bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing species density and abundance of tropical trees from remotely sensed data and geostatistics
Authors: Hernández‐Stefanoni J. Luis , Dupuy Juan Manuel , Castillo‐Santiago M. Angel 
Published: July 2009

AbstractQuestion: What relationships exist between remotely sensed measurements and field observations of species density and abundance of tree species? Can these relationships and spatial interpolation approaches be used to improve the accuracy of prediction of species density and abundance of tree species?Location: Quintana Roo, Yucatan peninsula, Mexico.Methods: Spatial prediction of species density and abundance of species for three functional groups was performed using regression kriging, which considers the linear relationship between dependent and explanatory variables, as well as the spatial dependence of the observations. These relationships were explored using regression analysis with species density and abundance of species of three functional groups as dependent variables, and reflectance values of spectral bands, computed NDVI (normalized difference vegetation index), standard deviation of NDVI and texture measurements of Landsat 7 Thematic Mapper (TM) imagery as explanatory variables. Akaike information criterion was employed to select a set of candidate models and calculate model‐averaged parameters. Variogram analysis was used to analyze the spatial structure of the residuals of the linear regressions.Results: Species density of trees was related to reflectance values of TM4, NDVI and spatial heterogeneity of land cover types, while the abundance of species in functional groups showed different patterns of association with remotely sensed data. Models that accounted for spatial autocorrelation improved the accuracy of estimates in all cases.Conclusions: Our approach can substantially increase the accuracy of the spatial estimates of species richness and abundance of tropical tree species and can help guide and evaluate tropical forest management and conservation.
Adaptive evolution of baker's yeast in a dough‐like environment enhances freeze and salinity tolerance
Authors: Aguilera Jaime , Andreu Pasqual , Randez‐Gil Francisca , Prieto Jose Antonio 
Published: July 2009

SummaryWe used adaptive evolution to improve freeze tolerance of industrial baker's yeast. Our hypothesis was that adaptation to low temperature is accompanied by enhanced resistance of yeast to freezing. Based on this hypothesis, yeast was propagated in a flour‐free liquid dough model system, which contained sorbitol and NaCl, by successive batch refreshments maintained constantly at 12°C over at least 200 generations. Relative to the parental population, the maximal growth rate (µmax) under the restrictive conditions, increased gradually over the time course of the experiment. This increase was accompanied by enhanced freeze tolerance. However, these changes were not the consequence of genetic adaptation to low temperature, a fact that was confirmed by prolonged selection of yeast cells in YPD at 12°C. Instead, the experimental populations showed a progressive increase in NaCl tolerance. This phenotype was likely achieved at the expense of others traits, since evolved cells showed a ploidy reduction, a defect in the glucose derepression mechanism and a loss in their ability to utilize gluconeogenic carbon sources. We discuss the genetic flexibility of S. cerevisiae in terms of adaptation to the multiple constraints of the experimental design applied to drive adaptive evolution and the technologically advantageous phenotype of the evolved population.
A rare tumour in the mandible of a young man: a case report and literature review of mesenchymal chondrosarcoma of the mandible
Authors: Myers R.P. , Jiang S. , Girotto J.A. 
Published: July 2009

AbstractMesenchymal chondrosarcoma (MCS) is a rare malignancy that was first described by Lichtenstein and Bernstein in 1959. This paper reports the latest case of mandibular MCS and provides a review of cases of mandibular MCS from 1971 to the present. The literature was searched using the PubMed and Ovid engines; bibliographies were cross referenced. A meta‐analysis of the reported cases was performed and Kaplan–Meier curves generated for all treatment options. In the paediatric population, MCS is a rare and aggressive tumour. Since 1971, only 15 cases of MCS have been reported in the mandible of patients less than 20 years old. Surgical treatment positively impacts survival and is not improved with radiation or chemotherapy. Local recurrence was frequent, aggressive and dramatically affects survival. This meta‐analysis shows that primary intervention with surgery remains the standard of care for MCS. The role for chemotherapy and radiation therapy in the treatment of MCS remains unclear.
Infrequent clinicopathologic features of keratocystic odontogenic tumour: a 29‐year multi‐institutional retrospective review
Authors: Ide F. , Horie N. , Shimoyama T. , Saito I. , Tanaka A. , Kusama K. 
Published: July 2009

AbstractAim:  Keratocystic odontogenic tumour (KCOT), formerly known as odontogenic keratocyst, is an interesting and challenging entity. This study addresses the spectrum of clinicopathologic features of KCOT other than those classically described.Materials and methods:  Three hundred forty‐seven cases of KCOT from the records of three institutions over a period of 29 years were retrospectively reviewed to analyse their clinical presentation, radiographic features, histopathology and biological behaviour.Results:  Six cases of KCOT with infrequent findings were retrieved, none of which was associated with the nevoid basal cell carcinoma syndrome. Two lesions gave an erroneous radiographic impression of radicular cyst and nasopalatine duct cyst, respectively; the former periapical KCOT showed recurrence. An additional small KCOT adjacent to the initially presenting lesion was incidentally discovered, and both periradicular KCOT recurred twice. In interradicular KCOT, the growth rate of 2.4 mm per year was successfully estimated on radiographs. One paediatric KCOT showed a deceptive feature of eruption cyst and recurrence was not evident, despite of the fenestration. Microscopic rarities included mural cartilaginous metaplasia in a recurrent periradicular KCOT.Conclusions:  This series of cases substantiates the preceding observations that KCOT has a reputation for clinically confusing jaw lesions, often resulting in a potential endodontic or periodontal misdiagnosis. Believed to exhibit occasional recurrent behaviour, missing a diagnosis of KCOT has serious implications for the patient. Both in principle and in practice, the differential diagnosis of KCOT deserves consideration in non‐healing radiolucencies associated with the roots of teeth.
Mandibular reconstruction after resection of benign tumours using non‐vascularised methods in a series of patients that did not undergo radiotherapy
Authors: Mehrotra D. , Kumar S. , Pradhan R. 
Published: July 2009

AbstractAim:  A case series analysis of 52 consequent subjects of immediate mandibular reconstruction after tumour resection using non‐vascularised methods, undertaken at U.P. King George's University of Dental Sciences and King George's Medical University, is being reported. To assess the success of reconstruction on subjective and objective evaluation based upon Mandibular Reconstruction Assessment Scale (MRAS) questionnaire.Methods:  Patients with benign mandibular tumours irrespective of age, sex, site and socio‐economic status were included. Primary reconstruction was carried out after resection in two surgical units on surgeon's choice using stainless steel wire (6/52; 12%), stainless steel reconstruction plate (10/52; 19%) or titanium reconstruction plate (36/52; 69%) without bone graft (23/52; 44%) or with bone graft (29/52; 56%). Bone grafts were harvested from iliac crest (21/52; 40%), rib (2/52; 4%) and an additional pectoralis major myocutaneous flap with iliac crest bone graft (6/52; 12%) to provide cover to the reconstruction plate was also used.Results:  The primary outcome measurements were wound healing, mouth opening, chewing efficiency, jaw movements, cosmetic achievement and speech on a five‐point scale, all of which improved significantly after surgery. The overall complication rate was 17%. Three patients (6%) had loosening of the screw, two (4%) showed dehiscence of the plate, two (4%) showed tumour recurrence and one (2%) had infection of the graft that was subsequently removed.Conclusion:  Titanium reconstruction plates with iliac crest graft provided good result in the absence of microvascular reconstruction because of unavailable long operating time and lack of expertise. Long‐term satisfactory rehabilitation can be achieved using removable dentures or prosthesis on dental implants on the contraption provided by the non‐vascularised tissue despite non‐calcified bone visible on the skiagram.
Actinomycosis of the infratemporal fossa: an unusual cause of trismus
Authors: Sethi A. , Bansal R. , Sareen D. , Jain S. 
Published: July 2009

AbstractWe report the case of a 43‐year‐old female who presented to us with trismus. She was found to have unilateral tonsillar enlargement on examination. A computerised tomography scan revealed an enhancing mass lesion involving the infratemporal fossa and the parapharyngeal space. A fine needle aspiration cytology of the enlarged tonsil revealed actinomycosis. The patient responded well to tonsillectomy followed by medical management and is asymptomatic 6 months following the completion of treatment.
Angiography for multiple dental extractions in Sturge–Weber Syndrome: report of a case
Authors: Siddiqi A. , Morkel J.A. , Zafar S. 
Published: July 2009

AbstractSturge–Weber Syndrome is a rare neurocutaneous syndrome. This case involves a possible complication of excessive intra‐operative bleeding. Surgical management of such patients may be challenging due to the risk of haemorrhage. The purpose of this case report is to discuss the importance of pre‐operative angiography in such patients for oral surgical procedures.
Identification ofYersinia enterocoliticaat the Species and Subspecies Levels by Fourier Transform Infrared Spectroscopy
Authors: Kuhm Andrea Elisabeth , Suter Daniel , Felleisen Richard , Rau Jörg 
Published: July 2009

ABSTRACTYersinia enterocoliticaand otherYersiniaspecies, such asY. pseudotuberculosis,Y. bercovieri, andY. intermedia, were differentiated using Fourier transform infrared spectroscopy (FT-IR) combined with artificial neural network analysis. A set of well definedYersiniastrains from Switzerland and Germany was used to create a method for FT-IR-based differentiation ofYersiniaisolates at the species level. The isolates ofY. enterocoliticawere also differentiated by FT-IR into the main biotypes (biotypes 1A, 2, and 4) and serotypes (serotypes O:3, O:5, O:9, and “non-O:3, O:5, and O:9”). For external validation of the constructed methods, independently obtained isolates of differentYersiniaspecies were used. A total of 79.9% ofY. enterocoliticasensu stricto isolates were identified correctly at the species level. The FT-IR analysis allowed the separation of allY. bercovieri,Y. intermedia, andY. rohdeistrains fromY. enterocolitica, which could not be differentiated by the API 20E test system. The probability for correct biotype identification ofY. enterocoliticaisolates was 98.3% (41 externally validated strains). For correct serotype identification, the probability was 92.5% (42 externally validated strains). In addition, the presence or absence of theailgene, one of the main pathogenicity markers, was demonstrated using FT-IR. The probability for correct identification of isolates concerning theailgene was 98.5% (51 externally validated strains). This indicates that it is possible to obtain information about genus, species, and in the case ofY. enterocoliticaalso subspecies type with a single measurement. Furthermore, this is the first example of the identification of specific pathogenicity using FT-IR.
Cell Surface Engineering of a β-Galactosidase for Galactooligosaccharide Synthesis
Authors: Li Yumei , Lu Lili , Wang Hongmei , Xu Xiaodong , Xiao Min 
Published: July 2009

ABSTRACT

A novel gene encoding transglycosylating β-galactosidase (BGase) was cloned from
Penicillium expansum
F3. The sequence contained a 3,036-bp open reading frame encoding a 1,011-amino-acid protein. This gene was subsequently expressed on the cell surface of
Saccharomyces cerevisiae
EBY-100 by galactose induction. The BGase-anchored yeast could directly utilize lactose to produce galactooligosaccharide (GOS), as well as the by-products glucose and a small quantity of galactose. The glucose was consumed by the yeast, and the galactose was used for BGase expression, thus greatly facilitating GOS synthesis. The GOS yield reached 43.64% when the recombinant yeast was cultivated in yeast nitrogen base-Casamino Acids medium containing 100 g/liter initial lactose at 25°C for 5 days. The yeast cells were harvested and recycled for the next batch of GOS synthesis. During sequential operations, both oligosaccharide synthesis and BGase expression were maintained at high levels with GOS yields of over 40%, and approximately 8 U/ml of BGase was detected in each batch.
Sporicidal Activity of Synthetic Antifungal Undecapeptides and Control of
Penicillium
Rot of Apples
Authors: Badosa Esther , Ferré Rafael , Francés Jesús , Bardají Eduard , Feliu Lidia , Planas Marta , Montesinos Emilio 
Published: July 2009

ABSTRACT

The antifungal activity of cecropin A(2-8)-melittin(6-9) hybrid undecapeptides, previously reported as active against plant pathogenic bacteria, was studied. A set of 15 sequences was screened in vitro against
Fusarium oxysporum
,
Penicillium expansum
,
Aspergillus niger
, and
Rhizopus stolonifer
. Most compounds were highly active against
F. oxysporum
(MIC < 2.5 μM) but were less active against the other fungi. The best peptides were studied for their sporicidal activity and for Sytox green uptake in
F. oxysporum
microconidia. A significant inverse linear relationship was observed between survival and fluorescence, indicating membrane disruption. Next, we evaluated the in vitro activity against
P. expansum
of a 125-member peptide library with the general structure R-X
1
KLFKKILKX
10
L-NH
2
, where X
1
and X
10
corresponded to amino acids with various degrees of hydrophobicity and hydrophilicity and R included different N-terminal derivatizations. Fifteen sequences with MICs below 12.5 μM were identified. The most active compounds were BP21 {Ac,F,V} and BP34 {Ac,L,V} (MIC < 6.25 μM), where the braces denote R, X
1
, and X
10
positions and where Ac is an acetyl group. The peptides had sporicidal activity against
P. expansum
conidia. Seven of these peptides were tested in vivo by evaluating their preventative effect of inhibition of
P. expansum
infection in apple fruits. The peptide Ts-FKLFKKILKVL-NH
2
(BP22), where Ts is a tosyl group, was the most active with an average efficacy of 56% disease reduction, which was slightly lower than that of a commercial formulation of the fungicide imazalil.
Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows
Authors: Zinger L. , Coissac E. , Choler P. , Geremia R. A. 
Published: July 2009

ABSTRACT
Understanding how microbial community structure and diversity respond to environmental conditions is one of the main challenges in environmental microbiology. However, there is often confusion between determining the phylogenetic structure of microbial communities and assessing the distribution and diversity of molecular operational taxonomic units (MOTUs) in these communities. This has led to the use of sequence analysis tools such as multiple alignments and hierarchical clustering that are not adapted to the analysis of large and diverse data sets and not always justified for characterization of MOTUs. Here, we developed an approach combining a pairwise alignment algorithm and graph partitioning by using MCL (Markov clustering) in order to generate discrete groups for nuclear large-subunit rRNA gene and internal transcript spacer 1 sequence data sets obtained from a yearly monitoring study of two spatially close but ecologically contrasting alpine soils (namely, early and late snowmelt locations). We compared MCL with a classical single-linkage method (Ccomps) and showed that MCL reduced bias such as the chaining effect. Using MCL, we characterized fungal communities in early and late snowmelt locations. We found contrasting distributions of MOTUs in the two soils, suggesting that there is a high level of habitat filtering in the assembly of alpine soil fungal communities. However, few MOTUs were specific to one location.
Anaerobic Fermentation of Glycerol in
Paenibacillus macerans
: Metabolic Pathways and Environmental Determinants
Authors: Gupta Ashutosh , Murarka Abhishek , Campbell Paul , Gonzalez Ramon 
Published: July 2009

ABSTRACT

Paenibacillus macerans
is one of the species with the broadest metabolic capabilities in the genus
Paenibacillus
, able to ferment hexoses, deoxyhexoses, pentoses, cellulose, and hemicellulose. However, little is known about glycerol metabolism in this organism, and some studies have reported that glycerol is not fermented. Despite these reports, we found that several
P. macerans
strains are capable of anaerobic fermentation of glycerol. One of these strains,
P. macerans
N234A, grew fermentatively on glycerol at a maximum specific growth rate of 0.40 h
−1
and was chosen for further characterization. The use of [U-
13
C]glycerol and further analysis of extracellular metabolites and proteinogenic amino acids via nuclear magnetic resonance (NMR) spectroscopy allowed identification of ethanol, formate, acetate, succinate, and 1,2-propanediol (1,2-PDO) as fermentation products and demonstrated that glycerol is incorporated into cellular components. A medium formulation with low concentrations of potassium and phosphate, cultivation at acidic pH, and the use of a CO
2
-enriched atmosphere stimulated glycerol fermentation and are proposed to be environmental determinants of this process. The pathways involved in glycerol utilization and synthesis of fermentation products were identified using NMR spectroscopy in combination with enzyme assays. Based on these studies, the synthesis of ethanol and 1,2-PDO is proposed to be a metabolic determinant of glycerol fermentation in
P. macerans
N234A. Conversion of glycerol to ethanol fulfills energy requirements by generating one molecule of ATP per molecule of ethanol synthesized. Conversion of glycerol to 1,2-PDO results in the consumption of reducing equivalents, thus facilitating redox balance. Given the availability, low price, and high degree of reduction of glycerol, the high metabolic rates exhibited by
P. macerans
N234A are of paramount importance for the production of fuels and chemicals.
Carbonate Crystals Precipitated by Freshwater Bacteria and Their Use as a Limestone Consolidant
Authors: Zamarreño Dania V. , Inkpen Robert , May Eric 
Published: July 2009

ABSTRACTBacterial carbonate precipitation is known to be a natural phenomenon associated with a wide range of bacterial species. Recently, the ability of bacteria to produce carbonates has been studied for its value in the conservation of limestone monuments and concrete. This paper describes investigations of carbonate crystals precipitated by freshwater bacteria by means of histological (Loeffler's methylene blue and alcian blue-periodic acid-Schiff stain) and fluorescence (CTC [5-cyano-2,3-ditolyl tetrazolium chloride]) stains, determination of cell viability inside carbonate crystals, and pore size reduction in limestone by image analysis. Carbonate crystals were found to be composed of bacteria embedded in a matrix of neutral and acid polysaccharides. Cell viability inside the carbonate crystals decreased with time. On stone, bacteria were found to form carbonate crystals, with only a few bacteria remaining as isolated cells or as cell aggregates. Pore size was reduced by about 50%, but no blockage was detected. Taken together, the results of this research provide some reassurance to conservators that biocalcification by bacteria could be a safe consolidation tool in a restoration strategy for building stone conservation.
Alteration of the Ileal Microbiota of Weanling Piglets by the Growth-Promoting Antibiotic Chlortetracycline
Authors: Rettedal Elizabeth , Vilain Sébastien , Lindblom Stacy , Lehnert Kelly , Scofield Clay , George Sajan , Clay Sharon , Kaushik Radhey S. , Rosa Artur J. M. , Francis David , Brözel Volker S. 
Published: July 2009

ABSTRACTAntibiotics such as chlortetracycline (CTC) have been used to promote growth of pigs for decades, but concerns over increased antibiotic-resistant infections in humans have prompted the development of alternative strategies. Developing alternatives to antibiotic growth promoters (AGPs) could be informed by information on the mechanisms of growth promotion, notably, how AGPs affect the microbial populations of the gastrointestinal tract. Pigs from three sows were aseptically delivered by cesarean section. Six piglets were distributed to each of two foster mothers until weaning, when piglets were fed a diet with or without 50 mg/kg CTC for 2 weeks. The ileal bacterial microbiota was characterized by using a cultivation-independent approach based on DNA extraction, PCR amplification, cloning, and sequencing of the 16S rRNA gene pool. The ileal and mucosal communities of these growing pigs were dominated byLactobacillusbacteria, various members of the familyClostridiaceae, and members of the poorly known genusTuricibacter. Overall, CTC treatment resulted in three shifts: a decrease inLactobacillusjohnsonii, an increase inL.amylovorus, and a decrease inTuricibacterphylotypes. The composition of the microbiota varied considerably between individual pigs, as revealed by shared operational taxonomic units (OTUs) and similarity (SONS) analysis (θYCvalues). While the observed variation between untreated pigs obscured the possible effect of CTC, ∫-LIBSHUFF and SONS analyses of pooled libraries indicated a significant shift due to CTC in both the lumen and the mucosa, with some OTUs unique to either treated or control ileum. DOTUR analysis revealed little overlap between control and treated communities at the 3% difference level, indicating unique ileal communities in the presence of CTC.
The
ARG9
Gene Encodes the Plastid-Resident
N
-Acetyl Ornithine Aminotransferase in the Green Alga
Chlamydomonas reinhardtii
Authors: Remacle Claire , Cline Sara , Boutaffala Layla , Gabilly Stéphane , Larosa Véronique , Barbieri M. Rosario , Coosemans Nadine , Hamel Patrice P. 
Published: July 2009

ABSTRACT

Here we report the characterization of the
Chlamydomonas reinhardtii
gene
ARG9
, encoding the plastid resident
N
-acetyl ornithine aminotransferase, which is involved in arginine synthesis. Integration of an engineered
ARG9
cassette in the plastid chromosome of the nuclear
arg9
mutant restores arginine prototrophy. This suggests that
ARG9
could be used as a new selectable marker for plastid transformation.