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PubMed2005

Clinical, pathological and immunohistochemical study of feline mammary fibroepithelial hyperplasia following a single injection of depot medroxyprogesterone acetate.

Feline mammary fibroepithelial hyperplasia (FMFH) following a single injection of depot medroxyprogesterone acetate (MPA) was observed in eight intact young queens. The repository compound is marketed as a veterinary product by a local pharmaceutical company with an indication for contraception in cats. The drug was administered according to the recommended doses and injection frequencies. Serum hormone assays performed immediately before neutering and 3 weeks after neutering detected persistently high levels of progesterone suggesting that depot MPA was still exerting its influence. No corpora lutea were found in those cases ruling out ovaries as the main site of progesterone. Immunohistochemistry performed on the hyperplastic mammary glands detected progesterone receptors in the nuclei of ductal cells, and growth hormone (GH) and insulin-like growth factor-I (IGF-I) in the cytoplasm of ductal epithelium. Overdosing should be considered here as the animals received at least 10 mg/kg of depot MPA in a single injection. Progestin-induced local synthesis of GH and IGF-I in mammary epithelial cells is suggested as one of the pathogenic mechanisms involved in the development of FMFH.

Animals↗

PubMed2006

Leaching of chromated copper arsenate (CCA)-treated wood in a simulated monofill and its potential impacts to landfill leachate.

The proper end-of-life management of chromated copper arsenate (CCA)-treated wood, which contains arsenic, copper, and chromium, is a concern to the solid waste management community. Landfills are often the final repository of this waste stream, and the impacts of CCA preservative metals on leachate quality are not well understood. Monofills are a type of landfill designed and operated to dispose a single waste type, such as ash, tires, mining waste, or wood. The feasibility of managing CCA-treated wood in monofills was examined using a simulated landfill (a leaching lysimeter) that contained a mix of new and weathered CCA-treated wood. The liquid to solid ratio (LS) reached in the experiment was 0.63:1. Arsenic, chromium, and copper leached from the lysimeter at average concentrations of 42 mg/L for arsenic, 9.4 mg/L for chromium, and 2.4 mg/L for copper. Complementary batch leaching studies using deionized water were performed on similar CCA-treated wood samples at LS of 5:1 and 10:1. When results from the lysimeter were compared to the batch test results, copper and chromium leachability appeared to be reduced in the lysimeter disposal environment. Of the three metals, arsenic leached to the greatest extent and was found to have the best correlation between the batch and the lysimeter experiments.

Arsenates↗

PubMed2006

Immobilization of cesium and strontium radionuclides in zeolite-cement blends.

Zeolites are preferred ion exchange materials for the removal of radioisotopes from aqueous nuclear wastes because of their selectivity, radiation and temperature stability, and good compatibility with the cement matrix. Loaded materials, which are not regenerated, are preferably embedded in a solid matrix prior to ultimate storage in a repository. The aim of the present study is to investigate the possibility of solidifying exhausted synthetic zeolite A, loaded with (137)Cs and/or (90)Sr radionuclides, in Ordinary Portland Cement (OPC). Several factors affecting the characteristics of the final solidified waste product towards safe disposal such as mechanical strength and leaching behavior of the radionuclides have been studied. A simplified mathematical model based on diffusion mechanism for cylindrical geometry waste matrix has been simulated to predict the release rates of the investigated radionuclides from cement matrix. The predicted values are discussed in relation to experimentally observed leach rates to confirm the proposed mechanism in the model. The obtained results showed that the presence of zeolite A in the final cemented wastes improve the mechanical characteristics of the solidified cement matrix (mechanical strength and setting times) towards the safety requirements and reduce considerably the radionuclides leach rates.

Cesium Radioisotopes↗

PubMed2006

Evaluation of engineering properties for the use of leached brown coal ash in soil covers.

The need to engineer cover systems for the successful rehabilitation or remediation of a wide variety of solid wastes is increasing. Some common applications include landfills, hazardous waste repositories, or mine tailings dams and waste rock/overburden dumps. The brown coal industry of the Latrobe Valley region of Victoria, Australia, produces significant quantities of coal ash and overburden annually. There are some site-specific acid mine drainage (AMD) issues associated with overburden material. This needs to be addressed both during the operational phase of a project and during rehabilitation. An innovative approach was taken to investigate the potential to use leached brown coal ash in engineered soil covers on this overburden dump. The basis for this is two-fold: first, the ash has favourable physical characteristics for use in cover systems (such as high storage capacity/porosity, moderately low permeability, and an ability to act as a capillary break layer generating minimal leachate or seepage); and second, the leachate from the ash is mildly alkaline (which can help to mitigate and reduce the risk of AMD). This paper will review the engineering issues involved in using leached brown coal ash in designing soil covers for potentially acid-forming overburden dumps. It presents the results of laboratory work investigating the technical feasibility of using leached brown coal ash in engineered solid waste cover systems.

Coal Mining↗

PubMed2006

Modeling the long-term leaching behavior of (137)Cs, (60)Co, and (152,154)Eu radionuclides from cement-clay matrices.

Leaching characteristics of some radionuclides that are commonly encountered in radioactive waste streams from immobilized waste matrices in different cement-clay grouts have been assessed to investigate the influence of the clay additives on the leaching behavior of the solid waste matrices. The International Atomic Energy's Agency (IAEA) standard leach method has been employed to study the leach pattern of (137)Cs, (60)Co, and (152,154)Eu radionuclides immobilized in ordinary Portland cement (OPC), OPC-bentonite, and OPC-red clay grouts. The examination of the leaching data revealed that adding clays to OPC reduces the leach pattern as OPC-bentonite<OPC-red clay<OPC for all studied radionuclides. The controlling leaching mechanism has been found to be diffusion and the mean apparent diffusion coefficients and leachability indices have been calculated for the studied waste matrices. Simplified analytical models have been derived to predict the cumulative leach fraction (CLF) of radionuclides over the studied experimental period. These simplified research models could be used as a screening tool to assess the performance of the waste matrix under repository conditions.

Aluminum Silicates↗

PubMed2025

ABCD-type phage cocktail targeting distinct LPS receptor sites demonstrates superior efficacy against multidrug-resistant Salmonella.

The narrow host range of phages poses a limitation in addressing multidrug-resistant bacteria, whereas phage cocktail therapy, targeting multiple bacterial receptors, broadens the phage host spectrum. This study establishes a comprehensive Salmonella phages repository through nationwide surveillance in China, isolating 242 phages classified into 29 genera, with genome sizes ranging from 5.4 to 350.3 Kb. Based on LPS specificity, phages were categorized into four types A-D. Here, we developed an ABCD-Type phage cocktail targeting four distinct LPS recognition sites, demonstrating superior efficacy versus single phages or phage cocktail with different receptors (CCR-Type). In vitro, ABCD-Type phage cocktail treatment sustained bactericidal activity > 36 h versus CCR's 8 h, effectively controlling Salmonella in lettuce, milk, and Galleria mellonella infection models. Moreover, ABCD-Type phage cocktail effectively cleared Salmonella biofilms and showed promising results in the treatment of animal infections, significantly reducing bacterial loads in infected chicks and improving their survival rates. Resistant mutants predominantly harbored mutations in the btuB gene and LPS biosynthesis genes. These mutants showed increased antibiotic sensitivity and attenuated virulence. Collectively, these findings underscore the therapeutic potential of Salmonella phages, specifically ABCD-Type phage cocktail formulations which contain the phages PJNS014, PJNS023, PJNS036, and PJNS038, for controlling Salmonella infections. This work provides a foundation for developing advanced phage-based therapeutics.

Salmonella Phages↗

PubMed2005

Molecular characterization of the circulating anti-HIV-1 gp120-specific B cell repertoire using antibody phage display libraries generated from pre-selected HIV-1 gp120 binding PBLs.

Human bone marrow is a major repository for maturated antibody-secreting plasma cells, which produce the majority of the antibodies found in serum, making it an attractive source for generating human immune antibody libraries. Unfortunately, bone marrow is not always readily available and, although human immune libraries can be generated from circulating B cells, the low frequency of antigen-specific B cells in the circulation yield few monoclonal antibodies of interest. We used a pre-selection strategy to enrich for antigen-specific B cells prior to library generation, and applied this approach to evaluate, at a molecular level, the nature of the human anti-HIV-1 gp120 repertoire encoded by circulating B cells. IgG antibody phage display libraries were generated from HIV-1 seropositive individuals using either affinity-selected anti-gp120 IgG-bearing circulating B cells, predominantly exhibiting memory/activated B cell phenotype, or unselected PBMCs. These libraries were selected against HIV-1 gp120, resulting in isolation of a panel of gp120-specific antibodies. Whereas only 2 gp120-specific antibodies were retrieved from the non-pre-selected HIV-1 library, 9 gp120-specific antibodies were retrieved from the 10-fold smaller library generated from the pre-selected B cells, demonstrating the feasibility of the approach. The anti-gp120 antibodies derived from the circulating B cells of HIV-1 donors generally resembles those from bone marrow plasma cells with respect to epitope specificity, affinity and neutralization ability. They exhibit high affinity for gp120, are directed against a variety of epitopes, but rarely exhibit the ability to neutralize HIV-1.

Amino Acid Sequence↗

PubMed2004

The Electronic Report on Adolescent Pregnancy (ERAP).

PURPOSE: To create a data management system that: (1) standardizes antecedent, program, and outcome variables relevant to the shared goals of adolescent-oriented maternity programs while allowing users to add variables pertaining to unique aspects of their work; (2) cues providers to physiologic and psychosocial characteristics that predispose teenagers to adverse pregnancy and parenting outcomes, (3) standardizes patient care by guiding providers through adolescent-oriented prenatal, postpartum, and well baby visits, and (4) establishes the infrastructure to collect data from a nationally representative sample of pregnant and parenting teens. METHOD: We adapted a powerful, state-of-the-art relational database framework (Microsoft Access 2000) to create an easy-to-use data management system-The Electronic Report on Adolescent Pregnancy (ERAP)-that requires minimal training to use on a personal computer. RESULTS: ERAP is designed to meet the administrative and analytic needs of adolescent-oriented maternity programs. It consists of six linked core data tables (teen, pregnancy, prenatal visits, child, interconception interval, and interconception interval visits), that allow users to analyze data from these multiple views while preserving the family structure. In addition, the database standardizes methods for collecting and storing the information and automatically computing the variables needed to monitor and evaluate an adolescent-oriented maternity program. Since by adding variables and appending supplementary tables, users can modify the core database to accommodate unique aspects of their programs and/or research, ERAP is also an ideal conduit for translating research findings into clinical practice. Similarly, because ERAP actually structures the care patients receive, the database provides the infrastructure needed to develop and implement best practice guidelines for treating teen-headed families. Finally, the confidentiality of all subject data is assured because ERAP is password-protected and automatically prepares files for batched external analyses by removing personal identifiers. CONCLUSIONS: ERAP provides the infrastructure needed to create a teen-pregnancy databank at the national level and an efficient patient monitoring system at the program level. By standardizing variable definitions and data collection techniques, serving as a repository for data collected at multiple sites, and tracking the multidisciplinary aspects of the care patients receive, ERAP has the potential to facilitate collaboration between adolescent-oriented maternity programs, increase the scientific rigor of teen pregnancy research, and improve the quality of care individual teen-headed families receive by prompting compliance with best practice guidelines.

Adolescent↗

PubMed2006

Ethical issues arising from the participation of children in genetic research.

With new tools derived from the Human Genome Project, genetic research is expanding from the study of rare, single gene disorders to the evaluation of genetic contributors to common, complex diseases. Many genetic studies include pediatric participants. The ethical concerns related to pediatric participation in genetic research derive from the study designs commonly employed in gene discovery and from the power accorded to genetic prediction in our society. In both family-based studies and large studies combining genetic and other health-related data, special attention should be placed on recruitment procedures, informed consent, and confidentiality protections. If data repositories are created for long-term use, we recommend re-consent of pediatric participants when they reach adulthood. In addition, the potential for disclosure of individual results should be considered as part of the institutional review of genetic studies, taking into account the validity of research data and the potential that such data could be used in health care. The potential for genetic results to pose harms of personal and group stigma is also a consideration. Because genetic information is often accorded special power in our society, careful attention should be paid to how genetic information is collected and used in research involving pediatric participants.

Child↗

PubMed2004

Effect of drought and rewatering on the metabolism of Lupinus albus organs.

Alterations in the metabolism of Lupinus albus organs that result from and subsequently follow a period of severe water deficit (WD) are described. By means of 13C-nuclear magnetic resonance (NMR), changes in the major metabolites were monitored in several plant organs (leaflets and petiole, roots, stem stele and cortex). During the stress, most of the leaves were lost and the stem functioned as a storage repository of sugars (glucose and sucrose) and amino acids (asparagine and proline). Upon rewatering, lupin plants rapidly re-established the relative water content (RWC) and produced new leaves. However, at the metabolic level, the events seem to be more complex, since proline (a stress related metabolite) disappeared rapidly while sugars and asparagine reached the initial pattern more slowly, particularly in the stem.

Asparagine↗

PubMed2005

Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology.

Three-dimensional electron microscopy (3DEM) has made significant contributions to structural biology. To accomplish this feat, many image-processing software packages were developed by various laboratories. The independent development of methods naturally implied the adoption of dissimilar conventions-penalizing users who want to take advantage of the wealth of algorithms from different packages. In addition, a public repository of 3DEM research results, the EM Data Bank, is now established. In an era where information exchange is important, standardizing conventions is a necessity. The 3DEM field requires a consistent set of conventions. We propose a set of common conventions named the "3DEM Image Conventions." They are designed as a standardized approach to image interpretation and presentation. In this regard, the conventions serve as a first step on which to build data-exchange solutions among existing software packages and as a vehicle for homogenous data representation in data archives, such as the EM Data Bank.

Algorithms↗

PubMed2025

Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study.

BACKGROUND: Rising antimicrobial resistance of Helicobacter pylori is a public health challenge. Genomic-based susceptibility testing allows for the identification of resistance-associated mutations, complementing conventional diagnostics and advancing towards pathogen-based personalised therapies. Our study aimed to identify genes and mutations involved in antimicrobial resistance in H pylori and evaluate the extent to which these markers can be used as predictors of phenotypic resistance against clarithromycin and levofloxacin. METHODS: In this retrospective phenotypic and genotypic observational study, we included 1011 H pylori whole-genome sequences and strains of known geographical origin from the H pylori Genome Project (HpGP) collection. We performed phenotypic clarithromycin and levofloxacin susceptibility testing on a subset of 419 HpGP strains using Etest at a centralised laboratory. A genomic analysis was conducted to identify 23S rRNA and gyrA variants and build a curated catalogue of mutations associated with resistance to clarithromycin (ie, 23S rRNA 2142A→G, 2142A→C, and 2143A→G) and levofloxacin (ie, gyrA A88V or A88P, N87K or N87I, and D91G, D91N, or D91Y). Genotype-phenotype concordance was assessed to estimate sensitivity and specificity, and the curated catalogue of resistance-associated mutations was applied to the complete HpGP set. Region-specific prevalence of resistance-associated mutations was calculated for a combined dataset including the HpGP genomes and 768 whole-genome sequences retrieved from the US National Center for Biotechnology Information Sequence Read Archive repository. Associations between resistance genotypes, H pylori subpopulations, and minimum inhibitory concentrations (MICs) were tested. FINDINGS: Clarithromycin-resistant and levofloxacin-resistant HpGP strains were estimated with a sensitivity and specificity of 100%, with all confidence intervals ranging from 96% to 100%. The combined analysis (n=1779) found the highest prevalence of clarithromycin resistance in the western Pacific region (173 [51·2%] of 338 in southeast Asia and 75 [29·8%] of 252 in eastern Asia), north African region (seven [38·9%] of 18), and western Asian region (12 [31·6%] of 38), whereas the highest prevalence of levofloxacin resistance was found in south Asia (14 [51·85%] of 27), Central America (48 [38·7%] of 124), eastern Europe (four [36·4%] of 11), and southern Africa (three [33·3%] of nine). Similarly, 23S rRNA and gyrA genotypes are variable across H pylori subpopulations. MIC values changed depending on the specific mutation in 23S rRNA (mean clarithromycin MIC 24·61 mg/L [95% CI 12·27-36·96] for 2143A→G and 142·25 mg/L [95% CI 77·88-206·61] for 2142A→G) and gyrA (mean levofloxacin MIC 9·66 mg/L [95% CI 6·75-12·56] for mutations on codon 91, and 27·97 mg/L [95% CI 25·82-30·11] for mutations on codon 87). INTERPRETATION: Mutations in specific genes are reliable indicators to clarithromycin and levofloxacin resistance in H pylori, making them useful markers for the development of diagnostic assays and molecular monitoring. Our results suggest that using clarithromycin and levofloxacin empirically, without previous susceptibility testing, is unsuitable in all geographical regions covered by this study. FUNDING: Intramural Research Program of the US National Cancer Institute, the European Research Council, and the Spanish Ministry of Science and Innovation.

Helicobacter pylori↗

PubMed2006

Bioaccumulation of heavy metals and radionuclides from seawater by encased embryos of the spotted dogfish Scyliorhinus canicula.

Encased embryos of spotted dogfish Scyliorhinus canicula absorbed six radio-isotopes (241Am, 109Cd, 57Co, 134Cs, 54Mn and 65Zn) directly from seawater during short-term experimental exposure, demonstrating the permeability of the egg-case to these contaminants. Embryo to water concentration factors (CFs) ranged from 0.14 for 134Cs to 7.4 for 65Zn. The 65Zn and 57Co CFs increased exponentially with embryo length, whereas the CF for 109Cd declined with length. Among different components of the encased embryo the egg case was the major repository (69-99%) of all six radio-isotopes that were distributed throughout its wall. Egg-case CFs were as high as 10(3) for 57Co and 65Zn, making it the major source of gamma radiation exposure to the embryo and potentially of radio-isotopes for continued absorption by the embryo, following the uptake phase of the experiment. The patterns of uptake by the egg-case approximated linearity for most isotopes and loss rates were isotope-specific; egg-case biokinetics were not greatly affected by the viability of the contained embryo. Within the embryo initial data on radio isotopic distribution show that the skin is their major site of uptake, as previously demonstrated for juveniles.

Animals↗

PubMed2006

Systematic tuning of parameters in support vector clustering.

Clustering algorithms divide a set of observations into groups so that members of the same group share common features. In most of the algorithms, tunable parameters are set arbitrarily or by trial and error, resulting in less than optimal clustering. This paper presents a global optimization strategy for the systematic and optimal selection of parameter values associated with a clustering method. In the process, a performance criterion for the optimization model is proposed and benchmarked against popular performance criteria from the literature (namely, the Silhouette coefficient, Dunn's index, and Davies-Bouldin index). The tuning strategy is illustrated using the support vector clustering (SVC) algorithm and simulated annealing. In order to reduce the computational burden, the paper also proposes an alternative to the adjacency matrix method (used for the assignment of cluster labels), namely the contour plotting approach. Datasets tested include the iris and the thyroid datasets from the UCI repository, as well as lymphoma and breast cancer data. The optimal tuning parameters are determined efficiently, while the contour plotting approach leads to significant reductions in computational effort (CPU time) especially for large datasets. The performance criteria comparisons indicate mixed results. Specifically, the Silhouette coefficient and the Davies-Bouldin index perform better, while the Dunn's index is worse on average than the proposed performance index.

Algorithms↗

PubMed2005

Current insights into the role of transforming growth factor-beta in bone resorption.

Transforming growth factor-beta (TGF-beta) elicits a variety of effects on cellular proliferation and differentiation. The major repository for TGF-beta is bone, where it possesses separate facilitative and suppressive actions on osteoclast differentiation and bone resorption. Without a direct enabling stimulus from TGF-beta monocytes cannot form osteoclasts but instead follow macrophage differentiation pathways. This facilitative action depends on an ability to promote a state in which precursors are resistant to anti-osteoclastic inflammatory signals. Following the initiation of resorption TGF-beta is released from bone matrix. This acts on osteoblasts to reduce the availability of the osteoclast differentiation factor, RANKL (receptor activator of NFkappaB ligand) and thereby indirectly limits further osteoclast formation. Thus TGF-beta has a fundamental role in the control of bone resorption having actions that first allow monocytes to develop into osteoclasts then subsequently limiting the extent and duration of resorption after its release from the bone matrix.

Animals↗

PubMed2004

Modulation of zinc toxicity by tissue plasminogen activator.

The tissue plasminogen activator (tPA)-plasmin proteolytic system mediates excitotoxin-induced neurodegeneration in vivo and in cell culture. tPA also confers neuroprotection from zinc toxicity in cell culture through a proteolysis-independent mechanism. This raises two questions: what is this non-enzymatic mechanism, and why tPA does not synergize with zinc to promote neuronal cell death? We show here that zinc binds to tPA and inhibits its activity in a dose-dependent fashion, thus terminating its protease-dependent neurotoxic capacity. We extend the previously reported culture findings to demonstrate that elevated zinc is neurotoxic in vivo, and even more so when tPA is absent. Thus, physiological levels of tPA confer protection from elevated free zinc. Mechanistically, tPA promotes movement of zinc into hippocampal neuron cells through voltage-sensitive Ca(2+) channels and Ca(2+)-permeable AMPA/KA channels. Therefore, zinc and tPA each appear to be able to limit the potential of the other to facilitate neurodegeneration, a reciprocal set of actions that may be critical in the hippocampus where tPA is secreted during the nonpathological conditions of learning and memory at sites known to be repositories of free and sequestered zinc.

Animals↗

PubMed2024

Multilevel Proteomics Reveals Epigenetic Signatures in BCG-Mediated Macrophage Activation.

The bacillus Calmette-Guérin BCG vaccine (Mycobacterium bovis) is primarily used to prevent tuberculosis (TB) infections but has wide-ranging immunogenic effects. One of its most notable properties is its ability to induce trained immunity, a memory-like response in innate immune cells such as macrophages. Through targeted analyses of well-established histone marks, prior research has shown that these changes are generated through epigenetic modification. Mass spectrometry-based proteomic approaches provide a way to globally profile various aspects of the proteome, providing data to further identify unexplored mechanisms of BCG-mediated immunomodulation. Here we use multi-level proteomics (total, histone, and phospho to identify networks and potential mechanisms that mediate BCG-induced immunomodulation in macrophages. Histone-focused proteomics and total proteomics were performed at the University of Cape Town (data available via ProteomeXchange with identifier PXD051187), while phosphoproteomics data was retrieved from the ProteomeXchange Repository (identifier PXD013171). We identify several epigenetic mechanisms that may drive BCG-induced training phenotypes. Evidence across the proteomics and histone-focused proteomics data set pair 6 epigenetic effectors (NuA4, NuRD, NSL, Sin3A, SIRT2, SIRT6) and their substrates.

Epigenesis, Genetic↗

PubMed2024

Proteomic Characterization of 1000 Human and Murine Neutrophils Freshly Isolated From Blood and Sites of Sterile Inflammation.

Neutrophils are indispensable for defense against pathogens. Injured tissue-infiltrated neutrophils can establish a niche of chronic inflammation and promote degeneration. Studies investigated transcriptome of single-infiltrated neutrophils which could misinterpret molecular states of these post mitotic cells. However, neutrophil proteome characterization has been challenging due to low harvests from affected tissues. Here, we present a workflow to obtain proteome of 1000 murine and human tissue-infiltrated neutrophils. We generated spectral libraries containing ∼6200 mouse and ∼5300 human proteins from circulating neutrophils. 4800 mouse and 3400 human proteins were recovered from 1000 cells with 102-108 copies/cell. Neutrophils from stroke-affected mouse brains adapted to the glucose-deprived environment with increased mitochondrial activity and ROS-production, while cells invading inflamed human oral cavities increased phagocytosis and granule release. We provide an extensive protein repository for resting human and mouse neutrophils, identify proteins lost in low input samples, thus enabling the proteomic characterization of limited tissue-infiltrated neutrophils.

Proteomics↗