Manipulating magnetic and magnetoresistive properties by oxygen vacancy complexes in GCMO thin films.

The effect ofin situannealing is investigated in Gd0.1Ca0.9MnO3(GCMO) thin films in oxygen and vacuum atmospheres. We show that the reduction of oxygen content in GCMO lattice by vacuum annealing induced more oxygen complex vacancies in both subsurface and interface regions and larger grain domains when compared with the pristine one. Consequently, the double exchange interaction is suppressed and the metallic-ferromagnetic state below Curie temperature turned into spin-glass insulating state. In contrast, the magnetic and resistivity measurements show that the oxygen treatment increases ferromagnetic phase volume, resulting in greater magnetization (MS) and improved magnetoresistivity properties below Curie temperature by improving the double exchange interaction. The threshold field to observe the training effect is decreased in oxygen treated film. In addition, the positron annihilation spectroscopy analysis exhibits fewer open volume defects in the subsurface region for oxygen treated film when compared with the pristine sample. These results unambiguously demonstrate that the oxygen treated film with significant spin memory and greater magnetoresistance can be a potential candidate for the future memristor applications.

Tuned AFM-FM coupling by the formation of vacancy complex in Gd0.6Ca0.4MnO3thin film lattice.

The effect ofin situoxygen and vacuum annealings on the low bandwidth manganite Gd1-xCaxMnO3(GCMO) thin film withx= 0.4 was investigated. Based on the magnetic measurements, the AFM-FM coupling is suppressed by the vacuum annealing treatment via destroying the double exchange interaction and increasing the unit cell volume by converting the Mn4+to the Mn3+. Consequently, resistance increases significantly compared to pristine film. The results are explained by a model obtained from the positron annihilation studies, where the vacuum annealing increased the annihilation lifetime in A and B sites due to the formation of vacancy complexesVA,B-VO, which was not the case in the pristine sample. The positron annihilation analysis indicated that most of the open volume defects have been detected in the interface region rather than on the subsurface layer and this result is confirmed by detailed x-ray reflection analysis. On the other hand, the effect of oxygen annealing on the unit cell volume and magnetization was insignificant. This is in agreement with positron annihilation results which demonstrated that the introduction of oxygen does not change the number of cation vacancies significantly. This work demonstrates that the modification of oxygen vacancies and vacancy complexes can tune magnetic and electronic structure of the epitaxial thin films to provide new functionalities in future applications.

Metastable ferromagnetic flux closure-type domains in strain relaxed Gd0.1Ca0.9MnO3thin films.

We have systematically studied the structural, electrical transport, and magnetic properties of Gd0.1Ca0.9MnO3thin films in function of thickness, which ranged from 22 nm up to 220 nm. We have found that, although no strong substrate-induced strain was detected for any thickness, a sudden change in the electric transport properties was observed when the film thickness increases above 80 nm. While thinner samples are insulating in the whole temperature range, the samples thicker than 80 nm show a clear insulator-to-metal transition (IMT) at around 100 K. The IMT coincides with the appearance of a ferromagnetic phase that is absent in the thinner samples. We associate this change in behavior with a critical film thickness that induces a sudden change in domain configuration, from in-plane domain to a closed flux-type domain with out-of-plane orientations. These out-of-plane oriented domains are meta-stable ferromagnetic in nature and result in an IMT which is accompanied by a hysteretic magnetoresistance behavior.

Does mpMRI improve clinical criteria in selecting men with prostate cancer for active surveillance?

BACKGROUND: Active surveillance (AS) has excellent short to medium term outcomes in well-selected prostate cancer patients. Traditional biopsy-based selection criteria have been criticized for inaccurate determination of cancer grade and extent. We evaluated the incremental benefit of multiparametric magnetic resonance imaging (mpMRI) in patient selection using various AS criteria. METHODS: We retrospectively evaluated men who received mpMRI before radical prostatectomy between 2011 and 2014. Patients were classified as suitable for AS using four criteria: (1) Epstein, (2) National Comprehensive Cancer Network (NCCN) low-risk or (3) extended criteria (Gleason ⩽3+4, PSA ⩽15 ng/ml, clinical stage ⩽T2b) using clinical parameters. The incremental value of mpMRI was evaluated against the referent standard of surgical pathology in determining suitability for AS using sensitivity, specificity, likelihood ratios (LRs) and area under receiver operating curves (AUCs). RESULTS: We evaluated 208 men. Only one man fulfilled Epstein criteria (1) at pathology, who was neither identified using clinical criteria nor mpMRI. Using (2), clinical criteria had a sensitivity of 80%, specificity 75%, LR+ 3.3, LR- 0.3, AUC 0.78, while combined clinical-mpMRI criteria achieved a sensitivity of 80%, specificity 99.5% (P<0.01), LR+ 162, LR- 0.2 and AUC 0.90 (P<0.01 compared to clinical). Using (3), clinical criteria had a sensitivity of 74%, specificity 47%, LR+ 1.4, LR- 0.6, AUC 0.60, while combined clinical-mpMRI criteria achieved a sensitivity of 26% (P<0.01), specificity 97% (P<0.01), LR+ 8.3, LR- 0.8 and AUC 0.62 (P=0.85). CONCLUSIONS: Addition of mpMRI significantly improved selection of men for AS using NCCN low-risk criteria. For selecting men with limited prognostic grade group 2, mpMRI significantly improved specificity at the expense of sensitivity.

Integrating cereal genomics to support innovation in the Triticeae.

The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.

Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.

Analysis of plant diversity with retrotransposon-based molecular markers.

Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.

Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers.

The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied for the first time within the genus Helianthus to assess intraspecific variability based on retrotransposon sequences among 36 wild accessions and 26 cultivars of Helianthus annuus L., and interspecific variability among 39 species of Helianthus. Two groups of LTRs, one belonging to a Copia-like retroelement and the other to a putative retrotransposon of unknown nature (SURE) have been isolated, sequenced and primers were designed to obtain IRAP fingerprints. The number of polymorphic bands in H. annuus wild accessions is as high as in Helianthus species. If we assume that a polymorphic band can be related to a retrotransposon insertion, this result suggests that retrotransposon activity continued after Helianthus speciation. Calculation of similarity indices from binary matrices (Shannon's and Jaccard's indices) show that variability is reduced among domesticated H. annuus. On the contrary, similarity indices among Helianthus species were as large as those observed among wild H. annuus accessions, probably related to their scattered geographic distribution. Principal component analysis of IRAP fingerprints allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned.

Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome.

LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.

Mapping of major spot-type and net-type net-blotch resistance genes in the Ethiopian barley line CI 9819.

Net blotch of barley (Hordeum vulgare L.), caused by the fungal phytopathogen Pyrenophora teres Drechs. f. teres Smedeg., constitutes one of the most serious constraints to barley production worldwide. Two forms of the disease, the net form, caused by P. teres f. teres, and the spot form, caused by P. teres f. maculata, are differentiated by the type of symptoms on leaves. Several barley lines with major gene resistance to net blotch have been identified. Earlier, one of these was mapped in the Rolfi x CI 9819 cross to barley chromosome 6H, using a mixture of 4 Finnish isolates of P. teres f. teres. In this study, we used the same barley progeny to map resistance to 4 spot-type isolates and 4 net-type isolates of P. teres. With all net-type isolates, a major resistance gene was located on chromosome 6H, in the same position as described previously, explaining up to 88% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt5. Several minor resistance genes were located on chromosomes 1H, 2H, 3H, 5H, and 7H. These minor genes were not genuinely isolate-specific, but their effect varied among isolates and experiments. When the spot-type isolates were used for infection, a major isolate-specific resistance gene was located on chromosome 5H, close to microsatellite marker HVLEU, explaining up to 84% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt6. No minor gene effects were detected in spot-type isolates. The Ethiopian 2-rowed barley line CI 9819 thus carries at least 2 independent major genes for net-blotch resistance: Rpt5, active against net-type isolates; and Rpt6, active against specific spot-type isolates.

A movable feast: diverse retrotransposons and their contribution to barley genome dynamics.

Cellular genes comprise at most 5% of the barley genome; the rest is occupied primarily by retrotransposons. Retrotransposons move intracellularly by a replicative mechanism similar to that of retroviruses. We describe the major classes of retrotransposons in barley, including the two nonautonomous groups that were recently identified, and detail the evidence supporting our current understanding of their life cycle. Data from analyses of long contiguous segments of the barley genome, as well as surveys of the prevalence of full-length retrotransposons and their solo LTR derivatives in the genus Hordeum, indicate that integration and recombinational loss of retrotransposons are major factors shaping the genome. The sequence conservation and integrative capacity of barley retrotransposons have made them excellent sources for development of molecular marker systems.

Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.

The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

Sebaceous adenocarcinoma of the external auditory canal in a New Zealand white rabbit.

A rare sebaceous gland carcinoma of the external auditory canal in a rabbit is described. The tumour was characterized histologically by foci and cords of markedly pleomorphic cells with abundant cytoplasm and variable numbers of vacuoles. A single pulmonary mass had similar histological characteristics. This is the first such tumour reported in a rabbit.

Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants.

Retrotransposons and retroviruses share similar intracellular life cycles and major encoded proteins, but retrotransposons lack the envelope (env) critical for infectivity. Retrotransposons are ubiquitous and abundant in plants and active retroviruses are known in animals. Although a few env-containing retroelements, gypsy-like Athila, Cyclops, and Calypso and copia-like SIRE-1, have been identified in plants, the general presence and functionality of the domain remains unclear. We show here that env-class elements are present throughout the flowering plants and are widely transcribed. Within the grasses, we show the transcription of the env domain itself for Bagy-2 and related retrotransposons, all members of the Athila group. Furthermore, Bagy-2 transcripts undergo splicing to generate a subgenomic env product as do those of retroviruses. Transcription and the polymorphism of their insertion sites in closely related barley cultivars suggests that at least some are propagationally active. The putative ENV polypeptides of Bagy-2 and rice Rigy-2 contain predicted leucine zipper and transmembrane domains typical of retroviral ENVs. These findings raise the prospect of active retroviral agents among the plants.

Surgical infection and the aging population.

With the general aging of the United States population we can expect to encounter increasing numbers of elderly patients with surgical infections. To further delineate this population, patient attributes, treatment characteristics, and outcomes were examined in elderly patients with surgical infection. All infections from December 1996 through May 2000 occurring on the inpatient, adult general, and trauma surgical services at a university hospital were studied prospectively. Characteristics, comorbidities, and outcomes were examined in patients > or = 70 years of age and compared with those of patients <70 years of age. Elderly patients had significantly higher Acute Physiology and Chronic Health Evaluation (APACHE) II scores (15.4 +/- 0.3 vs 11.2 +/- 0.2, P < 0.001) and greater numbers of comorbidities than the younger population. The Acute Physiology score; infecting organisms; and rates of pneumonia and intra-abdominal, central line, and bloodstream infection were similar between groups. Crude mortality (21.7% vs 8.1%, P < 0.001) and mortality associated with pneumonia (31.0% vs 17.2%, P = 0.005), central venous catheter infection (50.0% vs 17.4%, P < 0.001), bloodstream infection (32.3% vs 16.6%, P = 0.006), and intra-abdominal infection (23.2% vs 6.3%, P < 0.001) were significantly higher in the elderly. Logistic regression analysis identified APACHE II score, cerebrovascular disease, and fungal infection as independent predictors of mortality in the elderly population. Surgical infection in the elderly is associated with a high mortality and requires special consideration when treating this unique population.

The "July phenomenon" and the care of the severely injured patient: fact or fiction?

BACKGROUND: The "July phenomenon," a common belief in medical academia, refers to purported errors, inefficiency, and negative outcomes during the summertime transition of the house staff. We hypothesized that care in a trauma service is consistent throughout the year and that the July phenomenon therefore is a myth. METHODS: The records of adults admitted to a trauma service between July 1994 and September 1999 were evaluated. The care of and outcomes for patients admitted in July and August were compared with those of patients admitted in April and May. RESULTS: Nine hundred seventeen patients were evaluated over 5 years. Patients were well matched by the Injury Severity Score, the Glasgow Coma Score, by mechanism, and by survival probability. Patients admitted in the spring were significantly older, by a mean of 5.1 years. Length of stay and intensive care unit stay were similar. Emergency department times were similar, as were resuscitation times, infection rates, and hospital costs. The mortality of patients was similar between the 2 times. CONCLUSIONS: There was no evidence of an increase in negative outcomes early in the academic year compared with the end of the academic year. We believe that a systematic approach to the diagnosis, resuscitation, and treatment of trauma prevented a July phenomenon.

Active retrotransposons are a common feature of grass genomes.

A large fraction of the genomes of grasses, members of the family Graminae, is composed of retrotransposons. These elements resemble animal retroviruses in their structure and possess a life cycle similar to theirs that includes transcription, translation, and integration of daughter copies. We have investigated if retrotransposons are generally transcribed in the grasses and other plants, and whether the various families of elements are translationally and integrationally active in multiple grass species. A systematic search of 7.8 x 10(5) publicly available expressed sequence tags from plants revealed widespread retrotransposon transcripts at a frequency of one in 1,000. Monocot retrotransposons found relatively more expressed sequence tags from non-source species than did those of dicots. Antibodies were raised to the capsid protein, GAG, of BARE-1, a transcribed and translated copia-like retrotransposon of barley (Hordeum vulgare). These detected immunoreactive proteins of sizes identical to those of the BARE-1 GAG and polyprotein, respectively, in other species of the tribe Triticeae as well as in oats (Avena sativa) and rice (Oryza sativa). Retrotransposon-based markers showed integrational polymorphisms for BARE-1 in different subfamilies of the Graminae. The results suggest that grasses share families of transcriptionally, translationally, and integrationally active retrotransposons, enabling a comparative and integrative approach to understanding the life cycle of retrotransposons and their impact on the genome.

Shear bond strength of six restorative materials.

The purpose of this study was to determine and compare the shear bond strength of a conventional glass-ionomer cement, a resin modified glass-ionomer, a composite resin and three compomer restorative materials. Dentin of the occlusal surfaces from sixty extracted human permanent molars were prepared for shear bond strength testing. The specimens were randomly divided into six groups of 10 each. Dentinal surfaces were treated according to the instructions of manufacturers for each material. Each restorative material was placed inside nylon cylinders 2 mm high with an internal diameter of 3 mm, which were placed perpendicular to dentin surfaces. Shear bond strengths were determined using an Universal Testing Machine at crosshead speed of 0.5 mm/min in a compression mode. Conventional glass-ionomer, Ketac-Molar aplicap showed the lowest mean shear bond strength 3.77+/-1.76 (X +/- SD MPa) and the composite resin, Heliomolar showed the highest mean shear bond strength 16.54+/-1.65 while the mean bond strength of Fuji II LC was 9.55+/-1.06. The shear bond strengths of compomer restorative materials were 12.83+/-1.42, 10.64+/-1.42 and 11.19+/-1.19 for Compoglass, Hytac and Dyract respectively. ANOVA revealed statistically significant differences in the mean shear bond strengths of all groups (P<0.001). No statistically significant difference was found between the three compomer materials (P>0.5). Ketac-Molar and composite resin showed statistically significant difference (P<0.0005). The mode of fracture varied between materials. It is concluded that the compomer restorative materials show higher shear bond strength than conventional glass-ionomer and resin modified glass-ionomer, but less than composite resin. The fracture mode is not related to the shear bond strengths values.

Tumor development is retarded in mice lacking the gene for urokinase-type plasminogen activator or its inhibitor, plasminogen activator inhibitor-1.

In vivo tumor progression in mice with targeted deficiencies in urokinase-type plasminogen activator (UPA-/-) and its inhibitor, plasminogen activator inhibitor-1 (PAI-1-/-), was studied using a fibrosarcoma tumor model. Murine T241 fibrosarcoma cells were s.c. implanted into three groups of mice with the following genotypes, wild-type (WT), UPA-/-, and PAI-1-/-. A significantly diminished primary tumor growth in UPA-/- and PAI-1-/- mice occurred, relative to WT mice. Tumors in UPA-/- and PAI-1-/- mice displayed lower proliferative and higher apoptotic indices and displayed a different neovascular morphology, as compared with WT mice. These results are consistent with the decreased growth rates of this tumor in these gene-deleted mice. Immunohistochemical analyses of the tumors revealed a decrease in vascularity and vascular endothelial growth factor expression only in tumors in PAI-1-/- mice. Analyses of the relative extents of corneal angiogenesis in these same animals, induced by basic fibroblast growth factor, corroborated the resistance of PAI-1-/- mice to neovascularization. The results obtained suggest that the host fibrinolytic system plays an important role in tumor growth in this model. Alterations in host expression of components of this system may alter tumor growth and dissemination by affecting the balance between tumor cell death and proliferation, as well as extracellular matrix changes needed for invasiveness and angiogenesis.