Miracle-dz/UniFAR-FTUs huggingface dataset:
An Amino Acid Polymorphism in Histidine-rich Glycoprotein (HRG) Explains 59% of the Variance in Plasma HRG Levels

Summary A pedigree-based maximum likelihood method developed by Lange et al. (12) was used to study the contribution of a newly defined di-allelic polymorphism in histidine-rich glycoprotein (HRG) to the plasma levels of HRG. In four families (n = 99) and 20 volunteers we found a heritability of 70%, an age effect of 3% and an effect of individual environmental factors of 27%. These results are remarkably similar to the results found in a previous parent-twin study in which a heritability of 69% and an effect of random environment of 31% was found. The overall genetic influence in the present study can be subdivided into an effect of 59% by the HRG phenotype and 11% by residual genetic factors. The influence of the HRG phenotype of 59% can entirely be explained by adding up the effect of the two alleles that make up the phenotype. These results indicate a codominant inheritance pattern of HRG levels in which the genetic influence can almost completely be ascribed to the additive effect of the di-allelic HRG locus whereas only a small part is due to other loci.
An Exact and Inexact Data Matching Approach for Saving Time and Preventing Errors in Processing of Student Exam Results at the University of Botswana

The University of Botswana (UB) offers a comprehensive range of academic programmes, leading to a variety of undergraduate and postgraduate qualifications offered across its seven faculties. Like other universities, UB faces a problem of large enrolment creating a large numbers of students in some of the courses offered. Often this problem is seen in the university-wide General Education Courses which UB created to provide basic interdisciplinary skills for students. We study an examination problem using one such course, Computing and Information Skills Fundamentals I, with a registration of more than 4000 students. The exam questions are designed with multiple choice questions and the exam answer sheets are marked using an Optical Mark Recognition scanner. A recurring problem is observed where students do not shade their details perfectly, leading to a cumbersome problem when matching exam records with class list records. We implement a data matching solution and test it, yielding excellent results. We make use of an exact matching processing step, before use of standard data matching methods for indexing, comparison, and classification. We use q-gram indexing, edit-distance comparison, and Support Vector Machine classification methods. The results show that the impact is very high. First the processing time is reduced from a cumbersome process of more than 13 hours to less than 18 minutes, with no mistakes made in the automated processing phase. Secondly, record pairs which had too little information to match automatically and have to be matched manually are few hence manageable
Modulating Fis and IHF binding specificity, crosstalk and regulatory logic through the engineering of complex promoters

Bacterial promoters are usually formed by multiple cis-regulatory elements recognized by a plethora of transcriptional factors (TFs). From those, global regulators are key elements since these TFs are responsible for the regulation of hundreds of genes in the bacterial genome. For instance, Fis and IHF are two global regulators which play a major role in gene expression control in Escherichia coli and usually multiple cis-regulatory elements for these proteins co-occur at target promoters. Here, we investigated the relationship between the architecture of the cis-regulatory elements for Fis and IHF in E. coli. For this, we constructed 42 synthetic promoter variants harboring consensus cis-elements for Fis and IHF at different distances from a core −35/−10 region and in different numbers and combinations. We first demonstrated that although Fis preferentially recognizes its consensus cis-element, it can also recognize, to some extent, the consensus binding site for IHF, and the same was true for IHF, which was also able of recognizing Fis binding sites. However, changing the arrangement of the cis-elements (i.e., the position or the number of sites) can completely abolish unspecific binding of both TFs. More remarkably, we demonstrate that combining cis-elements for both TFs could result in Fis and IHF repressed or activated promoters depending on the final architecture of the promoters in an unpredictable way. Taken together, the data presented here demonstrate how small changes in the architecture of bacterial promoters could result in drastic changes in the final regulatory logic of the system, with important implications for the understanding of natural complex promoters in bacteria and their engineering for novel applications. Importance The understanding of the regulatory complex in bacteria is a key issue in modern microbiology. Here, we constructed synthetic bacterial promoters in order to investigate how binding of transcriptional factors to multiple target sites at the promoters can influence gene expression. Our results demonstrate in a systematic way that the arrangement and number of these cis-regulatory elements are crucial for the final expression dynamics of the target promoters. In particular, we show that TF binding specificity or promiscuity can be modulated using different promoter architectures based on consensus cis-regulatory elements, and that transcriptional repression and activation can also be affected by promoter architecture. These results are relevant both for the understanding of natural systems and for the construction of synthetic circuits for biotechnological applications.
A Hidden Markov Model for Analysis of Frontline Veterinary Data for Emerging Zoonotic Disease Surveillance

Surveillance systems tracking health patterns in animals have potential for early warning of infectious disease in humans, yet there are many challenges that remain before this can be realized. Specifically, there remains the challenge of detecting early warning signals for diseases that are not known or are not part of routine surveillance for named diseases. This paper reports on the development of a hidden Markov model for analysis of frontline veterinary sentinel surveillance data from Sri Lanka. Field veterinarians collected data on syndromes and diagnoses using mobile phones. A model for submission patterns accounts for both sentinel-related and disease-related variability. Models for commonly reported cattle diagnoses were estimated separately. Region-specific weekly average prevalence was estimated for each diagnoses and partitioned into normal and abnormal periods. Visualization of state probabilities was used to indicate areas and times of unusual disease prevalence. The analysis suggests that hidden Markov modelling is a useful approach for surveillance datasets from novel populations and/or having little historical baselines.
Nuclear Import of Hepatitis B Virus Capsids and Genome

Hepatitis B virus (HBV) is an enveloped pararetrovirus with a DNA genome, which is found in an up to 36 nm-measuring capsid. Replication of the genome occurs via an RNA intermediate, which is synthesized in the nucleus. The virus must have thus ways of transporting its DNA genome into this compartment. This review summarizes the data on hepatitis B virus genome transport and correlates the finding to those from other viruses.
Redefining the potential applications of dental stem cells: An asset for future

Recent exciting discoveries isolated dental stem cells from the pulp of the primary and permanent teeth, from the periodontal ligament, and from associated healthy tissues. Dental pulp stem cells (DPSCs) represent a kind of adult cell colony which has the potent capacity of self-renewing and multilineage differentiation. Stem cell-based tooth engineering is deemed as a promising approach to the making of a biological tooth (bio-tooth) or engineering of functional tooth structures. Dental professionals have the opportunity to make their patients aware of these new sources of stem cells that can be stored for future use as new therapies are developed for a range of diseases and injuries. The aim of this article is to review and understand how dental stem cells are being used for regeneration of oral and conversely nonoral tissues. A brief review on banking is also done for storing of these valuable stem cells for future use.
Explorer Polymorphic queries for P 2 P systems

When a query is posed on a centralized database, if it refers to attributes that are not defined in the database, the user is warranted to get either an error or an empty set. In contrast, when a query is posed on a peer in a P2P system and refers to attributes not found in the local database, the query should not be simply rejected if the relevant information is available at other peers. This paper proposes a query model for unstructured P2P systems to answer such queries. (a) We introduce a class of polymorphic queries, a revision of conjunctive queries by incorporating type variables to accommodate attributes not defined in the local database. (b) We define the semantics of polymorphic queries in terms of horizontal and vertical object expansions, to find attributes and tuples, respectively, missing from the local database. We show that both expansions can be conducted in a uniform framework. (c) We develop a top-K algorithm to approximately answer polymorphic queries. (d) We also provide a method to merge tuples collected from various peers, based on matching keys specified in polymorphic queries. Our experimental study verifies that polymorphic queries are able to find more sensible information than traditional queries supported by P2P systems, and that these queries can be evaluated efficiently. & 2011 Elsevier B.V. All rights reserved.
Comparison of Periodic and Event Based Sampling for Linear State Estimation

Abstract In this paper, the state estimation problem for continuous-time linear systems with two types of sampling is considered. First, the optimal state estimator under periodic sampling is presented. Then the state estimator with event-based updates is designed, i.e., when an event occurs the estimator is updated linearly by using the measurement of output, while between the consecutive event times the estimator is updated by minimum mean-squared error criteria. The average estimation errors under both sampling schemes are compared quantitatively for first and second order systems, respectively. A numerical example is given to compare the effectiveness of two state estimators.
A Quantitative Comparison of Epoch Extraction Algorithms for Telephone Speech

Telephone speech is one of the degradations involved in building speech systems in practical environments. The potential use of the speech systems depends on the speech analysis algorithms that can handle different acoustic variations and degradations often found in the human speech communication. Detection of epochs/glottal closure instants (GCIs) is typically required in such analysis stages. In this paper, the effect of telephone channel speech on the accuracy of detection of epochs using state-of-art epoch extraction methods is investigated. Epoch is the instant of significant excitation to the vocal tract system in voiced speech. Most of the existing epoch extraction algorithms are shown to perform excellently well on the speech data collected under lab environment. The efficiency of these algorithms for the analysis of telephone quality speech is quantitatively studied and the strengths and weaknesses of the methods are discussed here. The methods are evaluated on six large databases containing speech and simultaneous EGG recordings as the ground truth. The state-of-art epoch extraction algorithms considered in this study for comparison are: ZFF, YAGA, DYPSA, SEDREAMS, SE-VQ and MMF. The performance of the algorithms is evaluated in terms of both reliability and accuracy measures.
Mining Sequential Purchasing Behaviors from Customer Transaction Databases

Mining sequential patterns is to find the sequential purchasing behaviors for most of the customers, which only considers the number of the customers with the purchasing behaviors in a customer transaction database. Mining high utility sequential patterns considers both of the profits and purchased quantities for the items, which is to find the sequential patterns with high benefits for the business. The previous researches for mining high utility sequential patterns roughly defined the utility of a sequence contributed by a customer, such that the generated patterns are not really high utility. Moreover, the previous approaches need to generate a large number of the candidates and scan the whole database to calculate the utilities for all the generated candidates. Therefore, in this paper, we consider the actual purchasing behaviors for the customers and exactly define the high utility sequential patterns. Besides, we also propose an efficient algorithm for mining our well-defined high utility sequential patterns which can significantly reduce the number of the candidates. The experimental results also show that our algorithm significantly outperforms the previous approach for mining high utility sequential patterns.
Effects of mutant small, acid-soluble spore proteins from Bacillus subtilis on DNA in vivo and in vitro

alpha/beta-type small, acid-soluble spore proteins (SASP) of Bacillus subtilis bind to DNA and alter its conformation, topology, and photochemistry, and thereby spore resistance to UV light. Three mutations have been introduced into the B. subtilis sspC gene, which codes for the alpha/beta-type wild-type SASP, SspCwt. One mutation (SspCTyr) was a conservative change, as residue 29 (Leu) was changed to Tyr, an amino acid found at this position in other alpha/beta-type SASP. The other mutations changed residues conserved in all alpha/beta-type SASP. In one (SspCAla), residue 52 (Gly) was changed to Ala; in the second (SspCGln), residue 57 (Lys) was changed to Gln. The effects of the wild-type and mutant SspC on DNA properties were examined in vivo in B. subtilis spores and Escherichia coli as well as in vitro with use of purified protein. Both SspCwt and SspCTyr interacted similarly with DNA in vivo and in vitro, restoring much UV resistance to spores lacking major alpha/beta-type SASP, causing a large increase in plasmid negative supercoiling, and altering DNA UV photochemistry from cell type to spore type. In contrast, SspCAla had no detectable effect on DNA properties in vivo or in vitro, while SspCGln had effects intermediate between those of SspCAla and SspCwt. Strikingly, neither SspCAla nor SspCGln bound well to DNA in vitro. These results confirm the importance of the conserved primary sequence of alpha/beta-type SASP in the ability of these proteins to bind to spore DNA and cause spore UV resistance.
Decision Feedback Semi-blind Estimation Algorithm for Specular OFDM Channels

This paper deals with semi-blind channel estimation in Single-Input Single-Output (SISO) Orthogonal Frequency Division Multiplexing (OFDM) communications system. The proposed algorithm proceeds in two main stages. The first one addresses the pilot-based Time-Of-Arrival (TOA) estimation using subspace methods and then estimates the channel through its specular model. In the second stage, one considers a decision feedback equalizer that is used to refine the channel parameters estimates. Simulation results show that good performance can be reached with only one OFDM pilot symbol with appropriate windowing using only one iteration. A significant performance improvement as compared to the pilot-based TOA method is observed.
CGO: utilizing and integrating gene expression microarray data in clinical research and data management

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *. txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.
The Contagion Effect Between the Volatilities of the NASDAQ-100 and the IT.CA :A Univariate and A Bivariate Switching Approach

This article uses models with changes in regime and conditional variance to show the presence of co-movement between the American and the French New Technology indexes, the NASDAQ-100 and the IT.CAC respectively. For the past two years, American and French New Technology stock markets have been ﬂuctuating severely, and it has been observed that the IT.CAC is considerably affected by the NASDAQ- 100. In the ﬁrst part of this article, we study the volatilities of those two IT indexes, using univariate conditional variance and changes in regime models. We show that the volatilities of the two indexes have considerably increased exhibiting a certain level of correlation. We ﬁnd signs of a co-movement effect between the volatilities of the NASDAQ-100 and the IT.CAC. The hypothesis of a co-movement effect is discussed in the second part of this article, using a bivariate SWARCH model to show the dependence of the high and low volatility states of the IT.CAC on the NASDAQ-100, with no intermediate simultaneous high-low volatility states.
On the continuum limit of a discrete inverse spectral problem on optimal finite difference grids

We consider finite difference approximations of solutions of inverse Sturm‐Liouville problems in bounded intervals. Using three‐point finite difference schemes, we discretize the equations on so‐called optimal grids constructed as follows: For a staggered grid with 2 k points, we ask that the finite difference operator (a k × k Jacobi matrix) and the Sturm‐Liouville differential operator share the k lowest eigenvalues and the values of the orthonormal eigenfunctions at one end of the interval. This requirement determines uniquely the entries in the Jacobi matrix, which are grid cell averages of the coefficients in the continuum problem. If these coefficients are known, we can find the grid, which we call optimal because it gives, by design, a finite difference operator with a prescribed spectral measure. We focus attention on the inverse problem, where neither the coefficients nor the grid are known.
Haematocrit in Elite Athletes

It is possible to increase haemoglobin (Hb) and haematocrit (Ht) to non-physiological values by injecting recombinant human erythropoietin (rhEPO). Although this treatment may result in a better performance of athletes, it may also cause a health risk. To prevent doping with rhEPO, the Union Cycliste Internationale has decided to exclude male cyclists with Ht>0.50 and female cyclists with Ht>0.47 from competition. These cut-off values, however, may result in a non-justified exclusion of clean athletes. To test this hypothesis, we measured the Ht of elite athletes (50 men and 41 women) during a total study period of 43 months. Ht was compared with that in healthy control subjects (134 men and 144 women). No significant differences in Ht were detected between male elite athletes and their references and female elite athletes and their references (P>0.05). In both populations, however, male subjects were found with Ht>0.50, 6 controls and 5 elite athletes (4 highlanders and 1 lowlander). In the female subjects 5 controls but not one of the athletes exceeded a Ht>0.47. "Increased" Ht values among athletes were mainly seen in highlanders. The study shows that it is very difficult to set up a decision value for Ht with regard to doping by erythropoietin.
Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea

Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5′ to 3′ direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5′→3′ exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5′→3′ exonuclease with a preference to ssDNA; however, RecJ2 is a 3′→5′ exonuclease with a preference to ssRNA. The 5′ terminal phosphate promotes RecJ1 activity, but the 3′ terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.
Multiscale Entropy‐based Analysis of Soil Transect Data

A deeper understanding of the spatial variability of soil properties and the relationships between them is needed to scale up measured soil properties and to model soil processes. The object of this study was to describe the spatial scaling properties of a set of soil physical properties measured on a common 1024‐m transect across arable fields at Silsoe in Bedfordshire, east‐central England. Properties studied were volumetric water content (θ), total porosity (π), pH, and N2O flux. We applied entropy as a means of quantifying the scaling behavior of each transect. Finally, we examined the spatial intrascaling behavior of the correlations between θ and the other soil variables. Relative entropies and increments in relative entropy calculated for θ, π, and pH showed maximum structure at the 128‐m scale, while N2O flux presented a more complex scale dependency at large and small scales. The intrascale‐dependent correlation between θ and π was negative at small scales up to 8 m. The rest of the intrascale‐dependent correlation functions between θ with N2O fluxes and pH were in agreement with previous studies. These techniques allow research on scale effects localized in scale and provide the information that is complementary to the information about scale dependencies found across a range of scales.
Synchronization in Relaxation Oscillator Networks with Conduction Delays

We study locally coupled networks of relaxation oscillators with excitatory connections and conduction delays and propose a mechanism for achieving zero phase-lag synchrony. Our mechanism is based on the observation that different rates of motion along different nullclines of the system can lead to synchrony in the presence of conduction delays. We analyze the system of two coupled oscillators and derive phase compression rates. This analysis indicates how to choose nullclines for individual relaxation oscillators in order to induce rapid synchrony. The numerical simulations demonstrate that our analytical results extend to locally coupled networks with conduction delays and that these networks can attain rapid synchrony with appropriately chosen nullclines and initial conditions. The robustness of the proposed mechanism is verified with respect to different nullclines, variations in parameter values, and initial conditions.