bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Junk’ DNA and phenotypic evolution inSilenesectionSiphonomorpha
Authors: MEAGHER THOMAS R. , COSTICH DENISE E. 
Published: May 2008

SummaryOne of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size inSilene latifoliahas been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species inSilenesect.Elisanthe. Given the presence of sex chromosomes in dioeciousSilenespecies, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioeciousSileneis a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species ofSilenesect.Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect.Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect.Siphonomorphafor petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect.Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect.Elisanthe, and particularly inS. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa.
Vegetative growth, superoxide dismutase activity and ion concentration of salt-stressed watermelon as influenced by rootstock
Authors: GORETA SMILJANA , BUCEVIC-POPOVIC VILJEMKA , SELAK GABRIELA VULETIN , PAVELA-VRANCIC MAJA , PERICA SLAVKO 
Published: May 2008

SUMMARYWatermelon is a crop with a high water demand and is frequently grown under conditions of higher than normal root-zone salinity. In the present study, seedlings of watermelon (cv. Fantasy, Citrullus lanatus (Thunb.) Matsum & Nakai) were grown either ungrafted or grafted on three rootstocks: Strong Tosa, S1 (both Cucurbita maxima×Cucurbita moschata), or Emphasis (Lagenaria siceraria). All the plants were exposed to an NaCl-induced salinity stress (electrical conductivity, EC=2·2, 4·0, or 6·0 dS/m). The vegetative growth of all the plants substantially reduced after 2 weeks of exposure to 6·0 dS/m; however, growth of the plants grafted on Strong Tosa reduced less than that of the others. The leaf water content and specific leaf area (SLA, m2/g) decreased with an increasing salinity in grafted plants, but not in ungrafted plants. Salinity induced an increase of superoxide dismutase (SOD) activity in grafted plants up to two-fold depending on the rootstock, whereas it had no effect on this enzyme activity in ungrafted plants. Leaf Na+ concentration increased with increasing salinity in ungrafted and S1 grafted plants, whereas there was no significant leaf Na+ accumulation in Emphasis and Strong Tosa grafted plants. Leaf K+ concentration was affected by the rootstock but not by salinity, thus, the ability to keep a high K+/Na+ ratio was achieved mainly by limiting leaf Na+ concentration. The rootstock determined the leaf Cl− accumulation, with lower overall concentrations found if plants were grafted on the S1 rootstock than on Emphasis or ungrafted plants. Salinity significantly decreased the leaf NO3− concentration on Emphasis grafted plants only, while the NO3−/Cl− ratio was reduced in all the rootstocks. The capacity of Strong Tosa to withstand salt stress better than other tested rootstocks was probably due to the ability to induce anatomical adaptation (SLA) and SOD activity in response to salt stress, and also to the efficiency of Na+ exclusion from the shoot.
Molluscicidal and antiparasitic activity ofSolanum nigrumvillosumagainstGalba truncatulainfected or uninfected withFasciola hepatica
Authors: Hammami H. , Ayadi A. 
Published: May 2008

AbstractThe present study was based on assessments of the molluscicidal and antiparasitic activities ofSolanum nigrum villosum. This plant has been collected in Tozeur's traditional oases (south-western Tunisia). Molluscicidal activities of leaves, ripe fruit and unripe fruit extracts ofS. n. villosumhave been assessed in experimental and semi-field conditions on uninfectedGalba truncatula. Antiparasitic activities have also been assessed on larval stages (rediae, intraredial germinal masses and cercariae) of the parasiteFasciola hepaticainfectingG. truncatulanaturally. The unripe fruit extract (LC50 = 41.2 mg l− 1) was more toxic than the leaf (LC50 = 132.5 mg l− 1) and the ripe fruit (LC50 = 172.8 mg l− 1) extracts on the snail after 48 h of treatment. One mg l− 1of cupric chloride produced the death of 97% ofG. truncatulaafter 25 days of treatment.Solanum n. villosumextracts used at the lethal laboratory concentration in semi-field conditions were also toxic toG. truncatula. The unripe fruit extract was more toxic than the leaf and the ripe fruit extracts on larval stages ofF. hepatica. Maximum deterioration rates were obtained with the unripe fruit extract: 65.6% for rediae, 77.8% for cercariae and 27.6% for intraredial germinal masses after 48 h of treating the snails. The possibility of the unripe fruit extract application for the control ofG. truncatulaandF. hepaticalarval stages should be considered.
Screening for Indian isolates of egg-parasitic fungi for use in biological control of fascioliasis and amphistomiasis in ruminant livestock
Authors: De S. , Sanyal P.K. , Sarkar A.K. , Patel N.K. , Pal S. , Mandal S.C. 
Published: May 2008

AbstractWild isolates of the egg-parasitic fungiPaecilomyces lilacinusandVerticillium chlamydosporium, obtained from the organic environment of Durg, Chhattisgarh, India, were subjected to screening forin vitrogrowth using different media types, range of incubation temperature and pH, and their predatory activity to the eggs ofFasciola giganticaandGigantocotyle explanatum. Maximum growth ofP. lilacinuswas obtained in corn-meal agar compared to any other media types. The preferred medium for growth ofV. chlamydosporiumwas corn-meal agar, followed by potato-dextrose agar. After initial growth for 16 h of incubation, no growth was observed in water agar for both the fungi. Six different temperatures – 4°C, 10°C, 18°C, 26°C, 34°C and 40°C – were used to observe growth profiles of the fungi in corn-meal agar medium. While no and very little growth ofP. lilacinusandV. chlamydosporiumwas observed at 4°C and 10°C, respectively, growth profiles of both the fungi were optimal at 26–40°C. A range of pH (pH 4–8) supported growth of bothP. lilacinusandV. chlamydosporium. Full-grown plates of the fungi baited with viable eggs ofF. giganticaandG. explanatumrevealed thatV. chlamydosporiumwas more vigorous in its egg-parasitic ability compared toP. lilacinus. Distortion of the eggs started on day 2–3 of egg baiting in culture plates ofV. chlamydosporium, with complete distortion by day 7. On the contrary,P. lilacinusexhibited very limited egg-parasitic ability and some of the baited eggs even showed development of miracidia.
Stability analysis of the operational space control for industrial robots using their own joint velocity PI controllers
Authors: Camarillo Karla , Campa Ricardo , Santibáñez Víctor , Moreno-Valenzuela Javier 
Published: May 2008

SUMMARYOperational space control of industrial robots is addressed in this document. We analyze a two-loop hierarchical control with the resolved motion rate controller (RMRC) as outer loop and the joint velocity PI controller as inner loop; the latter is the typical velocity controller used in industrial robots. We prove, by the first time, that these simple controllers make the solutions of the closed-loop system uniformly ultimately bounded. Additionally, we give some simple guidelines for the selection of the control gains so as to ensure an explicit bound of the tracking error.
Fall detection in walking robots by multi-way principal component analysis
Authors: Karssen J. G. Daniël , Wisse Martijn 
Published: May 2008

SUMMARYLarge disturbances can cause a biped to fall. If an upcoming fall can be detected, damage can be minimized or the fall can be prevented. We introduce the multi-way principal component analysis (MPCA) method for the detection of upcoming falls. We study the detection capability of the MPCA method in a simulation study with the simplest walking model. The results of this study show that the MPCA method is able to predict a fall up to four steps in advance in the case of single disturbances. In the case of random disturbances the MPCA method has a successful detection probability of up to 90%.
On the intersection of free subgroups in free products of groups
Authors: DICKS WARREN , IVANOV S. V. 
Published: May 2008

AbstractLet (Gi|i∈I) be a family of groups, letFbe a free group, and let$G = F \ast \mathop{\text{\Large $*$}}_{i\in I} G_i,$the free product ofFand all theGi.Let$\mathcal{F}$denote the set of all finitely generated subgroupsHofGwhich have the property that, for eachg∈Gand eachi∈I,$H \cap G_i^{g} = \{1\}.$By the Kurosh Subgroup Theorem, every element of$\mathcal{F}$is a free group. For each free groupH, thereduced rankofH, denotedr(H), is defined as$\max \{\rank(H) -1, 0\} \in \naturals \cup \{\infty\} \subseteq [0,\infty].$To avoid the vacuous case, we make the additional assumption that$\mathcal{F}$contains a non-cyclic group, and we defineWe are interested in precise bounds for$\upp$. In the special case whereIis empty, Hanna Neumann proved that$\upp$∈ [1,2], and conjectured that$\upp$= 1; fifty years later, this interval has not been reduced.With the understanding that ∞/(∞ − 2) is 1, we defineGeneralizing Hanna Neumann's theorem we prove that$\upp \in [\fun, 2\fun]$, and, moreover,$\upp = 2\fun$wheneverGhas 2-torsion. Since$\upp$is finite,$\mathcal{F}$is closed under finite intersections. Generalizing Hanna Neumann's conjecture, we conjecture that$\upp = \fun$wheneverGdoes not have 2-torsion.
Food Stamp Program participation but not food insecurity is associated with higher adult BMI in Massachusetts residents living in low-income neighbourhoods
Authors: Webb Amy L , Schiff Andrew , Currivan Douglas , Villamor Eduardo 
Published: May 2008

AbstractObjectiveFood-insecure populations employ multiple strategies to ensure adequate household food supplies. These strategies may increase the risk of overweight and obesity. However, existing literature reports conflicting associations between these strategies and BMI. The objective of the present study was to examine whether food insecurity and strategies for managing food insecurity are associated with BMI in adults.Design, setting and subjectsIn 2005, RTI International and Project Bread conducted a representative survey of 435 adult residents of low-income census tracts in Massachusetts. Food insecurity was assessed using the US Department of Agriculture’s eighteen-item Household Food Security Module.ResultsThe prevalence of overweight and obesity was 51 % and 25 %, respectively. After adjusting for age, sex, sociodemographic characteristics and food insecurity, both participation in the Food Stamp Program (FSP) and participation in any federal nutrition programme 12 months prior to the survey were each associated with an approximate 3·0 kg/m2higher adult BMI. In the subset of current FSP participants (n77), participation for ≥6 months was associated with an 11·3 kg/m2lower BMI compared with participation for <6 months. Respondents who consumed fast foods in the previous month had a mean BMI that was 2·4 kg/m2higher than those who did not. Food insecurity was not associated with BMI after adjustment for sociodemographic characteristics and FSP participation.ConclusionsParticipation in federal nutrition programmes and consumption of fast food were each associated with higher adult BMI independent of food insecurity and other sociodemographic factors. However, prolonged participation in the FSP was associated with lower BMI.
A comparison of the socio-economic determinants of growth retardation in South African and Filipino infants
Authors: Jones Laura L , Griffiths Paula L , Adair Linda S , Norris Shane A , Richter Linda M , Cameron Noël 
Published: May 2008

AbstractObjectiveTo examine the association between household socio-economic status (SES) at birth and poor infant growth such as small for gestational age (SGA) and stunting across two different socio-cultural settings: South Africa and the Philippines.DesignData were from two longitudinal birth cohorts, the Birth to Twenty (Bt20) study in South Africa and the Cebu Longitudinal Health and Nutrition Survey (CLHNS) in the Philippines.SubjectsBt20 infants (n 2293 total; reduced to 758 (SGA), 450 (stunting 1 year) and 401 (stunting 2 years)) and CLHNS infants (n 2513 total; reduced to 2161 (SGA), 1820 (stunting 1 year) and 1710 (stunting 2 years)).ResultsCLHNS infants were significantly more likely to be born SGA (20·9 v. 11·7 %) and be stunted at 1 year (32·6 v. 8·7 %) and 2 years (48·9 v. 21·1 %) compared with Bt20 infants. Logistic regression analyses showed that SES (index) was a significant predictor of stunting at 1 and 2 years of age in the CLHNS cohort. SES (index or individual variables) was not a significant predictor of SGA in either cohort, or of stunting in the Bt20 cohort. Maternal education, ownership of a television and toilet facilities were all independent predictors of stunting in the CLHNS cohort.ConclusionsThe social and economic milieu within the Philippines appears to place CLHNS infants at greater risk of being born SGA and being stunted compared with Bt20 infants. The present research highlights the importance of investigating the individual SES variables that predict infantile growth faltering, to identify the key areas for context-specific policy development and intervention.
Design and implementation of aggregate functions in the DLV
system
Authors: FABER WOLFGANG , PFEIFER GERALD , LEONE NICOLA , DELL'ARMI TINA , IELPA GIUSEPPE 
Published: May 2008

AbstractDisjunctive logic programming (DLP) is a very expressive formalism. It allows for
expressing every property of finite structures that is decidable in the
complexity class ΣP2(=NPNP). Despite this high expressiveness, there
are some simple properties, often arising in real-world applications, which
cannot be encoded in a simple and natural manner. Especially properties that
require the use of arithmetic operators (like sum, times, or count) on a set or
multiset of elements, which satisfy some conditions, cannot be naturally
expressed in classic DLP. To overcome this deficiency, we extend DLP by
aggregate functions in a conservative way. In particular, we avoid the
introduction of constructs with disputed semantics, by requiring aggregates to
be stratified. We formally define the semantics of the extended language (called ), and illustrate how it can be profitably used for representing
knowledge. Furthermore, we analyze the computational complexity of , showing that the addition of aggregates does not bring a higher
cost in that respect. Finally, we provide an implementation of in DLV—a state-of-the-art DLP system—and
report on experiments which confirm the usefulness of the proposed extension
also for the efficiency of computation.
Preferred extensions as stable models
Authors: NIEVES JUAN CARLOS , CORTÉS ULISES , OSORIO MAURICIO 
Published: May 2008

AbstractGiven an argumentation frameworkAF, we introduce a mapping function that constructs a disjunctive logic programP, such that the preferred extensions ofAFcorrespond to the stable models ofP, after intersecting each stable model with the relevant atoms. The given mapping function is of polynomial size w.r.t.AF.In particular, we identify that there is a direct relationship between the minimal models of a propositional formula and the preferred extensions of an argumentation framework by working on representing the defeated arguments. Then we show how to infer the preferred extensions of an argumentation framework by using UNSAT algorithms and disjunctive stable model solvers. The relevance of this result is that we define a direct relationship between one of the most satisfactory argumentation semantics and one of the most successful approach of nonmonotonic reasoning i.e., logic programming with the stable model semantics.
Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
Authors: Martin-Cuadrado Ana-Belen , Rodriguez-Valera Francisco , Moreira David , Alba José C , Ivars-Martínez Elena , Henn Matthew R , Talla Emmanuel , López-García Purificación 
Published: May 2008

Abstract
Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.
Rapid purification of truncated Taq DNA polymerase Stoffel fragment by boiling lysis of bacterial expression cultures
Authors: Yang Zhengan , Ding Yumei , Zhang Yinghua , Liu Feihu 
Published: May 2008

A simplified and low‐cost method, boiling lysis, was developed and used to purify the truncated DNA polymerase Stoffel fragment after overproduction of the enzyme in Escherichia coli. The method is based on the thermostable properties of the Stoffel fragment. Conditions such as the boiling time and number of cycles employed were identified as determinants with which to achieve a high yield and activity of this truncated Taq enzyme. Under established conditions, a period of 8 min consisting of two cycles of boiling and centrifuging was ideal for the purification of the Taq protein, followed by dibasic phosphate and ethanol extraction in a single type of storage buffer to remove contaminating nucleic acid. The whole purification process could be achieved within 1 or 2 h. A total yield of 80 mg of truncated Taq enzyme with an activity of 1.6×107 units was purified from l litre of bacterial culture. The purified Taq enzyme had a molecular mass of 61 kDa, a value consistent with the truncated DNA polymerase Stoffel fragment reported previously.
Selection and characterization of Affibody® ligands to the transcription factor c‐Jun
Authors: Lundberg Emma , Brismar Hjalmar , Gräslund Torbjörn 
Published: May 2008

c‐Jun is a highly oncogenic transcription factor involved in the development of different types of cancer. In the present study we have generated c‐Jun‐binding‐affinity proteins from a phage‐displayed library of so‐called ‘Affibody® ligands’, developed by combinatorial engineering of a non‐immunoglobulin‐based scaffold protein. Homodimeric c‐Jun protein was recombinantly produced in Escherichia coli and, prior to selection, the quality of the target protein was investigated by binding analyses, which indicated specific binding to a double‐stranded DNA hairpin construct containing a c‐Jun response element, but not to a control sequence. Isolated Affibody® variants from the phage selection were expressed in E. coli, purified by affinity chromatography and their interaction with c‐Jun was analysed. In biosensor analyses, one Affibody® ligand, denoted ZcJun518, was shown to interact with immobilized c‐Jun protein with an apparent dissociation constant of 5 μM. By constructing a head‐to‐tail homodimeric version of ZcJun518, its apparent affinity for c‐Jun could be increased threefold, suggesting co‐operativity effects in the binding to the immobilized c‐Jun protein. Further characterization of the ZcJun518 Affibody® molecule demonstrated, in both affinity‐capture and Western‐blotting experiments, its ability to interact selectively with c‐Jun, even when the c‐Jun target was present in a complex protein background consisting of a bacterial cell lysate. ZcJun518 could also be used to stain the c‐Jun‐overexpressing cell line C8161 visualized by confocal fluorescence microscopy. Results from competition experiments indicated that the binding epitope on c‐Jun for the ZcJun518 Affibody® molecule was separate from the binding sites of both a polyclonal antibody raised against the unstructured N‐terminal domain and a double‐stranded DNA hairpin containing a c‐Jun response element. The potential intracellular use of Affibody® ligands directed against transcription factors and other oncogenic factors is discussed.