julilili42/papers huggingface dataset:
burial (version 1.0): a method for testing genetic similarity within small groups of individuals using fragmentary data sets
2001-09-01

Abstract Biologists are frequently facing the problem of dealing with data sets with a small amount of data and a high proportion of missing information. We were particularly interested in analysing fragmentary data sets generated by the application of molecular methods in palaeoanthropology in order to determine whether individuals are genetically related. In this note, we announce the release of the software burial (version 1.0) to test the null hypothesis that the observed grouping of individuals at a particular burial site reflects random placement of genotypes. The proposed test, however, can also be applied to data sets whose objects can be grouped according to nongenetic criteria such as the style of clothing, the kind of burial gifts or cultural artefacts. The C + + source code and binary executables for Windows and Linux are available for download at: http://www.uni‐tuebingen.de/uni/bcm/BURIAL/index.html .
[Protein analysis of enzyme tablets].
2001-09-01

Enzyme tablets with butyrylcholine esterase (CHE) and peroxidase (POD) partly lose enzymatic activity during compaction at a pressure of 495 MPa. Compared to solutions of the original enzyme, no changes of ultraviolet absorbance and fluorescence intensity in the tablet solutions were found. Only small changes were observed in the far ultraviolet circular dichroism spectra. Neither missing nor additional bands were detected with polyacrylamide gel electrophoresis. Heated (150 degrees C) solid starting material with CHE and POD showed still part of its original enzymatic activity. The ultraviolet absorbance increased with continued heating until precipitation occurred. The circular dichroism spectra are changed clearly.
Topological susceptibility of Yang-Mills center projection vortices
2001-09-05

The topological susceptibility induced by center projection vortices extracted from SU(2) lattice Yang-Mills configurations via the maximal center gauge is measured. Two different smoothing procedures, designed to eliminate spurious ultraviolet fluctuations of these vortices before evaluating the topological charge, are explored. They result in consistent estimates of the topological susceptibility carried by the physical thick vortices characterizing the Yang-Mills vacuum in the vortex picture. This susceptibility is comparable to the one obtained from the full lattice Yang-Mills configurations. The topological properties of the SU(2) Yang-Mills vacuum can thus be accounted for in terms of its vortex content.
Empty Categories in Sentence Processing
2001-09-06

This book reports a research program into one of the most controversial questions in the syntax — processing interface: The behavior of the parser at gap positions. While the work done is largely experimental, the results are analyzed both for their relevance to sentence processing and for their implications for competing syntactic frameworks. In particular the differing predictions of PPT and HPSG for structures with dislocated constituents are tested for their empirical adequacy. The author addresses a broad range of questions about gap processing and uses a broad range of methodologies to cut through the confounds which prevent previous work providing clear answers. Wh-movement, scrambling, raising, and equi structures are all addressed, and all current accounts of the experimental evidence evaluated. The results move the debate forward significantly, and provide clear confirmation of some non-trivial claims of generative grammar.
Quantum Energies of Interfaces
2001-09-10

We present a method for computing the one-loop, renormalized quantum energies of symmetrical interfaces of arbitrary dimension and codimension using elementary scattering data. Internal consistency requires finite-energy sum rules relating phase shifts to bound state energies.
Spectroscopic Studies on Iron Complexes of Different Anthracyclines in Aprotic Solvent Systems
2001-09-11

Iron complexes of daunorubicin, idarubicin, pirarubicin, and doxorubicin in anhydrous DMF were studied by UV/vis, CD, fluorescence, Mössbauer, and EPR spectroscopy. Titration studies of the metal-free anthracyclines showed one (UV-detectable) deprotonation step requiring 2 equiv of base, compared to 1 equiv for quinizarine. Metal complexation was studied at three different metal/ligand ratios, and with increasing amounts of base. The results obtained from optical spectroscopy show the existence of two different complex species and give clear indications for the requirements of metal complexation. Complex species I, formed at a low iron-to-ligand ratio, is less dependent on base addition than complex species II formed with equimolar ferric ion. EPR and Mössbauer experiments provide further insight into the structures of both complex species. Lack of spin density of the Mössbauer samples in EPR indicates spin coupling between the metal centers. Mössbauer spectra consist of single quadrupole doublets with values typical for high-spin ferric ion in an octahedral arrangement. The Mössbauer spectroscopic features at 7 T exclude the presence of S = 0 dimers. Complex I represents a monomeric ferric iron complex whereas complex II is consistent with a more or less aggregrated oligomeric Fe-anthracycline system.
The epithelial tumor antigen MUC1 is expressed in hematological malignancies and is recognized by MUC1-specific cytotoxic T-lymphocytes.
2001-09-15

The epithelial mucin MUC1 is overexpressed on the cell surface of many epithelial malignancies as well as on some B-cell lymphomas and multiple myelomas. Recently, we identified two HLA-A2-restricted T-cell epitopes derived from the MUC1 protein. To further extend the potential application of these peptides, we analyzed the expression of MUC1 on blast cells from patients with acute myelogenous leukemia (AML; n = 43) and several other hematological malignancies including acute lymphoblastic leukemia (n = 24), chronic lymphocytic leukemia (n = 36), hairy cell leukemia (n = 9), follicular lymphoma (n = 7), and multiple myeloma (n = 12). Using reverse transcription-PCR and MUC1-specific monoclonal antibodies, MUC1 expression was found in 67% of AML samples and 92% of myeloma samples. To analyze the presentation of MUC1 peptides by primary AML blasts, we induced MUC1-specific CTLs in vitro using peptide-pulsed dendritic cells from HLA-A2+ healthy donors as antigen-presenting cells. These CTLs efficiently lysed in an antigen-specific and HLA-A2-restricted manner not only target cells pulsed with the antigenic peptide but also tumor cell lines including multiple myeloma cells and primary AML blasts that constitutively expressed both MUC1 and HLA-A2. The specificity of the CTLs was confirmed in a cold target inhibition assay. Our data demonstrate that MUC1-derived peptides are tumor antigens in AML and several other hematological malignancies that could potentially be used for immunotherapeutic approaches.
Activation of Group I Metabotropic Glutamate Receptors Produces a Direct Excitation and Disinhibition of GABAergic Projection Neurons in the Substantia Nigra Pars Reticulata
2001-09-15

A pathological increase in excitatory glutamatergic input to substantia nigra pars reticulata (SNr) from the subthalamic nucleus (STN) is believed to play a key role in the pathophysiology of Parkinson's disease. We present an analysis of the physiological roles that group I metabotropic glutamate receptors (mGluRs) play in regulating SNr functions. Immunocytochemical analysis at the light and electron microscopic levels reveal that both mGuR1a and mGluR5 are localized postsynaptically in the SNr. Consistent with this, activation of group I mGluRs depolarizes SNr GABAergic neurons. Interestingly, although both group I mGluRs (mGluR1 and mGluR5) are expressed in these neurons, the effect is mediated solely by mGluR1. Light presynaptic staining for mGluR1a and mGluR5 was also observed in some terminals forming symmetric synapses and in small unmyelinated axons. Consistent with this, activation of presynaptic mGluR1a and mGluR5 decreases inhibitory transmission in the SNr. The combination of direct excitatory effects and disinhibition induced by activation of group I mGluRs could lead to a large excitation of SNr projection neurons. This suggests that group I mGluRs are likely to play an important role in the powerful excitatory control that the STN exerts on basal ganglia output neurons.
Spatially Resolved Single Bead Analysis: Homogeneity, Diffusion, and Adsorption in Cross-Linked Polystyrene
2001-09-17

Spatially resolved single bead analysis in the micrometer range was employed as a tool for evaluating homogeneity, diffusion, and adsorption in solid-phase supported reactions. Fluorescence microscopy (confocal and non-confocal) as well as IR microscopy were used to detect both the distribution of products and the formation of product gradients in representative reactions. For the first time, the optical slices of whole beads obtained by confocal fluorescence microscopy were compared with the fluorescence images of microtome-sliced beads. The experiments revealed that only physical slices of polystyrene beads deliver realistic representations of the distribution of fluorophores, and confirmed-in contrast to a recent report-the homogeneity of functional site distribution in polystyrene beads. Moreover, the pattern of product formation obtained from an acylation reaction as well as from an alkylation reaction were employed as probes to study the impact of bead size, diffusion, and adsorption on the reaction progress. A simulation of the diffusion process was conducted and compared with the experimental results. Diffusional control was found neither in the case of the alkylation nor in the case of the acylation reaction under investigation. As a consequence, the reaction progress was not a function of the bead sizes as proposed in the literature. Interestingly, in the case of rhodamine acylation with substoichiometric amounts an adsorption-controlled reaction was found. This result highlights the significance of adsorptive effects in solid-phase supported chemistry.
Cover Picture
2001-09-17

The cover picture shows a representation of a polystyrene resin bead recorded by confocal Raman spectroscopy (top left, recorded by Bradley et al.) as well as a picture of a microtome slice of a resin bead obtained by confocal fluorescence microscopy (top right, recorded by Rademann et al.). Both images indicate the homogeneous distribution of reactive sites throughout the resin bead. For Raman microscopy, 4-cyanobenzoic acid was coupled to the resin and employed as a probe. Different colours indicate the relative intensity of the Raman signal of the CN group, the respective Raman spectrum is displayed on the bottom left. For confocal fluorescence spectroscopy, 5,6-carboxytetramethylrhodamine was used as probe, the respective fluorescence spectrum is displayed on the bottom right. For further details on the investigation of the homogeneity, diffusion, and adsorption properties of cross-linked polystyrene beads see the papers by M. Bradley et al. on p. 3880 ff. and J. Rademann et al. on p. 3884 ff.
Structure–function relationships in the tryptophan‐rich, antimicrobial peptide indolicidin
2001-09-24

Abstract Indolicidin is a cationic 13 amino acid peptide amide produced in the granules of bovine neutrophils with the sequence H‐ILPWKWPWWPWRR‐NH 2 . Indolicidin is both antimicrobial and, to a lesser extent, haemolytic. In order to systematically investigate structure–function relationships, the solid‐phase synthesis of indolicidin and 48 distinct analogues are reported, as well as the characterization of their respective biological properties. Peptides synthesized and characterized include analogues with modified terminal functions, truncations from either terminus, an alanine scan to determine the role of each individual amino acid, specific amino acid exchanges of aromatic, charged and structural residues and several retro‐, inverso‐ and retroinverso‐analogues. Together, characterization of these analogues identifies specific residues involved in antimicrobial or haemolytic activity and suggests a core structure that may form a scaffold for the further development of peptidomimetic analogues of indolicidin. Copyright © 2001 European Peptide Society and John Wiley &amp; Sons, Ltd.
Cholesterol and Alzheimer’s disease
2001-09-25

The Abeta-amyloid peptide (Abeta), the main component of amyloid plaques, is derived by proteolytic cleavage from the amyloid precursor protein (APP). Epidemiologic and biochemical data suggest a link between cholesterol, APP processing, Abeta, and Alzheimer's disease. Two recent epidemiologic studies indicate that there is a decreased prevalence of AD associated with the use of cholesterol-lowering drugs that inhibit 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase inhibitors or statins). Experiments in cell culture and in vivo demonstrate that treatment with statins reduces production of Abeta. The authors discuss how cholesterol might modulate Abeta deposit formation. As neurons receive only small amounts of exogenous cholesterol, statins that efficiently cross the blood-brain barrier may reduce the amount of neuronal cholesterol below a critical level. Decreased neuronal cholesterol levels inhibit the Abeta-forming amyloidogenic pathway possibly by removing APP from cholesterol- and sphingolipid-enriched membrane microdomains. In addition, depletion of cellular cholesterol levels reduces the ability of Abeta to act as a seed for further fibril formation. These intriguing relationships raise the hopes that cholesterol-lowering strategies may influence the progression of AD.
Pancreatic neuroendocrine tumor with extensive vascularisation and parathyroid hormone-related protein (PTHrP) - associated hypercalcemia of malignancy
2001-09-25

We report the case of a 34 year old male presenting with symptomatic hypercalcemia due to excessive PTHrP secretion from a pancreatic neuroendocrine carcinoma with extensive hypervascularization and without any evidence for metastatic disease. In the early phase of the disease conventional chemotherapy with streptozocin and doxorubicin was able to control functional activity as well as tumor growth. However, after 2 years tumor escape was indicated by severe therapy-resistant hypercalcemia. Therapeutic options were reduced due to the excessive tumor vascularization and the patient died from his disease after a short period of intensified therapy. The role of PTHrP in hypercalcemia of malignancy (HHM) and its association with neuroendocrine pancreatic tumors as well as possible therapeutic options are reviewed.
ChemInform Abstract: FTICR‐Mass Spectrometry for High‐Resolution Analysis in Combinatorial Chemistry
2001-09-25

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Tetrameric Fluorophosphazene, (NPF2)4, Planar or Puckered?
2001-09-26

The results obtained in a comprehensive experimental study on the redetermination of the structure of N(4)P(4)F(8) with single-crystal X-ray diffraction, gas electron diffraction (GED), and differential scanning calorimetry (DSC) establish clearly that, in contrast to the previous report, the eight-membered heterocycle is not planar. Above the phase transition temperature of -74 degrees C, the ring appears pseudoplanar. However, the N(4)P(4) ring is disordered and is puckered above the phase transition when the disorder is modeled correctly. Below the phase transition the ring clearly resembles that of the saddle (K form) of N(4)P(4)Cl(8). The unit cell of the low-temperature phase is derived from that of the higher temperature phase by doubling the c-axis and removing one-half of the symmetry elements. Full structure optimizations were performed at the HF/6-31G and B3LYP/6-31G levels and fully support the experimental diffraction data.
Function and structure of heterodimeric amino acid transporters
2001-10-01

Heterodimeric amino acid transporters are comprised of two subunits, a polytopic membrane protein (light chain) and an associated type II membrane protein (heavy chain). The heavy chain rbAT (related to b 0,+ amino acid transporter) associates with the light chain b 0,+ AT (b 0,+ amino acid transporter) to form the amino acid transport system b 0,+ , whereas the homologous heavy chain 4F2hc interacts with several light chains to form system L (with LAT1 and LAT2), system y + L (with y + LAT1 and y + LAT2), system x[Formula: see text](with xAT), or system asc (with asc1). The association of light chains with the two heavy chains is not unambiguous. rbAT may interact with LAT2 and y + LAT1 and vice versa; 4F2hc may interact with b 0,+ AT when overexpressed. 4F2hc is necessary for trafficking of the light chain to the plasma membrane, whereas the light chains are thought to determine the transport characteristics of the respective heterodimer. In contrast to 4F2hc, mutations in rbAT suggest that rbAT itself takes part in the transport besides serving for the trafficking of the light chain to the cell surface. Heavy and light subunits are linked together by a disulfide bridge. The disulfide bridge, however, is not necessary for the trafficking of rbAT or 4F2 heterodimers to the membrane or for the functioning of the transporter. However, there is experimental evidence that the disulfide bridge in the 4F2hc/LAT1 heterodimer plays a role in the regulation of a cation channel. These results highlight complex interactions between the different subunits of heterodimeric amino acid transporters and suggest that despite high grades of homology, the interactions between rbAT and 4F2hc and their respective partners may be different.
How to Assess Spatial Neglect - Line Bisection or Cancellation Tasks?
2001-10-01

Spatial neglect is usually assessed using cancellation tests or line bisection. A recent comparison of these tests has revealed a double dissociation, in which one neglect patient was impaired in line bisection but not in star cancellation whereas another showed the reverse deficit. This dissociation has prompted the question whether 'neglect' is still a meaningful theoretical entity. We compared line bisection and cancellation tasks regarding their accuracy in detecting spatial neglect. We tested 35 patients with well-defined spatial neglect using a line bisection task and four different cancellation tasks. The line bisection test missed 40% of our neglect patients. Far superior were the letter cancellation and bells tests, each of which missed only 6% of the cases. A deviation in line bisection is not fundamentally related to spatial neglect, but may also arise from other causes (e.g., hemianopia, or which hand is used), and therefore, should be treated with caution in clinical diagnosis. Cancellation tests, such as the bells test and letter cancellation, are more helpful tools to detect spatial neglect.
Substances with estrogenic activity in effluents of sewage treatment plants in southwestern Germany. 1. Chemical analysis
2001-10-01

Abstract A gas chromatography/mass spectrometry method for the simultaneous quantitative determination of natural and synthetic estrogens (17β-estradiol, estrone, 17α-ethinylestradiol, and mestranol), phytoestrogens (genistein and β-sitosterol), and xenoestrogens (benzyl butyl phthalate, dibutyl phthalate, bisphenol A, 4-nonylphenol [NP], 4-nonylphenoxyacetic acid [NP1EC], 4-nonyl-phenol diethoxylate [NP2EO], and α-endosulfan) in effluents of sewage treatment plants (STPs) was developed. Identification and quantification were carried out with the standard addition method using analyte-specific and, in some cases, deuterium-labeled internal standards. The effluents of 18 STPs were investigated. Apart from α-endosulfan and mestranol, all selected substances were detected in the majority of samples. The median concentrations of steroidal estrogens were between 0.4 ng/L (17α-ethiny-lestradiol) and 1.6 ng/L (17β-estradiol). The metabolites of the nonylphenol polyethoxylates, NP, NP1EC, and NP2EO were found in concentrations ranging from the upper-ng/L-range (NP) to the lower-μg/L range (NP1EC). For all substances except mestranol and α-endosulfan, median values were calculated and compared to the results of other investigations in Europe and the United States. Possible dependencies of measured concentrations on the geographical location, the capacity, the influent composition, and the technical fitting of the STPs are discussed.
Comprehensive analysis of the genetic factors determining expression and function of hepatic CYP2D6
2001-10-01

Variable expression and function of the cytochrome P4502D6 (CYP2D6) leads to distinct phenotypes termed ultrarapid (UM), extensive (EM), intermediate (IM) and poor metabolizer (PM). Whereas the PM phenotype is known to be caused by two null-alleles leading to absence of functional CYP2D6 protein, the large variability among individuals with functional alleles remained largely unexplained. In this study, we systematically investigated 76 liver biopsies from individuals with known sparteine metabolic ratios (MRS) for the relationships between CYP2D6 genotype, microsomal protein expression, bufuralol 1′-hydroxylase activity and in-vivo phenotype. Average CYP2D6 protein levels ranged from undetectable in PMs (MRS> 20) to 2.6 ± 2.7 pmol/mg microsomal protein in IMs (1.2 < MRS< 20), 7.6 ± 4.7 in EMs (0.2 < MRS< 1.2) and 23.8 ± 7.7 in UMs (MRS< 0.2), respectively. Analysis with respect to genotype demonstrated gradually increased expression and function for individuals with no, one, two or three functional gene copies per genome. The recently discovered − 1584 C/G promoter polymorphism was identified as another major factor for expression and function with the mutant [−1584G] promoter type being consistently associated with significantly higher expression than [−1584C]. To investigate functional differences between the detected variant protein forms CYP2D6.1, 2D6.2, 2D6.9 and 2D6.10, we expressed them recombinantly in insect cells. The most significant difference was a decrease in the relative P450 holoprotein content of all allelic forms, including the common functional variant 2D6.2, in comparison to 2D6.1, whereas only modest Km changes were observed. Taken together, these data provide further insight into the complex mechanisms that govern the highly variable expression and function of CYP2D6.