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.

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.

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.

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.

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.

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.

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.

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.

Mapping the basal ganglia: fMRI evidence for somatotopic representation of face, hand, and foot.

OBJECTIVE: To noninvasively investigate the somatotopy of the basal ganglia in humans. METHODS: Functional MRI, 1.5-T, was performed on six normal right-handed volunteers during simple acoustically paced motor tasks involving the right hand, foot, and face. RESULTS: In a single-subject analysis, statistical parametric maps showed overlapping activation extending along the anteroposterior extent of the left lentiform nucleus (LLN) for the hand, foot, and face representations. Within the LLN, the centers of gravity of each body part, reflecting both the extent and gradient of activation, were all located in the retrocommissural portion of the putamen. Their spatial relationship followed a similar pattern across subjects-face was medial to toes and fingers, toes were dorsal and rostral to fingers. CONCLUSIONS: The somatotopic organization of hand, face, and foot representation in the human lentiform nucleus suggests a triangular pattern, rather than the linear pattern seen in primate studies. The overlap observed between the distinct body parts differs from the cortical sensorimotor representation, indicating a different organizational concept of the basal ganglia.

Blink reflex recovery in facial weakness: an electrophysiologic study of adaptive changes.

OBJECTIVE: To study the electrophysiologic effects of unilateral facial weakness on the excitability of the neuronal circuitry underlying blink reflex, and to localize the site of changes in blink reflex excitability that occur after facial weakness. BACKGROUND: Eyelid kinematic studies suggest that adaptive modification of the blink reflex occurs after facial weakness. Such adaptations generally optimize eye closure. A report of blepharospasm following Bell's palsy suggests that dysfunctional adaptive changes can also occur. METHODS: Blink reflex recovery was evaluated with paired stimulation of the supraorbital nerve at different interstimulus intervals. Comparisons were made between normal control subjects and patients with Bell's palsy who either recovered facial strength or who had persistent weakness. RESULTS: Blink reflex recovery was enhanced in patients with residual weakness but not in patients who recovered facial strength. Facial muscles on weak and unaffected sides showed enhancement. In patients with residual weakness, earlier blink reflex recovery occurred when stimulating the supraorbital nerve on the weak side. Sensory thresholds were symmetric. CONCLUSION: Enhancement of blink reflex recovery is dependent on ongoing facial weakness. Faster recovery when stimulating the supraorbital nerve on the paretic side suggests that sensitization may be lateralized, and suggests a role for abnormal afferent input in maintaining sensitization. Interneurons in the blink reflex pathway are the best candidates for the locus of this plasticity.

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.

Unchanged [3H]MK-801 binding and increased [3H]flunitrazepam binding in turtle forebrain during anoxia.

In order to determine if functional changes in N-methyl-D-aspartate receptors and GABAA receptors play a role in the remarkable anoxia tolerance of freshwater turtle brain, we used autoradiographic techniques to assay [3H]MK-801 and [3H]flunitrazepam binding in turtle forebrain after turtles had been subjected to anoxia for 2 or 6 h. The effects of glutamate, glycine, competitive N-methyl-D-aspartate antagonists, glycine antagonists, polyamines, magnesium, and zinc on [3H]MK-801 binding were the same in anoxic and control turtle forebrains. These results indicate that NMDA receptor regulation plays no role in the adaptive responses to anoxia in turtle brain. In contrast, [3H]flunitrazepam binding was significantly increased in the anoxic dorsal cortex and striatum. The most parsimonious explanation for elevated benzodiazepine receptor binding is that the rise in extracellular GABA levels known to accompany anoxia enhances benzodiazepine receptor affinity. It is possible, however, that GABAA receptor upregulation during anoxia increases the effectiveness of the inhibitory action of released GABA and contributes to the anoxia tolerance of turtles.

Calpain inhibitors protect auditory sensory cells from hypoxia and neurotrophin-withdrawal induced apoptosis.

Inhibitors of calpain have been shown to protect nerve growth factor (NGF)-deprived ciliary ganglion neurons and hypoxic cortical neurons. Calpains have been identified in the cochlea and are active during ischemic injury. Since apoptosis can be initiated by loss of neurotrophic support, hypoxia, and ototoxins (e.g., cisplatin, CDDP), the role of calpain inhibitors under these conditions was examined in auditory hair cells and neurons. Dissociated spiral ganglion neuron (SGN) cell cultures and organ of Corti explants from P3 rats were used to test the efficacy of calpain inhibitors as otoprotective molecules. Our results indicate that calpain inhibitor I, calpain inhibitor II, and leupeptin all provided significant protection of SGNs against neurotrophin-withdrawal and hypoxia-induced apoptosis. The increase in neuronal survival ranged from 2.16 to 2.31 times greater than in untreated neurotrophin-withdrawn SGN cell cultures. BOC-Asp(Ome)-Fluoromethyl Ketone (B-D-FMK), a general caspase inhibitor, increased neuronal survival 2.16 times more. Neuronal survival rates were from 1.88 to 2.27 times greater than in untreated, hypoxic neurons and hair cell survival rates were from 1.98 to 2.03 times greater than untreated, hypoxic organ of Corti explants. However, protection of auditory hair cells and neurons from CDDP-induced damage (10 and 6 micrograms/ml, respectively) was limited with any of these calpain inhibitors. Apoptotic pathways initiated by neurotrophin-deprivation and ototoxic stress (e.g., CDDP) have been shown to be different. Our results agree with this finding, with neurotrophin-withdrawal and hypoxia, but not CDDP damage-induced apoptosis being calpain-dependent.

Electroencephalographic measurement of motor cortex control of muscle activity in humans.

OBJECTIVE: To detect and measure correlation between cortical and muscle activities, coherence analysis was used. METHODS: The electroencephalogram (EEG) and electromyogram (EMG) were recorded in 9 normal volunteers during tonic contraction of upper and lower limb muscles on the right side. Coherence between EEG and EMG was computed to analyze their linear association. RESULTS: EEG over the contralateral sensorimotor area was coherent with EMG, with peak coherence at 11-36 Hz (mean, 22 Hz). For the abductor pollicis brevis (APB) muscle, peak coherence, as determined by functional brain mapping with focal transcranial magnetic stimulation (TMS), was over or slightly posterior to the hand area on the primary motor cortex determined by focal transcranial magnetic stimulation (TMS). Peak coherence over the scalp was somatotopically organized. The temporal relation between EEG and EMG was analyzed with a new model for interpreting the phase shift ('constant phase shift plus constant time lag' model). For the APB muscle, the phase relation between cortical and muscular oscillations differed in the frequency ranges of 3-13 Hz and 14-50 Hz, respectively, suggesting that different coupling mechanisms operate in different bands. Only the phase shift between cortical and motoneuronal firing at 14-50 Hz was reliably estimated by a linear model. At 14-50 Hz, motoneuronal firing was led by surface-negative cortical activity with a constant time lag that depended on the cortical-muscular distance. For the APB muscle, the time lag was slightly shorter than the cortical-muscular conduction time determined by TMS. Vibratory stimulation (100 Hz) of a muscle tendon during tonic contraction had no significant effect on cortical-muscular coherence, indicating that cortical oscillation reflected motor rather than sensory activity. CONCLUSIONS: The present findings suggest temporal coding of the oscillatory motor control system (3-13 Hz vs. 14-50 Hz), and confirm the functional importance of cortical beta and gamma rhythms in the motor efferent command. Cortical-muscular synchronization is most likely mediated by the direct corticospinal pathway within the frequency range of 14-50 Hz.

Gold-nickel alloys in dental prostheses.

A gold-nickel master alloy was prepared by arc melting in an inert atmosphere and from it, mechanical test specimens and dental prostheses were made by centrifugal casting. The cast alloy had a yield strength of about 7,400 kg/cm2, with an elongation of 12%. The alloy was clinically tested in the form of partial dentures and crown and bridge materials. For the 32-month period these prostheses have been in use, no tissue reaction, tarnish, or corrosion had been observed.

Correlation between macroscopic porosity location and liquid metal pressure in centrifugal casting technique.

Radiographic analysis of uniform cylindrical castings fabricated by the centrifugal casting technique has revealed that the macroscopic porosity is dependent on the location of the sprue attachment to the casting. This is attributed to the significant pressure gradient associated with the centrifugal casting technique. The pressure gradient results in different heat transfer rates at portions of the castings near and away from the free surface of the button. Consequently, the macroscopic porosity is invariably at portions of the casting close to the free surface of the button. In addition, some optimized sprue-reservoir combinations could be predicted and proved, based on this pressure gradient concept.

Urinary tract dilatation in pregnancy.

Two radiologists individually studied 220 intravenous urograms done during pregnancy in patients with apparently normal urinary tracts, and an observer-agreement technique was used to obtain the results. The few cases seen in early pregnancy show that dilatation of the urinary tract is uncommon, or at least mild, before mid term. Shortly thereafter, however, dilatation appears abruptly and remains virtually unchanged both in incidence and degree until full term. After mid term, the right side is dilated in about three-quarters of cases and the left side in about one-third. In only 10 % was the left side fuller than the right; in 86%, the right side was the fuller. Severe dilatation is infrequent, especially on the left. The dilatation never extends into the pelvis. The abdominal ureters are displaced outwards in a minority of cases, more often on the left. Little or no association was found between the dilatation and fetal position, maternal gravidity or urinary infection. These statistically derived conclusions should provide a firmer basis for what constitutes the limits of normality in the intravenous urogram during pregnancy.

Subpulmonary pneumothorax.

Seven cases of subpulmonary pneumothorax are presented: four due to penetrating injury, two to blunt trauma and one to osteosarcoma metastasis. The typical and diagnostic appearance is a basal band of radiolucency bounded above by the thin hair-line of visceral pleura paralleling the dome of the hemi-diaphragm. When partially clotted blood is also present, the appearance becomes less typical and has to be differentiated from traumatic diaphragmatic herniation of bowel and from traumatic pneumatocoele by barium studies and by decubitus radiographs respectively. It is the bridge-like disposition of the pleural cavity between the dome of the hemi-diaphragm and the hollowed concavity of the lung base which allows pneumothorax to collect in it. It is rarely seen because blebs and bullae which are the commonest causes of pneumothorax are most often located in the upper zones.