bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and dynamics of rare and of resident bacterial populations in coastal sands
Authors: Gobet Angélique , Böer Simone I , Huse Susan M , van Beusekom Justus E E , Quince Christopher , Sogin Mitchell L , Boetius Antje , Ramette Alban 
Published: October 2011

Abstract
Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities.
The Presequence of Arabidopsis Serine Hydroxymethyltransferase SHM2 Selectively Prevents Import into Mesophyll Mitochondria
Authors: Engel Nadja , Ewald Ralph , Gupta Kapuganti J. , Zrenner Rita , Hagemann Martin , Bauwe Hermann 
Published: October 2011

Abstract
Serine hydroxymethyltransferases (SHMs) are important enzymes of cellular one-carbon metabolism and are essential for the photorespiratory glycine-into-serine conversion in leaf mesophyll mitochondria. In Arabidopsis (Arabidopsis thaliana), SHM1 has been identified as the photorespiratory isozyme, but little is known about the very similar SHM2. Although the mitochondrial location of SHM2 can be predicted, some data suggest that this particular isozyme could be inactive or not targeted into mitochondria. We report that SHM2 is a functional mitochondrial SHM. In leaves, the presequence of SHM2 selectively hinders targeting of the enzyme into mesophyll mitochondria. For this reason, the enzyme is confined to the vascular tissue of wild-type Arabidopsis, likely the protoxylem and/or adjacent cells, where it occurs together with SHM1. The resulting exclusion of SHM2 from the photorespiratory environment of mesophyll mitochondria explains why this enzyme cannot substitute for SHM1 in photorespiratory metabolism. Unlike the individual shm1 and shm2 null mutants, which require CO2-enriched air to inhibit photorespiration (shm1) or do not show any visible impairment (shm2), double-null mutants cannot survive in CO2-enriched air. It seems that SHM1 and SHM2 operate in a redundant manner in one-carbon metabolism of nonphotorespiring cells with a high demand of one-carbon units; for example, during lignification of vascular cells. We hypothesize that yet unknown kinetic properties of SHM2 might render this enzyme unsuitable for the high-folate conditions of photorespiring mesophyll mitochondria.
Evaluation of Spermiation Indices with Multiple Sperm Collections in Endangered Sterlet (Acipenser ruthenus)
Authors: Shaliutina A , Dzyuba B , Hulak M , Boryshpolets S , Li P , Linhart O 
Published: October 2011

ContentsThis study investigated the effects of multiple collections of sperm on endangered sterlet (Acipenser ruthenus) sperm functional parameters [spermatozoa motility and curvilinear velocity (VCL)] as well as on protein concentration and osmolality of seminal plasma. The average sperm volume and mean spermatozoa concentration per male were significantly altered with multiple collections. On the other hand, no significant effect of multiple collections on protein concentration of seminal plasma was observed. In all experimental groups, moderate impact of sequential collection on osmolality (p < 0.05) of seminal plasma was observed. Ninety to 100% of motile spermatozoa were observed at 15 s after activation, with an average VCL of 181.12 ± 19.10 μm/s. After 90 s, average VCL decreased to 130 ± 26 μm/s. Motility was maintained for up to 4 min. The maximum percentage of motile spermatozoa was observed after the third collection of sperm. The spermatozoa VCL increased significantly with subsequent collections. The results of this study provide new data on the effects of multiple collections on quantitative and qualitative parameters of sperm in sterlet. The data confirmed that the sequential stripping has no negative effect on the percentage of motility and spermatozoa velocity. This should be beneficial for the development of sterlet aquaculture programs.
Poor numeracy skills are associated with glycaemic control in Type 1 diabetes
Authors: Marden S. , Thomas P. W. , Sheppard Z. A. , Knott J. , Lueddeke J. , Kerr D. 
Published: October 2011

Diabet. Med. 29, 662–669 (2012)AbstractAims  To assess the numeracy and literacy skills of individuals with Type 1 diabetes and determine if there is a relationship with achieved glycaemic control independent of their duration of diabetes, diabetes education, demographic and socio‐economic factors.Methods  One hundred and twelve patients completed the study (mean current age 43.8 ± 12.5 years, 47% male, mean duration of diabetes 22.0 ± 13.2 years) out of 650 randomly selected patients from the Bournemouth Diabetes and Endocrine Centre’s diabetes register. The Skills for Life Initial Assessments were used to measure numeracy and literacy. These indicate skills levels up to level 2, equivalent to the national General Certificate of Secondary Education grades A*–C. HbA1c was also measured. Pearson’s correlation was used to measure the correlation of numeracy and literacy scores with HbA1c. To compare mean HbA1c between those with or without level 2 skills, t‐tests were used, and multiple linear regression was used to investigate whether any differences were independent of duration of diabetes, diabetes education, demographic and socio‐economic factors.Results  Literacy was not associated with achieved HbA1c. In contrast, participants with numeracy skills at level 2 or above achieved an HbA1c lower than those with numeracy skills below level 2 (P = 0.027). Although higher socio‐economic status was associated with lower mean HbA1c, the relationship between numeracy and HbA1c appeared to be independent of socio‐economic factors.Conclusions  Low numeracy skills were adversely associated with diabetes control. Assessment of numeracy skills may be relevant to the structure of diabetes education programmes.
The nursing hypothesis: An evolutionary account of emotional modulation of the postauricular reflex
Authors: Johnson Gabriella M. , Valle‐Inclán Fernando , Geary David C. , Hackley Steven A. 
Published: October 2011

AbstractThe postauricular reflex (PAR) is anomalous because it seems to be potentiated during positive emotions and inhibited during negative states, unlike eyeblink and other components of the startle reflex. Two evolutionary explanations based on simian facial emotion expressions were tested. Reflexes were elicited while 47 young adult volunteers made lip pursing or grimacing poses and viewed neutral, intimidating, or appetitive photos. The PAR was enhanced during appetitive slides, but only as subjects carried out the lip‐pursing maneuver. These results support the nursing hypothesis, which assumes that infant mammals instinctively retract their pinnae while nursing in order to comfortably position the head. Appetitive emotions prime the ear‐retraction musculature, even in higher primates whose postauricular muscles are vestigial.
The ‘gating’ residues Ile199 and Tyr326 in human monoamine oxidase B function in substrate and inhibitor recognition
Authors: Milczek Erika M. , Binda Claudia , Rovida Stefano , Mattevi Andrea , Edmondson Dale E. 
Published: October 2011

The major structural difference between human monoamine oxidases A (MAO A) and B (MAO B) is that MAO A has a monopartite substrate cavity of ∼ 550 Å3 volume and MAO B contains a dipartite cavity structure with volumes of ∼ 290 Å3 (entrance cavity) and ∼ 400 Å3 (substrate cavity). Ile199 and Tyr326 side chains separate these two cavities in MAO B. To probe the function of these gating residues, Ile199Ala and Ile199Ala‐Tyr326Ala mutant forms of MAO B were investigated. Structural data on the Ile199Ala MAO B mutant show no alterations in active site geometries compared with wild‐type enzyme while the Ile199Ala‐Tyr326Ala MAO B mutant exhibits alterations in residues 100–103 which are part of the loop gating the entrance to the active site. Both mutant enzymes exhibit catalytic properties with increased amine KM but unaltered kcat values. The altered KM values on mutation are attributed to the influence of the cavity structure in the binding and subsequent deprotonation of the amine substrate. Both mutant enzymes exhibit weaker binding affinities relative to wild‐type enzyme for small reversible inhibitors. Ile199Ala MAO B exhibits an increase in binding affinity for reversible MAO B specific inhibitors which bridge both cavities. The Ile199Ala‐Tyr326Ala double mutant exhibits inhibitor binding properties more similar to those of MAO A than to MAO B. These results demonstrate that the bipartite cavity structure in MAO B plays an important role in substrate and inhibitor recognition to distinguish its specificities from those of MAO A and provide insights into specific reversible inhibitor design for these membrane‐bound enzymes.DatabaseThe atomic coordinates and structural factors of the structure of human MAO B Ile199Ala‐Tyr326Ala double mutant have been deposited in the Protein Data Bank under the accession number 3zyx.
Galactomannan Antigenemia after Infusion of Gluconate-Containing Plasma-Lyte
Authors: Petraitiene Ruta , Petraitis Vidmantas , Witt John R. , Durkin Michelle M. , Bacher John D. , Wheat L. Joseph , Walsh Thomas J. 
Published: October 2011

ABSTRACT

We demonstrated that sodium gluconate was the factor causing false-positive galactomannan (GM) antigenemia of Plasma-Lyte hydration solution. Infusion of sodium gluconate-containing solution but not gluconate-free Plasma-Lyte resulted in positive serum GM antigenemia. Serum GM concentrations also correlated with the volume and
in vitro
concentrations of GM within gluconate-containing solutions of infused Plasma-Lyte.
Multiplex PCR Method for Detection of Clostridium difficile tcdA,
tcdB
,
cdtA
, and
cdtB
and Internal In-Frame Deletion of
tcdC
Authors: Persson Søren , Jensen Joan N. , Olsen Katharina E. P. 
Published: October 2011

ABSTRACT

A multiplex PCR method was developed for the detection of
Clostridium difficile
toxin genes
tcdA
,
tcdB
,
ctdA
, and
cdtB
and the major in-frame deletion types (18, 39, and 54 bp) of
tcdC
. The method has high specificity for PCR ribotype 027 and may identify other
C
.
difficile
strains of clinical and epidemiological importance.
Genomic Analysis of the Vaccinia Virus Strain Variants Found in Dryvax Vaccine
Authors: Qin Li , Upton Chris , Hazes Bart , Evans David H. 
Published: October 2011

ABSTRACT
Smallpox was eradicated using variant forms of vaccinia virus-based vaccines. One of these was Dryvax, a calf lymph vaccine derived from the New York City Board of Health strain. We used genome-sequencing technology to examine the genetic diversity of the population of viruses present in a sample of Dryvax. These studies show that the conserved cores of these viruses exhibit a lower level of sequence variation than do the telomeres. However, even though the ends of orthopoxviruses are more genetically plastic than the cores, there are still many telomeric genes that are conserved as intact open reading frames in the 11 genomes that we, and 4 genomes that others, have sequenced. Most of these genes likely modulate inflammation. Our sequencing also detected an evolving pattern of mutation, with some genes being highly fragmented by randomly assorting mutations (e.g., M1L), while other genes are intact in most viruses but have been disrupted in individual strains (e.g., I4L in strain DPP17). Over 85% of insertion and deletion mutations are associated with repeats, and a rare new isolate bearing a large deletion in the right telomere was identified. All of these strains cluster in dendrograms consistent with their origin but which also surprisingly incorporate horsepox virus. However, these viruses also exhibit a “patchy” pattern of polymorphic sites characteristic of recombinants. There is more genetic diversity detected within a vial of Dryvax than between variola virus major and minor strains, and our study highlights how propagation methods affect the genetics of orthopoxvirus populations.
Concentrations of IGF-I and IGFBP-3 and Brain Tumor Risk in the European Prospective Investigation into Cancer and Nutrition
Authors: Rohrmann Sabine , Linseisen Jakob , Becker Susen , Allen Naomi , Schlehofer Brigitte , Overvad Kim , Olsen Anja , Tjønneland Anne , Melin Beatrice S. , Lund Eiliv , Vineis Paolo , Grioni Sara , Tumino Rosario , Palli Domenico , Mattiello Amalia , Bonet Catalina , Chirlaque Maria-Dolores , Sánchez María-José , Rodríguez Laudina , Dorronsoro Miren , Ardanaz Eva , Lagiou Pagona , Trichopoulou Antonia , Trichopoulos Dimitrios , Dossus Laure , Grote Verena A. , Boeing Heiner , Aleksandrova Krasimira , Bueno-de-Mesquita H. Bas , van Duijnhoven Fränzel J.B. , Peeters Petra H.M. , Khaw Kay-Tee , Wareham Nicholas J. , Key Timothy J. , Rinaldi Sabina , Romieux Isabelle , Gallo Valentina , Michaud Dominique S. , Riboli Elio , Kaaks Rudolf 
Published: October 2011

AbstractBackground: Insulin-like growth factor-1 (IGF-I) is important in normal brain development but in the adult brain, IGF-I overexpression may be a risk factor for tumor development.Methods: We examined the association between circulating concentrations of IGF-I and IGFBP-3 in relation to risk of gliomas (74 low-grade, 206 high-grade gliomas), meningiomas (n = 174) and acoustic neuromas (n = 49) by using a case–control design nested in the European Prospective Investigation into Cancer and Nutrition. IGF-I and IGFBP-3 were measured by ELISAs.Conditional logistic regression was used to compute ORs and corresponding 95% CIs.Results: The risk of low-grade gliomas was elevated with increased IGF-I (OR = 3.60, 95% CI: 1.11–11.7; top vs. bottom quartile) and decreased with elevated IGFBP-3 concentrations (OR = 0.28, 95% CI: 0.09–0.84) after mutual adjustment of these two factors; these results became nonsignificant after exclusion of the first year of follow-up. No association was observed for high-grade gliomas or meningiomas. Both high IGF-I and IGFBP-3 concentrations were associated with risk of acoustic neuromas (IGF-I: OR = 6.63, 95% CI: 2.27–19.4, top vs. bottom tertile; IGFBP-3: OR = 7.07, 95% CI: 2.32–21.6), even after excluding the first year of follow-up.Conclusion: High concentrations of IGF-I might be positively associated with risk of low-grade gliomas and acoustic neuromas, although we cannot exclude reverse causation, in particular for low-grade gliomas.Impact: Factors of the IGF axis might be involved in the etiology of some types of brain tumors. Cancer Epidemiol Biomarkers Prev; 20(10); 2174–82. ©2011 AACR.
Inflammation, Focal Atrophic Lesions, and Prostatic Intraepithelial Neoplasia with Respect to Risk of Lethal Prostate Cancer
Authors: Davidsson Sabina , Fiorentino Michelangelo , Andrén Ove , Fang Fang , Mucci Lorelei A. , Varenhorst Eberhard , Fall Katja , Rider Jennifer R. 
Published: October 2011

Abstract
Background: A challenge in prostate cancer (PCa) management is identifying potentially lethal disease at diagnosis. Inflammation, focal prostatic atrophy, and prostatic intraepithelial neoplasia (PIN) are common in prostate tumor specimens, but it is not clear whether these lesions have prognostic significance.
Methods: We conducted a case–control study nested in a cohort of men diagnosed with stage T1a-b PCa through transurethral resection of the prostate in Sweden. Cases are men who died of PCa (n = 228). Controls are men who survived more than 10 years after PCa diagnosis without metastases (n = 387). Slides were assessed for Gleason grade, inflammation, PIN, and four subtypes of focal prostatic atrophy: simple atrophy (SA), postatrophic hyperplasia (PAH), simple atrophy with cyst formation, and partial atrophy. We estimated OR and 95% CI for odds of lethal PCa with multivariable logistic regression.
Results: Chronic inflammation and PIN were more frequently observed in tumors with PAH, but not SA. No specific type of atrophy or inflammation was significantly associated with lethal PCa overall, but there was a suggestion of a positive association for chronic inflammation. Independent of age, Gleason score, year of diagnosis, inflammation, and atrophy type, men with PIN were 89% more likely to die of PCa (95% CI: 1.04–3.42).
Conclusion: Our data show that PIN, and perhaps presence of moderate or severe chronic inflammation, may have prognostic significance for PCa.
Impact: Lesions in tumor adjacent tissue, and not just the tumor itself, may aid in identification of clinically relevant disease. Cancer Epidemiol Biomarkers Prev; 20(10); 2280–7. ©2011 AACR.
Population Sciences, Translational Research, and the Opportunities and Challenges for Genomics to Reduce the Burden of Cancer in the 21st Century
Authors: Khoury Muin J. , Clauser Steven B. , Freedman Andrew N. , Gillanders Elizabeth M. , Glasgow Russ E. , Klein William M.P. , Schully Sheri D. 
Published: October 2011

Abstract
Advances in genomics and related fields are promising tools for risk assessment, early detection, and targeted therapies across the entire cancer care continuum. In this commentary, we submit that this promise cannot be fulfilled without an enhanced translational genomics research agenda firmly rooted in the population sciences. Population sciences include multiple disciplines that are needed throughout the translational research continuum. For example, epidemiologic studies are needed not only to accelerate genomic discoveries and new biological insights into cancer etiology and pathogenesis, but to characterize and critically evaluate these discoveries in well-defined populations for their potential for cancer prediction, prevention and response to treatment. Behavioral, social, and communication sciences are needed to explore genomic-modulated responses to old and new behavioral interventions, adherence to therapies, decision making across the continuum, and effective use in health care. Implementation science, health services, outcomes research, comparative effectiveness research, and regulatory science are needed for moving validated genomic applications into practice and for measuring their effectiveness, cost-effectiveness, and unintended consequences. Knowledge synthesis, evidence reviews, and economic modeling of the effects of promising genomic applications will facilitate policy decisions and evidence-based recommendations. Several independent and multidisciplinary panels have recently made specific recommendations for enhanced research and policy infrastructure to inform clinical and population research for moving genomic innovations into the cancer care continuum. An enhanced translational genomics and population sciences agenda is urgently needed to fulfill the promise of genomics in reducing the burden of cancer. Cancer Epidemiol Biomarkers Prev; 20(10); 2105–14. ©2011 AACR.
Common Genetic Variants in the Vitamin D Pathway Including Genome-Wide Associated Variants Are Not Associated with Breast Cancer Risk among Chinese Women
Authors: Dorjgochoo Tsogzolmaa , Delahanty Ryan , Lu Wei , Long Jirong , Cai Qiuyin , Zheng Ying , Gu Kai , Gao Yu-Tang , Zheng Wei , Shu Xiao Ou 
Published: October 2011

Abstract
Background: Previous studies evaluating the association of vitamin D–related genetic variants with breast cancer risk have produced inconsistent results.
Methods: We evaluated the association between breast cancer risk and 559 single-nucleotide polymorphisms (SNP) in 12 vitamin D–related genes, including 6 genes associated with circulating 25-hydroxyvitamin D [25(OH)D] level identified by recent genome-wide association studies (GWAS), using directly observed and imputed GWAS genotyping data from 2,919 breast cancer cases and 2,323 controls recruited in the Shanghai Breast Cancer Study.
Results: Of the SNPs studied, only rs12570116 in the ACADSB gene, rs4760658 in the VDR gene and rs6091822, rs8124792, and rs6097809 in the CYP24A1 gene, and rs10902845 in C10orf88 had a nominal association with breast cancer risk (P &lt; 0.05 for all). None of these associations persisted after adjustment for multiple comparisons. The most extensively studied SNPs including rs10735810, also known as rs2228570 (Fok1, VDR), rs1544410 (Bsm1, VDR), and rs2296241 (CYP24A1), were not associated with breast cancer risk. GWAS-identified genetic variants that were associated with 25(OH)D were also not related to breast cancer risk.
Conclusions: Our data suggest that genetic polymorphisms in vitamin D–related genes do not play a major role in breast cancer risk in Chinese women.
Impact: Although our study confirms previously documented breast cancer risk factor associations, our null results suggest that common genetic variants in vitamin D genes and loci associated with control of vitamin D levels are not risk factors for breast cancer in Chinese women. Our data contribute to filling the gap in this field of research. Cancer Epidemiol Biomarkers Prev; 20(10); 2313–6. ©2011 AACR.
Cancer Survivors: A Booming Population
Authors: Parry Carla , Kent Erin E. , Mariotto Angela B. , Alfano Catherine M. , Rowland Julia H. 
Published: October 2011

Abstract
Background: In this first article of what is planned to be an annual series, we examine the history of cancer prevalence reporting and the role that these annual figures play in guiding the direction of cancer control research, and specifically the science of cancer survivorship. For this inaugural year, we focus on the confluence of the growing number of survivors and population aging, and the impact these combined trends will have on cancer survivorship in the future.
Methods: State or metro area-level cancer incidence and prevalence data were collected from 9 registries via the Surveillance, Epidemiology, and End Results Program. The complete prevalence method was used to estimate prevalence for 2008 and the Prevalence, Incidence Approach Model method was used to project prevalence data through 2020, assuming flat cancer incidence and survival trends but dynamic U.S. population projections.
Results: As of January 2008, the number of cancer survivors is estimated at 11.9 million. Approximately 60% of cancer survivors are age 65 or older, and by the year 2020, it is estimated that 63% of cancer survivors will be age 65 or older.
Conclusions: Improved survival and population aging converge to generate a booming population of older adult cancer survivors, many of whom have multiple complex health conditions and unique survivorship needs. This demographic shift has important implications for future health care needs and costs of the U.S. population.
Impact: The findings provide information critical for guiding cancer prevention and control research and service provision. Cancer Epidemiol Biomarkers Prev; 20(10); 1996–2005. ©2011 AACR.