Miracle-dz/UniFAR-FTUs huggingface dataset:
Eleven Novel Polymorphic Microsatellite Loci for Oval Squid Sepioteuthis Lessoniana (Shiro-Ika Type)

The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future.
Robot-induced perturbations of human walking reveal a selective generation of motor adaptation

An exoskeleton reveals that walking humans adapt to changes in step length and height by maximizing locomotor stability. The processes underlying the generation of motor adaptation in response to mechanical perturbations during human walking have been subject to debate. We used a robotic system to apply mechanical perturbations to step length and step height over consecutive gait cycles. Specifically, we studied perturbations affecting only step length, only step height, and step length and height in combination. Both step-length and step-height perturbations disrupt normal walking patterns, but step-length perturbations have a far greater impact on locomotor stability. We found a selective process of motor adaptation in that participants failed to adapt to step-height perturbations but strongly adapted to step-length perturbations, even when these adaptations increased metabolic cost. These results indicate that motor adaptation during human walking is primarily driven by locomotor stability, and only secondarily by energy expenditure and walking pattern preservation. These findings have substantial implications for the design of protocols for robot-assisted gait rehabilitation.
Arabidopsis ABA-Activated Kinase MAPKKK18 is Regulated by Protein Phosphatase 2C ABI1 and the Ubiquitin–Proteasome Pathway

Phosphorylation and dephosphorylation events play an important role in the transmission of the ABA signal. Although SnRK2 [sucrose non-fermenting1-related kinase2] protein kinases and group A protein phosphatase type 2C (PP2C)-type phosphatases constitute the core ABA pathway, mitogen-activated protein kinase (MAPK) pathways are also involved in plant response to ABA. However, little is known about the interplay between MAPKs and PP2Cs or SnRK2 in the regulation of ABA pathways. In this study, an effort was made to elucidate the role of MAP kinase kinase kinase18 (MKKK18) in relation to ABA signaling and response. The MKKK18 knockout lines showed more vigorous root growth, decreased abaxial stomatal index and increased stomatal aperture under normal growth conditions, compared with the control wild-type Columbia line. In addition to transcriptional regulation of the MKKK18 promoter by ABA, we demonstrated using in vitro and in vivo kinase assays that the kinase activity of MKKK18 was regulated by ABA. Analysis of the cellular localization of MKKK18 showed that the active kinase was targeted specifically to the nucleus. Notably, we identified abscisic acid insensitive 1 (ABI1) PP2C as a MKKK18-interacting protein, and demonstrated that ABI1 inhibited its activity. Using a cell-free degradation assay, we also established that MKKK18 was unstable and was degraded by the proteasome pathway. The rate of MKKK18 degradation was delayed in the ABI1 knockout line. Overall, we provide evidence that ABI1 regulates the activity and promotes proteasomal degradation of MKKK18.
Cooperative output regulation for networked multi-agent systems based on the self-tuning adaptive distributed observer

In this paper, we first propose a self-tuning adaptive distributed observer for a multi-agent system, which is capable of providing the estimation of the leader's signal to various followers without assuming all the followers know the system matrix of the leader and which avoids calculating the observer gain off-line. We then further develop an adaptive distributed control law to solve the cooperative output regulation problem for linear heterogeneous multi-agent systems. This control law offers two advantages in that it makes the least use of the information of the network and the information of the leader system, and it avoids calculating the observer gain.
A Novel method of Data Stream Classification Based on Incremental Storage Tree

For the characteristics of large number, fast change, high cost of random access of data stream, this paper proposes a Bayesian classification data mining algorithm based on incremental storage tree to handle the problems. Use sliding window to process data stream and divide it into several basic units, apply Principal component analysis (PCA) to compress the data from window and produce dynamic incremental storage tree, use the second power strategy to continuously update several incremental storage tree. Then use multi-classifier integration technology combines with Bayesian classification to produce Bayesian classifier. At last, adjust the weight of classifier by cyclic test, and get high classification accuracy. Detailed simulation analysis demonstrates that the presented algorithm is of high efficiency of space and time and is more stable.
Change in Japanese Encephalitis Virus Distribution,Thailand

Japanese encephalitis virus (JEV) genotypes in Thailand were studied in pigs and mosquitoes collected near houses of confirmed human JEV cases in 2003–2005. Twelve JEV strains isolated belonged to genotype I, which shows a switch from genotype III incidence that started during the 1980s.
A Built-in-Self-Test Scheme for Online Evaluation of Physical Unclonable Functions and True Random Number Generators

In the emerging era of Internet of Things (IoT) where various physical entities are spontaneously communicating with each other and sharing sensitive information, it is prohibitive to have a global entity for maintaining the security of the complex web against environmental variations and active attacks. Therefore, it is crucial that each entity has the capability of safeguarding its security features on its own. Methods based on harnessing the random identification and authentication from the physical device and environment, such as physical unclonable functions (PUFs) and True Random Number Generators (TRNGs), if securely run, are promising primitives for protecting lightweight IoT devices. This paper presents the first Built-In-Self-Test scheme for on-the-fly evaluation of PUFs that can also be utilized for assessing the desired statistical properties of TRNGs. Unlike earlier known PUF evaluation suites that were software-based and offline, our methodology enables online assessment of the pertinent statistical and security properties all in hardware. Specifically, the BIST structure is designed to evaluate two main properties of PUFs: unpredictability and stability. Our work is the first online test suite that thoroughly evaluates the internal health of the entropy source of TRNGs along with the statistical properties of the generated bit stream. Comprehensive real-time evaluation by the BIST method is able to ensure robustness and security of both TRNG and PUF in the face of operational, structural, and environmental fluctuations due to variations, aging, or adversarial acts. Proof-of-concept implementation of our BIST methodology in FPGA demonstrates its reasonable overhead, effectiveness, and practicality.
Bias Properties of Budget Constrained Simulations

This paper addresses the bias characteristics of estimators produced from Monte Carlo simulations. If the computer time allocated to the simulation is t, then Nt, the number of replications completed by time t, is a renewal process. The simulation implications of a known exact expression for the expected value of a sample mean based on Nt replications are explored and a similar exact expression for a sample mean based on Nt + 1 replications is derived. Bias expansions for a sample mean based on Nt or Nt + 1 replications are obtained. The bias in the sample mean based on Nt replications is at most of order o1/t. Under suitable moment conditions, the bias decreases at a much faster rate than o1/t; on the other hand, the estimator based on Nt + 1 replications has bias of order 1/t. The exact expressions also lead to simple and totally unbiased estimators. Using Taylor series, the bias expansions of a general function of means based on Nt or Nt + 1 replications are determined. The leading terms in these expansions are of order 1/t, although the coefficients are different. Based on these expansions, a Tin-style adjusted estimator is proposed to reduce the bias. These expansions are specialized to the case of ratio estimation in regenerative simulation. Due to a cancellation effect, the ratio estimator based on Nt + 1 cycles is biased only to order o1/t providing confirmation and reinterpretation of a result of M. Meketon and P. Heidelberger.
A traffic flow-based and dynamic grouping-enabled resource allocation algorithm for LTE-D2D vehicular networks

Nowadays, Device-to-Device (D2D) communication in LTE system has been proposed as a possible candidate for vehicle-to-vehicle(V2V) communication. As V2V communications share the same licensed frequency spectrum pool with typical UEs communications in one LTE cell, efficient radio resource allocation is a challenging issue. In this paper, we proposed a traffic flow based dynamic resource allocation algorithm for vehicular communication networks, which could make radio resource to be utilized in a more efficient way with a flexible node-grouping algorithm. The simulation results show, compared with random allocation and greedy allocation algorithms, the proposed algorithm can significantly reduce running time and significantly improve spectrum utilization efficiency.
Systems Biology of Microbial Exopolysaccharides Production

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.
BER Analysis of the Alamouti Coding Scheme Using Receive Antenna Selection

In this paper, we present a comprehensive performance analysis of the 2x2 wireless MIMO Alamouti coding scheme using receive antenna selection. Complete knowledge at the receiver of the Channel State Information (CSI), i.e., perfect knowledge of both the symbol synchronisation and the channel gains, and a MIMO model of uncorrelated Rayleigh fading subchannels are assumed. A receive selection algorithm based on the maximizing Signal to Noise Ratio (SNR) is used to select two antennas. Under these conditions, we derive the exact average Bit Error Rate (BER) for Binary Phase Shift Keying (BPSK) modulation using the Moment Generating Function (MGF) and the order statistics associated with the instantaneous SNR at the two selected antennas.
ALTERATIONS IN BURST FIRING OF THALAMIC VPL NEURONS AND REVERSAL BY Nav 1 . 3 ANTISENSE FOLLOWING SPINAL CORD INJURY

We recently showed that spinal cord contusion injury (SCI) at the thoracic level induces painrelated behaviors and increased spontaneous discharges, hyperresponsiveness to innocuous and noxious peripheral stimuli, and enlarged receptive fields in neurons in the ventral posterolateral (VPL) nucleus of the thalamus. These changes are linked to the abnormal expression of Nav1.3, a rapidly repriming voltagegated sodium channel. In this study, we examined the burst firing properties of VPL neurons after SCI. Adult male Sprague-Dawley rats underwent contusion SCI at the T9 level. Four weeks later, when Nav1.3 protein was upregulated within VPL neurons, extracellular unit recordings were made from VPL neurons in intact animals, those with SCI, and in SCI animals after receiving lumbar intrathecal injections of Nav1.3 antisense or mismatch oligodeoxynucleotides for 4 days. Following SCI, VPL neurons with identifiable peripheral receptive fields showed rhythmic oscillatory burst firing with changes in discrete burst properties, and alternated among single-spike, burst, silent, and spindle wave firing modes. Nav1.3 antisense, but not mismatch, partially reversed alterations in burst firing after SCI. These results demonstrate several newly characterized changes in spontaneous burst firing properties of VPL neurons after SCI, and suggest that abnormal expression of Nav1.3 contributes to these phenomena.
Automatic Detection and Recognition of Tonal Bird Sounds in Noisy Environments

This paper presents a study of automatic detection and recognition of tonal bird sounds in noisy environments. The detection of spectro-temporal regions containing bird tonal vocalisations is based on exploiting the spectral shape to identify sinusoidal components in the short-time spectrum. The detection method provides tonal-based feature representation that is employed for automatic bird recognition. The recognition system uses Gaussian mixture models to model 165 different bird syllables, produced by 95 bird species. Standard models, as well as models compensating for the effect of the noise, are employed. Experiments are performed on bird sound recordings corrupted by White noise and real-world environmental noise. The proposed detection method shows high detection accuracy of bird tonal components. The employed tonal-based features show significant recognition accuracy improvements over the Mel-frequency cepstral coefficients, in both standard and noise-compensated models, and strong robustness to mismatch between the training and testing conditions.
Co-regulation of β-lactam resistance, alginate production and quorum sensing in Pseudomonas aeruginosa

Development of β-lactam resistance, production of alginate and modulation of virulence factor expression that alters host immune responses are the hallmarks of chronic Pseudomonas aeruginosa infection in cystic fibrosis patients. In this study, we propose that a co-regulatory network exists between these mechanisms. We compared the promoter activities of ampR, algT/U, lasR, lasI, rhlR, rhlI and lasA genes, representing the β-lactam antibiotic resistance master regulatory gene, the alginate switch operon, the las and rhl quorum-sensing (QS) genes, and the LasA staphylolytic protease, respectively. Four isogenic P. aeruginosa strains, the prototypic Alg− PAO1, Alg− PAOampR, the mucoid Alg+ PAOmucA22 (Alg+ PDO300) and Alg+ PAOmucA22ampR (Alg+ PDOampR) were used. We found that in the presence of AmpR regulator and β-lactam antibiotic, the extracytoplasmic function sigma factor AlgT/U positively regulated PampR, whereas AmpR negatively regulated PalgT/U. On the basis of this finding we suggest the presence of a negative feedback loop to limit algT/U expression. In addition, the functional AlgT/U caused a significant decrease in the expression of QS genes, whereas loss of ampR only resulted in increased PlasI and PlasR transcription. The upregulation of the las QS system is likely to be responsible for the increased lasA promoter and the LasA protease activities in Alg− PAOampR and Alg+ PDOampR. The enhanced expression of virulence factors in the ampR strains correlated with a higher rate of Caenorhabditis elegans paralysis. Hence, this study shows that the loss of ampR results in increased virulence, and is indicative of the existence of a co-regulatory network between β-lactam resistance, alginate production, QS and virulence factor production, with AmpR playing a central role.
Performance evaluation and comparison of parallel conjugate gradient on modern multi-core accelerator and massively parallel systems

Two parallel computer paradigms available today are multi-core accelerators such as the Sony, Toshiba and IBM Cell or Graphics Processing Unit (GPUs), and massively parallel message-passing machines such as the IBM Blue Gene (BG). The solution of systems of linear equations is one of the most central processing unit-intensive steps in engineering and simulation applications and can greatly benefit from the multitude of processing cores and vectorisation on today's parallel computers. We parallelise the conjugate gradient (CG) linear equation solver on the Cell Broadband Engine and the IBM Blue Gene/L machine. We perform a scalability analysis of CG on both machines across 1, 8 and 16 synergistic processing elements and 1–32 cores on BG with heptadiagonal matrices. The results indicate that the multi-core Cell system outperforms by three to four times the massively parallel BG system due to the Cell's higher communication bandwidth and accelerated vector processing capability.
The Master Negative Regulator REST/NRSF Controls Adult Neurogenesis by Restraining the Neurogenic Program in Quiescent Stem Cells

Transcriptional regulation is a critical mechanism in the birth, specification, and differentiation of granule neurons in the adult hippocampus. One of the first negative-acting transcriptional regulators implicated in vertebrate development is repressor element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF)—thought to regulate hundreds of neuron-specific genes—yet its function in the adult brain remains elusive. Here we report that REST/NRSF is required to maintain the adult neural stem cell (NSC) pool and orchestrate stage-specific differentiation. REST/NRSF recruits CoREST and mSin3A corepressors to stem cell chromatin for the regulation of pro-neuronal target genes to prevent precocious neuronal differentiation in cultured adult NSCs. Moreover, mice lacking REST/NRSF specifically in NSCs display a transient increase in adult neurogenesis that leads to a loss in the neurogenic capacity of NSCs and eventually diminished granule neurons. Our work identifies REST/NRSF as a master negative regulator of adult NSC differentiation and offers a potential molecular target for neuroregenerative approaches.
Looking for ‘System Integrity’ in Cognitive Epidemiology

Background: In the last decade, an increasing body of empirical evidence has gathered to establish an association between higher cognitive ability in youth and later mortality, less morbidity and better health. This field of research is known as cognitive epidemiology. The causes of these associations are not understood. Objective: Among the possible explanations for the associations is the suggestion that they might, in part, be accounted for by general bodily ‘system integrity’. That is, scoring well on cognitive ability tests might be an indicator of a more general tendency for complex systems in the body to be efficient. The construct of system integrity is critically assessed. Method: This viewpoint provides a critical presentation and an empirical and theoretical evaluation of the construct of system integrity as it is used in cognitive epidemiology. Results: A precedent of the system integrity suggestion is discovered. The empirical tests of the system integrity idea to date are critically evaluated. Other possible routes to testing system integrity are suggested. There is a critical re-evaluation of the idea and other, related concepts. Conclusion: The construct of system integrity is distinct from related constructs. It is still underdeveloped theoretically, and undertested empirically within cognitive epidemiology.
Vitamin D analogs, a new treatment for retinoblastoma: The first Ellsworth Lecture

Purpose: This lecture honors the memory of Dr. Robert M. Ellsworth, an important figure in the development of current treatments of retinoblastoma (RB), and reviews our studies of vitamin D analogs as treatments for retinoblastoma in two experimental mouse models. We identified vitamin D receptors in retinoblastoma and examined the effectiveness and mechanism of action of these analogs. Methods: Reverse-transcriptase polymerase chain reaction (RT-PCR) amplification was used to detect vitamin D receptor mRNAs in human and mouse retinoblastomas. The effectiveness and toxicity of vitamin D 2 , calcitroil, and synthetic analogs were studied in the athymic/Y-79 xenograft and transgenic mouse models of RB. Dosing was 5X/week for five weeks. Dose-response studies focused on tumor inhibition; toxicity studies investigated survival and serum calcium. The mechanism of action of vitamin D was investigated using terminal transferase dUTP labeling 3'-overhang ligation to measure apoptosis; immunohistochemistry measured p53-dependent gene expression and cell proliferation. Result: Vitamin D receptor mRNAs were detectable in Y-79 RB cells, LHß-Tag tumors, and human RB specimens using RT-PCR. Calcitriol inhibited cell growth in vitro . Calcitriol and vitamin D 2 inhibited in vivo growth in xenograft and transgenic models, but therapeutic levels were toxic due to hypercalcemia. Two analogs, 16,23-D 3 and 1a- OH-D 2 , inhibited tumors in animal models of RB with reduced toxicity. The mechanism of action appears related to increased p53-related gene expression resulting in increased apoptosis. Conclusion : 16,23-D 3 and 1a-OH-D2 are effective in tumor reduction in two mouse models of RB with low toxicity. These results warrant initiating phase 1 and phase 2 clinical studies in children.