bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly
Authors: Gong Haipeng , Shen Yang , Rose George D. 
Published: July 2007

AbstractWe have been analyzing the extent to which protein secondary structure determines protein tertiary structure in simple protein folds. An earlier paper demonstrated that three‐dimensional structure can be obtained successfully using only highly approximate backbone torsion angles for every residue. Here, the initial information is further diluted by introducing a realistic degree of experimental uncertainty into this process. In particular, we tackle the practical problem of determining three‐dimensional structure solely from backbone chemical shifts, which can be measured directly by NMR and are known to be correlated with a protein's backbone torsion angles. Extending our previous algorithm to incorporate these experimentally determined data, clusters of structures compatible with the experimentally determined chemical shifts were generated by fragment assembly Monte Carlo. The cluster that corresponds to the native conformation was then identified based on four energy terms: steric clash, solvent‐squeezing, hydrogen‐bonding, and hydrophobic contact. Currently, the method has been applied successfully to five small proteins with simple topology. Although still under development, this approach offers promise for high‐throughput NMR structure determination.
Pioglitazone shift circadian rhythm of blood pressure from non‐dipper to dipper type in type 2 diabetes mellitus
Authors: Anan F. , Masaki T. , Fukunaga N. , Teshima Y. , Iwao T. , Kaneda K. , Umeno Y. , Okada K. , Wakasugi K. , Yonemochi H. , Eshima N. , Saikawa T. , Yoshimatsu H. 
Published: July 2007

AbstractBackground  Insulin resistance significantly correlated with a non‐dipper type of essential hypertension. Thiazolidinediones (TZD), oral hypoglycaemic agents that act as insulin sensitizers, have been demonstrated in multiple in vivo and in vitro studies to possess antihypertensive properties. This study examined the efficacy of TZD therapy with pioglitazone at transforming the circadian rhythms of blood pressure from a non‐dipper to a dipper type.Materials  We examined 31 patients with type 2 diabetes mellitus during both a baseline period and a period of treatment with pioglitazone. Patients received 15 mg day−1 pioglitazone for four weeks and 30 mg day−1 for 12 weeks. Twenty‐four hour ambulatory blood pressure monitoring (ABPM) and laboratory data (blood tests for cardiovascular risk factors) were obtained at the beginning and end of the study.Results  In non‐dippers (n = 16), but not dippers (n = 15), we observed a significant interaction between pioglitazone therapy and nocturnal falls in systolic and diastolic blood pressure. This examination indicated that the magnitude of the nocturnal blood pressure fall was affected by pioglitazone therapy. In non‐dippers, but not dippers, a significant correlation was observed between the percent decrease in nocturnal BP and the homeostasis model assessment (HOMA) index (r = 0·774, P = 0·0007).Conclusions  The present study demonstrated that pioglitazone can restore the nocturnal BP declines in parallel to reductions in the HOMA index, suggesting that insulin resistance may play an important role in the genesis of circadian BP rhythms. TZD‐based treatment may thus have the additional therapeutic advantage of reducing the risk of cardiovascular complications by transforming the circadian rhythm of BP.
Family dynamics in families of severe COPD patients
Authors: Kanervisto Merja , Paavilainen Eija , Heikkilä Johanna 
Published: July 2007

Aim and objectives.  The purpose of this study was to describe family dynamics in families with severe chronic obstructive pulmonary disease (COPD) on the basis of Barnhill's framework for healthy family systems. The sample consisted of 35 severe COPD patients and 30 family members at Tampere University Hospital, Finland or in the neighbouring regions.Background.  Chronic obstructive pulmonary disease is a public health problem worldwide. It is a slowly progressive airway disease, producing a decline in lung function which is not fully reversible.Design.  The sample included the families of patients without oxygen therapy and the families of patients who had long‐term oxygen therapy (LTOT). The data were collected using the Family Dynamics Measure 2 (FDM2) and the Family Dynamics Questionnaire (FDQ).Method.  A quantitative research method was employed in the study. Frequency and percentage distributions, as well as cross‐tabulations, were used to describe the data. Mean values and standard deviations were calculated for the sum variables of six dimensions of the FDM2.Results.  In the dimensions of individuation, mutuality and flexibility, dynamics in the families of patients with LTOT was significantly better than of the patients without oxygen therapy. Especially in the dimension of mutuality, the families of LTOT patients functioned very well, while in the dimensions of communication and roles, family dynamics in these families was notably worse, although still good.Conclusion.  Poor self‐identity – enmeshment, isolation from others and lack of flexibility to varying conditions – in families with severe COPD can weaken the ability of the families to manage in everyday life.Relevance to clinical practice.  Families need family nursing to adapt to alterations occurring when a family member has severe COPD. Nurses can give support and help for these families for their roles of patient and caregiver, as well as opportunities to speak with someone about their situation.
Preceptoring a student in the final clinical placement: reflections from nurses in a Canadian Hospital
Authors: Bourbonnais Frances Fothergill , Kerr Evelyn 
Published: July 2007

Aim.  To capture personal reflections on being a preceptor and to identify the supports and challenges to enacting the role.Background.  Prior to graduation from a nursing programme, students begin the transition in roles from student to practicing health‐care professional. To ease this transition, preceptorship programmes have been implemented to foster professional socialization and help students achieve confidence in their practice during their final clinical placement (consolidation experience). Preparation for the preceptor role is dependent upon the information offered by the agency as well as by the educational institution. Nursing staff are requested for much of the calendar year to work with increasing numbers of undergraduate students at various levels, function as preceptors in the final clinical experience (consolidation) as well as be involved in the orientation of newly hired nurses.Methods.  This qualitative study used one‐on‐one tape recorded interviews with nurses who had previous experience as a preceptor. Thematic analysis of the transcribed data resulted in the emergence of an overall theme and categories.Results.  Eight nurses were interviewed from a variety of units including medical surgical as well as critical care. The overriding theme from the analysis was ‘safe passage’. This safe passage was for the patient and the student and was accomplished through the process of teaching and a clear view of the preceptor role. Challenges to the role were lack of recognition by other nursing staff as well as limited support from some faculty advisors. Supports for the role were the visible presence and ongoing support by faculty advisors as well as the hospital workshop.Conclusion.  This study highlighted the importance of support from nursing faculty as well as recognition by fellow nurses of the workload involved when being a preceptor.Relevance to clinical practice.  Preceptors play an important role with students prior to graduation. Both the hospital and educational institutions need to ensure that nurses are given the necessary support, recognition and resources.
Resistance of Pseudoperonospora cubensis to flumorph on cucumber in plastic houses
Authors: Zhu S. S. , Liu X. L. , Wang Y. , Wu X. H. , Liu P. F. , Li J. Q. , Yuan S. K. , Si N. G. 
Published: July 2007

Plastic‐house experiments were conducted over a 2‐year period (2004–05) to estimate the effects of successive applications of flumorph or a mixture of flumorph with mancozeb to cucumber plants on selection for flumorph resistance in the downy mildew oomycete, Pseudoperonospora cubensis. Application of flumorph alone favoured the selection of resistant isolates of Ps. cubensis. Resistant populations were detected at a frequency of 2·5% after six successive applications of flumorph alone in a plastic house in 2004. Resistant isolates were also detected (4·8%) after eight successive applications of the mixture of flumorph and mancozeb in 2004, although the mixture gave significantly better disease control than flumorph alone and produced a slight delay in the development of resistance. In a second cucumber crop in the same plastic houses in 2004, the frequency of resistant isolates increased to 100% after three successive applications of flumorph or four of flumorph + mancozeb. Under laboratory conditions, most flumorph‐resistant isolates showed high levels of resistance and their levels of pathogenicity and sporulation were as high as that of wild‐type isolates. Flumorph showed cross‐resistance with dimethomorph and iprovalicarb, but not with azoxystrobin, cyazofamid, cymoxanil or metalaxyl. These studies suggest a high risk for the occurrence of resistance to flumorph in Ps. cubensis in cucumber crops under plastic‐house conditions.
A RanGAP protein physically interacts with the NB‐LRR protein Rx, and is required for Rx‐mediated viral resistance
Authors: Sacco Melanie A. , Mansoor Shahid , Moffett Peter 
Published: July 2007

SummaryRace‐specific disease resistance in plants is mediated by the products of host disease resistance (R) genes. Plant genomes possess hundreds of R gene homologs encoding nucleotide‐binding and leucine‐rich repeat (NB‐LRR) proteins. NB‐LRR proteins induce a disease resistance response following recognition of pathogen‐encoded avirulence (Avr) proteins. However, little is known about the general mechanisms by which NB‐LRR proteins recognize Avr proteins or how they subsequently induce defense responses. The Rx NB‐LRR protein of potato confers resistance to potato virus X (PVX). Using a co‐purification strategy, we have identified a Ran GTPase‐activating protein (RanGAP2) as an Rx‐interacting protein. We show by co‐immunoprecipitation that this interaction is mediated in planta through the putative signaling domain at the Rx amino terminus. Overexpression of RanGAP2 results in activation of certain Rx derivatives. Likewise, knocking down RanGAP2 expression in Nicotiana benthamiana by virus‐induced gene silencing compromises Rx‐mediated resistance to PVX. Thus, we have demonstrated a novel role for a RanGAP in the function of a plant disease resistance response.
Predictable males and unpredictable females: sex difference in repeatability of parental care in a wild bird population
Authors: NAKAGAWA S. , GILLESPIE D. O. S. , HATCHWELL B. J. , BURKE T. 
Published: July 2007

AbstractRepeatability of parental care, let alone heritability of care, has been rarely measured, although there has been much research linking sexual selection to male parental care and also examining biparental care in relation to game theory models. We investigated within‐ and between‐year repeatabilities of incubation and nestling provisioning and how these two types of parental care were related in a sexually dimorphic species, the house sparrow, Passer domesticus. We found that between‐ and within‐year repeatabilities of feeding rate were high in males and low to moderate in females, but that between‐ and within‐year repeatabilities of incubation time were low to moderate in both sexes. Interestingly, the amount of time during which neither sex incubated significantly predicted the subsequent male feeding rate but not the female feeding rate. Our results suggest a need for a new theoretical framework that encompasses variation in the predictability and plasticity of parental investment by individuals.
Lifespan is unrelated to investment in reproduction in populations of mammals and birds in captivity
Authors: Ricklefs Robert E. , Cadena Carlos Daniel 
Published: July 2007

AbstractWe examined the relationship between number of offspring produced to a certain age and subsequent longevity in captive zoo populations of 18 species of mammal and 12 species of bird. The age cut‐offs in each analysis were set to include 50%, 75% and 90% of the offspring produced in each of the population samples. Only one of 68 regressions was significant, and its slope was positive. In addition, we examined the relationship between age at first reproduction up to a certain age and longevity after that age, generally 5 years (3–8), among 17 species of mammal and 12 species of bird. Only one of these regressions had a significantly positive slope, indicating that early reproduction rarely reduces lifespan. Overall, we found no evidence that producing offspring in a zoo environment influences the age at death. Thus, although trade‐offs might apply in natural populations under resource limitation, neither pregnancy, growth of the foetus and lactation in mammals, nor egg production in birds, reduces lifespan in the absence of such stress. If genetically based or other intrinsic antagonistic pleiotropy underlies the evolution of senescence, it was not evident in our analyses.
Long‐term reproductive behaviour of woody plants across seven Bornean forest types in the Gunung Palung National Park (Indonesia): suprannual synchrony, temporal productivity and fruiting diversity
Authors: Cannon Charles H. , Curran Lisa M. , Marshall Andrew J. , Leighton Mark 
Published: July 2007

AbstractFor 68 months, we observed the reproductive behaviour of 7288 woody plants (172 figs, 1457 climbers and 5659 trees) spanning major soil and elevational gradients. Two 2–3 month community‐wide supra‐annual fruiting events were synchronized across five forest types, coinciding with ENSO events. At least 27 genera in 24 families restricted their reproduction to these events, which involved a substantial proportion of tree diversity (> 80% of phylogenetic diversity). During these events, mean reproductive levels (8.5%) represented an almost four‐fold increase compared with other months. These patterns indicate a strong behavioural advantage to this unusual reproductive behaviour. Montane forest experienced a single, separate fruiting peak while the peat swamp forest did not participate. Excluding these events, no temporal reproductive pattern was detectible, at either the landscape or forest type. These phenological patterns have major implications for the conservation of frugivore communities, with montane and swamp forests acting as ‘keystone’ forests.
Applying population‐genetic models in theoretical evolutionary epidemiology
Authors: Day Troy , Gandon Sylvain 
Published: July 2007

AbstractMuch of the existing theory for the evolutionary biology of infectious diseases uses an invasion analysis approach. In this Ideas and Perspectives article, we suggest that techniques from theoretical population genetics can also be profitably used to study the evolutionary epidemiology of infectious diseases. We highlight four ways in which population‐genetic models provide benefits beyond those provided by most invasion analyses: (i) they can make predictions about the rate of pathogen evolution; (ii) they explicitly draw out the mechanistic way in which the epidemiological dynamics feed into evolutionary change, and thereby provide new insights into pathogen evolution; (iii) they can make predictions about the evolutionary consequences of non‐equilibrium epidemiological dynamics; (iv) they can readily incorporate the effects of multiple host dynamics, and thereby account for phenomena such as immunological history and/or host co‐evolution.
Hexavalent uranium supports growth of Anaeromyxobacter dehalogenans and Geobacter spp. with lower than predicted biomass yields
Authors: Sanford Robert A. , Wu Qingzhong , Sung Youlboong , Thomas Sara H. , Amos Benjamin K. , Prince Emily K. , Löffler Frank E. 
Published: July 2007

SummaryThe stimulation of bacteria capable of reducing soluble U(VI) to sparingly soluble U(IV) is a promising approach for containing U(VI) plumes. Anaeromyxobacter dehalogenans is capable of mediating this activity; however, its ability to couple U(VI) reduction to growth has not been established. Monitoring the increase in 16S rRNA gene copy numbers using quantitative real‐time PCR (qPCR) in cultures provided with U(VI) as an electron acceptor demonstrated growth, and 7.7–8.6 × 106 cells were produced per μmole of U(VI) reduced. This biomass yield was lower than predicted based on the theoretical free energy changes associated with U(VI)‐to‐U(IV) reduction. Lower than predicted growth yields with U(VI) as electron acceptor were also determined in cultures of Geobacter lovleyi and Geobacter sulfurreducens suggesting that U(VI) reduction is inefficient or imposes an additional cost to growing cells. These findings have implications for U(VI) bioremediation because Anaeromyxobacter spp. and Geobacter spp. contribute to radionuclide immobilization in contaminated subsurface environments.
Genome structure impacts molecular evolution at the AvrLm1 avirulence locus of the plant pathogen Leptosphaeria maculans
Authors: Gout Lilian , Kuhn Marie Line , Vincenot Lucie , Bernard‐Samain Sylvie , Cattolico Laurence , Barbetti Martin , Moreno‐Rico Onésimo , Balesdent Marie‐Hélène , Rouxel Thierry 
Published: July 2007

Summary Leptosphaeria maculans, a dothideomycete fungus causing stem canker on oilseed rape, develops gene‐for‐gene interactions with its host plants. It has the ability to rapidly adapt to selection pressure exerted by cultivars harbouring novel resistance genes as exemplified recently by the 3‐year evolution towards virulence at the AvrLm1 locus in French populations. The AvrLm1 avirulence gene was recently cloned and shown to be a solo gene within a 269 kb non‐coding, heterochromatin‐like region. Here we describe the sequencing of the AvrLm1 genomic region in one avirulent and two virulent isolates to investigate the molecular basis of evolution towards virulence at the AvrLm1 locus. For these virulent isolates, the gain of virulence was linked to a 260 kb deletion of a chromosomal segment spanning AvrLm1 and deletion breakpoints were identical or similar. Among the 460 isolates analysed from France, Australia and Mexico, a similar large deletion was apparent in > 90% of the virulent isolates. Deletion breakpoints were also strongly conserved in most of the virulent isolates, which led to the hypothesis that a unique deletion event leading to the avrLm1 virulence has diffused in pathogen populations. These data finally suggest that retrotransposons are key drivers in genome evolution and adaptation to novel selection pressure in L. maculans.
Estimating the Consequences of Unintended Fertility for Child Health and Education in Romania: An Analysis Using Twins Data*
Authors: Glick Peter J. , Marini Alessandra , Sahn David E. 
Published: July 2007

AbstractWe use the natural experiment of twins at first birth to estimate the effects of unplanned fertility on the nutritional status and school enrolment of children in Romania, a country with a unique fertility history. A first‐birth twins shock has negative impacts on children's human capital investments, particularly for later‐born siblings. We infer that harsh pronatalist policies prior to the 1989 Revolution had adverse consequences for the human capital of Romanian children, and that policies to make fertility control easier will have significant positive impacts on children's health and schooling.
Evaluation of the use of dried spots and of different storage conditions of plasma for HIV‐1 RNA quantification
Authors: Amellal B , Katlama C , Calvez V 
Published: July 2007

ObjectivesThe aim of the study was to evaluate the use of dried plasma spots to determine HIV‐1 RNA viral loads.MethodsThe viral loads of 30 liquid plasma samples were compared with those of corresponding dried plasma spots on filter paper (DPS‐FP) and in tubes (DPS‐T), both of which were left for 7 days at 22°C. Also, 10 liquid plasma samples with detectable viral load were stored at 4, 22 or 37°C for 7 days and five further liquid plasma samples were air‐dried for up to 54 h to assess the effects of temperature and the drying step on HIV‐1 viral load.ResultsThe viral loads of the 30 liquid plasma samples correlated significantly with those of the paired dried spots DPS‐FP and DPS‐T, but with median losses of 0.64 and 0.69 log10 HIV‐1 RNA copies/mL, respectively, and a limit of detection of 3 log10 copies/mL. The 10 liquid plasma samples stored for 1 week at 37°C showed a weaker correlation and had a significantly reduced median viral load (–0.92 log10; P=0.005) when compared with the viral load of the matched plasma stored at −80°C. Most of the loss happened during the drying step.ConclusionsReliable measurement of HIV‐1 RNA viral load requires good plasma storage conditions. HIV RNA stability was affected by desiccation and 1 week of storage at 37°C. However, our findings suggest that liquid plasma can be kept at 4 or 22°C for a week with no effect on viral load.
HIV forensics: pitfalls and acceptable standards in the use of phylogenetic analysis as evidence in criminal investigations of HIV transmission*
Authors: Bernard EJ , Azad Y , Vandamme AM , Weait M , Geretti AM 
Published: July 2007

BackgroundPhylogenetic analysis – the study of the genetic relatedness between HIV strains – has recently been used in criminal prosecutions as evidence of responsibility for HIV transmission. In these trials, the expert opinion of virologists has been of critical importance.PitfallsPhylogenetic analysis of HIV gene sequences is complex and its findings do not achieve the levels of certainty obtained with the forensic analysis of human DNA. Although two individuals may carry HIV strains that are closely related, these will not necessarily be unique to the two parties and could extend to other persons within the same transmission network.Acceptable standardsFor forensic purposes, phylogenetic analysis should be conducted under strictly controlled conditions by laboratories with relevant expertise applying rigorous methods. It is vitally important to include the right controls, which should be epidemiologically and temporally relevant to the parties under investigation. Use of inappropriate controls can exaggerate any relatedness between the virus strains of the complainant and defendant as being strikingly unique. It will be often difficult to obtain the relevant controls. If convenient but less appropriate controls are used, interpretation of the findings should be tempered accordingly.ConclusionsPhylogenetic analysis cannot prove that HIV transmission occurred directly between two individuals. However, it can exonerate individuals by demonstrating that the defendant carries a virus strain unrelated to that of the complainant. Expert witnesses should acknowledge the limitations of the inferences that might be made and choose the correct language in both written and verbal testimony.
SOME RECENT RESEARCH INTO HOME HEATING
Authors: PIMBERT S. L. , FISHMAN D. S. 
Published: July 2007

As part of an investigation into the performance of heating systems and the effectiveness of energy saving measures, temperatures have been monitored in forty centrally heated homes.The addition of extra insulation had no effect on the way people operated their heating system or on the temperature level set in the main living room. However, bedrooms were warmer and the importance of individual room temperature controls demonstrated.Differences between people's thermal requirements in domestic and office environments are considered.