julilili42/papers huggingface dataset:
Establishing Causality between Pollution and Effects at Different Levels of Biological Organization: The VALIMAR Project
2003-01-01

The study summarizes the objectives of the VALIMAR project and gives selected examples of biomarker responses that allow causal relationships to be established between exposure and biological effects at different levels of biological organization. In this project, active and passive biomonitoring experiments with brown trout (Salmo trutta f. fario) and stone loach (Barbatula barbatula) were performed in two small streams in southern Germany between 1995 and 1999 in parallel with investigations on contaminant mixtures in the laboratory in order to evaluate the suitability of biomarkers representing different levels of biological organization for the assessment of pollution in small streams. In addition to biomarker studies, the morphology of the test streams was characterized and limnological and chemical parameters were monitored. Early life stage tests and ecological studies of brown trout and stone loach population demography, of the fish assemblages, and the macro- and meiozoobenthos communities in the two test streams were included in the project. Several causality criteria were addressed by means of combined (1) laboratory and field studies, (2) chemical, biological, and statistical investigations, and (3) in vivo and in vitro studies that allowed establishment of cause-effect relationships at different biological levels. The comparison of results obtained at these levels allowed identification of mechanisms responsible for the respective effects (coherence of association, biological plausibility). Finally, individual responses (biomarkers, bioindicators) could be extrapolated to higher biological levels (population, community) thus addressing the criteria of 'time order' and 'coherence of association'.
Establishment of T cell lines to bovine beta-casein and beta-casein-derived epitopes in patients with type 1 diabetes
2003-01-01

Enhanced cellular immune response to bovine beta-casein has been reported in patients with type 1 diabetes. In this study we aimed to establish beta-casein-specific T cell lines from newly diagnosed type 1 diabetic patients and to characterise these cell lines in terms of phenotype and epitope specificity. Furthermore, since sequence homologies exist between beta-casein and putative beta-cell autoantigens, reactivity to the latter was also investigated. T cell lines were generated from the peripheral blood of nine recent onset type 1 diabetic patients with different HLA-DQ and -DR genotypes, after stimulation with antigen pulsed autologous irradiated antigen presenting cells (APCs) and recombinant human interleukin-2 (rhIL-2). T cell line reactivity was evaluated in response to bovine beta-casein, to 18 overlapping peptides encompassing the whole sequence of beta-casein and to beta-cell antigens, including the human insulinoma cell line, CM, and a peptide from the beta-cell glucose transporter, GLUT-2. T cell lines specific to beta-casein could not be isolated from HLA-matched and -unmatched control subjects. beta-Casein T cell lines reacted to different sequences of the protein, however a higher frequency of T cell reactivity was observed towards the C-terminal portion (peptides B05-14, and B05-17 in 5/9 and 4/9 T cell lines respectively). Furthermore, we found that 1 out of 9 beta-casein-specific T cell lines reacted also to the homologous peptide from GLUT-2, and that 3 out of 4 of tested cell lines reacted also to extracts of the human insulinoma cell line, CM. We conclude that T cell lines specific to bovine beta-casein can be isolated from the peripheral blood of patients with type 1 diabetes; these cell lines react with multiple and different sequences of the protein particularly towards the C-terminal portion. In addition, reactivity of beta-casein T cell lines to human insulinoma extracts and GLUT-2 peptide was detected, suggesting that the potential cross-reactivity with beta-cell antigens deserves further investigation.
Interfering with TGFbeta-induced Smad3 nuclear accumulation differentially affects TGFbeta-dependent gene expression.
2003-01-01

The data show that SB-202190 and SB-203580 suppress TGFbeta-dependent activation of genes that are important for the acquisition of invasive behavior, while having no effect on the expression of the natural TGFbeta inhibitor Smad7. This suggests that these compounds are potent inhibitors of malignant behavior of cancer cells.
Microarray technology--the future analyses tool in exercise physiology?
2003-01-01

Microarray analysis offers a set of analytical platforms that provide rapid, affordable and substantial information at the DNA, RNA or protein level. It enables the analysis of thousands of genes simultaneously in a parallel manner across samples derived from various biological sources and treatment regimens. This development became possible as a result of the combination of three technological advances achieved at the beginning of the 1990's, namely parallelism, miniaturization and automation. In regular physical checkups the microarray technology could be used to supplement the current spectrum of tests and therefore enhance the quality of the data obtained. Arrays for analyses of RNA expression will allow gene expression profiling also in exercise physiology. DNA chips may also be used for genetic screening and diagnostics to analyze polymorphisms and mutations which may underlie genetic diseases or interindividual variations between subjects. Using microarrays in exercise physiology will provide new insights into the complex molecular mechanisms of the exercise-induced stress response, adaptation to training and modulation of immune function. Gene expression profiling and genetic screening will probably help to characterize and predict the individually variable response to and efficiency of training.
Molecular phylogenetics employing modern and ancient DNA.
2003-01-01

Comparative studies of DNA in recent populations and characterisation of ancient hereditary material have contributed very interesting facts to our understanding of evolution of modern mankind. Analysis of DNA homology in related species, assessment of mutations and polymorphisms in various populations and new DNA sequence data from prehistoric finds allowed - via sophisticated DNA extraction techniques, PCR, sequencing and digitalised processing of genetic information - insights into possible roots of Homo sapiens and related species, migration patterns and ancient cultural habits, thus enrhing the palaeoanthropological discipline. However, a presentation of this development would not be complete without pointing towards the methodological limitations and manifold presentations burdened with artifacts, data misinterpretation and unjustified conclusions. Presently, this modern field of research is in its consolidation phase and new parameters for quality control and authentication are being implemented to avoid spectacular but unfounded reports. It is expected that most of the problems connected to old biomolecules may be closely related to fossilisation parameters. The future challenge will be the full understanding of the complex and multi-faceted processes underlying diagenesis, including the elucidation of nucleic acid postmortem damage".
Generation-adjusted discounting in long-term decision-making
2003-01-01

This paper analyses the choice of an inter-generational discount rate as well as a method for inter-generational discounting. It is shown that the pure time preference rate is irrelevant for inter-generational comparisons. However, the application of the growth time preference rate - with respect to consumption - is a necessary condition for inter-temporal utility maximisation. Opportunity costs should be taken into account not by discounting with their internal rate of return, but by calculating consumption equivalents (shadow prices of capital). Thus, an intergenerational discount rate has to be based on the time preference approach. These considerations lead us to the formulation of a new discounting technique, "Generation Adjusted Discounting" (GAD). It takes into account intra- as well as inter-generational aspects. Compared with conventional discounting techniques, we find that the present values obtained by using the GAD noticeably exceed those derived conventionally.
Early Outcome of Carotid Angioplasty and Stenting versus Carotid Endarterectomy in a Single Academic Center
2003-01-01

&lt;i&gt;Background:&lt;/i&gt; Evidence is accumulating that carotid angioplasty and stenting (CAS) might become an alternative to carotid endarterectomy (CEA) for the treatment of high-grade carotid artery disease (CAD). Evaluating the efficacy of this novel technique in single institutions in addition to performing further large trials can help to guide optimal patient management in everyday practice. &lt;i&gt;Methods:&lt;/i&gt; In this study we compared the early outcome of 100 prospectively followed patients who underwent CAS with a retrospectively reviewed group of 142 patients that underwent CEA over the same time period. Only patients who had received pre- and postsurgical evaluations by a neurologist were included. According to the criteria set forth by the large trials the occurrence of minor or major strokes, myocardial infarction and death within 30 days was analysed. &lt;i&gt;Results:&lt;/i&gt; Both groups had similar age and sex distributions, as well as cerebrovascular risk factors. In the group of CAS patients 63 (63%) and in the group of CEA patients 92 (65%) had a symptomatic carotid stenosis, respectively. For symptomatic patients the overall complication rate (any stroke or death) was 6.5% (3 minor and 3 major strokes) in the surgical and 8% (2 minor strokes, 2 major strokes, and 1 death) in the non-surgical group (n.s.). For asymptomatic patients there was one minor stroke (2%) in the surgical and no stroke or death in the non-surgical group. As a frequent non-neurological complication the post-procedural course was complicated by groin hematoma requiring surgery in 3 CAS patients, and neck hematoma requiring additional surgery in 3 CEA patients. &lt;i&gt;Conclusions:&lt;/i&gt; Within our academic institution we found comparable complication rates for CAS and CEA in patients with symptomatic or asymptomatic high-grade CAD. Although these early results are promising and support the notion that CAS may become an alternative treatment option for CAD in everyday practice, the long-term efficacy of CAS has to be evaluated critically by means of further prospective studies.
Flip the Tip: An Automated, High Quality, Cost-Effective Patch Clamp Screen
2003-01-01

The race for creating an automated patch clamp has begun. Here, we present a novel technology to produce true gigaseals and whole cell preparations at a high rate. Suspended cells are flushed toward the tip of glass micropipettes. Seal, whole-cell break-in, and pipette/liquid handling are fully automated. Extremely stable seals and access resistance guarantee high recording quality. Data obtained from different cell types sealed inside pipettes show long-term stability, voltage clamp and seal quality, as well as block by compounds in the pM range. A flexible array of independent electrode positions minimizes consumables consumption at maximal throughput. Pulled micropipettes guarantee a proven gigaseal substrate with ultraclean and smooth surface at low cost.
Finite structure query
2003-01-01

Finite structure query (fsq for short) is a tool for querying syntactically annotated corpora. fsq employs a query language of high expressive power, namely full first order logic. It can be used to query arbitrary finite structures, not just trees.
Influence of different types of exercise on the expression of haem oxygenase-1 in leukocytes
2003-01-01

Haem-oxygenase-1 (HO-1) is an antioxidant stress protein that is mainly induced by reactive oxygen species, inflammatory cytokines and hyperthermia. We assessed the influence of different types of exercise on HO-1 expression in leukocytes of the peripheral blood in three groups of male participants: a short exhaustive run above the lactate steady state (n = 15), eccentric exercise (n = 12) and an intensive endurance run (half-marathon, n = 12). Blood samples were taken at rest and up to 24 h after exercise. Blood lactate concentration after exercise was 9.0 +/- 2.1, 3.8 +/- 1.6 and 5.1 +/- 2.2 mmol x l(-1) (mean +/- s) for the exhaustive run, eccentric exercise and half-marathon groups, respectively (P < 0.05). Creatine kinase concentration was highest 24 h after exercise: 133 +/- 91, 231 +/- 139 and 289 +/- 221 U x l(-1) for the exhaustive run, eccentric exercise and half-marathon groups, respectively (P < 0.05). The maximal increase in leukocyte counts after exercise was 11.5 +/- 19.2, 6.2 +/- 1.4 and 14.7 +/- 2.1 x 10(9) x l(-1). There was no change in HO-1 as a result of the short exhaustive run or the eccentric exercise, whereas the half-marathon had a significant stimulatory effect on HO-1-expression in lymphocytes, monocytes and granulocytes (P < 0.001) using flow cytometry analyses. In conclusion, eccentric exercise alone or short-term heavy exercise are not sufficient to stimulate the antioxidative stress protein HO-1 in peripheral leukocytes
Stable isotopic indication for the cyst formation depth of Campanian/Maastrichtian calcareous dinoflagellates
2003-01-01

Abstract δ18O and δ13C values for the calcareous dinoflagellate species Orthopithonella? globosa (Fütterer 1984) Lentin and Williams 1985 and Pirumella krasheninnikovii (Bolli 1974) Lentin and Williams 1993 from latest Campanian and earliest Maastrichtian of ODP Hole 690C (Weddell Sea, Antarctic Ocean) have been studied in order to evaluate the species' depth habitat in the water column and their applicability in paleoceanographic studies. The calcareous dinoflagellates show isotopic values comparable to probably shallow-dwelling planktic foraminifera from the same samples in δ18O, but have an offset of about −5‰ to −7‰ in δ13C. This suggests that calcareous dinoflagellate oxygen isotopes may provide information for paleoceanographic reconstructions of sea-surface water temperatures, whereas their extremely light carbon isotope values are probably due to photosynthetic processes.
Inhibition of interferon-γ expression by osmotic shrinkage of peripheral blood lymphocytes
2003-01-01

A hypertonic environment, as it prevails in renal medulla or in hyperosmolar states such as hyperglycemia of diabetes mellitus, has been shown to impair the immune response, thus facilitating the development of infection. The present experiments were performed to test whether hypertonicity influences activation of T lymphocytes. To this end, peripheral blood lymphocytes (PBL) of cytomegalovirus (CMV)-positive donors were stimulated by human leukocyte antigen (HLA)-A2-restricted CMV epitope NLVPMVATV to produce interferon (IFN)-γ at varying extracellular osmolarity. As a result, increasing extracellular osmolarity during exposure to the CMV antigen indeed decreased IFN-γ formation. Addition of NaCl was more effective than urea. A 50% inhibition was observed at 350 mosM by addition of NaCl. The combined application of the Ca 2+ ionophore ionomycin (1 μg/ml) and the phorbol ester phorbol 12-myristate 13-acetate (PMA; 5 μg/ml) stimulated IFN-γ production, an effect again reversed by hyperosmolarity. Moreover, hyperosmolarity abrogated the stimulating effect of ionomycin (1 μg/ml) and PMA (5 μg/ml) on the transcription factors activator protein (AP)-1, nuclear factor of activated T cells (NFAT), and NF-κB but not Sp1. In conclusion, osmotic cell shrinkage blunts the stimulatory action of antigen exposure on IFN-γ production, an effect explained at least partially by suppression of transcription factor activation.
AN OVERVIEW OF THE SPATIAL ARCHAEOLOGY OF THE GEELBEK DUNES, WESTERN CAPE, SOUTH AFRICA
2003-01-01

situated 90 km north of Cape Town in the West Coast National Park (Fig. 1). The deflation hollows located between the wind-blown, mobile sand dunes have long been recognized as a source of mammalian fossils and Stone Age artifacts. In 1998 a team from the Department of Early Prehistory and Quaternary Ecology of the University of Tubingen began fieldwork to systematically study archaeological occurrences in this active dune system (Conard et al. 1999). Over the course of the following field seasons from 1998 through 2001, the team spent over seven months in the field surveying the dunes, collecting samples of the faunal and artifactual remains, and excavating large areas. The team studied the geology and geomorphology of the dunes by excavating test pits, obtaining soil and organic samples for dating and other physical testing, measuring movement of the dunes, and setting up experiments to monitor the movement of objects placed in the dune system.
Ergonomics in the operating room – from the anesthesiologist's point of view
2003-01-01

Over the past years, progress in medicine and the development of a multitude of new devices have made the tasks to be performed in operating rooms increasingly complex; at the same time, more and more equipment is necessary to perform these tasks and make surgery as safe as possible for the patients. These developments are also relevant for the field of anesthetic care; when planning new operating rooms or restructuring existing ones, attention should be paid to provide the anesthesia team with an adequate work environment so that all anesthetic procedures can be carried out safely and efficiently and an optimal workflow can be established in the OR environment. The present paper illuminates this topic from various angles, discussing questions of space requirements, monitoring, alarm systems, equipment design, documentation and human factors. All these individual considerations should ultimately be integrated into a coherent approach which could serve as guidance in the planning of effective and ergonomic anesthesia workplaces for the future.
An Architecture for Hierarchical Collision Detection
2003-01-01

We present novel algorithms for efficient hierarchical collision detection and propose a hardware architecture for a single-chip accelerator. We use a hierarchy of bounding volumes defined by k-DOPs for maximum performance. A new hierarchy traversal algorithm and an optimized triangle-triangle intersection test reduce bandwidth and computation costs. The resulting hardware architecture can process two object hierarchies and identify intersecting triangles autonomously at high speed. Real-time collision detection of complex objects at rates required by force-feedback and physically-based simulations can be achieved.
X‐Ray Single Crystal Refinement and Superconductivity of La3Ni2B2N3
2003-01-01

Abstract Crystalline samples of La 3 Ni 2 B 2 N 3 were synthesized using solid state metathesis reactions from combinations of La, LaCl 3 , NiCl 2 together with Li 3 BN 2 . The structure was determined by single crystal X‐ray diffraction (I4/mmm (No. 139), a = 372.95(2) pm, c = 2056.3(2) pm, R 1 = 0.027, wR 2 = 0.062) and confirmed earlier results from neutron powder diffraction. La 3 Ni 2 B 2 N 3 contains BN units capping square planar Ni layers. Isolated nitrogen atoms reside in La 6 octahedra. Magnetic measurements on several bulk samples exhibit superconductivity at temperatures below 14.6 K.
Late Visean/early Namurian conodont succession from the Esla area of the Cantabrian Mountains, Spain
2003-01-01

Conodont fauna recovered from pelagic nodular limestone sequence exposed near Santa Olaja de la Varga precisely dates the upper part of the Alba Formation in the Esla area of the Cantabrian Mountains. In terms of goniatite stratigraphy, the formation ranges into the early Namurian E2 interval which has been identified by the occurrence of the conodont Gnathodus bollandensis . The investigated conodont fauna includes exclusively deep-water forms and is dominated by species of Gnathodus and Lochriea . The former genus is represented primarily by the bilineatus lineage, in which a new species Gnathodus cantabricus sp. nov. has been recognized and is described herein. Representatives of the another gnathodontid girtyi lineage,generally present in the late Visean/early Namurian deep-water faunas, are extremely rare. The vertical succession of Lohriea species is closely comparable to those recognized in Northern England, Poland and Ukraine. The Visean/Namurian boundary is thus placed at the first occurrence of Lochriea cruciformis , 4.7 m below the top of the Alba Formation.
Sedimentary response to tectonics in extensional basins: the Pechelbronn Beds (Late Eocene to early Oligocene) in the northern Upper Rhine Graben, Germany
2003-01-01

Abstract The deposition of the late Eocene to early Oligocene Pechelbronn Beds in the northern Upper Rhine Graben was controlled by changes in accommodation space, sediment supply and basin physiography, imposed by the syn-rift tectonic framework. Base-level cycles, defined by variations of the ratio of accommodation space to sediment supply (A/S ratio), allow untangling of the depositional history in this complex structural setting. A transfer zone divided the northern part of the Upper Rhine Graben into a southern and a northern sub-basin and created major depositional gradients. The low A/S ratio in the transfer zone led to sediment bypassing and cannibalisation. Only asymmetric cycles of fluvial and alluvial fan deposits developed, as the sediment was transported to the sub-basins. The higher A/S ratio on the major gradient of the southern sub-basin, which increased from the transfer zone to the south, allowed the formation of symmetric delta/shoreface and lacustrine cycles. At times starvation occurred in the transfer-zone-distal parts of the sub-basin. On subordinate scale, within the southern sub-basin, tilt-blocks bounded by growth faults created halfgrabens with inferior depositional gradients. On the footwall crest, due to low A/S ratio, bypassing and erosion occurred. Here asymmetric cycles of coarse-grained channel fill deposits were preserved. On the hangingwall, close to the normal fault, high A/S conditions were present and symmetric cycles developed. The creation of accommodation space kept pace and even outpaced the footwall-derived sediment supply, which created thick shallow water deposits.
Bounded Property Checking with Symbolic Simulation.
2003-01-01

Steadily increasing design sizes, make the verification a bottleneck in modern design flows of digital hardware and embedded software systems. Up to 75 % of the overall design costs are due to the verification task. Formal methods have been proposed to accompany commonly used simulation approaches. In this paper we combine property checking and symbolic simulation to make these techniques applicable to larger designs and to seamlessly integrate formal verification and standard simulation. Our experimental results show a run time gain over standard symbolic model checking and SATbased bounded model checking for certain classes of circuits and properties.