bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of level-walking aperiodicity
Authors: Pecoraro Fabrizio , Mazzà Claudia , Zok Mounir , Cappozzo Aurelio 
Published: December 2006

Abstract

Background:
In gait analysis, walking is assumed to be periodic for the sake of simplicity, despite the fact that, strictly speaking, it can only approximate periodicity and, as such, may be referred to as pseudo-periodic. This study aims at: 1) quantifying gait pseudo-periodicity using information concerning a single stride; 2) investigating the effects of walking pathway length on gait periodicity; 3) investigating separately the periodicity of the upper and lower body parts movement; 4) verifying the validity of foot-floor contact events as markers of the gait cycle period.

Methods:
Ten young healthy subjects (6 males, 23 ± 5 years) were asked to perform various gait trials, first along a 20-m pathway that allowed reaching a steady-state condition, and then along an 8-m pathway. A stereophotogrammetric system was used to reconstruct the 3D position of reflective markers distributed over the subjects' body. Foot contact was detected using an instrumented mat. Three marker clusters were used to represent the movement of the whole body, the upper body (without upper limbs), and the lower body, respectively. Linear and rotational kinetic, and gravitational and elastic potential "energy-like" quantities were used to calculate an index J(t) that described the instantaneous "mechanical state" of the analysed body portion. The variations of J(t) in time allowed for the determination of the walking pseudo-period and for the assessment of gait aperiodicity.

Results:
The suitability of the proposed approach was demonstrated, and it was shown that, for young, healthy adults, a threshold of physiological pseudo-periodicity of walking at natural speed could be set. Higher pseudo-periodicity values were found for the shorter pathway only for the upper body. Irrespective of pathway length, the upper body had a larger divergency from periodicity than the lower body. The error that can be made in estimating the gait cycle duration for the upper body from the heel contacts was shown to be significant.

Conclusion:
The proposed method can be easily implemented in gait laboratories to verify the consistency of a recorded stride with the hypothesis of periodicity.
Concordane of OSTA and lumbar spine BMD by DXA in identifying risk of osteoporosis
Authors: Lu ChunYan , Chen DeCai , Cai YunHua , Wei SongQuan 
Published: December 2006

Abstract

Objective
To investigate the accuracy of Osteoporosis Self-assessment Tool for Asians (OSTA) in identifying the risk of osteoporosis in postmenopausal women. To validate use of OSTA risk index by comparing it with the bone mineral density (BMD) of lumbar spine measured by dual energy X-ray absorptiometry (DXA).

Methods
The data of lumbar spine BMD (LS BMD) measurements by DXA of 218 postmenopausal women of Han nationality in Sichuan province were compared with OSTA risk index. The concordance of OSTA and LS BMD were calculated and analyzed by fourfold table and receiver operating characteristic (ROC) curve.

Results
The prevalence of osteoporosis in these women was 40.4% and 61.5%, with the LS BMD T score cutoffs -2.5 and -2.0, respectively. The sensitivity, specificity, and accuracy of OSTA risk index compared with T score cutoff -2.5 of LS BMD were 59.1%, 56.9% and 57.8%, respectively, while they were 57.5%, 63.1%, 59.6% by T score cutoff -2.0.

Conclusion
For identifying risk of osteoporosis, the concurrence was lower than those reported studies when comparing LS BMD measurements to OSTA risk index in Chinese Han nationality postmenopausal women of Sichuan province. Physicians should identify women who need BMD measurement according to more factors rather than age and body weight.
Lipoprotein Lipase mRNA Expression in Whole Blood Is a Prognostic Marker in B Cell Chronic Lymphocytic Leukemia
Authors: Van Bockstaele Femke , Pede Valerie , Janssens Ann , Callewaert Filip , Offner Fritz , Verhasselt Bruno , Philippé Jan 
Published: December 2006

Abstract
Background: Chronic lymphocytic leukemia (CLL) is characterized by high individual variability in clinical course and the need for therapy. Differentiation of prognostic subgroups is based primarily on the mutation status of the genes for the variable region of the immunoglobulin heavy chain (IGHV). The time- and labor-intensive nature of this analysis necessitates the use of easily applicable surrogate markers.
Methods: We developed a quantitative PCR (qPCR) method for determining lipoprotein lipase (LPL) mRNA expression and analyzed samples of lysed whole blood and CD19-selected cells from 50 CLL patients. Associations of LPL and ZAP70 [ζ-chain (TCR) associated protein kinase 70 kDa] expression with IGHV mutation status, overall survival (OS), and treatment-free survival (TFS) were investigated.
Results: Lysed samples of whole blood and CD19-selected cells were similar with respect to LPL expression (R = 0.88; P &lt;0.0001). LPL expression was significantly associated with IGHV mutation status [χ2(1) = 15.3; P &lt;0.0001] and showed an 89.3% specificity, a 68.2% sensitivity, an 83.3% positive predictive value, and a 78.1% negative predictive value for IGHV mutation status. LPL expression was significantly associated with both OS and TFS in log-rank tests (both P values = 0.002). LPL-positive patients had a significantly shorter median TFS time (23 months) than LPL-negative patients (88 months) (P = 0.002).
Conclusions: LPL mRNA expression is a valuable prognostic marker in CLL. The method does not require cell purification, and its applicability with archived samples facilitates its use in the clinical routine and other studies.
Mos1Mutagenesis Reveals a Diversity of Mechanisms Affecting Response ofCaenorhabditis elegansto the Bacterial PathogenMicrobacterium nematophilum
Authors: Yook Karen , Hodgkin Jonathan 
Published: December 2006

AbstractA specific host–pathogen interaction exists between Caenorhabditis elegans and the gram-positive bacterium Microbacterium nematophilum. This bacterium is able to colonize the rectum of susceptible worms and induces a defensive tail-swelling response in the host. Previous mutant screens have identified multiple loci that affect this interaction. Some of these loci correspond to known genes, but many bus genes [those with a bacterially unswollen (Bus) mutant phenotype] have yet to be cloned. We employed Mos1 transposon mutagenesis as a means of more rapidly cloning bus genes and identifying new mutants with altered pathogen response. This approach revealed new infection-related roles for two well-characterized and much-studied genes, egl-8 and tax-4. It also allowed the cloning of a known bus gene, bus-17, which encodes a predicted galactosyltransferase, and of a new bus gene, bus-19, which encodes a novel, albeit ancient, protein. The results illustrate advantages and disadvantages of Mos1 transposon mutagenesis in this system.
The Impact of Male-Killing Bacteria on Host Evolutionary Processes
Authors: Engelstädter Jan , Hurst Gregory D D 
Published: December 2006

Abstract
Male-killing bacteria are maternally inherited endosymbionts that selectively kill male offspring of their arthropod hosts. Using both analytical techniques and computer simulations, we studied the impact of these bacteria on the population genetics of their hosts. In particular, we derived and corroborated formulas for the fixation probability of mutant alleles, mean times to fixation and fixation or extinction, and heterozygosity for varying male-killer prevalence. Our results demonstrate that infections with male-killing bacteria impede the spread of beneficial alleles, facilitate the spread of deleterious alleles, and reduce genetic variation. The reason for this lies in the strongly reduced fitness of infected females combined with no or very limited gene flow from infected females to uninfected individuals. These two properties of male-killer-infected populations reduce the population size relevant for the initial emergence and spread of mutations. In contrast, use of Wright's equation relating sex ratio to effective population size produces misleading predictions. We discuss the relationship to the similar effect of background selection, the impact of other sex-ratio-distorting endosymbionts, and how our results affect the interpretation of empirical data on genetic variation in male-killer-infected populations.
The Population Biology of Bacterial Plasmids: A Hidden Markov Model Approach
Authors: Ponciano José M , De Gelder Leen , Top Eva M , Joyce Paul 
Published: December 2006

AbstractHorizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process using a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.
The SU(VAR)3-9/HP1 Complex Differentially Regulates the Compaction State and Degree of Underreplication of X Chromosome Pericentric Heterochromatin in Drosophila melanogaster
Authors: Demakova Olga V , Pokholkova Galina V , Kolesnikova Tatyana D , Demakov Sergey A , Andreyeva Eugenia N , Belyaeva Elena S , Zhimulev Igor F 
Published: December 2006

Abstract
In polytene chromosomes of Drosophila melanogaster, regions of pericentric heterochromatin coalesce to form a compact chromocenter and are highly underreplicated. Focusing on study of X chromosome heterochromatin, we demonstrate that loss of either SU(VAR)3-9 histone methyltransferase activity or HP1 protein differentially affects the compaction of different pericentric regions. Using a set of inversions breaking X chromosome heterochromatin in the background of the Su(var)3-9 mutations, we show that distal heterochromatin (blocks h26–h29) is the only one within the chromocenter to form a big “puff”-like structure. The “puffed” heterochromatin has not only unique morphology but also very special protein composition as well: (i) it does not bind proteins specific for active chromatin and should therefore be referred to as a pseudopuff and (ii) it strongly associates with heterochromatin-specific proteins SU(VAR)3-7 and SUUR, despite the fact that HP1 and HP2 are depleted particularly from this polytene structure. The pseudopuff completes replication earlier than when it is compacted as heterochromatin, and underreplication of some DNA sequences within the pseudopuff is strongly suppressed. So, we show that pericentric heterochromatin is heterogeneous in its requirement for SU(VAR)3-9 with respect to the establishment of the condensed state, time of replication, and DNA polytenization.
Effects of Introgression and Recombination on Haplotype Structure and Linkage Disequilibrium Surrounding a Locus EncodingBymovirusResistance in Barley
Authors: Stracke Silke , Presterl Thomas , Stein Nils , Perovic Dragan , Ordon Frank , Graner Andreas 
Published: December 2006

AbstractWe present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.
Combining Sperm Typing and Linkage Disequilibrium Analyses Reveals Differences in Selective Pressures or Recombination Rates Across Human Populations
Authors: Clark Vanessa J , Ptak Susan E , Tiemann Irene , Qian Yudong , Coop Graham , Stone Anne C , Przeworski Molly , Arnheim Norman , Rienzo Anna Di 
Published: December 2006

AbstractA previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.
Onset of the DNA Replication Checkpoint in the Early Drosophila Embryo
Authors: Crest Justin , Oxnard Nathan , Ji Jun-Yuan , Schubiger Gerold 
Published: December 2006

AbstractThe Drosophila embryo is a promising model for isolating gene products that coordinate S phase and mitosis. We have reported before that increasing maternal Cyclin B dosage to up to six copies (six cycB) increases Cdk1–Cyclin B (CycB) levels and activity in the embryo, delays nuclear migration at cycle 10, and produces abnormal nuclei at cycle 14. Here we show that the level of CycB in the embryo inversely correlates with the ability to lengthen interphase as the embryo transits from preblastoderm to blastoderm stages and defines the onset of a checkpoint that regulates mitosis when DNA replication is blocked with aphidicolin. A screen for modifiers of the six cycB phenotypes identified 10 new suppressor deficiencies. In addition, heterozygote dRPA2 (a DNA replication gene) mutants suppressed only the abnormal nuclear phenotype at cycle 14. Reduction of dRPA2 also restored interphase duration and checkpoint efficacy to control levels. We propose that lowered dRPA2 levels activate Grp/Chk1 to counteract excess Cdk1–CycB activity and restore interphase duration and the ability to block mitosis in response to aphidicolin. Our results suggest an antagonistic interaction between DNA replication checkpoint activation and Cdk1–CycB activity during the transition from preblastoderm to blastoderm cycles.
Two Events Are Responsible for an Insertion in a Paternally Inherited Mitochondrial Genome of the Mussel Mytilus galloprovincialis
Authors: Burzyński Artur 
Published: December 2006

Abstract
Frequent nonhomologous recombination has been previously postulated to explain the 1045-bp insertion in one mitochondrial sperm-transmitted haplotype of Mytilus galloprovincialis. Such recombination would lead to the disruption of gene order and so the existence of a specific mechanism for maintaining the same gene order in both mitochondrial genomes of Mytilus has been proposed. Here the simpler explanation of the observed structure, involving a tandem duplication and a deletion, is presented. Their occasional occurrence in Mytilus mtDNA proves the similarity, not the difference, between animals with and without DUI.
Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers
Authors: Sekino Masashi , Hara Motoyuki 
Published: December 2006

Abstract
This study presents linkage maps for the Pacific abalone (Haliotis discus hannai) based on 180 microsatellite DNA markers. Linkage mapping was performed using three F1 outbred families, and a composite linkage map for each sex was generated by incorporating map information from the multiple families. A total of 160 markers are placed on the consolidated female map and 167 markers on the male map. The numbers of linkage groups in the composite female and male maps are 19 and 18, respectively; however, by aligning the two maps, 18 linkage groups are formed, which are consistent with the haploid chromosome number of H. discus hannai. The female map spans 888.1 cM (Kosambi) with an average spacing of 6.3 cM; the male map spans 702.4 cM with an average spacing of 4.7 cM. However, we encountered several linkage groups that show a high level of heterogeneity in recombination rate between families even within the same sex, which reduces the precision of the consolidated maps. Nevertheless, we suggest that the composite maps are of significant potential use as a scaffold to further extend the coverage of the H. discus hannai genome with additional markers.
Importance of the Hsp70 ATPase Domain in Yeast Prion Propagation
Authors: Loovers Harriët M , Guinan Emma , Jones Gary W 
Published: December 2006

AbstractThe Saccharomyces cerevisiae non-Mendelian genetic element [PSI+] is the prion form of the translation termination factor Sup35p. The ability of [PSI+] to propagate efficiently has been shown previously to depend upon the action of protein chaperones. In this article we describe a genetic screen that identifies an array of mutants within the two major cytosolic Hsp70 chaperones of yeast, Ssa1p and Ssa2p, which impair the propagation of [PSI+]. All but one of the mutants was located within the ATPase domain of Hsp70, which highlights the important role of regulation of Hsp70–Ssa ATP hydrolysis in prion propagation. A subset of mutants is shown to alter Hsp70 function in a way that is distinct from that of previously characterized Hsp70 mutants that alter [PSI+] propagation and supports the importance of interdomain communication and Hsp70 interaction with nucleotide exchange factors in prion propagation. Analysis of the effects of Hsp70 mutants upon propagation of a second yeast prion [URE3] further classifies these mutants as having general or prion-specific inhibitory properties.
Generating Novel Allelic Variation ThroughActivatorInsertional Mutagenesis in Maize
Authors: Bai Ling , Singh Manjit , Pitt Lauren , Sweeney Meredith , Brutnell Thomas P 
Published: December 2006

AbstractThe maize transposable element Activator (Ac) has been exploited as an insertional mutagen to disrupt, clone, and characterize genes in a number of plant species. To develop an Ac-based mutagenesis platform for maize, a large-scale mutagenesis was conducted targeting the pink scutellum1 locus. We selected 1092 Ac transposition events from a closely linked donor Ac, resulting in the recovery of 17 novel ps1 alleles. Multiple phenotypic classes were identified corresponding to Ac insertions in the 5′-UTR and coding region of the predicted Ps1 gene. To generate a stable allelic series, we employed genetic screens and identified 83 germinally heritable ps1 excision alleles. Molecular characterization of these excision alleles revealed a position-dependent bias in excision allele frequencies and the predominance of 7- and 8-bp footprint products. In total, 19 unique ps1 excision alleles were generated in this study, including several that resulted in weak mutant phenotypes. The analysis of footprint alleles suggests a model of Ac excision in maize that is consistent with recent in vitro studies of hAT element excision. Importantly, the genetic and molecular methods developed in this study can be extended to generate novel allelic variation at any Ac-tagged gene in the genome.
Evaluation of Formalin and Hydrogen Peroxide Treatment Regimes on Rainbow Trout Eyed Eggs
Authors: Barnes Michael E , Soupir Craig A 
Published: December 2006

Abstract
This study examined the use of antifungal chemicals at nonstandard treatment concentrations or treatment intervals during the incubation of eyed eggs of rainbow trout Oncorhynchus mykiss until hatch in vertically stacked incubation trays. Daily chemical treatments of 500, 1,000, and 1,667 mg of commercial formalin (containing 37% formaldehyde)/L for 15 min and a nonchemical, dead-egg-removal control were included in three trials. The second and third trials added a true control (no antifungal measures) and the third trial also incorporated a treatment of formalin at 1,667 mg/L for 15 min every other day. In these three trials, formalin at 1,000 or 1,667 mg/L daily or 1,667 mg/L every other day significantly improved egg survival to hatch relative to the other treatments and completely controlled fungal growth. A fourth trial evaluated treatments of formalin at 750 mg/L for 15 min daily or every other day, hydrogen peroxide at 500 mg/L for 15 min daily or every other day, and control groups for both treatments. Egg survival to hatch was significantly different among the treatments; the daily 750-mg/L formalin treatment produced the greatest number of hatched fry, followed by the treatment with 750 mg/L formalin every other day, the dead-egg-removal control, and daily hydrogen peroxide treatment. Survival in the every-other-day hydrogen peroxide treatment and the true control could only be estimated because of extreme fungal growth, and was substantially less than the other treatments. Only daily 750 mg/L formalin treatments and dead egg removal completely controlled fungal growth. To adequately control fungus and maximize egg survival, either daily 15-min treatments of formalin at concentrations of at least 750 mg/L or every-other-day treatments of formalin at 1,667 mg/L are recommended.