bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Lactobacillus casei in ileal and fecal samples from healthy volunteers after consumption of a fermented milk containingLactobacillus caseiDN-114 001Rif
Authors: Rochet Violaine , Rigottier-Gois Lionel , Levenez Florence , Cadiou Julie , Marteau Philippe , Bresson Jean-Louis , Goupil-Feillerat Nathalie , Doré Joël 
Published: September 2008

Lactobacillus casei DN-114 001 is a probiotic strain able to interact with the immune system and to interfere with gastrointestinal pathogens. The derived strain DN-114 001Rifwas studied during its transit through the upper and distal intestine of human volunteers. Seven volunteers participated in the study, which involved intestinal intubation to sample ileal contents and collection of fecal samples, with a wash-out period of 8 days between the 2 steps. The retrieval of the probiotic was analyzed in the ileum every 2 h for 8 h following the ingestion of one dose of the test product and in the feces prior to, during, and after daily consumption of the test product for 8 days. Persistence of the probiotic amplifiable DNA was assessed using temporal temperature gradient gel electrophoresis and real-time PCR. Fluorescent in situ hybridization allowed analysis of the composition of the dominant digestive microbiota. The ingestion of L. casei DN-114 001Rifled to a significant and transient increase of its amplifiable DNA in ileal and fecal samples. This is related to a high stability in the composition of dominant groups of the gut microbiota. Data from ileal samples are scarce and our study confirms the potentiality for interaction between probiotics and the human immune system.
Use of the 16S–23S ribosomal genes spacer region for the molecular typing of sphingomonads
Authors: Tokajian Sima , Al-Medawar Siba , Hashwa Fuad 
Published: September 2008

The ability of sphingomonads in drinking water to cause community- and hospital-acquired opportunistic infections has raised the need to establish reproducible identification assays. In this study, a total of 129 isolates recovered from drinking water with yellow- to orange-pigmented colonies were distributed among 10 biotypes on the basis of colony morphology. Polymorphisms, based on the amplification and restriction digestion of the intergenic transcribed spacer (ITS) region within the 10 assigned biotypes and 18 ATCC reference strains, were used to investigate the ability of this approach to differentiate closely related sphingomonads. ITS size, which ranged between 400 and 1100 bp, did not vary enough among the different genera. However, 16 distinct banding patterns within the ATCC reference strains and 9 within the 10 biotypes were obtained through ITS restriction digestion, and the majority of the tested biotypes produced patterns similar to those generated by the ATCC strains. To our knowledge, this study is not only the first comprehensive record of the size of the ITS region in sphingomonads, it is also the first study that describes the use of ITS restriction digestion to subtype those isolates.
Novel extracellular proteolytic activity inPediococcus acidilacticiATCC 8042
Authors: Llorente-Bousquets Adriana , Pérez-Munguía Sandra , Farrés Amelia 
Published: September 2008

Proteolytic systems are common in lactic acid bacteria, but there are few reports about proteases or peptidases in the genus Pediococcus . To evaluate the presence of these types of enzymes, Pediococcus acidilactici ATCC 8042 was cultured in MRS broth. Supernatants collected during the log phase showed proteolytic activity towards an elastin dispersion when assayed using a spectrophotometer. Zn2+showed a stimulatory effect, and the proteolytic activity reached its maximum when 200 mmol/L NaCl was included in the reaction buffer. On the other hand, activity was reduced when 5 mmol/L EDTA, 10 mmol/L phenylmethylsulfonyl fluoride, and 10 mmol/L 1,10-phenanthroline were used or when the sample was heat treated. Zymograms showed two different proteolytic bands when gelatin was used as a substrate (>200 and 107 kDa), but only the higher molecular mass band was detected when casein or elastin was used. The gelatinolytic activity was not detected with zymograms of the 107 kDa band, which was the one inactivated by heat treatment. The use of a renaturing SDS–PAGE gel with embedded Micrococcus lysodeikticus cells allowed for the detection of a band with peptidoglycan hydrolase activity migrating at about 110 kDa. This activity was lost when 10 mmol/L EDTA was added to the renaturing buffer. Therefore, Pediococcus showed at least three different extracellular enzymes that were produced during the logarithmic growth phase and acted on peptide substrates. Each showed different substrate specificity, ion requirements, and thermostability.
Variation of cell surface hydrophobicity and biofilm formation among genotypes ofCandida albicansandCandida dubliniensisunder antifungal treatment
Authors: Borecká-Melkusová Silvia , Bujdáková Helena 
Published: September 2008

Candida infections are frequently associated with formation of biofilms on artificial medical devices. This work studied variation of cell surface hydrophobicity (CSH) and formation of biofilm in relation to Candida albicans and Candida dubliniensis genotypes and an effect of some conventional antifungal agents on both CSH and biofilm. The 50 isolates of C. albicans and C. dubliniensis were classified into genotypes A, B, C, and D, genotype D being exclusively represented by C. dubliniensis. No significant differences between CSH of genotypes A and B and B and C were observed with respect to cultivation temperature 25 or 37 °C. Candida dubliniensis showed increased CSH in comparison with other C. albicans genotypes (p < 0.001) regardless of temperature used. Using XTT reduction assay and dry masses, genotypes B and C showed reduced ability to form biofilm in comparison with genotype A (p < 0.05) and C. dubliniensis (p < 0.001). Fluconazole reduced biofilm in C. albicans genotypes A, B, and C (p < 0.05) but not CSH. The opposite effect was observed in C. dubliniensis. Voriconazole effectively reduced both biofilm formation and CSH in all tested genotypes of C. albicans and C. dubliniensis (p < 0.05).
Gene cloning, protein purification, and enzymatic properties of multicopper oxidase, fromKlebsiellasp. 601
Authors: Li Yang , Yin Jiao , Qu Guosheng , Lv Luchao , Li Yadong , Yang Sheng , Wang Xing-Guo 
Published: September 2008

A gene encoding a putative multicopper oxidase (MCO) was cloned from the soil bacterium Klebsiella sp. 601 and its corresponding enzyme was overexpressed in an Escherichia coli strain. Klebsiella sp. 601 MCO is composed of 536 amino acids with a molecular mass of 58.2 kDa. Theoretical calculation gave a pI value of 6.11. The amino acid sequence of Klebsiella sp. 601 MCO is strongly homologous to that of E. coli CueO with a similarity of 90% and an identity of 78%. Unlike E. coli CueO, Klebsiella sp. 601 MCO contains an extra 20 amino acids close to its C-terminus. The enzyme was purified to homogeneity by Ni-affinity chromatography. The purified enzyme was capable of using DMP (2,6-dimethoxyphenol), ABTS (2,2′-azino-bis(3-ethylbenzthiazolinesulfonic acid)), and SGZ (syringaldazine) as substrates with an optimal pH of 8.0 for DMP, 3.0 for ABTS, and 7.0 for SGZ. Klebsiella sp. 601 MCO was quite stable at pH 7.0 in which its activity was constant for 25 h without any significant change. Kinetic studies gave Km, kcat, and kcat/Kmvalues of 0.49 mmol·L–1, 1.08 × 103s–1, and 2.23 × 103s–1·mmol–1·L, respectively, for DMP, 5.63 mmol·L–1, 6.64 × 103s–1, and 1.18 × 103s–1·mmol–1·L for ABTS, and 0.023 mmol·L–1, 11 s–1, and 4.68 × 102s–1·mmol–1·L for SGZ.
Direct detection ofCampylobacter jejuniin human stool samples by real-time PCR
Authors: Lin Shiyong , Wang Xinying , Zheng Haoxuan , Mao Zhengguo , Sun Yong , Jiang Bo 
Published: September 2008

Our purpose was to establish a quick and accurate real-time PCR (rtPCR) method to detect Campylobacter jejuni directly from human diarrheal stool as an alternative to traditional culture methods. To determine the consistency of rtPCR and culture method, 256 clinical diarrheal stool samples and 50 normal stool samples from healthy individuals were examined, and the whole process was double-blinded. Our data showed that the sensitivity of rtPCR in pure cultures and stool was 102CFU·mL–1and 103CFU·g–1, respectively. Of the 256 diarrheal samples, 10 specimens were successfully detected by both methods, whereas two specimens were PCR positive but culture negative. No positive results were found by these two methods in 50 normal specimens. Our data suggested that rtPCR was convenient in operation and time-saving (turnaround time 3.5–4 h), so it could be used for clinical diagnostic and epidemiological purposes.
Impact of sheep urine deposition and plant species on ammonia-oxidizing bacteria in upland grassland soil
Authors: Rooney Deirdre C. , Clipson Nicholas 
Published: September 2008

The effects of different concentrations of synthetic sheep urine and plant species on ammonia-oxidizing bacterial (AOB) communities in an upland grassland soil were investigated using a microcosm approach. Plant species characteristic of unimproved and improved agricultural pastures ( Agrostis capillaris and Lolium perenne , respectively) were planted in soil microcosms, and different levels of synthetic sheep urine were applied, with harvests 10 and 50 days following urine application. Shifts in the community structure of the AOB were investigated using terminal restriction fragment length polymorphism of amoA amplicons. Species richness and diversity were significantly altered by synthetic sheep urine addition and time depending on plant species type. Principal coordinate analysis revealed that AOB community structure was largely dependent on interactions between sheep urine deposition, plant species, and time after urine application, while significant changes in AOB structure were also revealed by similarity percentage analysis. The results of this study suggested that high levels of sheep urine, combined with floristic changes that are characteristic of agricultural intensification, can contribute to temporal and spatial changes in the structure of key bacterial communities in upland grassland soil. Changes in AOB community structure could potentially affect important soil processes, such as nitrification, with subsequent implications for nutrient cycling in agricultural systems.
Use of insertional mutagenesis to tag putative parasitic fitness genes in the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi
Authors: Plourde Karine V. , Jacobi Volker , Bernier Louis 
Published: September 2008

We used insertional mutagenesis to produce genetically tagged mutants of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. We first optimized transformation of O. novo-ulmi protoplasts by the restriction enzyme mediated integration method. A concentration of 80 U of HindIII with 108 fungal protoplasts and 5 μg of plasmid DNA was the most efficient for generating a high number of O. novo-ulmi mutants carrying a single insertion in their genome. Mycelium- and yeast-like growth kinetics of 24 O. novo-ulmi mutants were evaluated in vitro. Flanking sequences were successfully recovered in 8% of the transformants analyzed. Some mutant phenotypes appeared to result from gene disruption events, whereas others likely involved modifications of noncoding regions. Several nuclear loci that control vegetative growth and could potentially impact parasitic fitness were successfully tagged.
Antioxidant, antihypertensive, and antibacterial properties of endophyticPestalotiopsisspecies from medicinal plants
Authors: Tejesvi Mysore V. , Kini Kukkundoor R. , Prakash Harishchandra S. , Subbiah Ven , Shetty Hunthrike S. 
Published: September 2008

Pestalotiopsis species were most dominant endophytic species isolated from four medicinal plants including Terminalia arjuna , Terminalia chebula , Azadirachta indica , and Holarrhena antidysenterica . Thirty Pestalotiopsis species isolated from different parts of the medicinal plants were selected for the study. The antioxidant and antihypertensive properties of Pestalotiopsis isolates were determined by measuring 1,1-diphenyl-2-picrylhydrazyl inhibitory activity, lipid peroxidation, and angiotensin-converting enzyme inhibition activity. Pestalotiopsis isolates of T. arjuna origin exhibited maximum radical scavenging activity compared with the others. The IC50values of Pestalotiopsis extracts for 1,1-diphenyl-2-picrylhydrazyl scavenging activity ranged from 14 to 27 μg/mL compared with 15 and 6 μg/mL for butylated hydroxytoluene and ascorbic acid, respectively. The DNA damage study was also done for three isolates, TC-315, TA-37, and TA-60; TA-37 gave 80% protection. The IC50values of Pestalotiopsis extracts for lipid peroxidation ranged between 30 and 35.5 μg/mL, while for the positive control butylated hydroxytoluene, it was 26 μg/mL. Out of 32 fungal extracts screened for antihypertensive assay, five (TA-37, TA-60, TA-102, TA-103, and TC-320) showed >60% inhibition of angiotensin-converting enzyme. The IC50values for five extracts ranged from 21 to 37 μg/mL and was 20 μg/mL for captopril used as a positive control. The antibacterial activity was measured by the microplate-based turbidity measurement method. Four Pestalotiopsis extracts (TA-04, TA-37, TA-60, and TA-102) showed >75% inhibition against five bacterial strains including Bacillus subtilis , Escherichia coli , Pseudomonas fluorescens , Xanthomonas axonopodis pv. malvacearum, and Staphylococcus aureus . The antioxidant, antibacterial, and antihypertensive activities demonstrated the potential of Pestalotiopsis extracts as therapeutic targets.
Vital effects and beyond: a modelling perspective on developing palaeoceanographical proxy relationships in foraminifera
Authors: Zeebe Richard E. , Bijma Jelle , Hönisch Bärbel , Sanyal Abhijit , Spero Howard J. , Wolf-Gladrow Dieter A. 
Published: September 2008

Abstract

This paper mainly reviews our recent work on the biology and geochemistry of foraminifera with respect to their use as palaeoceanographic proxies. Our approach to proxy validation and development is described, primarily from a modeler's point of view. The approach is based on complementary steps in understanding the inorganic chemistry, inorganic isotope fractionation, and biological controls that determine palaeo-tracer signals in organisms used in climate reconstructions. Integration of laboratory experiments, field and culture studies, theoretical considerations and numerical modelling holds the key to the method's success. We describe effects of life-processes in foraminifera on stable carbon, oxygen, and boron isotopes as well as Mg incorporation into foraminiferal calcite shells. Stable boron isotopes will be used to illustrate our approach. We show that a mechanism-based understanding is often required before primary climate signals can be extracted from the geologic record because the signals can be heavily overprinted by secondary, non-climate related phenomena. Moreover, for some of the proxies, fundamental knowledge on the thermodynamic, inorganic basis is still lacking. One example is stable boron isotopes, a palaeo-
p
H proxy, for which the boron isotope fractionation between the dissolved boron compounds in seawater was not precisely known until recently. Attempts to overcome such hurdles are described and implications of our work for palaeoceanographic reconstructions are discussed.
Foraminifer test preservation and diagenesis: comparison of high latitude Eocene sites
Authors: Pearson Paul N. , Burgess Catherine E. 
Published: September 2008

Abstract

Foraminifer tests are prone to diagenetic recrystallization on a micron scale that can affect their geochemical composition, hence it is important to identify fossil material that is well-preserved. Here we illustrate the textures of tests from several high-latitude Eocene sites using a combination of Reflected Light Microscopy and high-resolution Scanning Electron Microscopy. The sites are Ocean Drilling Program (ODP) Site 647 in the Labrador Sea (53°N), ODP Site 689 at Maud Rise in the Weddell Sea (64°S), ODP Site 1135 (Kerguelen Plateau
c
. 59°S) and outcrop samples from Hampden Beach, New Zealand (palaeolatitude
c
. 55°S). The foraminifera studied from Site 647 and Hampden Beach have glassy, transparent tests that show only minor signs of diagenetic alteration, whereas the foraminifera from Sites 690 and 1135 are opaque and recrystallized. We associate the better state of foraminifer preservation at the former sites with the high clay content of the sediments. Our observations suggest that Site 647 and Hampden Beach may be useful for the establishment of high-latitude sea-surface temperatures and hence global temperature gradients in the Eocene.
The influences of growth rates on planktic foraminifers as proxies for palaeostudies – a review
Authors: Schmidt D. N. , Elliott T. , Kasemann S. A. 
Published: September 2008

Abstract
Size dependent changes in element concentrations in planktic foraminifers have long been recognized to influence their reliability as an archive for climate change. Traditionally, these changes have been interpreted as changes in element partitioning during the ontogeny of the organism with faster growth rates in the earlier part of the development. These changes, in the light of new culture experiments, can also be interpreted as changes in growth rate throughout the entire life of the organism, with larger, faster-growing specimens discriminating less efficiently against trace element incorporation into the calcite shell. Growth rates of foraminifera are influenced by the environment and hence change geographically and temporally at various scales, e.g. glacial-interglacial or rapid millennial events such as the Younger Dryas. These changes in growth rate can account for some changes in element to calcium ratio between glacial and interglacials, which were previously linked to changes in seawater element ratios.
Open answer set programming with guarded programs
Authors: Heymans Stijn , Nieuwenborgh Davy Van , Vermeir Dirk 
Published: September 2008

Open answer set programming (OASP) is an extension of answer set programming where one may ground a program with an arbitrary superset of the program's constants. We define a fixed-point logic (FPL) extension of Clark's completion such that open answer sets correspond to models of FPL formulas and identify a syntactic subclass of programs, called (loosely)guarded programs. Whereas reasoning with general programs in OASP is undecidable, the FPL translation of (loosely) guarded programs falls in the decidable (loosely) guarded fixed-point logic (μ(L)GF). Moreover, we reduce normal closed ASP to loosely guarded OASP, enabling, for the first time, a characterization of an answer set semantics by μLGF formulas.We further extend the open answer set semantics for programs with generalized literals. Suchgeneralized programs (gPs)have interesting properties, for example, the ability to express infinity axioms. We restrict the syntax of gPs such that both rules and generalized literals areguarded. Via a translation to guarded fixed-point logic, we deduce 2-EXPTIME-completeness of satisfiability checking in suchguarded gPs(GgPs).Bound GgPsare restricted GgPs with EXPTIME-complete satisfiability checking, but still sufficiently expressive to optimally simulatecomputation tree logic(CTL). We translate Datalog lite programs to GgPs, establishing equivalence of GgPs under an open answer set semantics, alternation-free μGF, and Datalog LITE.
Workload-aware anonymization techniques for large-scale datasets
Authors: LeFevre Kristen , DeWitt David J. , Ramakrishnan Raghu 
Published: September 2008

Protecting individual privacy is an important problem in microdata distribution and publishing. Anonymization algorithms typically aim to satisfy certain privacy definitions with minimal impact on the quality of the resulting data. While much of the previous literature has measured quality through simple one-size-fits-all measures, we argue that quality is best judged with respect to the workload for which the data will ultimately be used.
This article provides a suite of anonymization algorithms that incorporate a target class of workloads, consisting of one or more data mining tasks as well as selection predicates. An extensive empirical evaluation indicates that this approach is often more effective than previous techniques. In addition, we consider the problem of scalability. The article describes two extensions that allow us to scale the anonymization algorithms to datasets much larger than main memory. The first extension is based on ideas from scalable decision trees, and the second is based on sampling. A thorough performance evaluation indicates that these techniques are viable in practice.
A type system equivalent to a model checker
Authors: Naik Mayur , Palsberg Jens 
Published: September 2008

Type systems and model checking are two prevalent approaches to program verification. A prominent difference between them is that type systems are typically defined in a syntactic and modular style whereas model checking is usually performed in a semantic and whole-program style. This difference between the two approaches makes them complementary to each other: type systems are good at explaining why a program was accepted while model checkers are good at explaining why a program was rejected.
We present a type system that is equivalent to a model checker for verifying temporal safety properties of imperative programs. The model checker is natural and may be instantiated with any finite-state abstraction scheme such as predicate abstraction. The type system, which is also parametric, type checks exactly those programs that are accepted by the model checker. It uses a variant of function types to capture flow sensitivity and intersection and union types to capture context sensitivity. Our result sheds light on the relationship between type systems and model checking, provides a methodology for studying their relative expressiveness, is a step towards sharing results between the two approaches, and motivates synergistic program analyses involving interplay between them.
The new features of Fortran 2008
Authors: Reid John 
Published: September 2008

The aim of this paper is to summarize the new features of the draft Fortran 2008 standard (ISO/IEC 2008). We take as our starting point Fortran 2003 (ISO/IEC 2008). An official extension for enhanced module facilities (ISO/IEC 2005) that has been published as a Type 2 Technical Report (TR), and WG5 is committed to include this in Fortran 2008. For an informal description of Fortran 2003 and Enhanced Module Facilities see Metcalf, Reid, and Cohen (2004). The major proposed extension consists of coarrays for parallel computing. Since the author has already summarised coarrays in another WG5 paper (Reid 2008), we refer the reader to this for further details.
This is not an official document and has not been approved by either of the Fortran committees WG5 or J3.
Compiler support for the Fortran 2003 standard
Authors: Chivers Ian D. , Sleightholme Jane 
Published: September 2008

This is a repeating article in Fortran Forum. The first version appeared in Fortran Forum in April 2007. The basis for the entries in the list of features was a report by John Reid. An electronic version can be found at: ftp://ftp.nag.co.uk/sc22wg5/N1601-N1650/N1648.pdf
The next edition of the article will include support for the Fortran 2008 standard, and again the basis for the entries will be a John Reid article!
If you are a compiler vendor and would like to be included in future versions of this table please email one of us with details and they will be added to the table and published in Fortran Forum.