Miracle-dz/UniFAR-FTUs huggingface dataset:
Space hopping scheme under short range Rician multipath fading environment

An array antenna system requires the same number of RF circuit sections as that of the antennas. This paper presents the novel concept of "space hopping" scheme which requires only "one" RF circuit to enable the array antenna system at very low cost. The scheme also shows excellent BER characteristics for the array antenna system. We focus on the improvement of BER in the array antenna configuration in the short range Rician distribution multipath fading environment. A multipath simulation bench is studied and designed to evaluate the space hopping performance. Several simulations are made to confirm the expected performance of the space hopping scheme and to obtain a good configuration of the array antenna.
Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses

Although an exchange of genetic information by recombination plays an important role in the evolution of viruses, it is not clear how it generates diversity. {\it Geminiviruses} are plant viruses which have ambisense single-stranded circular DNA genomes and one of the most economically important plant viruses in agricultural production. Small circular single-stranded DNA satellites, termed DNA-$\beta$, have recently been found associated with some geminivirus infections. In this paper we analyze a satellite molecule DNA-$\beta$ of geminiviruses for recombination events using phylogenetic and statistical analysis and we find that one strain from ToLCMaB has a recombination pattern and is possibly recombinant molecule between two strains from two species, PaLCuB-[IN:Chi:05] (major parent) and ToLCB-[IN:CP:04] (minor parent).
On a mechanistic process of macroparasite aggregation

Parasite aggregation, a recurring pattern in macroparasite infections, is considered one of the “laws” in parasite ecology. Few hosts have a large number of parasites while most hosts have a low number of parasites. This pattern has been widely studied using phenomenological models, by using the negative binomial distribution. However, to infer the mechanisms of aggregation, a mechanistic model is essential. Here we formulate such a mechanistic model of parasite aggregation in hosts without initially assuming a negative binomial distribution. Our results show that a simple model of parasite accumulation still results in an aggregated pattern, as shown by the derived mean and variance of the parasite distribution. By incorporating the derived mean and variance to the host-parasite interaction, we can predict how aggregation affects the population dynamics of the hosts and parasites through time. Thus, our results can directly be applied to observed data as well as can be utilised in designing statistical sampling procedures. Overall, we have shown how a plausible mechanistic process can result in the often observed phenomenon of parasite aggregation occurring in numerous ecological scenarios. Key Findings Parasite aggregation is considered one of the “laws” in parasite ecology – few hosts harbouring a large number of parasites. While examples abound, there is lack of mechanistic models available to explain the phenomenon Taking a bottom up approach we construct a simple model of host-parasite population dynamics which naturally results in parasite aggregation – negative binomial distribution of parasites in the host population While providing a plausible mechanism our model can be readily deployed in field work when designing sampling methodology or analysis of available data.
Assessment of natural variability in leaf morphological and physiological traits in maize inbreds and their related hybrids during early vegetative growth

ABSTRACT The superior growth of maize hybrids and some inbreds may be linked to key leaf growth features and critical components in carbon and nitrogen metabolism. Here, we performed simultaneous growth, physiological and heterosis analyses of morpho-physiological traits in four maize inbreds (B73, Mo17, Sids7, Sids63) and two hybrids (B73 × Mo17&Sids7 × Sids63). B73 and Sids7 exhibited alternate superiority over Mo17 and Sids63 in most growth traits. Both hybrids gained an early advantage over their parental inbreds in growth. They showed relatively similar behavior in many growth traits but differed significantly in biomass accumulation. Physiologically, B73 and Sids7 predominated in total pigments. Further, B73 contained the highest levels of sucrose, glucose, amino-N, and total N among inbreds. Both hybrids did not significantly differ in sucrose and total soluble sugars. However, Sids7 × Sids63 had consistently higher N fractions than B73 × Mo17. Both hybrids showed common and specific heterotic patterns. The superior growth of B73, Sids7, and hybrids is positively correlated with a set of leaf morphological (leaf area, leaf breadth, and LAI) and physiological (total chlorophyll, total pigments, and total N) traits. Advantages in these traits and efficient resource utilization support the superior growth of maize genotypes.
VlbZIP30 of grapevine functions in drought tolerance via the abscisic acid core signaling pathway

Drought stress limits the growth and development of grapevines, thereby reducing productivity, but the mechanisms by which grapevines respond to drought stress remain largely uncharacterized. Here, we characterized a group A bZIP gene from ‘Kyoho’ grapevine, VlbZIP30, which was shown to be induced by abscisic acid (ABA) and dehydration stress. Overexpression of VlbZIP30 in transgenic Arabidopsis enhanced dehydration tolerance during seed germination, and in the seedling and adult stages. Transcriptome analysis revealed that a major proportion of ABA- and/or drought-responsive genes are transcriptionally regulated by VlbZIP30 during ABA or mannitol treatment at the cotyledon greening stage. We identified an A. thaliana G-box motif (CACGTG) and a potential grapevine G-box motif (MCACGTGK) in the promoters of the 39 selected A. thaliana genes up-regulated in the transgenic plants and in the 35 grapevine homologs, respectively. Subsequently, using two grapevine-related databases, we found that 74% and 84% (a total of 27 genes) of the detected grapevine genes were significantly up-regulated by ABA and drought stress, respectively, suggesting that these 27 genes involve in ABA or dehydration stress and may be regulated by VlbZIP30 in grapevine. We propose that VlbZIP30 functions as a positive regulator of drought-responsive signaling in the ABA core signaling pathway. Highlight VlbZIP30 positively regulate plant drought tolerance through regulated the expression of 27 grapevine candidate genes via G-box cis-element (MCACGTGK) in ABA signaling pathway.
Estrés oxidativo y el uso de antioxidantes en la producción in vitro de embriones mamíferos. Revisión

La producción de embriones in vitro es una de las biotecnologías de la reproducción animal que ha presentado mayor desarrollo en las últimas dos décadas; sin embargo, los resultados exitosos en estos procedimientos dependen de múltiples factores, entre ellos la presencia de especies reactivas de oxígeno, debido a que el proceso de fertilización in vitro y la manipulación de los gametos y embriones expone a las células a factores endógenos y exógenos que pueden afectar los mecanismos de defensa antioxidante y por consiguiente la calidad de los gametos y embriones. En esta revisión se discutirán algunas fuentes de especies reactivas de oxígeno, el uso de antioxidantes enzimáticos, no enzimáticos y polifenólicos para disminuir el estrés oxidativo en los procesos de producción in vitro de embriones, y su efecto sobre la calidad de los oocitos y embriones, la expresión génica y su competencia para el desarrollo embrionario.
A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo PacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.
New Social Collaborative Filtering Algorithms for Recommendation on Facebook

This thesis examines the problem of designing efficient, scalable, and accurate social collaborative filtering (CF) algorithms for personalized link recommendation on Facebook. Unlike standard CF algorithms using relatively simple user and item features (possibly just the user ID and link ID), link recommendation on social networks like Facebook poses the more complex problem of learning user preferences from a rich and complex set of user profile and interaction information. Most existing social CF (SCF) methods have extended traditional CF matrix factorization (MF) approaches, but have overlooked important aspects specific to the social setting; specifically, existing SCF MF methods (a) do not permit the use of item or link features in learning user similarity based on observed interactions, (b) do not permit directly modeling useruser information diffusion according to the social graph structure, and (c) cannot learn that that two users may only have overlapping interests in specific areas. This thesis proposes a unified SCF optimization framework that addresses (a)–(c) and compares these novel algorithms with a variety of existing baslines. Evaluation is carried out via live user trials in a custom-developed Facebook App involving data collected over three months from over 100 App users and their nearly 30,000 friends. Not only do we show that our novel proposals to address (a)–(c) outperform existing approaches, but we also identify which offline ranking and classigication evaluation metrics correlate most with human judgment of algorithm performance. Overall, this thesis represents a critical step forward in extending SCF recommendation algorithms to fully exploit the rich content and structure of social networks like Facebook.
A functional study of all 40 C. elegans insulin-like peptides

The human genome encodes ten insulin-like genes, whereas the C. elegans genome remarkably encodes forty insulin-like genes. The roles of insulin/insulin-like peptide ligands (INS) in C. elegans are not well understood. The functional redundancy of the forty INS genes makes it challenging to address their functions by using knock out strategies. Here, we individually overexpressed each of the forty ins genes pan-neuronally, and monitored multiple phenotypes including: L1 arrest life span, neuroblast divisions under L1 arrest, dauer formation and fat accumulation, as readouts to characterize the functions of each INS in vivo. Of the 40 INS peptides, we found functions for 35 INS peptides and functionally categorized each as agonists, antagonists or of pleiotropic function. In particular, we found that 9 of 16 agonistic INS peptides shortened L1 arrest life span and promoted neuroblast divisions during L1 arrest. Our study revealed that a subset of β-class INS peptides that contain a distinct F peptide sequence are agonists. Our work is the first to categorize the structures of INS peptides and relate these structures to the functions of all forty INS peptides in vivo. Our findings will promote the study of insulin function on development, metabolism, and aging-related diseases. Author Summary Insulin and insulin-like growth factors are found in all animals and regulate many physiological and developmental processes. The human genome has 10 insulin-like peptides including the well characterized insulin hormone. The nematode C. elegans has 40 insulin-like (INS) peptide genes. All 40 INS peptides have been knocked out but no single INS gene knock out resembles the loss of the C. elegans insulin receptor suggesting that the other INS peptides can compensate when one INS is lost. We have used a genetic approach to overexpress each of the 40 INS peptides in C. elegans and have identified in vivo function for 35 of the 40 INS peptides. Like the human insulin and IGF-1, C. elegans INS peptides are derived from a precursor protein and we have shown that INS peptides with an associated peptide called the F peptide are strong activators of the C. elegans insulin-like receptor. We also identified several INS peptides that inhibit the insulin-like receptor and these inhibitory INS peptides may have therapeutic potential.
Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes

Germline genome defense evolves to recognize and suppress retrotransposons. One of defensive mechanisms is the PIWI-associated RNA (piRNA) pathway, which employs small RNAs for sequence-specific post-transcriptional and transcriptional repression. The loss of the piRNA pathway in mice causes male sterility while females remain fertile. Unlike spermatogenic cells, mouse oocytes have also RNA interference (RNAi), another small RNA pathway capable of retrotransposon suppression. To examine whether RNAi compensates the loss of the piRNA pathway in mouse oocytes, we produced a new RNAi pathway mutant DicerSOM and crossed it with a catalytically-dead mutant of Mili, an essential piRNA gene. Normal follicular and oocyte in double mutants showed that RNAi does not suppress a strong piRNA knock-out phenotype. However, we observed redundant and non-redundant targeting of specific retrotransposons. Intracisternal A Particle retrotransposon was mainly targeted by the piRNA pathway, MT and RLTR10 retrotransposons were targeted mainly by RNAi. Importantly, only double mutants showed increased background levels of transcripts potentially originating from intact LINE-1 elements. Our results thus show that while both small RNA pathways are simultaneously expendable defense pathways for ovarian oocyte development, yet another transcriptional silencing mechanism must mediate LINE-1 repression in female germ cells. Author summary Retrotransposons are mobile genomic parasites causing mutations. Germ cells need protection against retrotransposons to prevent heritable transmission of their new insertions. The piRNA pathway is an ancient germline defense system analogous to acquired immunity: once a retrotransposons jumps into a specific “genomic checkpoint”, it is recognized and suppressed. Remarkably, the murine piRNA pathway is essential for spermatogenesis but not oocyte development. In contrast, zebrafish lacking the piRNA pathway do not develop any germ cells. It was hypothesized that RNA interference pathway could rescue oocyte development in mice lacking the piRNA pathway. RNA interference also targets retrotransposons and is particularly enhanced in mouse oocytes. To test this hypothesis, we engineered mice lacking both pathways and observed that oocytes in these mice develop normally, which argues against the hypothesis. Furthermore, analysis of individual retrotransposon groups revealed that in specific cases the two pathways can mutually compensate each other. However, this ability is restricted to specific retrotransposon groups and seems to evolve stochastically. Finally, our results also indicate that there must be yet another layer of retrotransposon silencing in mouse oocytes, which prevents high retrotransposon activity in the absence of piRNA and RNA interference pathways.
Mechanism of the Effect of Walking Walk on the Motor Function of Injured Muscles

To study the mechanism of the influence of walking walk on the muscle function of injured athletes. Methods: 10 athletes were selected as reference. The XX Management Center competed for male athletes (8) and a high-level walking athlete (2). Gas metabolism data and muscle electrical signal data were recorded using an active treadmill, a portable cardiopulmonary telemeter, and a surface electromyography collector. RESULTS: The changes in oxygen uptake of the subjects were almost the same as the changes in the intensity of the test protocol. They all increased in a stepwise manner. VO2 initially showed a rapid increase. The general time was between 15 seconds and 25 seconds. After that, VO2 will grow slowly trend. This is consistent with the trend of oxygen uptake in the study test; in the muscle electrical strength performance, each muscle involved in exercise, the number of movement units will be different, but from the overall trend of myoelectric strength It is on the rise; MPF will rise first, and later the decline in MPF may be related to the fatigue of fast muscle fibers and the extra recruitment of slow muscle fibers. Conclusion: By analyzing the indicators of athletes, it is found that the walking movement has a certain degree of influence on the muscle function of the injured muscles. Attention should always be paid to the prevention of various aspects of the athlete's body.
Iterative Estimation and Detection for Single Carrier Block Transmission

T HIS thesis deals with efficient receiver design for digital point-to-point communications. A single carrier block transmission scheme, including channel coding, shall serve as a basis. At the receiver neither knowledge of the channel impulse response (CIR) nor the signal-to-noise ratio (SNR) is assumed. Accordingly, those parameters have to be estimated for power-efficient data detection. In particular, an iterative solution for joint parameter estimation and data detection based on the turbo principle is investigated. As a result of an in-depth study of various decisiondirected SNR estimation techniques, a novel estimator using a priori probabilities of data symbols is derived for Gaussian channels with binary modulation. The potential of the algorithm is evaluated for the example of iterative decoding of concatenated convolutional codes. In the case of multipath channels, the CIR has to be estimated, too and equalization is additionally necessary. Iterative equalization and decoding (turbo equalization) is chosen as a powerful technique for data detection with moderate computational complexity. A decision-directed channel estimator based on the least-mean-square (LMS) algorithm is suggested that adapts its step size according to the quality of the data estimates and that does not require SNR knowledge. Numerical results for a turbo equalization setup support that the proposed channel estimator performs well for arbitrary signal constellations. Furthermore, the performance of turbo equalization itself is addressed. An optimization algorithm for bit-to-symbol mappings is presented that enhances power efficiency by means of iterative demapping. The algorithm can be applied to any equalization technique if the equalizer’s output variance is known or can be estimated. Finally, the use of estimation error statistics is investigated. Its advantage for turbo equalization and the relationship to decision-directed channel estimation is shown by an extrinsic information transfer (EXIT) analysis.
Genomic and structural features of the Yellow Fever virus from the 2016-2017 Brazilian outbreak

Brazil has been suffering a severe sylvatic epidemic of yellow fever virus (YFV) since late 2016. Analysis of full-length YFV genomes from all hosts involved in the Brazilian 2017 outbreak reveals that they belong to sub-lineage 1E within modern-lineage, but display several unique amino acid substitutions in highly conserved positions at NS3 and NS5 viral proteins. Evolutionary analyses indicate that YFV carrying that set of amino acid substitution circulates in the Southern Brazilian region for several months before being detected in December 2016. Structural and selection analyses support that some of these substitutions were under positive selection and could impact enzyme structure and function. Altogether, this evidence demonstrated that the current Brazilian YFV carries unique amino acid signatures in the non-structural proteins and support the hypothesis that those substitutions may be affecting the viral fitness and transmissibility.
ZAG-1/ZEB prevents the expression of repressors and protects neuronal cell fate in Caenorhabditis elegans

Summary statement : Transcriptional repressors regulate binary fate choices through reciprocal inhibition during terminal neuronal differentiation. Specifically, ZEB family transcription factor indirectly promotes fate specification of sensory neuron by inhibiting TEA domain-containing repressor. Abstract Terminal differentiation generates the specialized structures and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called “terminal selectors” that directly activate a set of effector genes. Using the mechanosensory touch receptor neurons (TRNs) in Caenorhabditis elegans , we extend this concept by identifying the ZEB family transcriptional repressor ZAG-1 as a non-selector regulator of cell fate. ZAG-1 does not activate TRN genes directly but promotes TRN differentiation by preventing the expression of the TEA domain transcription factor EGL-44 and its binding partner EGL-46, which are potent repressors of TRN fate. The EGL-44/EGL-46 complex normally blocks the activation of TRN genes by the terminal selectors, UNC-86 and MEC-3, in the multidendritic nociceptor FLP neurons, whose fate also requires UNC-86 and MEC-3. Thus, TRN and FLP neurons share the same terminal selectors and a common ground state. Diversification beyond this ground state is controlled by ZAG-1 and EGL-44, which form a negative feedback loop through the reciprocal inhibition to regulate the choice between the two neuronal fates.
Simulation of PN Code Sequences for Cellular Systems

PN sequences are an important part of Code Division Multiple Access (CDMA) based wireless cellular systems. This report investigates the generation of m-sequences, Gold sequences, Gold-like sequences and Kasami sequences, which are special families of PN sequences. The autocorrelation and cross-correlation of these sequences are compared and analysed. The PN sequences specified in IS-95 CDMA and WCDMA standards are generated and stored for use in system level simulations.
Extracting Associations from Kidney Transplantations Dataset

Data Mining is one of the most motivating area of research which become increasingly popular in healthcare. Studies in heath scope used data mining techniques for diagnosing diseases and much less in prognosis stage of diseases. The records of the members of The Sudanese Kidney Transplanted Associations has been collected and their follow-up data from Cardiac Surgery & Renal Transplantations Center at Ahmed Qassim hospital in Khartoum North. We used Clementine, ARMADA association mining tool and MatLab to develop a program based on Apriori algorithm for extracting association rules. There are some differences in the results, but they all shows the essentially factors that impacts on renal functions.