julilili42/papers huggingface dataset:
On the evolution of the resonant planetary system HD 128311
2006-05-04

\\n Context.A significant number of the known multiple exoplanetary systems\\n contain a pair of giant planets engaged in low-order mean-motion\\n resonance. Such a resonant condition protects the dynamics of these planets\\n resulting in very stable orbits. According to recent studies, this capture\\n into a resonance is the result of a planetary migration process induced\\n by interaction of the planets with a protoplanetary disk.\\n If the migration is slow enough (adiabatic) near a mean motion\\n resonance, the two planets will also be in apsidal corotation.\\n Aims.The recently refined orbital parameters of the system HD 128311\\n suggest that the two giant planets are in a 2:1 mean motion\\n resonance, however, without exhibiting apsidal corotation. Thus the evolution of\\n this system cannot be described by an adiabatic migration process alone. \\n We present possible evolution scenarios of this system by combining migration \\n processes and sudden perturbations.\\n Methods.We model migration scenarios through numerical\\n integration of the gravitational N-body problem with additional non-conservative forces. \\n Planet-planet scattering has been investigated by N-body simulations.\\n Results.We show that the present dynamical state of the system HD 128311 may be\\n explained by such evolutionary processes.\\n
Nucleonic gamma-ray production in Vela X
2006-05-04

\\n Context.\\nThe recently discovered extended very high energy gamma-ray\\n( eV) emission\\nfrom at least three pulsar wind nebula systems (MSH 15-52, G18.0-07,\\nand <ext-link ext-link-type="aoi">Vela X</ext-link>) could be hinting at \\na possibly new class of objects which is called in the following “TeV\\nplerions”. In some of these systems, particle acceleration could be driven \\nby ions in the relativistic pulsar wind. These ions are expected to \\nproduce gamma-ray emission via inelastic scattering with the ambient medium. \\n\\n Aims.\\nThe gamma-ray emission from the Vela TeV plerion associated with the\\n pulsar <ext-link ext-link-type="aoi">PSR B0833-45</ext-link> is investigated\\n\\n Methods.\\nWe calculate the gamma-ray emission \\n in the framework of nucleonic gamma-ray production\\nincluding the synchrotron and inverse Compton emission from primary and \\nsecondary electrons and compare the model with observational data.\\n\\n Results.\\nThe spectra calculated in this model give a very good description of the gamma-ray data.\\nThe required energy in nuclei is erg for protons and erg\\nfor iron nuclei released in the pulsar wind. \\nThe secondary electrons produce optical to soft X-ray emission at\\nthe level of ≈1032 erg/s.\\nWe give a prediction for the \\nand neutrino emission including a simple parameterization of the flux useful\\nfor calculating detection rates in next generation neutrino telescopes.\\n\\n Conclusions.\\nThe observed gamma-ray emission can be produced by a pulsar wind which carries\\na large fraction of the spin down luminosity in the form of\\nrelativistic nuclei. We predict the neutrino flux as a unique signature for this\\nmodel. \\nBased upon this prediction, the Vela TeV plerion would be one of the best\\nknown candidates for detection with next generation neutrino telescopes.\\n\\n
The Arabidopsis Major Intrinsic Protein NIP5;1 Is Essential for Efficient Boron Uptake and Plant Development under Boron Limitation
2006-05-05

Boron (B) is essential in plants but often present at low concentrations in the environment. To investigate how plants survive under conditions of B limitation, we conducted a transcriptome analysis and identified NIP5;1, a member of the major intrinsic protein family, as a gene upregulated in B-deficient roots of Arabidopsis thaliana. Promoter-beta-glucuronidase fusions indicated that NIP5;1 is strongly upregulated in the root elongation zone and the root hair zone under B limitation, and green fluorescent protein-tagged NIP5;1 proteins localized to the plasma membrane. Expression in Xenopus laevis oocytes demonstrated that NIP5;1 facilitated the transport of boric acid in addition to water. Importantly, two T-DNA insertion lines of NIP5;1 displayed lower boric acid uptake into roots, lower biomass production, and increased sensitivity of root and shoot development to B deficiency. These results identify NIP5;1 as a major plasma membrane boric acid channel crucial for the B uptake required for plant growth and development under B limitation.
<b>GAS CHROMATOGRAPHIC AND SPECTROSCOPIC ANALYSIS OF EPOXIDISED CANOLA OIL</b>
2006-05-08

Peroxyformic acid prepared <i>in</i>-<i>situ</i> was employed for epoxidation of canola oil in the presence of toluene. Gas chromatographic analysis of the product revealed the following species: C16:0; C18:0; C18:1; C18:2; C18:3; monoepoxy C18:0; monoepoxy C18:1; monoepoxy C18:2; diepoxy C18:0; diepoxy C18:1 and triepoxy C18:0, that were well separated and easily quantified. Result also revealed that epoxidation of canola oil was almost complete after 8 h using 4.0 moles of 85% formic acid in excess hydrogen peroxide. The <sup>1</sup>H and <sup>13</sup>C NMR of the products are discussed.
Model-based hybrid tracking for medical augmented reality
2006-05-08

Camera pose estimation is one of the most important, but also one of the most challenging tasks in augmented reality. Without a highly accurate estimation of the position and orientation of the digital video camera, it is impossible to render a spatially correct overlay of graphical information. This requirement is even more crucial in medical applications, where the virtual objects are supposed to be correctly aligned with the patient. Many medical AR systems use specialized tracking devices, which can be of limited suitability for real-world scenarios. We have developed an AR framework for surgical applications based on existing medical equipment. A surgical navigation device delivers tracking information measured by a built-in infrared camera system, which is the basis for the pose estimation of the AR video camera. However, depending on the conditions in the environment, this infrared pose data can contain discernible tracking errors. One main drawback of the medical tracking device is the fact that, while it delivers a very high positional accuracy, the reported camera orientation can contain a relatively large error.In this paper, we present a hybrid tracking scheme for medical augmented reality based on a certified medical tracking system. The final pose estimation takes the inital infrared tracking data as well as salient features in the camera image into account. The vision-based component of the tracking algorithm relies on a pre-defined graphical model of the observed scene. The infrared and vision-based tracking data are tightly integrated into a unified pose estimation algorithm. This algorithm is based on an iterative numerical optimization method. We describe an implementation of the algorithm and present experimental data showing that our new method is capable of delivering a more accurate pose estimation.
Theoretical considerations for cyclic (pd)π systems
2006-05-08

In most of the cyclic (pd)π systems which may be formed by use of either outer or inner d orbitals, cyclic delocalization through the d-orbital center is possible and leads to an increase in stability, but in no case will the (pd)π system alone lead to an extraordinary ground-state stabilization which can be classified as aromatic.
Platelets secrete stromal cell–derived factor 1α and recruit bone marrow–derived progenitor cells to arterial thrombi in vivo
2006-05-08

The accumulation of smooth muscle and endothelial cells is essential for remodeling and repair of injured blood vessel walls.Bone marrow-derived progenitor cells have been implicated in vascular repair and remodeling; however, the mechanisms underlying their recruitment to the site of injury remain elusive.Here, using real-time in vivo fl uorescence microscopy, we show that platelets provide the critical signal that recruits CD34 + bone marrow cells and c-Kit + Sca-1 + Lin -bone marrow-derived progenitor cells to sites of vascular injury.Correspondingly, specifi c inhibition of platelet adhesion virtually abrogated the accumulation of both CD34 + and c-Kit + Sca-1 + Lin -bone marrow-derived progenitor cells at sites of endothelial disruption.Binding of bone marrow cells to platelets involves both P-selectin and GPIIb integrin on platelets.Unexpectedly, we found that activated platelets secrete the chemokine SDF-1, thereby supporting further primary adhesion and migration of progenitor cells.These fi ndings establish the platelet as a major player in the initiation of vascular remodeling, a process of fundamental importance for vascular repair and pathological remodeling after vascular injury.
Epidemiology of a primary pneumonic plague in Kantoshu, Manchuria, from 1910 to 1911: statistical analysis of individual records collected by the Japanese Empire
2006-05-09

The increase in doubling time demonstrates the efficient and rapid countermeasures employed. Since the short interval from onset to death implies the importance of rapid responses, the challenge in confronting a future bioterrorist attack is to implement rapid and appropriate integration of control measures both at the individual and community level to prevent further transmissions as well as lower case fatality.
Freehand three-dimensional assessment of left ventricular volumes and ejection fraction with ultrasound contrast agent LK565
2006-05-09

LK565 improves feasibility of endocardial border delineation in 3D echocardiography, leading to better correlation of left ventricular volumetry with reference methods. Efficacy and safety of LK565 are equivalent to those of conventional UCAs.
Hybrid graphs as a framework for the small-world effect
2006-05-10

In this paper we formalize the small-world effect which describes the surprising fact that a hybrid graph composed of a local graph component and a very sparse random graph has a diameter of O(ln n) whereby the diameter of both components alone is much higher. We show that a large family of these hybrid graphs shows this effect and that this generalized family also includes classic small-world models proposed by various authors although not all of them are captured by the small-world definition given by Watts and Strogatz. Furthermore, we give a detailed upper bound of the hybrid's graph diameter for different choices of the expected number of random edges by applying a new kind of proof pattern that is applicable to a large number of hybrid graphs. The focus in this paper is on presenting a flexible family of hybrid graphs showing the small-world effect that can be tuned closely to real-world systems.
Incubation period as a clinical predictor of botulism: analysis of previous izushi-borne outbreaks in Hokkaido, Japan, from 1951 to 1965
2006-05-10

This study investigated 21 foodborne type-E botulism outbreaks, without antitoxin administration, from 1951 to 1965 in Hokkaido, Japan, to characterize the descriptive epidemiology and evaluate the relationship between case fatality and incubation period. The median (25–75% quartile) attack rate and case fatality, which were evaluated by outbreak, were 58·3% (38·0–73·2) and 25·7% (0·1–50·0) respectively. Individual records of 64 diagnoses, including 31 deaths, were also examined using logistic regression analysis, revealing that a shorter incubation period is likely to result in a significantly higher risk of death ( P =0·01). The observed case fatality was more than 50% for those who developed symptoms within the first 18 h after exposure, possibly reflecting underlying dose-dependent mechanisms. In the event of intentional contamination of food with botulinum toxin, rapidly determining the incubation periods may be critical for guiding public health response efforts.
Quantitative sensory testing in the German Research Network on Neuropathic Pain (DFNS): Standardized protocol and reference values
2006-05-12

The nationwide multicenter trials of the German Research Network on Neuropathic Pain (DFNS) aim to characterize the somatosensory phenotype of patients with neuropathic pain. For this purpose, we have implemented a standardized quantitative sensory testing (QST) protocol giving a complete profile for one region within 30 min. To judge plus or minus signs in patients we have now established age- and gender-matched absolute and relative QST reference values from 180 healthy subjects, assessed bilaterally over face, hand and foot. We determined thermal detection and pain thresholds including a test for paradoxical heat sensations, mechanical detection thresholds to von Frey filaments and a 64 Hz tuning fork, mechanical pain thresholds to pinprick stimuli and blunt pressure, stimulus/response-functions for pinprick and dynamic mechanical allodynia, and pain summation (wind-up ratio). QST parameters were region specific and age dependent. Pain thresholds were significantly lower in women than men. Detection thresholds were generally independent of gender. Reference data were normalized to the specific group means and variances (region, age, gender) by calculating z-scores. Due to confidence limits close to the respective limits of the possible data range, heat hypoalgesia, cold hypoalgesia, and mechanical hyperesthesia can hardly be diagnosed. Nevertheless, these parameters can be used for group comparisons. Sensitivity is enhanced by side-to-side comparisons by a factor ranging from 1.1 to 2.5. Relative comparisons across body regions do not offer advantages over absolute reference values. Application of this standardized QST protocol in patients and human surrogate models will allow to infer underlying mechanisms from somatosensory phenotypes.
Characterization of the Tandem GAF Domain of Human Phosphodiesterase 5 Using a Cyanobacterial Adenylyl Cyclase as a Reporter Enzyme
2006-05-12

We analyzed cGMP signaling by the human phosphodiesterase 5 (hPDE5) tandem GAF domain based on a functional activation assay. The C-terminal catalytic domain of the cyanobacterial adenylyl cyclase (AC) cyaB1 was used as a reporter enzyme. We demonstrate functional coupling between the hPDE5 GAF ensemble and the AC resulting in a chimera stimulated 10-fold by cGMP. The hPDE5 GAF domain has an inhibitory effect on AC activity, which is released upon cGMP activation. Removal of 109 amino acids from the N terminus resulted in partial disengagement of the GAF domain and AC, i.e. in a 10-fold increase in basal activity, and affected cGMP affinity. The Ser-102 phosphorylation site of hPDE5 increased cGMP affinity, as shown by a 5-fold lower K(D) for cGMP in a S102D mutant, which mimicked complete modification. The function of the NKFDE motif, which is a signature of all GAF domains with known cyclic nucleotide binding capacity, was elucidated by targeted mutations. Data with either single and double mutants in either GAF A or GAF B or a quadruple mutant affecting both subdomains simultaneously indicated that it is impossible to functionally assign cGMP binding and intramolecular signaling to either GAF A or B of hPDE5. Both subdomains are structurally and functionally interdependent and act in concert in regulating cycaB1 AC and, most likely, also hPDE5.
Effect of Crystallization on the Lamellar Orientation in Thin Films of Symmetric Poly(styrene)-b-poly(l-lactide) Diblock Copolymer
2006-05-13

The effect of crystallization on the lamellar orientation of poly(styrene)-b-poly(l-lactide) (PS−PLLA) semicrystalline diblock copolymer in thin films has been investigated by atomic force microscopy (AFM), transmission electronic microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). In the melt state, microphase separation leads to a symmetric wetting structure with PLLA blocks located at both polymer/substrate and polymer/air interfaces. The lamellar period is equal to the long period L in bulk determined by small-angle X-ray scattering (SAXS). Symmetric wetting structure formed in the melt state provides a model structure to study the crystallization of PLLA monolayer tethered on glassy (Tc < Tg,PS) or rubber (Tc > Tg,PS) PS substrate. In both cases, it is found that the crystallization of PLLA results in a "sandwich" structure with amorphous PS layer located at both folding surfaces. For Tc ≤ Tg,PS, the crystallization induces a transition of the lamellar orientation from parallel to perpendicular to substrate in between and front of the crystals. In addition, the depletion of materials around the crystals leads to the formation of holes of 1/2L, leaving the adsorbed monolayer exposure at the bottom of the holes. In contrast, the adsorbed monolayer on the substrate with thickness of 1/2L does not change in parallel orientation and thickness upon crystallization. When Tc > Tg,PS, no perpendicular lamellae and holes could be observed due to the high mobility of molecules.
A resolution for the coiling direction paradox in Neogloboquadrina pachyderma
2006-05-15

We present new data on genotypic differences and biogeographic distribution of coiling types in the living planktonic foraminiferal morphospecies Neogloboquadrina pachyderma . The genetic evidence demonstrates that coiling direction in N. pachyderma is a genetic trait, heritable through time, and is not a morphological feature reflecting ecophenotypic variation. The two opposite coiling morphotypes appear to have diverged during the late Miocene, and they have distinctly different ecologies. In combination with fossil evidence, biogeography, and ecology the degree of genetic distinction between the two coiling types of N. pachyderma strongly implies that they should be considered different species. We propose the adoption of the widely recognized name N. incompta for the right coiling morphospecies. The genetic evidence also demonstrates a low level (&lt;3%) of aberrant coiling associated with both morphotypes. The abundance of these aberrant specimens has no relationship with the environment. These findings have important consequences for the use of N. pachyderma and N. incompta as paleoceanographic signal carriers in polar and subpolar waters.
Progression-Specific Genes Identified by Expression Profiling of Matched Ductal Carcinomas In situ and Invasive Breast Tumors, Combining Laser Capture Microdissection and Oligonucleotide Microarray Analysis
2006-05-15

Abstract Becoming invasive is a crucial step in breast cancer oncogenesis. At this point, a lesion carries the potential for spreading and metastasis—a process, whose molecular characteristics still remain poorly understood. In this article, we describe a matched-pair analysis of ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) of nine breast ductal carcinomas to identify novel molecular markers characterizing the transition from DCIS to IDC. The purpose of this study was to better understand the molecular biology of this transition and to identify candidate genes whose products might serve as prognostic markers and/or as molecular targets for treatment. To obtain cellular-based gene expression profiles from epithelial tumor cells, we combined laser capture microdissection with a T7-based two-round RNA amplification and Affymetrix oligonucleotide microarray analysis. Altogether, a set of 24 tumor samples was analyzed, comprised of nine matched DCIS/IDC and replicate DCIS/IDC preparations from three of the nine tumors. Cluster analysis on expression data shows the robustness and reproducibility of the techniques we established. Using multiple statistical methods, 546 significantly differentially expressed probe sets were identified. Eighteen candidate genes were evaluated by RT-PCR. Examples of genes already known to be associated with breast cancer invasion are BPAG1, LRRC15, MMP11, and PLAU. The expression of BPAG1, DACT1, GREM1, MEF2C, SART2, and TNFAIP6 was localized to epithelial tumor cells by in situ hybridization and/or immunohistochemistry, confirming the accuracy of laser capture microdissection sampling and microarray analysis. (Cancer Res 2006; 66(10): 5278-86)
Alveolar recruitment during prone position: time matters
2006-05-15

Alveolar recruitment is one of the beneficial effects of prone positioning in patients with ARDS (acute respiratory distress syndrome). However, responses vary among patients and, therefore, we hypothesized that alveolar recruitment is an individual time-dependent process and its measurement might be helpful to ‘dose’ prone positioning individually. In 13 patients diagnosed with ARDS, EELV (end-expiratory lung volume) was measured in the supine position, immediately after turning to the prone position, at 1, 2, 4 and 8 h in the prone position and after returning to the supine position. Responders were defined based on a 30% increase in oxygenation. EELV increased in responders, whereas it remained constant in non-responders. The time course was different in individual patients. In some responders, a plateau was reached as early as 2–4 h, whereas, in others, 8 h of prone positioning was not sufficient to allow complete recruitment. The increase in lung volume was associated with both an increase in arterial oxygenation and a decrease in venous admixture. Furthermore, responders had significantly lower baseline EELVs than non-responders. In conclusion, alveolar recruitment during prone positioning has been characterized as an individual time-dependent process. Its measurement might be useful to apply prone positioning more individually and might also help to identify responders.
Activity of the major staphylococcal autolysin Atl
2006-05-16

The major autolysin of Staphylococcus aureus (AtlA) and of Staphylococcus epidermidis (AtlE) are well-studied enzymes. Here we created an atlA deletion mutant in S. aureus that formed large cell clusters and was biofilm-negative. In electron micrographs, the mutant cells were distinguished by rough outer cell surface. The mutant could be complemented using the atlE gene from S. epidermidis. To study the role of the repetitive sequences of atlE, we expressed in Escherichia coli the amidase domain encoded by the gene, carrying no repeat regions (amiE) or two repeat regions (amiE-R1,2), or the three repeat regions alone (R1,2,3) as N-terminal His-tag fusion proteins. Only slight differences in the cell wall lytic activity between AmiE and AmiE-R1,2 were observed. The repetitive sequences exhibit a good binding affinity to isolated peptidoglycan and might contribute to the targeting of the amidase to the substrate. AmiE and AmiE-R1,2 have a broad substrate specificity as shown by similar activities with peptidoglycan lacking wall teichoic acid, O-acetylation, or both. As the amidase activity of AtlA and AtlE has not been proved biochemically, we used purified AmiE-R1,2 to determine the exact peptidoglycan cleavage site. We provide the first evidence that the amidase indeed cleaves the amide bond between N-acetyl muramic acid and L-alanine.