julilili42/papers huggingface dataset:
Diffraction of a Bose-Einstein Condensate from a Magnetic Lattice on a Microchip
2005-10-20

We experimentally study the diffraction of a Bose-Einstein condensate from a magnetic lattice, realized by a set of 372 parallel gold conductors which are microfabricated on a silicon substrate. The conductors generate a periodic potential for the atoms with a lattice constant of 4 microm. After exposing the condensate to the lattice for several milliseconds we observe diffraction up to fifth order by standard time of flight imaging techniques. The experimental data can be quantitatively interpreted with a simple phase imprinting model. The demonstrated diffraction grating offers promising perspectives for the construction of an integrated atom interferometer.
Sequence diversity of the peptaibol antibiotic suzukacillin-A from the moldTrichoderma viride
2005-10-21

From the culture broth of the mold Trichoderma viride, strain 63 C-I, the polypeptide antibiotic suzukacillin (SZ) was isolated. A peptide mixture named SZ-A was obtained by crystallization from crude SZ. Individual peptides from SZ-A were isolated by semipreparative HPLC and sequences were determined by HPLC-ESI-MS. The data confirm a general sequence of SZ-A published previously and in addition establish the individual sequences of 15 acetylated eicosa peptides with C-terminal alcohols. The major peptide SZ-A4 (21% of all peptides) shows the sequence:Ac-Aib-Ala-Aib-Ala-Aib-Ala(6)-Gln-Aib-Lx(9)-Aib-Gly-Aib(12)-Aib-Pro-Vx(15)-Aib-Vx(17)-Gln-Gln-Fol. Amino acid exchanges of the peptaibol are located in position 6 (Ala/Aib), 9 (Vx/Lx), 12 (Aib/Lx), 17 (Aib/Vx) and possibly at position15 (Val/Iva) (uncommon abbreviations: Aib (alpha-aminoisobutyric acid); Iva (D-isovaline); Lx (L-leucine or L-isoleucine); Vx (L-valine or D-isovaline); Fol (L-phenylalaninol)).
X-ray properties of NGC 300
2005-10-21

We present X-ray properties of NGC 300 point sources, extracted from 66 ks of XMM-Newton data taken in 2000 December and 2001 January. A total of 163 sources were detected in the energy range of 0.3–6 keV. We report on the global properties of the sources detected inside the D 25&#13;\\noptical disk, such as the hardness ratio and X-ray fluxes, and on the properties of their optical counterparts found in B, V, and R images from the 2.2 m MPG/ESO telescope. Furthermore, we cross-correlate the X-ray sources with SIMBAD, the USNO-A2.0 catalog, and radio catalogues.&#13;\\n
The heat shock protein Hsp70 enhances antigen-specific proliferation of human CD4+ memory T cells
2005-10-24

Heat shock proteins (HSP) can interact with a wide variety of peptides and the resulting HSP:peptide complexes are known to be highly immunogenic. The ability of HSP:peptide complexes to elicit CD8+ T cell responses by cross-presentation of exogenous antigen via MHC class I is well known. In contrast, their role in the activation of CD4+ T cells is less clearly defined, although several recent studies in mice and T cell lines suggest an involvement of HSP in the presentation of antigenic peptides via MHC class II. In this study we have investigated the potential of antigenic peptides from tetanus toxin and influenza hemagglutinin complexed to the human stress-inducible Hsp70 to enhance activation and proliferation of human memory CD4+ T cells. Hsp70:peptide complexes were found to amplify the proliferation of antigen-specific CD4+ T cells as confirmed by HLA-DR tetramer staining. Complex formation of the antigenic peptide with Hsp70 was absolutely required to elicit an antigen-specific amplification. This effect was most pronounced at low doses of antigen and decreasing APC/CD4+ T cell ratios. Taken together, we show the potential of Hsp70 to enhance antigen-specific CD4+ T cell proliferation and to increase the immunogenicity of presented peptides in human CD4+ T cells.
The accumulation of abundant soluble proteins changes early in the development of the primary roots of maize ( Zea mays L.)
2005-10-24

Abstract A reference database of the major soluble proteins of the primary root of the maize inbred line B73 was generated 5 days after germination (DAG) using a combination of 2‐DE and MALDI‐TOF MS. A total of 302 protein spots were detected with CBB in a pH 4–7 range and 81 proteins representing 74 distinct Genbank accessions were identified. Only 28% of the major proteins identified in 5 DAG primary roots were identified in similarly analyzed 9 DAG primary roots documenting remarkable changes in the accumulation of abundant soluble proteins early in primary root development.
Hydrolytic enzymes as virulence factors of Candida albicans
2005-10-25

Summary Candida albicans is a facultative pathogenic micro‐organism that has developed several virulence traits enabling invasion of host tissues and avoidance of host defence mechanisms. Virulence factors that contribute to this process are the hydrolytic enzymes. Most of them are extracellularly secreted by the fungus. The most discussed hydrolytic enzymes produced by C. albicans are secreted aspartic proteinases (Saps). The role of these Saps for C. albicans infections was carefully evaluated in numerous studies, whereas only little is known about the physiological role of the secreted phospholipases (PL) and almost nothing about the involvement of lipases (Lip) in virulence. They may play an important role in the pathogenicity of candidosis and their hydrolytic activity probably has a number of possible functions in addition to the simple role of digesting molecules for nutrition. Saps as the best‐studied member of this group of hydrolytic enzymes contribute to host tissue invasion by digesting or destroying cell membranes and by degrading host surface molecules. There is also some evidence that hydrolytic enzymes are able to attack cells and molecules of the host immune system to avoid or resist antimicrobial activity. High hydrolytic activity with broad substrate specificity has been found in several Candida species, most notably in C. albicans . This activity is attributed to multigene families with at least 10 members for Saps and Lips and several members for PL B. Distinct members of these gene families are differentially regulated in various Candida infections. In future, prevention and control of Candida infections might be achieved by pharmacological or immunological tools specifically modulated to inhibit virulence factors, e.g. the family of Saps.
Amplification ofPlasmodium falciparumMultidrug Resistance Gene 1 in Isolates from Gabon
2005-10-25

The study of molecular markers of drug resistance is particularly important in surveillance studies of drugs, such as mefloquine, that still retain efficacy in sub-Saharan Africa yet have encountered resistance elsewhere. In a recent study in Thailand, we identified amplification of the Plasmodium falciparum multidrug resistance gene 1 (pfmdr1) as being the most important predictor of in vitro drug resistance and in vivo failure of mefloquine monotherapy. Here we report amplification of pfmdr1 in >5% of patient samples from Lambarene, Gabon, collected in 1995. None of the samples collected 7 years later showed pfmdr1 amplification, suggesting that parasites with increased numbers of pfmdr1 copies have not substantially spread through the population. Nevertheless, the detection of multicopy pfmdr1 in African parasites suggests a high potential for rapid selection for resistance, implying that mefloquine use in Africa should be considered only as part of combination therapy.
Rosai-Dorfman disease involving the cranial base, paranasal sinuses and spinal cord.
2005-10-26

Rosai-Dorfman disease is a lymphoproliferative disease that rarely involves the central nervous system. A 32-year-old patient with an extensive process involving the petroclival region, cavernous sinuses, suprasellar region, anterior cranial fossa, paranasal sinuses, nasal cavity and spinal cord is reported. Sinus histiocytosis with massive lymphadenopathy lesions may be dural-based and located in the skull base. As these lesions may clinically and radiologically mimic meningiomas as well as other disorders, Rosai-Dorfman disease should be included in the differential diagnosis of extensive lesions involving the intracranial and spinal compartments along with meningiomatosis and inflammatory diseases. The individual management of Rosai-Dorfman disease may be challenging due to diffuse involvement of neurovascular structures at the skull base.
Phosphinothricin Tripeptide Synthetases in Streptomyces viridochromogenes Tu494
2005-10-26

ABSTRACT The tripeptide backbone of phosphinothricin (PT) tripeptide (PTT), a compound with herbicidal activity from Streptomyces viridochromogenes , is assembled by three stand-alone peptide synthetase modules. The enzyme PhsA (66 kDa) recruits the PT-precursor N -acetyl-demethylphosphinothricin ( N -Ac-DMPT), whereas the two alanine residues of PTT are assembled by the enzymes PhsB and PhsC (129 and 119 kDa, respectively). During or after assembly, the N-Ac-DMPT residue in the peptide is converted to PT by methylation and deacetylation. Both phsB and phsC appear to be cotranscribed together with two other genes from a single promoter and they are located at a distance of 20 kb from the gene phsA , encoding PhsA, in the PTT biosynthesis gene cluster of S. viridochromogenes . PhsB and PhsC represent single nonribosomal peptide synthetase elongation modules lacking a thioesterase domain. Gene inactivations, genetic complementations, determinations of substrate specificity of the heterologously produced proteins, and comparison of PhsC sequence with the amino terminus of the alanine-activating nonribosomal peptide synthetase PTTSII from S. viridochromogenes confirmed the role of the two genes in the bialanylation of Ac-DMPT. The lack of an integral thioesterase domain in the PTT assembly system points to product release possibly involving two type II thioesterase genes ( the1 and the2 ) located in the PTT gene cluster alone or in conjunction with an as yet unknown mechanism of product release.
Hypothalamic‐pituitary gonadal axis and immune response imbalance during chronic filarial infections
2005-10-26

Summary Bi‐directional relationships operate between the hypothalamic‐pituitary‐gonadal axis and the immune system. Cytokines, peptide hormones and their shared receptors/ligands are used as a common biological language for communication within and between the immune and neuroendocrine systems. Such communication suggests an immunoregulatory role for the brain and a sensory function for the immune system. We used a radioimmunoassay to measure the concentrations of steroid hormones (cortisol, testosterone, estradiol and progesterone) and pituitary hormones [follicle stimulating hormone (FSH), luteinizing hormone (LH) human chorionic gonadotropin (HCG) and prolactin] in peripheral blood plasma from 78 young Gabonese women with chronic filarial infections. We used an enzyme‐linked immunosorbent assay to determine the concentrations of four proinflammatory cytokines [tumor necrosis factor‐alpha (TNF‐ α ), gamma interferon (IFN‐ γ ), interleukin‐1 (IL‐1) and IL‐6] in the same plasma samples. Progesterone was unchanged and all other steroid hormone plasma concentrations were lower in microfilaremic women than in amicrofilaremic women. The concentration of LH was higher in amicrofilaremic women, whereas the prolactin concentration was higher in microfilaremics. The plasma concentrations of TNF‐ α , IFN‐ γ , IL‐1 and IL‐6 were higher in microfilaremic women. A strong negative correlation was found between the steroid and pituitary hormones and the pro‐inflammatory cytokines. Conversely, a strong positive correlation was found between prolactin and the same cytokines. These data provide first evidence of immune system and hormonal system disturbance during chronic filarial infections and suggest that the observed imbalance should be taken into account in the diagnosis and treatment of filarial infections.
Intranasal Immunization Strategy To Impede Pilin-Mediated Binding ofPseudomonas aeruginosato Airway Epithelial Cells
2005-10-26

ABSTRACT Prevention of pulmonary Pseudomonas aeruginosa infections represents a critical unmet medical need for cystic fibrosis (CF) patients. We have examined the tenet that a mucosal immunization approach can reduce interactions of a piliated form of this opportunistic pathogen with respiratory epithelial cells. Vaccinations were performed using ntPEpilinPAK, a protein chimera composed of a nontoxic form of P. aeruginosa exotoxin A (ntPE), where the C-terminal loop amino acid sequence of the PAK strain pilin protein was inserted in place of the ntPE Ib domain. Intranasal (i.n.) immunization of BALB/c mice with ntPEpilinPAK generated both serum and saliva immune responses. A series of in vitro studies showed that diluted samples of saliva obtained from immunized mice reduced pilin-dependent P. aeruginosa binding to polarized human tracheal epithelial cells, protected human pulmonary epithelial cells from cytotoxic actions associated with bacterial challenge, and reduced exotoxin A toxicity. Overall, i.n. administration of ntPEpilinPAK induced mucosal and systemic immune responses that may be beneficial for blocking early stage adhesion and/or infection events of epithelial cell- P. aeruginosa interactions at oropharyngeal surfaces.
Ruthenium Complexes with the Stanna‐closo‐dodecaborate Ligand: Coexistence of η1(Sn) and η3(BH) Coordination
2005-10-26

Abstract Four stanna‐ closo ‐dodecaborate complexes of ruthenium have been prepared and characterized by multinuclear NMR studies in solution and in the solid state. The solid‐state structures of the dimeric zwitterions [{Ru(dppb)(SnB 11 H 11 )} 2 ] ( 2 ) (dppb=bis(diphenylphosphino)butane), [{Ru(PPh 3 ) 2 (SnB 11 H 11 )} 2 ] ( 3 ), and the dianionic ruthenium complex [Bu 3 MeN] 2 [Ru(dppb){2,7,8‐(μ‐H) 3 ‐ exo ‐SnB 11 H 11 }(SnB 11 H 11 )] ( 4 ) were determined by X‐ray crystal structure analysis; they establish an unprecedented structural motif in the chemistry of heteroboranes and transition‐metal fragments with the stanna‐ closo ‐dodecaborate moiety as a two‐faced ligand that exhibits η 1 (Sn) as well as η 3 (BH) coordination. The η 3 ‐coordinated stannaborate in 4 and in the isostructural compound [Bu 3 MeN] 2 [Ru(PPh 3 ) 2 {2,7,8‐(μ‐H) 3 ‐ exo ‐SnB 11 H 11 }(SnB 11 H 11 )] ( 5 ) shows fluxional behavior, which was studied in detail by using 31 P{ 1 H} EXSY and DNMR experiments. The activation parameters for the dynamic process of 5 are given.
Break on through to the Other Side—Biophysics and Cell Biology Shed Light on Cell‐Penetrating Peptides
2005-10-27

Abstract Cell‐penetrating peptides (CPPs) have become widely used vectors for the cellular import of molecules in basic and applied biomedical research. Despite the broad acceptance of these molecules as molecular carriers, the details of the mode of cellular internalization and membrane permeation remain elusive. Within the last two years endocytosis has been demonstrated to be a route of uptake shared by several CPPs. These findings had a significant impact on CPP research. State‐of‐the‐art cell biology is now required to advance the understanding of the intracellular fate of the CPP and cargo molecules. Owing to their presumed ability to cross lipid bilayers, CPPs also represent highly interesting objects of biophysical research. Numerous studies have investigated structure–activity relationships of CPPs with respect to their ability to bind to a lipid bilayer or to cross this barrier. Endocytosis route only relocates the membrane permeation from the cell surface to endocytic compartments. Therefore, biophysical experiments are key to a mechanistic molecular understanding of the cellular uptake of CPPs. However, biophysical investigations have to consider the molecular environment encountered by a peptide inside and outside a cell. In this contribution we will review biophysical and cell‐biology data obtained for several prominent CPPs. Furthermore, we will summarize recent findings on the cell‐penetrating characteristics of antimicrobial peptides and the antimicrobial properties of CPPs. Peptides of both groups have overlapping characteristics. Therefore, both fields may greatly benefit from each other. The review will conclude with a perspective of how biophysics and cell biology may synergize even more efficiently in the future.
Differential detection of S100A8 in transitional cell carcinoma of the bladder by pair wise tissue proteomic and immunohistochemical analysis
2005-10-27

Abstract The search for novel molecular markers of tumor invasion is vital if strategies are to become more effective in the diagnostic and prognostic management of transitional cell carcinoma of the bladder. Up to 50% of tumors detected at stage 1 (pT1) progress to a higher grade even after endoscopic surgical resection, and there are currently no protein markers of this aggressive, invasive phenotype. We have combined SELDI‐TOF‐MS, ClinProt magnetic bead enrichment, Nano‐LC‐ESI‐ion trap tandem mass spectrometry and immunohistochemical analysis to the study of 12 invasive bladder cancer tissue biopsies paired with normal bladder tissue samples obtained from the same patients for the definition and identification of proteins up‐regulated in the tumors. We report the inflammation‐associated calcium binding protein S100A8 (MRP‐8, calgranulin A) to be highly expressed in tumor cells in contrast to normal urothelium in 50% of the samples, as well as two unidentified protein markers at 5.75 and 6.89 kDa that were differentially detected in 9/12 and 10/12 tumor samples, respectively. These new markers, when fully characterized, may contribute to new target proteins for the prediction of aggressive, invasive bladder tumors.
Anaemia in cancer patients: pathophysiology, incidence and treatment
2005-10-27

Abstract This review focuses on the pathophysiology, incidence and treatment of anaemia in cancer patients. Causative factors such as different chemotherapy regimens and patient risk factors for the development of anaemia are discussed in order to identify the patient group that is most likely to receive red blood cell transfusions and would thus have the largest benefit from treatment with erythropoietic proteins. The data available with recombinant human erythropoietin alfa, recombinant human erythropoietin beta and darbepoetin alfa are described in more detail and the significant benefit of treating cancer anaemia by these molecules is outlined. Finally, differences in treatment approaches between these erythropoietic proteins are discussed in order to guide treatment decisions specific for the individual patients’ situation.
A model for linear dragging
2005-10-27

We try to carry over, as closely as possible, the well-known results for rotational dragging (Thirring, Brill and Cohen) to dragging due to linearly accelerated masses. To this end, a spherical, charged mass shell is linearly accelerated by a (weak) external, axisymmetric and dipolar charge distribution. It is shown that the interior of this (Reissner–Nordström-like) shell stays flat. The dragging of neutral test particles inside the shell, defined by their acceleration, scaled by the overall acceleration of the (rigid) shell, is calculated for the weak field case for a highly massive but weakly charged shell and for the general strong field case. The results compare favourably with the corresponding results for rotational dragging.
Dimethyldioxirane and Acetone Are Not in Equilibrium
2005-10-27

Abstract The potential transfer of an oxygen atom from dioxiranes to a ketonic carbonyl group is disproved by appropriate D‐ and 13 C‐labelling. As shown by 13 C NMR spectroscopy bis(trideuteriomethyl)dioxirane and [carbonyl‐ 13 C]acetone are not in equilibrium with [D 6 ]acetone and [3‐ 13 C]dimethyldioxirane. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Supramolecular Conjugates of Carbon Nanotubes and DNA by a Solid-State Reaction
2005-10-28

DNA-wrapped nanotubes of both multiwalled and single-walled carbon nanotubes were obtained by a solid-state mechanochemical reaction. Scanning electron microscopic images show that the nanotubes were cut into shorter lengths and were fully covered with DNA, which was further confirmed by fluorescence microscopy. This resulted in a high aqueous solubility of the products with a stability of >6 months. The results show that nanotubes were cut also with uniform distribution where >90% of the multiwalled products were 500 nm to 3 μm and 80% of the single-walled products were 250 nm to 1 μm in length, respectively. UV−vis spectra and gel electrophorosis show that the DNA in the product is intact. This facile technique for obtaining supramolecularly masked, water-soluble carbon nanotubes by a solid-state reaction has a great potential for both biological and nonbiological applications of nanotubes.
Endocytosis and Cationic Cell-Penetrating Peptides - A Merger of Concepts and Methods
2005-10-28

With the identification of fixation as a major source of artefacts in the cell biological research on cell-penetrating peptides (CPPs), the past two years have witnessed a dramatic development in the CPP field. At least for some of these molecules, endocytosis is now considered to be the major if not the exclusive route of cellular import. However, endocytosis comprises a variety of different pathways with very different implications for the delivery of bioactive molecules to the cytoplasm and nucleus. The endocytosis of CPPs is governed by complex mechanisms similar to those responsible for the internalization of other molecules. Therefore the investigation of uptake and intracellular trafficking of CPPs can benefit enormously from the understanding of the endocytic machinery as well as from the tools that have already been developed for the analysis of endocytosis. This review will introduce aspects of endocytosis relevant to the analysis of CPPs. In addition to the methods, that have already been used for the analysis of CPP trafficking, we will also present other tools and approaches which can be helpful for the research of CPP uptake. Furthermore this review will analyze and summarize recent data providing new insights in endocytosis and intracellular trafficking of CPPs.
Sebacinales form ectendomycorrhizas with Cavendishia nobilis, a member of the Andean clade of Ericaceae, in the mountain rain forest of southern Ecuador
2005-10-31

Cavendishia nobilis var. capitata is an endemic member of the Ericaceae growing as a hemiepiphyte in the tropical mountain rain forest of southern Ecuador. Mycorrhizas were collected from 20 individuals along an altitudinal gradient between 1850 and 2300 m. Transmission electron microscopy was used to study the symbiotic association in detail, and phylogenetic analyses based on nuclear rDNA coding for the ribosomal large subunit (nucLSU) were carried out to identify the associated mycorrhizal fungi. Microscopic and ultrastructural investigations showed the formation of a hyphal sheath, intercellular penetration of fine hyphae and colonization of the cortical cells by swollen hyphae of the same fungus. These structures were formed by hymenomycetes and ascomycetes. Molecular phylogenetic analysis detected seven groups of mycorrhizal fungi belonging to the Sebacinales. This is the first study to obtain evidence of ectendomycorrhizas in the Vaccinioideae. The ascomycetous nucLSU sequences belonged to members of the Leotiomycetes. The ectendomycorrhiza of C. nobilis with Sebacinales is discussed as a specific, hitherto undescribed mycorrhizal subcategory of ectomycorrhizas. We propose the term 'cavendishioid mycorrhiza'. This subcategory is most likely specific for the Andean clade of Ericaceae.