julilili42/papers huggingface dataset:
Potential Function of Added Minerals as Nucleation Sites and Effect of Humic Substances on Mineral Formation by the Nitrate-Reducing Fe(II)-Oxidizer Acidovorax sp. BoFeN1
2012-05-29

The mobility of toxic metals and the transformation of organic pollutants in the environment are influenced and in many cases even controlled by iron minerals. Therefore knowing the factors influencing iron mineral formation and transformation by Fe(II)-oxidizing and Fe(III)-reducing bacteria is crucial for understanding the fate of contaminants and for the development of remediation technologies. In this study we followed mineral formation by the nitrate-reducing Fe(II)-oxidizing strain Acidovorax sp. BoFeN1 in the presence of the crystalline Fe(III) (oxyhydr)oxides goethite, magnetite and hematite added as potential nucleation sites. Mössbauer spectroscopy analysis of minerals precipitated by BoFeN1 in (57)Fe(II)-spiked microbial growth medium showed that goethite was formed in the absence of mineral additions as well as in the presence of goethite or hematite. The presence of magnetite minerals during Fe(II) oxidation induced the formation of magnetite in addition to goethite, while the addition of humic substances along with magnetite also led to goethite but no magnetite. This study showed that mineral formation not only depends on the aqueous geochemical conditions but can also be affected by the presence of mineral nucleation sites that initiate precipitation of the same underlying mineral phases.
A Novel Look at Astrocytes
2012-05-29

Aquaporin-4 (AQP4) water channels are located at the basolateral membrane domain of many epithelial cells involved in ion transport and secretion. These epithelial cells separate fluid compartments by forming apical tight junctions. In the brain, AQP4 is located on astrocytes in a polarized distribution: At the border to blood vessels or the pial surface, its density is very high. During ontogeny and phylogeny, astroglial cells go through a stage of expressing tight junctions, separating fluid compartments differently than in adult mammals. In adult mammals, this barrier is formed by arachnoid, choroid plexus, and endothelial cells. The ontogenetic and phylogenetic barrier transition from glial to endothelial cells correlates with the regenerative capacity of neuronal structures: Glial cells forming tight junctions, and expressing no or unpolarized AQP4 are found in the fish optic nerve and the olfactory nerve in mammals both known for their regenerative ability. It is hypothesized that highly polarized AQP4 expression and the lack of tight junctions on astrocytes increase ionic homeostasis, thus improving neuronal performance possibly at the expense of restraining neurogenesis and regeneration.
Langkolide, a 32-Membered Macrolactone Antibiotic Produced by Streptomyces sp. Acta 3062
2012-05-29

A new 32-membered macrolactone antibiotic, named langkolide, was isolated from the mycelium of Streptomyces sp. Acta 3062. The langkolide structure was determined by HR-MS and 1D and 2D NMR as a 32-membered macrolactone connected from an overhanging polyketide tail to a naphthoquinone unit mediated by two carbohydrate moieties. The producing strain was isolated from a rhizosphere soil of Clitorea sp. collected at Burau Bay, Langkawi, Malaysia, and was characterized by its morphological and chemotaxonomic features in addition to its 16S rRNA gene sequence. It was identified as a member of the Streptomyces galbus clade. Langkolide exhibited various bioactivities including antimicrobial and antiproliferative activities. Furthermore, langkolide inhibited human recombinant phosphodiesterase 4 with an IC(50) value of 0.48 μM.
Non-contact, Label-free Monitoring of Cells and Extracellular Matrix using Raman Spectroscopy
2012-05-29

Non-destructive, non-contact and label-free technologies to monitor cell and tissue cultures are needed in the field of biomedical research.(1-5) However, currently available routine methods require processing steps and alter sample integrity. Raman spectroscopy is a fast method that enables the measurement of biological samples without the need for further processing steps. This laser-based technology detects the inelastic scattering of monochromatic light.(6) As every chemical vibration is assigned to a specific Raman band (wavenumber in cm(-1)), each biological sample features a typical spectral pattern due to their inherent biochemical composition.(7-9) Within Raman spectra, the peak intensities correlate with the amount of the present molecular bonds.(1) Similarities and differences of the spectral data sets can be detected by employing a multivariate analysis (e.g. principal component analysis (PCA)).(10) Here, we perform Raman spectroscopy of living cells and native tissues. Cells are either seeded on glass bottom dishes or kept in suspension under normal cell culture conditions (37 °C, 5% CO(2)) before measurement. Native tissues are dissected and stored in phosphate buffered saline (PBS) at 4 °C prior measurements. Depending on our experimental set up, we then either focused on the cell nucleus or extracellular matrix (ECM) proteins such as elastin and collagen. For all studies, a minimum of 30 cells or 30 random points of interest within the ECM are measured. Data processing steps included background subtraction and normalization.
Magnetic resonance imaging based determination of body compartments with the versatile, interactive sparse sampling (VISS) method
2012-05-29

Abstract Purpose: To investigate the inhomogeneity of radiofrequency fields at higher field strengths that can interfere with established volumetric methods, in particular for the determination of visceral ( VAT ) and subcutaneous adipose tissue ( SCAT ). A versatile, interactive sparse sampling ( VISS ) method is proposed to determine VAT, SCAT, and also total body volume (TBV). Materials and Methods: VISS is based on a separation of major components by contour lines, followed by a sparse sampling algorithm, and eventually a quick manual correction. T1‐weighted whole body scans of 24 subjects were evaluated (12 at 1.5T, 12 at 3.0T). Results: (a) Coefficients of variance (CV) and intra class correlation coefficients ( ICC ) determined within 3 raters (24 subjects) showed high consistency for SCAT (CV 2.2%, ICC 0.993) and VAT (CV 4.9%, ICC 0.987), (b) comparison with an established volumetric method revealed good agreement (Bland‐Altman, VAT −0.68L to 1.07L, SCAT −2.18L to 8.39L), and (c) comparison of weights calculated from TBV with values measured on a scale resulted in an even better accuracy for VISS (Bland‐Altman −1.98 kg to 4.09 kg) than for the reference method (−5.60 kg to 1.60 kg). Conclusion: VISS is reproducible in particular within the same rater, accurate as compared with established methods, and robust against low contrast and inhomogeneity artifacts. J. Magn. Reson. Imaging 2012;36:951–960. © 2012 Wiley Periodicals, Inc.
Non-contact, Label-free Monitoring of Cells and Extracellular Matrix using Raman Spectroscopy
2012-05-29

Non-destructive, non-contact and label-free technologies to monitor cell and tissue cultures are needed in the field of biomedical research.1-5 However, currently available routine methods require processing steps and alter sample integrity. Raman spectroscopy is a fast method that enables the measurement of biological samples without the need for further processing steps. This laser-based technology detects the inelastic scattering of monochromatic light.6 As every chemical vibration is assigned to a specific Raman band (wavenumber in cm-1), each biological sample features a typical spectral pattern due to their inherent biochemical composition.7-9 Within Raman spectra, the peak intensities correlate with the amount of the present molecular bonds.1 Similarities and differences of the spectral data sets can be detected by employing a multivariate analysis (e.g. principal component analysis (PCA)).10 Here, we perform Raman spectroscopy of living cells and native tissues. Cells are either seeded on glass bottom dishes or kept in suspension under normal cell culture conditions (37 °C, 5% CO2) before measurement. Native tissues are dissected and stored in phosphate buffered saline (PBS) at 4 °C prior measurements. Depending on our experimental set up, we then either focused on the cell nucleus or extracellular matrix (ECM) proteins such as elastin and collagen. For all studies, a minimum of 30 cells or 30 random points of interest within the ECM are measured. Data processing steps included background subtraction and normalization.
Brain–computer interfaces for communication with nonresponsive patients
2012-05-30

Abstract A substantial number of patients who survive severe brain injury progress to a nonresponsive state of wakeful unawareness, referred to as a vegetative state (VS). They appear to be awake, but show no signs of awareness of themselves, or of their environment in repeated clinical examinations. However, recent neuroimaging research demonstrates that some VS patients can respond to commands by willfully modulating their brain activity according to instruction. Brain–computer interfaces (BCIs) may allow such patients to circumvent the barriers imposed by their behavioral limitations and communicate with the outside world. However, although such devices would undoubtedly improve the quality of life for some patients and their families, developing BCI systems for behaviorally nonresponsive patients presents substantial technical and clinical challenges. Here we review the state of the art of BCI research across noninvasive neuroimaging technologies, and propose how such systems should be developed further to provide fully fledged communication systems for behaviorally nonresponsive populations. Ann Neurol 2012;72:312–323
Variants of Toll-like Receptor 4 Predict Cardiac Recovery in Patients with Dilated Cardiomyopathy
2012-05-30

The clinical course of patients with dilated cardiomyopathy (DCM) varies from cardiac recovery to end stage heart failure. The etiology of this variability is largely unknown. In this study, we investigated the impact of coding polymorphisms of the innate immune protein Toll-like receptor 4 (TLR4) on left ventricular performance in patients with DCM. Two variants of TLR4 (rs4986790, TLR4 c.1187A→G, p.299D→G and rs4986791,TLR4 c.1487C→T, p.T399I) were investigated in 158 patients with DCM. Other reasons for heart failure were excluded by coronary angiography, myocardial biopsy, and echocardiography. Risk factors, age, gender, or treatment did not differ among the groups. At the follow-up evaluation (median 4.0-5.4 months), patients carrying the TLR4 wild type gene displayed cardiac recovery under intense medical heart failure therapy indexed by reduced left ventricular dilation, improved left ventricular ejection fraction, and reduced NT-probrain natriuretic peptide blood level when compared with the initial evaluation. In contrast, patients carrying both the rs4986790 and the rs4986791 variant showed significantly reduced improvement of left ventricular ejection fraction (p = 0.006) and left ventricular dilation (p = 0.015) at the follow-up evaluation when compared with carriers of the wild type gene under the same treatment conditions. In addition, NT-probrain natriuretic peptide level in carriers of both TLR4 variants did not change significantly at the follow up when compared with the first evaluation. Among patients with DCM, the presence of the TLR4 variants rs4986790 and rs4986791 predicts impaired cardiac recovery independently of medical treatment or cardiac risk factors.
Characterisation of the Cell Line HC-AFW1 Derived from a Pediatric Hepatocellular Carcinoma
2012-05-30

Current treatment of paediatric hepatocellular carcinoma (HCC) is often inefficient due to advanced disease at diagnosis and resistance to common drugs. The aim of this study was to generate a cell line derived from a paediatric HCC in order to expand research in this field. We established the HC-AFW1 cell line from a liver neoplasm of a 4-year-old boy through culturing of primary tumor specimens. The cell line has been stable for over one year of culturing and has a doubling time of 40 h. The tumour cells have an epithelial histology and express HCC-associated proteins such as Alpha-fetoprotein (AFP), Glypican 3, E-cadherin, CD10, CD326, HepPar1 and Vimentin. Forty-nine amino acids in exon 3 of β-Catenin that involve the phosphorylation sites of GSK3 were absent and β-Catenin is detectable in the cell nuclei. Cytogenetic analysis revealed large anomalies in the chromosomal map. Several alterations of gene copy numbers were detected by genome-wide SNP array. Among the different drugs tested, cisplatin and irinotecan showed effective inhibition of tumour cell growth in a proliferation assay at concentrations below 5 μg/ml. Subcutaneous xenotransplantation of HC-AFW1 cells into NOD/SCID mice resulted in fast growing dedifferentiated tumours with high levels of serum AFP. Histological analyses of the primary tumour and xenografts included national and international expert pathological review. Consensus reading characterised the primary tumour and the HC-AFW1-derived tumours as HCC. HC-AFW1 is the first cell line derived from a paediatric HCC without a background of viral hepatitis or cirrhosis and represents a valuable tool for investigating the biology of and therapeutic strategies for childhood HCC.
GITR Ligand Provided by Thrombopoietic Cells Inhibits NK Cell Antitumor Activity
2012-05-31

Abstract Thrombocytopenia inhibits tumor growth and especially metastasis in mice, whereas additional depletion of NK cells reverts this antimetastatic phenotype. It has therefore been speculated that platelets may protect hematogenously disseminating tumor cells from NK-dependent antitumor immunity. Tumor cells do not travel through the blood alone, but are rapidly coated by platelets, and this phenomenon has been proposed to shield disseminating tumor cells from NK-mediated lysis. However, the underlying mechanisms remain largely unclear. In this study, we show that megakaryocytes acquire expression of the TNF family member glucocorticoid-induced TNF-related ligand (GITRL) during differentiation, resulting in GITRL expression by platelets. Upon platelet activation, GITRL is upregulated on the platelet surface in parallel with the α-granular activation marker P-selectin. GITRL is also rapidly mobilized to the platelet surface following interaction with tumor cells, which results in platelet coating. Whereas GITRL, in the fashion of several other TNF family members, is capable of transducing reverse signals, no influence on platelet activation and function was observed upon GITRL triggering. However, platelet coating of tumor cells inhibited NK cell cytotoxicity and IFN-γ production that could partially be restored by blocking GITR on NK cells, thus indicating that platelet-derived GITRL mediates NK-inhibitory forward signaling via GITR. These data identify conferment of GITRL pseudoexpression to tumor cells by platelets as a mechanism by which platelets may alter tumor cell immunogenicity. Our data thus provide further evidence for the involvement of platelets in facilitating evasion of tumor cells from NK cell immune surveillance.
PET and MRI Reveal Early Evidence of Neurodegeneration in Spinocerebellar Ataxia Type 17
2012-05-31

MRI volumetry, as well as (11)C-raclopride and (18)F-FDG PET, reveal neuronal dysfunction and neurodegeneration even in the presymptomatic stage and may serve as markers for disease activity in upcoming interventional trials on SCA17.
OSR1-sensitive regulation of Na+/H+ exchanger activity in dendritic cells
2012-05-31

The oxidative stress-responsive kinase 1 (OSR1) is activated by WNK (with no K kinases) and in turn stimulates the thiazide-sensitive Na-Cl cotransporter (NCC) and the furosemide-sensitive Na-K-2Cl cotransporter (NKCC), thus contributing to transport and cell volume regulation. Little is known about extrarenal functions of OSR1. The present study analyzed the impact of decreased OSR1 activity on the function of dendritic cells (DCs), antigen-presenting cells linking innate and adaptive immunity. DCs were cultured from bone marrow of heterozygous WNK-resistant OSR1 knockin mice ( osr KI ) and wild-type mice ( osr WT ). Cell volume was estimated from forward scatter in FACS analysis, ROS production from 2′,7′-dichlorodihydrofluorescein-diacetate fluorescence, cytosolic pH (pH i ) from 2′,7′- bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein fluorescence, and Na + /H + exchanger activity from Na + -dependent realkalinization following ammonium pulse and migration utilizing transwell chambers. DCs expressed WNK1, WNK3, NCC, NKCC1, and OSR1. Phosphorylated NKCC1 was reduced in osr KI DCs. Cell volume and pH i were similar in osr KI and osr WT DCs, but Na + /H + exchanger activity and ROS production were higher in osr KI than in osr WT DCs. Before LPS treatment, migration was similar in osr KI and osr WT DCs. LPS (1 μg/ml), however, increased migration of osr WT DCs but not of osr KI DCs. Na + /H + exchanger 1 inhibitor cariporide (10 μM) decreased cell volume, intracellular reactive oxygen species (ROS) formation, Na + /H + exchanger activity, and pH i to a greater extent in osr KI than in osr WT DCs. LPS increased cell volume, Na + /H + exchanger activity, and ROS formation in osr WT DCs but not in osr KI DCs and blunted the difference between osr KI and osr WT DCs. Na + /H + exchanger activity in osr WT DCs was increased by the NKCC1 inhibitor furosemide (100 nM) to values similar to those in osr KI DCs. Oxidative stress (10 μM tert-butyl-hydroperoxide) increased Na + /H + exchanger activity in osr WT DCs but not in osr KI DCs and reversed the difference between genotypes. Cariporide virtually abrogated Na + /H + exchanger activity in both genotypes and blunted LPS-induced cell swelling and ROS formation in osr WT mice. In conclusion, partial OSR1 deficiency influences Na + /H + exchanger activity, ROS formation, and migration of dendritic cells.
Impact of total hip arthroplasty on pain, walking ability, and cardiovascular fitness
2012-05-31

Abstract We tested the hypothesis that total hip arthroplasty (THA) patients have less pain and are able to walk longer post‐operatively than pre‐operatively, and that THA patients before and after have higher heart rates and compromised gas exchange determinants at rest and following exercise compared to healthy subjects with a post‐operative improvement. Fifty‐two patients completed questionnaires and an incremental walking stress test pre‐operatively and 6‐months after THA. Twenty‐four age‐matched control subjects completed the same stress test. Fifty‐one patients had less pain 6‐months after THA compared to pre‐operative levels. Forty‐three patients showed an improvement of at least one walking duration category. Patients had compromised cardiovascular fitness compared to the control group with a tendency to improve after THA. Hence, 6‐months following THA, deficits exist other than reduced strength as reported in the literature. Prior to THA, the ability to walk longer is compromised by pain and not by poor cardiovascular fitness. Studies on specific rehabilitation programs of varying intensities may demonstrate opportunities to improve the cardiovascular fitness of this population. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:2025–2030, 2012
Dual polarity directions in basaltic-andesitic dykes-reversal record or self-reversed magnetization?
2012-05-31

Rock magnetic analyses were performed on basaltic-andesitic dyke samples from the Lhasa Block, which were previously used for palaeomagnetic investigations of the India–Asia collision. The aim of the study is to prove whether antipodal directions separated in these samples represent different polarities of the Earth's magnetic field or a self-reversal magnetization. Reflected light microscopy, domain pattern observations and energy dispersive X-ray analyses revealed two generations of titanomagnetite (TM) grains, one consisting of large-sized (∼20 μm to more than 100 μm) and inhomogeneous Ti-poor TM, and another with small (smaller than ∼10 μm) and rather homogeneous Ti-rich TM grains. Partial thermoremant magnetization experiments and reflected light microscopy show that magnetostatic or superexchange interaction between these two phases is unlikely. Temperature dependence of saturation magnetization and low-temperature curves of isothermal remanent magnetization disprove a possible N-type behaviour of the samples. A self-reversal due to ionic reordering can be ruled out as it requires a high degree of oxidation of the Ti-rich TMs, which was not observed. In summary, a self-reversal magnetization is very unlikely in the studied dyke samples, and therefore the observed antipodal directions most probably represent a record of different polarity epochs of the Earth's magnetic field. This conclusion implies that the time of remanence acquisition in the studied dykes was sufficiently long to average out paleosecular variation, supporting the significance and reliability of the palaeomagnetic results.
Habent sua fata libelli: thoughts on an early parody of Max Müller and other classics in comparative religious studies
2012-05-31

‘Books that have become classics’, Thomas Bailey Aldrich once noted, ‘always remind me of venerable colonels and majors and captains who, having reached the age limit, find themselves retired on half pay.’1 1Aldrich 1903: 20–21. To some extent, some of the earliest classics in the comparative study of religions may be said to share this fate, being today more frequently referred or alluded to than studied in any detail. Nevertheless, the author argues that there is still a good deal of unpublished material which may yet be put to good use in elucidating the context in which these authors lived, worked, and wrote. In fact, this material may even induce us to revise current notions and question popular assumptions. This article deals firstly with a parody of F. Max Müller's solar mythology, first published anonymously in 1870, examining it in the light of its contemporary reception and of what is known about its author (the theological writer Richard Frederick Littledale) and his circle of friends. Secondly, it considers the approaches to the study of religions taken by such scholars as F. Max Müller, William Robertson Smith, James George Frazer, and Theodor Nöldeke, discussing the extent to which the spirit of the times, personal experience, professional training, and other factors contributed to shaping these approaches. Special attention is paid to the private letters of these scholars, many of which have only recently been published or are as yet unpublished, suggesting that our insight into the origins of comparative religious studies as an academic discipline may be considerably enhanced by a more extensive use of these manuscript sources. In conclusion, the article considers the complex interrelationship between primary sources, secondary literature, and the modern historiography of scholarship, examining, by way of illustration, some points of interest in recent monographs in the field.
Standardized Assessment of Reading Performance: The New International Reading Speed Texts IReST
2012-06-01

The low within-subject variability shows the equivalence of the texts. The IReST (second edition) can now be provided in 17 languages allowing standardized assessment of reading speed, as well as comparability of results before and after interventions, and is a useful tool for multi-language studies (for further information see www.amd-read.net).