bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing standard and genetic parameters in 220 patients with multiple myeloma with complete data sets: superiority of molecular genetics
Authors: Shaughnessy John D. , Haessler Jeffrey , Van Rhee Frits , Anaissie Elias , Pineda‐Roman Mauricio , Cottler‐Fox Michele , Hollmig Klaus , Zangari Maurizio , Mohiuddin Abid , Alsayed Yazan , Grazziutti Monica , Epstein Joshua , Crowley John , Barlogie Bart 
Published: May 2007

SummaryPrognostic models for multiple myeloma have been fraught with tremendous heterogeneity in outcome among subgroups. In the context of Total Therapy 2, a tandem transplant trial for newly diagnosed myeloma, comprehensive information was available in 220 patients on standard prognostic factors (SPF), magnetic resonance imaging (MRI)‐defined focal lesions, cytogenetic abnormalities (CA), fluorescence‐in‐situ‐hybridisation (FISH)‐derived amplification of chromosome 1q21 (amp1q21) and deletion of 13q14, as well as gene expression profiling (GEP). Five multivariate analysis‐based survival models were derived, utilising SPF only (model 1), with progressive addition of CA (model 2), MRI (model 3), FISH (model 4) and GEP (model 5). TheR2value, a measure of accounting for clinical outcome variability, increased progressively from 18% in model 1 to 38% in model 5. The hazard ratio for overall survival was highest for GEP (3·07,P < 0·001) followed by amp1q21 (1·71,P = 0·05). According to the presence of none (49%), one (35%) or both of these two risk features (16%), 3‐year survival decreased progressively from 92% to 78% to 43% (P < 0·0001). Thus, the dominance over other prognostic parameters of molecular genetics justifies the generation of quantitative reverse transcription polymerase chain reaction methodology (‘MM genetic kit’) for the optimal risk stratification of patients participating in therapeutic trials.
Shell decay rates of native and alien freshwater bivalves and implications for habitat engineering
Authors: STRAYER DAVID L. , MALCOM HEATHER M. 
Published: May 2007

Summary1. Spent shells of bivalves can provide habitat for other organisms, as well as playing important roles in biogeochemical cycles. The amount of spent shell material that will accumulate at a site depends on rates of both shell production and decay, although the latter is rarely considered.2. We measured the instantaneous decay rates of four species of freshwater bivalves across a range of sites in south‐eastern New York, and found that rates varied by more than 500‐fold across sites and species.3. Differences in decay rates were related to water chemistry (Ca, pH, dissolved inorganic C), the presence of a current, and the size of the bivalve shell.4. Combining these decay rates with estimates of shell production derived from the literature, we conclude that the Unionidae, Corbicula, and Dreissena are all capable of producing large accumulations (>10 kg dry mass m−2) of spent shells, while members of the Sphaeriidae probably rarely will produce such large accumulations.5. Hence the replacement of native unionid bivalves by the alien Corbicula and Dreissena may have little effect on standing stocks of spent shells, unless the aliens invade sites where unionids are scarce or absent.
Automatic differentiation in geophysical inverse problems
Authors: Sambridge M. , Rickwood P. , Rawlinson N. , Sommacal S. 
Published: May 2007

Summary
Automatic differentiation (AD) is the technique whereby output variables of a computer code evaluating any complicated function (e.g. the solution to a differential equation) can be differentiated with respect to the input variables. Often AD tools take the form of source to source translators and produce computer code without the need for deriving and hand coding of explicit mathematical formulae by the user. The power of AD lies in the fact that it combines the generality of finite difference techniques and the accuracy and efficiency of analytical derivatives, while at the same time eliminating ‘human’ coding errors. It also provides the possibility of accurate, efficient derivative calculation from complex ‘forward’ codes where no analytical derivatives are possible and finite difference techniques are too cumbersome. AD is already having a major impact in areas such as optimization, meteorology and oceanography. Similarly it has considerable potential for use in non-linear inverse problems in geophysics where linearization is desirable, or for sensitivity analysis of large numerical simulation codes, for example, wave propagation and geodynamic modelling. At present, however, AD tools appear to be little used in the geosciences. Here we report on experiments using a state of the art AD tool to perform source to source code translation in a range of geoscience problems. These include calculating derivatives for Gibbs free energy minimization, seismic receiver function inversion, and seismic ray tracing. Issues of accuracy and efficiency are discussed.
Glycogen synthase kinase 3 activity during development of bone marrow‐derived dendritic cells (DCs) essential for the DC function to induce T helper 2 polarization
Authors: Ono Takenori , Yanagawa Yoshiki , Iwabuchi Kazuya , Nonomura Katsuya , Onoé Kazunori 
Published: May 2007

SummaryDendritic cells (DCs) polarize naive CD4+ T cells to either T helper 1 (Th1) or Th2 cells. We examined the role of glycogen synthase kinase 3 (GSK3) activity during DC development from murine bone marrow (BM) cells. DCs were generated by culturing lineage‐marker‐negative BM cells with granulocyte–macrophage colony‐stimulating factor in the presence or absence of a specific inhibitor of GSK3 (Gi), SB415286, for 6 days. DCs generated in the presence (GiDC) or absence (control DC) of SB415286 similarly exhibited a conventional DC phenotype (CD11b+ B220– CD8–). These DCs were mixed with allogeneic CD4+ T cells and the ability to polarize Th1 or Th2 cells was evaluated. The GiDCs exhibited markedly impaired function to induce Th2 polarization compared to control DCs. In contrast, the ability of GiDCs to generate Th1 cells was slightly higher than that of control DCs. CD86 expression and CD40‐mediated interleukin‐6 production were completely diminished in GiDCs, which might be associated with the impaired ability of the GiDCs to induce Th2 differentiation. These results suggest that the GSK3 activity during DC development is essential for the establishment of the DC function to induce Th2, but not Th1, differentiation.
Aberrant T‐cell ontogeny and defective thymocyte and colonic T‐cell chemotactic migration in colitis‐prone Gαi2‐deficient mice
Authors: Elgbratt Kristina , Bjursten Malin , Willén Roger , Bland Paul W. , Hörnquist Elisabeth Hultgren 
Published: May 2007

SummaryGαi2‐deficient mice, which spontaneously develop colitis, have previously been reported to have an increased frequency of mature, single positive thymocytes compared to wild‐type mice. In this study we further characterized the intrathymic changes in these mice before and during overt colitis. Even before the onset of colitis, Gαi2–/– thymi weighed less and contained fewer thymocytes, and this was exacerbated with colitis development. Whereas precolitic Gαi2–/– mice had unchanged thymocyte density compared to Gαi2+/– mice of the same age, this was significantly decreased in mice with colitis. Thymic atrophy in Gαi2–/– mice involved mainly the cortex. Using a five‐stage phenotypic characterization of thymocyte maturation based on expression of CD4, CD8, TCRαβ, CD69 and CD62L, we found that both precolitic and colitic Gαi2–/– mice had significantly increased frequencies of mature single‐positive CD4+ and CD8+ medullary thymocytes, and significantly reduced frequencies and total numbers of immature CD4+ CD8+ double‐positive thymocytes compared to Gαi2+/– mice. Furthermore, cortical and transitional precolitic Gαi2–/– thymocytes showed significantly reduced chemotactic migration towards CXCL12, and a trend towards reduced migration to CCL25, compared to wild‐type thymocytes, a feature even more pronounced in colitic mice. This impaired chemotactic migration of Gαi2–/– thymocytes could not be reversed by increased chemokine concentrations. Gαi2–/– thymocytes also showed reduced expression of the CCL25 receptor CCR9, but not CXCR4, the receptor, for CXCL12. Finally, wild‐type colonic lamina propria lymphocytes migrated in response to CXCL12, but not CCL25 and, as with thymocytes, the chemokine responsiveness was significantly reduced in Gαi2–/– mucosal lymphocytes.
Instruction of naive CD4+ T‐cell fate to T‐bet expression and T helper 1 development: roles of T‐cell receptor‐mediated signals
Authors: Ariga Haruyuki , Shimohakamada Yoko , Nakada Makiyo , Tokunaga Takeshi , Kikuchi Takeshi , Kariyone Ai , Tamura Toshiki , Takatsu Kiyoshi 
Published: May 2007

SummaryUsing T‐cell receptor (TCR) transgenic mice, we demonstrate that TCR stimulation of naive CD4+ T cells induces transient T‐bet expression, interleukin (IL)‐12 receptor β2 up‐regulation, and GATA‐3 down‐regulation, which leads to T helper (Th)1 differentiation even when the cells are stimulated with peptide‐loaded I‐Ab‐transfected Chinese hamster ovary cells in the absence of interferon‐γ (IFN‐γ) and IL‐12. Sustained IFN‐γ and IL‐12 stimulation augments naive T‐cell differentiation into Th1 cells. Intriguingly, a significant Th1 response is observed even when T‐bet–/– naive CD4+ T cells are stimulated through TCR in the absence of IFN‐γ or IL‐12. Stimulation of naive CD4+ T cells in the absence of IFN‐γ or IL‐12 with altered peptide ligand, whose avidity to the TCR is lower than that of original peptide, fails to up‐regulate transient T‐bet expression, sustains GATA‐3 expression, and induces differentiation into Th2 cells. These results support the notion that direct interaction between TCR and peptide‐loaded antigen‐presenting cells, even in the absence of T‐bet expression and costimulatory signals, primarily determine the fate of naive CD4+ T cells to Th1 cells.
Salmonella‐induced SipB‐independent cell death requires Toll‐like receptor‐4 signalling via the adapter proteins Tram and Trif
Authors: Cook Pamela , Tötemeyer Sabine , Stevenson Catherine , Fitzgerald Katherine A. , Yamamoto Masahiro , Akira Shizuo , Maskell Duncan J. , Bryant Clare E. 
Published: May 2007

Summary Salmonella enterica serovar typhimurium (S. typhimurium) is an intracellular pathogen that causes macrophage cell death by at least two different mechanisms. Rapid cell death is dependent on the Salmonella pathogenicity island‐1 protein SipB whereas delayed cell death is independent of SipB and occurs 18–24 hr post infection. Lipopolysaccharide (LPS) is essential for the delayed cell death. LPS is the main structural component of the outer membrane of Gram‐negative bacteria and is recognized by Toll‐like receptor 4, signalling via the adapter proteins Mal, MyD88, Tram and Trif. Here we show that S. typhimurium induces SipB‐independent cell death through Toll‐like receptor 4 signalling via the adapter proteins Tram and Trif. In contrast to wild type bone marrow derived macrophages (BMDM), Tram–/– and Trif–/– BMDM proliferate in response to Salmonella infection.
Corticosterone impairs dendritic cell maturation and function
Authors: Elftman Michael D. , Norbury Christopher C. , Bonneau Robert H. , Truckenmiller Mary E. 
Published: May 2007

SummaryDendritic cells (DC) play a critical role in initiating and directing adaptive immune responses against pathogens and tumours. Immature DC are thought to act as sentinels in peripheral tissues where their main function is to capture antigen at sites of infection, whereas mature DC are highly efficient at priming T‐cell‐mediated immune responses against infectious pathogens. The DC maturation process is thought to be an important step in the efficient generation of cytotoxic T lymphocytes (CTL). It is well established that many aspects of immune function, including CTL‐mediated antiviral immunity, are modulated by neuroendocrine‐derived products. Corticosterone (CORT), an adrenal hormone produced at increased concentrations during a stress response, has been shown to play a role in impaired CTL responses in stressed animals, leading to high mortality in mice normally resistant to viral infection. While direct effects of neuroendocrine mediators on CTL have been studied, little is known about their effects on DC that are critical for CTL priming. Here, we found that physiologically relevant concentrations of CORT, acting via the glucocorticoid receptor, functionally compromise DC maturation. DC exposed to CORT remained phenotypically and functionally immature after stimulation with lipopolysaccharide and were impaired for the production of interleukin (IL)‐6, IL‐12, and tumour necrosis factor‐α. These effects were biologically significant, as CORT treatment resulted in a marked reduction in the ability of DC to prime naive CD8+ T cells in vivo. These findings offer a potential mechanism underlying stress‐associated immunosuppression.
Rates of mass gain and energy deposition in red knot on their final spring staging site is both time‐ and condition‐dependent
Authors: ATKINSON PHILIP W. , BAKER ALLAN J. , BENNETT KAREN A. , CLARK NIGEL A. , CLARK JACQUIE A. , COLE KIMBERLY B. , DEKINGA ANNE , DEY AMANDA , GILLINGS SIMON , GONZÁLEZ PATRICIA M. , KALASZ KEVIN , MINTON CLIVE D. T. , NEWTON JASON , NILES LAWRENCE J. , PIERSMA THEUNIS , ROBINSON ROBERT A. , SITTERS HUMPHREY P. 
Published: May 2007

Summary

Millions of shorebirds migrate each year through a small number of highly productive staging areas where they often conflict with fisheries interests. Delaware Bay, USA, is a major shorebird stopover site where, in spring, many thousands of shorebirds undergo rapid mass gain by feeding on the eggs of commercially harvested horseshoe crabs Limulus polyphemus.
Environmental factors may cause deviations from the best migration schedule. We used within‐year mass gain data from red knot Calidris canutus caught in Delaware Bay between 1998 and 2005 to determine the degree of flexibility individuals have to vary migration speed.
Mass gain by birds below 133 g was shown to comprise 15·3% fat (39 kJ g−1), the remainder being lean mass (6 kJ g−1). Above this critical level, fat comprised 83·9% of mass deposition. The rates of energy deposition (kJ d−1) were therefore fundamentally different between the two states but were among the highest ever recorded among vertebrates (5–7 × basic metabolic rate).
A total of 36–62% of the variation in observed rates of energy deposition between 1998 and 2002 was explained by a year factor, date and mass at initial capture and interaction terms, such that light‐weight birds at the end of May had rates of mass gain or energy deposition two to three times higher than birds of similar mass in mid‐May, indicating that birds were attempting to achieve a certain mass by a certain date. In 2003 and 2005, this relationship broke down as a result of lower densities of eggs.
Synthesis and application. The maintenance of high densities of crab eggs required for high rates of mass gain in red knot requires severe cuts in, or the complete cessation of, the crab harvest, reduced human and raptor‐related disturbance as well as management of beaches to provide sufficient crab‐spawning habitat. These findings are widely applicable to other systems where harvesting activities come into conflict with migrating animals and show that certain sections of the population, in this case the long‐distance migrants from South America, will be impacted more than short‐distance migrants whose physiology may give them access to alternative food resources.
Susceptibility of salmonid alphavirus to a range of chemical disinfectants
Authors: Graham D A , Cherry K , Wilson C J , Rowley H M 
Published: May 2007

AbstractA range of commercially available disinfectants were tested for efficacy against salmonid alphavirus under a range of different conditions including variations in concentration, temperature, contact time, water type and presence or absence of organic matter. Testing was based on the protocol defined in the draft European Standard prEN 14675, for which the effective standard is a 4 log(10) reduction in viral titre. All disinfectants were found to be effective under at least some of the conditions tested. However, the presence of organic matter in particular was shown to be detrimental in some cases, either through rendering some disinfectants ineffective, or by production of a visible inhomogeneity.
Yersinia ruckeri infections in salmonid fish
Authors: Tobback E , Decostere A , Hermans K , Haesebrouck F , Chiers K 
Published: May 2007

Abstract Yersinia ruckeri is the causative agent of yersiniosis or enteric redmouth disease leading to significant economic losses in salmonid aquaculture worldwide. Infection may result in a septicaemic condition with haemorrhages on the body surface and in the internal organs. Despite the significance of the disease, very little information is available on the pathogenesis, hampering the development of preventive measures to efficiently combat this bacterial agent. This review discusses the agent and the disease it causes. The possibility of the presence of similar virulence markers and/or pathogenic mechanisms between the Yersinia species which elicit disease in humans and Y. ruckeri is also examined.
Self‐determination, social abilities and the quality of life of people with intellectual disability
Authors: Nota L. , Ferrari L. , Soresi S. , Wehmeyer M. 
Published: May 2007

SummaryBackground  The international literature has documented that self‐determination is impacted by environmental factors, including living or work settings; and by intraindividual factors, including intelligence level, age, gender, social skills and adaptive behaviour. In addition, self‐determination has been correlated with improved quality of life (QoL). This study sought to contribute to the growing literature base in this area by examining the relationship among and between personal characteristics, self‐determination, social abilities and the environmental living situations of people with intellectual disabilities (ID).Methods  The study involved 141 people with ID residing in Italy. Healthcare professionals and social workers who had known participants for at least 1 year completed measures of self‐determination, QoL and social skills. Analysis of variance was conducted to verify whether different levels of intellectual impairment were associated with different degrees of the dependent variables. The Pearson product–moment correlation was used to examine any relationships among dependent variables and IQ scores. Finally, discriminant function analysis was used to examine the degree to which IQ score, age, self‐determination and social abilities predicted membership in groups that were formed based on living arrangement, and on QoL status (high vs. low).Results  The anova determined, as expected, that participants with more severe ID showed the lowest levels of self‐determination, QoL and social abilities. Discriminant function analysis showed that (a) individuals attending day centres were distinguished from those living in institutions in that they were younger and showed greater autonomy of choice and self‐determination in their daily activities; (b) basic social skills and IQ score predicted membership in the high or low QoL groups; and (c) the IQ score predicted membership in the high or low self‐determination groups. A manova conducted to examine gender‐ and age‐level differences on self‐determination found gender differences; women had higher self‐determination scores than men.Conclusions  These findings contribute to an emerging knowledge base pertaining to the role of intraindividual and environmental factors in self‐determination and QoL. In general, the study replicated findings pertaining to the relative contribution of intelligence to self‐determination and QoL, added information about the potential contribution of social abilities, and pointed to the potentially important role of opportunities to make choices as a particularly important aspect of becoming more self‐determined, at least in the context of residential settings.
Predictors of depressive symptoms in primary caregivers of young children with or at risk for developmental delay
Authors: Feldman M. , McDonald L. , Serbin L. , Stack D. , Secco M. L. , Yu C. T. 
Published: May 2007

AbstractBackground  Despite extensive research with families raising children with or at risk for developmental delay (DD), it is not clear whether primary caregivers of these children are at increased risk for depressive symptoms. Discrepant findings in the literature may be owing to heterogeneity of child problems. More research is needed on child, parent and family variables that may increase risk for, or resilience to, caregiver depressive symptoms. Some studies have found that parental resources (e.g. social support and coping strategies) may buffer the effects of parental distress, while other studies have highlighted the role of parental self‐efficacy.Methods  We examined Beck Depression Inventory (BDI) scores in 178 primary caregivers (mainly biological mothers) who had 2‐year‐old children with or at risk for DD owing to: (a) low birthweight, prematurity or multiple birth (n = 58), (b) other known reasons (e.g. Down syndrome, spina bifida) (n = 67), or (c) unknown reasons (n = 69).Results  We found that 20% (n = 35) of the caregivers scored above the BDI clinical cut‐off for depression. Analysis of variance revealed that caregivers with elevated BDI scores had higher child behaviour problem and escape‐avoidance coping scores, and lower social support and parent self‐efficacy, compared with caregivers without depressive symptoms. Caregivers with children who had DD for unknown reasons had higher BDI scores than caregivers of the other two groups of children. Regression analyses showed that child behaviour problems, escape‐avoidance coping strategies and social support predicted caregiver BDI scores, but caregiver self‐efficacy only did so when entered independently of social support. Only social support mediated and (marginally) moderated the relationship between child behaviour problems and caregiver depressive symptoms.Conclusions  These findings suggest that early intervention programmes should carefully consider the interaction of child characteristics (e.g. Diagnosis and behaviour problems), caregiver resources (e.g. coping strategies and social support), and parental mental health and mood when planning and tailoring services for families of children with or at risk for DD.
Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?
Authors: Hobman Jon L. , Penn Charles W. , Pallen Mark J. 
Published: May 2007

Summary Escherichia coli stands unchallenged as biology's premier model organism. However, we propose, equipped with insights from the post‐genomic era, a contrary view: that microbiology's chief idol has feet of clay. E. coli laboratory strains, particularly E. coli K‐12, are far from model citizens, but instead degenerate and deceitful delinquents growing old disgracefully in our scientific institutions. E. coli K‐12 is neither archetype nor ancestor. In addition, it has a far from optimal provenance for a model organism, with strong grounds for believing that current versions of the strain are quite distinct from any original wild‐type free‐living ancestor. In addition, it is usually studied under conditions far removed from its natural habitats and in ignorance of the selective pressures that have shaped its evolution. Fortunately, a flood of information from high‐throughput genome sequencing, together with a new ‘eco‐evo’ view of this model organism, promises to help put K‐12 better into context.