Phyllotaxis involves auxin drainage through leaf primordia

The spatial arrangement of leaves and flowers around the stem, known as phyllotaxis, is controlled by an auxin-dependent reiterative mechanism that leads to regular spacing of the organs and thereby to remarkably precise phyllotactic patterns. The mechanism is based on the active cellular transport of the phytohormone auxin by cellular influx and efflux carriers, such as AUX1 and PIN1. Their important role in phyllotaxis is evident from mutant phenotypes, but their exact roles in space and time are difficult to address due to the strong pleiotropic phenotypes of most mutants in phyllotaxis. Models of phyllotaxis invoke the accumulation of auxin at leaf initials and removal of auxin through their developing vascular strand, the midvein. We have developed a precise microsurgical tool to ablate the midvein at high spatial and temporal resolution in order to test its function in leaf formation and phyllotaxis. Using amplified femtosecond laser pulses, we ablated the internal tissues in young leaf primordia of tomato (Solanum lycopersicum) without damaging the overlying L1 and L2 layers. Our results show that ablation of the future midvein leads to a transient accumulation of auxin in the primordia and to an increase in their width. Phyllotaxis was transiently affected after midvein ablations, but readjusted after two plastochrons. These results indicate that the developing midvein is involved in the basipetal transport of auxin through young primordia, which contributes to phyllotactic spacing and stability.

Supersymmetric quantum mechanics on the lattice: II. Exact results

Simulations of supersymmetric field theories with spontaneously broken supersymmetry require in addition to the ultraviolet regularisation also an infrared one, due to the emergence of the massless Goldstino. The intricate interplay between ultraviolet and infrared effects towards the continuum and infinite volume limit demands careful investigations to avoid potential problems. In this paper – the second in a series of three – we present such an investigation for N=2 supersymmetric quantum mechanics formulated on the lattice in terms of bosonic and fermionic bonds. In one dimension, the bond formulation allows to solve the system exactly, even at finite lattice spacing, through the construction and analysis of transfer matrices. In the present paper we elaborate on this approach and discuss a range of exact results for observables such as the Witten index, the mass spectra and Ward identities.

Progress in Simulations with Twisted Mass Fermions at the Physical Point

In this contribution, results from Nf = 2 lattice QCD simulations at one lattice spacing using twisted mass fermions with a clover term at the physical pion mass are presented. The mass splitting between charged and neutral pions (including the disconnected contribution) is shown to be around 20(20) MeV. Further, a first measurement using the clover twisted mass action of the average momentum fraction of the pion is given. Finally, an analysis of pseudoscalar meson masses and decay constants is presented involving linear interpolations in strange and charm quark masses. Matching to meson mass ratios allows the calculation of quark mass ratios: ms=ml = 27:63(13), mc=ml = 339:6(2:2) and mc=ms = 12:29(10). From this mass matching the quantities fK = 153:9(7:5) MeV, fD = 219(11) MeV, fDs = 255(12) MeV and MDs = 1894(93) MeV are determined without the application of finite volume or discretization artefact corrections and with errors dominated by a preliminary estimate of the lattice spacing.

STUDY OF THE EFFECTS OF TOTAL MODULATION TRANSFER FUNCTION CHANGES ON OBSERVER PERFORMANCE USING CLINICAL MAMMOGRAMS

The main goal of this study was to relate physical changes in image quality measured by Modulation Transfer Function (MTF) to diagnostic accuracy.^ One Hundred and Fifty Kodak Min-R screen/film combination conventional craniocaudal mammograms obtained with the Pfizer Microfocus Mammographic system were selected from the files of the Department of Radiology, at M.D. Anderson Hospital and Tumor Institute.^ The mammograms included 88 cases with a variety of benign diagnosis and 62 cases with a variety of malignant biopsy diagnosis. The average age of the patient population was 55 years old. 70 cases presented calcifications with 30 cases having calcifications smaller than 0.5mm. 46 cases presented irregular bordered masses larger than 1 cm. 30 cases presented smooth bordered masses with 20 larger than 1 cm.^ Four separated copies of the original images were made each having a different change in the MTF using a defocusing technique whereby copies of the original were obtained by light exposure through different thicknesses (spacing) of transparent film base.^ The mammograms were randomized, and evaluated by three experienced mammographers for the degree of visibility of various anatomical breast structures and pathological lesions (masses and calicifications), subjective image quality, and mammographic interpretation.^ 3,000 separate evaluations were anayzed by several statistical techniques including Receiver Operating Characteristic curve analysis, McNemar test for differences between proportions and the Landis et al. method of agreement weighted kappa for ordinal categorical data.^ Results from the statistical analysis show: (1) There were no statistical significant differences in the diagnostic accuracy of the observers when diagnosing from mammograms with the same MTF. (2) There were no statistically significant differences in diagnostic accuracy for each observer when diagnosing from mammograms with the different MTF's used in the study. (3) There statistical significant differences in detail visibility between the copies and the originals. Detail visibility was better in the originals. (4) Feature interpretations were not significantly different between the originals and the copies. (5) Perception of image quality did not affect image interpretation.^ Continuation and improvement of this research ca be accomplished by: using a case population more sensitive to MTF changes, i.e., asymptomatic women with minimum breast cancer, more observers (including less experienced radiologists and experienced technologists) must collaborate in the study, and using a minimum of 200 benign and 200 malignant cases.^

Validation of a Spatially Continuous EDEN Water-Surface Model for the Everglades, Florida

The Everglades Depth Estimation Network (EDEN) is an integrated network of realtime water-level monitoring, ground-elevation modeling, and water-surface modeling that provides scientists and managers with current (2000-present), online water-stage and water-depth information for the entire freshwater portion of the Greater Everglades. Continuous daily spatial interpolations of the EDEN network stage data are presented on grid with 400-square-meter spacing. EDEN offers a consistent and documented dataset that can be used by scientists and managers to: (1) guide large-scale field operations, (2) integrate hydrologic and ecological responses, and (3) support biological and ecological assessments that measure ecosystem responses to the implementation of the Comprehensive Everglades Restoration Plan (CERP) (U.S. Army Corps of Engineers, 1999). The target users are biologists and ecologists examining trophic level responses to hydrodynamic changes in the Everglades. The first objective of this report is to validate the spatially continuous EDEN water-surface model for the Everglades, Florida developed by Pearlstine et al. (2007) by using an independent field-measured data-set. The second objective is to demonstrate two applications of the EDEN water-surface model: to estimate site-specific ground elevation by using the validated EDEN water-surface model and observed water depth data; and to create water-depth hydrographs for tree islands. We found that there are no statistically significant differences between model-predicted and field-observed water-stage data in both southern Water Conservation Area (WCA) 3A and WCA 3B. Tree island elevations were derived by subtracting field water-depth measurements from the predicted EDEN water-surface. Water-depth hydrographs were then computed by subtracting tree island elevations from the EDEN water stage. Overall, the model is reliable by a root mean square error (RMSE) of 3.31 cm. By region, the RMSE is 2.49 cm and 7.77 cm in WCA 3A and 3B, respectively. This new landscape-scale hydrological model has wide applications for ongoing research and management efforts that are vital to restoration of the Florida Everglades. The accurate, high-resolution hydrological data, generated over broad spatial and temporal scales by the EDEN model, provides a previously missing key to understanding the habitat requirements and linkages among native and invasive populations, including fish, wildlife, wading birds, and plants. The EDEN model is a powerful tool that could be adapted for other ecosystem-scale restoration and management programs worldwide.

The role of sensory neuron outgrowth in long-term sensitization of the tail-elicited tail-siphon withdrawal reflex of Aplysia

Neuronal outgrowth has been proposed in many systems as a mechanism underlying memory storage. For example, sensory neuron outgrowth is widely accepted as an underlying mechanism of long-term sensitization of defensive withdrawal reflexes in Aplysia. The hypothesis is that learning leads to outgrowth and consequently to the formation of new synapses, which in turn strengthen the neural circuit underlying the behavior. However, key experiments to test this hypothesis have never been performed. ^ Four days of sensitization training leads to outgrowth of siphon sensory neurons mediating the siphon-gill withdrawal response in Aplysia . We found that a similar training protocol produced robust outgrowth in tail sensory neurons mediating the tail siphon withdrawal reflex. In contrast, 1 day of training, which effectively induces long-term behavioral sensitization and synaptic facilitation, was not associated with neuronal outgrowth. Further examination of the effect of behavioral training protocols on sensory neuron outgrowth indicated that this structural modification is associated only with the most persistent forms of sensitization, and that the induction of these changes is dependent on the spacing of the training trials over multiple days. Therefore, we suggest that neuronal outgrowth is not a universal mechanism underlying long-term sensitization, but is involved only in the most persistent forms of the memory. ^ Sensory neuron outgrowth presumably contributes to long-term sensitization through formation of new synapses with follower motor neurons, but this hypothesis has never been directly tested. The contribution of outgrowth to long-term sensitization was assessed using confocal microscopy to examine sites of contact between physiologically connected pairs of sensory and motor neurons. Following 4 days of training, the strength of both the behavior and sensorimotor synapse and the number of appositions with follower neurons was enhanced only on the trained side of the animal. In contrast, outgrowth was induced on both sides of the animal, indicating that although sensory neuron outgrowth does appear to contribute to sensitization through the formation of new synapses, outgrowth alone is not sufficient to account for the effects of sensitization. This indicates that key regulatory steps are downstream from outgrowth, possibly in the targeting of new processes and activation of new synapses. ^

Multiple gradient echo propeller (MGREP) MRI: Technical development and potential applications

The PROPELLER (Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction) magnetic resonance imaging (MRI) technique has inherent advantages over other fast imaging methods, including robust motion correction, reduced image distortion, and resistance to off-resonance effects. These features make PROPELLER highly desirable for T2*-sensitive imaging, high-resolution diffusion imaging, and many other applications. However, PROPELLER has been predominantly implemented as a fast spin-echo (FSE) technique, which is insensitive to T2* contrast, and requires time-inefficient signal averaging to achieve adequate signal-to-noise ratio (SNR) for many applications. These issues presently constrain the potential clinical utility of FSE-based PROPELLER. ^ In this research, our aim was to extend and enhance the potential applications of PROPELLER MRI by developing a novel multiple gradient echo PROPELLER (MGREP) technique that can overcome the aforementioned limitations. The MGREP pulse sequence was designed to acquire multiple gradient-echo images simultaneously, without any increase in total scan time or RF energy deposition relative to FSE-based PROPELLER. A new parameter was also introduced for direct user-control over gradient echo spacing, to allow variable sensitivity to T2* contrast. In parallel to pulse sequence development, an improved algorithm for motion correction was also developed and evaluated against the established method through extensive simulations. The potential advantages of MGREP over FSE-based PROPELLER were illustrated via three specific applications: (1) quantitative T2* measurement, (2) time-efficient signal averaging, and (3) high-resolution diffusion imaging. Relative to the FSE-PROPELLER method, the MGREP sequence was found to yield quantitative T2* values, increase SNR by ∼40% without any increase in acquisition time or RF energy deposition, and noticeably improve image quality in high-resolution diffusion maps. In addition, the new motion algorithm was found to improve the performance considerably in motion-artifact reduction. ^ Overall, this work demonstrated a number of enhancements and extensions to existing PROPELLER techniques. The new technical capabilities of PROPELLER imaging, developed in this thesis research, are expected to serve as the foundation for further expanding the scope of PROPELLER applications. ^

Hepatitis B vaccination of high risk pregnant women: A clinical trial at Parkland Memorial Hospital

Hepatitis B infection is a major public health problem of global proportions. It is estimated that 2 billion people worldwide are infected by the Hepatitis B virus (HBV) at some point, and 350 million are chronic carriers. The Centers for Disease Control and Prevention (CDC) report an incidence in the United States of 140,000–320,000 infections each year (asymptomatic and symptomatic), and estimate 1–1.25 million people are chronically infected. Hepatitis B and its chronic complications (cirrhosis of the liver, liver failure, hepatocellular carcinoma) responsible for 4,000–5,000 deaths in America each year. ^ One quarter of those who become chronic carriers develop progressive liver disease, and chronic HBV infection is thought to be responsible for 60 million cases of cirrhosis worldwide, surpassing alcohol as a cause of liver disease. Since there are few treatment options for the person chronically infected with Hepatitis B, and what is available is expensive, prevention is clearly best strategy for combating this disease. ^ Since the approval of the Hepatitis B vaccine in 1981, national and international vaccination campaigns have been undertaken for the prevention of Hepatitis B. Despite encouraging results, however, studies indicate that prevalence rates of Hepatitis B infection have not been significantly reduced in certain high risk populations because vaccination campaigns targeting those groups do not exist and opportunities for vaccination by individual physicians in clinical settings are often missed. Many of the high-risk individuals who go unvaccinated are women of childbearing age, and a significant proportion of these women become infected with the Hepatitis B virus (HBV) during pregnancy. Though these women are often seen annually or for prenatal care (because of the close spacing of their children and their high rate of fertility), the Hepatitis B vaccine series is seldom recommended by their health care provider. In 1993, ACOG issued a statement recommending Hepatitis B vaccination of pregnant women who were defined as high-risk by diagnosis of a sexually transmitted disease. ^ Hepatitis B vaccine has been extensively studied in the non-pregnant population. The overall efficacy of the vaccine in infants, children and adults is greater than 90%. In the small clinical trials to date, the vaccine seemed to be effective in those pregnant women receiving 3 doses; however, by using the usual 0, 1 and 6 month regimen, most pregnant women were unable to complete a full series during pregnancy. There is data now available supporting the use of an "accelerated" dosing schedule at 0, 1 and 4 months. This has not been evaluated in pregnant women. A clinical trial proving the efficacy of the 0, 1, 4 schedule and its feasibility in this population would add significantly to the body of research in this area, and would have implications for public health policy. Such a trial was undertaken in the Parkland Memorial Hospital Obstetrical Infectious Diseases clinic. In this study, the vaccine was very well tolerated with no major adverse events reported, 90% of fully vaccinated patients achieved immunity, and only Body Mass Index (BMI) was found to be a significant factor affecting efficacy. This thesis will report the results of the trial and compare it to previous trials, and will discuss barriers to implementation, lessons learned and implications for future trials. ^

EGFR and Notch signaling pathways are regulated by distinct isoforms of Drosophila cbl

Activation of cell surface receptors transduces extracellular signals into cellular responses such as proliferation, differentiation and survival. However, the appropriate spatial and temporal down-regulation of signaling receptors is essential for normal development and homeostasis. The Cbl family of E3-ubiquitin ligases plays a major role for the ligand-dependent inactivation of growth factor receptors through ubiquitin-mediated endocytosis and lysosomal degradation. Here, we report the D-cbl mutant phenotypes in the Drosophila eye. D-cbl mutants display overgrowth, inhibition of apoptosis, differentiation defects and increased ommatidial spacing. Many of these phenotypes are caused by lack of down-regulation of the Drosophila EGFR signaling. However, not all D-cbl phenotypes can be explained by inappropriate EGFR activity. We found that D-Cbl also negatively regulates Notch activity during eye and wing development. D-cbl produces two isoforms by alternative splicing. Strikingly, the long isoform, D-CblL, preferentially regulates the EGFR, whereas the short isoform, D-CblS, preferentially regulates Notch. Taken together, these data suggest that D-Cbl controls at least two signaling pathways, EGFR and Notch, through production of two alternatively spliced isoforms during development in Drosophila.^

L -Sox5 and Sox6: Architectural transcription factors in chondrogenesis

Transcription factors often determine cell fate and tissue development. Chondrogenesis is the developmental process by which cartilages form. Recently, gene targeting studies have shown that two transcription factors, L-Sox5 and Sox6, play essential and redundant roles in chondrogenesis in vivo by converting precartilaginous cell condensations into cartilages. Both are highly similar High-Mobility-Group (HMG)-domain proteins that bind and subsequently bend DNA containing the 7bp HMG site (A/T)(A/T)CAA(A/T)G. They have no transactivation domain, but homo- and hetero-dimerize and preferentially bind DNA containing two HMG sites. They are thought to play an architectural role in transactivation by facilitating long-range DNA and protein interactions. To understand their molecular mechanism of action, we investigated how phasing, orientation, and spacing between HMG sites affect L-Sox5 and Sox6 DNA-binding. We determined that L-Sox5 and Sox6 dimers bind with high affinity to paired HMG sites in DNA rather than a single HMG site. Binding of paired sites is independent of DNA helical phasing, orientation of paired HMG sites and independent of distance up to 255 base pairs between sites. Mutational analysis demonstrated that binding of L-Sox5 and Sox6, independent of orientation of the sites, is critically dependent on the presence of paired HMG sites rather than one HMG site alone. Our data support a unique and novel model whereby L-Sox5 and Sox6 dimerize and bind DNA with pronounced spatial flexibility, possibly by a flexible hinge, and act as architectural transcription factors that bring distant DNA sites and proteins together to form higher order transcriptional complexes that are essential for the activation of their target genes in chondrogenesis. ^

Converting Land from Poplar Tree Bioenergy Planting to Cropland: An Example

Many landowners ask about the process and costs for returning land to crop production after trees are cut for biomass. A field on the Squaw Creek bottom, Story County, Iowa was planted to hybrid poplar trees in spring 2000. The trees were planted in rows with a 10-ft spacing. The trees were cut in spring 2010. The resulting field was four acres, and this is the account of the first corn crop in 2011 on the area.

Evaluation of Narrow Row Soybeans

Producers continue to look at different management practices to increase corn and soybean yields. One area of interest is planting corn and soybeans in narrow rows. Traditionally, these crops have been planted in row widths of 30 to 38 in. Planters on the market today have the capability to plant corn and soybeans in 15- and 20-in. rows, as well as in twin rows that are spaced eight inches apart. This study was set up to evaluate the yield impact of planting soybeans in 15-in. rows versus the traditional 30-in. row spacing.

Benthic foraminiferal stable isotope record from ODP Site 138-849 on the East Pacific Rise

Benthic foraminifer and delta13C data from Site 849, on the west flank of the East Pacific Rise (0°11 'N, 110°31'W; 3851 m), give relatively continuous records of deep Pacific Ocean stable isotope variations between 0 and 5 Ma. The mean sample spacing is 4 k.y. Most analyses are from Cibicides wuellerstorfi, but isotopic offsets relative to Uvigerina peregrina appear roughly constant. Because of its location west of the East Pacific Rise, Site 849 yields a suitable record of mean Pacific Ocean delta13C, which approximates a global oceanic signal. The ~100-k.y.-period climate cycle, which is prevalent in delta18O does not dominate the long-term delta13C record. For delta13C, variations in the ~400- and 41-k.y. periods are more important. Phase lags of delta13C relative to ice volume in the 41- and 23-k.y. bands are consistent with delta13C as a measure of organic biomass. A model-calculated exponential response time of 1-2 k.y. is appropriate for carbon stored in soils and shallow sediments responding to glacial-interglacial climate change. Oceanic delta13C leads ice volume slightly in the 100-k.y. band, and this suggests another process such as changes in continental weathering to modulate mean river delta13C at long periods. The delta13C record from Site 849 diverges from that of Site 677 in the Panama Basin mostly because of decay of 13C-depleted organic carbon in the relatively isolated Panama Basin. North Atlantic to Pacific delta13C differences calculated using published data from Sites 607 and 849 reveal variations in Pliocene deep water within the range of those of the late Quaternary. Maximum delta13C contrast between these sites, which presumably reflects maximum influx of high-delta13C northern source water into the deep North Atlantic Ocean, occurred between 1.3 and 2.1 Ma, well after the initiation of Northern Hemisphere glaciation. Export of high-delta13C North Atlantic Deep Water from the Atlantic to the circumpolar Antarctic, as recorded by published delta13C data from Subantarctic Site 704, appears unrelated to the North Atlantic-Pacific delta13C contrast. To account for this observation, we suggest that deep-water formation in the North Atlantic reflects northern source characteristics, whereas export of this water into the circumpolar Antarctic reflects Southern Hemisphere wind forcing. Neither process appears directly linked to ice-volume variations.

Diatom biostratigraphy and datum levels of sediments from ODP Leg 167 sites

Ocean Drilling Program Leg 167 represents the first time since 1978 that the North American Pacific margin was drilled to study ocean history. More than 7500 m of Quaternary to middle Miocene (14 Ma) sediments were recovered from 13 sites, representing the most complete stratigraphic sequence on the California margin. Diatoms are found in most samples in variable abundance and in a moderately well-preserved state throughout the sequence, and they are often dominated by robust, dissolution-resistant species. The Neogene North Pacific diatom zonation of Yanagisawa and Akiba (1998, doi:10.5575/geosoc.104.395) best divides the Miocene to Quaternary sequences, and updated ages of diatom biohorizons estimated based on the geomagnetic polarity time scale of Cande and Kent (1995, doi:10.1029/94JB03098) are slightly revised to adjust the differences between the other zonations. Most of the early middle Miocene through Pleistocene diatom datum levels that have been proven to be of stratigraphic utility in the North Pacific appear to be nearly isochronous within the level of resolution constrained by sample spacing. The assemblages are characterized by species typical of middle-to-high latitudes and regions of high surface-water productivity, predominantly by Coscinodiscus marginatus, Stephanopyxis species, Proboscia barboi, and Thalassiothrix longissima. Latest Miocene through Pliocene assemblages in the region of the California Current, however, are intermediate between those of subarctic and subtropical areas. As a result, neither the existing tropical nor the subarctic (high latitude) zonal schemes were applicable for this region. An interval of pronounced diatom dissolution detected throughout the Pliocene sequence apparently correspond to a relatively warmer paleoceanographic condition resulting in a slackening of the southward flow of the California Current.

Insoluble residues of the fine-grained sediments from DSDP Leg 67 Holes

Insoluble residues of Late Cretaceous to Quaternary deep-sea samples from slope, trench, and oceanic plate sites south of Guatemala were examined, specifically for the distribution of clay minerals in the <2-µm fraction and of silt grains in the 20-63-µm fraction. Widespread "oceanic" particles (biogenic opal, rhyolitic glass) and their diagenetic products (smectite, clinoptilolite, heulandite) were distinguished from terrigenous material - illite, kaolinite, chlorite, plagioclase, quartz, and heavy minerals. The main results of this investigation are: (1) At Site 494 on the slope immediately adjacent to the trench, terrigenous supplies testify to a slope position of the whole sequence back to the Late Cretaceous. (2) At Site 495 on the Pacific Cocos Plate, "oceanic" and terrigenous sedimentation are clearly separated. Whereas the pelagic sedimentation prevailed in the early Miocene, terrigenous minerals appeared in the middle Miocene in the clay fraction, and in the early Pliocene in the coarse silt fraction. These terrigenous supplies are interpreted as having been transported by suspension clouds crossing the slope and even the trench. The alternative, however, an eolian transport, cannot be excluded.