bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
Authors: Huang Hui-Lin , Lin I-Che , Liou Yi-Fan , Tsai Chia-Ta , Hsu Kai-Ti , Huang Wen-Lin , Ho Shinn-Jang , Ho Shinn-Ying
Published: February 2011

Background

Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors.

Results

This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc.

Conclusions

The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences.
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
Authors: Duitama Jorge , Kennedy Justin , Dinakar Sanjiv , Hernández Yözen , Wu Yufeng , Măndoiu Ion I
Published: February 2011

Background

Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping.

Results

In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage. A software package implementing our algorithm, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/GeneSeq/.

Conclusions

Integration of LD information leads to significant improvements in genotype calling accuracy compared to prior LD-oblivious methods, rendering low-coverage sequencing as a viable alternative to microarrays for conducting large-scale genome-wide association studies.
Incorporating Ab Initio energy into threading approaches for protein structure prediction
Authors: Shao Mingfu , Wang Sheng , Wang Chao , Yuan Xiongying , Li Shuai Cheng , Zheng Weimou , Bu Dongbo
Published: February 2011

Background

Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates.

Results

In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function.

Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison.

Conclusions

Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
Musculoskeletal comorbidities in cardiovascular disease, diabetes and respiratory disease: the impact on activity limitations; a representative population-based study
Authors: Slater Morgan , Perruccio Anthony V , Badley Elizabeth M
Published: February 2011

Background

The purpose of this study was to quantify the contribution of comorbidity to activity limitations in populations with chronic cardiovascular disease, diabetes or respiratory disease (index conditions), with emphasis on musculoskeletal comorbidity (arthritis or back problems).

Methods

Analysis of the 2005 Canadian Community Health Survey 3.1 (age 20+ years, n = 115,915). Prevalence ratios for activity limitations in people with the index conditions and co-occurring musculoskeletal disease, adjusted for age, gender, and socioeconomic factors, were used to estimate population associated fractions (PAF).

Results

Comorbid arthritis and back problems significantly increased the risk of activity limitations across all index conditions with prevalence ratios of 1.60 and 1.46 for cardiovascular disease, 1.51 and 1.36 for diabetes, and 1.38 and 1.44 for respiratory disease for arthritis and back problems respectively. Arthritis and back problems accounted for at least 13% and 9% of activity limitations in the index populations.

Conclusions

While chronic musculoskeletal conditions are not always considered priorities in chronic disease prevention, they account for a substantial proportion of activity restrictions seen in people with cardiovascular disease, diabetes and respiratory disease, with implications for prevention and control strategies.
Factors affecting commencement and cessation of betel quid chewing behaviour in Malaysian adults
Authors: Ghani Wan MN , Razak Ishak A , Yang Yi-Hsin , Talib Norain A , Ikeda Noriaki , Axell Tony , Gupta Prakash C , Handa Yujiro , Abdullah Norlida , Zain Rosnah B
Published: February 2011

Background

Betel quid chewing is a common habit widely practiced in Southern Asian populations. However, variations are seen in the content of a betel quid across the different countries. Factors associated with commencement and cessation of this habit has been numerously studied. Unfortunately, data on Malaysian population is non-existent. This study aims to determine the factors associated with the inception and also cessation of betel quid chewing behaviour among Malaysian adults.

Method

This study is part of a nationwide survey on oral mucosal lesions carried out among 11,697 adults in all fourteen states in Malaysia. The questionnaire included sociodemographic information and details on betel quid chewing habit such as duration, type and frequency. The Kaplan-Meier estimates were calculated and plotted to compare the rates for the commencement and cessation of betel quid chewing behaviour. Cox proportional hazard regression models were used to calculate the hazard rate ratios for factors related to commencement or cessation of this habit.

Results

Of the total subjects, 8.2% were found to be betel quid chewers. This habit was more prevalent among females and, in terms of ethnicity, among the Indians and the Indigenous people of Sabah and Sarawak. Cessation of this habit was more commonly seen among males and the Chinese. Females were found to be significantly more likely to start (p < 0.0001) and less likely to stop the quid chewing habit. Females, those over 40 years old, Indians and a history of smoking was found to significantly increase the likelihood of developing a quid chewing habit (p < 0.0001). However, those who had stopped smoking were found to be significantly more likely to promote stopping the habit (p = 0.0064). Cessation was also more likely to be seen among those who chewed less than 5 quids per day (p < 0.05) and less likely to be seen among those who included areca nut and tobacco in their quid (p < 0.0001).

Conclusion

Factors that influence the development and cessation of this behaviour are gender, age, ethnicity, and also history of smoking habit while frequency and type of quid chewed are important factors for cessation of this habit.
Ion beam-induced shaping of Ni nanoparticles embedded in a silica matrix: from spherical to prolate shape
Authors: Kumar Hardeep , Ghosh Santanu , Avasthi Devesh Kumar , Kabiraj Debdulal , Mücklich Arndt , Zhou Shengqiang , Schmidt Heidemarie , Stoquert Jean-Paul
Published: February 2011

Present work reports the elongation of spherical Ni nanoparticles (NPs) parallel to each other, due to bombardment with 120 MeV Au+9 ions at a fluence of 5 × 1013 ions/cm2. The Ni NPs embedded in silica matrix have been prepared by atom beam sputtering technique and subsequent annealing. The elongation of Ni NPs due to interaction with Au+9 ions as investigated by cross-sectional transmission electron microscopy (TEM) shows a strong dependence on initial Ni particle size and is explained on the basis of thermal spike model. Irradiation induces a change from single crystalline nature of spherical particles to polycrystalline nature of elongated particles. Magnetization measurements indicate that changes in coercivity (Hc) and remanence ratio (Mr/Ms) are stronger in the ion beam direction due to the preferential easy axis of elongated particles in the beam direction.
New Si-based multilayers for solar cell applications
Authors: Nalini R Pratibha , Dufour Christian , Cardin Julien , Gourbilleau Fabrice
Published: February 2011

In this article, we have fabricated and studied a new multilayer structure Si-SiO2/SiN
x
by reactive magnetron sputtering. The comparison between SiO2 and SiN
x
host matrices in the optical properties of the multilayers is detailed. Structural analysis was made on the multilayer structures using Fourier transform infrared spectroscopy. The effect of specific annealing treatments on the optical properties is studied and we report a higher visible luminescence with a control over the thermal budget when SiO2 is replaced by the SiN
x
matrix. The latter seems to be a potential candidate to replace the most sought SiO2 host matrix.
Interactions between Sex Hormones and a 1,2-Di-O-myristoyl-sn-glycero-3-phosphocholine Molecular Layer: Characteristics of the Liposome, Surface Area versus Surface Pressure of the Monolayer, and Microscopic Observation
Authors: Nakata Satoshi , Ikeguchi Ayaka , Shiota Takaya , Komori Ryouhei , Kumazawa Noriyuki , Tsutsumi Moe , Denda Mitsuhiro
Published: February 2011

The interactions between sex hormones (estradiol and testosterone) and a 1,2-di-O-myristoyl-sn-glycero-3-phosphocholine (DMPC) molecular layer were investigated by observing the liposome and the surface area (A) vs. surface pressure (π) of the DMPC monolayer at an air–water interface. The shape and size of the liposome changed with the addition of estradiol and testosterone. The π–A isotherm, the time variation of the surface pressure, and the microscopic observation of monolayer were examined to clarify the different effects of the steroid hormones. These experimental results are discussed in relation to the formation of a rigid membrane due to hydrogen bonding between estradiol and DMPC.
A Molecular Dynamic Simulation of Crosslinking of Bisphenol and Triazine by United Atom Model: A Polycyanurate Model
Authors: Ikeno Taketo , Tsubuku Makoto , Katagiri Masayuki , Tsujimoto Tomoo
Published: February 2011

Polycyanurate networks were densely built by crosslinking of bisphenols and triazine. A molecular dynamics study of the networks from bisphenol A, bisphenol E, and fluorene bisphenol qualitatively reproduced the glass-transition temperatures in correct orders.
Managing Global Brand Investments at DHL
Authors: Fischer Marc , Giehl Wolfgang , Freundt Tjark
Published: February 2011

In this paper, we introduce the customer-insight based approach that Deutsche Post DHL adopted to improve its global express delivery business. DHL has used the operations research based brand assessment tool in more than 20 large countries on four continents since 2004. The tool supports local brand managers in allocating marketing resources to activities that grow the global brand in their country market. Its application led to an estimated increase in brand value of USD 1.32 billion over five years. This corresponds to a return on investment of 38 percent and an internal rate of return of 24 percent. The tool's implementation also had a major impact on DHL's strategy and organization.
Breaking the Deadlock: Improving Water-Release Policies on the Delaware River Through Operations Research
Authors: Kolesar Peter , Serio James
Published: February 2011

The Delaware River provides half of New York City's drinking water, is a habitat for wild trout and American shad, and has suffered three major floods in the last five years. The water releases from three New York City dams on the Delaware River's headwaters impact the reliability of the city's water supply, the potential for floods, and the quality of the aquatic habitat. This project's objective was to revise the release policies to benefit river habitat and fisheries without increasing New York City's drought risk. Changes in the release policies were constrained by the dictates of two US Supreme Court Decrees and the need for unanimity among four states and New York City. We describe the analyses and the politics that led the Delaware River Basin Commission to implement our operations-research–based adaptive release framework in October 2007. In addition to meeting our habitat improvement goals and drought-risk constraint, our algorithm conservatively decreases end-of-summer reservoir levels more in wet years, thereby modestly increasing flood protection during the hurricane season, and is substantially simpler to administer.
Public health knowledge utilisation by policy actors: an evaluation study in Midden-Holland, the Netherlands
Authors: de Goede Joyce , Steenkamer Betty , Treurniet Henriëtte , Putters Kim , van Oers Hans
Published: February 2011

A comprehensive report has been prepared on the state of public health and healthcare in the Midden-Holland region of the Netherlands. This study describes the development of the report and the mechanisms behind public health knowledge utilisation by three groups of health policy actors: local authorities, public health professionals and regional care providers. The processes are studied in various qualitative ways. The mechanisms explaining the use of the report were found to be complex and different for each group of policy actors. Interaction between researchers and users is not the only factor that explains usage, but rather serves as an intermediate factor.
Connecting evidence and policy: bringing researchers and policy makers together for effective evidence-based health policy in the Netherlands: a case study
Authors: van Egmond Stans , Bekker Marleen , Bal Roland , van der Grinten Tom
Published: February 2011

The use of evidence in health promotion has become the gold standard, and obliges rethinking how to increase the (often limited) use of evidence in public health policy. Recently calls have been made to reconceptualise science policy relations as dynamic, interactive and coconstructive practices. Building on a qualitative investigation of an information tool for the Dutch government, the authors show how the nature of evidence is closely linked to its usefulness for policy, and how a specific infrastructural organisation of science-policy interactions contributes to an effective participation and interaction between both scientists and policy makers and the translation of research findings.
Switching of Na+, K+-ATPase isoforms by salinity and prolactin in the gill of a cichlid fish
Authors: Tipsmark C K , Breves J P , Seale A P , Lerner D T , Hirano T , Grau E G
Published: February 2011

We identified and investigated the changes in expression of two gill Na+, K+-ATPase α-subunit isoforms (α-1a and α-1b) in relationship with salinity acclimation in a cichlid fish, Mozambique tilapia. Transfer of freshwater (FW)-acclimated fish to seawater (SW) resulted in a marked reduction in α-1a expression within 24 h and a significant increase in α-1b expression with maximum levels attained 7 days after the transfer. In contrast, transfer of SW-acclimated fish to FW induced a marked increase in α-1a expression within 2 days, while α-1b expression decreased significantly after 14 days. Hypophysectomy resulted in a virtual shutdown of α-1a mRNA expression in both FW- and SW-acclimated fish, whereas no significant effect was observed in α-1b expression. Replacement therapy by ovine prolactin (oPrl) fully restored α-1a expression in FW-acclimated fish, while cortisol had a modest, but significant, stimulatory effect on α-1a expression. In hypophysectomized fish in SW, replacement therapy with oPrl alone or in combination with cortisol resulted in a marked increase in α-1a mRNA to levels far exceeding those observed in sham-operated fish. Expression of α-1b mRNA was unaffected by hormone treatment either in FW-acclimated fish or in SW-acclimated fish. The mRNA expression of fxyd-11, a regulatory Na+, K+-ATPase subunit, was transiently enhanced during both FW and SW acclimation. In hypophysectomized fish in FW, oPrl and cortisol stimulated fxyd-11 expression in a synergistic manner. The clear Prl dependence of gill α-1a expression may partially explain the importance of this hormone to hyperosmoregulation in this species.
STAT genes display differential evolutionary rates that correlate with their roles in the endocrine and immune system
Authors: Gorissen Marnix , de Vrieze Erik , Flik Gert , Huising Mark O
Published: February 2011

We identified orthologues of all mammalian Janus kinase (JAK) and signal transducer and activator of transcription (STAT) genes in teleostean fishes, indicating that these protein families were already largely complete before the teleost tetrapod split, 450 million years ago. In mammals, the STAT repertoire consists of seven genes (STAT1, -2, -3, -4, -5a, -5b, and -6). Our phylogenetic analyses show that STAT proteins that are recruited downstream of endocrine hormones (STAT3 and STAT5a and -5b) show a markedly higher primary sequence conservation compared with STATs that convey immune signals (STAT1-2, STAT4, and STAT6). A similar dichotomy in evolutionary conservation is observed for the JAK family of protein kinases, which activate STATs. The ligands to activate the JAK/STAT-signalling pathway include hormones and cytokines such as GH, prolactin, interleukin 6 (IL6) and IL12. In this paper, we examine the evolutionary forces that have acted on JAK/STAT signalling in the endocrine and immune systems and discuss the reasons why the JAK/STAT cascade that conveys classical immune signals has diverged much faster compared with endocrine JAK/STAT paralogues.
Szemlélet- és gyakorlatváltozás a rectalis digitális vizsgálat indikációjában és kivitelezésben appendicitis acuta gyanúja esetén gyermekkorban
Authors: Kutasy Balázs , Mohay Gabriella , Pintér András
Published: February 2011

Absztrakt

A laboratóriumi és képalkotó diagnosztika fejlődésével a nem kielégítő hatékonyságú, kellemetlen és fájdalmas rectalis digitális vizsgálat heveny vakbélgyulladás esetén nem szükségszerűen a fizikális vizsgálat része. Ugyanakkor egyes kérdéses esetekben hasznos. Ilyenkor azonban a megváltozott jogi és társadalmi környezet miatt a vizsgálat altatásban történő végzése mérlegelendő.
Posztkondicionálás kísérletes vizsgálata vékonybél ischaemiás-reperfusiós modelljében
Authors: Rosero Olivér , Ónody Péter , Stangl Rita , Hegedűs Viktor , Lotz Gábor , Blázovics Anna , Kupcsulik Péter , Szijártó Attila
Published: February 2011

Absztrakt

Bevezetés:A vékonybél ischaemiás-reperfusiós károsodása – mely az arteria mesenterica superior occlusiója vagy keringési redistributio során jelentkezik leggyakrabban – jelentős mortalitású kórkép. Kísérletünk során a posztkondicionálás felmerülő protektív hatását vizsgáltuk patkányvékonybél ischaemiás-reperfusiós modelljében.Módszer:Hím Wistar-patkányokon az arteria mesenterica superior 60 perces kirekesztését végeztük. Az állatokat négy – áloperált, kontroll- és két posztkondicionált csoportra osztottuk. A posztkondicionált csoportokban a kirekesztést követően háromszor 1 perces, illetve 10 másodperces reperfusiós-reocclusiós ciklusok ismétlése után került sor 60 perc reperfusióra. A vékonybél microcirculatióját laser Doppler-flowmeterrel detektáltuk. A reperfusio első órájának végén vér- és szöveti mintavétel történt. Szérum-necroenzim- és IL-6-szinteket, fénymikroszkópos szöveti képet, mesenterialis vénás vérgázértékeket és nyálkahártya-antioxidáns-statust vizsgáltunk.Eredmények:A microcirculatiót jellemző paraméterek mindkét posztkondicionált csoportban szignifikánsan javultak. A gyulladásos válaszjelenségek és a szövetkárosodás mértéke szignifikáns módon csökkent, mely a necroenzimszint-csökkenéssel is korrelált. Megfigyelhető volt továbbá az antioxidáns-statusra gyakorolt kedvező hatás és a pH késleltetett normalizálódása is.Következtetés:A posztkondicionálás alkalmas sebésztechnikai módszer lehet a vékonybél túlélési esélyének javítására arteria mesenterica superior occlusiója során kialakuló ischaemiás-reperfusiós károsodás esetén.
Compaction and design of gypsiferous fill for hot desert road pavements
Authors: Razouki Sabah S , Kuttah Dina K , Abood Maha H
Published: February 2011

A comparative study between a homogeneous road embankment constructed of gypsiferous soil and compacted throughout its full height at the dry optimum moisture content (DOMC) and an exactly similar embankment but with improved active zone (top 50 cm of the embankment compacted at the wet optimum moisture content WOMC), is presented. Two soils A and B were examined. Soil A was sandy lean clay (CL) containing about 35% total soluble salt (TSS) of which 33% was gypsum; soil B had a 28% TSS and a gypsum content of 25·6%. California bearing ratio (CBR) soil samples, prepared at DOMC and WOMC for soil A and at WOMC for soil B, showed serious reductions in soil strength and stiffness due to soaking, especially when the soil had been compacted at DOMC. A soaking period of 4 days was considered very reasonable and conservative for hot dry regions. Swelling of the soil during soaking was observed, especially when the soil was compacted at DOMC. For pavement design, it appears to be more economical to introduce an active zone compacted at WOMC instead of DOMC. The cost of the additional water required for compaction at WOMC instead of DOMC is much less than the savings in cost of sub-base material due to increased subgrade soil strength. It is concluded that the gypsiferous soil which occurs widely in the Middle East can be used to build embankments for hot desert road pavements.
Is the quasi-steady state a real behaviour? A micromechanical perspective
Authors: YANG J. , DAI B.B.
Published: February 2011

Whether the so-called quasi-steady state is a real material response is a fundamental yet controversial question in the study of undrained shear behaviour of sand. An attempt is made here to clarify the question from a micromechanical viewpoint by means of a grain-scale modelling technique combined with statistical analyses. The study shows that the quasi-steady state is a real behaviour rather than a test-induced phenomenon; it is a transition state, and can be regarded as the result of spatial rearrangement of discrete particles sheared under the constant-volume condition. The quasi-steady state has distinct features that make it different from the steady state at both the macro scale and micro scale. During the loading process, the average number of contacts per particle decreases with strain until the quasi-steady state emerges, and after that it increases gradually to an approximately constant value at large deformations associated with the steady state. This result suggests that the loss of contacts is most pronounced at the quasi-steady state. The study also shows that the contact normal forces and particle rotations play a major role in the deformation process, whereas the contributions of contact tangential forces and particle sliding appear to be minor.
OHSAS 18001 in a UK county highways and transportation department
Authors: Winter Michael , Norman Tim
Published: February 2011

This paper considers the case for introducing a formal occupational health and safety management system, which meets the requirements of the UK occupational health and safety assessment specification, OHSAS 18001, into the highways and transportation department of a local authority. It describes the existing arrangements within Dorset Engineering Consultancy (DEC), Dorset County Council’s in-house highways and transportation professional services provider, and how they were reviewed to identify the developments necessary to secure OHSAS 18001 registration. The existing health and safety procedures were extended and fully integrated with an established quality management system before training members of staff in the new approaches to be taken. Compliance auditing was used to ensure that the new procedures were being adopted. Challenges in meeting the requirements of OHSAS 18001 and how they were overcome are described. This is followed by an account of the assessment process that was necessary to achieve third-party registration. Finally, the benefits that have accrued from implementing OHSAS 18001 are considered before outlining future development plans.
Genetic Analysis of “8101” Soybean Containing Three Genes for Resistance to Soybean Mosaic Virus
Authors: Liao L. , Chen P. , Rajcan I. , Buss G. R. , Tolin S. A.
Published: February 2011

Soybean mosaic virus (SMV) occurs in most soybean [Glycine max (L.) Merr.] growing areas around the world. The use of soybean cultivars with resistance to SMV is the most effective way of controlling this disease. Three independent genetic loci (Rsv1, Rsv3, and Rsv4) with multiple alleles for SMV resistance have been identified. The objective of this study was to evaluate the genetic composition of a Chinese soybean line 8101 for SMV resistance. In this study, 8101 was crossed with susceptible cultivars Lee 68, Essex, and Hefeng No. 25. The genotype 8101 was also crossed with resistant lines PI 96983, L29, and V94‐5152 carrying Rsv1, Rsv3, and Rsv4, respectively, to examine the allelic relationship between the genes in 8101 and the previously reported genes at these three loci. The results indicated that 8101 carries three independent dominant genes for resistance to SMV. One of them is at the Rsv1 locus but carries a different allele than the Rsv1 in PI 96983. This new allele confers resistance to SMV G1 but a susceptible reaction to SMV G7. The second gene is at the Rsv3 locus conferring resistance to SMV G7 but a susceptible reaction to SMV G1. The third gene is at the Rsv4 locus and confers resistance to both SMV G1 and G7. The presence of these three genes in 8101 confers resistance to SMV strains G1 through G3 and G5 through G7. The line 8101 is the first genotype identified as carrying all three SMV resistance genes, Rsv1, Rsv3, and Rsv4 Research is underway to further characterize the three resistance genes in 8101.
QTL Analysis of Soybean Seed Coat Discoloration Associated with II TT Genotype
Authors: Oyoo Maurice E. , Benitez Eduardo R. , Kurosaki Hideki , Ohnishi Shizen , Miyoshi Tomoaki , Kiribuchi‐Otobe Chikako , Horigane Akira , Takahashi Ryoji
Published: February 2011

In soybean [Glycine max (L.) Merr.], the dominant allele of the T locus for tawny pubescence is associated with chilling tolerance and is useful for breeding for chilling tolerance. Yellow hilum cultivars with the dominant I allele are preferred in Japan because of a better external appearance. However, the II TT allelic combination darkens the entire seed coat and degrades the external appearance. This study was conducted to investigate the genetic basis of seed coat discoloration using DNA markers. F2 populations derived from crosses between soybean breeding lines 0518BW‐8 with slight discoloration and 0734BW‐1 with severe discoloration were grown at Memuro in 2003 and Kunneppu in 2007. Seed coat discoloration was measured by the L* value with a two‐dimensional colorimeter. A total of 104 simple sequence repeat markers were classified into 20 linkage groups (LGs) spanning 1025 cM in 2003 and 19 LGs spanning 789 cM in 2007. A quantitative trait locus (QTL), discol1, was identified by composite interval mapping in LG A2 (chromosome 8) across years and locations. It had an LOD score of 5.58 explaining 22.0% of phenotypic variance in 2003 and a LOD score of 5.62 explaining 20.2% of variance in 2007. The allele from 0518BW‐8 increased the L* value at the QTL. Position of discol1 was close to the I locus corresponding to the chalcone synthase (CHS) multigene family cluster. No sequence differences were observed between the two lines in nucleotide sequences of CHS1 and CHS3 genes and the intergenic region between CHS1 and CHS3.
Evaluation and Validation of Ecogeographical Core Collections using Phenotypic Data
Authors: Parra‐Quijano Mauricio , Iriondo José M. , Torres Elena , De la Rosa Lucía
Published: February 2011

This study evaluated the phenotypic representativeness of core collections generated independently with ecogeographical data or with morphological data. The Spanish Phaseolus vulgaris L. collection was the target germplasm collection, and one map of ecogeographical categories and 15 morphological variables were used to create core collections. Three ecogeographical and 12 morphological core collections were produced combining different grouping methods (categories from ecogeographical land characterization map [CEM], two‐step clustering [TSC], Ward–modified location model clustering [WM], and unweighted pair‐group method using arithmetic average [UPGMA]) and allocation strategies (constant [C], proportional [P], logarithmic [L], and Gower's distance [D]). An additional morphological core collection was created using a modified least distance stepwise sampling (LDSSm) method. Core collections were evaluated with morphological data using parameters for qualitative and quantitative variables that were summarized in a new synthetic evaluation parameter (SEP). Synthetic evaluation parameter results showed that the ecogeographical core collections had high phenotypic representativeness, similar to that of morphological core collections generated by the combination of WM and TSC grouping methods and P allocation strategy. A graphical evaluation of core collections supported these results. In conclusion, ecogeographical information was confirmed as a good alternative or complement to other types of data to create reliable and representative core collections.
Environmental Variation and Correlation of Seed Components in Nontransgenic Soybeans: Protein, Oil, Unsaturated Fatty Acids, Tocopherols, and Isoflavones
Authors: Carrera Constanza , Martínez María José , Dardanelli Julio , Balzarini Mónica
Published: February 2011

The environment has a significant influence on the expression of traits contributing to soybean nutritional and/or industrial value. The aim of this study was to explore and describe the variability of nontransgenic soybean seed chemical components by investigating the environmental correlations among protein (Pr), oil (O), oleic (Ol), linoleic (La), and linolenic (Ln) acids, oleic to linolenic acid ratio (Ol:Ln) alpha‐ (AT), beta‐ (BT), gamma‐ (GT), delta‐ (DT), and total tocopherols (TT) and total isoflavones (TI) by means of principal component analysis. We analyzed seeds from multienvironment trials involving 23 field trials grown in Argentina (24 to 38° S latitude). A wide range of variability was observed for Ol, Ln, Ol:Ln, AT, BT, and TI. The strongest environment‐induced relationships found were the negative correlation between DT and AT and the positive correlation between DT and Ln. Increased Ol:Ln was negatively correlated with Ln. High values of DT, Ln, and Pr were associated with cool environments, TI content was greater in temperate to cool environments, and AT, O, and Ol:Ln were associated with warm environments. Warm environments would be suitable for obtaining products with higher O concentration of low oxidation capacity and greater vitamin E content. In turn, temperate to cool environments would be suitable for the production of soybean with higher TI, La, Ln, and TT content; in addition, these environments would favor seeds of higher Pr concentration.
Identification of Creeping Foxtail Germplasm with High Dry Matter Yield and Nutritive Value
Authors: Robins Joseph G. , Jensen Kevin B.
Published: February 2011

While creeping foxtail (Alopecurus arundinaceus Poir.) is widely grown in wet meadows and pastures throughout temperate regions of the United States and world, only the cultivars ‘Garrison’ and ‘Retain’ have been developed in the United States. These cultivars represent a narrow genetic base and substantial improvement of creeping foxtail may be realized by incorporating additional germplasm resources into a cultivar development program. The study described herein compared the agronomic and nutritive value of 47 creeping foxtail accessions to that of Garrison and Retain in a field study conducted over two production years at a site near Richmond, UT. The effect of accessions was separated into the component due to the region of origin and the component due to the accession per se. Differences were limited among region of origin, although significant differences occurred for dry matter yield and in vitro true digestibility. The U.S. cultivars had the numerically highest dry matter yield (116 g plot−1) and the Mongolian accessions (945 g kg−1) had higher in vitro true digestibility than the other regions. Differences among the individual accessions occurred for all traits except rhizome spread. A group of seven accessions from Afghanistan, Iran, Russia, and Turkey exhibited high dry matter yield and neutral detergent fiber digestibility. These accessions could be combined with the cultivar Garrison to develop a broad base population for further creeping foxtail improvement and cultivar development.
Nonstructural Carbohydrate Content in the Stem at Full Heading Contributes to High Performance of Ripening in Heat‐Tolerant Rice Cultivar Nikomaru
Authors: Morita S. , Nakano H.
Published: February 2011

Rice (Oryza sativa L.) grain yields in western Japan have recently decreased as a result of higher temperatures during ripening. The improvement of rice cultivars for stable production is a pressing need because of climate change. In this study, the features of good ripening of the new rice cultivar Nikomaru were analyzed through a 3‐yr field experiment. Nikomaru showed a yield increase of 7 to 8% compared with the leading cultivar in western Japan, Hinohikari, even though these cultivars have similar source size (available carbohydrate during ripening) and sink size (total spikelet number and rough grain size). The greater ripening index (percentage of ripened grains × 1000‐grain weight) in Nikomaru, which determined the varietal yield differences in this study, was attributed to the translocated dry matter for ripening (ΔT) but not to the newly assimilated dry matter during ripening (ΔW). In addition, ΔT was positively correlated with the nonstructural carbohydrate content in the stem at full heading (NSCh). There was positive correlation between the NSCh and the percentage of ripened grains in the hotter years (2005 and 2007). It was suggested that a large NSCh as the main source of the ΔT contributes to the maintenance of a higher ripening rate especially under high temperatures.
The Relevancy of Forage Quality to Beef Production
Authors: Phillips W. A. , Horn G. W. , Cole N. A.
Published: February 2011

Low cost and abundant fossil fuels have driven the U.S. beef industry toward greater dependence on feed grains as the major feedstuff for finished beef cattle production. Further, it has led to a centralized beef cattle feeding and processing system concentrated in the High Plains states. Low cost fuel and mechanization of harvesting of forages allowed cow‐calf producers to calve in late winter, which produced older heavier calves in the fall. The stocker industry evolved as a cushion between the cow‐calf producer, stabilizing the flow of cattle into the feedlots and resulting in a steady flow out of the feedlots, through the processing plants, and into the retail market. In the future, other domesticated species and biofuel demands will out bid beef cattle for feed grains and transportation cost of live and processed beef cattle will increase. As a result, a greater proportion of our finished beef supply must come from forage‐based diets harvested by grazing beef cattle and the final product will be processed nearer to the consumer to lower food miles and total cost of the finished product. Improving forage quality, extending the grazing season, selecting beef cattle that are efficient converters of forages into body weigh gain, and developing sustainable forage‐based grazing production systems will be imperative.
Leaf Transpiration Efficiency of Sweet Corn Varieties from Three Eras of Breeding
Authors: Bunce James A.
Published: February 2011

When measured under midday field conditions, modern varieties of maize (Zea mays L.) often have substomatal carbon dioxide concentration (Ci) values in excess of those required to saturate the photosynthetic carbon dioxide assimilation rate (A). This results in lower leaf transpiration efficiency (TE), the ratio of photosynthesis to transpiration, than potentially achievable for a given rate of photosynthesis. In some other crops, breeding has indirectly resulted in a large increase in stomatal conductance (gs), which would decrease TE. I tested whether this occurred in sweet corn by comparing five open‐pollinated varieties released before 1903 with four standard hybrid varieties released in the mid‐1900s and four varieties released after 1990. Leaf gas exchange of each variety was measured under ambient midday field conditions on eight sunny days over two seasons in Beltsville, MD. Although there were significant differences among varieties in gs, A, Ci, and TE, no effect of era was significant for any variable except A. Of the four modern varieties tested, two had the highest gs and two had the lowest gs of any of the varieties compared, with high gs associated with low TE. These four varieties were further compared in a third year and were found to differ consistently in leaf TE but not in A. It is concluded that breeding over the last century has not increased gs or decreased leaf TE in sweet corn but that there is significant variation in TE among modern sweet corn varieties.
The Use of Ultrasonography, Transient Elastography, APRI and FIB-4 to Measure Liver Steatosis and Fibrosis in HIV-Positive Patients Not Co- Infected with Hepatitis Viruses with Hypertransaminasemia of Unknown Etiology on HAART
Authors: Izzo Ilaria , Biasi Luciano , Mendeni Monia , Prestini Katiela , Vavassori Andrea , Foca Emanuele , Quiros-Roldan Eugenia , Carosi Giampiero , Torti Carlo
Published: February 2011

Background:

HIV positive patients may be affected by hypertransaminasemia notwithstanding they are not coinfected
with HCV and HBV.

Aims:

To understand the causes of this abnormality and what correlates are in terms of ultrasonic transient elastography
(UTE) and ultrasonography (U) features and fibrosis scores.

Methods:

HIV positive patients with hypertransaminasemia have been studied. They underwent UTE and U. Non-invasive
fibrosis scores (APRI and FIB-4) were calculated. Moreover, they underwent immunological and virological tests to
exclude known causes of liver damage (including alcohol abuse).

Results:

Among 24 patients, 3 presented a progressive fibrosis at UTE. 3/3 with progressive fibrosis and further 14
patients among the entire sample had steatosis at U. Using non-invasive fibrosis scores, no patients had significant
fibrosis, while 5 patients had mild fibrosis. 14 patients had hepatomegaly independently from steatosis. One patient has
progressive fibrosis at UTE and mild fibrosis at both APRI and FIB-4, while 2 patients had fibrosis only at UTE, 2 only at
APRI and 1 at both APRI and FIB-4, but not at UTE. Alcoholaemia was negative in all patients, confirming anamnestic
information. No other causes of liver disease were found.

Conclusions:

In this series, more than 50% of patients had steatosis at U. Discordance between the non-invasive methods
to estimate liver fibrosis were found. Further prospective studies are necessary to assess concordance between these
methods and liver biopsy and assess the prognostic value of UTE, APRI and FIB-4 for liver complications in HIV monoinfected
patients so as to improve diagnostic algorithms.
Satisfaction with Renal Replacement Therapy and Education
Authors: Fadem Stephen Z. , Walker David R. , Abbott Greg , Friedman Amy L. , Goldman Richard , Sexton Sue , Buettner Kim , Robinson Kris , Peters Thomas G.
Published: February 2011

Background and objectives

This study was undertaken by the American Association of Kidney Patients (AAKP) to better understand ESRD patients' satisfaction with their current renal replacement therapy (RRT) and the education they received before initiating therapy.

Design, setting, participants, & measurements

In addition to an open invitation on the AAKP website, nearly 9000 ESRD patients received invitations to complete the survey, which consisted of 46 questions. Satisfaction was measured on a 1 (extremely dissatisfied) to 7 (extremely satisfied) scale.

Results

Survey respondents were younger, more highly educated, and more likely to be white as well as employed as compared with the U.S. dialysis population. A total of 977 patients responded. Overall patient satisfaction with current RRT treatment varied from a low of 4.5 for in-center hemodialysis (ICHD) to a high of 6.1 in transplant (TX) patients. Peritoneal dialysis (PD) and home hemodialysis (HHD) mean scores were 5.2 and 5.5, respectively. PD, HHD, and TX patients' satisfaction scores were significantly higher than those of ICHD patients (P < 0.05). Approximately 31% of respondents felt that the therapies were not equally and fairly presented as treatment options, and 32% responded that they were not educated regarding HHD.

Conclusions

ESRD patients are not uniformly advised about all possible treatment methods and hence were only moderately satisfied with their pretreatment education. Once on RRT, those on a home therapy or with a kidney TX are more satisfied than those with ICHD.
Inferior Vena Cava Diameter and Left Atrial Diameter Measure Volume but Not Dry Weight
Authors: Agarwal Rajiv , Bouldin J. Michael , Light Robert P. , Garg Ashok
Published: February 2011

Background and objectives

Hypervolemia is an important and modifiable cause of hypertension. Hypertension improves with probing dry weight, but its effect on echocardiographic measures of volume is unknown.

Design, setting, participants, & measurements

Shortly after dialysis, echocardiograms were obtained at baseline and longitudinally every 4 weeks on two occasions. Among 100 patients in the additional ultrafiltration group, 198 echocardiograms were performed; among 50 patients in the control group, 104 echocardiograms were performed.

Results

Baseline inferior vena cava (IVC)insp diameter was approximately 5.1 mm/m2; with ultrafiltration, change in IVCinsp diameter was −0.95 mm/m2 more compared with the control group at 4 weeks and −1.18 mm/m2 more compared with the control group at 8 weeks. From baseline IVCexp diameter of approximately 8.2 mm/m2, ultrafiltration-induced change at 4 weeks was −1.06 mm/m2 more and at 8 weeks was −1.07 mm/m2 more (P = 0.044). From a baseline left atrial diameter of 2.1 cm/m2, ultrafiltration-induced change at 4 weeks was −0.14 cm/m2 more and at 8 weeks was −0.15 cm/m2 more. At baseline, there was no relationship between interdialytic ambulatory BP and echocardiographic parameters of volume. The reduction in interdialytic ambulatory BP was also independent of change in the echocardiographic volume parameters.

Conclusions

The inferior vena cava and left atrial diameters are echocardiographic parameters that are responsive to probing dry weight; thus, they reflect excess volume. However, echocardiographic volume parameters are poor determinants of interdialytic BP, and their change does not predict the BP response to probing dry weight.
On the lower and upper solution method for higher order functional boundary value problems
Authors: Graef John , Kong Lingju , Minhós Feliz , Fialho João
Published: February 2011

The authors consider the nth-order differential equation ?(?(u(n?1)(x)))?=
f(x, u(x), ..., u(n?1)(x)), for 2?(0, 1), where ?: R? R is an increasing
homeomorphism such that ?(0) = 0, n?2, I:= [0,1], and f : I ?Rn ? R is a
L1-Carath?odory function, together with the boundary conditions gi(u, u?,
..., u(n?2), u(i)(1)) = 0, i = 0, ..., n? 3, gn?2 (u, u?, ..., u(n?2),
u(n?2)(0), u(n?1)(0)) = 0, gn?1 (u, u?, ..., u(n?2), u(n?2)(1), u(n?1)(1))
= 0, where gi : (C(I))n?1?R ? R, i = 0, ..., n?3, and gn?2, gn?1 :
(C(I))n?1?R2 ? R are continuous functions satisfying certain monotonicity
assumptions. The main result establishes sufficient conditions for the
existence of solutions and some location sets for the solution and its
derivatives up to order (n?1). Moreover, it is shown how the monotone
properties of the nonlinearity and the boundary functions depend on n and
upon the relation between lower and upper solutions and their derivatives.