bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene Clusters
Authors: Ghanem Noël , Jarinova Olga , Amores Angel , Long Qiaoming , Hatch Gary , Park Byung Keon , Rubenstein John L.R. , Ekker Marc 
Published: April 2003

Dlx homeobox genes of vertebrates are generally arranged as three bigene clusters on distinct chromosomes. The Dlx1/Dlx2,Dlx5/Dlx6, and Dlx3/Dlx7 clusters likely originate from duplications of an ancestral Dlx gene pair. Overlaps in expression are often observed between genes from the different clusters. To determine if the overlaps are a result of the conservation of enhancer sequences between paralogous clusters, we compared theDlx1/2 and the Dlx5/Dlx6 intergenic regions from human, mouse, zebrafish, and from two pufferfish, Spheroides nephelus and Takifugu rubripes. Conservation between all five vertebrates is limited to four sequences, two inDlx1/Dlx2 and two in Dlx5/Dlx6. These noncoding sequences are >75% identical over a few hundred base pairs, even in distant vertebrates. However, when compared to each other, the four intergenic sequences show a much more limited similarity. Each intergenic sequence acts as an enhancer when tested in transgenic animals. Three of them are active in the forebrain with overlapping patterns despite their limited sequence similarity. The lack of sequence similarity between paralogous intergenic regions and the high degree of sequence conservation of orthologous enhancers suggest a rapid divergence of Dlx intergenic regions early in chordate/vertebrate evolution followed by fixation ofcis-acting regulatory elements.[Supplemental material is available online at www.genome.org.]
Ran's C-terminal, Basic Patch, and Nucleotide Exchange Mechanisms in Light of a Canonical Structure for Rab, Rho, Ras, and Ran GTPases
Authors: Neuwald Andrew F. , Kannan Natarajan , Poleksic Aleksandar , Hata Naoya , Liu Jun S. 
Published: April 2003

Proteins comprising the core of the eukaryotic cellular machinery are often highly conserved, presumably due to selective constraints maintaining important structural features. We have developed statistical procedures to decompose these constraints into distinct categories and to pinpoint critical structural features within each category. When applied to P-loop GTPases, this revealed within Rab, Rho, Ras, and Ran a canonical network of molecular interactions centered on bound nucleotide. This network presumably performs a crucial structural and/or mechanistic role considering that it has persisted for more than a billion years after the divergence of these families. We call these ‘FY-pivot’ GTPases after their most distinguishing feature, a phenylalanine or tyrosine that functions as a pivot within this network. Specific families deviate somewhat from canonical features in interesting ways, presumably reflecting their functional specialization during evolution. We illustrate this here for Ran GTPases, within which two highly conserved histidines, His30 and His139, strikingly diverge from their canonical counterparts. These, along with other residues specifically conserved in Ran, such as Tyr98, Lys99, and Phe138, appear to work in conjunction with FY-pivot canonical residues to facilitate alternative conformations in which these histidines are strategically positioned to couple Ran's basic patch and C-terminal switch to nucleotide exchange and effector binding. Other core components of the cellular machinery are likewise amenable to this approach, which we termContrastHierarchicalAlignment andInteractionNetwork (CHAIN) analysis.[Supplemental material is available online atwww.genome.org.]
The First-Generation Whole-Genome Radiation Hybrid Map in the Horse Identifies Conserved Segments in Human and Mouse Genomes
Authors: Chowdhary Bhanu P. , Raudsepp Terje , Kata Srinivas R. , Goh Glenda , Millon Lee V. , Allan Veronica , Piumi François , Guérin Gérard , Swinburne June , Binns Matthew , Lear Teri L. , Mickelson Jim , Murray James , Antczak Douglas F. , Womack James E. , Skow Loren C. 
Published: April 2003

A first-generation radiation hybrid (RH) map of the equine (Equus caballus) genome was assembled using 92 horse × hamster hybrid cell lines and 730 equine markers. The map is the first comprehensive framework map of the horse that (1) incorporates type I as well as type II markers, (2) integrates synteny, cytogenetic, and meiotic maps into a consensus map, and (3) provides the most detailed genome-wide information to date on the organization and comparative status of the equine genome. The 730 loci (258 type I and 472 type II) included in the final map are clustered in 101 RH groups distributed over all equine autosomes and the X chromosome. The overall marker retention frequency in the panel is ∼21%, and the possibility of adding any new marker to the map is ∼90%. On average, the mapped markers are distributed every 19 cR (4 Mb) of the equine genome—a significant improvement in resolution over previous maps. With 69 new FISH assignments, a total of 253 cytogenetically mapped loci physically anchor the RH map to various chromosomal segments. Synteny assignments of 39 gene loci complemented the RH mapping of 27 genes. The results added 12 new loci to the horse gene map. Lastly, comparison of the assembly of 447 equine genes (256 linearly ordered RH-mapped and additional 191 FISH-mapped) with the location of draft sequences of their human and mouse orthologs provides the most extensive horse–human and horse–mouse comparative map to date. We expect that the foundation established through this map will significantly facilitate rapid targeted expansion of the horse gene map and consequently, mapping and positional cloning of genes governing traits significant to the equine industry.[Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Brandon, G. Lindgren, and I. Tammen.]
Staphylococcus lugdunensis
Infections: High Frequency of Inguinal Area Carriage
Authors: van der Mee-Marquet N. , Achard A. , Mereghetti L. , Danton A. , Minier M. , Quentin R. 
Published: April 2003

ABSTRACT

Following a change in surgical practice, we noted that the rate at which
Staphylococcus lugdunensis
was isolated from samples from the plastic surgery unit of our hospital increased considerably. We investigated the sources of these
S. lugdunensis
strains, and we found that in the case of drain colonization or surgical site infection, the strain was more likely to have come from the patient's skin bacteria when the pubic site had been shaved preoperatively. To test the hypothesis of pubic site colonization, we evaluated the prevalence of
S. lugdunensis
carriage among the cutaneous flora of the inguinal area. We found that 22% of 140 incoming patients carried
S. lugdunensis
in this area and that carriage at both inguinal folds was frequent (68% of carriers). A study of the genetic structure of the total population, including the clinical (
n
= 18) and the commensal (
n
= 53) strains, revealed that the diversity of the species was low and that the population was composed of two major groups that diverged at a distance of 35%. No particular characteristics made it possible to distinguish between clinical and commensal strains. Only isolates producing β-lactamase were homogeneous; six of the eight β-lactamase-positive strains displayed the same pulsed-field gel electrophoresis pattern.
Prevalence of Genes Encoding Pyrogenic Toxin Superantigens and Exfoliative Toxins among Strains of
Staphylococcus aureus
Isolated from Blood and Nasal Specimens
Authors: Becker Karsten , Friedrich Alexander W. , Lubritz Gabriele , Weilert Maria , Peters Georg , von Eiff Christof 
Published: April 2003

ABSTRACT

A total of 429 different
Staphylococcus aureus
isolates encompassing 219 blood isolates and 210 isolates taken from anterior nares were systematically searched by two multiplex PCR-DNA enzyme immunoassays (PCR-DEIA) for exfoliative toxin (ET) genes
eta
and
etb
, as well as for the classical members of the pyrogenic toxin superantigen (PTSAg) gene family comprising the staphylococcal enterotoxin (SE) genes
sea
-
see
and the toxic shock syndrome toxin 1 gene
tst
. In addition, a third PCR-DEIA was established to investigate the possession of four recently described SE genes, viz.
seg
-
sej
. The most frequent PTSAg/ET genes amplified were
seg
and
sei
, which were found strictly in combination in 55.0% of the
S. aureus
isolates tested. Other frequently detected toxin genes were
tst
(20.3%),
sea
(15.9%), and
sec
(11.2%). Only five isolates harbored ET genes. Regarding the origin of the
S. aureus
isolates, a significant difference (
P
= 0.037) was found for the possession of the
sed/sej
gene combination (10.5% of blood isolates versus 3.3% of nasal strains). Overall, about half of
S. aureus
isolates tested harbored genes of the classical members of the PTSAg family and ETs (50.8%), whereas 73.0% of
S. aureus
isolates were toxin gene positive if the recently described SE genes were included. This notable higher prevalence indicates that the possession of PTSAg genes in particular seems to be a habitual feature of
S. aureus
. Moreover, mainly due to the fixed combinations of
seg
plus
sei
, as well as
sed
plus
sej
, the possession of multiple PTSAg genes (62.9%) is more frequent than assumed so far.
Evaluation of PCR as a Diagnostic Mass-Screening Tool To Detect
Leishmania
(
Viannia
) spp. in Domestic Dogs (
Canis familiaris
)
Authors: Reithinger Richard , Espinoza Juan Canales , Courtenay Orin , Davies Clive R. 
Published: April 2003

ABSTRACT

Several studies have suggested that the PCR could be used in epidemiological mass-screening surveys to detect
Leishmania
(
Viannia
) spp. infection in human and animal hosts. Dogs from an area of
Leishmania braziliensis
and
Leishmania peruviana
endemicity were screened for American cutaneous leishmaniasis (ACL) infection by established PCR-based and enzyme-linked immunosorbent antibody test (ELISA) protocols. PCR detected
Leishmania
(
Viannia
) infection in a total of 90 of 1,066 (8.4%) dogs: 32 of 368 (8.7%), 65 of 769 (8.5%), and 7 of 42 (16.7%) dogs were PCR positive by testing of whole blood, buffy coat, and bone marrow aspirates, respectively. ELISA detected infection in 221 of 1,059 (20.9%) tested dogs. The high prevalence of
Leishmania
(
Viannia
) detected by PCR and ELISA in both asymptomatic (7.5 and 19.2%, respectively) and symptomatic (32 and 62.5%, respectively) dogs is further circumstantial evidence for their suspected role as reservoir hosts of ACL. However, the low sensitivity of PCR (31%) compared to ELISA (81%) indicates that PCR cannot be used for mass screening of samples in ACL epidemiological studies. Unless more-sensitive PCR protocols were to be developed, its use should be restricted to the diagnosis of active (canine and human) cases and to the parasitological monitoring of patients after chemotherapy.
Clinical Evaluation of Two Methods for Genotyping Hepatitis C Virus Based on Analysis of the 5′ Noncoding Region
Authors: Nolte Frederick S. , Green Alicia M. , Fiebelkorn Kristin R. , Caliendo Angela M. , Sturchio Cynthia , Grunwald Aileen , Healy Mimi 
Published: April 2003

ABSTRACT

We compared the performance characteristics of a standardized direct sequencing method (TRUGENE HCV 5′NC; Visible Genetics Inc., Toronto, Ontario, Canada) and a reverse hybridization line probe assay (INNO-LiPA HCV II; Bayer Corp., Tarrytown, N.Y.) for genotyping of hepatitis C virus (HCV). Both methods are based on detection of sequence heterogeneity in the 5′ noncoding (5′NC) region. Concordance between the genotyping methods was assessed by testing 172 samples representing the six major genotypes. Sequence analysis of the more phylogenetically informative nonstructural 5B (NS5B) region was also done with 148 (86%) samples to confirm the accuracy of and resolve discrepancies between the 5′NC genotyping results. The sensitivities of the methods were assessed by using the 5′NC amplicon from both the qualitative and quantitative AMPLICOR HCV tests (Roche Diagnostics Corp., Indianapolis, Ind.). The ability of the methods to detect mixed-genotype infections was determined with mixtures of two different genotypes at relative concentrations ranging from 1 to 50%. Both 5′NC methods were able to genotype 99.4% of the samples with type agreement for 99.5% and subtype agreement for 68.2% of the samples. No or ambiguous subtype results were found by the line probe assay for 16.5% and by the TRUGENE 5′NC test for 17.1% of the samples. Discrepancies occurred between the line probe assay and NS5B results at the type level for 1.4% of the samples and at the subtype level for 14.2% of the samples. Discrepancies also occurred between the TRUGENE 5′NC and NS5B results at the type level for 2% of the samples and at the subtype level for 8.1% of the samples. We also found two distinct strains of HCV classified as type 2 by analysis of the 5′NC region that were type 1 by analysis of the NS5B region. The sensitivities of the two 5′NC genotyping methods were comparable and dependent on the amplification test used (∼10
3
IU/ml with the qualitative HCV RNA tests and ∼10
5
IU/ml with the quantitative HCV RNA tests). Genotype mixtures were successfully identified at a relative concentration of 5% by the line probe assay and 10% by the TRUGENE 5′NC test. In conclusion, the performance characteristics of the 5′NC methods were similar and both methods produced accurate results at the genotype level but neither method should be used for subtyping.
Use of Monoclonal Antibodies to Lipopolysaccharide for Antigenic Analysis of
Coxiella burnetii
Authors: Hotta Akitoyo , Kawamura Midori , To Ho , Andoh Masako , Yamaguchi Tsuyoshi , Fukushi Hideto , Amano Ken-Ichi , Hirai Katsuya 
Published: April 2003

ABSTRACT

Antigenic differences among
Coxiella burnetii
strains were analyzed. The monoclonal antibodies against the lipopolysaccharide outer core did not react with the strains containing a QpRS plasmid or with plasmidless strains, whereas they reacted with strains containing a QpH1 or QpDV plasmid.
C. burnetii
isolates could be divided into two groups immunologically.
AN OBSTRUCTION TO EMBEDDING 4-TANGLES IN LINKS
Authors: KREBES DAVID A. 
Published: April 2003

We consider the ways in which a 4-tangle T inside a unit cube can be extended outside the cube into a knot or link L. We present two links n(T) and d(T) such that the greatest common divisor of the determinants of these two links always divides the determinant of the link L. In order to prove this result we give a two-integer invariant of 4-tangles. Calculations are facilitated by viewing the determinant as the Kauffman bracket at a fourth root of -1, which sets the loop factor to zero. For rational tangles, our invariant coincides with the value of the associated continued fraction.
DISCRETE TIME DYNAMIC GAMES WITH CONTINUUM OF PLAYERS II: SEMI-DECOMPOSABLE GAMES
Authors: WISZNIEWSKA-MATYSZKIEL AGNIESZKA 
Published: April 2003

In this paper we consider dynamic games with continuum of players which can constitute a framework to model large financial markets. They are called semi-decomposable games. In semi-decomposable games the system changes in response to a (possibly distorted) aggregate of players' decisions and the payoff is a sum of discounted semi-instantaneous payoffs. The purpose of this paper is to present some simple properties and applications of these games. The main result is an equivalence between dynamic equilibria and families of static equilibria in the corresponding static perfect-foresight games, as well as between dynamic and static best response sets. The existence of a dynamic equilibrium is also proven. These results are counterintuitive since they differ from results that can be obtained in games with a finite number of players. The theoretical results are illustrated with examples describing large financial markets: markets for futures and stock exchanges.
1/f NOISE AS A DIAGNOSTIC TOOL TO INVESTIGATE THE QUALITY OF ANISOTROPIC CONDUCTIVE ADHESIVE (ACA) BONDS FOR BALL GRID ARRAYS (BGA'S)
Authors: JONGEN R. J. J. M. , VANDAMME L. K. J. , BONNÉ H. H. , DE VRIES J. W. C. 
Published: April 2003

Reliability assessment of conductive adhesive bonds by humidity and temperature tests is time consuming and does not provide enough information about the details of the onset of degradation. There is a need for measurements that can give an early warning about the contact quality with more quantitative details about its degradation. Here 1/f noise of such contact arrays is investigated before and after temperature and humidity stress tests with different durations. 1/f Noise stems from conductance fluctuations. We investigated the constriction resistance 1/f noise SR of the contact constriction resistance RC before accelerated aging and during aging at temperatures of 85°C and 110°C with an 85% relative humidity. Noise analysis on non-degraded samples is also a fast diagnostic tool for reliability characterization. From the analysis based on a noise model for a multispot contact, the onset of constriction resistance increase goes hand in hand with a strong increase in resistance noise. This is understood and can be characterized by a reduction in the electrical contact area Ae . The degree of contact degradation is expressed in a reduction of the real electrical contact area Ae of a multispot contact and is quantitatively given by the D-factor.
Sequestration of p27Kip1 protein by cyclin D1 in typical and blastic variants of mantle cell lymphoma (MCL): implications for pathogenesis
Authors: Quintanilla-Martinez Leticia , Davies-Hill Theresa , Fend Falko , Calzada-Wack Julia , Sorbara Lynn , Campo Elias , Jaffe Elaine S. , Raffeld Mark 
Published: April 2003

Abstract
p27 is a cyclin-dependent kinase inhibitor that plays a critical role in regulating G1/S progression, and whose activity is, in part, regulated through interactions with D-type cyclins. Mantle cell lymphoma (MCL) is characterized by the t(11;14) translocation resulting in deregulated cyclin D1. We previously showed that p27 expression in MCL, as assessed by immunohistochemistry (IHC), does not show the usual inverse relationship to proliferate seen in most other lymphomas that do not overexpress cyclin D1. This suggested that the normal expression or control of p27 activity on cell growth might be altered through potential interactions with cyclin D1. Using Western blot and coimmunoprecipitation studies, we assessed the interrelationship between cyclin D1 and p27 in several cyclin D1+ cell lines and primary MCL cases. Similar to our previous results by IHC, typical MCLs showed lower expression of p27 when compared to the more highly proliferative blastic cases or cell lines (mean arbitrary units: 58 versus 236 versus 120). Cyclin D1 was expressed at variable levels in both typical and blastic MCLs. p27 protein could be consistently coimmunoprecipitated with cyclin D1 from both cell lines and cases. Using techniques of exhaustive immunoprecipitation, we could demonstrate that most p27 protein was sequestered into complexes containing cyclin D1. We hypothesize that mantle cell lymphomagenesis results not only from direct consequences of inappropriate cyclin D1 expression, but also from the ability of overexpressed cyclin D1 to buffer physiologic changes in p27 levels, thereby rendering p27 ineffective as an inhibitor of cellular growth.
Roles of neutrophil β2 integrins in kinetics of bacteremia, extravasation, and tick acquisition of Anaplasma phagocytophila in mice
Authors: Borjesson Dori L. , Simon Scott I. , Hodzic Emir , DeCock Hilde E. V. , Ballantyne Christie M. , Barthold Stephen W. 
Published: April 2003

AbstractTick saliva contains anti-inflammatory and immunosuppressive substances that facilitate blood feeding and enhance tick-vectored pathogen transmission, including Anaplasma phagocytophila,an etiologic agent of granulocytic ehrlichiosis. As such, inflammation at a tick-feeding site is strikingly different than that typically observed at other sites of inflammation. Up-regulation of CD11b/CD18 occurs in host granulocytes following interaction or infection withA phagocytophila, and the absence of CD11b/CD18 results in early increases in bacteremia. We hypothesized that β2 integrin–dependent infection kinetics and leukocyte extravasation are important determinants of neutrophil trafficking to, and pathogen acquisition at, tick-feeding sites.A phagocytophila infection kinetics were evaluated in CD11a/CD18, CD11b/CD18, and CD18 knock-out mice using quantitative polymerase chain reaction (PCR) of blood, ticks, and skin biopsies in conjunction with histopathology. A marked increase in the rate ofA phagocytophila infection of neutrophils and pathogen burden in blood followed tick feeding. Infection kinetics were modified by β2 integrin expression and systemic neutrophil counts. Significant neutrophil-pathogen trafficking was observed to both suture and tick sites. Despite the prominent role for β2 integrins in neutrophil arrest in flowing blood, successful pathogen acquisition by ticks occurred in the absence of β2 integrins. Establishment of feeding pools that rely less on leukocyte trafficking and more on small hemorrhages may explain the ready amplification of A phagocytophila DNA from ticks infested on CD11/CD18-deficient mouse strains.
Signal transducer and activator of transcription proteins in leukemias
Authors: Benekli Mustafa , Baer Maria R. , Baumann Heinz , Wetzler Meir 
Published: April 2003

AbstractSignal transducer and activator of transcription (STAT) proteins are a 7-member family of cytoplasmic transcription factors that contribute to signal transduction by cytokines, hormones, and growth factors. STAT proteins control fundamental cellular processes, including survival, proliferation, and differentiation. Given the critical roles of STAT proteins, it was hypothesized that inappropriate or aberrant activation of STATs might contribute to cellular transformation and, in particular, leukemogenesis. Constitutive activation of mutated STAT3 has in fact been demonstrated to result in transformation. STAT activation has been extensively studied in leukemias, and mechanisms of STAT activation and the potential role of STAT signaling in leukemogenesis are the focus of this review. A better understanding of mechanisms of dysregulation of STAT signaling pathways may serve as a basis for designing novel therapeutic strategies that target these pathways in leukemia cells.