pkd2 is a calcium channel known to be necessary for specification of the left-right axis in vertebrates. Embryos with knockdown of miR-202* also demonstrate a 2:1 atrioventricular node (AV) block, where the atrium conducts twice for every ventricular conduction. The molecular mechanism for 2:1 AV block remains unknown, but elucidating the targets responsible for the phenotype will give insight into human diseases with similar conduction abnormalities.In summary, the studies described here identify two miRNAs as being necessary for normal development and/or function of the heart. Future studies further elucidating the role of miR-138 and miR-202* in mammals will provide insight into connections between these miRNAs and human disease.
Multiple-clue Sensory Information Fusion Model of Fashion Silhouette Perception in Coastal City

ABSTRACT Qin, F. ; Kuang, C.Y. , and Jiang, Y. , 2020. Multiple-clue sensory information fusion model of fashion silhouette perception in coastal city. In: Guido Aldana, P.A. and Kantamaneni, K. (eds.), Advances in Water Resources, Coastal Management, and Marine Science Technology. Journal of Coastal Research, Special Issue No. 104, pp. 891–895. Coconut Creek (Florida), ISSN 0749-0208. Sensory perception about clothing, such as color, silhouette and texture, comes from the fusion, interpretation and analysis of sensory information. Therefore, research on clothing design that focuses on human perception must begin with consumers' perception about clothing. After analysis of available perceptual design theories and research progress, we find that few studies have been made on the fusion of sensory information. This paper takes references from the theory of the fusion of multiple-clue sensory information and performs a SD experiment to investigate observers' perceptual changes and the fusion of visual clues in coastal city. Visual clues are usually generated by information sources. The paper starts from clothing silhouette and adopts silhouette elements that are able to affect perception as information sources. Finally, the paper puts forward a psychological model on the fusion of multiple-clue sensory information based on clothing silhouette perception and establishes a mathematical model. It will provide practical methods for researchers on clothing sensory perception to integrate color, texture and other aspects of sensory information.
Neuropeptide Y Is an Immunomodulatory Factor: Direct and Indirect

Neuropeptide Y (NPY), which is widely distributed in the nervous system, is involved in regulating a variety of biological processes, including food intake, energy metabolism, and emotional expression. However, emerging evidence points to NPY also as a critical transmitter between the nervous system and immune system, as well as a mediator produced and released by immune cells. In vivo and in vitro studies based on gene-editing techniques and specific NPY receptor agonists and antagonists have demonstrated that NPY is responsible for multifarious direct modulations on immune cells by acting on NPY receptors. Moreover, via the central or peripheral nervous system, NPY is closely connected to body temperature regulation, obesity development, glucose metabolism, and emotional expression, which are all immunomodulatory factors for the immune system. In this review, we focus on the direct role of NPY in immune cells and particularly discuss its indirect impact on the immune response.
Raw Milk Microbiota Modifications as Affected by Chlorine Usage for Cleaning Procedures: The Trentingrana PDO Case

Milk microbiota represents a key point in raw milk cheese production and contributes to the development of typical flavor and texture for each type of cheese. The aim of the present study was to evaluate the influence of chlorine products usage for cleaning and sanitizing the milking equipment on (i) raw milk microbiota; (ii) the deriving whey-starter microbiota; and (iii) Trentingrana Protected Designation of Origin (PDO) cheese microbiota and volatilome. Milk samples from three farms affiliated to a Trentingrana PDO cheese factory were collected three times per week during a 6-weeks period in which a sodium hypochlorite detergent (period C) was used and during a subsequent 6-weeks period of non-chlorine detergent usage (period NC). Samples were subjected to microbiological [Standard Plate Count; coliforms; coagulase-positive staphylococci; and lactic acid bacteria (LAB)] and metagenomic analysis (amplification of V3-V4 regions of 16S rRNA gene performed on Illumina MiSeq platform). In addition, cheese volatilome was determined by SPME-GC-MS. In the transition from period C to period NC, higher SPC and LAB counts in milk were recorded. Milk metagenomic analysis showed a peculiar distinctive microbiota composition for the three farms during the whole experimental period. Moreover, differences were highlighted comparing C and NC periods in each farm. A difference in microbial population related to chlorine usage in bulk milk and vat samples was evidenced. Moreover, chlorine utilization at farm level was found to affect the whey-starter population: the usually predominant Lactobacillus helveticus was significantly reduced during NC period, whereas Lactobacillus delbrueckii had the exact opposite trend. Alpha- and beta-diversity revealed a separation between the two treatment periods with a higher presence of L. helveticus, L. delbrueckii, and Streptococcus thermophilus in cheese samples after NC detergent period. Cheese volatilome analysis showed a slight decrease in lipolysis during C period in the inner part of the cheese wheel. Although preliminary, these results suggest a profound influence on milk and cheese microbiota, as well as on raw milk cheese production and quality, due to the use of chlorine. However, further studies will be needed to better understand the complex relationship between chlorine and microbiota along all the cheese production steps.
SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment

The emergence and rapid spread of SARS-CoV-2 in December 2019 has brought the world to a standstill. While less pathogenic than the 2002–2003 SARS-CoV, this novel betacoronavirus presents a global threat due to its high transmission rate, ability to invade multiple tissues, and ability to trigger immunological hyperactivation. The identification of the animal reservoir and intermediate host were important steps toward slowing the spread of disease, and its genetic similarity to SARS-CoV has helped to determine pathogenesis and direct treatment strategies. The exponential increase in cases has necessitated fast and reliable testing procedures. Although RT-PCR remains the gold standard, it is a time-consuming procedure, paving the way for newer techniques such as serologic tests and enzyme immunoassays. Various clinical trials using broad antiviral agents in addition to novel medications have produced controversial results; however, the advancement of immunotherapy, particularly monoclonal antibodies and immune modulators is showing great promise in clinical trials. Non-orthodox medications such as anti-malarials have been tested in multiple institutions but definitive conclusions are yet to be made. Adjuvant therapies have also proven to be effective in decreasing mortality in the disease course. While no formal guidelines have been established, the multitude of ongoing clinical trials as a result of unprecedented access to research data brings us closer to halting the SARS-CoV-2 pandemic.
Robust Power Textile Based on Triboelectrification for Self-Powered Smart Textiles

Harvesting energy from human body motions is an appropriate option as an assistant or even subversive way for powering the booming wearable electronics, in which smart textiles are important components. Here, we fabricate a robust power textile with working mechanism of triboelectrification effect and electrostatic induction effect by simply integrating the normal textiles and polydimethylsiloxane (PDMS)/conductive yarns electrodes. Maximum peak loading voltage and current reaching 230 V and 11.6 μA are obtained by rubbing our power textile, and this alternating and irregular electricity can be accumulated in a capacitor or directly light up 20 blue LEDs. The recovered energy generation ability of the power textile after washing successfully demonstrate its robustness, showing the potential application in powering the electronics in smart textiles.
Mobile Cloud Computing Readiness Assessment Framework in Upstream Oil and Gas Using RAMI 4.0

Indonesia Industry 4.0 Readiness Index, also known as INDI 4.0, was launched by the Indonesian government where it stated that oil and gas sector was one of the sectors given low priority. The readiness assessment towards INDI 4.0 should be different for each industry. Specific industry value chains need to be examined and their readiness needs to be assessed prior to digitalization project. Mobility is the nature of the Upstream Oil and Gas industry due to remote and vast work areas. Thus, an adoption of digitalization without considering mobility aspects will be less effective. Efficiency expectations from using cloud infrastructure will also be difficult to achieve. Through RAMI 4.0 approach, it is expected that a reference can be obtained grouping value chains in clear hierarchical dimension so that readiness towards INDI 4.0 in the Upstream Oil and Gas industry can be assessed more specifically and accurately. The assessment framework reference is extracted from several sources in order to obtain aspect dimension in the form of people, process and platform. By using these two dimensions, which are hierarchical and aspect dimension, it is expected that the results of the assessment can help making the strategy of implementing Mobile Cloud Computing in the Upstream Oil and Gas industry more specific but still provide flexibility so that the adoption stages can be realistic in accordance to strategic road map.
Vehicle-to-Grid Integration for Enhancement of Grid: A Distributed Resource Allocation Approach

In the future grids, to reduce greenhouse gas emissions Electric Vehicles (EVs) seems to be an important means of transportation. One of the major disadvantages of the future grid is the demand-supply mismatch which can be mitigated by incorporating the EVs into the grid. The paper introduces the concept of the Distributed Resource Allocation (DRA) approach for incorporating a large number of Plug-in EV (PEVs) with the power grid utilizing the concept of achieving output consensus. The charging/discharging time of all the participating PEVs are separated with respect to time slots and are considered as strategies. The major aim of the paper is to obtain a favorable charging strategy for each grid-connected PEVs in such a way that it satisfies both grid objectives in terms of load profile smoothening and minimizing of load shifting as well as economic and social interests of vehicle owners i.e. a fair share of the rate of charging for all connected PEVs. The three-fold contribution of the paper in smoothening of load profile, load shifting minimization, and fair charging rate is validated using a representative case study. The results confirm improvement in load profile and also highlight a fair deal in the charging rate for each PEV.
Reconstructing the Developmental Trajectories of Multiple Subtypes in Pulmonary Parenchymal Epithelial Cells by Single-Cell RNA-seq

Background Some lung diseases are cell type-specific. It is essential to study the cellular anatomy of the normal human lung for exploring the cellular origin of lung disease and the cell development trajectory. Methods We used the Seurat R package for data quality control. The principal component analysis (PCA) was used for linear dimensionality reduction. UMAP and tSNE were used for dimensionality reduction. Muonocle2 was used to extract lung epithelial cells to analyze the subtypes of epithelial cells further and to study the development of these cell subtypes. Results We showed a total of 20154 high quality of cells from human normal lung tissue. They were initially divided into 17 clusters cells and then identified as seven types of cells, namely macrophages, monocytes, CD8 + T cells, epithelial cells, endothelial cells, adipocytes, and NK cells. 4240 epithelial cells were extracted for further analysis and they were divided into seven clusters. The seven cell clusters include alveolar cell, alveolar endothelial progenitor, ciliated cell, secretory cell, ionocyte cell, and a group of cells that are not clear at present. We show the development track of these subtypes of epithelial cells, in which we speculate that alveolar epithelial progenitor (AEP) is a kind of progenitor cells that can develop into alveolar cells, and find six essential genes that determine the cell fate, including AGER, RPL10, RPL9, RPS18, RPS27, and SFTPB. Conclusion We provide a transcription map of human lung cells, especially the in-depth study on the development of epithelial cell subtypes, which will help us to study lung cell biology and lung diseases.
Autonomous Distributed System for Gait Generation for Single-Legged Modular Robots Connected in Various Configurations

To date, many gait generation strategies have been designed for robots with leg configurations that model those of natural creatures. However, their leg configurations are limited to the $2\times N$ type, such as hexapod or myriapod; hence, simultaneously, the potential ability of legged robots is implicitly limited. We consider single-legged modular robots that can be arranged to form a cluster with arbitrary 2-D leg configurations. By choosing configurations appropriately, these robots have the potential to perform several types of tasks, as is the case for reconfigurable modular robots. However, to use appropriate configurations for a given task, a unified gait generation system for various configurations of a cluster is required. In this article, we propose an autonomous distributed control system for each single-legged modular robot to collectively achieve static walking of the cluster with various leg configurations on planar ground. Moreover, our system is an autonomous distributed system with scalability and fault tolerance, in which each module determines the moving pattern of its foot through local communication without global information, such as the entire leg configuration of the cluster. We verified that several types of clusters achieved static walking using our system not only in dynamic simulations, but also in real robot experiments.
Design of Energy Modulation Massive SIMO Transceivers via Machine Learning

This paper considers a massive single-input multiple-output (SIMO) system, where multiple single-antenna transmitters simultaneously communicate with a receiver equipped with a large number of antennas. Different from the conventional noncoherent transceivers which require a certain level of the statistical information on the channel fading, we propose a joint transceiver design method based on machine learning, requiring a limited number of channel realizations. In the proposed method, the multiple transmitters, the channel, and the receiver are represented with a deep neural network (NN), and an autoencoder is adopted to minimize the end-to-end transmission error probability. Simulation results show that the proposed NN-based transceiver achieves lower transmission error probability in typical scenarios, and is more robust against the channel parameters variation compared with the existing methods.
Enhanced Chlorophyll Degradation Triggers the Pod Degreening of “Golden Hook,” a Special Ecotype in Common Bean (Phaseolus vulgaris L.)

To reveal genetic factors or pathways involved in the pod degreening, we performed transcriptome and metabolome analyses using a yellow pod cultivar of the common bean “golden hook” ecotype and its green pod mutants yielded via gamma radiation. Transcriptional profiling showed that expression levels of red chlorophyll catabolite reductase (RCCR, Phvul.008G280300) involved in chlorophyll degradation was strongly enhanced at an early stage (2 cm long) in wild type but not in green pod mutants. The expression levels of genes involved in cellulose synthesis was inhibited by the pod degreening. Metabolomic profiling showed that the content of most flavonoid, flavones, and isoflavonoid was decreased during pod development, but the content of afzelechin, taxifolin, dihydrokaempferol, and cyanidin 3-O-rutinoside was remarkably increased in both wild type and green pod mutant. This study revealed that the pod degreening of the golden hook resulting from chlorophyll degradation could trigger changes in cellulose and flavonoids biosynthesis pathway, offering this cultivar a special color appearance and good flavor.
Novel Porcine Retina Cultivation Techniques Provide Improved Photoreceptor Preservation

Age-related macular degeneration (AMD) is the leading cause of blindness in industrialized countries among people over 60 years. It has multiple triggers and risk factors, but despite intense research efforts, its pathomechanisms are currently not completely understood. AMD pathogenesis is characterized by soft drusen in Bruch’s membrane and involves the retinal pigment epithelium–Bruch’s membrane-choroid complex and adjacent structures, like photoreceptors. This study explores the potential of novel cultivation techniques to preserve photoreceptors in retinal explants to gain better insights in AMD pathology. The porcine retina explants were cultured for 4 and 8 days using three different explantation techniques, namely, control (photoreceptors facing down, touching the filter), filter (photoreceptors facing up, turned sample using a filter), and tweezers (photoreceptors facing up, turned sample using tweezers). Optical coherence tomography revealed that the tweezers method had the best capacity to limit thinning of the retinal explants. Both novel methods displayed advantages in maintaining outer segment thickness. Additionally, immunofluorescence evaluation revealed a better preservation of opsin+ cells and rhodopsin signal intensity in both novel methods, especially the tweezers method. Furthermore, RT-qPCR analysis demonstrated an upregulation of OPSIN and RHODOPSIN mRNA expression in tweezers samples at 8 days. Amacrine and bipolar cell numbers were not altered at day 4 of cultivation, while cultivation until 8 days led to reduced bipolar cell numbers. At 4 days, CALRETININ mRNA was upregulated in filter samples, but protein kinase C alpha expression was downregulated. Retinal ganglion cells were diminished in both novel techniques due to a direct physical contact with the insert. Remarkably, no difference in TUBB3 mRNA expression was detected among the techniques. Nevertheless, both novel methods exhibited an improved retention of photoreceptor cells. In conclusion, the tweezers technique was the most promising one. Due to the high homology of the porcine to the human retina, it provides a reasonable alternative to in vivo rodent models. Consequently, an adapted coculture system based on the current findings may serve as an ex vivo model suitable to analyze AMD pathomechanisms and novel therapeutic approaches.