julilili42/papers huggingface dataset:
Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence
2003-02-01

Plasmid SCP2* is a 31 kb, circular, low-copy-number plasmid originally identified in Streptomyces coelicolor A3(2) as a fertility factor. The plasmid was completely sequenced. The analysis of the 31 317 bp sequence revealed 34 ORFs encoding putative proteins from 31 to 710 aa long, most of them lacking similarity to known proteins. Three functional regions had been identified previously: the replication region, the transfer and spreading region, and the stability region. Three genes were identified in the stability region which contribute to the stability of SCP2 as shown by plasmid stability testing. The first gene, mrpA, encodes a new member of the lambda integrase family of site-specific recombinases. The two genes downstream of mrpA were called parA and parB. The gene product, ParA, shows similarity to a family of ATPases involved in plasmid partition. An increase of plasmid stability could be seen only when both genes were present. By deletion analysis, the replication region could be narrowed down to a 1.6 kb region, consisting of a 650 bp non-coding region and two genes, repI and repII, encoding proteins of 161 and 131 aa. Only RepI exhibits similarities to DNA binding elements and contains a putative helix-turn-helix motif. The traA gene that is essential for DNA transfer and pock formation was identified previously. Upstream of traA, 10 ORFs were found in the same orientation as traA which might be involved in conjugation and DNA spreading, together with one gene in the opposite orientation with similarities to transcriptional regulators of DNA transfer. Two transposable elements were found on SCP2*. IS1648 belongs to the IS3 family of insertion sequences. The second element, Tn5417, shows the highest similarity to the Tn4811 element located in the terminal inverted repeats of the Streptomyces lividans chromosome.
Synthesis and Structure of Redox‐Active Heterotetranuclear Molecular Polygons by Self‐Assembly of Two Ferrocene‐Bridged Bis(pyridines) with Two Transition Metals
2003-02-01

Abstract The macrocyclic complexes [(η 5 ‐C 5 H 4 C 2 ‐4‐py) 2 Fe] 2 Ni 2 (NO 3 ) 4 ( 2 ), [(η 5 ‐C 5 H 4 C 2 ‐3‐py) 2 Fe] 2 Ag 2 (ClO 4 ) 2 ( 4 ), and [(η 5 ‐C 5 H 4 C 2 ‐3‐py) 2 Fe] 2 Pd 2 Cl 4 ( 5 ) were obtained by reaction of [Ni(H 2 O) 6 ](NO 3 ) 2 , AgClO 4 , and PdCl 2 (COD) with the ligands (η 5 ‐C 5 H 4 C 2 ‐4‐py) 2 Fe ( 1 ) and (η 5 ‐C 5 H 4 C 2 ‐3‐py) 2 Fe ( 3 ), respectively, under high dilution conditions (Scheme 1). The molecular motifs of 2 , 4 , and 5 were studied by single‐crystal X‐ray structural investigations. Elemental analyses and 1 H NMR and IR spectra were also used to confirm the structures. Compound 2 represents an unsymmetric paddlewheel, in which the centers of the four Cp rings define a nearly ideal rectangle with dimensions of 20.2 × 3.3 Å. In principle, macrocycles 4 and 5 can also be described as rectangles, however, due to the 3‐positioned nitrogen donors with deformed edges (17.4 × 3.3 Å for 4 ). In contrast to the offset packing of the molecules in 2 , the macrocycles in the crystal of 4 are aligned, with trapped acetonitrile molecules in between. The intra‐ and intermolecular Ag−Ag distances are 3.50 and 3.79 Å, respectively. Cyclovoltammetric studies reveal chemically reversible ferrocene‐based redox reactions of 1 − 4 . Although no electronic communication was observed between the two identical ferrocene units, a weak through‐bond electronic interaction between ferrocene and nickel, or silver, was established. In 2 a weak antiferromagnetic interaction between the nickel atoms was also found. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Centre and surround responses of marmoset lateral geniculate neurones at different temporal frequencies
2003-02-01

The responses of marmoset lateral geniculate neurones to stimuli that were composed of a sinusoidally modulating centre stimulus and a surround that was modulated in counterphase were measured. The size of the stimulus centre was varied. These measurements were repeated at different temporal frequencies between 1 and 30 Hz. The response amplitudes and phases depended in a characteristic manner on the stimulus centre size. The response behaviour could be modelled by assuming Gaussian responsivity profiles of the cells' receptive field (RF) centres and surrounds and a phase delay in the RF surround responses, relative to the centre, enabling the description of RF centre and surround response characteristics. We found that the RF centre‐to‐surround phase difference increased linearly with increasing temporal frequency, indicating a constant delay difference of about 4.5 to 6 ms. A linear model, including low‐pass filters, a lead lag stage and a delay, was used to describe the mean RF centre and surround responses. The separate RF centre and surround responses were less band pass than the full receptive field responses of the cells. The linear model provided less satisfactory fits to M‐cell responses than to those of P‐cells, indicating additional nonlinearities.
HIGHER ORDER ABSTRACT CAUCHY PROBLEMS: THEIR EXISTENCE AND UNIQUENESS FAMILIES
2003-02-01

Let X,Y be Banach spaces. Of concern are the higher order abstract Cauchy problem (ACPn) in X and its inhomogeneous version (IACPn). A new operator family of bounded linear operators from Y to X is introduced, called an existence family for (ACPn), so that the existence and continuous dependence on initial data of the solutions of (ACPn) and (IACPn) can be studied, and some basic results in a quite general setting can be obtained. A sufficient and necessary condition ensuring that (ACPn) possesses an exponentially bounded existence family, in terms of Laplace transforms, is presented. As a partner of the existence family, for (ACPn), a uniqueness family of bounded linear operators on X is defined to guarantee the uniqueness of solutions. These two operator families for (ACPn) are generalizations of the classical strongly continuous semigroups and sine operator functions, the C-regularized semigroups and sine operator functions, the existence and uniqueness families for (ACP1), and the C-propagation families for (ACPn). They have a special function in treating those ill-posed (ACPn) and (IACPn) whose coefficient operators lack commutativity.
The Effect of Progesterone and Synthetic Progestins on Serum- and Estradiol-Stimulated Proliferation of Human Breast Cancer Cells
2003-02-01

The results from the Women's Health Initiative study on enhanced breast cancer risk in postmenopausal women using an estrogen/progestin combination clearly indicate the need for a comparison of different progestins with regard to cancer risk. To shed some light on this issue, we have investigated the influence of progesterone and various synthetic C19- and C21-progestins on cell proliferation of a human breast cancer cell line in vitro. Of special interested was the comparison of two different regimens commonly used in HRT, sequential and continuous combination with estradiol. We used the human breast cancer cell line MCF-7 as a model. Progesterone (P), chlormadinone acetate (CMA), dienogest (DNG), gestodene (GSD), 3-ketodesogestrel (KDG), levonorgestrel (LNG), medroxyprogesterone acetate (MPA), and norethisterone (NET) were investigated in the range of 0.01nm to 10 micro M alone and in combination with 10 nM estradiol. Cell proliferation was measured after 7 days using the ATP chemosensitivity test. Tested alone, CMA, DNG, GSD, KDG, MPA and NET significantly stimulated cell proliferation, but only at high dosages. Sequentially combined with estradiol, only CMA inhibited cell proliferation over the whole concentration range. Slight effects were found for DNG, GSD and KDG, whereas P and MPA only showed an effect at the highest concentration. NET had no significant effect on cell proliferation. Continuously combined, all progestins exhibited an inhibitory effect over the whole concentration range. The most prominent effects were found for P, CMA, GSD, and KDG. Only slight effects were found for DNG, MPA and NET. Our in vitro results indicate that the influence on breast cancer risk using HRT in postmenopausal women might depend on the type of progestin used as well as on the regimen applied. However, the net inhibitory in vitro effect of the progestins at clinically relevant dosages is rather minimal, and whether progestins in general can reduce breast cancer risk in long-term treatment remains uncertain. Further clinical trials are urgently needed to clarify this issue.
Activity and subcellular distribution of cathepsins in primary human monocytes
2003-02-01

Abstract Cathepsins (Cat) in antigen presenting cells (APC) control antigen processing as well as major histocompatibility complex class II transport and function. The set of active Cat and the subcellular architecture of the class II antigen presentation compartment are largely unknown in primary human APC, including peripheral blood monocytes. We used novel chemical tools to visualize Cat in an activity-dependent manner. Primary human monocytes cntained active CatS, -B, and -H, while CatL was absent. Expression and activity patterns of Cat in human myelo-monocytoid cell lines were distinct from those found in primary cells. On a subcellular scale, the bulk of active Cat was concentrated in lysosomes in primary monocytes. In late endosomes, only active CatS was found in sizable amounts, colocalizing with C-terminal processing of the class II invariant chain and with cystatin C, the major endogenous Cat inhibitor. Late endosomes of human peripheral blood monocytes contain a well-controlled proteolytic machinery distinct from lysosomes, which is likely to play a key role in class II function.
Pro‐inflammatory (IL‐1β, IL‐18) cytokines and IL‐8 chemokine release by PBMC in response to Echinococcus multilocularis metacestode vesicles
2003-02-01

SUMMARY In humans infected with Echinococcus multilocularis , larval metacestodes will develop, proliferate and progressively infiltrate the surrounding host tissues by exogenous budding of parasitic microvesicles or cell lines which detach from the original tumour and thus become transported through blood or lymph vessels into other organs. Cellular effector mechanisms constitute the most effective means to restrict parasite persistence and proliferation, and here we demonstrate that E. multilocularis vesicle antigens will induce pro‐inflammatory, regulatory and chemokine release by PBMC from patients. The pro‐inflammatory cytokines IL‐1β and IL‐18 were reduced in echinococcosis patients, regulatory IL‐10 was similar, but parasite vesicle‐induced IL‐8 was dominant and clearly elevated in patients. Such selective and opposite dynamics of inflammatory cytokines and chemokine release may prevent overwhelming and pathogenic inflammation, and constitute an appropriate response for attraction of effector cells into the periparasitic tissues with the capacity to limit E. multilocularis metacestode proliferation and dissemination.
Stability of the viscously spreading ring
2003-02-01

We study analytically and numerically the stability of the pressure-less, viscously spreading accretion ring. We show that the ring is unstable to small non-axisymmetric perturbations. To perform the perturbation analysis of the ring we use a stretching transformation of the time coordinate. We find that to 1st order, one-armed spiral structures, and to 2nd order additionally two-armed spiral features may appear. Furthermore, we identify a dispersion relation determining the instability of the ring. The theoretical results are confirmed in several simulations, using two different numerical methods. These computations prove independently the existence of a secular spiral instability driven by viscosity, which evolves into persisting leading and trailing spiral waves. Our results settle the question whether the spiral structures found in earlier simulations of the spreading ring are numerical artifacts or genuine instabilities.
Isolated Internal Cerebral Venous Thrombosis in a Neonate with Increased Lipoprotein (a) Level: Diagnostic and Therapeutic Considerations
2003-02-01

Background. Internal cerebral venous thrombosis is a life-threatening condition, which requires immediate therapy. Being infrequent in childhood, internal venous thrombosis is very rare in the neonate and has never been observed without concomitant occlusion of further dural sinuses. Case Description. We report a neonate born at term, who developed seizures on the third day of life after normal pregnancy and uneventful delivery. Ultrasound and CT disclosed bilateral intraventricular and intracerebral hemorrhage with an unusual distribution for germinal matrix hemorrhage. MRI disclosed thrombotic occlusion of the straight sinus and the internal cerebral veins with concomitant bleeding into the ventricles, the basal ganglia, thalamus and the periventricular hemispheres. The other sinuses were not affected. The clinical condition of the child improved after initiation of a low-dose heparin treatment with subsequent partial recanalization of the occluded vessels. The screening for risk factors disclosed an elevated lipoprotein (a) level, also present in both parents. Conclusion. Internal cerebral venous thrombosis may be encountered in neonates and must be included in the list of differential diagnosis of perinatal intraventricular and intracerebral bleeding. MRI allows the diagnosis even in the absence of widespread dural sinus occlusion. Low dose heparin may be a therapeutic option in these cases. This is the first report of neonatal internal venous thrombosis due to hereditary lipoprotein (a) level elevation, which must be included in the list of possible predisposing conditions.
Immunohistochemical and Molecular Biological Investigations Regarding the Pathogenesis of Extrahepatic Biliary Atresia
2003-02-01

Most tissue preparations from children operated on during the 4th-8th week of life show only small leukocyte infiltrations and in the majority of cases no immunocompetent lymphocytes. This leads to the conclusion that a virus infection as an underlying cause for EHBA is very unlikely. Most probably, the observed leukocyte infiltrations are due to an unspecific phagocytotic activity. Comparing our results to reports from Hadchouel et al (9) and Landing et al (12) led us to believe that a pathologic immunoreaction with a possible defective antigen elimination could also be considered as a reason for EHBA.
Issues for further refinement of family interventions in schizophrenia.
2003-02-01

While medication is vital for people with schizophrenia, it is only one part of the treatment regimen. Treatment of individuals with schizophrenia requires a co-ordinated multidisciplinary approach. With the patient's consent, families and carers should be involved from the outset. In the acute phase, an experienced health professional should provide information to patients, families and carers on the illness, aetiology, course, treatment, and service options. After assessment and during the transition to the stabilisation phase, family intervention should be implemented in most cases. These interventions include psychoeducation, analysis of family relationships and functioning, and special sessions to address problems of the family. Of the psychosocial treatments, family interventions have proven the most promising in affecting patient outcome in schizophrenia. Family interventions clearly augment pharmacotherapy, resulting in reduced relapse rates, improved symptomatology, and better social and vocational functioning. The typical reduction of risk of relapse or rehospitalization is about 20 to 30% over 2 years. Research also suggests that family interventions improve quality of family relationships. Despite these achievements, there are a variety of critical issues which are currently a topic of intense discussion in Germany. I will present a few of them.
Common Surface‐AntigenvarGenes of Limited Diversity Expressed byPlasmodium falciparumPlacental Isolates Separated by Time and Space
2003-02-01

Plasmodium falciparum placental parasites from Cameroon have been shown to express surface variant var genes encoding Duffy binding-like (DBL)-gamma domains that bind chondroitin sulfate A. All 5 domains exhibited sequences with 39%-55% amino acid (aa) identities and appear sufficiently conserved to function in receptor binding. Transcripts of 2 samples showed complete conservation over 4 kb, demonstrating for the first time distinct conserved placental var genes. Four placental isolates from Gabon collected 4 years later expressed DBL-gamma sequences with 85%-99% aa identities to those from Cameroon, confirming the conserved nature of placental variants separated by time and location. Five peripheral parasites from children also displayed DBL-gamma sequences with 75%-97% homologies. From this, it can be concluded that P. falciparum parasites expressing unique var DBL-gamma genes can cause placental malaria, referred to as varPAM genes. This demonstration of structurally/functionally constrained DBL-gamma chondroitin sulfate A-binding domains is relevant to understanding pregnancy-associated malaria pathogenesis and to vaccine development.
NORMAL RIBOFLAVIN STATUS IN MALARIA PATIENTS IN GABON
2003-02-01

Previous publications reported commonly the occurrence of riboflavin deficiency and a positive correlation between riboflavin status and parasitemia in patients with Plasmodium falciparum malaria. In these studies, riboflavin status was determined by erythrocyte glutathione reductase activation coefficients (EGRACs). Inherited low erythrocyte glutathione reductase activity is highly prevalent in malarial regions, however. To rule out falsely diagnosed riboflavin deficiency in affected patients, we conducted an investigation using a high-performance liquid chromatography method (HPLC) instead of the EGRAC method. In 29 infants (age range, 1–5 years), 22 schoolchildren (age range, 6–12 years), and 33 adolescents and adults (age range, 13–74 years) from Lambaréné, Gabon, with acute P. falciparum malaria, plasma concentrations of riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) were measured by HPLC. Results were correlated with parasite densities. Profiles of plasma concentrations of all 3 flavin compounds were within the normal range in all patients. Concentrations of free riboflavin were not different between the 3 age groups. In adolescents and adults, FMN and FAD concentrations were higher than in infants ( P = 0.002 and P = 0.001) and schoolchildren ( P = 0.003 and P = 0.002). Comparing children with hyperparasitemic and uncomplicated malaria, no difference in the concentrations of either flavin compound was found. Neither the concentrations of free riboflavin nor the concentrations of one of the flavin nucleotides correlated with parasitemia within subgroups of age or of children with uncomplicated and hyperparasitemic malaria. Our data indicate that nutritional riboflavin deficiency might have been overestimated in previous malaria studies and do not support a relationship between flavin concentrations and parasitemia in P. falciparum malaria.
Optical identifications in the Marano field XMM‐Newton survey
2003-02-01

Abstract The “Marano field”, a deep optical quasar survey field, has been observed by the XMM Newton EPIC camera with 16 overlapping pointings totalling at ∼ 120 ksec integration time. Source detection in the merged observations resulted in more than 600 X‐ray sources. Here we present the status of optical follow up observations which were undertaken to identify and classify the newly found X‐ray sources.
Comparison of Volume-rendered and Surface-rendered MR Colonography
2003-02-01

In the United States and Europe, colorectal cancer is the second leading cause of cancer-related deaths. It is well known that colorectal carcinomas may originate from preexisting adenomas. For the visualization of colorectal cancer and other pathologic changes such as polyps, two 3D methods (volume-rendering (VR) and surface-rendering (SR)) in MR colonography were compared in our study. MR colonography was carried out in 17 patients on a 1.5 T MR scanner using a 10 mmolar gadolinium water solution enema. Coronal as well as rotated VR and SR views were compared in order to examine the technical quality (TQ) of the visualization model and grade of confidence (GC) in the pathological findings. Colonoscopic findings revealed 8 colorectal carcinoma, 10 patients with polyps, 4 diverticular disease, and 2 with redundant bowel loops. Based on a total of 248 colonic segments for both visualization methods, volume rendering were significantly superior to surface rendering for both, TQ (p&lt;0.0001) and GC (p&lt;0.0001). Volume rendering and surface rendering were not dependent on individual colon segments (p=0.13 for TQ and p=0.18 for GC) or on image rotation (p=0.06 for TQ and p=0.062 for GC). It is also independent of the type of pathology (p=0.31 for TQ and p=0.42 for GC) and the reviewers (p=0.62 for TQ and p=0.88 for GC). This indicates, that for the purpose of interpreting the technical quality and pathological findings, volume rendering is superior to surface rendering in MR colonography. Volume rendering could be used as an 3D visualization tool, enabling MR colonography examinations to be completed sooner in cases where colon distension is sufficient, and it would also provide an overview of potential mass lesions.
DESIGNING PARALLEL ALGORITHMS FOR HIERARCHICAL SMP CLUSTERS
2003-02-01

Clusters of symmetric multiprocessor nodes (SMP clusters) are one of the most important parallel architectures at the moment. The architecture consists of shared-memory nodes with multiple processors and a fast interconnection network between the nodes. New programming models try to exploit this architecture by using threads in the nodes and using message-passing-libraries for inter-node communication. In order to develop efficient algorithms, it is necessary to consider the hybrid nature of the architecture and of the programming models. We present the κNUMA-model and a methodology that build a good base for designing efficient algorithms for SMP clusters. The κNUMA-model is a computational model that extends the bulk-synchronous parallel (BSP) model with the characteristics of SMP clusters and new hybrid programming models. The κNUMA-methodology suggests to develop efficient overall algorithms by developing efficient algorithms for each level in the hierarchy. We use the problem of personalized one-to-all-broadcast and the dense matrix-vector-multiplication for the presentation. The theoretical results of the analysis of the dense matrix-vector-multiplication are verified practically. We show results of experiments, made on a Linux-cluster of dual Pentium-III nodes.