Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides

Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
Impaired Cognitive Function after Perineuronal Net Degradation in the Medial Prefrontal Cortex

Abstract Perineuronal nets (PNNs) are highly organized components of the extracellular matrix that surround a subset of mature neurons in the CNS. These structures play a critical role in regulating neuronal plasticity, particularly during neurodevelopment. Consistent with this role, their presence is associated with functional and structural stability of the neurons they ensheath. A loss of PNNs in the prefrontal cortex (PFC) has been suggested to contribute to cognitive impairment in disorders such as schizophrenia. However, the direct consequences of PNN loss in medial PFC (mPFC) on cognition has not been demonstrated. Here, we examined behavior after disruption of PNNs in mPFC of Long–Evans rats following injection of the enzyme chondroitinase ABC (ChABC). Our data show that ChABC-treated animals were impaired on tests of object oddity perception. Performance in the cross-modal object recognition (CMOR) task was not significantly different for ChABC-treated rats, although ChABC-treated rats were not able to perform above chance levels whereas control rats were. ChABC-treated animals were not significantly different from controls on tests of prepulse inhibition (PPI), set-shifting (SS), reversal learning, or tactile and visual object recognition memory. Posthumous immunohistochemistry confirmed significantly reduced PNNs in mPFC due to ChABC treatment. Moreover, PNN density in the mPFC predicted performance on the oddity task, where higher PNN density was associated with better performance. These findings suggest that PNN loss within the mPFC impairs some aspects of object oddity perception and recognition and that PNNs contribute to cognitive function in young adulthood.
Effect of Admission Time on the Outcomes of Liver Cirrhosis with Acute Upper Gastrointestinal Bleeding: Regular Hours versus Off-Hours Admission

Background and Aims Acute upper gastrointestinal bleeding (AUGIB) is a lethal complication of liver cirrhosis. We aimed to compare the outcomes of patients with liver cirrhosis and AUGIB who were admitted to hospital on regular hours and off-hours. Methods This retrospective study screened all cirrhotic patients with AUGIB who were admitted to our hospital from January 2010 to June 2014 for the test cohort and from December 2014 to March 2018 for the validation cohort. A 1:1 propensity score matching analysis was performed to adjust the Child-Pugh and MELD scores. In-hospital mortality, 5-day rebleeding rate, length of stay, and total payment were primary outcomes. Results Overall, 826 and 173 patients with liver cirrhosis and AUGIB were included in the test and validation cohorts, respectively. After propensity score matching, 226 and 40 patients were included in the test and validation cohorts, respectively. The overall analysis of the test cohort found significantly higher Child-Pugh score (P=0.006), 5-day rebleeding rate (18.69% versus 10.72%, P=0.001), and total payment (¥25,906.83 versus ¥22,017.42, P<0.001) in patients admitted on off-hours. By contrast, the overall analysis of the validation cohort did not find any difference in Child-Pugh score, 5-day rebleeding, in-hospital mortality, length of stay, or hospital payment between patients admitted on regular hours and off-hours. Similarly, the propensity score matching analyses of both test and validation cohorts found no difference in these primary outcomes between the two groups. Conclusions Off-hours admission might not be negatively associated with the outcomes of patients with liver cirrhosis and AUGIB.
Global Interactomics Connect Nuclear Mitotic Apparatus Protein NUMA1 to Influenza Virus Maturation

Influenza A virus (IAV) infections remain a major human health threat. IAV has enormous genetic plasticity and can rapidly escape virus-targeted anti-viral strategies. Thus, there is increasing interest to identify host proteins and processes the virus requires for replication and maturation. The IAV non-structural protein 1 (NS1) is a critical multifunctional protein that is expressed to high levels in infected cells. Host proteins that interact with NS1 may serve as ideal targets for attenuating IAV replication. We previously developed and characterized broadly cross-reactive anti-NS1 monoclonal antibodies. For the current study, we used these mAbs to co-immunoprecipitate native IAV NS1 and interacting host proteins; 183 proteins were consistently identified in this NS1 interactome study, 124 of which have not been previously reported. RNAi screens identified 11 NS1-interacting host factors as vital for IAV replication. Knocking down one of these, nuclear mitotic apparatus protein 1 (NUMA1), dramatically reduced IAV replication. IAV genomic transcription and translation were not inhibited but transport of viral structural proteins to the cell membrane was hindered during maturation steps in NUMA1 knockdown (KD) cells.
Facilitators and Barriers of Assistive Technology and Learning Environment for Children with Special Needs

The purpose of this research was to study the facilitators and barriers of assistive technology (AT) and the learning environment for children with special needs in special education schools in Chiang Mai, Thailand. The informants were one hundred and sixteen children with special needs, who studied in nursery to Grade 12, or with their caregivers. The instrument was a questionnaire applied by the International Classification of Functioning, Disability and Health (ICF) and examined for content validity by five specialists. The results in terms of AT showed that a majority of children with physical disability needed it for mobility and use of school buildings and those with hearing disability for communication. However, most of the children did not need to use AT for culture, recreation, or sports, while many considered it as a facilitator for education. In terms of the learning environment, most characteristics of the physical environment were facilitators for children with special needs, as were those of the social environment for all groups of such children. The results of this study were useful in providing information for AT and design of a learning environment relating to the varied characteristics of children with special needs in special education schools.
Remote Phonon Scattering in Two-Dimensional InSe FETs with High-κ Gate Stack

This work focuses on the effect of remote phonon arising from the substrate and high-κ gate dielectric on electron mobility in two-dimensional (2D) InSe field-effect transistors (FETs). The electrostatic characteristic under quantum confinement is derived by self-consistently solving the Poisson and Schrödinger equations using the effective mass approximation. Then mobility is calculated by the Kubo–Greenwood formula accounting for the remote phonon scattering (RPS) as well as the intrinsic phonon scatterings, including the acoustic phonon, homopolar phonon, optical phonon scatterings, and Fröhlich interaction. Using the above method, the mobility degradation due to remote phonon is comprehensively explored in single- and dual-gate InSe FETs utilizing SiO2, Al2O3, and HfO2 as gate dielectric respectively. We unveil the origin of temperature, inversion density, and thickness dependence of carrier mobility. Simulations indicate that remote phonon and Fröhlich interaction plays a comparatively major role in determining the electron transport in InSe. Mobility is more severely degraded by remote phonon of HfO2 dielectric than Al2O3 and SiO2 dielectric, which can be effectively insulated by introducing a SiO2 interfacial layer between the high-κ dielectric and InSe. Due to its smaller in-plane and quantization effective masses, mobility begins to increase at higher density as carriers become degenerate, and mobility degradation with a reduced layer number is much stronger in InSe compared with MoS2.
RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway

TBK1 phosphorylates RAB7A-S72 to support multiple downstream steps in PARKIN-dependent mitophagy. Removal of damaged mitochondria is orchestrated by a pathway involving the PINK1 kinase and the PARKIN ubiquitin ligase. Ubiquitin chains assembled by PARKIN on the mitochondrial outer membrane recruit autophagy cargo receptors in complexes with TBK1 protein kinase. While TBK1 is known to phosphorylate cargo receptors to promote ubiquitin binding, it is unknown whether TBK1 phosphorylates other proteins to promote mitophagy. Using global quantitative proteomics, we identified S72 in RAB7A, a RAB previously linked with mitophagy, as a dynamic target of TBK1 upon mitochondrial depolarization. TBK1 directly phosphorylates RAB7AS72, but not several other RABs known to be phosphorylated on the homologous residue by LRRK2, in vitro, and this modification requires PARKIN activity in vivo. Interaction proteomics using nonphosphorylatable and phosphomimetic RAB7A mutants revealed loss of association of RAB7AS72E with RAB GDP dissociation inhibitor and increased association with the DENN domain–containing heterodimer FLCN-FNIP1. FLCN-FNIP1 is recruited to damaged mitochondria, and this process is inhibited in cells expressing RAB7AS72A. Moreover, nonphosphorylatable RAB7A failed to support efficient mitophagy, as well as recruitment of ATG9A-positive vesicles to damaged mitochondria. These data reveal a novel function for TBK1 in mitophagy, which parallels that of LRRK2-mediated phosphorylation of the homologous site in distinct RABs to control membrane trafficking.
Hierarchical Cognition Causes Task-Related Deactivations but Not Just in Default Mode Regions

Abstract The well-known deactivation of the default mode network (DMN) during external tasks is usually thought to reflect the suppression of internally directed mental activity during external attention. In three experiments with human participants we organized sequences of task events identical in their attentional and control demands into larger task episodes. We found that DMN deactivation across such sequential events was never constant, but was maximum at the beginning of the episode, then decreased gradually across the episode, reaching baseline towards episode completion, with the final event of the episode eliciting an activation. Crucially, this pattern of activity was not limited to a fixed set of DMN regions but, across experiments, was shown by a variable set of regions expected to be uninvolved in processing the ongoing task. This change in deactivation across sequential but identical events showed that the deactivation cannot be related to attentional/control demands which were constant across the episode, instead, it has to be related to some episode related load that was maximal at the beginning and then decreased gradually as parts of the episode got executed. We argue that this load resulted from cognitive programs through which the entire episode was hierarchically executed as one unit. At the beginning of task episodes, programs related to their entire duration is assembled, causing maximal deactivation. As execution proceeds, elements within the program related to the completed parts of the episode dismantle, thereby decreasing the program load and causing a decrease in deactivation.
The C677T Polymorphism of the Methylenetetrahydrofolate Reductase Gene and Susceptibility to Late-onset Alzheimer’s Disease

Abstract Folate metabolism makes a crucial contribution towards late-onset Alzheimer’s disease (LOAD). Moreover, methylenetetrahydrofolate reductase (MTHFR) constitutes the primary enzyme of the folate pathway. We hypothesize that there is an association of C677T polymorphism in the MTHFR gene with the susceptibility to LOAD. Previous published research has investigated the link between the MTHFR C677T polymorphisms and LOAD susceptibility; nevertheless, the findings have continued to be not only controversial, but also indecisive. Accordingly, we carried out the present meta-analysis for the assessment of the potential link that exists between the MTHFR C677T polymorphism and the susceptibility to LOAD. Furthermore, we carried out a literature search of the PubMed, EMBASE, Cochrane Library, and WanFang database up to August 10, 2018. The odds ratios (ORs) with the respective 95% confidence interval (95%CI) were put to use for the evaluation of the robustness of the link of the MTHFR C677T polymorphism with the vulnerability to LOAD. All statistical analyses were carried out using STATA 15.0. An aggregate of 14 case-control research works was retrieved, involving 2,467 LOAD patients as well as 2,877 controls. We found that a substantial link exists between C677T polymorphism and LOAD risk in a codominant framework (TC vs. CC: OR=1.22, 95%CI=1.00-1.49, P=0.049). In addition to the stratified analysis based on ethnicity, which suggested that C677T polymorphism was likely linked only to an augmented threat of LOAD in Asians, it did not exist among Caucasians. Furthermore, in the subgroup analysis carried out using APOE ɛ4 status, a substantial increase in the susceptibility to LOAD was detected in APOE ɛ4 carriers as well as non-APOE ɛ4 carriers. In sum, the current meta-analysis revealed that MTHFR C677T polymorphism was associated with susceptibility to LOAD. Further extensive case-control studies are required.
TDDFT Investigation of the Hybrid Organic Inorganic Perovskite: CH3NH3PbC3

Hybrid organic-inorganic metal perovskites (chemical formula: ABX3, A-organic cation, B-metal ion, X-halide) are the latest advancement for increasing efficiency in thin-film solar cells or Dye Solar Cells (DSC). They have become the fastest growing technology in solar cells, rising in efficiency from 3% to 22.7% in less than a decade. This work focuses on a time-dependent density-functional theory (TDDFT) study of $\pmb{\text{CH}_{3}\text{NH}_{3}\text{PbCl}_{3}}$ -methyl ammonium lead chloride- a perovskite material of potential and current research interest. The work focuses on the cubic phase. Electronic and optical properties including transition energy, band gap, and vibrational frequencies are examined. The Density of States (DOS) spectrum, IR and UV-VIS spectra are calculated. It is observed that the cubic phase of $\pmb{\text{CH}_{3}\text{NH}_{3}\text{PbCl}_{3}}$ shows responsivity for optical excitation between wavelength ranges from 180 nm to 350 nm, with the peak observed at 240 nm. This work will help significantly to understand charge transport and optical properties, and design optimized solar cells involving these materials.
Group Recommendation Method Based on Item Type Proportion Factor

Group recommendation has attracted significant research attention in recent years. In view of low accuracy and lacking of integration strategy of existing group recommendation methods, we propose an novel method called GRIP (Group Recommendation method based on Item type Proportion factor) to improve preference fusion strategy increaandse the accuracy. We use an improved similarity formula by integrating the co-scored item proportion factor (CIPF) in order to get the personal prediction rating. Further more, we improve the preference fusion strategy by introducing item type proportion factor to calculate the type similarity between group type preference and user type preference, and designing a score fusion formula with the type similarity mentioned above to predict the final item score for the group. To validate GRIP, we carry out experiments and compare GRIP with several classic group recommendation methods using Movielens dataset. The results show that our method achieves higher recommendation accuracy than all the baseline methods.
Query Support for Data Processing and Analysis on Ethereum Blockchain

Blockchain technology has gained immense popularity because many researchers believe that it could solve numerous problems and could be applied in various fields of study. Unfortunately, behind its potentials, blockchain also possessed many challenges and limitations. The highlighted problem is the usability aspect of blockchain technology examined from developer and user perspective. This paper tried to address this problem by proposing query functionalities, with the help of query layer system, to facilitate the developer and the user to access blockchain data easily. There are three main query functionalities that will be discussed in this paper: (1) finding blockchain data based on multiple search parameters (retrieval query), (2) providing simple statistical analysis from a collection of blockchain data (aggregate query) and (3) sorting blockchain data according to its blockchain component (ranking query). For the implementation stage, Ethereum is used as platform to provide blockchain network, MongoDB is used as cloud storage service and REST API is used as web services. For the testing stage, throughput and time response are used to evaluate the performance of the developed query functionalities in the query layer system. The results are: (1) the throughput of query layer system is lower than Ethereum service for blockchain data retrieval and (2) the time response of query layer system is affected by the number of thread and the amount of data stored in cloud storage.
MSME Recommendation Application using Collaborative Filtering Method and Realtime Database (Case Study: Salatiga City)

Micro small medium enterprise (MSMEs) is one of the important supports in the economic development of a certain region, including Salatiga. According to Salatiga’s industry and cooperative office (Disperindagkop), there are 3.663 MSMEs in Salatiga and 1.450 of which have already registered. The main problem for the owners of MSMEs is the lack of facility in promoting the products, thereby it indicates that there should be media to help promoting MSMEs products. This research uses Collaborative Filtering method which is developed based on Android Platform to count the similarity value between products based on the rating given by the users, to get the recommended products for each user. A batch of datasets which will be processed first, are saved into cloud storage by utilizing Google firebase services.
Intelligent Vehicle Collision-Avoidance System with Deep Learning

In this paper, we demonstrate and evaluate a method to perform real-time object detection with unmanned vehicle using the state of the art, MobileNets, with object detection algorithm running on an NVIDIA Jetson TX2, an GPU platform targeted at power constrained mobile applications that use neural networks under the hood. This, as a result of comparing several cutting edge object detection algorithms. Multiple evaluations we present provide insights that help choose the optimal object detection configuration given certain frame rate and detection accuracy requirements. We propose how this setup running on-board a unmanned vehicle can be used to process a video feedback during emergencies in real-time, and feed a decision support warning system using the generated detections.
Multi-Set Space-Time Shift Keying Assisted Adaptive Inter-Layer FEC for Wireless Video Streaming

The scalable video coding extension of H.265/high efficiency video coding is capable of supporting diverse video resolutions. Due to the fact that the enhancement layer (EL) is encoded and decoded with the aid of the base layer (BL), the decodability of ELs is conditioned on that of the BL. Hence, the EL frames occasionally have to be discarded as a result of corrupted BL frames. Therefore, potent unequal error protection schemes have been conceived for providing a stronger protection to the BL by invoking a lower coding rate based forward error correction (FEC) or a higher transmit power for a specific multiple-input multiple-output sub-channel. This stronger protection is essential for the BL for the sake of both avoiding the waste of resources caused by the dropped undecodable EL bits and for improving the reconstructed video quality. In this treatise, we propose an adaptive system for transmitting the layered video bit stream over the wireless channel. The proposed system is capable of selecting an appropriate interlayer (IL) operation-aided FEC (IL-FEC) scheme in order to maintain the robustness of the system by comparing the near-instantaneous signal-to-noise ratio (SNR) to pre-recorded reconfiguration thresholds. Our simulation results show that the proposed adaptive system is capable of providing better video quality over a large proportion of the channel SNR range than its corresponding fixed-mode counterparts.
Subharmonic Resonance in Magnetic Levitation of the High-Temperature Superconducting Bulks YBa2Cu3O7‐x Under Harmonic Excitation

High-temperature superconducting (HTS) bulk YBa2Cu3O7‐x (YBCO) can achieve self-stable magnetic levitation (maglev) over a permanent magnet (PM) for its inherent flux pinning effect, which has considerable potential for engineering applications. The complicated vibration response, however, is lacking in research for the nonlinearity of the interaction force between the HTS bulks and PMs. This paper mainly focuses on the subharmonic resonance of the HTS bulks YBCO levitating above the PMs in Halbach array, which are in reciprocating motion, by numerical simulations. In general, the motion of HTS bulks is approximately harmonic under limited excitation. When the amplitude and frequency of the excitation satisfy certain conditions, the dynamical system undergoes a period-double bifurcation, and then, the subharmonic resonance occurs. Moreover, the period-double bifurcation brings the jump phenomenon when the frequency of excitation increases and decreases at the double of eigenfrequency nearby. Simulations show that a suitable damping is able to reduce the vibration markedly. The subharmonic resonance region in an amplitude-frequency plane is presented in this paper finally. In a word, the subharmonic resonance would occur in an HTS maglev system under certain conditions and its prediction is numerically studied here with a nonlinear mathematics model of the levitation force.