Miracle-dz/UniFAR-FTUs huggingface dataset:
Management of gene promoter mutations in molecular diagnostics.

BACKGROUND Although promoter mutations are known to cause functionally important consequences for gene expression, promoter analysis is not a regular part of DNA diagnostics. CONTENT This review covers different important aspects of promoter mutation analysis and includes a proposed model procedure for studying promoter mutations. Characterization of a promoter sequence variation includes a comprehensive study of the literature and databases of human mutations and transcription factors. Phylogenetic footprinting is also used to evaluate the putative importance of the promoter region of interest. This in silico analysis is, in general, followed by in vitro functional assays, of which transient and stable transfection assays are considered the gold-standard methods. Electrophoretic mobility shift and supershift assays are used to identify trans-acting proteins that putatively interact with the promoter region of interest. Finally, chromatin immunoprecipitation assays are essential to confirm in vivo binding of these proteins to the promoter. SUMMARY Although promoter mutation analysis is complex, often laborious, and difficult to perform, it is an essential part of the diagnosis of disease-causing promoter mutations and improves our understanding of the role of transcriptional regulation in human disease. We recommend that routine laboratories and research groups specialized in gene promoter research cooperate to expand general knowledge and diagnosis of gene-promoter defects.
Escherichia coli detection in different types of water

Escherichia coli detection in different types of water is proposed in this paper. In this study, a theoretical investigation has been carried out to determine the relation between temperature and dielectric constant of different types of water with the growth of E. coli bacteria in each water. Both dielectric constant and temperature plays and important roles in this study. The basic principle of this study is to monitor the wavelength of radiation and reduce the physical size of probe which is an antenna by immersing, transmitting, and receiving it and target into a high dielectric constant material, which is water. The temperature that suitable for growth of E. coli in each types of water was identified and the effect of temperature to its growth is observed. Thus, a V-slotted rectangular patch antenna was designed and presented in this paper. The simulation of antenna was done using Computer and Simulation Technology (CST) software. The measurement result was obtained by using Programmable Network Analyzer (PNA) after fabrication of the antenna. The antenna design shows a great performance by simulation and measurement. It can be said that E. coli survive at different temperature range in different kinds of water.
Gas-Solid Reaction Route toward the Production of Intermetallics from Their Corresponding Oxide Mixtures

Near-net shape forming of metallic components from metallic powders produced in situ from reduction of corresponding pure metal oxides has not been explored to a large extent. Such a process can be probably termed in short as the “Reduction-Sintering” process. This methodology can be especially effective in producing components containing refractory metals. Additionally, in situ production of metallic powder from complex oxides containing more than one metallic element may result in in situ alloying during reduction, possibly at lower temperatures. With this motivation, in situ reduction of complex oxides mixtures containing more than one metallic element has been investigated intensively over a period of years in the department of materials science, KTH, Sweden. This review highlights the most important features of that investigation. The investigation includes not only synthesis of intermetallics and refractory metals using the gas solid reaction route but also study the reaction kinetics and mechanism. Environmentally friendly gases like H2, CH4 and N2 were used for simultaneous reduction, carburization and nitridation, respectively. Different techniques have been utilized. A thermogravimetric analyzer was used to accurately control the process conditions and obtain reaction kinetics. The fluidized bed technique has been utilized to study the possibility of bulk production of intermetallics compared to milligrams in TGA. Carburization and nitridation of nascent formed intermetallics were successfully carried out. A novel method based on material thermal property was explored to track the reaction progress and estimate the reaction kinetics. This method implies the dynamic measure of thermal diffusivity using laser flash method. These efforts end up with a successful preparation of nanograined intermetallics like Fe-Mo and Ni-W. In addition, it ends up with simultaneous reduction and synthesis of Ni-WN and Ni-WC from their oxide mixtures in single step.
Recombinant human granulocyte colony-stimulating factor in preterm neonates with sepsis and relative neutropenia: a randomized, single-blind, non-placebo-controlled trial.

We performed a prospective, randomized, single-blind, non-placebo-controlled trial on preterm (<37 weeks) neonates (birth weight <2000g) with sepsis and absolute neutrophil counts (ANC) <5000 cells mm(-3) to study the effect of recombinant human granulocyte colony-stimulating factor (rhG-CSF) on all-cause-neonatal mortality and hematological parameters (total leucocyte (TLC, ANC, absolute monocyte and absolute platelet counts). The rhG-CSF group (n = 20) received 10 µg/kg/day of intravenous infusion of rhG-CSF once daily for 5 days along with conventional therapy, and the control group (n = 20) received conventional therapy alone. Hematological parameters on Days 0, 1, 3, 5, 7 and 14 of study entry and all-cause mortality rates at discharge were recorded. Baseline characteristics between the rhG-CSF and control group including mean birth weight (1395 ± 289 vs. 1500 ± 231g), mean gestational age (31.5 ± 2.68 vs. 32.6 ± 2.23 weeks), initial neonatal complaints and maternal characteristics were comparable. Mortality rates were significantly less among the rhG-CSF group (3/20 (15%) vs. 7/20 (35%), p < 0.05). By Day 5 (for TLC) and Day 3 (for ANC) of start of the intervention, rhG-CSF group had significantly higher TLC (8189 ± 1570 vs. 6936 ± 1128 cells mm(-3), p < 0.05) and ANC (4756 ± 1089 vs. 4213 ± 354 cells mm(-3), p < 0.05) compared to controls. ANC levels recovered to levels >5000 cells mm(-3) faster in the rhG-CSF group, with 80% babies having ANC >5000 cells mm(-3) by Day 7 of study entry compared with 35% in the control group (p < 0.05). Preterm neonates with sepsis and neutropenia treated with rhG-CSF adjunctive therapy have decreased all-cause mortality at discharge and a quicker recovery of their total leucocyte and ANC.
Examining the Barriers to e-Government Adoption

e-Government initially began as process where government entities developed websites and began populating these sites with information. After mastering this information dissemination aspect, government units moved toward processing online transactions. Subsequent to mastering transaction processing, governments moved across a continuum and engaged citizens online in a participatory framework; that is, offering Internet applications that connect citizens with public administrators, decision-makers, and perhaps elected officials. While the subsequent progression and potential benefits of e-Government applications are without limits, there are a number of barriers that impede the implementation of such applications. Using survey data collected by the International City/County Management Association (ICMA), this paper examines the factors that most impede the adoption of e-Government applications. Central research questions include: what are the differences between municipalities that have comprehensive eGovernment platforms and those that do not, and to what extent do certain barriers explain these differences? Multiple regression results indicate that e-Government adoption is a function of financial, technical, and human resources. Holding all other factors constant, municipalities with higher operating budgets, more full-time IT staff, and technical resources are more likely to implement a comprehensive e-Government platform. Political support is a key and fairly robust determinant of municipal e-Government adoption as well.
Optimal Signal Design for Multi-Parameter Estimation Problems

In this paper, the optimal stochastic design of multiple parameters is investigated for an array of fixed estimators both in the absence and presence of an average power constraint. Two different performance criteria are considered: the total Bayes risk criterion and the maximum Bayes risk criterion. It is obtained that in the presence of K parameters and the average power constraint, the optimal stochastic parameter design results in randomization (time sharing) among at most two and (K+1) different signals for the total Bayes risk and the maximum Bayes risk criteria, respectively. The average transmitted signal powers corresponding to the optimal parameter design approaches are specified, and the characterization of the optimal approaches is provided in various scenarios. In addition, sufficient conditions are derived to specify when the stochastic parameter design or the deterministic parameter design is optimal. Finally, numerical examples are presented to investigate the theoretical results, and to illustrate performance improvements achieved via the proposed approaches.
A generalisation of the matroid lift construction

This paper introduces a general matroid-theoretic construction which includes, as special cases, elementary lifts of matroids and bias matroids of biased graphs. Elementary lifts are obtained when the submodular function chosen is the rank function of M. We define what is meant by a k-induced matroid. These matroids simultaneously generalise matroids of graphs, transversal matroids and Dilworth truncations
Studies of the earliest generated cells of the cat's visual cortex: cogeneration of subplate and marginal zones

The earliest generated cells of the cat's telencephalon that may play a role in the formation of the primary visual cortex are the subject of this study. Using [3H]thymidine autoradiography, we have found that these cells are generated between embryonic day 24 (E24) and E30 (gestation is 65 days) and that they are present in very low numbers in the white matter of the adult brain. These cells are rarely labeled by injections made after E30, when the cells destined for the cortical layers are generated. Examination of the labeling pattern in the fetal brain 10 days or more after administration of [3H]thymidine between E24 and E30 revealed a bistratified distribution of these early generated cells. Labeled cells were found in large numbers in two embryonic zones flanking the developing cortical plate: above in the marginal zone and below in the subplate. (Some if not all of the marginal zone cells constitute the population of Cajal-Retzius cells of the cat's telencephalon.). These experiments indicate that cells of the subplate and marginal zones are cogenerated in time during the days just preceding the genesis of the cortical plate. We also examined the distribution of the early generated cells shortly after their genesis-- on E30, a time when cells of the cortical plate are just being generated at the ventricular zone. In this case, the labeling pattern at the occipital pole was not bistratified. Rather, labeled cells were situated within a single zone extending from the pial surface inward to the border of the ventricular zone. This finding indicates that the cells of the subplate and marginal zones are generated as a contiguous population that is subsequently split apart by the insertion of cells forming the cortical plate. A comparison between the number of early generated cells found in fetal and newborn brains with that found in adult brains suggests that these cells are generated initially in substantial numbers but then largely disappear during early postnatal life, since injections of [3H]thymidine between E24 and E30 yielded large numbers of labeled cells in the white matter and layer 1 at birth, but very few at 2 months postnatal. This significant loss contrasted with the results from injections made just a few days later (E33) that resulted in large numbers of labeled cells in cortical layer 6 not only at birth but also in adulthood.
IrisNet: An Architecture for Compute-Intensive Wide-Area Sensor Network Services

Previous work on sensor networks has targeted ad hoc wireless networks of closely-colocated, resourceconstrained scalar sensor motes. Such work has overlooked richer sensor types such as webcams and microphones, which are typically attached to Internetconnected machines with significant computing power and storage. In this paper, we describe IrisNet (Internetscale Resource-Intensive Sensor Network services), an architecture for wide-area sensor networks based on these more capable sensing nodes. IrisNet provides a common, scalable software infrastructure that enables the flexible creation of sensor-based Internet services. It dramatically reduces network bandwidth utilization through the use of senselets, binary code fragments that perform intensive data filtering at the sensing nodes, leveraging the available processing power and memory. IrisNet employs a two-tier hierarchy of sensing nodes and query processing nodes. Key features of IrisNet include flexible data partitioning, efficient and protected sharing of sensor nodes, low-latency queries, partial match caching, query-specified freshness tolerances, and monitoring and logging support. This paper reports on experiments with a working IrisNet prototype running a parking space finder service, demonstrating the effectiveness of IrisNet’s features in achieving scalability and reducing query response times.
Fabrication

This report summarized the development w^ork perforraed, and the p r o c e s s es established, for the fabrication of Hastelloy X clad, U-ZrH fuel elements. P r o c e s s es described include: U-Zr ' X alloy melting and extrusion, U - Zr hydriding, Gd_0„ vapor depo sition on U-ZrH fuel rods, machining helical fins in Hastelloy X cladding, Hastelloy X electron beam welding, ceramic coating of Hastelloy X, and final assembly operations. and test data on developmental fuel elements are presented, which demon strate that the dimensional and performance test requirements of the 5-kwe zirconium hydride reactor could be met.
Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,.,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10). (11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.
Using Ontology Repository to Support Data Mining

Ontology plays the central role in the information system. A novel framework for data mining process is proposed, using ontology repository to integrate domain knowledge. Ontobase ontology repository is an implementation of our design to allow users and agents to retrieve ontologies and metadata through open Web standards and ontology service. Key features of the system include the use of XML metadata interchange to represent and import ontologies and metadata, the support for smooth transformation and transparent integration using ontology mapping and the use of ontology services to share and reuse domain knowledge in a generic way. Some examples show that Ontobase is useful in supporting data mining process
Overview of the Basic Biology of Bacillus thuringiensis with Emphasis on Genetic Engineering of Bacterial Larvicides for Mosquito Control

The insecticidal bacterium, Bacillus thuringiensis, consists of a wide variety of subspecies, most of which are insecticidal for either lepidopteran, coleopteran, or dipteran insect larvae. Subspecies such as B. thuringiensis subsp. kurstaki have been used with remarkable safety for more than forty years to control lepidopteran pests in agriculture and forestry, and over the past thirty years, B. thruingeinsis subsp. israelensis, has proven to be a safe and effective larvicide for controlling mosquito and black fly larvae. Studies of the basic biology of B. thuringiensis have shown that it produces a variety of insecticidal proteins produced during vegetative growth and sporulation that determines its activity for insect species belonging to different orders, with the most important of these being the Cry proteins active against lepidopteran and coleopteran pests, and a combination of Cry and Cyt proteins for mosquitoes and blackflies. After intoxication by these proteins, spores typically germinate and invade larvae, contributing to insect mortality. Whereas strains of many wild type isolates have been commercialized and are now used worldwide, the use of recombinant DNA techniques, i.e., genetic engineering, has been used over the past decade to recombine the proteins of different B. thuringiensis strains with those of B. sphaericus to generate recombinant larvicides as much as ten-fold more toxic than the parental strains. In this chapter, we begin with a general overview of the basic biology of B. thuringiensis and B. sphaericus, then show how studies of its molecular genetics combined with recombinant DNA techniques have been used to generate highly improved bacterial larvicides for control of nuisance and vector mosquitoes.
Design of ultrahigh-speed low-voltage CMOS CML buffers and latches

A comprehensive study of ultrahigh-speed current-mode logic (CML) buffers along with the design of novel regenerative CML latches will be illustrated. First, a new design procedure to systematically design a chain of tapered CML buffers is proposed. Next, two new high-speed regenerative latch circuits capable of operating at ultrahigh-speed data rates will be introduced. Experimental results show a higher performance for the new latch architectures compared to the conventional CML latch circuit at ultrahigh-frequencies. It is also shown, both through the experiments and by using efficient analytical models, why CML buffers are better than CMOS inverters in high-speed low-voltage applications.
THE LATTICE DIMENSION OF BENZENOID SYSTEMS

A labeling of vertices of a benzenoid system B is proposed that reflects the graph distance in B and is significantly shorter that the labeling obtained from a hypercube embedding of B. The new labeling corresponds to an embedding of B into the integer lattice Zd and is shown to be optimal for all practical purposes. A coordinatization algorithm is presented and it is demonstrated that it can be easily carried out by hand.
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species

We describe here the results of the first genome-wide survey of candidate exon repetition events in expressed sequences from human, mouse, rat, chicken, zebrafish and fly. Exon repetition is a rare event, reported in <10 genes, in which one or more exons is tandemly duplicated in mRNA but not in the gene. To identify candidates, we analysed database sequences for mRNA transcripts in which the order of the spliced exons does not follow the linear genomic order of the individual gene [events we term rearrangements or repetition in exon order (RREO)]. Using a computational approach, we have identified 245 genes in mammals that produce RREO events. RREO in mRNA occurs predominantly in the coding regions of genes. However, exon 1 is never involved. Analysis of the open reading frames suggests that this process may increase protein diversity and regulate protein expression via nonsense-mediated RNA decay. The sizes of the exons and introns involved around these events suggest a gene model structure that may facilitate non-linear splicing. These findings imply that RREO affects a significant subset of genes within a genome and suggests that non-linear information encoded within the genomes of complex organisms could contribute to phenotypic variation.
Factors predicting the age when type 2 diabetes is diagnosed in Hong Kong Chinese subjects.

OBJECTIVE To examine the factors predicting age at diagnosis of type 2 diabetes in Hong Kong Chinese. RESEARCH DESIGN AND METHODS The relationships between age at diagnosis and parental history of diabetes as well as an array of clinical and metabolic factors were examined using a hospital clinic-based diabetes registry involving 3,414 index patients with type 2 diabetes Patterns of age at diagnosis in successive generations were also examined using 21 affected child-parent pairs and 7 affected child-parent-grandparent trios. RESULTS Approximately 29% of the index patients were diagnosed with type 2 diabetes at < or = 35 years of age (hereby defined as early-onset). Compared with the patients diagnosed at >35 years of age (hereby defined as late-onset) the early-onset patients had higher rates of positive paternal (16 vs. 5%) and maternal (22 vs. 12%) history of diabetes (both at P < 0.01) and had poorer metabolic profiles. In the overall index patients, male sex, higher HbA1c waist-to-hip ratio (WHR), and systolic blood pressure (sBP); lower HDL cholesterol level; and a positive paternal was well as maternal history of diabetes predicted younger age at diagnosis. More senior age and higher BMI and diastolic blood pressure predicted olderq age at diagnosis. Predictors for younger age at diagnosis in the male patients were higher HbA1c and sBP and a positive paternal history of diabetes Predictors for younger age at diagnosis in the female patients were higher HbA1c WHR, and sBP and a paternal as well as maternal history of diabetes. In the affected child parent pairs and clild-parent-grandparent trios there was a decrease in age at diagnosis in successive generations. CONCLUSIONS Our data indicate that both familial (possibly genetic) and metabolic factors affect the age of onset of type 2 diabetes in the Chinese population. The results also suggest an onset and progression pattern of the disease that is compatible with the phenomenon of anticipation.