bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila
topo IIIα is required for the maintenance of mitochondrial genome and male germ-line stem cells
Authors: Wu Jianhong , Feng Liping , Hsieh Tao-shih 
Published: March 2010

Topoisomerase IIIα (topo IIIα), a member of the conserved Type IA subfamily of topoisomerases, is required for the cell proliferation in mitotic tissues, but has a lesser effect on DNA endoreplication. The
top3α
gene encodes two forms of protein by utilizing alternative translation initiation sites: one (short form) with the nuclear localization signal only, exclusively localized in the nuclei, and the other (long form), retaining a mitochondrial import sequence at the N-terminus and the nuclear localization sequence at the C-terminus, localized primarily in the mitochondria, though with a small portion in the nuclei. Both forms of topo IIIα can rescue the viability of null mutants of
top3α
. No apparent defect is associated with the flies rescued by the long form; short-form-rescued flies (referred to as
M1L
), however, exhibit defects in fertilities.
M1L
females are sterile. They can lay eggs but with mitochondrial DNA (mtDNA) copy number and ATP content decreased by 20- and 2- to 3-fold, respectively, and they fail to hatch. Of the newly eclosed
M1L
males, 33% are completely sterile, whereas the rest have residual fertilities that are quickly lost in 6 days. The fertility loss of
M1L
males is caused by the disruption of the individualization complex and a progressive loss of germ-line stem cells. This study implicates topo IIIα in the maintenance of mtDNA and male germ-line stem cells, and thus is a causative candidate for genetic disorders associated with mtDNA depletion.
Tin-containing zeolites are highly active catalysts for the isomerization of glucose in water
Authors: Moliner Manuel , Román-Leshkov Yuriy , Davis Mark E. 
Published: March 2010

The isomerization of glucose into fructose is a large-scale reaction for the production of high-fructose corn syrup (HFCS; reaction performed by enzyme catalysts) and recently is being considered as an intermediate step in the possible route of biomass to fuels and chemicals. Here, it is shown that a large-pore zeolite that contains tin (Sn-Beta) is able to isomerize glucose to fructose in aqueous media with high activity and selectivity. Specifically, a 10% (wt/wt) glucose solution containing a catalytic amount of Sn-Beta (1∶50 Sn:glucose molar ratio) gives product yields of approximately 46% (wt/wt) glucose, 31% (wt/wt) fructose, and 9% (wt/wt) mannose after 30 min and 12 min of reaction at 383 K and 413 K, respectively. This reactivity is achieved also when a 45 wt% glucose solution is used. The properties of the large-pore zeolite greatly influence the reaction behavior because the reaction does not proceed with a medium-pore zeolite, and the isomerization activity is considerably lower when the metal centers are incorporated in ordered mesoporous silica (MCM-41). The Sn-Beta catalyst can be used for multiple cycles, and the reaction stops when the solid is removed, clearly indicating that the catalysis is occurring heterogeneously. Most importantly, the Sn-Beta catalyst is able to perform the isomerization reaction in highly acidic, aqueous environments with equivalent activity and product distribution as in media without added acid. This enables Sn-Beta to couple isomerizations with other acid-catalyzed reactions, including hydrolysis/isomerization or isomerization/dehydration reaction sequences [starch to fructose and glucose to 5-hydroxymethylfurfural (HMF) demonstrated here].
Do the Poor Pay More for Food? Evidence from the United Kingdom
Authors: Beatty Timothy K.M. 
Published: March 2010

AbstractDoes food cost more for low‐income households? This paper compares two well‐known approaches to answering this question. I find that quantity discounts for a broad range of foods are statistically significant and economically important. However quantity discounting does not lead to the poor paying more for food. I find that the poor pay less than average for the food they purchase. This is explained by the poor spending a greater share of their income on foods where quantity discounting occurs.
varLD: a program for quantifying variation in linkage disequilibrium patterns between populations
Authors: Ong Rick Twee-Hee , Teo Yik-Ying 
Published: March 2010

Abstract
Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studies (GWAS). However, such inter-population LD differences can be leveraged to narrow the search for common causal variants responsible for the association signals observed. The ability to assess and quantify LD variations among populations is thus expected to contribute to both replication and fine-mapping stages of GWAS.
Availability: The program varLD is available for download from http://www.nus-cme.org.sg/software/varld.html
Contact: statyy@nus.edu.sg
A comparison of bathymetry mapped with the Simrad ME70 multibeam echosounder operated in bathymetric and fisheries modes
Authors: Cutter George R. , Berger Laurent , Demer David A. 
Published: March 2010

Abstract
Cutter, G. R. Jr, Berger, L., and Demer, D. A. 2010. A comparison of bathymetry mapped with the Simrad ME70 multibeam echosounder operated in bathymetric and fisheries modes. – ICES Journal of Marine Science, 67: 1301–1309. The Simrad ME70 multibeam echosounder was designed for quantitative fisheries research and is currently installed on Ifremer's fishery survey vessel (FSV) “Thalassa” and each of the new, quiet, NOAA FSVs. The ME70 has configurable beams and transmits in the range 70–120 kHz to provide calibrated, acoustic-backscattering data throughout the detection range (fisheries mode, FM). With optional hardware and software, the ME70 can also collect soundings that potentially meet International Hydrographic Organization's S–44 Order 1 standards (bathymetric mode, BM). Furthermore, with custom algorithms and software, bathymetric data can be obtained from the ME70 operating in FM, and volume backscatter can be sampled from the ME70 operating in BM. This flexibility allows data to be concurrently collected on fish and their seabed habitat. A method is described for processing the echo amplitude and phase data from multiple split-beams formed in FM to estimate seabed range, slope, and roughness. The resulting bathymetry is compared with that collected with the ME70 operating in BM in the same area of the Bay of Biscay. A proposal is made for software development to facilitate dual-use data processing.
Age, growth, and mortality of Loligo vulgaris wild paralarvae: implications for understanding of the life cycle and longevity
Authors: González Ángel F. , Otero Jaime , Pierce Graham J. , Guerra Ángel 
Published: March 2010

Abstract
González, Á. F., Otero, J., Pierce, G. J., and Guerra, Á. 2010. Age, growth, and mortality of Loligo vulgaris wild paralarvae: implications for understanding of the life cycle and longevity. – ICES Journal of Marine Science, 67: 1119–1127. Age, growth, and mortality were estimated for the first time in wild paralarvae of the common squid, Loligo vulgaris, by examining growth increments in the statoliths of 273 animals collected off the Ría de Vigo (NW Spain, NE Atlantic). Hatching was all year round for the period 2003–2005, with a peak during late spring and a secondary peak during early autumn. Paralarvae varied from 1260 to 7580 µm, and their abundance decreased abruptly as they grew. Statolith increments were clearly visible without grinding in almost all material, allowing reliable estimation of age. Paralarvae are planktonic for at least 3 months. Growth in dorsal mantle length (DML) during that period fitted an exponential equation. The instantaneous relative growth rates were 2.11, 2.15, and 1.82% DML d−1 for 2003, 2004, and 2005, respectively, and there were no significant differences in size-at-age between the 3 years. Taking into account the growth rates estimated for the whole cycle of L. vulgaris, we suggest that the lifespan may previously have been underestimated by 3 months, because the proximity of the rings deposited during paralarval and early juvenile stages would prevent accuracy in enumerating the number of growth increments in later stages. The estimated instantaneous rate of total mortality during the first 90 d of a paralarva life was 9.6, 5.3, and 4.8% d−1 for 2003, 2004, and 2005, respectively. Eye diameter was a reliable and rapid way of estimating DML and age.
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
Authors: Sheldrick George M. 
Published: March 2010

The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXE by the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue α-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap.
With phases: how two wrongs can sometimes make a right
Authors: Roversi Pietro , Johnson Steven , Lea Susan M. 
Published: March 2010

In isolation, both weak isomorphous/anomalous difference signals from heavy-atom derivatization and phases from partial molecular-replacement solutions for a subset of the asymmetric unit often fall short of producing interpretable electron-density maps. Phases generated from very partial molecular-replacement models (if generated carefully) can be used to reliably locate heavy-atom sites, even if the signal is not sufficiently strong to allow robust finding of the sites using Patterson interpretation or direct methods. Additional advantages are that using molecular-replacement phases to define the heavy-atom substructure avoids the need for subsequent hand determination and/or origin-choice reconciliation and that the partial model can be used to aid the mask determination during solvent flattening. Two case studies are presented in which it was only by combining experimental and molecular-replacement phasing approaches that the crystal structures could be determined.
Experimental phasing: best practice and pitfalls
Authors: McCoy Airlie J. , Read Randy J. 
Published: March 2010

Developments in protein crystal structure determination by experimental phasing are reviewed, emphasizing the theoretical continuum between experimental phasing, density modification, model building and refinement. Traditional notions of the composition of the substructure and the best coefficients for map generation are discussed. Pitfalls such as determining the enantiomorph, identifying centrosymmetry (or pseudo-symmetry) in the substructure and crystal twinning are discussed in detail. An appendix introduces combined real–imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.
Features and development of Coot
Authors: Emsley P. , Lohkamp B. , Scott W. G. , Cowtan K. 
Published: March 2010

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
Phymatotrichum (cotton) root rot caused by Phymatotrichopsis omnivora: retrospects and prospects
Authors: UPPALAPATI SRINIVASA RAO , YOUNG CAROLYN A. , MAREK STEPHEN M. , MYSORE KIRANKUMAR S. 
Published: March 2010

SUMMARYPhymatotrichum (cotton or Texas) root rot is caused by the soil‐borne fungus Phymatotrichopsis omnivora (Duggar) Hennebert. The broad host range of the fungus includes numerous crop plants, such as alfalfa and cotton. Together with an overview of existing knowledge, this review is aimed at discussing the recent molecular and genomic approaches that have been undertaken to better understand the disease development at the molecular level with the ultimate goal of developing resistant germplasm.Taxonomy: Phymatotrichopsis omnivora (Duggar) Hennebert [synonym Phymatotrichum omnivorum (Shear) Duggar] is an asexual fungus with no known sexual stage. Mitosporic botryoblastospores occasionally form on epigeous spore mats in nature, but perform no known function and do not contribute to the disease cycle. The fungus has been affiliated erroneously with the polypore basidiomycete Sistotrema brinkmannii (Bres.) J. Erikss. Recent phylogenetic studies have placed this fungus in the ascomycete order Pezizales.Host range and disease symptoms: The fungus infects most dicotyledonous field crops, causing significant losses to cotton, alfalfa, grape, fruit and nut trees and ornamental shrubs in the south‐western USA, northern Mexico and possibly parts of central Asia. However, this fungus does not cause disease in monocotyledonous plants. Symptoms include an expanding tissue collapse (rot) of infected taproots. In above‐ground tissues, the root rot results in vascular discoloration of the stem and rapid wilting of the leaves without abscission, and eventually the death of the plant. Characteristic mycelial strands of the pathogen are typically present on the root's surface, aiding diagnosis.Pathogenicity: Confocal imaging of P. omnivora interactions with Medicago truncatula roots revealed that infecting hyphae do not form any specialized structures for penetration and mainly colonize cortical cells and eventually form a mycelial mantle covering the root's surfaces. Cell wall‐degrading enzymes have been implicated in penetration and symptom development. Global gene expression profiling of infected M. truncatula revealed roles for jasmonic acid, ethylene and the flavonoid pathway during disease development. Phymatotrichopsis omnivora apparently evades induced host defences and may suppress the host's phytochemical defences at later stages of infection to favour pathogenesis.Disease control: No consistently effective control measures are known. The long‐lived sclerotia and facultative saprotrophism of P. omnivora make crop rotation ineffective. Chemical fumigation methods are not cost‐effective for most crops. Interestingly, no genetic resistance has been reported in any of the susceptible crop species.
Expression patterns and association analysis of the porcine DHX58 gene
Authors: Li X. Y. , Han C. M. , Wang Y. , Liu H. Z. , Wu Z. F. , Gao Q. H. , Zhao S. H. 
Published: March 2010

Summary RIG‐1 signalling is responsible for the detection of cytoplasmic viral RNA molecules. DEXH (Asp‐Glu‐X‐His) box polypeptide 58 (encoded by DHX58) is a negative regulator of the RIG‐1 signalling pathway. In human, the DHX58 gene can be upregulated and can inhibit the RIG‐1 signalling pathway during viral infection. In this study, porcine DHX58 gene expression patterns were studied. According to our results, the porcine DHX58 gene was upregulated not only by the stimulation of Poly I:C but also by the stimulation of 1ipopolysaccharides (LPS). One polymorphism (g.4919G>C), detected in the ninth intron, was significantly associated with some blood parameters including the red cell distribution width of 1‐day‐old pigs and white blood cell counts, lymphocyte absolute counts, and platelet distribution width of 17‐day‐old pigs (P < 0.05). Moreover, the individuals with the genotype GG have a significantly higher mean white blood cell count than individuals with genotype CC or GC (P < 0.05). Our study indicates that DHX58 is an important gene that is associated with the immune response in swine.
Dietary habits and health status of African‐Caribbean adults
Authors: Earland J. , Campbell J. , Srivastava A. 
Published: March 2010

AbstractBackground:  Although African‐Caribbeans in the UK are more likely to suffer from a number of diet‐related health conditions, including obesity, hypertension and type II diabetes, there have been few dietary studies on this group. The present study is based on a small survey of food and nutrient intakes and traditional dietary habits of African‐Caribbean adults living in Staffordshire.Methods:  A questionnaire, designed to collect demographic data and information on medical status, physical activities, dietary, cooking and food shopping habits was administered to a convenience sample of 39 adults. Detailed information on food intakes was gathered using a modified existing Food Frequency Questionnaire with 169 items. Height and weight were measured for the calculation of body mass index.Results:  The average age of the subjects was 47 years (range 19–65 years). The prevalence of obesity was 39% and one‐third of subjects reported having at least one health condition. Physical activities, outside of work, were undertaken by 95% of the sample. Traditional foods were used by 92% of respondents, including fruit and vegetables purchased at markets outside of their local area. A wide variety of foods were consumed and the percentages of energy provided by fats and carbohydrates (30% and 53%, respectively) appeared to be meeting government recommendations. However, absolute energy intakes were high and salt consumption, often in the form of commercial seasonings, exceeded government recommendations.Conclusions:  The positive aspects of the diets of this population need to be encouraged. Interventions need to focus on ways of reducing total energy intakes, as well as levels of salt consumption.
Attitudes to breastfeeding among adolescents
Authors: Giles M. , Connor S. , McClenahan C. , Mallet J. 
Published: March 2010

AbstractBackground:  Breastfeeding is a major public health concern and a decision to breastfeed has important health benefits for both the infant and mother. Breastfeeding rates are low in many Western countries, and evidence is accumulating to suggest that breastfeeding should be promoted in schools. The present study aimed to employ the theory of planned behaviour (TPB) to predict and explain young people’s motivations to breastfeed with a view to designing an intervention to positively promote breastfeeding among adolescents.Methods:  Senior schools in Northern Ireland were sorted by a number of key stratification variables, and then randomly sampled. In anticipation of a nonresponse, a first and second reserve list was drawn using matched replacements. Selected schools were contacted by letter, followed by a telephone call. Thirty‐six schools agreed to take part in the research, and a cross‐sectional survey was conducted with 2021 Year 10 pupils.Results:  Having been breastfed as a child and having seen a mother breastfeeding significantly correlated with intention among both females and males. In descending order of importance, the TPB direct constructs were all significantly correlated with intention among males and females. A hierarchical multiple regression was performed with the intention to breastfeed/encourage partner to breastfeed as the dependent variable, and the TPB successfully predicted intention among males and females.Conclusions:  The findings obtained in the present study suggest that the TPB is a useful framework on which to base the design of an intervention to promote attitude change, and highlight the importance of key theoretical constructs in predicting intentions to breastfeed.
Nutritional status, nutrition practices and post‐operative complications in patients with gastrointestinal cancer
Authors: Garth A. K. , Newsome C. M. , Simmance N. , Crowe T. C. 
Published: March 2010

AbstractBackground:  Malnutrition and its associated complications are a considerable issue for surgical patients with upper gastrointestinal and colorectal cancer. The present study aimed to determine whether specific perioperative nutritional practices and protocols are associated with improved patient outcomes in this group.Methods:  Patients admitted for elective upper gastrointestinal or colorectal cancer surgery (n = 95) over a 19‐month period underwent a medical history audit assessing weight changes, nutritional intake, biochemistry, post‐operative complications and length of stay. A subset of patients (n = 25) underwent nutritional assessment by subjective global assessment prior to surgery in addition to assessment of post‐operative medical outcomes, nutritional intake and timing of dietetic intervention.Results:  Mean (SD) length of stay for patients was 14.0 (12.2) days, with complication rates at 35%. Length of stay was significantly longer in patients who experienced significant preoperative weight loss compared to those who did not [17.0 (15.8) days versus 10.0 (6.8) days, respectively; P < 0.05]. Low albumin and post‐operative weight loss were also predictive of increased length of stay. Of patients who underwent nutritional assessment, 32% were classified as mild–moderately malnourished and 16% severely malnourished. Malnourished patients were hospitalised twice as long as well‐nourished patients [15.8 (12.8) days versus 7.6 (3.5) days; P < 0.05]. Time taken [6.9 (3.6) days] to achieve adequate nutrition post surgery was a factor in post‐operative outcomes, with a positive correlation with length of stay (r = 0.493; P < 0.01), a negative correlation with post‐operative weight change (r = −0.417; P < 0.05) and a greater risk of complications (52% versus 13%; P < 0.01).Conclusions:  Malnutrition is prevalent among surgical patients with gastrointestinal cancer. Poor nutritional status coupled with delayed and inadequate post‐operative nutrition practices are associated with worse clinical outcomes.