bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of the
hupB
Gene Encoding a Histone-Like Protein of
Mycobacterium tuberculosis
as a Target for Detection and Differentiation of
M. tuberculosis
and
M. bovis
Authors: Prabhakar S. , Mishra A. , Singhal A. , Katoch V. M. , Thakral S. S. , Tyagi J. S. , Prasad H. K. 
Published: June 2004

ABSTRACT

The gene for histone-like protein (
hupB
[
Rv2986c
]) of
Mycobacterium tuberculosis
has been identified as a singular target which allows differentiation of two closely related mycobacterial species, namely,
M. tuberculosis
and
M. bovis
of the MTB complex, by a PCR assay. The N and S primer-generated PCR amplicons differed in
M. tuberculosis
and
M. bovis
; these amplicons were determined to be 645 and 618 bp, respectively. This difference was localized to the C-terminal part of the gene by using primers M and S. The C-terminal PCR amplicons of
M. tuberculosis
and
M. bovis
were determined to be 318 and 291 bp, respectively. The differences in the C-terminal portion of the gene were confirmed by restriction fragment length polymorphism analysis and sequencing. Sequence analysis indicated that in
M. bovis
there was a deletion of 27 bp (9 amino acids) in frame after codon 128 in the C-terminal part of the
hupB
gene. In the present study 104 mycobacterial strains and 11 nonmycobacterial species were analyzed for
hupB
gene sequences. Of the 104 mycobacterial strains included, 62 belonged to the MTB complex and 42 were non-MTB complex strains and species. Neither the
hupB
gene-specific primers (N and S) nor the C-terminal primers (M and S) amplify DNA from any other mycobacteria, making the assay suitable for distinguishing members of the MTB complex from other mycobacterial species, as well as for differentiating between members of the MTB complex, namely,
M. tuberculosis
and
M. bovis
.
Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India
Authors: Siddappa Nagadenahalli B. , Dash Prashanta K. , Mahadevan Anita , Jayasuryan Narayana , Hu Fen , Dice Bethany , Keefe Randy , Satish Kadappa S. , Satish Bhuthiah , Sreekanthan Kuttan , Chatterjee Ramdas , Venu Kandala , Satishchandra Parthasarathy , Ravi Vasanthapuram , Shankar Susarla K. , Shankarappa Raj , Ranga Udaykumar 
Published: June 2004

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and
gag
in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-κB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.
Use of a Recombinant Envelope Protein Subunit Antigen for Specific Serological Diagnosis of West Nile Virus Infection
Authors: Beasley David W. C. , Holbrook Michael R. , Travassos da Rosa Amelia P. A. , Coffey Lark , Carrara Anne-Sophie , Phillippi-Falkenstein Kathrine , Bohm Rudolf P. , Ratterree Marion S. , Lillibridge Kristy M. , Ludwig George V. , Estrada-Franco Jose , Weaver Scott C. , Tesh Robert B. , Shope Robert E. , Barrett Alan D. T. 
Published: June 2004

ABSTRACTSerological diagnosis of West Nile virus (WNV) infection is complicated by extensive antigenic cross-reactivity with other closely related flaviviruses, such as St. Louis encephalitis virus. Here we describe a recombinant, bacterially expressed antigen equivalent to structural domain III of the WNV envelope protein that has allowed clear discrimination of antibody responses to WNV from those against other related flaviviruses in indirect enzyme-linked immunosorbent assays using standardized control antisera and field-collected samples.
Identification of Enterohepatic
Helicobacter
Species in Patients Suffering from Inflammatory Bowel Disease
Authors: Bohr Ulrich R. M. , Glasbrenner Bernhard , Primus Anett , Zagoura Alexandra , Wex Thomas , Malfertheiner Peter 
Published: June 2004

ABSTRACT

Using a group-specific PCR assay, we investigated the presence of enterohepatic
Helicobacter
species in gut specimens from patients with inflammatory bowel disease. Enterohepatic
Helicobacter
species were detected in 12% (3 of 25) of the patients with Crohn's disease, in 17% (3 of 18) of the ulcerative colitis samples, and in 4% (1 of 23) of the controls.
Clinical Significance and Mechanism of Gas Formation of Pyogenic Liver Abscess Due toKlebsiella pneumoniae
Authors: Lee Hsin-Ling , Lee Hsin-Chun , Guo How-Ran , Ko Wen-Chien , Chen Kuan-Wen 
Published: June 2004

ABSTRACTWe enrolled 22 patients with gas-forming pyogenic liver abscess in a study to assess the mechanism of gas formation.Klebsiella pneumoniaewas cultured from specimens from all patients. Gas and pus samples from abscesses revealed four major components: nitrogen, oxygen, carbon dioxide, and hydrogen; this implicates mixed acid fermentation of glucose as the mechanism of gas formation.
Immunoreactivity of Cryptococcal Antigen Is Not Stable under Prolonged Incubations in Human Serum
Authors: McFadden Diane C. , Zaragoza Oscar , Casadevall Arturo 
Published: June 2004

ABSTRACT

The stability of cryptococcal antigen from
Cryptococcus neoformans
serotype A and D strains at different temperatures in serum and other solvents was studied. Samples stored at −20 or 4°C had equivalent stabilities as measured by the Premier Cryptococcal Antigen kit and the Cryptococcal Antigen Latex Agglutination System (CALAS) kit. However, using the Premier Cryptococcal Antigen kit, there was a 91% loss of reactivity in samples incubated in human serum for 4 weeks at 37°C. A loss of reactivity of more than 99% was observed after incubation at 45°C for 4 weeks. The capsular antigen was not detected by the Premier Cryptococcal Antigen kit after 16 weeks at elevated temperatures. Antigen titers were also reduced in a latex agglutination assay (CALAS) after 4 weeks at 37 and 45°C. The loss of antigen reactivity was a function of pH and temperature.
Multiple Outbreaks of
Yersinia pseudotuberculosis
Infections in Finland
Authors: Jalava Katri , Hallanvuo S. , Nakari U.-M. , Ruutu P. , Kela E. , Heinäsmäki T. , Siitonen A. , Nuorti J. P. 
Published: June 2004

ABSTRACT

During 2001, 89 culture-confirmed cases of
Yersinia pseudotuberculosis
were reported in Finland; 55 (62%) were serotype O:1, and 34 (38%) were serotype O:3. Four major pulsed-field gel electrophoresis profiles were identified. A case-control study of 25 case patients and 71 healthy controls identified eating outside the home as a risk factor for infection.
Prevalence ofBorrelia burgdorferi,Bartonellaspp.,Babesia microti, andAnaplasma phagocytophilainIxodes scapularisTicks Collected in Northern New Jersey
Authors: Adelson Martin E. , Rao Raja-Venkitesh S. , Tilton Richard C. , Cabets Kimberly , Eskow Eugene , Fein Lesley , Occi James L. , Mordechai Eli 
Published: June 2004

ABSTRACTPCR analysis ofIxodes scapularisticks collected in New Jersey identified infections withBorrelia burgdorferi(33.6%),Babesia microti(8.4%),Anaplasma phagocytophila(1.9%), andBartonellaspp. (34.5%). TheI. scapularistick is a potential pathogen vector that can cause coinfection and contribute to the variety of clinical responses noted in some tick-borne disease patients.
Molecular Characterization and Phylogenetic Study of Newcastle Disease Virus Isolates from Recent Outbreaks in Eastern Uganda
Authors: Otim Maxwell O. , Christensen Henrik , Jørgensen Poul H. , Handberg Kurt J. , Bisgaard Magne 
Published: June 2004

ABSTRACT
Newcastle disease virus isolates from chickens in eastern Uganda in 2001 were found to be velogenic by fusion protein cleavage site sequence analysis and biological characterization; the intracerebral pathogenicity index was 1.8. Analysis of their hemagglutinin-neuraminidase protein gene sequences revealed a novel genotype unrelated to those that caused previous outbreaks.
Survey of Ferroxidase Expression and Siderophore Production in Clinical Isolates of
Pseudomonas aeruginosa
Authors: Huston Wilhelmina M. , Potter Adam J. , Jennings Michael P. , Rello Jordi , Hauser Alan R. , McEwan Alastair G. 
Published: June 2004

ABSTRACT

Ferroxidase (encoded by the
mco
gene), a component of a ferrous iron uptake pathway in
Pseudomonas aeruginosa
, was detected in all of the 35 respiratory clinical isolates surveyed; in contrast, considerable variation in siderophore expression was observed. The ubiquitous expression of this periplasmic ferroxidase suggests that it plays a key role in iron uptake in this opportunistic pathogen.
Clonality of
Streptococcus pneumoniae
Serotype 1 Isolates from Pediatric Patients in the United States
Authors: Gonzalez Blanca E. , Hulten Kristina G. , Kaplan Sheldon L. , Mason Edward O. 
Published: June 2004

ABSTRACT

We compared
Streptococcus pneumoniae
serotype 1 isolates causing disease among children in six geographic regions of the United States to determine genetic relatedness. Genomic fingerprints were determined by repetitive element polymorphism PCR (Rep-PCR). Multilocus sequence type characterization was performed on selected isolates. Four different genomic banding patterns were identified by Rep-PCR. One profile (clone 1) was predominant and matched sequence type 227.
Hospital- and Laboratory-Based Investigations of Hospitalized Children with Central Nervous System-Related Symptoms To Assess Japanese Encephalitis Virus Etiology in Cuddalore District, Tamil Nadu, India
Authors: Kabilan Lalitha , Ramesh S. , Srinivasan S. , Thenmozhi V. , Muthukumaravel S. , Rajendran R. 
Published: June 2004

ABSTRACT
A collaborative investigation of hospitalized encephalitic children in south India, between July 2002 and February 2003, has indicated that Japanese encephalitis was confirmed in 27.3% of these children. In developing countries, assessment of actual Japanese encephalitis disease burden requires strengthening of diagnostic laboratory capacities at hospitals.
Comparison of the Sensitivities of the Version 1.5 and Version 1.0 Ultrasensitive Roche AMPLICOR HIV-1 MONITOR Kits at Low Concentrations of Human Immunodeficiency Virus RNA
Authors: Brambilla Donald J. , Jennings Cheryl , Morack Ralph , Granger Suzanne , Bremer James W. 
Published: June 2004

ABSTRACT
The sensitivities of the version 1.5 and 1.0 Roche UltraSensitive AMPLICOR HIV-1 MONITOR tests were compared using panels of coded samples of subtype B human immunodeficiency virus type 1 spiked into plasma at predetermined concentrations. Results indicate that the version 1.5 kit is more sensitive than the version 1.0 kit.
Multiplex PCR Assay for Rapid Detection and Genotyping of
Helicobacter pylori
Directly from Biopsy Specimens
Authors: Chattopadhyay Santanu , Patra Rajashree , Ramamurthy T. , Chowdhury Abhijit , Santra Amal , Dhali G. K. , Bhattacharya S. K. , Berg Douglas E. , Nair G. Balakrish , Mukhopadhyay Asish K. 
Published: June 2004

ABSTRACT

We developed and evaluated a simple, novel multiplex PCR assay for rapid detection of
Helicobacter pylori
infection and for the determination of
vacA
and
cagA
genotypes directly from gastric biopsy specimens. This assay did not require culturing of strains or extraction of DNA from biopsy samples. This multiplex PCR assay would be of particularly great value for laboratories in developing countries.
Identification of a Novel
Brevibacterium
Species Isolated from Humans and Description of
Brevibacterium sanguinis
sp. nov
Authors: Wauters Georges , Haase Gerhard , Avesani Véronique , Charlier Jacqueline , Janssens Michèle , Van Broeck Johan , Delmée Michel 
Published: June 2004

ABSTRACT

Six coryneforms isolated from blood and dialysate fluid were phenotypically similar to
Brevibacterium casei
, but 16S rRNA gene sequencing and DNA-DNA hybridization indicate that they belong to a new species for which the name
Brevibacterium sanguinis
is proposed.
WAVE PROPAGATION IN A 3-D OPTICAL WAVEGUIDE
Authors: ALEXANDROV OLEG , CIRAOLO GIULIO 
Published: June 2004

In this paper we study the problem of electromagnetic wave propagation in a 3-D optical fiber. The goal is to obtain a solution for the time-harmonic field caused by a source in a cylindrically symmetric waveguide. The geometry of the problem, corresponding to an open waveguide, makes the problem challenging. To solve it, we construct a transform theory which is a nontrivial generalization of a method for solving a 2-D version of this problem given by Magnanini and Santosa.3 The extension to 3-D is made complicated by the fact that the resulting eigenvalue problem defining the transform kernel is singular both at the origin and at infinity. The singularities require the investigation of the behavior of the solutions of the eigenvalue problem. Moreover, the derivation of the transform formulas needed to solve the wave propagation problem involves nontrivial calculations. The paper provides a complete description on how to construct the solution to the wave propagation problem in a 3-D optical waveguide with cylindrical symmetry. A follow-up article will study the particular cases of a step-index fiber and of a coaxial waveguide. In those cases we will obtain concrete formulas for the field and numerical examples.
FISCHER DECOMPOSITIONS OF ENTIRE FUNCTIONS OF HILBERT–SCHMIDT HOLOMORPHY TYPE
Authors: PETERSSON HENRIK 
Published: June 2004

A Fischer pair (FP) for a vector space E is a pair (u, v) of linear maps on E, not necessarily everywhere defined, such that E= ker u⊕ Im v (Fischer decomposition). Thus, in particular, every densely defined closed operator u on a Hilbert space E forms a Fischer pair together with its adjoint u*, whenever Im u, or equivalently, Im u* is closed since then Im u*= ker u⊥. The question of when a given pair of maps (u, v) is a FP is related to the well-posedness of the (abstract) Cauchy–Goursat problem for u, v in E. We establish some Fischer pairs, for spaces that are built up by homogeneous Hilbert–Schmidt polynomials on a Hilbert space, consisting of differential and multiplication operators. In particular we study Fischer decompositions of the space of entire functions of Hilbert–Schmidt type. As a basis we generalize Fischers theorem for homogeneous polynomials in n variables to Hilbert–Schmidt polynomials.
THE LIFE CYCLE DIMENSION OF NEW PRODUCT DEVELOPMENT PERFORMANCE MEASUREMENT
Authors: SUOMALA PETRI 
Published: June 2004

This paper is concerned with comprehensive performance measurement (PM) of new product development (NPD). The idea of "life cycle conscious" NPD performance measurement is introduced by conducting a conceptual analysis combining product life cycle (PLC) thinking and NPD Performance Measurement (NPD PM). The empirical base of the paper is six case studies that focus on product life cycles and their characteristics within different industrial environments. The paper indicates that there are several ways that NPD PM would benefit from life cycle thinking. Life cycle orientation would provide companies with a feasible framework for constructing the performance measures of NPD, and the framework is likely to reduce the short-termism typically associated with NPD PM. In addition, life cycle could provide help for weighting the criteria and the measures utilized in NPD, for finding a balance for the measurement system, and for directing proper attention towards the comprehensive effects of new products.
Outcome with the hyper-CVAD regimens in lymphoblastic lymphoma
Authors: Thomas Deborah A. , O'Brien Susan , Cortes Jorge , Giles Francis J. , Faderl Stefan , Verstovsek Srdan , Ferrajoli Alessandra , Koller Charles , Beran Miloslav , Pierce Sherry , Ha Chul S. , Cabanillas Fernando , Keating Michael J. , Kantarjian Hagop 
Published: June 2004

Abstract
Therapy of lymphoblastic lymphoma (LL) has evolved with use of chemotherapy regimens modeled after those for acute lymphocytic leukemia (ALL). We treated 33 patients with LL with the intensive chemotherapy regimens hyper-CVAD (fractionated cyclophosphamide, vincristine, Adriamycin, and dexamethasone) or modified hyper-CVAD used for ALL at our institution. Induction consolidation was administered with 8 or 9 alternating cycles of chemotherapy over 5 to 6 months with intrathecal chemotherapy prophylaxis, followed by maintenance therapy. Consolidative radiation therapy was given to patients with mediastinal disease at presentation. No consolidation with autologous or allogeneic stem cell transplantation was performed. At diagnosis, 80% were T-cell immunophenotype, 70% were stages III to IV, 70% had mediastinal involvement, and 9% had central nervous system (CNS) disease. Of the patients, 30 (91%) achieved complete remission, and 3 (9%) achieved partial response. Within a median of 13 months, 10 patients (30%) relapsed or progressed. Estimates for 3-year progression-free and overall survival for the 33 patients were 66% and 70%, respectively. Estimates for the patients with known T-cell immunophenotype were 62% and 67%, respectively. No parameters (eg, age, stage, serum lactate dehydrogenase [LDH], β2 microglobulin) appeared to influence outcome except for CNS disease at presentation. Modification of the hyper-CVAD regimen with anthracycline intensification did not improve outcome. Other modifications of the program could include incorporation of monoclonal antibodies and/or nucleoside analogs, particularly for slow responders or those with residual mediastinal disease. (Blood. 2004;104:1624-1630)
Cardiac-like behavior of an insect flight muscle
Authors: Tu Michael S. , Daniel Thomas L. 
Published: June 2004

SUMMARYThe synchronous wing depressor muscles of the hawkmoth Manduca sexta undergo large amplitude motions at lengths that lie entirely on the ascending region of their twitch length–tension curve. Moreover, these muscles bear a striking functional resemblance to mammalian cardiac muscle in both the shape of their length–tension curve and in their working length range. Although operation on the ascending region of the twitch length–tension curve sacrifices maximal force, it does permit the generation of larger forces at greater strains. In the case of cardiac muscle,this mechanical behavior is critical for accommodating the increasing stresses associated with greater ventricular filling. Similar characteristics in moth flight muscle suggest an analogous regulatory mechanism for skeletal muscles performing repetitive oscillatory work; the strong length dependence of force over their working length range should give the wing depressors the capacity to generate larger forces as wing stroke amplitude increases. These results support the notion that the length–tension relationship of muscle can be tuned to function in locomotor muscles.
Morphological and physiological specialization for digging in amphisbaenians, an ancient lineage of fossorial vertebrates
Authors: Navas Carlos A. , Antoniazzi Marta M. , Carvalho José Eduardo , Chaui-Berlink José Guilherme , James Rob S. , Jared Carlos , Kohlsdorf Tiana , Pai-Silva Maeli Dal , Wilson Robbie S. 
Published: June 2004

SUMMARYAmphisbaenians are legless reptiles that differ significantly from other vertebrate lineages. Most species dig underground galleries of similar diameter to that of the animal. We studied the muscle physiology and morphological attributes of digging effort in the Brazilian amphisbaenid Leposternon microcephalum (Squamata; Amphisbaenia), which burrows by compressing soil against the upper wall of the tunnel by means of upward strokes of the head. The individuals tested (&lt;72 g) exerted forces on the soil of up to 24 N. These forces were possible because the fibres of the longissimus dorsi, the main muscle associated with burrowing, are highly pennated, thus increasing effective muscle cross-sectional area. The muscle is characterized by a metabolic transition along its length: proximal, medial and distal fibres are fast contracting and moderately oxidative, but fibres closer to the head are richer in citrate synthase and more aerobic in nature. Distal fibres, then, might be active mainly at the final step of the compression stroke, which requires more power. For animals greater than a given diameter,the work required to compress soil increases exponentially with body diameter. Leposternon microcephalum, and probably some other highly specialized amphisbaenids, are most likely constrained to small diameters and can increase muscle mass and effective muscle cross-sectional area by increasing body length, not body diameter.
Switching destinations: memory change in wood ants
Authors: Durier Virginie , Graham Paul , Collett Thomas S. 
Published: June 2004

SUMMARY
We have studied the changing use of spatial memories in wood ants by charting how the ants' paths transform when ants are first trained to feed at one site and must then switch to another site. Because ants, which are trained to approach a single feeding site from a single starting point, are attracted directly to that goal when started from unfamiliar positions, we describe the ants' paths in terms of the use of two stored snapshots. Each snapshot consists of retinotopic views of the ants' surroundings acquired at one of the two feeding sites. When a snapshot is activated, it draws an ant to the related site from a wide range of directions. Here, we focus on routes that occur before ants have learnt to go directly from the start to the second site. The initial direction of the ant's path is then mostly aimed either at the first site or between the two sites. On 62.2% of all recorded paths, this segment is followed by an abrupt turn, after which the ant often aims directly at the second feeding site. The details of this behaviour suggest that, after the turn, control of the path switches from the snapshot recorded at the first feeding site (or some combination of the two snapshots) to the snapshot recorded at the second feeding site. We discuss different ways in which control might be transferred from one snapshot to the other.