Miracle-dz/UniFAR-FTUs huggingface dataset:
The genomic basis of adaptation to the deep water ‘twilight zone’ in Lake Malawi cichlid fishes

Deep water environments are characterized by low levels of available light at increasingly narrow spectra, great hydrostatic pressure and reduced dissolved oxygen - conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 100 metres. We use population-level RAD-seq data to investigate whether four endemic deep water species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology and haemoglobin, many not previously implicated in cichlid adaptive radiations. Co-localization of functionally linked genes suggests co-adapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions in candidate genes. Our data provide unique insights into genomic adaptation to life at depth, and suggest genome-level specialisation for deep water habitat as an important process in cichlid radiation.
Statistical Modeling to Information Retrieval for Searching from Big Text Data and Higher Order Inference for Reliability

This thesis examined two research projects: probabilistic information retrieval modeling and third-order inference on reliability. In the first part of this dissertation, two research topics in the information retrieval are carried out and experimented on large-scale text data set. First, we conduct an in-depth study of relationship between information of document length and document relevance to user need. Two statistical methods are proposed which incorporates document length as a substantial weighting factor to achieve higher retrieval performance. Second, we utilize the property of survival function to propose a cost-based re-ranking method to promote ranking diversity for biomedical information retrieval, and to model the proximity between query terms to improve retrieval performance. Through extensive experiments on standard TREC collections, our proposed models perform significantly better than the classical probabilistic information retrieval models. In the second part of this dissertation, a small sample asymptotic method is proii posed for higher order inference in the stress-strength reliability model, R = P (Y < X), where X and Y are independently distributed. A penalized likelihood method is proposed to handle the numerical complications of maximizing the constrained likelihood model. Simulation studies are conducted on two distributions: Burr type X distribution and exponentiated exponential distribution. Results from simulation studies show that the proposed method is very accurate even when the sample sizes are small.
Advanced Blind Signal Processing for MIMO Communications

The ever growing interest for higher transmission rates, bandwidth efficiency, coverage, and reliability in the third generation (3G) of wireless communication systems and beyond, has initiated an intensive research in the field of multi-antenna communications. Moreover, orthogonal frequency-division multiplexing (OFDM) has recently emerged as a favorable candidate for future generation of wireless communication systems due to its efficient utilization of bandwidth, simplicity of equalization, and robustness to multipath fading. Motivated by these facts, multiple-input multiple-output (MIMO) systems in association with the OFDM transmission are promising schemes widely adopted in recent wireless network standards such as Long Term Evolution (LTE) and Worldwide interoperability for Microwave Access (WiMAX). Space-time coding (STC) techniques are capable of exploiting the spatial diversity offered by multi-antenna systems. STC techniques have also been combined with MIMOOFDM wireless communication systems to both improve reliability and to increase higher transmission rates compared to single-antenna systems. In particular, the so-called orthogonal space-time block codes (OSTBCs) represent a popular class of STC techniques which are known to not only maximize the spatial diversity gain, but also offer simple decoding schemes. However, to obtain the theoretical promises of orthogonally coded MIMO-OFDM systems, accurate channel state information (CSI) is required at the receiver. The lack of CSI at the receiver is associated with a severe performance degradation of the MIMO-OFDM
Mathematical Chemistry! Is It? And if so, What Is It?

Mathematical chemistry entailing the development of novel mathe- matics for chemical applications is argued to exist, and to manifest an extreme- ly diverse range of applications. Yet further it is argued to have a substantial history of well over a century, though the field has perhaps only attained a de- gree of recognition with a formal widely accepted naming in the last few dec- ades. The evidence here for the broad range and long history is by way of nu- merous briefly noted example sub-areas. That mathematical chemistry was on- ly recently formally recognized is seemingly the result of its having been somewhat disguised for a period of time - sometimes because it was viewed as just an unnamed part of physical chemistry, and sometimes because the rather frequent applications in other chemical areas were not always viewed as math- ematical (often involving somewhat 'non-numerical' mathematics). Mathemat- ical chemistry's relation to and distinction from computational chemistry & theoretical chemistry is further briefly addressed.
Early survival and delayed death of developmentally-born dentate gyrus neurons

The storage and persistence of memories depends on plasticity in the hippocampus. Adult neurogenesis produces new neurons that mature through critical periods for plasticity and cellular survival, which determine their contributions to learning and memory. However, most granule neurons are generated prior to adulthood; the maturational timecourse of these neurons is poorly understood compared to adult-born neurons, but is essential to identify how the dentate gyrus, as a whole, contributes to behavior. To characterize neurons born in the early postnatal period, we labeled dentate gyrus neurons born on postnatal day 6 (P6) with BrdU and quantified maturation and survival across early (1 hour to 8 weeks old) and late (2-6 months old) cell ages. We find that the dynamics of developmentally-born neuron survival is essentially the opposite of neurons born in adulthood: P6-born neurons did not go through a period of cell death during their immature stages (from 1-8 weeks). In contrast, 17% of P6-born neurons died after reaching maturity, between 2-6 months of age. Delayed death was evident from the loss of BrdU+ cells as well as pyknotic BrdU+caspase3+ neurons within the superficial granule cell layer. Patterns of DCX, NeuN and activity-dependent Fos expression indicate that developmentally-born neurons mature over several weeks and a sharp peak in zif268 expression at 2 weeks suggests that developmentally-born neurons mature faster than adult-born neurons (which peak at 3 weeks). Collectively, our findings are relevant for understanding how developmentally-born dentate gyrus neurons contribute to memory and disorders throughout the lifespan. High levels of early survival and zif268 expression may promote learning, while also rendering neurons sensitive to insults at defined stages. Late neuronal death in young adulthood may result in the loss of hundreds of thousands of dentate gyrus neurons, which could impact memory persistence and contribute to hippocampal/dentate gyrus atrophy in disorders such as depression.
Extended query language and composition for the XR data model

The XR data model allows capturing rich semistructured corpora of documents (XML) with annotations (RDF triples). A simple query language for XR was presented in previous work, which allowed to retrieve results from from XR databases but not to build new XR content. This work makes two contributions. First, we present an extension of the query language giving powerful content structuring and grouping capabilities which enables flexible generation of new XR results. Second, we provide a query-view composition algorithm which enables the efficient evaluation of XR queries over previously defined XR views.
Incertezas e erros na estimativa de vazões usando modelagem hidrológica e precipitação por RADAR

This work presents an analysis of uncertainties and errors of the SCS-CN model of the Hydrologic Engineering Center - Hydrologic Modeling System (HEC-HMS), for hydrological events using observed and RADAR-estimated precipitation data of the Sao Miguel River Basin in State of Alagoas, which covers an area of 296 km². Physiographic data of the basin were used to find the initial estimates of the SCS-CN parameters. Then, using simultaneous measurements of precipitation and observed flow, the parameters were calibrated. Using independent data series, calibrated parameters were validated. The performance coefficient showed Nash-Sutcliffe values of 0.93 in the calibration phase and between 0.81 and 0.87 in the validation phase. The model was then used for past hydrological events, using RADAR-estimated precipitation data. This resulted in Nash-Sutcliffe coefficients between 0.75 and 0.79. The SCS-CN model with RADAR-estimated precipitation represented the time of the peak flow adequately; however, it underestimated the magnitude of the peak with errors up to 26% in some events. The methodology had satisfactory results for this basin and can be a useful tool for the prediction of flooding in other watersheds.
Cognitive Radio MAC Protocols

In cognitive radio networks, methods to allow the efficient sharing of the radio spectrum without causing any harmful interference to the primary users and to solve the spectrum scarcity problem are necessary. Identifying the available spectrum resources through spectrum sensing, coordinating with other users for spectrum access, improving channel utility, reducing collision rates, and improving sensing overhead are the major factors in cognitive radio medium access control protocols. Efficient use of radio spectrum largely depends on accurate spectrum sensing, spectrum sharing, spectrum mobility, and spectrum decisions. Hence, cognitive radio technology can significantly solve the spectrum scarcity problem by exploiting radio spectrum unused by licensed users. However, many technical problems still need to be solved for the proper functioning of cognitive radio networks. The medium access control protocols for cognitive radio networks should provide a comprehensive description of common control channels, spectrum sensing, harmful interference to primary users, variation of the spectrum availability, infrastructure support, the need for time synchronization, and the number of radio transceivers. In this paper, we present an overview of current medium access control protocols. Moreover, the classifications of medium access control protocols with their relative advantages and disadvantages are thoroughly investigated. We also highlight and explore some important research issues and challenges that could drive future research in this area.
USING MCNP5 for Medical Physics Applications

MCNP is a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport. MCNP5 has a wide range of abilities which make it useful for medical physics calculations. These abilities span its geometry representation, physics models, and source, tally and variance reduction capabilities. This workshop will demonstrate how MCNP5 can be used to calculate dose, simulate a radiograph, or even use CT data to create a voxel model of a human or phantom. A general review of MCNP5 source and tally capabilities, as well as new and future capabilities will also be included.
Human enhancers associated with immune response harbor specific sequence composition, activity, and genome organization

23 The FANTOM5 consortium recently characterized 38,554 robust hu24 man enhancers from 808 cell and tissue types using the Cap Analysis of 25 Gene Expression technology. We used the distribution of guanine and 26 cytosine nucleotides at enhancer regions to distinguish two classes of en27 hancers harboring distinct DNA structural properties. A functional anal28 ysis of their predicted gene targets highlighted one class of enhancers as 29 significantly enriched for associations with immune response genes. More30 over, these enhancers were specifically enriched for regulatory motifs rec31 ognized by TFs involved in immune response. We observed that immune 32 response enhancers were cell type specific, preferentially activated upon 33 bacterial infection, and with long-lasting response activity. Looking at 34 chromatin capture data, we found that the two classes of enhancers were 35 lying in distinct topologically-associated domains and chromatin loops. 36 Our results suggest that specific DNA sequence patterns encode for classes 37 of enhancers that are functionally distinct and specifically organized in the 38 human genome. 39
Use of Retroviral and Lentiviral Vectors to Deliver New Gene Therapies

Submit Manuscript | http://medcraveonline.com variants in different individuals to assess its association with a genetic trait and the pathological consequences. Researchers recognized that the observed genetic heterogeneity amongst individuals and genetic traits constitutes a Herculean challenge to develop new treatments. With this new personalized medicine information approach, the advance in genetic engineering was fast to act to try and help solving genetic abnormalities. Understanding the observed functional genetic diversity helps to correlate pathology phenotypes with the specific responses to therapeutic treatments. Finding the causal genetic mutations is crucial to define a precise strategy to correct the genetic imperfection. Retroviruses and lentiviruses were soon considered a viable approach to manipulate the human genome taking advantage of the mechanisms viruses use to invade and exploit the host genome.
Mechanisms of Immune Suppression Utilized by Canine Adipose and Bone Marrow-Derived Mesenchymal Stem Cells

Mesenchymal stem cells (MSCs) from rodents and humans have been shown to suppress T cells by distinct primary pathways, with nitric oxide (NO)-dependent pathways dominating in rodents and indoleamine 2,3-deoxygenase (IDO)-dependent pathways dominating in humans. However, the immune suppressive pathways utilized by canine MSC have not been thoroughly studied, nor have bone marrow-derived MSC (BM-MSC) and adipose-derived MSC (Ad-MSC) been directly compared for their immune modulatory potency or pathway utilization. Therefore, canine BM-MSC and Ad-MSC were generated in vitro and their potency in suppressing T cell proliferation and cytokine production was compared, and differential gene expression. Mechanisms of T cells suppression were also investigated for both MSC types. We found that BM-MSC and Ad-MSC were roughly equivalent in terms of their ability to suppress T cell activation. However, the two MSC types used both shared and distinct biochemical pathways to suppress T cell activation. Ad-MSC utilized .
The non-stationary dynamics of fitness distributions: asexual model with epistasis and standing variation

Various models describe asexual evolution by mutation, selection and drift. Some focus directly on fitness, typically modelling drift but ignoring or simplifying both epistasis and the distribution of mutation effects (travelling wave models). Others follow the dynamics of quantitative traits determining fitness (Fisher’s geometrical model), imposing a complex but fixed form of mutation effects and epistasis, and often ignoring drift. In all cases, predictions are typically obtained in high or low mutation rate limits and for long-term stationary regimes, thus loosing information on transient behaviors and the effect of initial conditions. Here, we connect fitness-based and trait-based models into a single framework, and seek explicit solutions even away from stationarity. The expected fitness distribution is followed over time via its cumulant generating function, using a deterministic approximation that neglects drift. In several cases, explicit trajectories for the full fitness distribution are obtained, for arbitrary mutation rates and standing variance. For non-epistatic mutation, especially with beneficial mutations, this approximation fails over the long term but captures the early dynamics, thus complementing stationary stochastic predictions. The approximation also handles several diminishing return epistasis models (e.g. with an optimal genotype): it can then apply at and away from equilibrium. General results arise at equilibrium, where fitness distributions display a ‘phase transition’ with mutation rate. Beyond this phase transition, in Fisher’s geometrical model, the full trajectory of fitness and trait distributions takes simple form, robust to details of the mutant phenotype distribution. Analytical arguments are explored for why and when the deterministic approximation applies. Significance statement How fast do asexuals evolve in new environments? Asexual fitness dynamics are well documented empirically. Various corresponding theories exist, to which they may be compared, but most typically describe stationary regimes, thus losing information on the shorter timescale of experiments, and on the impact of the initial conditions set by the experimenter. Here, a general deterministic approximation is proposed that encompasses many previous models as subcases, and shows surprising accuracy when compared to stochastic simulations. It can yield predictions over both short and long timescales, hopefully fostering the quantitative test of alternative models, using data from experimental evolution in asexuals.
Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

The interpretation of genetic variants identified during clinical sequencing has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC). Genuinely pathogenic variants, particularly in genes associated with severe autosomal dominant conditions, are assumed to be absent or extremely rare in these databases. Clinical exome sequencing of a six-year-old female patient with seizures, global developmental delay, dysmorphic features and failure to thrive identified an ASXL1 variant that was previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype matched the presentation of the patient, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Interrogation of the literature revealed that acquired somatic mosaicism of ASXL1 variants (including known pathogenic variants) during hematopoietic clonal expansion may be concomitant with aging in healthy individuals. We examined all high quality ASXL1 predicted truncating variant calls in the ExAC database and determined the majority could be attributed to this phenomenon. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like Bohring-Opitz syndrome have reduced penetrance, or the misclassification of potentially pathogenic variants.
Genetic and Environmental Biomarkers Associated with Triglyceride Levels in Two Groups of Slovak Women.

OBJECTIVE This study analyzed the association between the MLXIPL gene polymorphism (rs3812316) and triglyceride (TG) levels and selected environmental biomarkers in Slovak women at risk for cardiovascular disease compared to a reference sample. MATERIALS AND METHODS The studied sample consisted of 200 women at cardiovascular risk (mean age 52.96 ± 6.01 years) and 244 healthy women (mean age 47.52 ± 5.34 years). Participants gave details of their health and lifestyle during their medical examination, and peripheral blood samples were used for biochemical analyses and DNA genotyping. A nested polymerase chain reaction-restriction fragment length polymorphism assay was used to detect the rs 3812316 SNP. RESULTS We determined that there were significantly different genotype distributions in two TG categories: (1) subjects with normal TG values had a significantly higher G allele frequency than those with elevated TG levels (χ2 = 6.1556, df = 2, p = 0.046); and (2) the rare G allele frequency was 0.11 in the cardiovascular risk group and 0.15 in the reference group. Binary regression analysis showed that women with at least one G allele had a significantly lower relative risk of hypertriglyceridemia than women with the CC genotype (OR = 0.399, p = 0.022, 95% CI = 0.182-0.876). CONCLUSION This cross-sectional study suggests that MLXIPL rs3812316 genotypes may be associated with TG levels. However, further analysis is advisable because of study limitations.
A wide dynamic range receiver channel for a pulsed time-of-flight laser radar

An integrated receiver channel for a pulsed time-of-flight (TOF) laser rangefinder has been designed and tested. The bandwidth of the receiver channel is 170 MHz, the transimpedance can be controlled in the range from 1.1 k/spl Omega/ to 260 k/spl Omega/, and the input-referred noise is /spl sim/6 pA//spl radic/Hz. The distance measurement accuracy is /spl plusmn/4.7 mm (average of 10000 measurements), taking into account walk error (input signal amplitude varies in the range 1:624) and jitter. A considerable increase in the input dynamic range of the receiver has been achieved by placing an integrated current buffer with variable attenuation between the external photodetector and the transimpedance preamplifier. Integrated electronic gain control structures together with the small size and low power consumption achieved by the use of full custom integrated technology considerably simplifies rangefinding devices for many applications. The circuit was implemented in an 0.8-/spl mu/m BiCMOS process.
Mathematical Modelling and Simulation of Human Systemic Arterial System

the purpose of this study is to develop a model of arterial system using lumped parameter approach. The model contains systemic arterial circulation, starting from aorta, and follows upper and lower edges vessels. Anatomic and physiological data for circuit parameters, have been taken from medical textbooks and articles and where needed calculated using appropriate formulas. The developed mathematical model has been simulated by MATLAB software. Each compartment includes Resistor-Capacitor-Inductor (RCL) elements. The normal arterial operation is characterized by the pressure curves in various part of the system. The presented model is a one of the useful tool in studying the physiology of cardiovascular system and the related diseases. We can able to calculate pressure and blood flow in particular artery at the given time.