julilili42/papers huggingface dataset:
Developmental changes in rat surfactant lipidomics in the context of species variability
2007-07-20

Abstract Lung surfactant comprises mainly phosphatidylcholine (PC) species together with phosphatidylglycerols and surfactant proteins (SP) SP‐A to ‐D. Changes in the concentrations of its principal components dipalmitoyl‐PC, palmitoylmyristoyl‐PC, palmitoylpalmitoleoyl‐PC relative to developmental, structural and physiological differences are only partially understood. Particularly, their attribution to differences in air–liquid interface curvature, compared with dynamic parameters, such as respiratory rate, are controversial. We postulated that during alveolarization the changes in these principal PC components of surfactant differ from those in other phospholipid parameters, and that across endothermic vertebrates their concentrations are related to lung physiology rather than structure. We therefore investigated in rats from postnatal day (d)1 to d42 the pattern of surfactant phospholipids relative to alveolarization (d4–d14), and we discuss these changes in terms of molecular adaptation to pulmonary structure or physiology. Contrary to mammals with advanced alveolarization and increased respiratory rate (RR) at term, concentrations of dipalmitoyl‐PC (49–52%) and palmitoylmyristoyl‐PC (7–9%) in lung lavage fluid were identical at d1 and d42. At d7–d14, when in rats RR is increased, palmitoyl‐myristoyl‐PC transiently increased by 2.5‐ to 3.9‐fold at the expense of dipalmitoyl‐PC (−32% to 34%) and palmitoyl‐palmitoleoyl‐PC (−16%). Other lipidomic changes followed essentially different patterns of increase or decrease. Palmitoyl‐myristoyl‐PC was increased in large aggregates suggesting that it is an integral component of active surfactant. In the overall context of vertebrates, irrespective of age and lung structure, fractions of palmitoyl‐myristoyl‐PC, dipalmitoyl‐PC and palmitoyl‐palmitoleoyl‐PC correlate with differences in RR rather than alveolar curvature. In adult mammals, however, only concentrations of palmitoyl‐palmitoleoyl‐PC correlate with RR. Pediatr Pulmonol. 2007; 42:794–804. © 2007 Wiley‐Liss, Inc.
Extended Mycophenolate Mofetil and Shortened Cyclosporine Failed to Reduce Graft-versus-Host Disease after Unrelated Hematopoietic Cell Transplantation with Nonmyeloablative Conditioning
2007-07-21

We previously reported data from 103 patients with hematologic malignancies (median age 54 years) who received peripheral blood stem cell (PBSC) grafts from HLA-matched unrelated donors after nonmyeloablative conditioning and were given postgrafting immunosuppression consisting of mycophenolate mofetil (MMF; administered from day 0 until day +40 with taper through day +96) and cyclosporine (CSP; given from day -3 to day +100, with taper through day 180) (historical patients). The incidences of grade II-IV acute and extensive chronic graft-versus-host disease (aGVHD, cGVHD) were 52% and 49%, respectively, and the 1-year probabilities of relapse, nonrelapse mortality (NRM), and progression-free survival (PFS) were 26%, 18%, and 56%, respectively. Here, we treated 71 patients with hematologic malignancies (median age 56 years) with unrelated PBSC grafts and investigated whether postgrafting immunosuppression with an extended course of MMF, given at full dosing until day +150 and then tapered through day +180, and a shortened course of CSP, through day +80, would promote tolerance induction and reduce the incidence of GVHD (current patients). We observed 77% grade II-IV aGVHD and 45% extensive cGVHD (P=.03, and P=.43, respectively, in current compared to historical patients). The 1-year probabilities of relapse, NRM, and PFS were 23%, 29%, and 47%, respectively (P=.89, P=.02, and P=.08 compared to the historical patients). We conclude that postgrafting immunosuppression with extended MMF and shortened CSP failed to decrease the incidence of GVHD among unrelated PBSC recipients given nonmyeloablative conditioning.
Multimodal Signaling in Male and Female Foot‐Flagging Frogs Staurois guttatus (Ranidae): An Alerting Function of Calling
2007-07-23

Abstract In multimodal communication, individuals use several sensory modalities for information transfer. We report on novel observations of foot‐flagging in the Bornean ranid frog Staurois guttatus that is temporally linked to advertisement calling. In addition, we document the first case of foot‐flagging in a female anuran as well as additional visual displays in both males and females including arm‐waving, vocal‐sac pumping and open‐mouth display. In males, advertisement calls and foot‐flags were given throughout most of the day, suggesting that acoustic and visual signals form a multicomponent and multimodal display. We tested the efficacy‐based alerting signal hypothesis of multimodal communication using acoustic playback experiments with males. This hypothesis predicts that an initial signal draws the receiver's attention to the location of a subsequent more informative signal. Several lines of evidence supported the alerting hypothesis. First, the latency between foot‐flags and advertisement calls was significantly higher than that between advertisement calls and foot‐flags, suggesting a functional linkage with calls drawing attention to foot‐flags. Secondly, advertisement calling had a signaling function with males responding significantly more often with both calls and foot‐flags compared with pre‐ and post‐playback control periods. Finally, and most notably, all males tested turned towards the playback stimulus, suggesting that the advertisement call serves to focus their attention on subsequent signals. We discuss the potential of multimodal signaling for conspecific and heterospecific communication and the circumstances under which such a multimodal communication system could evolve.
A Pilot Open-Label Study of the Efficacy of Subanesthetic Isomeric S(+)-Ketamine in Refractory CRPS Patients
2007-07-23

S(+)-ketamine can be gradually titrated to large doses (500 mg/day) without clinically relevant side effects. There was no pain relief or change in QST measurements in this series of long-standing severe CRPS patients.
Design and Synthesis of a Tag‐Free Chemical Probe for Photoaffinity Labeling
2007-07-23

Abstract The novel aromatic diazirine‐containing benzoic acid 22 was prepared via the diazirine 11 as the key intermediate. After formylation of the aryl ring and cleavage of the methyl ether function of aldehyde 12 , the phenolic hydroxy group was converted into the ether 21 terminating in an alkyne function. Oxidation of the aldehyde to the carboxylic acid provided the chemical probe 22 designed for tag‐free photoaffinity labeling. In a proof‐of‐concept study it could be shown that irradiation of the simple ester 23 indeed yields the methanol insertion product 24 . A subsequent click reaction with benzyl azide 20 led to the triazole 25 . A more complicated example was realized with the esterification of bafilomycin A 1 ( 27 ) with acid 22 . (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Accelerated partial breast irradiation
2007-07-23

Abstract BACKGROUND. Breast‐conserving surgery followed by whole‐breast radiotherapy (WBRT) has become the standard treatment for the majority of patients with early breast cancer. Whereas the indications for systemic adjuvant treatment have continuously expanded, there is a tendency to restrict postoperative radiotherapy to accelerated partial breast irradiation (APBI) instead of WBRT. METHODS. The different techniques of APBI are described and their respective advantages or potential drawbacks outlined. Moreover, the results described in the literature are briefly reviewed as a basis for the consensus statements and recommendations of the German Society of Radiation Oncology, the German Society of Senology, and the Working Group for Gynecological Oncology of the German Cancer Society. RESULTS. The methods mainly used for APBI are: interstitial radiotherapy with multicatheter technique, intraoperative radiotherapy (IORT) using either electrons produced by linear accelerators or 50 kV x‐rays (Intrabeam), the balloon‐catheter technique (MammoSite), or 3D conformal external beam radiotherapy. These techniques have marked differences in dose distribution and homogeneity. The published range of local recurrence rates varies between 0% to 37%, the median follow‐up from 8 to 72 months. CONCLUSIONS. To date, follow‐up times mostly do not yet permit a definite judgment concerning the long‐term effectiveness and side effects of APBI. The relevant societies in Germany support randomized clinical studies comparing APBI with WBRT in a well‐defined subset of low‐risk patients. However, the authors expressly discourage the routine use of APBI outside clinical trials. Until definite results show that APBI neither impairs therapeutic outcome nor cosmetic results, WBRT remains the gold standard in the treatment of early breast cancer. Cancer 2007. © 2007 American Cancer Society.
Molecular Basis of Resistance to Muramidase and Cationic Antimicrobial Peptide Activity of Lysozyme in Staphylococci
2007-07-24

It has been shown recently that modification of peptidoglycan by O-acetylation renders pathogenic staphylococci resistant to the muramidase activity of lysozyme. Here, we show that a Staphylococcus aureus double mutant defective in O-acetyltransferase A (OatA), and the glycopeptide resistance-associated two-component system, GraRS, is much more sensitive to lysozyme than S. aureus with the oatA mutation alone. The graRS single mutant was resistant to the muramidase activity of lysozyme, but was sensitive to cationic antimicrobial peptides (CAMPs) such as the human lysozyme-derived peptide 107R-A-W-V-A-W-R-N-R115 (LP9), polymyxin B, or gallidermin. A comparative transcriptome analysis of wild type and the graRS mutant revealed that GraRS controls 248 genes. It up-regulates global regulators (rot, sarS, or mgrA), various colonization factors, and exotoxin-encoding genes, as well as the ica and dlt operons. A pronounced decrease in the expression of the latter two operons explains why the graRS mutant is also biofilm-negative. The decrease of the dlt transcript in the graRS mutant correlates with a 46.7% decrease in the content of esterified d-alanyl groups in teichoic acids. The oatA/dltA double mutant showed the highest sensitivity to lysozyme; this mutant completely lacks teichoic acid-bound d-alanine esters, which are responsible for the increased susceptibility to CAMPs and peptidoglycan O-acetylation. Our results demonstrate that resistance to lysozyme can be dissected into genes mediating resistance to its muramidase activity (oatA) and genes mediating resistance to CAMPs (graRS and dlt). The two lysozyme activities act synergistically, as the oatA/dltA or oatA/graRS double mutants are much more susceptible to lysozyme than each of the single mutants.
Ribosomal DNA in plant hybrids: Inheritance, rearrangement, expression
2007-07-25

Abstract Ribosomal RNA genes (rDNA) represent a useful tool to study reticulate evolution. In allopolyploid plant species biparental or uniparental inheritance of 35S rDNA was demonstrated. Uniparental inheritance; as a result of differential elimination of one of the parental rDNA, can be accompanied by structural rearrangements of rDNA ofthe other parent and by formation of new rDNA variants. Particularly, homo‐genization of rDNA in allopolyploids appears to be an example of fast concerted evolution of repeated sequences. At the functional level, interaction between parental 35S rDNA loci in hybrids/allopolyploids leads to differential transcription/silencing, known as nucleolar dominance (ND). Depending on the combination of parental species, ND may be strong and stable, or weak, unstable and even reversible. Differential transcription of parental rDNA is regulated via cytosine methylation of DNA, histone modifications, and chromatin remodelling factors, but mechanisms providing discrimination of parental rDNA remain poorly understood. Probably, interplay between several factors such as local structural features of rDNA (especially subrepeated elements in the intergenic spacer region), unlinked loci, and the chro‐mosomal/genomic context determine ND. The ND and rDNA rearrangements reflect the dynamic nature and evolutionary plasticity of the genome in allopolyploids. Key words: allopolyploidyreticulate speciationmolecular evolutionphylogeny Notes Corresponding author. Email: roman.volkov@uni‐tuebingen.de
Plant highly repeated satellite DNA: Molecular evolution, distribution and use for identification of hybrids
2007-07-25

Abstract Relationships among genomes are often revealed by the occurrence of common or related satellite DNA (satDNA) types. A typical satDNA characterized by specific sites for one (or more) restriction endonuclease(s) is called 'restriction satellite DNA'. Restriction satDNA comprises ‐ in addition to transposons and retrotransposable elements ‐ often highly repeated genome components present in most higher plants. Large arrays of satDNA elements are concentrated at subtelo‐meric and/or centromeric regions (intermingled with other retrotransposon‐derived elements), however, they can be also located as large intercalating blocks along the chromosome. The head‐to‐tail tandemly arranged repeat units (monomers) of satDNA mostly exhibit lengths of 160 to 180 bp or 320 to 370 bp, but other lengths were also found in plants. In particular, in interspecific hybrids between more distantly related species, which often exist only after polyploidization, the individual repetitive DNA of the crossing partners contribute to recombination and rearrangement processes in the hybrids, thereby stimulating genome evolution. Here, we concentrate on the possible origin, molecular evolution, organization and distribution of highly repeated satDNA in various higher plants with emphasis on hybrids and allopolyploids.
MODULATOR OF PIN genes control steady‐state levels of Arabidopsis PIN proteins
2007-07-25

Summary Polar transport of the phytohormone auxin controls numerous growth responses in plants. Molecular characterization of auxin transport in Arabidopsis thaliana has provided important insights into the mechanisms underlying the regulation of auxin distribution. In particular, the control of subcellular localization and expression of PIN‐type auxin efflux components appears to be fundamental for orchestrated distribution of the growth regulator throughout the entire plant body. Here we describe the identification of two Arabidopsis loci, MOP2 and MOP3 (for M ODULATOR O F P IN ), that are involved in control of the steady‐state levels of PIN protein. Mutations in both loci result in defects in auxin distribution and polar auxin transport, and cause phenotypes consistent with a reduction of PIN protein levels. Genetic interaction between PIN2 and both MOP loci is suggestive of functional cross‐talk, which is further substantiated by findings demonstrating that ectopic PIN up‐regulation is compensated in the mop background. Thus, in addition to pathways that control PIN localization and transcription, MOP2 and MOP3 appear to be involved in fine‐tuning of auxin distribution via post‐transcriptional regulation of PIN expression.
Quantitative assessment of ventricular function using three‐dimensional SSFP magnetic resonance angiography
2007-07-25

Abstract Purpose To evaluate three‐dimensional (3D), free‐breathing, steady‐state free precession (SSFP) magnetic resonance angiography (MRA) for volumetric assessment of ventricular function. Materials and Methods In 18 subjects (mean age = 21.5 years) 3D datasets of the heart and great vessels were acquired using an ECG‐triggered, free‐breathing SSFP technique with a T2‐preparation prepulse. Data were acquired during end‐systole (ES) and end‐diastole (ED) for assessment of stroke volumes (SVs). Through‐plane flow measurements of the great arteries were performed as well as 2D‐cine SSFP imaging for comparison. For image analysis of the 3D SSFP datasets a simplex mesh model was used. Papillary muscles were excluded from ventricular volumes using thresholds. Intra‐ and interobserver variability (Bland‐Altman analysis) and correlations (Pearson's coefficient) between volumetric and flow measurements were assessed. Results ES and ED datasets were acquired successfully in all subjects. The best correlation was observed between flow vs. 3D SSFP SV for the LV (r = 0.85, mean difference = −1.0 mL) and the RV (r = 0.89, mean difference = −2.2 mL) with high intra‐ (LV: r = 0.93; RV: r = 0.94) and interobserver (LV: r = 0.91; RV: r = 0.93) reproducibility. Conclusion 3D SSFP datasets combined with semiautomatic segmentation algorithms allow highly accurate and reproducible assessment of left (LV) and right ventricular (RV) SVs in free‐breathing subjects. J. Magn. Reson. Imaging 2007;26:288–295. © 2007 Wiley‐Liss, Inc.
Psychophysical investigation of facial expressions using computer animated faces
2007-07-25

The human face is capable of producing a large variety of facial expressions that supply important information for communication. As was shown in previous studies using unmanipulated video sequences, movements of single regions like mouth, eyes, and eyebrows as well as rigid head motion play a decisive role in the recognition of conversational facial expressions. Here, flexible but at the same time realistic computer animated faces were used to investigate the spatiotemporal coaction of facial movements systematically. For three psychophysical experiments, spatiotemporal properties were manipulated in a highly controlled manner. First, single regions (mouth, eyes, and eyebrows) of a computer animated face performing seven basic facial expressions were selected. These single regions, as well as combinations of these regions, were animated for each of the seven chosen facial expressions. Participants were then asked to recognize these animated expressions in the experiments. The findings show that the animated avatar in general is a useful tool for the investigation of facial expressions, although improvements have to be made to reach a higher recognition accuracy of certain expressions. Furthermore, the results shed light on the importance and interplay of individual facial regions for recognition. With this knowledge the perceptual quality of computer animations can be improved in order to reach a higher level of realism and effectiveness.
Morph Moulder: Teaching Software for HPSG and Description Logics
2007-07-25

The graphical software Morph Moulder (MoMo) presented here was originally created for teaching the logical foundations of Head-Driven Phrase Structure Grammar (HPSG) in an e-Learning environment. It has then been extended to a treatment of description logics (DL), which are at present the standard formalism for building ontologies. With MoMo, students can construct interpretations of sets of formulae and check whether their interpretations model these formulae (called theory in HPSG and axioms in DL). MoMo also supports reasoning such as the construction of well-formed interpretations in the feature logic of HPSG and the automatic extraction of subsumption hierarchies in DL. It has been used successfully in several courses on HPSG linguistics, on computational grammar implementation and on the logical foundations of constraint-based grammar frameworks.
AXL and AXR1 have redundant functions in RUB conjugation and growth and development in Arabidopsis
2007-07-26

Summary Cullin‐RING ubiquitin‐protein ligases such as the Skp1, cullin, F‐box protein (SCF) have been implicated in many growth and developmental processes in plants. Normal SCF function requires that the CUL1 subunit be post‐translationally modified by related to ubiquitin (RUB), a protein related to ubiquitin. This process is mediated by two enzymes: the RUB‐activating and RUB‐conjugating enzymes. In Arabidopsis, the RUB‐activating enzyme is a heterodimer consisting of AXR1 and ECR1. Mutations in the AXR1 gene result in a pleiotropic phenotype that includes resistance to the plant hormone auxin. Here we report that the AXL ( AXR1‐like ) gene also functions in the RUB conjugation pathway. Overexpression of AXL in the axr1‐3 background complements the axr1‐3 phenotype. Biochemical analysis indicates that AXL overexpression restores CUL1 modification to the wild‐type level, indicating that AXR1 and AXL have the same biochemical activity. Although the axl mutant resembles wild‐type plants, the majority of axr1 axl‐1 double mutants are embryo or seedling lethal. Furthermore, the axl‐1 mutation reveals novel RUB‐dependent processes in embryo development. We conclude that AXR1 and AXL function redundantly in the RUB conjugating pathway.
Constraint preserving implicit finite element discretization of harmonic map flow into spheres
2007-07-26

Abstract. Discretization of harmonic map \\now on the sphere often uses a penalization or projection strategy, where the rst suers from proper tuning of an additional parameter, and the latter from lack of discrete energy law, and concomitant restrictive mesh-constraints. We propose an implicit scheme that preserves the sphere condition at every node, enjoys discrete energy law, and unconditionally converges to weak solutions of the harmonic map heat \\now.
PD-1–PD-L1 Pathway Is Involved in Suppressing Alloreactivity of Heart Infiltrating T Cells During Murine GVHD Across Minor Histocompatibility Antigen Barriers
2007-07-26

Our data indicate that immunomodulatory molecules such as PD-L1 rather than Tregs play pivotal roles in the tissue-specific regulation of alloresponses. Further studies are needed to refine the significance of the PD-L1 pathway in GVHD and its versatility for therapeutic intervention.
Hypothalamic-Pituitary-Adrenal Axis Hyporesponsiveness to Restraint Stress in Mice Deficient for Large-Conductance Calcium- and Voltage-Activated Potassium (BK) Channels
2007-07-27

Stress activates the hypothalamic-pituitary-adrenal (HPA) axis, releasing ACTH from the anterior pituitary gland and glucocorticoids from the adrenal cortex. Stress also activates the sympathetic nervous system, evoking adrenaline release from the adrenal medulla. Large-conductance calcium- and voltage-activated potassium (BK) channels have been implicated in regulation of cellular excitability in these systems. Here, we examine the functional role of BK channels in HPA axis regulation in vivo using female mice genetically deficient (BK−/−) for the pore-forming subunits of BK channels. BK−/− phenotype in the HPA was confirmed by immunohistochemistry, Western blot analysis, and corticotrope patch-clamp recording. Restraint stress-induced plasma concentrations of ACTH and corticosterone were significantly blunted in BK−/− mice compared with wild type (WT) controls. This stress hyporesponsiveness was associated with reduced activation of hypothalamic paraventricular nucleus (PVN) neurons. Basal expression of CRH, but not arginine vasopressin mRNA in the PVN was significantly lower in BK−/− mice compared with WT controls. Total anterior pituitary ACTH peptide content, but not proopiomelanocortin mRNA expression or corticotrope number, was significantly reduced in BK−/− mice compared with WT. However, anterior pituitary corticotropes from BK−/− mice fully supported ACTH output, releasing a significantly greater proportion of stored ACTH in response to secretagogue in vitro compared with WT. These results support an important role for BK channels in both the neural circuitry and endocrine output of the HPA axis and indicate that the stress hyporesponsiveness in BK−/− mice primarily results from reduced activation of hypothalamic PVN neurosecretory neurons.