Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence rearrangement in the AT-rich minisatellite of the novel rice transposable element Basho.

In the process of characterizing a rice wx deletion mutant, an AT-rich minisatellite sequence that consisted of units of approximately 80 bp was detected about 2.3 kb downstream of the wx gene. This AT-rich minisatellite was a multiple-copy element (1 x 10(3) to 2 x 10(3) copies per haploid genome) and interspersed in the rice genome. By BLAST homology search it was indicated that not only the tandem repeat but also both flanking sequences were conserved among copies. According to the characteristics of the termini (5'-CHH . CTAG-3') and a target site preference for T, this AT-rich minisatellite accompanying the flanking sequences was classified into a novel transposon, Basho. The results of direct amplification of Basho showed that relatively large variation in size existed in the Basho family. We estimate the variation to be generated by not only alteration of the number of units in the minisatellite but also by duplications of larger blocks including the conserved flanking sequences caused by single-strand mispairing (SSM) at noncontiguous repeats. Because the AT-rich minisatellite contained in Basho possessed several motifs of the matrix attachment region (MAR) in its repeat unit, the functional role as MAR in the rice genome was discussed.
Use of mix of clay/solid waste from steel works for civil construction materials

The present study focuses on the use of solid waste generated by the steel works in Brazil for manufacturing clay-based structural products. The waste sample was characterized regarding chemical composition, X-ray diffraction, particle size, morphology, specific surface and plastic properties. The waste was added in gradual proportions to a kaolinitic clay from zero up to 3 wt. %. Ceramic bodies were formed by vacuum extrusion and fired at 950° C. The physical-mechanical properties (linear shrinkage, water absorption, apparent density and flexural strength) of the resulting clay/solid waste mixtures were determined. In addition, leaching tests were performed according Brazilian Standards as well as a preliminary analysis of gases evolved during the thermal process. It was found that the solid waste is formed by irregular particles, ranging in size from 1 to 500 μm. The test results indicate that solid wastes generated by steel works can be used as filler in construction materials, thereby increasing reuse in an environmentally safe manner.
Relevance of residue 116 of HLA‐B27 in determining susceptibility to ankylosing spondylitis

Ankylosing spondylitis (AS) is an autoimmune disorder strongly associated with HLA‐B27. A direct role of B27 molecules in the disease pathogenesis has been postulated, possibly by presenting to T cells an as‐yet unidentified arthritogenic peptide that triggers the autoimmune response. There are nine HLA‐B27 alleles differing from each other at one or more amino acid positions. It is important, for the identification of the arthritogenic peptide, to define which alleles, and therefore which polymorphic positions, predispose to the disease. Here, we report that HLA‐B★2709 is not associated with AS, as it was not found in patients. HLA‐B★2709 differs from the most frequent and disease‐associated HLA‐B★2705 allele for a single substitution (His vs. Asp) at position 116. Amino acid 116 is located at the bottom of the groove where the antigenic peptide sits, and it has been proven to influence the peptide‐binding specificity of HLA class I molecules. The most likely interpretation of these data is that the differences in charge and size that accompany the His‐to‐Asp substitution exclude the acceptance of the arthritogenic peptide.
Host-Nonspecific Iron Acquisition Systems and Virulence in the Zoonotic Serovar of Vibrio vulnificus

ABSTRACT The zoonotic serovar of Vibrio vulnificus (known as biotype 2 serovar E) is the etiological agent of human and fish vibriosis. The aim of the present work was to discover the role of the vulnibactin- and hemin-dependent iron acquisition systems in the pathogenicity of this zoonotic serovar under the hypothesis that both are host-nonspecific virulence factors. To this end, we selected three genes for three outer membrane receptors (vuuA, a receptor for ferric vulnibactin, and hupA and hutR, two hemin receptors), obtained single and multiple mutants as well as complemented strains, and tested them in a series of in vitro and in vivo assays, using eels and mice as animal models. The overall results confirm that hupA and vuuA, but not hutR, are host-nonspecific virulence genes and suggest that a third undescribed host-specific plasmid-encoded system could also be used by the zoonotic serovar in fish. hupA and vuuA were expressed in the internal organs of the animals in the first 24 h of infection, suggesting that they may be needed to achieve the population size required to trigger fatal septicemia. vuuA and hupA were sequenced in strains representative of the genetic diversity of this species, and their phylogenies were reconstructed by multilocus sequence analysis of selected housekeeping and virulence genes as a reference. Given the overall results, we suggest that both genes might form part of the core genes essential not only for disease development but also for the survival of this species in its natural reservoir, the aquatic environment.
Genome Analysis of the First Marseilleviridae Representative from Australia Indicates that Most of Its Genes Contribute to Virus Fitness

ABSTRACT The family Marseilleviridae consists of Acanthamoeba-infecting large DNA viruses with icosahedral particles ∼0.2 μm in diameter and genome sizes in the 346- to 380-kb range. Since the isolation of Marseillevirus from a cooling tower in Paris (France) in 2009, the family Marseilleviridae has expanded rapidly, with representatives from Europe and Africa. Five members have been fully sequenced that are distributed among 3 emerging Marseilleviridae lineages. One comprises Marseillevirus and Cannes 8 virus, another one includes Insectomime virus and Tunisvirus, and the third one corresponds to the more distant Lausannevirus. We now report the genomic characterization of Melbournevirus, the first representative of the Marseilleviridae isolated from a freshwater pond in Melbourne, Australia. Despite the large distance separating this sampling point from France, Melbournevirus is remarkably similar to Cannes 8 virus and Marseillevirus, with most orthologous genes exhibiting more than 98% identical nucleotide sequences. We took advantage of this optimal evolutionary distance to evaluate the selection pressure, expressed as the ratio of nonsynonymous to synonymous mutations for various categories of genes. This ratio was found to be less than 1 for all of them, including those shared solely by the closest Melbournevirus and Cannes 8 virus isolates and absent from Lausannevirus. This suggests that most of the 403 protein-coding genes composing the large Melbournevirus genome are under negative/purifying selection and must thus significantly contribute to virus fitness. This conclusion contrasts with the more common view that many of the genes of the usually more diverse large DNA viruses might be (almost) dispensable. IMPORTANCE A pervasive view is that viruses are fast-evolving parasites and carry the smallest possible amount of genomic information required to highjack the host cell machinery and perform their replication. This notion, probably inherited from the study of RNA viruses, is being gradually undermined by the discovery of DNA viruses with increasingly large gene content. These viruses also encode a variety of DNA repair functions, presumably slowing down their evolution by preserving their genomes from random alterations. On the other hand, these viruses also encode a majority of proteins without cellular homologs, including many shared only between the closest members of the same family. One may thus question the actual contribution of these anonymous and/or quasi-orphan genes to virus fitness. Genomic comparisons of Marseilleviridae, including a new Marseillevirus isolated in Australia, demonstrate that most of their genes, irrespective of their functions and conservation across families, are evolving under negative selection.
Linear and angular head accelerations during heading of a soccer ball.

PURPOSE Cognitive deficits observed in professional soccer players may be related to heading of a soccer ball. To assess the severity of a single instance of heading a soccer ball, this study experimentally and theoretically evaluated the linear and angular accelerations experienced by the human head during a frontal heading maneuver. METHODS Accelerations were measured using a set of three triaxial accelerometers mounted to the head of each of four adult male subjects. These measurements (nine signals) were used to estimate the linear acceleration of the mass center and the angular acceleration of the head. Results were obtained for ball speeds of 9 and 12 m.s(-1) (approximately 20 and 26 mph). A simple mathematical model was derived for comparison. RESULTS At 9 m.s(-1), peak linear acceleration of the head was 158 +/- 19 m.s(-2) (mean +/- standard deviation) and peak angular acceleration was 1302 +/- 324 rad.s(-2); at 12 m.s(-1), the values were 199 +/- 27 m.s-2 and 1457 +/- 297 rad.s-2, respectively. The initial acceleration pulses lasted approximately 25 ms. Measured head accelerations confirmed laboratory headform measurements reported in the literature and fell within the ranges predicted by the theoretical model. CONCLUSIONS Linear and angular acceleration levels for a single heading maneuver were well below those thought to be associated with traumatic brain injury, as were computed values of the Gadd Severity Index and the Head Injury Criterion. However, the effect of repeated acceleration at this relatively low level is unknown.
Effects of Environmentally Relevant Mixtures of Persistent Organic Pollutants on the Developmental Neurobiology in Rats

We report the developmental neuropathology for rat pups at postnatal day (PND) 37 and PND 77 and the molecular biomarkers for PND 35, 75, and 350 after perinatal exposure to a reconstituted mixture of persistent organochlorine pollutants (POPs) based on the blood profiles of people living in the Great Lake Basin. The developmental neuropathology included routine histopathology evaluation, quantification of cell proliferation and death in the subventricular zone, linear morphometric measurements, and transcriptional analysis. No histopathological, structural, or stereological changes were observed in animals treated with the POPs or Aroclor 1254, on PND 37 or PND 77. While no transcriptional changes were found in Arcolor-treated animals, significant transcriptional changes were observed on PND 350 in female offspring perinatally exposed to 0.13 mg/kg of the POP mixture. Markers of the cholinergic system including acetylcholinesterase and the muscarinic receptors (subtypes M1–M5) were downregulated 2- to 6-fold. In addition, structural genes including neurofilaments (NFLs) and microtubule-associated protein (MAP-2) were downregulated at least 2-fold or greater. Our results support that in utero and lactational exposure to the chemical mixture of POPs lead to developmental changes in adult rat brains.
Neurobehavioural deficits after severe traumatic brain injury (TBI)

Objectives: Debilitating neurobehavioural sequalae often complicate traumatic brain injury (TBI). Cognitive deficits, particularly of attention, memory, information-processing speed and problems in self-perception, are very common following severe TBI. Method: The Neurobehavioural Rating Scale (NRS) is a multi-dimensional clinical-based assessment instrument designed and validated to measure neurobehavioural disturbances following TBI. This study examined 41 patients who were admitted to the intensive care unit of the Department of General Neurosurgery at Cologne University Hospital after severe TBI between January 1995 and July 2003. All 27 items of the NRS were assessed 6 and 12 months post-injury. Results: Subjects after severe TBI (GCS<9) showed relatively high overall scores on the NRS, reflecting a high degree of overall neurobehavioural dysfunction. NRS items did not change significantly between 6 and 12 months post-trauma for anxiety, expressive deficit, emotional withdrawal, depressive mood, hostility, suspiciousness, fatigability, hallucinatory behaviour, motor retardation, unusual thought content, liability of mood and comprehension deficit. There was a tendency of improvement for inattention, somatic concern, disorientation, guilt feelings, excitement, poor planning and articulation deficits. For conceptual disorganization, disinhibition, memory deficit, agitation, inaccurate self-appraisal, decreased initiative, blunted affect and tension even a tendency for further deterioration in the post-traumatic follow-up was detected. Changes between 6 and 12 months post-TBI were statistically significant for disorientation (improvement), inattention/reduced alertness (improvement) and excitement (deterioration). Conclusion: The data shows that neurobehavioural deficits after TBI do not show a general tendency to disappear over time. Some aspects related to self-appraisal, conceptual disorganization and affect may even deteriorate, thereby presenting a challenging problem for both the patients and relatives. This is in contrast to the parallel improvement of post-traumatic sensomotoric deficits.
Imaging of organ-confined prostate cancer: functional ultrasound, MRI and PET/computed tomography

Purpose of review To review the current status of advanced imaging techniques in identification of organ-confined prostate cancer with a focus on their impact on patient management. Recent findings Transrectal ultrasound suffers from poor accuracy despite significant technical improvements. Generally used to distinguish cancers with extraprostatic spread, MRI is now focusing on intraprostatic prostate cancer identification. At 1.5T, the most recent high-resolution pelvic phased-array coils provide excellent imaging of the whole gland, including this challenging anterior part. Improvements in accuracy for cancer detection and volume estimation result from dynamic contrast-enhanced and diffusion-weighted imaging sequences. Histological correlations showed high sensitivity/specificity for significant volume cancers. 3T MRI scanners will improve these results. Most of the recent PET/computed tomography imaging studies use choline derivatives (11C-choline and 18F-fluorocholine). Their results are promising but insufficient to be currently recommended in routine practice. Summary Considerable advances have been made in the identification of organ-confined prostate cancer with multiparametric MRI. Only prebiopsy MRI can provide best quality of cancer assessment and allows for targeting biopsies. It is hoped that advances in 3T MRI as well as in radiotracers for PET/computed tomography will further improve diagnosis, treatment selection, planning and outcomes.
Does precursor regulation make a difference?

Cunningham & Liu (2003) find that three different methamphetamine precursor regulations—imposed in 1989, 1995 and 1997—each led to sharp reductions in methamphetamine-related hospital admissions in three western US states; the failure of a fourth one comes as little surprise since it was not well targeted. This analysis is welcome both for its nature (enforcement programs are infrequently evaluated quantitatively) and findings (enforcement has a mixed track record in such evaluations). However, this interesting study raises two important questions that merit further exploration: (1) how can this time series analysis on one indictor be reconciled with other events and indicators? ; and (2) how large were the benefits of these interventions relative to their costs (assessed in comparable units)? As a prelude, let us first ask why precursor regulations should affect hospital admissions. Precursor control is a supply-side intervention that should drive up prices. As it becomes more difficult to find precursors, production costs rise until suppliers develop new sources (perhaps in other countries) or new technologies. Higher prices should lead to fewer persons using and/or lower quantities consumed per user. Cunningham & Liu (2003) analyse hospital admissions only and make no broader statement as to whether the regulations affected methamphetamine use. However, it is implicit that reductions in prevalence or total consumption are the source of the decline in admissions, since there is nothing about the regulations that would have reduced the harmfulness of each dose of methamphetamine—the other potential source of a decline in hospital admissions. Hence, one would expect to see comparable evidence in other, drug-use-related indicators
Composed adaptive control of a bio-diesel engine with EGR & VGT

In this paper, a Third-order dimensional nonlinear model is proposed for a bio-diesel engine equipped with a Variable Geometry Turbocharger (VGT) and an Exhaust Gas Recirculation (EGR) valve. The referred model which takes into account the engine air-path dynamics and its corresponding uncertain dynamics is a non-minimum phase unstable system. The fuel flow rate Wf which is considered as input for the engine crankshaft subsystem acts as an external perturbation for the three-order dimensional non-minimum phase air-path subsystem. The global control objectives are to track desired values of exhaust manifold pressure and compressor flow mass rate which can be suitably chosen according to low emission criterions. For the considered objectives a composed adaptive robust stabilization control is proposed: an inner uncertain dynamics compensation sub-control and an outer Piecewise Continuous Hybrid Systems (PCHS) based stabilization sub-control. The inner compensation sub-control considers a unknown input observer which realizes the compensation of the uncertain system dynamics. The outer loop concerns the PCHS based EGR & VGT control. With the inner compensation sub-control, this outer stabilization loop ensures both the desired exhaust manifold pressure and the desired compressor mass flow rate trajectory tracking. The robustness and efficiency of the proposed method are demonstrated by simulation results.
Dynamic Performance of Electrical Balance Duplexing in a Vehicular Scenario

Electrical balance duplexers (EBDs) can achieve high transmit-to-receive (Tx–Rx) isolation, but can be affected by interaction between the antenna and the environment. Circuit simulations incorporating measured time-variant antenna impedance data have been used to quantify performance variation and determine circuit adaptation requirements for EBDs operating in vehicular scenarios at 875 and 1900 MHz. Results show that the interaction between the antennas and the external environment is limited and vehicle motion does not necessitate high-speed EBD adaptation. However, the impedance of dashboard mounted antennas can vary due to interaction with the windscreen wipers, causing substantial variation in the Tx–Rx isolation and requiring EBD rebalancing intervals of 5 ms or less to maintain performance.
Nutrition of the snowshoe hare (Lepus americanus).

Protein and maintenance energy requirements of the adult snowshoe hare in May and June were examined using complete nitrogen and energy balances (respiration calorimetry) and a digestion trial. Isocaloric diets varying from 10 to 26% crude protein were used. Ad libitum dry matter intake of experimental diets was 6.4% of body weight. Metabolic fecal nitrogen was 0.6 g/100 g diet dry matter. Indirect evidence was found that digestible protein requirement of a 1.5-kg hare is 2.6 g/kg metabolic body weight (W0.75) or less. Daily intakes of digestible, metabolizable, and net energy necessary to maintain body energy equilibrium at 18 to 20C with minimal physical activity were determined to be 122, 116, and 91 kcal/kg W0.75, respectively. These data may serve as a first step in estimating maximum carrying capacity of hare habitat provided quantity and nutritive value of applicable natural foods are known.
MISO uniform theory of diffraction based channel model for mobile wireless communications in urban areas

In urban areas, wireless communications experience severe fading problems due to the signal reflections and diffractions on the building walls and edges and the mobility of receivers. Currently, most of the existing channel models can only characterize the signal propagation in fixed environments. Existing researches on the impact of the vehicles are all limited to experimental results. This paper will introduce a new channel model in urban areas. In this way, we consider multiple antennas at the transmitter and single antenna at the receiver; moreover, we use Uniform Theory of Diffraction (UTD) and Fresnel's reflection coefficients for modeling rays that impinge on buildings. Against prior models, this model calculates the channel capacity rigorously and does not use any random variables and distribution functions. Furthermore, the vehicle positions in the urban areas are modeled as random Process. Therefore, the proposed model can improve the theoretical approaches for forecasting more realistic MISO channel capacity in cellular mobile communications, where diffraction and reflection from a number of buildings and mobility of receivers have to be considered.
Morpholino phenocopies of endothelin 1 (sucker) and other anterior arch class mutations

The pharyngeal cartilages of zebrafish endothelin 1 (sucker or edn1) mutants are severely defective (Miller et al., 2000). Similar but milder defects are present in mutants for any of three other still molecularly unknown “anterior arch” class genes (Kimmel et al., 1998; Piotrowski et al., 1996). These milder phenotypes might be the result of partial loss of Endothelin 1 signaling, as we now examine directly by injecting a concentration series of endothelin1-morpholino oligonucleotides (edn1-MO) to gradually reduce edn1 function. We observe that high amounts (5–15 ng) phenocopy the facial and pharyngeal cartilage phenotypes of edn1 mutants, and lower amounts (0.5–1.5 ng) phenocopy the milder phenotypes of the other anterior arch class mutants (Table 1, Fig. 1a–f). edn1-MO-injected and mutant phenotypes strikingly correspond; for example, joints are more sensitive to slight reduction of edn1 function than ventral cartilage, as in the original mutant phenotypic series (Kimmel et al., 1998). We verified that the high level injections eliminated the same specific expression domains of the edn1 target genes dHAND and goosecoid as eliminated in edn1 mutants (Fig. 1g–l; see Miller et al., 2000). Hence our experiments show that edn1-MOs allow edn1 function to be reduced in a graded fashion, and provide strong support for the hypothesis that all of the anterior arch loci function in the edn1 pathway.