julilili42/papers huggingface dataset:
Genome‐wide linkage scan of nonsyndromic orofacial clefting in 91 families of central European origin
2009-11-24

Abstract Orofacial clefts are among the most common of all congenital disorders. Nonsyndromic cases of cleft lip with or without cleft palate (NSCL/P) and cleft palate only (NSCPO) are considered to have a multifactorial etiology which involves both genetic and environmental factors. We present the results of a genome‐wide linkage scan in 91 families of central European descent with nonsyndromic orofacial clefts (NSC). The sample included 74 NSCL/P families, 15 NSCPO families, and 2 mixed families (a total of 217 affected and 230 unaffected individuals were genotyped). We genotyped 542 microsatellite markers (average intermarker distance = 6.9 cM). Multipoint nonparametric linkage analysis was performed using Allegro 2.0f. In addition to the factors investigated in previous genome‐wide linkage analyses, we searched for sex‐specific susceptibility loci, loci demonstrating parental imprinting and loci that are shared by NSCL/P and NSCPO. Several genomic regions likely to contain susceptibility loci for NSC were identified at the level of nominal significance. Some of these overlap with regions identified in previous studies. Suggestive evidence of linkage was obtained for the loci 4q21‐q26 and 1p31‐p21, with the chromosome 1 locus showing a male‐specific genetic effect. Our study has identified promising chromosomal regions for the identification of NSC‐associated genes, and demonstrates the importance of performing detailed statistical analyses which take into account complex genetic mechanisms such as sex‐specific effects and genomic imprinting. Further research in large patient samples is necessary to identify factors common to NSCL/P and NSCPO. © 2009 Wiley‐Liss, Inc.
Tetrabrominated Lead Naphthalocyanine for Optical Power Limiting
2009-11-24

Abstract The complex 2,(3)‐tetrabromo‐3,(2)‐tetra[(3,5‐di‐ tert ‐butyl)phenyloxy]‐naphthalocyaninato lead [Br 4 ( t Bu 2 C 6 H 3 O) 4 NcPb, 1 ] has been prepared and its optical limiting properties for ns light pulses have been measured. Complex 1 behaves as a reverse saturable absorber within the spectral range 440–720 nm with a limiting threshold of 0.1 J cm −2 at 532 nm. The lifetime of the absorbing triplet excited state has been evaluated as 3.8×10 −7 s and the quantum yield of triplet formation has been measured as 0.07 in toluene. The nonlinear optical transmission properties of complex 1 have also been determined in Plexiglas [naphthalocyanine content: 5.0×10 −4 M (0.1 % by weight)]. A reversible nonlinear absorption was again observed for a fluence above 0.4 J cm −2 , but through different excited‐state dynamics. This may be rationalized in terms of aggregation of the molecule in the polymer matrix.
A torque formula for non-isothermal type I planetary migration - I. Unsaturated horseshoe drag
2009-11-25

We study the torque on low-mass planets embedded in protoplanetary discs in\\nthe two-dimensional approximation, incorporating non-isothermal effects. We\\ncouple linear estimates of the Lindblad (or wave) torque to a simple, but\\nnon-linear, model of adiabatic corotation torques (or horseshoe drag),\\nresulting in a simple formula that governs Type I migration in non-isothermal\\ndiscs. This formula should apply in optically thick regions of the disc, where\\nviscous and thermal diffusion act to keep the horseshoe drag unsaturated. We\\ncheck this formula against numerical hydrodynamical simulations, using three\\nindependent numerical methods, and find good agreement.\\n
Immunoglobulin Superfamily Virus Receptors and the Evolution of Adaptive Immunity
2009-11-26

Obligate intracellular pathogens depend on cell-surface molecules to attach and enter into host cells. Pathogen receptors may be highly specialized proteins, such as complement receptors or neurotransmitter receptors, or more ubiquitous components of cell membranes, such as integrins or sialic acid–containing oligosaccharides. The immunoglobulin superfamily (IgSF) of molecules contains several members that are expressed at the cell surface, bind diverse ligands, and contribute to a variety of cellular activities, including adhesion and immune responses. Many viruses have usurped the adhesive properties of IgSF proteins to mediate attachment (Table 1). Strategies used by viruses to engage IgSF receptors provide clues to general mechanisms by which IgSF proteins bind different types of ligands, including antigens.
Determination of leaching behaviour of polycyclic aromatic hydrocarbons from contaminated soil by column leaching test
2009-11-26

Column leaching tests become increasingly important for assessing the risk of release of pollutants from a wide variety of solid materials into water. In this study a column leaching test was designed to provide insight into the fate of selected polycyclic aromatic hydrocarbons (PAHs) in soils and their leaching behaviour. The results showed relatively high initial concentrations of naphthalene, anthracene, and pyrene for column B2. Two proportions of contaminated soil (5 and 20%) used in the columns yielded different leaching behaviour. Different contact time applied in columns B1 and B2 affected the initial amounts of leached PAHs. Results indicated that the distribution pattern of PAH compounds in solid phase considerably affected leached concentrations of PAHs. Released amounts of PAH compounds decreased with increasing molecular size, or rather the hydrophobicity of the compound. The effect of dissolved organic carbon on PAH leaching was also investigated in this study. The mobilization of colloids did not show any significant effect on leached concentrations of PAH compounds. Approximately 4.6 and 2.2% of the total initial amounts of studied PAHs in the soil were leached in columns B1 and B2, respectively. Therefore high PAH concentrations in the solid phase does not imply serious groundwater contamination risk during a leaching event (e.g. raining) and significant amount of contaminants may stay in the soil layer for a long time and do not leach down into groundwater.
Treatment Strategies for Follicular Center Cell Non-Hodgkin’s Lymphoma
2009-11-27

Non-Hodgkin's lymphomas (NHL), a heterogenous group of malignancies arising from lymphoid tissue, account for almost 5% of all cancers occurring in the United States [1]. With an estimated 63,190 new cases and 18,660 cancer deaths projected in 2007 in the United States, NHL is the fifth most common malignant neoplasm after the breast, prostate, lung, and colon [2]. The incidence and mortality rates were reported to have risen steadily in Western countries over the past decades and have doubled between 1950 and 1989, from 5.9 to 13.7 per 100,000 persons per year [3] but the incidence rate had slowed to 1-2% in the 1990s [4, 5].
(2Z)-2-Fluoro-N-{4-[5-(4-fluorophenyl)-2-methylsulfanyl-1H-imidazol-4-yl]-2-pyridyl}-3-phenylacrylamide
2009-11-28

The asymmetric unit of the title compound, C(24)H(18)F(2)N(4)OS, contains two crystallographically independent mol-ecules, A and B, which are linked into two chains of A and B mol-ecules by inter-molecular N-H⋯O hydrogen bonds. The three-dimensional network is stabilized by π-π inter-actions between the pyridine rings and phenyl rings of different residues, with centroid-centroid distances of 3.793 (1) and 3.666 (2) Å. The mol-ecular conformation is stabilized by intra-molecular N-H⋯F hydrogen bonds (2.15/2.15Å). The imidazole rings make dihedral angles of 39.5 (2)/38.5 (2) and 31.8 (2)/33.2 (2)° with the 4-fluoro-phenyl rings and the pyridine rings, respectively. The methyl group of molecule A is disorderd in a 0.60:0.40 ratio.
Comprehensive genotype–phenotype analysis in 230 patients with tetralogy of Fallot
2009-11-30

Background Tetralogy of Fallot (ToF), the most frequent cyanotic congenital heart disease, is associated with a wide range of intra- and extracardiac phenotypes. In order to get further insight into genotype–phenotype correlation, a large cohort of 230 unselected patients with ToF was comprehensively investigated. Methods and results 230 patients with ToF were studied by karyotyping, comprehensive 22q11.2 deletion testing and sequencing of TBX1, NKX2.5 and JAG1 , as well as molecular karyotyping in selected patients. Pathogenic genetic aberrations were found in 42 patients (18%), with 22q11.2 deletion as the most common diagnosis (7.4%), followed by trisomy 21 (5.2%) and other chromosomal aberrations or submicroscopic copy number changes (3%). Mutations in JAG1 were detected in three patients with Alagille syndrome (1.3%), while NKX2.5 mutations were seen in two patients with non-syndromic ToF (0.9%). One patient showed a recurrent polyalanine stretch elongation within TBX1 which represents a true mutation resulting in loss of transcriptional activity due to cytoplasmatic protein aggregation. Conclusion This study shows that 22q11.2 deletion represents the most common known cause of ToF, and that the associated cardiac phenotype is distinct for obstruction of the proximal pulmonary artery, hypoplastic central pulmonary arteries and subclavian artery anomalies. Atrioventricular septal defect associated with ToF is very suggestive of trisomy 21 and almost excludes 22q11.2 deletion. We report a further patient with a recurrent polyalanine stretch elongation within TBX1 and for the first time link TBX1 cytoplasmatic protein aggregation to congenital heart defects.
Requirements for control of B‐cell lymphoma by NK cells
2009-11-30

Abstract The role of NK cells in the control of endogenously arising tumors is still unclear. We monitored activation and effector functions of NK cells in a c‐myc ‐transgenic mouse model of spontaneously arising lymphoma. At early stages, tumors demonstrated reduced MHC class I expression and increased expression of natural killer group 2D ligands (NKG2D‐L). NK cells in these tumors showed an activated phenotype that correlated with the loss of tumor MHC class I. With increasing tumor load however, NK‐cell effector functions became progressively paralyzed or exhausted. In later stages of disease, tumors re‐expressed MHC class I and lost NKG2D‐L, suggesting a role of these two signals for NK cell‐mediated tumor control. Testing a panel of lymphoma cell lines expressing various MHC class I and NKG2D‐L levels suggested that NK cell‐dependent tumor control required a priming and a triggering signal that were provided by MHC class I down‐regulation and by NKG2D‐L, respectively. Deleting either of the “two signals” resulted in tumor escape. At early disease stages, immune stimulation through TLR‐ligands in vivo efficiently delayed lymphoma growth in a strictly NK cell‐dependent manner. Thus, NK‐receptor coengagement is crucial for NK‐cell functions in vivo and especially for NK cell‐mediated tumor surveillance.
Glucocorticoids increase α5 integrin expression and adhesion of synovial fibroblasts but inhibit ERK signaling, migration, and cartilage invasion
2009-11-30

Abstract Objective In rheumatoid arthritis (RA), integrins mediate cell adhesion, migration, and invasion, and their expression is regulated by cytokines and growth factors. The aim of this study was to investigate whether hormones such as cortisol or other steroids can influence integrin expression and function in the synovial cells of patients with RA. Methods We performed immunofluorescence and fluorescence‐activated cell sorting analyses to quantify surface integrin levels. Adhesion and migration assays were performed to study the function of synovial fibroblasts (SFs). ERK activation was measured by cellular activation of a signaling enzyme‐linked immunosorbent assay. Invasion of SFs into cartilage was determined in the SCID mouse coimplantation model of RA in vivo. Results In RA, expression of integrin subunits α5, αv, and β1 was higher at the site of invasion compared with the sublining zone. Testosterone and 17β‐estradiol had no influence on integrin levels, but cortisol up‐regulated expression of the α5 subunit in a time‐dependent and dose‐dependent manner. In addition, cortisol increased the adhesion of SFs to fibronectin and inhibited ERK signaling upon integrin activation or upon stimulation with tumor necrosis factor. Small interfering RNA or a neutralizing antibody to α5 integrin increased SF migration, indicating that up‐regulated α5 integrin is responsible for an immobile phenotype. In addition, in the SCID mouse model, SF invasion into cartilage was attenuated by glucocorticoid treatment in vivo. Conclusion Glucocorticoids increase integrin expression and the adhesion of cells to fibronectin, inhibit ERK signaling, and down‐regulate the invasiveness of SFs in vivo. This study demonstrates that an important antiinflammatory aspect of glucocorticoids is regulating the expression and function of α5 integrin.
Characterization of binding affinities in a chromatographic system by suspended state HR/MAS NMR spectroscopy
2009-11-30

Abstract In the current work a racemate of ( R )‐ and ( S )‐benzylmandelate was separated with a stereoselective polysaccharide‐based chiral stationary phase by HPLC. To elucidate the occurring chiral molecular recognition processes in the heterogeneous system used, NMR spectroscopy was chosen under high resolution/magic angle spinning (HR/MAS) NMR conditions in the suspended state. Therefore, and as a proof of concept, a combination of several NMR methods such as spin–lattice relaxation time ( T 1 ) measurements ( T 1 ), the saturation transfer difference, and the 2D experiment of the transferred nuclear overhauser enhancement spectroscopy technique were applied. With HR/MAS NMR it is feasible to combine NMR and chromatography to achieve further insights into the separation process. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Heat Shock Protein Cognate 70-4 and an E3 Ubiquitin Ligase, CHIP, Mediate Plastid-Destined Precursor Degradation through the Ubiquitin-26S Proteasome System inArabidopsis
2009-12-01

Abstract Plastid-targeted proteins pass through the cytosol as unfolded precursors. If proteins accumulate in the cytosol, they can form nonspecific aggregates that cause severe cellular damage. Here, we demonstrate that high levels of plastid precursors are degraded through the ubiquitin-proteasome system (UPS) in Arabidopsis thaliana cells. The cytosolic heat shock protein cognate 70-4 (Hsc70-4) and E3 ligase carboxy terminus of Hsc70-interacting protein (CHIP) were highly induced in plastid protein import2 plants, which had a T-DNA insertion at Toc159 and showed an albino phenotype and a severe defect in protein import into chloroplasts. Hsc70-4 and CHIP together mediated plastid precursor degradation when import-defective chloroplast-targeted reporter proteins were transiently expressed in protoplasts. Hsc70-4 recognized specific sequence motifs in transit peptides and thereby led to precursor degradation through the UPS. CHIP, which interacted with Hsc70-4, functioned as an E3 ligase in the Hsc70-4–mediated protein degradation. The physiological role of Hsc70-4 was confirmed by analyzing Hsc70-4 RNA interfernce plants in an hsc70-1 mutant background. Plants with lower Hsc70 levels exhibited abnormal embryogenesis, resulting in defective seedlings that displayed high levels of reactive oxygen species and monoubiquitinated Lhcb4 precursors. We propose that Hsc70-4 and CHIP mediate plastid-destined precursor degradation to prevent cytosolic precursor accumulation and thereby play a critical role in embryogenesis.
PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase-Mediated Recruitment into GNOM-Independent Trafficking inArabidopsis
2009-12-01

Abstract The phytohormone auxin plays a major role in embryonic and postembryonic plant development. The temporal and spatial distribution of auxin largely depends on the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation and crucially contributes to the regulation of apical-basal PIN polarity. The GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially mediates PIN recycling at the basal side of the cell. Interference with GNOM activity leads to dynamic PIN transcytosis between different sides of the cell. Our genetic, pharmacological, and cell biological approaches illustrate that PID and GNOM influence PIN polarity and plant development in an antagonistic manner and that the PID-dependent PIN phosphorylation results in GNOM-independent polar PIN targeting. The data suggest that PID and the protein phosphatase 2A not only regulate the static PIN polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN transcytosis. We propose a model that includes PID-dependent PIN phosphorylation at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent pathway for polarity alterations during developmental processes, such as lateral root formation and leaf vasculature development.
Multiplex microsphere‐based flow cytometric platforms for protein analysis and their application in clinical proteomics – from assays to results
2009-12-01

Abstract Advances in high‐throughput screening, together with rapid progress in genomic and proteomic sciences, have considerably stimulated the development of a variety of biomarker discovery tools and have contributed to the improvement of clinical diagnosis. Major challenges include the obtaining of high‐quality data sets based on assays that are rapid, reliable, and inexpensive, but still highly sensitive and easy to perform. The microsphere‐based flow cytometric technology is a platform that is currently entering the diagnostic market. This article reviews the development and the applications of microsphere‐based flow cytometric platforms in basic and applied proteomic research, and discusses bead‐based assays used in clinical applications.
“Building a New Socialist Countryside” – Only a Political Slogan?
2009-12-01

In March 2006, China's National People's Congress officially promulgated the central government's intention to “build a new socialist countryside”, a new policy initiative and approach to rural development. Drawing on fieldwork conducted in two Chinese counties in 2008 and 2009, this article investigates how the new policy is being substantiated and implemented at the local level. It argues that by combining China's new fiscal system of transfer payments to poor local governments with administrative reforms, intensified internal project evaluation, and efforts to increase the rural income through a mixture of infrastructural investment, agricultural specialization, the expansion of social welfare, and accelerated urbanization, “building a new socialist countryside” constitutes more than a political slogan and has the potential to successfully overcome rural poverty and the rural-urban divide.
The ConMap approach for terrain‐based digital soil mapping
2009-12-01

We present a new digital terrain analysis framework for digital soil mapping, referred to as contextual elevation mapping (ConMap). In contrast to common regression approaches based on features from digital terrain analysis, ConMap is not based on standard terrain attributes, but on elevation differences from the centre pixel to each pixel in circular neighbourhoods only. These differences are used as features in random forest regressions. We applied and validated the framework by predicting topsoil silt content in a loess region of 1150 km 2 in Rhineland‐Palatinate and Hesse, Germany. Three hundred and forty‐two samples and a 20‐m resolution digital elevation model were used for this illustration and validation. We compared ConMap with standard and multi‐scale terrain analysis approaches as well as with ordinary kriging interpolations. Cross‐validation root mean square error ( RMSE) decreased from 16.1 when the standard digital terrain analysis was used to 11.2 when ConMap was used. This corresponds to an increase in variance explained ( R 2 ) from 15 to 61%. Even though ordinary kriging out‐performed standard terrain analysis as well, the variance explained was 6% smaller compared with that using ConMap. The results show that the geomorphic settings in the study area must have induced the spatial trend, which can be accounted for by ConMap over different scales. We conclude that ConMap shows great potential for digital soil mapping studies.
Study of Gene-Targeted Mouse Models of Splicing Factor GenePrpf31Implicated in Human Autosomal Dominant Retinitis Pigmentosa (RP)
2009-12-01

The results imply that Prpf31 is necessary for survival, and there is no compensation mechanism in mouse for the lack of this splicing factor. The authors suggest that p.A216P mutation in Prpf31 does not exert a dominant negative effect and that one Prpf31 wild-type allele is sufficient for maintenance of the healthy retina in mice.
Isolation and Culture of Ventral Mesencephalic Precursor Cells and Dopaminergic Neurons from Rodent Brains
2009-12-01

Abstract The ability to isolate ventral midbrain (VM) precursor cells and neurons provides a powerful means to characterize their differentiation properties and to study their potential for restoring dopamine (DA) neurons degenerated in Parkinson's disease (PD). Preparation and maintenance of DA VM in primary culture involves a number of critical steps to yield healthy cells and appropriate data. Here, we offer a detailed description of protocols to consistently prepare VM DA cultures from rat and mouse embryonic fetal‐stage midbrain. We also present methods for organotypic culture of midbrain tissue, for differentiation as aggregate cultures, and for adherent culture systems of DA differentiation and maturation, followed by a synopsis of relevant analytical read‐out options. Isolation and culture of rodent VM precursor cells and DA neurons can be exploited for studies of DA lineage development, of neuroprotection, and of cell therapeutic approaches in animal models of PD. Curr. Protoc. Stem Cell Biol . 11:2D.5.1‐2D.5.21. © 2009 by John Wiley &amp; Sons, Inc.
Spectrum of magnetic resonance imaging appearances of juvenile temporomandibular joints (tmj) in non-rheumatic children
2009-12-01

Background: Temporomandibular joints (TMJ) are frequently involved in children with juvenile idiopathic arthritis (JIA), and gadolinium-enhanced magnetic resonance imaging (MRI) is the only modality for an early diagnosis. However, only very few data exist on the appearance of contrast-enhanced MRI of normal juvenile TMJ. Purpose: To define the spectrum of normal MRI findings of juvenile TMJ, and to assess a possible overlap with findings typical for active synovitis in JIA. Material and Methods: 96 children (192 TMJ), 51 boys and 45 girls with a median age of 7.8 years (range 3–13 years), underwent a head MRI. The presence of autoimmune disease, including JIA, was excluded via chart history, available laboratory findings, and the absence of known typical pathological MRI changes (degree of synovial enhancement, hyperintense signal on T2-weighted images in the synovia or bone marrow, and morphologic changes of the mandibular condyle) of the TMJ affected by JIA. Results: In 90 (94%) children, the TMJ showed no MRI abnormalities compatible with arthritis. In three children (3%), the only abnormal MRI finding was a small bilateral joint effusion. A further three children (3%) had a mild synovial enhancement seen on both axial and coronal MR planes in one child and only in the axial plane in the other two children. Signal hyperintensity on T2-weighted images and other corresponding characteristics of TMJ inflammation were lacking in all these six patients. Conclusion: The vast majority of juvenile TMJ in non-rheumatic children shows no MRI abnormalities. Exceptions, including a discrete enhancement of the synovial membrane (3%) or small joint effusions (3%), can occur in a minority of patients, but none of them are accompanied by other signs of inflammation or morphological changes of the TMJ.