julilili42/papers huggingface dataset:
THE COMPUTATIONAL COMPLEXITY OF AVOIDING FORBIDDEN SUBMATRICES BY ROW DELETIONS
2006-12-01

We initiate a systematic study of the ROW DELETION(B) problem on matrices: Given an input matrix A and a fixed "forbidden submatrix" B, the task is to remove a minimum number of rows from A such that no row or column permutation of B occurs as a submatrix in the resulting matrix. An application of this problem can be found, for instance, in the construction of perfect phylogenies. Establishing a strong connection to variants of the NP-complete HITTING SET problem, we describe and analyze structural properties of B that make ROW DELETION(B)NP-complete. On the positive side, the close relation with HITTING SET problems yields constant-factor polynomial-time approximation algorithms and fixed-parameter tractability results.
Majorana neutrino masses and the neutrinoless double-beta decay
2006-12-01

Neutrinoless double-beta decay is forbidden in the Standard Model of electroweak and strong interaction but allowed in most Grand Unified Theories (GUTs). Only if the neutrino is a Majorana particle (identical with its antiparticle) and if it has a mass is neutrinoless double-beta decay allowed. Apart from one claim that the neutrinoless double-beta decay in 76Ge is measured, one has only upper limits for this transition probability. But even the upper limits allow one to give upper limits for the electron Majorana neutrino mass and upper limits for parameters of GUTs and the minimal R-parity-violating supersymmetric model. One further can give lower limits for the vector boson mediating mainly the right-handed weak interaction and the heavy mainly right-handed Majorana neutrino in left-right symmetric GUTs. For that, one has to assume that the specific mechanism is the leading one for neutrinoless double-beta decay and one has to be able to calculate reliably the corresponding nuclear matrix elements. In the present work, one discusses the accuracy of the present status of calculating of the nuclear matrix elements and the corresponding limits of GUTs and supersymmetric parameters.
In Memoriam - Andreas Flach
2006-12-01

Andreas Flach was an important contributor to German pediatric surgery and, in particular, to pediatric urology. I first met him 1965 when I still was a medical student. He was a surgical senior house officer at the University Hospital of Tübingen. His interest in surgery of children and his surgical talent were already evident but he still intended to gain more experience in neonatal surgery. Therefore he spent some time with Max Grob, former head of the Department of Pediatric Surgery at the University of Zürich.
Reconstructive urology
2006-12-01

Purpose: To enhance our understanding of sonographically visible alterations in bladder wall thickness, we delineated phenotypic changes occurring in developing smooth muscle cells of the fetal and postnatal bladder with respect to gender specific differences.Materials and Methods: Bladders of 30 male and 18 female fetuses and 4 stillborn infants were immunostained with an alpha-smooth muscle actin antibody.Morphological and morphometric assessment was performed with the assistance of an image analysis system.Results: Alpha-smooth muscle actin expression in fetal bladder wall was detectable at 9 weeks of gestation.Bladder wall thickness and mean profile area of smooth muscle bundles increased significantly with advancing gestation, mediated by linear growth patterns.Fetal bladder wall development occurred uniformly, unrelated to gender.
The Early Transcriptional Response of Human Granulocytes to Infection withCandida albicansIs Not Essential for Killing but Reflects Cellular Communications
2006-12-05

ABSTRACT Candida albicans is a polymorphic opportunistic fungus that can cause life-threatening systemic infections following hematogenous dissemination in patients susceptible to nosocomial infection. Neutrophils form part of the innate immune response, which is the first line of defense against microbes and is particularly important in C. albicans infections. To compare the transcriptional response of leukocytes exposed to C. albicans , we investigated the expression of key cytokine genes in polymorphonuclear and mononuclear leukocytes after incubation with C. albicans for 1 h. Isolated mononuclear cells expressed high levels of genes encoding proinflammatory signaling molecules, whereas neutrophils exhibited much lower levels, similar to those observed in whole blood. The global transcriptional profile of neutrophils was examined by using an immunology-biased human microarray to determine whether different morphological forms or the viability of C. albicans altered the transcriptome. Hyphal cells appeared to have the broadest effect, although the most strongly induced genes were regulated independently of morphology or viability. These genes were involved in proinflammatory cell-cell signaling, cell signal transduction, and cell growth. Generally, genes encoding known components of neutrophil granules showed no upregulation at this time point; however, lactoferrin, a well-known candidacidal peptide, was secreted by neutrophils. Addition to inhibitors of RNA or protein de novo synthesis did not influence the killing activity within 30 min. These results support the general notion that neutrophils do not require gene transcription to mount an immediate and direct attack against microbes. However, neutrophils exposed to C. albicans express genes involved in communication with other immune cells.
Aspects of automatic ontology extension: adapting and regeneralizing dynamic updates
2006-12-05

Ontologies are widely used in text technology and artificial intelligence. The need to develop large ontologies for real-life applications provokes researchers to automatize ontology extension procedures. Automatic updates without the control of a human expert can generate potential conflicts between original and new knowledge. As a consequence the resulting ontology can contain inconsistencies. On the other hand, even if the information extracted from the external sources automatically is consistent with the original ontology it can be generalized unsystematically and conceptually wrong. This in turn can lead to mistakes in applications of the extended ontology. We propose an algorithm that models the process of the adaptation of an ontology to new information and regeneralizes the resulting ontology in a more intuitive way inserting additional knowledge where this is possible.
The New Ternary Boride Mg8Pt4B and the New Intermetallic Compound PtMg2.
2006-12-05

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Synthesis of Both Enantiomers of Conduritol C Tetraacetate and of meso‐Conduritol D Tetraacetate by Oxidation of Benzoquinone Bis(ethylene acetal)
2006-12-05

Abstract Epoxidation of p ‐benzoquinone bis(ethylene acetal) ( 1 ) with m ‐chloroperbenzoic acid or hydrogen peroxide/benzonitrile afforded corresponding monoepoxide 2 , which was converted into p ‐benzoquinone mono(ethylene acetal) monoepoxide 5 with perchloric acid. Dihydroxylation of 1 with osmium tetroxide or ruthenium trichloride/sodium periodate afforded corresponding cis ‐diol 6 , which was subsequently acetylated to give diacetate 7 . One ethyleneacetal moiety in 7 could be selectively hydrolyzed with silica gel/ferric chloride under solvent‐free conditions to give ketone 8 , which, upon reduction with sodium borohydride and subsequent acetylation of the formed alcohol group, afforded two diastereomeric triacetates 10 . Hydrolysis of the remaining acetal functions in the two diastereomers 10 , followed by reduction of the second carbonyl group as described above, afforded racemic conduritol C and meso ‐conduritol D tetraacetates 12 and 13 , respectively. Enzymatic resolution of the racemic arabino ‐configured triacetate 10 with Lipozym failed, while the ribo ‐configured counterpart reacted smoothly to give enantiomerically pure D ‐ ribo ‐ and L ‐ ribo ‐configured triacetates 10 . The latter pair of enantiomerically pure triacetates were converted into both enantiomers of conduritol C tetraacetate 13 as described for the racemic compounds. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Expression of the target receptor CD33 in CD34+/CD38−/CD123+ AML stem cells
2006-12-06

Abstract Background CD33 (Siglec‐3) is becoming increasingly important as a target of antibody‐mediated therapy in acute myeloid leukaemia (AML). In normal myelopoiesis, expression of CD33 is restricted to advanced stages of differentiation, whereas primitive stem cells do not express CD33. In the present study, we asked whether leukaemic stem cells in patients with AML express CD33. Materials and methods A multicolour‐staining technique was applied in 11 patients with AML, and leukaemic progenitors defined as CD34 + /CD38 − /CD123 + cells. AML stem cells were purified by cell sorting and were examined for expression of CD33 mRNA by reverse transcriptase–polymerase chain reaction (RT–PCR). Results In all patients in whom the majority of myeloblasts expressed CD33 ( n = 8), AML progenitors reacted with the CD33 antibody P67·6. Repopulation experiments utilizing irradiated NOD/SCID mice confirmed that AML stem cells in these patients reside within the CD33 + subpopulation of the leukaemic clone. Moreover, highly purified AML stem cells (&gt; 98% purity) from patients with CD33 + AML were found to express CD33 mRNA in RT–PCR analyses. CD33 was neither detectable on CD34 + /CD38 − cells in normal bone marrow nor on leukaemic stem cells in patients with CD33‐negative AML. Conclusions Leukaemic stem cells in patients with CD33 + AML express CD33. This observation is in favour of novel treatment concepts employing CD33‐targeting antibodies in AML.
Microarray Analysis of the Fetal Hippocampus in the <i>Emx2</i> Mutant
2006-12-06

Deficiency in the transcription factor &lt;i&gt;Emx2&lt;/i&gt; causes a specific alteration of hippocampal development, which has been well analyzed morphologically. We are currently using microarrays and in situ hybridization to characterize gene expression in the &lt;i&gt;Emx2&lt;/i&gt; mutant hippocampus. In this report on our preliminary results for the fetal stage, we identify a group of genes for most of which a putative relation to &lt;i&gt;Emx2&lt;/i&gt; pathways has not been previously recognized. Some candidates are development genes or are involved in functional maturation, and show expression in the hippocampal plate and/or developing dentate gyrus. A second class of candidates label neuronal, glial or vascular structures in the outer marginal zone, and likely represent markers for cell populations specifically absent in the mutant. Our results point at pathways and processes altered in the mutant, particularly the &lt;i&gt;Notch&lt;/i&gt; and chemokine pathways, the processes of cell migration, axonal guidance and angiogenesis, and the relation of pia and Cajal-Retzius cells with hippocampal morphogenesis.
Super sizing the giants: first cartilage preservation at a sauropod dinosaur limb joint
2006-12-07

Re-examination of the sauropod dinosaur Cetiosauriscus greppini von Huene 1922 (Reuchenette Formation; Kimmeridgian, Late Jurassic) from northwestern Switzerland has revealed a well-preserved cartilage capsule at the distal extremity of the right humerus. The capsule represents hyaline cartilage together with fibrocartilage and can be distinguished by colour, surface structure and histology from the periosteum of the bone. This is the first fossil evidence for articular cartilage in a sauropodomorph dinosaur. It indicates the presence of a large articular capsule on sauropod forelimbs, which was only hypothesized until now, and shows that the forelimb length of sauropods was larger than previously assumed.
Infectiousness of smallpox relative to disease age: estimates based on transmission network and incubation period
2006-12-07

SUMMARY This study investigated the infectiousness of smallpox relative to the onset of fever using a likelihood-based estimation procedure based on the observed transmission network ( n =223) and on the distribution of the incubation period ( n =379). Who-infected-whom information enabled us to back-calculate the infectiousness by disease age, employing a step function model for infectiousness. Frequency of secondary transmissions was highest between 3 and 6 days after onset of fever, yielding an expected daily frequency of 20·6% (95% CI 15·1–26·4) of the total number of secondary transmissions, which is consistent with previous observations. The estimated cumulative frequency suggests that 91·1% of secondary transmissions occurred up to 9 days after onset of fever. The proposed method appeared to be useful for diseases with an acute course of illness, where transmission was not hampered by depletion of susceptible contacts.
Treatment of Cystic Nephroma and Cystic Partially Differentiated Nephroblastoma—A Report From the SIOP/GPOH Study Group
2006-12-10

In cystic renal tumors radiological findings should always be reviewed by the reference radiologist of the treatment protocol study group. Irrespective of the chosen therapy, outcome of cystic nephroma and cystic partially differentiated nephroblastoma is favorable. Even in large international trials the number of patients with cystic nephroma or cystic partially differentiated nephroblastoma is too small for statistical analysis.
Micro traps for quantum information processing and precision force sensing
2006-12-12

Abstract We review recent experimental progress towards quantum information processing and precision force sensing using neutral atoms in micro traps. Microscopic potential structures as generated by optical or electronic microstructures (micro traps) allow for a versatile manipulation of quantum states of atoms and of ultracold atomic quantum gases. Most recent experimental results include the implementation of single‐qubit‐operations in both, optical and magnetic micro traps, as well as in the demonstration of matter‐wave interferometer using Bose‐Einstein condensates coherently split in micro traps.
Comprehensive association analysis of the NOS2A gene with Parkinson disease
2006-12-12

Inducible nitric oxide synthase (NOS2A) may be involved in the oxidative stress pathology of Parkinson disease (PD). Two previous studies reported an association of a single nucleotide polymorphism (rs1060826) with PD. A replication study of 340 German patients and 680 controls showed no significant association between 12 genotyped polymorphisms and PD. NOS2A is therefore not a major susceptibility locus in our relatively young sample population.
Global singularity-free solution of the Iordanskii force problem
2006-12-12

We present a derivation of the transverse force acting on a hydrodynamic vortex in the presence of an incoming sound wave from a global solution of the scattering problem, using the method of matched asymptotic expansions. The solution presented includes a detailed treatment of the interaction of the incident wave with the vortex core, and is free from the singularities in the momentum exchange between vortex and sound wave which have led to contradictory results for the value of the transverse force in the literature.
Cerebrotendinous xanthomatosis
2006-12-12

Neuroscience and technological medicine in general increasingly faces us with the imminent reality of cyborgs—integrated part human and part machine complexes. If my brain functions in a way that is supported by and exploits intelligent technology both external and implantable, then how should I be treated and what is my moral status—am I a machine or am I a person? I explore a number of scenarios where the balance between human and humanoid machine shifts, and ask questions about the moral status of the individuals concerned. The position taken is very much in accordance with the Aristotelian idea that our moral behaviour is of a piece with our social and personal skills and forms a reactive and reflective component of those skills.
Primitive nest architecture and small monogynous colonies in basal Attini inhabiting sandy beaches of southern Brazil
2006-12-13

Abstract The species Mycetophylax conformis, M. simplex and Cyphomyrmex morschi, all belonging to the basal Attini, occur exclusively on beaches along the Atlantic shores of South America. In Brazil C. morschi colonies were found sympatrically with the two Mycetophylax species which, however, had no overlap in their geographic distribution. We recorded species‐specific nesting site preferences resulting in a zonal colonization of dune and restinga areas, with distinct preferences in microhabitat choice. After excavating subterraneous nests, we were able to describe details of nest architecture, especially with regard to the number and position of the fungus chambers. The nest structure is similar in all species, but the colony size differed with the highest number of workers in M. simplex. All nests were headed by a single mated queen. First attempts were undertaken to maintain colonies under laboratory conditions. Resumo As espécies Mycetophylax conformis, M. simplex e Cyphomyrmex morschi fazem parte do grupo dos Attini basais e ocorrem exclusivamente em praias do Atlântico na América do Sul. No Brasil C. morschi ocorre simpatricamente com as espécies de Mycetophylax, mas as duas espécies de Mycetophylax não tem uma sobreposição na sua distribuição geográfica. Também detectamos preferências específicas na escolha da área da nidificação o que resulta em uma colonização zonal das dunas e restingas com preferências distintas na escolha do microhabitat. Com escavações cuidadosas de um número representativo de ninhos obtivemos detalhes sobre a arquitetura, em especial o número e posição das câmaras de fungo. A estrutura subterrânea dos ninhos é similar nas espécies estudadas mas o tamanho da população difere entre as espécies com o maior número de operárias em M. simplex. Todas as colônias tem uma rainha que copulou apenas uma única vez. Primeiras tentativas de manutenção de colônias no laboratório foram feitas. Keywords: Brazilcoastal sand habitatscolony structure Cyphomyrmex Mycetophylax nest architecturebasal Attini Acknowledgments We would like to thank Dinair Couto Lima, Benedito C. Lopes, Rogerio Rosa da Silva, Bodo Hasso Dietz and Marisa Vianna Ferraz for help with the field work. The authors received support in Brazil from CAPES, CNPq, FAPESP, the Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, the Museu de Zoologia da Universidade de São Paulo, and in Germany from GRAFÖG, University of Tübingen, DAAD, and the Natural History Museum Karlsruhe.
Comparative analysis of Hox downstream genes inDrosophila
2006-12-14

Functional diversification of body parts is dependent on the formation of specialized structures along the various body axes. In animals,region-specific morphogenesis along the anteroposterior axis is controlled by a group of conserved transcription factors encoded by the Hox genes. Although it has long been assumed that Hox proteins carry out their function by regulating distinct sets of downstream genes, only a small number of such genes have been found, with very few having direct roles in controlling cellular behavior. We have quantitatively identified hundreds of Hox downstream genes in Drosophila by microarray analysis, and validated many of them by in situ hybridizations on loss- and gain-of-function mutants. One important finding is that Hox proteins, despite their similar DNA-binding properties in vitro, have highly specific effects on the transcriptome in vivo, because expression of many downstream genes respond primarily to a single Hox protein. In addition, a large fraction of downstream genes encodes realizator functions, which directly affect morphogenetic processes, such as orientation and rate of cell divisions, cell-cell adhesion and communication,cell shape and migration, or cell death. Focusing on these realizators, we provide a framework for the morphogenesis of the maxillary segment. As the genomic organization of Hox genes and the interaction of Hox proteins with specific co-factors are conserved in vertebrates and invertebrates, and similar classes of downstream genes are regulated by Hox proteins across the metazoan phylogeny, our findings represent a first step toward a mechanistic understanding of morphological diversification within a species as well as between species.
Complete extirpation of benign breast lesions with an ultrasound‐guided vacuum biopsy system
2006-12-14

Abstract Objectives To investigate whether ultrasound‐guided vacuum biopsy (VB) with curative intent is suitable for the complete extirpation of selected sonographically detectable benign lesions of the breast, and to establish the limitations of the method with regard to lesion size and complications, the extent of scar formation and the prognostic value. Methods One hundred and nine patients underwent hand‐held, ultrasound‐guided VB (8G or 11G needle) between June 2000 and September 2003. Of these, 45 (41%) women underwent ultrasound‐guided extirpation of 46 lesions, and 42 women with 43 lesions were followed up clinically and sonographically for an average of 5.9 months. The complete extirpation rate, residual lesions, and patient satisfaction with the intervention were evaluated. Results Removal of all sonographic evidence of lesions (median diameter, 13 mm) was achieved in 86% of cases (8G needle, 80%; 11G needle, 89%). 19% of the patients had suspected scar formation at the biopsy site. A palpable lesion in the breast could be removed by VB in 90% of cases. None of the patients developed infections and there were no hemorrhages requiring intervention, or damage to the skin or chest wall. A total of 95% of the patients stated that they would prefer this approach to open excision for possible future intervention. Conclusions VB is an ambulatory procedure associated with a low degree of pain. It has a high degree of patient acceptance and, as a minimally invasive biopsy technique for benign lesions, is a good alternative to open excision. The rate of complications is low and is similar to that observed with conventional microbiopsy. Copyright © 2006 ISUOG. Published by John Wiley &amp; Sons, Ltd.
Differentiation between malignant and benign solitary pulmonary nodules with proton density weighted and ECG-gated magnetic resonance imaging.
2006-12-14

Despite discrepancies in morphologic appearance, no significant difference of accuracy between MRI and CT was determined. Further investigations are necessary to demonstrate the clinical use in combination with functional parameters, establishing MRI as a comprehensive diagnostic modality for SPN.