bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subtyping Method for
Escherichia coli
Shiga Toxin (Verocytotoxin) 2 Variants and Correlations to Clinical Manifestations
Authors: Persson Søren , Olsen Katharina E. P. , Ethelberg Steen , Scheutz Flemming 
Published: April 2007

ABSTRACT

Shiga toxin 2 (Stx2) from Shiga toxin-producing
Escherichia coli
(STEC) was subtyped by a method involving partial sequencing of the
stx
AB
2
operon. Of 255 strains from the Danish STEC cohort, all 20 cases of hemolytic-uremic syndrome were associated with subtype Stx2 (11 cases), subtype Stx2c (1 case), or the two combined (8 cases).
Infectious Bursal Disease Virus Capsid Assembly and Maturation by Structural Rearrangements of a Transient Molecular Switch
Authors: Luque Daniel , Saugar Irene , Rodríguez José F. , Verdaguer Nuria , Garriga Damiá , Martín Carmen San , Velázquez-Muriel Javier A. , Trus Benes L. , Carrascosa José L. , Castón José R. 
Published: April 2007

ABSTRACT

Infectious bursal disease virus
(IBDV), a double-stranded RNA (dsRNA) virus belonging to the
Birnaviridae
family, is an economically important avian pathogen. The IBDV capsid is based on a single-shelled T=13 lattice, and the only structural subunits are VP2 trimers. During capsid assembly, VP2 is synthesized as a protein precursor, called pVP2, whose 71-residue C-terminal end is proteolytically processed. The conformational flexibility of pVP2 is due to an amphipathic α-helix located at its C-terminal end. VP3, the other IBDV major structural protein that accomplishes numerous roles during the viral cycle, acts as a scaffolding protein required for assembly control. Here we address the molecular mechanism that defines the multimeric state of the capsid protein as hexamers or pentamers. We used a combination of three-dimensional cryo-electron microscopy maps at or close to subnanometer resolution with atomic models. Our studies suggest that the key polypeptide element, the C-terminal amphipathic α-helix, which acts as a transient conformational switch, is bound to the flexible VP2 C-terminal end. In addition, capsid protein oligomerization is also controlled by the progressive trimming of its C-terminal domain. The coordination of these molecular events correlates viral capsid assembly with different conformations of the amphipathic α-helix in the precursor capsid, as a five-α-helix bundle at the pentamers or an open star-like conformation at the hexamers. These results, reminiscent of the assembly pathway of positive single-stranded RNA viruses, such as nodavirus and tetravirus, add new insights into the evolutionary relationships of dsRNA viruses.
Altered Interaction of the Matrix Protein with the Cytoplasmic Tail of Hemagglutinin Modulates Measles Virus Growth by Affecting Virus Assembly and Cell-Cell Fusion
Authors: Tahara Maino , Takeda Makoto , Yanagi Yusuke 
Published: April 2007

ABSTRACTClinical isolates of measles virus (MV) use signaling lymphocyte activation molecule (SLAM) as a cellular receptor, whereas vaccine and laboratory strains may utilize the ubiquitously expressed CD46 as an additional receptor. MVs also infect, albeit inefficiently, SLAM−cells, via a SLAM- and CD46-independent pathway. Our previous study with recombinant chimeric viruses revealed that not only the receptor-binding hemagglutinin (H) but also the matrix (M) protein of the Edmonston vaccine strain can confer on an MV clinical isolate the ability to grow well in SLAM−Vero cells. Two substitutions (P64S and E89K) in the M protein which are present in many vaccine strains were found to be responsible for the efficient growth of recombinant virus in Vero cells. Here we show that the P64S and E89K substitutions allow a strong interaction of the M protein with the cytoplasmic tail of the H protein, thereby enhancing the assembly of infectious particles in Vero cells. These substitutions, however, are not necessarily advantageous for MVs, as they inhibit SLAM-dependent cell-cell fusion, thus reducing virus growth in SLAM+B-lymphoblastoid B95a cells. When the cytoplasmic tail of the H protein is deleted, a virus with an M protein possessing the P64S and E89K substitutions no longer grows well in Vero cells yet causes cell-cell fusion and replicates efficiently in B95a cells. These results reveal a novel mechanism of adaptation and attenuation of MV in which the altered interaction of the M protein with the cytoplasmic tail of the H protein modulates MV growth in different cell types.
Human Immunodeficiency Virus Type 1 Protease Cleaves Procaspase 8 In Vivo
Authors: Nie Zilin , Bren Gary D. , Vlahakis Stacey R. , Schimnich Alicia Algeciras , Brenchley Jason M. , Trushin Sergey A. , Warren Sarah , Schnepple David J. , Kovacs Colin M. , Loutfy Mona R. , Douek Daniel C. , Badley Andrew D. 
Published: April 2007

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) infection causes apoptosis of infected CD4 T cells as well as uninfected (bystander) CD4 and CD8 T cells. It remains unknown what signals cause infected cells to die. We demonstrate that HIV-1 protease specifically cleaves procaspase 8 to create a novel fragment termed casp8p41, which independently induces apoptosis. casp8p41 is specific to HIV-1 protease-induced death but not other caspase 8-dependent death stimuli. In HIV-1-infected patients, casp8p41 is detected only in CD4
+
T cells, predominantly in the CD27
+
memory subset, its presence increases with increasing viral load, and it colocalizes with both infected and apoptotic cells. These data indicate that casp8p41 independently induces apoptosis and is a specific product of HIV-1 protease which may contribute to death of HIV-1-infected cells.
The Lifespans of the Patriarchs: Schematic Orderings in the Chrono-genealogy
Authors: Northcote Jeremy 
Published: April 2007

AbstractA remarkable numerical schema is revealed when the lifespan notices for the generations from Adam to Moses in the Masoretic version of the Pentateuch are added together—12,600 years. It is suggested that this schema has eschatological connotations that relates to the 1,260 days mentioned in Daniel and Revelation. The possibility that the lifespan notices developed from an earlier, progenitor chronology that originally tallied 12,000 years is also discussed, and the relationship between this schema, the surrounding patriarchal narratives and other Near East chronological traditions is examined in terms of the textual development of the Old Testament lifespan tradition.
Atomoxetine increases salivary cortisol in healthy volunteers
Authors: Chamberlain Samuel R. , Müller Ulrich , Cleary Sarah , Robbins Trevor W. , Sahakian Barbara J. 
Published: April 2007

It has been proposed that acute hypothalamo-pituitary-adrenal (HPA) axis challenge using noradrenergic drugs may be of utility in assessing the functional integrity of central noradrenaline pathways. Atomoxetine (formerly tomoxetine) is a highly selective noradrenaline reuptake inhibitor, which has recently been licensed for the treatment of attention deficit hyperactivity disorder (ADHD). The aim of this study was to assess the effects of acute atomoxetine on salivary cortisol levels for the first time. A total of 60 healthy male volunteers received 60 mg atomoxetine, 30 mg citalopram, or placebo per os in a double-blind parallel groups design ( n = 20 per group). Salivary cortisol, blood pressure and pulse rates were recorded at baseline and at +1.0, +1.5, +2.5 and +3.5 hours after capsule administration. 60 mg atomoxetine led to highly significant increases in salivary cortisol and a moderate increase in pulse rate, in the absence of significant effects on blood pressure. 30 mg citalopram had no significant effects on cortisol or cardiovascular parameters. These data support the utility of atomoxetine neuroendocrine chalenge for evaluating central noradrenaline pathways, which may be of future use in neuropsychiatric patient studies. Furthermore, the effects of atomoxetine on HPA axis function may have clinical implications given the use of this agent in the treatment of ADHD.
Extracting biology from high-dimensional biological data
Authors: Quackenbush John 
Published: April 2007

SUMMARYThe promise of the genome project was that a complete sequence would provide us with information that would transform biology and medicine. But the`parts list' that has emerged from the genome project is far from the `wiring diagram' and `circuit logic' we need to understand the link between genotype,environment and phenotype. While genomic technologies such as DNA microarrays,proteomics and metabolomics have given us new tools and new sources of data to address these problems, a number of crucial elements remain to be addressed before we can begin to close the loop and develop a predictive quantitative biology that is the stated goal of so much of current biological research,including systems biology. Our approach to this problem has largely been one of integration, bringing together a vast wealth of information to better interpret the experimental data we are generating in genomic assays and creating publicly available databases and software tools to facilitate the work of others. Recently, we have used a similar approach to trying to understand the biological networks that underlie the phenotypic responses we observe and starting us on the road to developing a predictive biology.
Common aging pathways in worms, flies, mice and humans
Authors: Kim Stuart K. 
Published: April 2007

SUMMARYDevelopment of functional genomics tools has made it possible to define the aging process by performing genome-wide scans for transcriptional differences between the young and the old. Global screens for age regulation have been performed for worms and flies, as well as many tissues in mice and humans. Recent work has begun to analyze the similarities and differences in transcriptional changes in aging among different species. Most age-related expression changes are specific for a given species, but genes in one pathway(the electron transport chain pathway) show common age regulation in species from worms to humans. Evolutionary theories of aging provide a basis to understand how age regulation of a genetic pathway might be preserved between distantly related species.
A new paradigm for developmental biology
Authors: Mattick John S. 
Published: April 2007

SUMMARYIt is usually thought that the development of complex organisms is controlled by protein regulatory factors and morphogenetic signals exchanged between cells and differentiating tissues during ontogeny. However, it is now evident that the majority of all animal genomes is transcribed, apparently in a developmentally regulated manner, suggesting that these genomes largely encode RNA machines and that there may be a vast hidden layer of RNA regulatory transactions in the background. I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks, with cell–cell signalling required to provide important positional information and to correct stochastic errors in the endogenous RNA-directed program.
Provision of laboratory services for lipid analysis in the United Kingdom
Authors: Hutchesson A C J , O'Kane M J , Neely R D , Oleesky D A 
Published: April 2007

Background: National guidelines have been developed in the UK to reduce coronary heart disease mortality. This audit assesses provision of lipid analyses by UK Clinical Biochemistry services to support their implementation. Methods: Audit standards were derived from published guidelines. A questionnaire based on these was circulated to all UK Clinical Biochemistry laboratories. Results: Of 108 replies, routine lipid profiles included triglycerides, HDL-, LDL-cholesterol and total:HDL cholesterol ratio in 98, 85, 72 and 44%, respectively. Only 33% and 27% analysed triglycerides and HDL, respectively, when asked simply to measure cholesterol. Seventy-six percent of the reports stated whether specimens were collected after fasting. For primary prevention, 46% of laboratories stated results should be interpreted in association with other risk factors; 20% referred explicitly to national/local guidelines. Only 19 laboratories quoted secondary prevention treatment thresholds for total cholesterol or LDL-cholesterol. Sixty laboratories occasionally added extra tests and/or interpretive comments. Eight laboratories appeared to provide no input from senior medical/scientific staff into report validation. Conclusions: These results indicate scope for improvement in the provision of lipid analyses and of information to support their interpretation. We recommend laboratories should routinely provide LDL- and non-HDL-cholesterol results, and that reports should quote treatment thresholds/targets in keeping with current guidelines.
The effect of potassium EDTA on the stability of parathyroid hormone in whole blood
Authors: English Emma , McFarlane Ian , Taylor Kevin P , Halsall David J 
Published: April 2007

Background: The stability of parathyroid hormone (PTH) in whole blood has not been well characterized. Previous studies show EDTA plasma samples to be more stable than serum samples. Methods: Blood from 17 haemodialysis patients and five healthy volunteers was collected into serum separator tubes (SSTs) and potassium EDTA tubes (EDTA-Ts) and incubated at room temperature before separation and storage for PTH analysis using the Bayer Advia Centaur. Results: Initial PTH concentrations were 7% higher (95% confidence interval [CI] 2-16%, P=0.016) in EDTA-Ts compared to the SSTs in the renal cohort. PTH concentrations in SSTs were significantly lower after 8 (10%, 95% CI 3-17%) and 20 h (22%, 95% CI 11-31%) but did not change significantly in EDTA-Ts ( P=0.1543). PTH concentration in EDTA-Ts from healthy volunteers was also independent of incubation time ( P=0.1165). Conclusion: The greater stability of PTH in whole blood anticoagulated with potassium EDTA allows PTH analysis to be offered to sites such as satellite clinics and primary care sites which do not have centrifugation and refrigeration facilities.
Salivary cortisol reflects serum cortisol: analysis of circadian profiles
Authors: Dorn Lorah D , Lucke Joseph F , Loucks Tammy L , Berga Sarah L 
Published: April 2007

Background: Technical hurdles limit the characterization of key hormonal rhythms. Frequent sampling increases detection of changes in magnitude or circadian and ultradian patterns, but limits feasibility for clinical or research settings. These caveats are particularly pertinent for cortisol, a hormone that displays a prominent circadian rhythm and whose magnitude is tightly regulated in the absence of biobehavioural challenge. Ideally, one would like to obtain samples non-invasively from a matrix of interest at frequent intervals. While many investigations have reported a high correlation between serum and salivary cortisol assays, the degree to which salivary cortisol reflects the circadian patterns of circulating cortisol concentrations has not been established across a 24 h period. Methods: We obtained hourly serum and salivary samples over a 24 h period in nine adults in an inpatient setting. The circadian patterns for serum and salivary cortisol were analysed by harmonic regression. Results: For all but two subjects (both on oral contraceptives), the salivary cortisol concentration was synchronous with the serum concentration, indicating that the salivary assay could be substituted for the serum assay to assess circulating rhythmicity across the 24 h time frame. Conclusions: This statistical model has distinct improvement over the correlational approach of examining serum and saliva cortisol relationships. Saliva cortisol appears to represent serum cortisol across the 24 h period, except for those on oral contraceptives.
Why do heterosexual young adults who use reliable contraception also use condoms? Results from a diary‐based prospective longitudinal study
Authors: de Visser Richard 
Published: April 2007

Objectives.To identify characteristics of individuals and characteristics of sexual encounters that predict whether people using contraception will also use condoms (dual use), and to determine whether dual use is prompted by concerns about unplanned pregnancy and/or sexually transmitted infections (STIs).Design.A longitudinal prospective design was used to identify characteristics of individuals and characteristics of specific sexual encounters that predict condom use.Methods.A sample of 349 sexually active heterosexual young adults was recruited at universities and trade colleges in Melbourne, Australia. Participants completed a self‐administered questionnaire, and a representative subsample (N= 103) completed a structured condom use diary in which they reported on up to 10 instances of vaginal intercourse. Respondents reported use of condoms and other forms of contraception during 919 instances of vaginal intercourse.Results.In multivariate analyses, dual use of condoms in addition to other contraception was predicted by attitudes toward condoms, intentions to use condoms, partner type and discussion of condom use with sexual partners. Dual use was not related to greater concern about HIV/STIs or unplanned pregnancy.Conclusion.Encouraging heterosexual young adults to discuss condom use, and developing their skills for negotiation of condom use will increase rates of condom use, thereby reducing current high rates of unplanned pregnancy and STIs.
Utilization and Diagnostic Yield of Neurogenetic Testing at a Tertiary Care Facility
Authors: Edlefsen Kerstin L , Tait Jonathan F , Wener Mark H , Astion Michael 
Published: April 2007

Abstract
Background: Institutions face increasing charges related to molecular genetic testing for neurological diseases. The literature contains little information on the utilization and performance of these tests.
Methods: A retrospective utilization review was performed to determine the diagnostic yield of neurogenetic tests ordered during calendar year 2005 at a large academic medical center in the western United States.
Results: Overall, a relevant mutation was identified in 30.2% of the 162 patients tested and in 21.5% of the 121 probands, defined as patients for whom no mutation has been previously identified in a family member. Patients with muscle weakness (n = 65) had a mutation detected in 26.2% of all patients and 23.5% of probands (n = 51), with an estimated testing cost per positive result of $3190. Patients tested for neuropathy (n = 36) had a mutation detected in 27.8% of patients and 22.6% of probands (n = 31), with an estimated cost per positive result of $5955. Patients with chorea (n = 25) had a positive result obtained in 68% of patients and 71.4% of probands (n = 7); the estimated cost per positive test was $440. Other diagnostic categories evaluated include ataxias (n = 18; yield, 11.1%; $7620 per positive), familial stroke or dementia syndromes (n = 8; yield, 12.5%; $6760 per positive), and multisystem mitochondrial disorders (n = 10; yield, 20%; $6485 per positive).
Conclusions: Expert clinicians at a tertiary care center who ordered neurogenetic tests obtained a positive result in 21.5% of patients without previously identified familial mutations. These results can be used for comparison and to help establish utilization guidelines for neurogenetic testing.
Suppressors ofzyg-1Define Regulators of Centrosome Duplication and Nuclear Association inCaenorhabditis elegans
Authors: Kemp Catherine A , Song Mi Hye , Addepalli Murali Krishna , Hunter Ginger , O'Connell Kevin 
Published: April 2007

AbstractIn Caenorhabditis elegans, the kinase ZYG-1 is required for centrosome duplication. To identify factors that interact with ZYG-1, we used a classical genetic approach and identified 21 szy (suppressor of zyg-1) genes that when mutated restore partial viability to a zyg-1 mutant. None of the suppressors render animals completely independent of zyg-1 activity and analysis of a subset of the suppressors indicates that all restore the normal process of centrosome duplication to zyg-1 mutants. Thirteen of these suppressor mutations confer phenotypes of their own and cytological examination reveals that these genes function in a variety of cellular processes including cell cycle timing, microtubule organization, cytokinesis, chromosome segregation, and centrosome morphology. Interestingly, several of the szy genes play a role in attaching the centrosome to the nuclear envelope. We have found that one such szy gene is sun-1, a gene encoding a nuclear envelope component. We further show that the role of SUN-1 in centrosome duplication is distinct from its role in attachment. Our approach has thus identified numerous candidate regulators of centrosome duplication and uncovered an unanticipated regulatory mechanism involving factors that tether the centrosome to the nucleus.
Spawning by Female Chinook Salmon Can Be Detected by Electromyogram Telemetry
Authors: Berejikian Barry A. , Endicott Robert C. , Van Doornik Donald M. , Brown Richard S. , Tatara Christopher P. , Atkins Jeffery 
Published: April 2007

AbstractNew methods to detect spawning of anadromous salmonids in their natural environment are needed to improve understanding of breeding behavior patterns, natural selection on reproductive traits (e.g., spawn timing), and interactions between artificially propagated and wild fish. We implanted maturing female Chinook salmon Oncorhynchus tshawytscha with coded electromyogram (CEMG) transmitters and continuously recorded spawning activity to develop an algorithm capable of accurately detecting spawning events from CEMG data. Marked increases in female digging frequencies immediately after spawning (cover digging) strongly correlated with CEMG values. The algorithm detected averages of 65% and 86% of the actual spawning events in 2003 and 2004, respectively. The algorithm accurately detected zero spawning events for the two female salmon that did not spawn. The presence of CEMG transmitters did not affect the digging frequency, number of nests constructed, or the reproductive life span of implanted fish. However, the CEMG tagging procedure or the presence of tags significantly increased egg retention. Pedigree analyses of DNA confirmed that females implanted with CEMG transmitters exhibited significantly lower individual reproductive success relative to that of nontagged females (73% and 66% reduction in two separate experiments). Subsequent research in adult steelhead O. mykiss has indicated that alternative implantation techniques hold promise for reducing the effects of the tags on reproductive success. We suggest that remote monitoring of salmonid spawning behavior is now possible with CEMG technology and should be tested in natural habitats.