julilili42/papers huggingface dataset:
Identification of an epitope derived from the cancer testis antigen HOM-TES-14/SCP1 and presented by dendritic cells to circulating CD4+ T cells
2005-07-20

Abstract Because of their frequent expression in a wide spectrum of malignant tumors but not in normal tissue except testis, cancer testis antigens are promising targets. However, except for HOM-TES-14/SCP1, their expression in malignant lymphomas is rare. SCP1 (synaptonemal complex protein 1) has been shown to elicit antibody responses in the autologous host, but no T-cell responses against HOM-TES-14/SCP1 have been reported. Using the SYFPEITHI algorithm, we selected peptides with a high binding affinity to major histocompatibility complex class 2 (MHC 2) molecules. The pentadecamer epitope p635-649 induced specific CD4+ T-cell responses that were shown to be restricted by HLA-DRB1*1401. The responses could be blocked by preincubation of T cells with anti-CD4 and antigen-presenting cells with anti–HLA-DR, respectively, proving the HLA-DR–restricted presentation of p635-649 and a CD4+ T-cell–mediated effector response. Responding CD4+ cells did not secrete interleukin-5 (IL-5), indicating that they belong to the TH1 subtype. The natural processing and presentation of p635-649 were demonstrated by pulsing autologous and allogeneic dendritic cells with a protein fragment covering p635-649. Thus, p635-649 is the first HOM-TES-14/SCP1–derived epitope to fulfill all prerequisites for use as a peptide vaccine in patients with HOM-TES-14/SCP1–expressing tumors, which is the case in two thirds of peripheral T-cell lymphomas.
Human SK-Mel 28 melanoma cells resume neural crest cell migration after transplantation into the chick embryo
2005-07-20

Melanocytes are derived from the neural crest. We questioned whether the migratory mechanism during the invasive growth of melanoma cells is the same as that in neural crest cell migration. We transplanted human SK-Mel 28 melanoma cells into the neural tube of the chick embryo stage 11-13 and, after up to 6 days of total incubation, traced the cells by immunohistochemistry in serial paraffin sections. SK-Mel 28 cells were integrated into the host neural crest and were found in the roof plate of the neural tube, along the medial neural crest cell pathway, in the sclerotome and, finally, in developing sympathetic ganglia. At stage 21, massive segmental emigration between myotome and disintegrating dermatome was observed at the level of the upper limb bud. The melanoma cells, in contrast with the chick neural crest cells, were HNK-1-negative. They retained the premelanosome epitope HMB-45. For definite identification and exclusion of fusion with chick embryo cells, in situ hybridization with the human-specific Alu sequence was performed. The results showed that human SK-Mel 28 melanoma cells were capable of resuming neural crest cell migration in the embryo.
Muscarinic cholinergic receptors in the human melanoma cell line SK-Mel 28: modulation of chemotaxis
2005-07-20

Summary Primary and metastatic human melanomas express muscarinic receptors. In embryonic tissues, expression of muscarinic receptors is correlated with morphogenesis. The hypothesis has been put forward that muscarinic receptors are involved in morphogenetic movements in the embryo, and in cellular movements in melanoma cells during invasive growth. The purpose of the present study was to characterize the muscarinic receptors in the human melanoma cell line SK-Mel 28 and to test in a Boyden chamber assay whether the chemotactic activity towards fibronectin can be influenced by muscarinic stimulation. In Western blots with the monoclonal antibody M35, muscarinic receptors were localized in a strong band at 66 kDa, and in a weak band at 63 kDa. Western blot with M3 subtype specific antibodies reproduced the line at 66 kDa. RT-PCR revealed mRNA for subtypes M3 and M5. These findings suggest that SK-Mel 28 cells express a large number of subtype M3 and a small number of subtype M5 receptors. Microscopic observation of calcium mobilization after muscarinic stimulation indicated that all cells carried functional muscarinic receptors. A standardized chemotaxis assay was established in modified Boyden chambers using fibronectin as chemotactic agent. After addition of carbachol to the upper compartment, an increase of fibronectin induced chemotaxis of ∼30% was observed, an effect abrogated by atropine. These results demonstrate that muscarinic cholinergic treatment has a modulatory effect on fibronectin-induced chemotaxis in SK-Mel 28 melanoma cells, indicating that the muscarinic system is involved in regulation of cell movement.
Role of Postchemotherapy Surgery in the Management of Patients With Liver Metastases From Germ Cell Tumors
2005-07-20

The high rate of viable cancer and teratoma found in liver specimens, differing histologic results at residual tumor locations, and the high survival rate achieved support a multidisciplinary approach including resection of liver masses since no accurate selection of patients can narrow the use of surgery.
Magnetic interaction analysis of basaltic samples and pre-selection for absolute palaeointensity measurements
2005-07-20

For a successful palaeointensity experiment a sample should only consists of non-interacting single domain (SD) particles. As this cannot be completely guarantied for natural samples we applied two different interaction methods (ΔM plots and FORC-diagrams) on basaltic samples from Fernando de Noronha, Brazil, in order to determine the degree of interaction and estimate their use as a preselection tool for palaeointensity experiments. An independent classification of the samples in terms of SD/MD contribution and the occurrence of partial self-reversals is obtained by rockmagnetic means, Thellier-like experiments and continuous thermal demagnetization. The samples show a variable amount of mean interaction fields, which tends to be higher for samples with partial self-reversal. Nevertheless, high mean interaction fields can also be present in samples of successful palaeointensity experiments with high mean coercivities. This suggests, that the recording potential of a sample depends on the interplay of magnetic interaction and its mean coercivity, i.e. samples of higher mean coercivity resist higher mean interaction fields. As this is difficult to assess by normal rockmagnetic means, interaction measurements, especially the ΔM plot derived parameters ΔM 1 and 2, provide a fast tool for preselection.
Image reconstruction and image quality evaluation for a 64‐slice CT scanner with ‐flying focal spot
2005-07-21

We present a theoretical overview and a performance evaluation of a novel ‐sampling technique for multidetector row CT (MDCT), relying on a periodic motion of the focal spot in the longitudinal direction ( ‐flying focal spot) to double the number of simultaneously acquired slices. The ‐flying focal spot technique has been implemented in a recently introduced MDCT scanner. Using collimation, this scanner acquires 64 overlapping 0.6 mm slices per rotation in its spiral (helical) mode of operation, with the goal of improved longitudinal resolution and reduction of spiral artifacts. The longitudinal sampling distance at isocenter is 0.3 mm. We discuss in detail the impact of the ‐flying focal spot technique on image reconstruction. We present measurements of spiral slice sensitivity profiles (SSPs) and of longitudinal resolution, both in the isocenter and off‐center. We evaluate the pitch dependence of the image noise measured in a centered 20 cm water phantom. To investigate spiral image quality we present images of an anthropomorphic thorax phantom and patient scans. The full width at half maximum (FWHM) of the spiral SSPs shows only minor variations as a function of the pitch, measured values differ by less than 0.15 mm from the nominal values 0.6, 0.75, 1, 1.5, and 2 mm. The measured FWHM of the smallest slice ranges between 0.66 and 0.68 mm at isocenter, except for pitch 0.55 (0.72 mm). In a centered ‐resolution phantom, bar patterns up to can be visualized independent of the pitch, corresponding to 0.33 mm longitudinal resolution. 100 mm off‐center, bar patterns up to are visible, corresponding to an object size of 0.36 mm that can be resolved in the direction. Image noise for constant effective mAs is almost independent of the pitch. Measured values show a variation of less than 7% as a function of the pitch, which demonstrates correct utilization of the applied radiation dose at any pitch. The product of image noise and square root of the slice width (FWHM of the respective SSP) is the same constant for all slices except 0.6 mm. For the thinnest slice, relative image noise is increased by 17%. Spiral windmill‐type artifacts are effectively suppressed with the ‐flying focal spot technique, which has the potential to maintain a low artifact level up to pitch 1.5, in this way increasing the maximum volume coverage speed that can be clinically used.
Accuracy of navigation‐guided socket drilling before implant installation compared to the conventional free‐hand method in a synthetic edentulous lower jaw model
2005-07-21

Abstract: In this study, the three‐dimensional (3D) accuracy of navigation‐guided (NG) socket drilling before implant installation was compared to the conventional free‐hand (CF) method in a synthetic edentulous lower jaw model. The drillings were performed by two surgeons with different years of working experience. The inter‐individual outcome was assessed. NG drillings were performed using an optical computerized tomography (CT)‐based navigation system. CF drillings were performed using a surgical template. The coordinates of the drilled sockets were determined on the basis of CT scans. A total of n =224 drillings was evaluated. Inter‐individual differences in terms of the surgeons' years of work experience were without statistical significance. The mean deviation of the CF drilled sockets ( n =112) on the vestibulo‐oral and mesio‐distal direction was 11.2±5.6° (range: 4.1–25.3°). With respect to the NG drilled sockets ( n =112), the mean deviation was 4.2±1.8° (range: 2.3–11.5). The mean distance to the mandibular canal was 1.1±0.6 mm (range: 0.1–2.3 mm) for CF‐drilled sockets and 0.7±0.5 mm (range: 0.1–1.8 mm) for NG drilled sockets. The differences between the two methods were highly significant ( P &lt;0.01). A potential benefit from image‐data‐based navigation in implant surgery is discussed against the background of cost‐effectiveness.
A synthesis route for carbon-centered triprismo-hexatungsten cluster compounds and the crystal structure of Cs[W6CCl18]·CH3OH
2005-07-21

Li x [W 6 CCl 18 ] was synthesized by the reaction of WCl 4 with Li 2 CN 2 , and used as source material for the synthesis of a new carbon-centered triprismo-hexatungsten cluster compound. Black crystals of Cs[W 6 CCl 18 ]·CH 3 OH were obtained by cation-exchange reaction of Li x [W 6 CCl 18 ] with CsCl in methanol. The air-stable compound crystallizes orthorhombic with unit-cell parameters a = 9.6957(5) Å, b = 14.046(1) Å, and c = 20.238(1) Å in the space group P 2 1 2 1 2 1 (No. 19). The crystal structure of Cs[W 6 CCl 18 ]·CH 3 OH contains isolated [W 6 CCl 18 ] – ions. If these ions are considered as spheres, their arrangement in the structure follows the principle of hexagonal closest packing, with cesium ions and methanol molecules filling voids in the hexagonal cluster layers. .
Functional role of Na+–HCO3− cotransport in migration of transformed renal epithelial cells
2005-07-22

Cell migration is crucial for immune defence, wound healing or formation of tumour metastases. It has been shown that the activity of the Na + –H + exchanger (NHE1) plays an important role in cell migration. However, so far it is unknown whether Na + – HCO 3 − cotransport (NBC), which has similar functions in the regulation of intracellular pH (pH i ) as NHE1, is also involved in cell migration. We therefore isolated NHE‐deficient Madin‐Darby canine kidney (MDCK‐F) cells and tested whether NBC compensates for NHE in pH i and cell volume regulation as well as in migration. Intracellular pH was measured with the fluorescent pH indicator 2′7′‐bis(carboxyethyl)‐5‐carboxyfluorescein (BCECF). The expression of NBC isoforms was determined with semiquantitative PCR. Migration was monitored with time‐lapse video microscopy and quantified as the displacement of the cell centre. We found that MDCK‐F cells express the isoform NBC1 ( SLCA4A gene product) at a much higher level than the isoform kNBC3 ( SLCA4A8 gene product). This difference is even more pronounced in NHE‐deficient cells so that NBC1 is likely to be the major acid extruder in these cells and the major mediator of propionate‐induced cell volume increase. NHE‐deficient MDCK‐F cells migrate more slowly than normal MDCK‐F cells. NBC activity promotes migration during an acute intracellular acid load and increases migratory speed and displacement on a short timescale (&lt; 30 min) whereas it has no effect on the long‐term behaviour of migrating MDCK‐F cells. Taken together, our results show that NBC actvity, despite many functional similarities, does not have the same importance for cell migration as NHE1 activity.
Pairing in a two-component ultracold Fermi gas: Phases with broken-space symmetries
2005-07-22

We explore the phase diagram of a two-component ultracold atomic Fermi gas\\ninteracting with zero-range forces in the limit of weak-coupling. We focus on\\nthe dependence of the pairing gap and the free energy on the variations in the\\nnumber densities of the two species while the total density of the system is\\nheld fixed. As the density asymmetry is increased, the system exhibits a\\ntransition from a homogenous Bardeen-Cooper-Schrieffer (BCS) phase to phases\\nwith spontaneously broken global space symmetries. One such realization is the\\ndeformed Fermi surface superfluidity (DFS) which exploits the possibility of\\ndeforming the Fermi-surfaces of the species into ellipsoidal form at zero total\\nmomentum of Cooper pairs. The critical asymmetries at which the transition from\\nthe DFS to the unpaired state occurs are larger than those for the BCS phase.\\nIn this precritical region the DFS phase lowers the condensation energy of the\\nasymmetric BCS state. We compare quantitatively the DFS phase to another\\nrealization of superconducting phases with broken translational symmetry - the\\nsingle plane wave Larkin-Ovchinnikov-Fulde-Ferrell (LOFF)phase, which is\\ncharacterized by a non-vanishing center-of-mass momentum of the Cooper pairs.\\nThe possibility of the detection of the DFS phase in the time-of-flight\\nexperiments is discussed and quantified for the case of Li atoms trapped in\\ntwo different hyperfine states.\\n
Virulence of the Fungal Pathogen Candida albicans Requires the Five Isoforms of Protein Mannosyltransferases
2005-07-23

ABSTRACT The PMT gene family in Candida albicans encodes five isoforms of protein mannosyltransferases (Pmt proteins Pmt1p, Pmt2p, Pmt4p, Pmt5p, and Pmt6p) that initiate O mannosylation of secretory proteins. We compared virulence characteristics of pmt mutants in two complex, three-dimensional models of localized candidiasis, using reconstituted human epithelium (RHE) and engineered human oral mucosa (EHOM); in addition, mutants were tested in a mouse model of hematogenously disseminated candidiasis (HDC). All pmt mutants showed attenuated virulence in the HDC model and at least one model of localized candidiasis. The pmt5 mutant, which lacks in vitro growth phenotypes, was less virulent in the EHOM and HDC assays but had no consistent phenotype in the RHE assay. In contrast, the pmt4 and pmt6 mutants were less virulent in the RHE and HDC assays but not in the EHOM assay. The results stress the contribution of all Pmt isoforms to the virulence of C. albicans and suggest that the importance of individual Pmt isoforms may differ in specific host niches. We propose that Pmt proteins may be suitable targets for future novel classes of antifungal agents.
Dynamic purine signaling and metabolism during neutrophil–endothelial interactions
2005-07-24

During episodes of hypoxia and inflammation, polymorphonuclear leukocytes (PMN) move into underlying tissues by initially passing between endothelial cells that line the inner surface of blood vessels (transendothelial migration, TEM). TEM creates the potential for disturbances in vascular barrier and concomitant loss of extravascular fluid and resultant edema. Recent studies have demonstrated a crucial role for nucleotide metabolism and nucleoside signaling during inflammation. These studies have implicated multiple adenine nucleotides as endogenous tissue protective mechanisms invivo. Here, we review the functional components of vascular barrier, identify strategies for increasing nucleotide generation and nucleoside signaling, and discuss potential therapeutic targets to regulate the vascular barrier during inflammation.
Neural cell adhesion molecule (NCAM –/– ) null mice show impaired sensitization of the startle response
2005-07-25

The neural cell adhesion molecule (NCAM) plays important roles in development of the nervous system and in synaptic plasticity and memory formation in the adult. The present study sought to further investigate the role of NCAM in learning by testing habituation and footshock sensitization learning of the startle response (SR) in NCAM null mutant ( NCAM –/– ) and wildtype littermate ( NCAM +/+ ) mice. Whereas habituation is a form of non‐associative learning, footshock sensitization is induced by rapid contextual fear conditioning. Habituation was tested by repetitive presentation of acoustic and tactile startle stimuli. Although NCAM –/– mice showed differences in sensitivity in both stimulus modalities, habituation learning was intact in NCAM –/– mice, suggesting that NCAM does not play a role in the mechanisms underlying synaptic plasticity in the startle pathway. Footshock sensitization was elicited by presentation of electric footshocks between two series of acoustic stimuli. In contrast to habituation, footshock sensitization learning was attenuated in NCAM –/– mice: the acoustic SR increase after the footshocks was lower in the mutant than in wildtype mice, indicating that NCAM plays an important role in the relevant brain areas, such as amygdala and/or the hippocampus.
Characterization of mouse amino acid transporter B0AT1 (slc6a19)
2005-07-26

The mechanism of the mouse (m)B0AT1 (slc6a19) transporter was studied in detail using two electrode voltage-clamp techniques and tracer studies in the Xenopus oocyte expression system. All neutral amino acids induced inward currents at physiological potentials, but large neutral non-aromatic amino acids were the preferred substrates of mB0AT1. Substrates were transported with K0.5 values ranging from approx. 1 mM to approx. 10 mM. The transporter mediates Na+–amino acid co-transport with a stoichiometry of 1:1. No other ions were involved in the transport mechanism. An increase in the extracellular Na+ concentration reduced the K0.5 for leucine, and vice versa. Moreover, the K0.5 values and Vmax values of both substrates varied with the membrane potential. As a result, K0.5 and Vmax values are a complex function of the concentration of substrate and co-substrate and the membrane potential. A model is presented assuming random binding order and a positive charge associated with the ternary [Na+–substrate–transporter] complex, which is consistent with the experimental data.
Notch ligands Delta-like1, Delta-like4 and Jagged1 differentially regulate activation of peripheral T helper cells
2005-07-26

The Notch pathway is involved in cell differentiation processes in various organs and at several developmental stages. The importance of Notch for early T lymphocyte development is well established. Recently, Notch has been implicated in directing naive T helper cell differentiation towards the Th1, Th2 or regulatory T cell lineages. However, the molecular events underlying these processes are poorly understood. We show that the Notch ligands Delta-like1, Delta-like4 and Jagged1 differentially affect early T cell activation and proliferation following T cell receptor cross-linking. Delta-like1 and Jagged1 induce a dose-dependent inhibition of early activation markers CD69 and CD25, as well as inhibition of proliferation after anti-CD3 stimulation of purified CD4+ T cells. Similarly, the rapid activation of transcription factors NF-AT, AP-1 and NF-kappaB is suppressed. In contrast, triggering of Notch by Delta-like4 enhances T cell activation and proliferation. The observed effects are dependent on simultaneous cross-linking of TCR and Notch but independent of gamma-secretase-mediated cleavage of Notch. These data suggest direct interference between Notch and early TCR signal transduction events, independent of the classical Notch pathway via release of the Notch intracellular domain. A Notch-mediated alteration of TCR signaling strength may contribute to the recently described modulation of naïve T cell differentiation by Notch ligands.
Invasive pulmonary aspergillosis: frequency and meaning of the “hypodense sign” on unenhanced CT
2005-07-26

The purpose of this study was to establish the diagnostic value of central hypointensity ("hypodense sign") in lung consolidations or nodules, in severely immunocompromised or neutropenic patients, suspected of having invasive pulmonary aspergillosis (IPA), and to assess its recognition on unenhanced CT scans. Serial CT scans of the lung were retrospectively reviewed in 43 consecutive immunosuppressed patients with IPA, and assessed for the presence of the hypodense sign using standard mediastinal and lung windowing settings, as well as a special, narrower window setting (width 110-140 HU; level 15-40 HU). The temporal relationship between the occurrence of the first CT-finding suspicious of IPA and the appearance of the hypodense sign, as well as between this and the occurrence of the crescent sign, cavitation or reduction in lesion size, was evaluated. Additionally, CT-scans from 89 immunocompromised patients with viral (n=45) or bacterial (n=44) pneumonia, investigated in the same time period at our institution were reviewed, with respect to the presence of the "hypodense" sign. Unenhanced CT scans revealed the hypodense sign in 11 neutropenic patients and 2 severely immunocompromised patients, out of a total of 43 patients with IPA evaluated in this study (30.2%). The mean time between the appearance of the first CT-findings of IPA (large nodule or consolidation +/- positive halo sign) and the hypodense sign was 7.8 days, while the time interval between the hypodense sign and the occurrence of crescent sign, cavitation, or decrease of the lesion's size was 8.3 days. The hypodense sign did not occur in any of the patients with viral or bacterial pneumonia, in the control series. We consider the hypodense sign to be a supplementary tool in the diagnosis of IPA. Its sensitivity was low in our series, but the high specificity makes it valuable in predicting IPA, anticipating the occurrence of cavitation or crescent sign, which are considered specific, but late findings of IPA. The hypodense sign is recognizable also on unenhanced CT, when a narrower lung window setting is used.