Miracle-dz/UniFAR-FTUs huggingface dataset:
International Journal for Parasitology 18 "0888# 220ð228

A nested PCR for the ssrRNA gene detects Trypanosoma binneyi in the platypus and Trypanosoma sp[ in wombats and kangaroos in Australia Abstract Trypanosome infections in their natural hosts are frequently di.cult to detect by microscopy\ and culture methods are unreliable and not suitable for all species of Trypanosoma[ A nested PCR strategy for detecting and identifying Trypanosoma species\ suitable for detecting both known and unknown trypanosomes\ is presented[ Thirty! two blood samples from 12 species of Australian birds and mammals were screened by a nested PCR for the presence of Trypanosoma sp[ ssrRNA[ Three infections were detected\ one in an eastern grey kangaroo "Macropus giganteus#\ one in a common wombat "Vombatus ursinus# and one in a platypus "Ornithorhynchus anatinus#[ The kangaroo and wombat are new host records for Trypanosoma sp[^ the platypus parasite was Trypanosoma binneyi[ The three parasites could be distinguished by restriction fragment length polymorphisms of the ampli_ed fragment of the ssrRNA gene[ The kangaroo and wombat parasites were also isolated in a semi! solid blood agar medium[ The culture forms of the kangaroo trypanosome had an expanded ~agellar sheath in which structures similar to hemidesmosomes were detected by EM[ The nested PCR was at least as sensitive as culture\ and analysis of the PCR products gave parasite! speci_c _ngerprints[ Therefore this method could be suitable for rapidly screening host animals for the presence of trypanosomes and identifying the infecting strain[ Þ 0888 Australian Society for Parasitology[ Published by Elsevier Science Ltd[ All rights reserved[ Keywords] Macropus giganteus^ Ornithorhynchus anatinus^ Ortholfersia macleayi^ Trypanosoma binneyi^ Trypanosoma cruzi^ Vombatus ursinus^ Guanidine thiocyanate
Depression Viewed as a GABA/Glutamate Imbalance in the Central Nervous System

Despite of the last few decades of investigations concerning the pathophysiology of affective disorders and their efficient treatment, the number of patients suffering from the diseases is growing every year. Compared to the data from the 1950s the percentage of people diagnosed with monopolar depression increased by nearly 7 times, and now it is estimated that more than 15% of the population suffers from the illness (Healy, 1999). Depressive episodes deeply influence the familiar and professional life of the patients, thus become both a clinical and social problem. The costs connected with the treatment are not only due to medical care, but also involve indirect wastes related to long-term disturbances in normal functioning. Statistical analysis reveal that depressive episodes became the most costly group of central nervous system (CNS) disorders in Europe and in the USA (in the recent decade they reached about 105 billion Euro and 83 Billion USD, respectively) (Andlin-Sobocki et al., 2005; Greenberg et al., 2003). Moreover, the problem of depression and mood disorders is hard to overestimate as only 1 out of 4 cases is either recognized or adequately treated, and approx. 15% of depressed people commit suicide (Brody et al., 1998).
Protein Secretion Systems in Pseudomonas aeruginosa: An Essay on Diversity, Evolution, and Function

Protein secretion systems are molecular nanomachines used by Gram-negative bacteria to thrive within their environment. They are used to release enzymes that hydrolyze complex carbon sources into usable compounds, or to release proteins that capture essential ions such as iron. They are also used to colonize and survive within eukaryotic hosts, causing acute or chronic infections, subverting the host cell response and escaping the immune system. In this article, the opportunistic human pathogen Pseudomonas aeruginosa is used as a model to review the diversity of secretion systems that bacteria have evolved to achieve these goals. This diversity may result from a progressive transformation of cell envelope complexes that initially may not have been dedicated to secretion. The striking similarities between secretion systems and type IV pili, flagella, bacteriophage tail, or efflux pumps is a nice illustration of this evolution. Differences are also needed since various secretion configurations call for diversity. For example, some proteins are released in the extracellular medium while others are directly injected into the cytosol of eukaryotic cells. Some proteins are folded before being released and transit into the periplasm. Other proteins cross the whole cell envelope at once in an unfolded state. However, the secretion system requires conserved basic elements or features. For example, there is a need for an energy source or for an outer membrane channel. The structure of this review is thus quite unconventional. Instead of listing secretion types one after each other, it presents a melting pot of concepts indicating that secretion types are in constant evolution and use basic principles. In other words, emergence of new secretion systems could be predicted the way Mendeleïev had anticipated characteristics of yet unknown elements.
Abdominal Aortic Aneurysms, Increasing Infrarenal Aortic Diameter, and Risk of Total Mortality and Incident Cardiovascular Disease Events: 10-Year Follow-Up Data From the Cardiovascular Health Study

Background— Long-term data describing small abdominal aortic aneurysms (AAAs) and increasing infrarenal aortic diameters and their relationship to future surgical repair, total mortality, and incident cardiovascular disease (CVD) events, particularly among women, are sparse. Methods and Results— In 1992 to 1993, 4734 Cardiovascular Health Study participants ≥65 years old had an abdominal aortic ultrasound evaluation. Of those screened, 416 had an AAA (infrarenal aortic diameter ≥3.0 cm or an infrarenal/suprarenal ratio ≥1.2). By 2002, there were 56 surgical AAA repairs and 10 AAA-related deaths. A single ultrasound screening demonstrated that aneurysm dilation ≥3 cm identified 68% of all AAA repairs over the next 10 years and 6 of the 10 AAA-related deaths in 4% of the total population and that a ≥2.5-cm dilation identified 91% of all AAA repairs and 9 of the 10 deaths in 10% of the total population. With adjusted Cox proportional hazard models, AAAs were associated with a higher risk of total mortality (hazard ratio 1.44, 95% confidence interval 1.25 to 1.66) and incident CVD events (hazard ratio 1.52, 95% confidence interval 1.25 to 1.85). Compared with diameters <2.0 cm, infrarenal aortic diameters 2.0 to <3.0 cm were associated with increased risk of incident CVD events in women and total mortality in men. Conclusions— This study suggests that a 1-time screening of the abdominal aorta can acceptably identify individuals with a clinically significant AAA. Infrarenal aortic diameters >2.0 cm are associated with a significantly increased risk of future CVD events and total mortality.
Repeated testing of prepulse inhibition and habituation of the startle reflex: a study in healthy human controls

The aim of this study was to examine the effect of repeated testing on prepulse inhibition (PPI) and habituation of the startle reflex. Fifteen healthy control subjects (eight males, mean age 30 years; seven females, mean age 29 years) were tested on three occasions across the same day separated by a minimum of 2 h. An acoustic probe of 40-msec bursts of 116 dB(A) white noise over a continuous background noise of 70 dB(A) was presented binaurally through headphones and the eye-blink component of the startle response was measured taking electromyographic recordings from the right orbicularis oculi. The test session was identical at each time point and consisted of two blocks of 12 randomly mixed trials of four pulse-alone, four 60-msec prepulse and four 120-msec prepulse trials enclosed by two blocks each of six pulse-alone trials. There was huge variation in individual response magnitude that was independent of subsequent PPI in both women and men. Women showed greater PPI in the second half of sessions with the 120-msec prepulse only; but PPI was not altered significantly in either group between sessions across the day. In general, there was good test-retest reliability of PPI especially within trial type. Normal reflex habituation occurred across sessions and this effect was preserved in sessions across the day. Latency of response was significantly reduced in a session by the 60-msec trial type compared to the 120-msec trial type, as previously reported. Our results suggest that measures of PPI and habituation of the startle response are appropriate and reliable for a within-subject, test-retest design.
Compact 3-D Slot-Loaded Folded Dipole Antenna With Unidirectional Radiation and Low Impulse Distortion for Head Imaging Applications

A compact 3-D antenna for microwave-based head imaging systems is presented. The antenna, which is fed by a coplanar waveguide, consists of a slot-loaded folded dipole structure with four furled sides. Because of the presence of stronger currents on the top layer and reflections from the slightly extended bottom layer, the antenna exhibits directional radiation in the frequency domain in both near and far fields. The transient response of the antenna is also analyzed. Despite the existence of multiple slot loading and folding in the proposed antenna, the investigation of the time domain responses reveals a directional low-distorted radiation (impulse fidelity factor of more than 80%) toward the boresight direction in both near and far fields. The antenna has the compact size and low profile, with respect to the lowest operating wavelength, of 0.29 × 0.08, and 0.04, respectively, and 67% fractional bandwidth over 1.1-2.2 GHz. Since the antenna is designed to operate within an array for head imaging, a 16-element array of the antenna is tested in a realistic simulation environment to confirm a safe radiation exposure level. Finally, the array is employed on a realistic human head model to successfully detect and locate a hemorrhagic brain injury.
Negative Tree Reweighted Belief Propagation

We introduce a new class of lower bounds on the log partition function of a Markov random field which makes use of a reversed Jensen's inequality. In particular, our method approximates the intractable distribution using a linear combination of spanning trees with negative weights. This technique is a lower-bound counterpart to the tree-reweighted belief propagation algorithm, which uses a convex combination of spanning trees with positive weights to provide corresponding upper bounds. We develop algorithms to optimize and tighten the lower bounds over the non-convex set of valid parameter values. Our algorithm generalizes mean field approaches (including naive and structured mean field approximations), which it includes as a limiting case.
The Use of SNP Markers for Linkage Mapping in Diploid and Tetraploid Peanuts

Single nucleotide polymorphic markers (SNPs) are attractive for use in genetic mapping and marker-assisted breeding because they can be scored in parallel assays at favorable costs. However, scoring SNP markers in polyploid plants like the peanut is problematic because of interfering signal generated from the DNA bases that are homeologous to those being assayed. The present study used a previously constructed 1536 GoldenGate SNP assay developed using SNPs identified between two A. duranensis accessions. In this study, the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis × A. stenosperma) and one tetraploid [A. hypogaea cv. Runner IAC 886 × synthetic tetraploid (A. ipaënsis × A. duranensis)4×]. The scoring was performed using the software GenomeStudio version 2011.1. For the diploid, polymorphic markers provided excellent genotyping scores with default software parameters. In the tetraploid, as expected, most of the polymorphic markers provided signal intensity plots that were distorted compared to diploid patterns and that were incorrectly scored using default parameters. However, these scorings were easily corrected using the GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, approximately 10% showed no distortion at all behaving as expected for single-dose markers, and another 30% showed low distortion and could be considered high-quality. The genotyped markers were incorporated into diploid and tetraploid genetic maps of Arachis and, in the latter case, were located almost entirely on A genome linkage groups.
Racism and resilience in Australian Aboriginal graduates' experiences of higher education

The Indigenous populace in Australia is vastly underrepresented in higher education, and many students leave before receiving their award (Bradley, Noonan, Nugent, & Scales, 2009). There is a need to understand the difficulties faced by Indigenous students and the factors that aid their participation. This study examined two case studies of Indigenous graduates’ resilience through an interpretative phenomenological lens. Data from in-depth interviews illuminated challenges faced by Indigenous students, discussed in terms of context-specific understanding of resilience and implications for Universities, generating of an inclusive community environment, assessing the relevancy of offered courses and increasing flexibility of higher education for Indigenous students.
Blame and family conflict: symptomatic children as scapegoats

The study’s aim was to examine the relation between children’s symptom type, specifically externalized vs. internalized symptoms, and children’s perception of being blamed by family members for various family conflicts. The research hypothesis was based on theories of family therapy, in particular on the concept of scapegoating and projective identification processes. The subjects were chosen from treatment centres for children and adolescents, using the Achenbach Self-Report Questionnaire. Subjects included males and females, aged 10–17, who had either internalized or externalized symptoms and no history of organic or psychotic disorders. The control group consisted of non-symptomatic children. The research groups also included each child’s sibling closest in chronological age, who served as an additional control group. A total of 161 children participated in the study. It was found that externalizing children reported greater subjection to parental blame than did the other children.
Antialiasing of curves by discrete pre-filtering

Pre-filtering is generally considered the ideal approach to antialiasing but is difficult to perform exactly for complex geometries such as curves or for arbitrary choice of filters. We present a discrete pre-filtering technique for anti-aliasing Bezier curves using arbitrary filters which is numerically and geometrically robust and whose accuracy is controllable. CR
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases

Motivation DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web (SW). Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected Linked Open Data (LOD). Availability http://rdf.disgenet.org/ Contact support@disgenet.org
Cosmic reionization constraints on the nature of cosmological perturbations

We study the reionization history of the Universe in cosmological models with non-Gaussian density fluctuations, taking them to have a renormalized Χ 2 probability distribution function parametrized by the number of degrees of freedom, v. We compute the ionization history using a simple semi-analytical model, considering various possibilities for the astrophysics of reionization. In all our models we require that reionization is completed prior to z = 6, as required by the measurement of the Gunn-Peterson optical depth from the spectra of high-redshift quasars. We confirm previous results demonstrating that such a non-Gaussian distribution leads to a slower reionization as compared to the Gaussian case. We further show that the recent WMAP three-year measurement of the optical depth due to electron scattering, τ = 0.09 ± 0.03, weakly constrains the allowed deviations from Gaussianity on the small scales relevant to reionization if a constant spectral index is assumed. We also confirm the need for a significant suppression of star formation in minihaloes, which increases dramatically as we decrease v.
A Dirichlet process characterization of a class of reflected diffusions

For a class of stochastic differential equations with reflection for which a certain L p continuity condition holds with p > 1, it is shown that any weak solution that is a strong Markov process can be decomposed into the sum of a local martingale and a continuous, adapted process of zero p-variation. When p = 2, this implies that the reflected diffusion is a Dirichlet process. Two examples are provided to motivate such a characterization. The first example is a class of multidimensional reflected diffusions in polyhedral conical domains that arise as approximations of certain stochastic networks, and the second example is a family of two-dimensional reflected diffusions in curved domains. In both cases, the reflected diffusions are shown to be Dirichlet processes, but not semimartingales.
DNA methylation profiling reveals a predominant immune component in breast cancers

Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimizing treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease are still poorly understood. By means of DNA methylation profiling of 248 breast tissues, we have highlighted the existence of previously unrecognized breast cancer groups that go beyond the currently known ‘expression subtypes’. Interestingly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment, and in particular a T lymphocyte infiltration of the tumours. Further, we highlighted a set of immune genes having high prognostic value in specific tumour categories. The immune component uncovered here by DNA methylation profiles provides a new perspective for the importance of the microenvironment in breast cancer, holding implications for better management of breast cancer patients.
A double‐blind comparison of zimelidine and desipramine in endogenous depression

ABSTRACT– Zimelidine, a specific 5HT uptake inhibitor (final dose 225 mg), and desipramine, mainly a noradrenaline uptake inhibitor (final dose 150 mg), were given in random order to 24 in‐ and out‐patients fulfilling the Research Diagnostic Criteria for Major Depressive Disorder, definite or probable endogenous type, for a 3‐week treatment period. Nonresponders were crossed over to the other drug for another 3 weeks. There was a nonsignificant trend towards more overall improvement on desipramine. Some patients in both groups showed very little change during 3 weeks, indicating a bimodal distribution of response to either drug. Several nonresponders improved markedly upon direct crossing over to the other drug. There were few and mild side effects on both drugs, with no significant difference between them. No significant correlation was found between improvement and plasma concentrations of zimelidine, norzimelidine, or desipramine, whereas a significant positive correlation was found between improvement and platelet serotonin uptake inhibition (measured in fresh platelets incubated in diluted plasma from the patients) in zimelidine‐treated patients.
New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.
The Epstein-Barr Virus Protein Kinase BGLF4 and the Exonuclease BGLF5 Have Opposite Effects on the Regulation of Viral Protein Production

ABSTRACT The Epstein-Barr virus BGLF4 and BGLF5 genes encode a protein kinase and an alkaline exonuclease, respectively. Both proteins were previously found to regulate multiple steps of virus replication, including lytic DNA replication and primary egress. However, while inactivation of BGLF4 led to the downregulation of several viral proteins, the absence of BGLF5 had the opposite effect. Using recombinant viruses that lack both viral enzymes, we confirm and extend these initial observations, e.g., by showing that both BGLF4 and BGLF5 are required for proper phosphorylation of the DNA polymerase processivity factor BMRF1. We further found that neither BGLF4 nor BGLF5 is required for baseline viral protein production. Complementation with BGLF5 downregulated mRNA levels and translation of numerous viral genes, though to various degrees, whereas BGLF4 had the opposite effect. BGLF4 and BGLF5 influences on viral expression were most pronounced for BFRF1 and BFLF2, two proteins essential for nuclear egress. For most viral genes studied, cotransfection of BGLF4 and BGLF5 had only a marginal influence on their expression patterns, showing that BGLF4 antagonizes BGLF5-mediated viral gene shutoff. To be able to exert its functions on viral gene expression, BGLF4 must be able to escape BGLF5's shutoff activities. Indeed, we found that BGLF5 stimulated the BGLF4 gene's transcription through an as yet uncharacterized molecular mechanism. The BGLF4/BGLF5 enzyme pair builds a regulatory loop that allows fine-tuning of virus protein production, which is required for efficient viral replication.
A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.