bluuebunny/crossref_metadata_2025_split huggingface dataset:
A FINITELY PRESENTED GROUP WITH ALMOST SOLVABLE CONJUGACY PROBLEM
Authors: Kalorkoti K. 
Published: December 2009

The algorithmic unsolvability of the conjugacy problem for finitely presented groups was demonstrated by Novikov in the early 1950s. Various simplifications and alternative proofs were found by later researchers and further questions raised. Recent work by Borovik, Myasnikov and Remeslennikov has considered the question of what proportion of the number of elements of a group (obtained by standard constructions) falls into the realm of unsolvability. In this paper we provide a straightforward construction, as a Britton tower, of a finitely presented group with solvable word problem but unsolvable conjugacy problem of any r.e. (recursively enumerable) Turing degree a. The question of whether two elements are conjugate is bounded truth-table reducible to the question of whether the elements are both conjugate to a single generator of the group. We also define computable normal forms, based on the method of Bokut', that are suitable for the conjugacy problem. We consider (ordered) pairs of normal words U, V for the conjugacy problem whose lengths add to l and show that the proportion of such pairs for which conjugacy is undecidable (in the case a ≠ 0) is strictly less than l2/(2λ - 1)l where λ > 4. The construction is based on modular machines, introduced by Aanderaa and Cohen. For the purposes of this construction it was helpful to extend the notion of configuration to include pairs of m-adic integers. The notion of computation step was also extended and is referred to as s-fold computation where s ∈ ℤ (the usual notion coresponds to s = 1). If gcd (m, s) = 1 then determinism is preserved, i.e., if the modular machine is deterministic then it remains so under the extended notion. Furthermore there is a simple correspondence between s-fold and standard computation in this case. Otherwise computation is non-deterministic and there does not seem to be any straightforward correspondence between s-fold and standard computation.
Observed Long-Term Trends for Agroclimatic Conditions in Canada
Authors: Qian Budong , Zhang Xuebin , Chen Kai , Feng Yang , O’Brien Ted 
Published: December 2009

Abstract
A set of agroclimatic indices representing Canadian climatic conditions for field crop production are analyzed for long-term trends during 1895–2007. The indices are categorized for three crop types: cool season, warm season, and overwintering. Results indicate a significant lengthening of the growing season due to a significantly earlier start and a significantly later end of the growing season. Significant positive trends are also observed for effective growing degree-days and crop heat units at most locations across the country. The occurrence of extremely low temperatures has become less frequent during the nongrowing season, implying a more favorable climate for overwinter survival. In addition, the total numbers of cool days, frost days, and killing-frost days within a growing season have a decreasing trend. This means that crops may also be less vulnerable to cold stress and injury during the growing season. Extreme daily precipitation amounts and 10-day precipitation totals during the growing season have been increasing. Significant trends associated with increased availability of water during the growing season are identified by the standardized precipitation index and seasonal water deficits. The benefit of the increased precipitation may have been offset by an upward trend in evaporative demand; however, this would depend on the amount of growth and productivity resulting from increased actual evapotranspiration.
Structure and Mechanisms of the Southern Hemisphere Summertime Subtropical Anticyclones
Authors: Miyasaka Takafumi , Nakamura Hisashi 
Published: December 2009

Abstract
The three-dimensional structure and dynamics of the climatological-mean summertime subtropical anticyclones in the Southern Hemisphere (SH) are investigated. As in the Northern Hemisphere (NH), each of the surface subtropical anticyclones over the South Pacific, South Atlantic, and South Indian Oceans is accompanied by a meridional vorticity dipole aloft, exhibiting barotropic and baroclinic structures in its poleward and equatorward portions, respectively, in a manner that is dynamically consistent with the observed midtropospheric subsidence. Their dynamics are also similar to their NH counterpart. It is demonstrated through the numerical experiments presented here that each of the SH surface anticyclones observed over the relatively cool eastern oceans can be reproduced as a response to a local near-surface cooling–heating couplet. The cooling is mainly due to radiative cooling associated with low-level maritime clouds, and the heating to the east is due to sensible heat flux over the dry, heated continental surface. The low-level clouds act to maintain the coolness of the underlying ocean surface, which is also maintained by the alongshore surface southerlies. As in the NH, the presence of a local atmosphere–ocean–land feedback loop is thus suggested, in which the summertime subtropical anticyclones and continental cyclones to their east are involved. Both the model experiments conducted here and the diagnosed upward flux of Rossby wave activity suggest that, in addition to continental deep convective heating, the land–sea heating–cooling contrasts across the west coasts of the three continents can contribute to the formation of the summertime upper-level planetary wave pattern observed in the entire subtropical SH, characterized by the zonal wavenumber-3 component. Though rather subtle, there are some interhemispheric differences in the summertime subtropical anticyclones, including their smaller magnitudes in the SH and the stronger equatorward propagation of upper-level Rossby wave activity emanating from the SH surface anticyclones.
Changes in the Risk of Cool-Season Tornadoes over Southern Australia due to Model Projections of Anthropogenic Warming
Authors: Timbal B. , Kounkou R. , Mills G. A. 
Published: December 2009

Abstract
Anthropogenic climate change is likely to be felt most acutely through changes in the frequency of extreme meteorological events. However, quantifying the impact of climate change on these events is a challenge because the core of the climate change science relies on general circulation models to detail future climate projections, and many of these extreme events occur on small scales that are not resolved by climate models. This note describes an attempt to infer the impact of climate change on one particular type of extreme meteorological event—the cool-season tornadoes of southern Australia. The Australian Bureau of Meteorology predicts threat areas for cool-season tornadoes using fine-resolution numerical weather prediction model output to define areas where the buoyancy of a near-surface air parcel and the vertical wind shear each exceed specified thresholds. The diagnostic has been successfully adapted to coarser-resolution climate models and applied to simulations of the current climate, as well as future projections of the climate over southern Australia. Simulations of the late twentieth century are used to validate the models’ ability to reproduce the climatology of the risk of cool-season tornado formation by comparing these with similar computations based on historical reanalyses. Model biases are overcome by setting model specific thresholds to define the cool-season tornado risk. The diagnostic, applied to simulations of the twenty-first century, is then used to quantify the impact of the projected climate change on cool-season tornado risk. The sign of the response is consistent across all models: a decrease of the risk of formation during the twenty-first century is projected, driven by the thermodynamical response. The thermal response is modulated by the dynamical response, which varies between models. The projected decrease in tornadoes risk during the cool season is consistent with the projection of positive southern annular mode trends and the known influence of this mode of variability on interannual to intraseasonal time-scale variations in cool-season tornado occurrence.
Pharmacokinetics of vancomycin in adult cancer patients
Authors: Al-Kofide Hadeel , Zaghloul Iman , Al-Naim Lamya 
Published: December 2009

Background and Objectives. Gram-positive infections are prevalent among cancer patients and vancomycin therapy is often initiated empirically. A typical vancomycin pharmacokinetics is observed in such patients. The aim of the study was to evaluate the pharmacokinetics of vancomycin in this patient population and compare it to that of normal population. Method and Results. The pharmacokinetics of vancomycin was examined retrospectively in two groups of patients — 18 cancer patients (age 43.4 ± 22.1 years) and 13 patients without cancer (age 48.5 ± 20.2 years). Following the administration of intermittent intravenous infusion of 15 mg/kg of vancomycin, peak and trough vancomycin serum concentration were determined after the third dose or at steady state as per standard of care. Vancomycin data were analyzed according to a one-compartment open model. Pharmacokinetic parameters such as clearance (CL), volume of distribution (Vd), and K elimination (ke) were calculated. Both Vd and CL were significantly higher in the cancer group (Mean Vd was 70 ± 45 L in the cancer group and 31.1 ± 8.3 L in the noncancer group, p-value 0.002; CL mean was 110.1 ± 42 mL/min in the cancer group and 71.2 ± 22.2 mL/min in the noncancer group, p-value 0.005). There was no significant difference in K elimination and half-life (t1/2). Conclusion. Cancer patients may require higher than usual dosing regimens to ensure optimal therapeutic concentrations, since vancomycin CL and Vd is significantly higher in these patients, a dosing schedule as high as 60 mg/kg/day may be needed for cancer patients.
Fetal hemoglobin in sickle cell anemia: genome-wide association studies suggest a regulatory region in the 5′ olfactory receptor gene cluster
Authors: Solovieff Nadia , Milton Jacqueline N. , Hartley Stephen W. , Sherva Richard , Sebastiani Paola , Dworkis Daniel A. , Klings Elizabeth S. , Farrer Lindsay A. , Garrett Melanie E. , Ashley-Koch Allison , Telen Marilyn J. , Fucharoen Supan , Ha Shau Yin , Li Chi-Kong , Chui David H. K. , Baldwin Clinton T. , Steinberg Martin H. 
Published: December 2009

AbstractIn a genome-wide association study of 848 blacks with sickle cell anemia, we identified single nucleotide polymorphisms (SNPs) associated with fetal hemoglobin concentration. The most significant SNPs in a discovery sample were tested in a replication set of 305 blacks with sickle cell anemia and in subjects with hemoglobin E or β thalassemia trait from Thailand and Hong Kong. A novel region on chromosome 11 containing olfactory receptor genes OR51B5 and OR51B6 was identified by 6 SNPs (lowest P = 4.7E−08) and validated in the replication set. An additional olfactory receptor gene, OR51B2, was identified by a novel SNP set enrichment analysis. Genome-wide association studies also validated a previously identified SNP (rs766432) in BCL11A, a gene known to affect fetal hemoglobin levels (P = 2.6E−21) and in Thailand and Hong Kong subjects. Elements within the olfactory receptor gene cluster might play a regulatory role in γ-globin gene expression.
Global transcriptional response after exposure of fission yeast cells to ultraviolet light
Authors: Skjølberg Henriette C , Fensgård Øyvind , Nilsen Hilde , Grallert Beáta , Boye Erik 
Published: December 2009

AbstractBackgroundIn many cell types, including the fission yeastSchizosaccharomyces pombe, a set of checkpoints are induced by perturbations of the cell cycle or by DNA damage. Many of the checkpoint responses include a substantial change of the transcriptional pattern. As part of characterising a novel G1/S checkpoint in fission yeast we have investigated whether a transcriptional response is induced after irradiation with ultraviolet light.ResultsMicroarray analyses were used to measure the global transcription levels of all open reading frames of fission yeast after 254 nm ultraviolet irradiation, which is known to induce a G1/S checkpoint. We discovered a surprisingly weak transcriptional response, which is quite unlike the marked changes detected after some other types of treatment and in several other checkpoints. Interestingly, the alterations in gene expression after ultraviolet irradiation were not similar to those observed after ionising radiation or oxidative stress. Pathway analysis suggests that there is little systematic transcriptional response to the irradiation by ultraviolet light, but a marked, coordinated transcriptional response was noted on progression of the cells from G1 to S phase.ConclusionThere is little response in fission yeast to ultraviolet light at the transcriptional level. Amongst the genes induced or repressed after ultraviolet irradiation we found none that are likely to be involved in the G1/S checkpoint mechanism, suggesting that the checkpoint is not dependent upon transcriptional regulation.
Evidence that phosphatidylinositol 3-kinase is involved in sperm-induced tyrosine kinase signaling in Xenopus egg fertilization
Authors: Mammadova Gunay , Iwasaki Tetsushi , Tokmakov Alexander A , Fukami Yasuo , Sato Ken-ichi 
Published: December 2009

Abstract

Background
Studies have examined the function of PI 3-kinase in the early developmental processes that operate in oocytes or early embryos of various species. However, the roles of egg-associated PI 3-kinase and Akt, especially in signal transduction at fertilization, are not well understood.

Results
Here we show that in Xenopus eggs, a potent inhibitor of phosphatidylinositol 3-kinase (PI 3-kinase), LY294002 inhibits sperm-induced activation of the tyrosine kinase Src and a transient increase in the intracellular concentration of Ca2+ at fertilization. LY294002 also inhibits sperm-induced dephosphorylation of mitogen-activated protein kinase, breakdown of cyclin B2 and Mos, and first embryonic cleavage, all of which are events of Ca2+-dependent egg activation. In fertilized eggs, an 85-kDa subunit of PI 3-kinase (p85) undergoes a transient translocation to the low-density, detergent-insoluble membranes (membrane microdomains) where Src tyrosine kinase signaling is operating. However, the tyrosine phosphorylation of p85 in fertilized eggs is not as evident as that in H2O2-activated eggs, arguing against the possibility that PI 3-kinase is activated by Src phosphorylation. Nevertheless, sperm-induced activation of PI 3-kinase has been demonstrated by the finding that Akt, a serine/threonine-specific protein kinase, is phosphorylated at threonine-308. The threonine-phosphorylated Akt also localizes to the membrane microdomains of fertilized eggs. Application of bp(V), an inhibitor of PTEN that dephosphorylates PIP3, the enzymatic product of PI 3-kinase, promotes parthenogenetic activation of Xenopus eggs. In vitro kinase assays demonstrate that PIP3 activates Src in a dose-dependent manner.

Conclusions
These results suggest that PI 3-kinase is involved in sperm-induced egg activation via production of PIP3 that would act as a positive regulator of the Src signaling pathway in Xenopus fertilization.
Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers
Authors: Krogius-Kurikka Lotta , Lyra Anna , Malinen Erja , Aarnikunnas Johannes , Tuimala Jarno , Paulin Lars , Mäkivuokko Harri , Kajander Kajsa , Palva Airi 
Published: December 2009

Abstract

Background
A growing amount of scientific evidence suggests that microbes are involved in the aetiology of irritable bowel syndrome (IBS), and the gastrointestinal (GI) microbiota of individuals suffering from diarrhoea-predominant IBS (IBS-D) is distinguishable from other IBS-subtypes. In our study, the GI microbiota of IBS-D patients was evaluated and compared with healthy controls (HC) by using a high-resolution sequencing method. The method allowed microbial community analysis on all levels of microbial genomic guanine plus cytosine (G+C) content, including high G+C bacteria.

Methods
The collective faecal microbiota composition of ten IBS-D patients was analysed by examining sequences obtained using percent G+C (%G+C) -based profiling and fractioning combined with 16S rRNA gene clone library sequencing of 3267 clones. The IBS-D library was compared with an analogous healthy-control library of 23 subjects. Real-time PCR analysis was used to identify phylotypes belonging to the class Gammaproteobacteria and the order Coriobacteriales.

Results
Significant differences were found between clone libraries of IBS-D patients and controls. The microbial communities of IBS-D patients were enriched in Proteobacteria and Firmicutes, but reduced in the number of Actinobacteria and Bacteroidetes compared to control. In particular, 16S rDNA sequences belonging to the family Lachnospiraceae within the phylum Firmicutes were in greater abundance in the IBS-D clone library.

Conclusions
In the microbiota of IBS-D sufferers, notable differences were detected among the prominent bacterial phyla (Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria) localized within the GI tract.
Early severe morbidity and resource utilization in South African adults on antiretroviral therapy
Authors: de Cherif Teresa K Smith , Schoeman Jan H , Cleary Susan , Meintjes Graeme A , Rebe Kevin , Maartens Gary 
Published: December 2009

AbstractBackgroundHigh rates of mortality and morbidity have been described in sub-Saharan African patients within the first few months of starting highly active antiretroviral therapy (HAART). There is limited data on the causes of early morbidity on HAART and the associated resource utilization.MethodsA cross-sectional study was conducted of medical admissions at a secondary-level hospital in Cape Town, South Africa. Patients on HAART were identified from a register and HIV-infected patients not on HAART were matched by gender, month of admission, and age group to correspond with the first admission of each case. Primary reasons for admission were determined by chart review. Direct health care costs were determined from the provider's perspective.ResultsThere were 53 in the HAART group with 70 admissions and 53 in the no-HAART group with 60 admissions. The median duration of HAART was 1 month (interquartile range 1-3 months). Median baseline CD4 count in the HAART group was 57 × 106cells/L (IQR 15-115). The primary reasons for admission in the HAART group were more likely to be due to adverse drug reactions and less likely to be due to AIDS events than the no-HAART group (34% versus 7%; p < 0.001 and 39% versus 63%; p = 0.005 respectively). Immune reconstitution inflammatory syndrome was the primary reason for admission in 10% of the HAART group. Lengths of hospital stay per admission and inpatient survival were not significantly different between the two groups. Five of the 15 deaths in the HAART group were due to IRIS or adverse drug reactions. Median costs per admission of diagnostic and therapeutic services (laboratory investigations, radiology, intravenous fluids and blood, and non-ART medications) were higher in the HAART group compared with the no-HAART group (US$190 versus US$111; p = 0.001), but the more expensive non-curative costs (overhead, capital, and clinical staff) were not significantly different (US$1199 versus US$1128; p = 0.525).ConclusionsCauses of early morbidity are different and more complex in HIV-infected patients on HAART. This results in greater resource utilization of diagnostic and therapeutic services.
The neck-region polymorphism of DC-SIGNR in peri-centenarian from Han Chinese Population
Authors: Li Hui , Wang Cheng-Ye , Wang Jia-Xin , Tang Nelson Leung-Sang , Xie Liang , Gong Yuan-Ying , Yang Zhao , Xu Liang-You , Kong Qing-Peng , Zhang Ya-Ping 
Published: December 2009

AbstractBackgroundDC-SIGNR (also called CD209L) has been extensively studied on its role in host genetic predisposition to viral infection. In particular, variable number tandem repeat (VNTR) of the neck-region of DC-SIGNR is highly polymorphic and the polymorphism has been investigated for genetic predisposition to various infectious diseases, though conflicting results had been reported. As infection is a major cause of human death and a mechanism of natural selection, we hypothesized that VNTR polymorphism of DC-SIGNR might have an effect on human life span.MethodsHere we collected 361 peri-centenarian individuals (age ≥94 for female and age ≥90 for male) and 342 geographically matched controls (age 22-53, mean 35.0 ± 12.0) from Han Chinese. The VNTR polymorphism of the neck region was determined by PCR and genotype was called by separating the PCR products in agarose gel.ResultsA total of 11 genotypes and 5 alleles were found in our population. The genotype distribution, allele frequencies and homozygote proportion did not show a significant difference between peri-centenarian and control group. As gender differences in lifespan are ubiquitously observed throughout the animal kingdom, we then stratified the samples by gender. There was more 6/7 genotypes in female peri-centenarian group than that in female control group, at a marginal level of significance (5.56 vs. 1.28%, p = 0.041). The difference was not significant after correction by Bonferroni method. It suggests a possible differential effect of DC-SIGNR VNTR genotypes between sexes. Further studies are warranted to confirm our preliminary findings and investigate the mechanisms of the underlying functions.ConclusionsOur study indicated that there was absence of association between the neck region polymorphism of DC-SIGNR and longevity in Han Chinese population. But the question of whether the DC-SIGNR could affect longevity in a gender-specific pattern remains open.
Rapid detection of SMARCB1 sequence variation using high resolution melting
Authors: Dagar Vinod , Chow Chung-Wo , Ashley David M , Algar Elizabeth M 
Published: December 2009

Abstract

Background
Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1.

Methods
Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes.

Results
The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue.

Conclusions
This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening.