julilili42/papers huggingface dataset:
Replication of simian virus 40 (SV40) DNA in virus-infected CV1 cells selectively permeabilized for small molecules by Staphylococcus aureus α-toxin: involvement of mitochondria in the fast O2-dependent regulation of SV40 DNA replication
2005-03-08

SV40 (simian virus 40)-infected CV1 cells were permeabilized with Staphylococcus aureus α-toxin for small molecules (&amp;lt;2 kDa) in a medium that supports DNA replication. Incorporation of [α-32P]dATP was shown to proceed at an essentially constant rate for at least 1 h. 32P-labelled DNA replication intermediates and products were analysed by alkaline sucrose density centrifugation. The results suggested that SV40 DNA replication in α-toxin-permeabilized CV1 cells occurred essentially as in vivo. After bromodeoxyuridine 5′-triphosphate-labelling and isopycnic banding, significant amounts of DNA density-labelled in both strands were detected from 110 min of permeabilization onwards, indicating repeated rounds of viral DNA replication in the permeabilized cells. Incubation of permeabilized SV40-infected cells under hypoxic culture conditions caused inhibition of SV40 DNA replication. As seen in unpermeabilized cells, SV40 DNA replication was inhibited at the stage of initiation. The inhibition of DNA replication induced by hypoxia was mimicked by AA (antimycin A), an inhibitor of mitochondrial respiration, and also by the replacement of glutamate, a substrate of mitochondrial respiration, by Hepes in the permeabilization medium. Inhibition of DNA replication was not mediated by intracellular ATP depletion. AA also inhibited SV40 DNA replication in unpermeabilized, normoxically incubated cells. Moreover, as in hypoxically incubated cells, the addition of glucose to SV40-infected cells incubated for several hours with AA induced a burst of new initiations followed by a nearly synchronous round of viral DNA replication. Taken together, these results indicate that mitochondria are involved in the oxygen-dependent regulation of SV40 DNA replication.
Microglial Expression of the B7 Family Member B7 Homolog 1 Confers Strong Immune Inhibition: Implications for Immune Responses and Autoimmunity in the CNS
2005-03-09

Inflammation of the CNS is usually locally limited to avoid devastating consequences. Critical players involved in this immune regulatory process are the resident immune cells of the brain, the microglia. Interactions between the growing family of B7 costimulatory ligands and their receptors are increasingly recognized as important pathways for costimulation and/or inhibition of immune responses. Human and mouse microglial cells constitutively express B7 homolog 1 (B7-H1) in vitro . However, under inflammatory conditions [presence of interferon-γ (IFN-γ) or T-helper 1 supernatants], a significant upregulation of B7-H1 was detectable. Expression levels of B7-H1 protein on microglial cells were substantially higher compared with astrocytes or splenocytes. Coculture experiments of major histocompatibility complex class II-positive antigen-presenting cells (APC) with syngeneic T cells in the presence of antigen demonstrated the functional consequences of B7-H1 expression on T-cell activation. In the presence of a neutralizing anti-B7-H1 antibody, both the production of inflammatory cytokines (IFN-γ and interleukin-2) and the upregulation of activation markers (inducible costimulatory signal) by T cells were markedly enhanced. Interestingly, this effect was clearly more pronounced when microglial cells were used as APC, compared with astrocytes or splenocytes. Furthermore, B7-H1 was highly upregulated during the course of myelin oligodendrocyte glycoprotein-induced and proteolipid protein-induced experimental allergic encephalomyelitis in vivo . Expression was predominantly localized to areas of strongest inflammation and could be colocalized with microglial cells/macrophages as well as T cells. Together, our data propose microglial B7-H1 as an important immune inhibitory molecule capable of downregulating T-cell activation in the CNS and thus confining immunopathological damage.
Al-alloyed MgB2: correlation of superconducting properties, microstructure, and chemical composition
2005-03-09

Al-alloyed MgB2 was prepared by solid state reaction of Mg (1-x)A1(x) alloy and crystalline B powder particles. The nominal composition of the samples was Mg1-xAlxB2, with x = 0, 0.1, 0.2, and 0.3. Microstructure and chemical composition have been investigated by scanning electron microscopy (SEM), electron probe microanalysis (EPMA), and preliminary transmission electron microscopy (TEM). The Al concentration of the matrix is close to, but less than, the nominal Al concentration and the difference increases with increasing nominal Al concentration. Al is incorporated into MgB2 grains of similar to 1 mu m size by substitution of Mg lattice sites with Al. Al was found to be distributed inhomogeneously, which partially explains the broadening of the superconducting transition width (Delta T-c) with increasing Al mole fraction. Al-alloyed samples contain large (similar to 15 mu m) and small (similar to 2 mu m) secondary phases embedded in the (Mg, Al)B-2 matrix. The composition of large secondary phases is found to be (Mg, Al)B7+delta with the mole fraction of excess boron (6) increasing from 0.99 at.% in the pure sample to 4.14 at.% in the highest alloyed sample. The Al to Mg mole fraction ratio in these large secondary phases is about half of that in the matrix. The size and density of the large secondary phases increased with increase in Al mole fraction. The secondary phases constitute less than 4% of the total sample volume and are thus not likely to affect the bulk superconductivity. Magnesium diffusion and evaporation governed the formation of secondary phases and can be explained by considering the effects of annealing temperature, annealing time, and boron powder particle size. The residual resistivity (p(0)) of pure MgB2., (x = 0) and Al-alloyed MgB2 (X = 0. 1, 0.2, 0.3), measured by the four-probe technique is comparable to the single crystals, indicating the excellent quality of these samples. The lattice parameters c and a decrease at a rate of 1. 15 pin and 0. 17 pm/at. % Al, respectively. The superconducting transition temperature (Tc) determined by measuring the resistive superconducting transition decreases with increasing A] alloying at a rate of 1.56 K/at.% Al.
Devonian/Lower Carboniferous stratigraphy, facies patterns and palaeogeography of Iran Part II. Northern and central Iran
2005-03-10

Apart from a few small remnants of the Turan Plate in the north, Iran during the Palaeozoic was part of the northern margin of Gondwana. On the basis of 65 sections, the majority of them covering the time-span from the Late Silurian into the Early Carboniferous, the stratigraphy and facies pattern of this area have been elucidated. Biostratigraphical calibration and correlation of the sections, mostly by means of conodonts and brachiopods, show the evolution from a shallow carbonate-dominated shelf in the Silurian which, by a drop of sea-level, was transformed into a siliciclastic shelf during the Early Devonian. Fully marine conditions were subsequently re-established in the Middle Devonian to early Frasnian and persisted into the early Late Carboniferous. A widespread uplift in the latest Carboniferous turned the entire area into a continental regime before the onset of a new marine cycle during the late Early Permian. With the exception of the northern zone (Talesh Range, Aghdarband), the Palaeozoic of Iran is characterized by continental to shallow marine deposits showing that enormous portions of the northern margin of this sector of Gondwana have been subducted during the convergence of the Turan and Iran Plates and the elimination of the Palaeotethys during the Late Triassic.
Extended pathoanatomical studies point to a consistent affection of the thalamus in spinocerebellar ataxia type 2
2005-03-10

The involvement of the thalamus during the course of the currently known polyglutamine diseases is still a matter of debate. While it is well‐known that this diencephalic nuclear complex undergoes neurodegeneration in some polyglutamine diseases such as Huntington's disease (HD), it has remained unclear whether and to what extent the thalamus is also involved in spinocerebellar ataxia type 2 (SCA2) patients. Encouraged by our recent post‐mortem findings in one German SCA2 patient and the results of a recent nuclear magnetic resonance (NMR) study, we extended our pathoanatomical analysis to serial thick sections stained for lipofuscin granules and Nissl substance through the thalami of four additional German and Cuban SCA2 patients. According to this analysis the thalamus is consistently affected by the destructive process of SCA2. In particular, during our study we observed a consistent involvement of the lateral geniculate body, the lateral posterior, ventral anterior, ventral lateral, ventral posterior lateral, and ventral posterior medial thalamic nuclei as well as the extraterritorial reticular nucleus. In four of the SCA2 cases studied additional damage was seen in the inferior and lateral nuclei of the pulvinar, whereas in the minority of the patients a subset of the limbic nuclei of the thalamus (i.e. anterodorsal, anteroprincipal, laterodorsal, fasciculosus, mediodorsal, central lateral, central medial, cucullar, and paracentral nuclei, medial nucleus of the pulvinar) underwent neurodegeneration. These interindividual differences in the distribution pattern of thalamic neurodegeneration indicate that the thalamic nuclei differ in their proclivities to degenerate in SCA2 and may suggest that they become involved at different phases in the evolution of the underlying degenerative process.
Clinical use of multislice spiral computed tomography in 210 highly preselected patients: experience with 4 and 16 slice technology
2005-03-10

Objective: To report an initial experience with multislice spiral computed tomography (MSCT) coronary imaging, as well as differences in diagnostic accuracy between 4 slice and 16 slice MSCT technology. Methods and results: 210 patients underwent MSCT coronary angiography (4 slices, n = 120; 16 slices, n = 90; suspicion of coronary artery disease, n = 158; suspicion of restenosis, n = 52). Recommendations for further diagnostic tests were based on the MSCT results. Patients were interviewed by telephone after a mean (SD) of 449 (169) days to evaluate their further clinical course. MSCT detected significant lesions in 90 of 210 (43%) patients and invasive coronary angiography (ICA) was recommended. MSCT excluded significant lesions in 120 of 210 (57%) patients. ICA was actually performed in 44 of 210 (21%) patients (corresponding results, 27 of 44 (61%); false positive, 11 of 44 (25%); false negative, 6 of 44 (14%)). No significant differences were found between 4 and 16 slice imaging. No major cardiac event occurred during follow up. Conclusions: MSCT was found to be useful to evaluate the need for invasive diagnostic procedures. However, the false negative results underline that further improvements of image quality are required before MSCT can replace ICA in carefully selected patients.
A new Middle Jurassic xinjiangchelyid turtle (Testudines; Eucryptodira) from China (Xinjiang, Junggar Basin)
2005-03-11

Abstract A new Middle Jurassic xinjiangchelyid turtle from China, Xinjiangchelys chowi sp. nov., is described from the Toutunhe Formation of the southern Junggar Basin, southwest of Urumchi (NW China). The material consists of a nearly complete carapace and the right hypoplastron. It shows important autapomorphies of the family Xinjiangchelyidae and the genus Xinjiangchelys: first neural larger than second, anterior peripherals guttered, posterior peripherals expanded, a reduced first thoracic rib, and lateral pegs of the bridge of the plastron. It is distinguished from all other species of Xinjiangchelys by the following autapomorphies: a first costal rib with free rib end, at least two anterolateral peripheral fontanelles of the carapace, a thin plastron with large lateral fontanelles, and a median hypoplastral suture with strong pegs. These features indicate that X. chowi is the most derived xinjiangchelyid turtle hitherto known. Together with X. tianshanensis, this is the oldest xinjiangchelyid turtle known so far. Therefore, a long ghost lineage must be claimed for the Xinjiangchelyidae.
Hyperquarks and generation number
2005-03-11

In a model in which quarks and leptons are built up from two spin 1/2 preons as fundamental entities, a new class of fermionic bound states (hyperquarks) arises. It turns out that these hyperquarks are necessary to fulfill the 't Hooft anomaly constraint, which then links the number of fermionic generations to the number of colors and hypercolors.
Crystallization and preliminary X-ray analysis of immunophilin-like FKBP42 fromArabidopsis thaliana
2005-03-12

Two fragments of FKBP42 from Arabidopsis thaliana covering differing lengths of the molecule have been expressed, purified and crystallized. For each construct, crystals belonging to two different space groups were obtained and subjected to preliminary X-ray analysis.
Nucleosome, the Main Autoantigen in Systemic Lupus Erythematosus, Induces Direct Dendritic Cell Activation via a MyD88-Independent Pathway: Consequences on Inflammation
2005-03-15

Abstract Nucleosome is the major autoantigen in systemic lupus erythematosus. It is found as a circulating complex in the sera of patients and seems to play a key role in disease development. In this study, we show for the first time that physiologic concentrations of purified nucleosomes directly induce in vitro dendritic cell (DC) maturation of mouse bone marrow-derived DC, human monocyte-derived DC (MDDC), and purified human myeloid DC as observed by stimulation of allogenic cells in MLR, cytokine secretion, and CD86 up-regulation. Importantly, nucleosomes act as free complexes without the need for immune complex formation or for the presence of unmethylated CpG DNA motifs, and we thus identified a new mechanism of DC activation by nucleosomes. We have clearly demonstrated that this activation is nucleosome-specific and endotoxin-independent. Particularly, nucleosomes induce MDDC to secrete cytokines known to be detected in high concentrations in the sera of patients. Moreover, activated MDDC secrete IL-8, a neutrophil chemoattractant also detected in patient sera, and thus might favor the inflammation observed in patients. Both normal and lupus MDDC are sensitive to nucleosome-induced activation. Finally, injection of purified nucleosomes to normal mice induces in vivo DC maturation. Altogether, these results strengthen the key role of nucleosomes in systemic lupus erythematosus and might explain how peripheral tolerance is broken in patients.
DC-NK cell cross talk as a novel CD4+ T-cell–independent pathway for antitumor CTL induction
2005-03-16

It is generally accepted that priming of antitumor CD8+ cytotoxic T lymphocytes (CTLs) needs help that can be provided by CD4+ T cells. We show that interactions between dendritic cells (DCs) and natural killer (NK) cells can bypass the T helper arm in CTL induction. Bone marrow–derived DCs caused rejection of the A20 lymphoma and induced tumor-specific long-term memory, although they were not loaded with tumor-derived antigen. Experiments using CD40- knock-out mice and cell depletion showed that this effect did not require CD4+ cells. Both primary rejection and long-term CTL memory were the result of NK cell activation by DCs. NK cytotoxicity, which was necessary for primary rejection, was dependent on expression of natural killer group 2 D (NKG2D) ligands on tumor cells. Blocking of these ligands using NKG2D tetramers abrogated tumor killing in vitro and in vivo. The long-term response was due to CTLs directed against antigen(s) expressed on A20 and in vitro–differentiated DCs. The mechanism leading to CD4+ helper cell–independent CTL responses was elucidated as a cascade that was initiated by NK cell activation. This pathway was dependent on inter-feron-γ expression and involved priming endogenous DCs for interleukin-12 production. Our data suggest a novel pathway linking innate and adaptive immunity.
Electrochemiluminescence from Organic Emitters
2005-03-16

Electrically induced light emission from conjugated organic molecules in a condensed phase has constituted one of the most investigated phenomena in the recent past for a variety of reasons. The considerable development achieved in this field has been mainly based on the search of new configurations for luminescent devices such as flexible large area light-emitting diodes, and in the synthesis of improved light-emitting organic materials. In the present review a particular aspect of electrically induced light-emission phenomena from organic materials is considered, namely, organic electrochemiluminescence, which is the phenomenon of light emission from excited organic molecules generated upon occurrence of electrochemically driven redox reactions. Such processes can produce luminescence in the visible range if the resulting oxidized/reduced forms of the conjugated organic molecules form excited species capable of emitting photons within the energy range 1.5-3.5 eV. Electrochemi luminescence from organic emitters in a condensed phase has led to the creation of devices such as light-emitting electrochemical cells, whose realization was decisive in the development of effective light-emitting devices. In the present review the description of the phenomena at the basis of organic electrochemiluminescence is given together with the description of materials and devices configurations for light-emitting electrochemical cells.
Adipocytokines: Fat-Derived Humoral Mediators of Metabolic Homeostasis
2005-03-17

The metabolic syndrome currently reaches epidemic proportions in the Western industrialized world. Its hallmarks obesity, type 2 diabetes mellitus, and atherosclerosis are closely associated, and we are just beginning to understand the reasons for this relationship: adipose tissue-derived proteohormones (adipocytokines), under normal weight conditions, guarantee homeostasis of glucose and lipid metabolism, but their dysregulated production in the obese state promotes insulin resistance, inflammation, as well as atherosclerotic events. This review will focus on the current understanding of the adipocytokines' molecular role in metabolism and metabolic disease.
A prioriidentifiability of a one-compartment model with two input functions for liver blood flow measurements
2005-03-17

An extended dual-input Kety-Schmidt model can be applied to positron emission tomography data for the quantification of local arterial (f(a)) and local portal-venous blood flow (f(p)) in the liver by freely diffusible tracers (e.g., [15O]H2O). We investigated the a priori identifiability of the three-parameter model (f(a), f(p) and distribution volume (Vd)) under ideal (noise-free) conditions. The results indicate that the full identifiability of the model depends on the form of the portal-venous input function (c(p)(t)), which is assumed to be a sum of m exponentials convolved with the arterial input function (c(a)(t)). When m>or=2, all three-model parameters are uniquely identifiable. For m=1 identifiability of f(p) fails if c(p)(t) coincides with tissue concentration (q(t)/Vd), which occurs if c(p)(t) is generated from an intestinal compartment with transit time Vd/f(a). Any portal input, f(p) c(p)(t), is balanced by the portal contribution, f(p) q(t)/Vd, to the liver efflux, leaving q(t) unchanged by f(p) and only f(a) and Vd are a priori uniquely identifiable. An extension to this condition of unidentifiability is obtained if we leave the assumption of a generating intestinal compartment system and allow for an arbitrary proportionality constant between c(p)(t) and q(t). In this case, only f(a) remains a priori uniquely identifiable. These findings provide important insights into the behaviour and identifiability of the model applied to the unique liver environment.
Perioperative monitoring of flow and patency in native and grafted internal mammary arteries using a combined MR protocol
2005-03-17

The objective of this study was to evaluate graft flow (f) and patency (p) in patients with internal mammary artery (f,p) and venous (p only) grafts using a combined MR protocol with phase-contrast technique and MR angiography. 42 patients with 42 left internal mammary artery (LIMA) and 63 venous grafts were examined pre and 6 months post coronary artery bypass graft (CABG) surgery. Phase-contrast flow measurements were applied to the IMA. Post-operatively, a contrast enhanced MR angiogram was performed to assess bypass patency. LIMA/venous grafts were occluded in 3/42 and 13/63, respectively. Flow in LIMA decreased from 19.4+/-10.4 ml min(-1) m(-2) pre-operatively to 13.4+/-9.7 ml min(-1) m(-2) post-operatively (p<0.002). In contrast, flow in the native right IMA increased from 17.6+/-8.7 ml min(-1) m(-2) pre-operatively to 24.8+/-9.0 ml min(-1) m(-2) post-operatively (p<0.001). MRI allows a combined assessment of bypass patency and flow. This study protocol may be applicable to perioperative follow-up studies in patients after CABG surgery.
Standardized assessment of whole body adipose tissue topography by MRI
2005-03-18

Abstract Purpose To assess standardized whole body adipose tissue topography in a cohort of subjects at an increased risk for type 2 diabetes and to compare fat distribution in subgroups regarding anthropometric (age, body mass index [BMI]) and metabolic parameters (insulin sensitivity). Materials and Methods A total of 80 volunteers (40 females, 40 males) underwent T1‐weighted MR imaging of the entire body. Standardized adipose tissue (AT) profiles were calculated considering the different body structure of the participants. The measured data were interpolated to a defined number of sampling points enabling a direct comparison of the profiles independent on body structure. Resulting mean profiles and region‐dependent standard deviations of four age groups and three BMI‐groups were compared for females and males. Correlations between insulin sensitivity and body fat distribution were analyzed. Results Reliable adipose tissue profiles could be obtained from all volunteers. In BMI‐matched subgroups, females show significant higher AT and subcutaneous abdominal AT ( P &lt; 0.05 both), but lower visceral AT (P &lt; 0.01) compared to the males. Furthermore, visceral AT increases with age, as shown in the matched age groups. In both gender groups, insulin‐resistant subjects are characterized by higher visceral adipose tissue (VAT) compared to insulin‐sensitive subjects. In addition, profiles of insulin‐resistant subjects show more AT in the shoulder/neck region but less AT in the upper extremities. Conclusion Standardized assessment of whole body AT profiles based on T1‐weighted MRI provides a reliable basis for interindividual comparison of the body fat distribution and allows a fast and reliable quantification of total body adipose tissue and the distribution of different AT components as subcutaneous and visceral fat in different body regions. Differences in standardized profiles might enable an early identification of people at risk of metabolic disorders, as not only the amount but also the distribution of AT is expected to play an essential role in the pathogenesis of metabolic diseases. J. Magn. Reson. Imaging 2005;21:455–462. © 2005 Wiley‐Liss, Inc.
AFP/β-HCG Secreting CNS Germ Cell Tumors: Long-Term Outcome with Respect to Initial Symptoms and Primary Tumor Resection. Results of the Cooperative Trial MAKEI 89
2005-03-18

Cisplatin-based three agent chemotherapy followed by resection of the residual tumor and craniospinal irradiation (CSI) with tumor boost is a successful and well-tolerated treatment for secCNSGCTs. The possibility of a clinical diagnosis based on MRI and tumor markers together with the use of modern neurosurgical techniques gives us the chance to postpone or even avoid major surgery. This gives an additional chance to reduce acute morbidity and further decrease late effects.