bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inheritance of bacterial blight resistance in the rice cultivar Ajaya and high-resolution mapping of a major QTL associated with resistance
Authors: SUJATHA K. , NATARAJKUMAR P. , LAHA G. S. , MISHRA B. , RAO K. SRINIVASA , VIRAKTAMATH B. C. , KIRTI P. B. , HARI Y. , BALACHANDRAN S. M. , RAJENDRAKUMAR P. , RAM T. , HAJIRA S. K. , MADHAV M. SHESHU , NEERAJA C. N. , SUNDARAM R. M. 
Published: December 2011

SummaryThe cultivar Ajaya (IET 8585) exhibits durable broad-spectrum resistance to bacterial blight (BB) disease of rice and is widely used as a resistance donor. The present study was carried out to decipher the genetics of BB resistance in Ajaya and map the gene(s) conferring resistance. Genetic analysis in the F2indicated a quantitative/additive nature of resistance governed by two loci with equal effects. Linked marker analysis and allelic tests revealed that one of the resistance genes isxa5. Sequence analysis of a 244 bp region of the second exon of the gene-encoding Transcription factor IIAγ (the candidate gene forxa5) confirmed the presence ofxa5. Bulked-segregant analysis (BSA) revealed the putative location of the two quantitative trait loci (QTLs)/genes associated with resistance on chromosomes 5 and 8. Composite interval mapping located the first locus on Chr. 5S exactly in the genomic region spanned byxa5and the second locus (qtl BBR 8.1) on Chr. 8L. Owing to its differential disease reaction with a set of seven hyper-virulent isolates ofXanthomonas oryzae, a map location on Chr. 8L, which was distinct fromxa13and data from allelism tests, the second resistance locus in Ajaya was determined to be novel and was designated asxaAj. A contig map spanningxaAjwas constructedin silicoand the genomic region was delimited to a 13·5 kb physical interval.In silicoanalysis of the genomic region spanningxaAjidentified four putatively expressed candidate genes, one of which could be involved in imparting BB resistance in Ajaya along withxa5.
Physical properties of surface outcrop cataclastic fault rocks, Alpine Fault, New Zealand
Authors: Boulton C. , Carpenter B. M. , Toy V. , Marone C. 
Published: December 2011

We present a unified analysis of physical properties of cataclastic fault rocks collected from surface exposures of the central Alpine Fault at Gaunt Creek and Waikukupa River, New Zealand. Friction experiments on fault gouge and intact samples of cataclasite were conducted at 30–33 MPa effective normal stress (σn′) using a double‐direct shear configuration and controlled pore fluid pressure in a true triaxial pressure vessel. Samples from a scarp outcrop on the southwest bank of Gaunt Creek display (1) an increase in fault normal permeability (k = 7.45 × 10−20 m2 to k = 1.15 × 10−16 m2), (2) a transition from frictionally weak (μ = 0.44) fault gouge to frictionally strong (μ = 0.50–0.55) cataclasite, (3) a change in friction rate dependence (a‐b) from solely velocity strengthening, to velocity strengthening and weakening, and (4) an increase in the rate of frictional healing with increasing distance from the footwall fluvioglacial gravels contact. At Gaunt Creek, alteration of the primary clay minerals chlorite and illite/muscovite to smectite, kaolinite, and goethite accompanies an increase in friction coefficient (μ = 0.31 to μ = 0.44) and fault‐perpendicular permeability (k = 3.10 × 10−20 m2 to k = 7.45 × 10−20 m2). Comminution of frictionally strong (μ = 0.51–0.57) cataclasites forms weaker (μ = 0.31–0.50) foliated cataclasites and fault gouges with behaviors associated with aseismic creep at low strain rates. Combined with published evidence of large magnitude (Mw ∼ 8) surface ruptures on the Alpine Fault, petrological observations indicate that shear failure involved frictional sliding within previously formed, velocity‐strengthening fault gouge.
Bacteroidales ectosymbionts of gut flagellates shape the nitrogen-fixing community in dry-wood termites
Authors: Desai Mahesh S , Brune Andreas 
Published: December 2011

Abstract
Although it is well documented that the lack of nitrogen in the diet of wood-feeding termites is compensated by the nitrogen-fixing capacity of their gut microbiota, the bacteria responsible for this activity are largely unknown. Here, we analyzed the diversity and expression of nitrogenase genes (homologs of nifH) in four species of dry-wood termites (Kalotermitidae), which thrive on a particularly nitrogen-poor resource. Although each species harbored a highly diverse suite of termite-specific homologs in their microliter-sized hindgut, only a core set related to nifH genes of Treponema and Azoarcus spp., ‘Azobacteroides pseudotrichonymphae’, the first member of the Bacteroidales identified as a diazotroph, and termite-gut-specific anfH genes of hitherto unknown origin were preferentially expressed. Transcription patterns corroborated that the populations of active diazotrophs differ fundamentally between termite genera. Capillary-picked suspensions of the flagellates Devescovina arta and Snyderella tabogae revealed that their bacterial ectosymbionts each possess two paralogs of nifH, which apparently have been acquired consecutively during evolution of Bacteroidales, but only one of them (anfH) is actively expressed. Transcription patterns correlated neither with the molybdenum content of the diet nor with intestinal hydrogen concentrations, measured with microsensors. We propose that the nitrogen-fixing community in different dry-wood termites is shaped by the symbionts of their specific flagellate populations. Our findings suggest that the diazotrophic nature of ‘Armantifilum devescovinae’ has an important role in the nitrogen metabolism of dry-wood termites and is the driving force of co-evolution with its flagellate host.
High-yield oil palm expansion spares land at the expense of forests in
the Peruvian Amazon
Authors: Gutiérrez-Vélez Víctor H , DeFries Ruth , Pinedo-Vásquez Miguel , Uriarte María , Padoch Christine , Baethgen Walter , Fernandes Katia , Lim Yili 
Published: December 2011

Abstract
High-yield agriculture potentially reduces pressure on forests by requiring less land
to increase production. Using satellite and field data, we assessed the area
deforested by industrial-scale high-yield oil palm expansion in the Peruvian Amazon
from 2000 to 2010, finding that 72% of new plantations expanded into forested areas.
In a focus area in the Ucayali region, we assessed deforestation for high- and
smallholder low-yield oil palm plantations. Low-yield plantations accounted for most
expansion overall (80%), but only 30% of their expansion involved forest conversion,
contrasting with 75% for high-yield expansion. High-yield expansion minimized the
total area required to achieve production but counter-intuitively at higher expense
to forests than low-yield plantations. The results show that high-yield agriculture
is an important but insufficient strategy to reduce pressure on forests. We suggest
that high-yield agriculture can be effective in sparing forests only if coupled with
incentives for agricultural expansion into already cleared lands.
Vitamin D and its role in allergic disease
Authors: Reinholz M. , Ruzicka T. , Schauber J. 
Published: December 2011

SummaryIn Western countries, the incidence of atopy and allergic diseases is high and further rising. While genetic factors certainly play a role, epigenetic or even nutritional factors might also be important in the pathogenesis of allergies. Vitamin D – the ‘sunshine hormone’ – exerts profound effects on both adaptive and innate immune functions involved in the development and course of allergic diseases. As also the incidence of vitamin D insufficiency is surprisingly high in the general population, clinical and experimental studies have started to investigate if correcting vitamin D levels [measured as serum 25 hydroxy vitamin D ‐25(OH)D] is beneficial or even protective in patients with allergies or children at risk. This review highlights current data on the effects of vitamin D on the allergy‐mediating immune system and the vitamin D status in atopic patients. Furthermore, the benefits and risks of vitamin D supplementation during pregnancy, childhood and in adults with respect to the development and course of allergic disease are discussed.
An equivalent medium model for wave simulation in fractured porous rocks
Authors: Qi‐Zhen Du , Xue‐Mei Wang , Jing Ba , Qiang Zhang 
Published: December 2011

ABSTRACTSeismic wave propagation in reservoir rocks is often strongly affected by fractures and micropores. Elastic properties of fractured reservoirs are studied using a fractured porous rock model, in which fractures are considered to be embedded in a homogeneous porous background. The paper presents an equivalent media model for fractured porous rocks. Fractures are described in a stress‐strain relationship in terms of fracture‐induced anisotropy. The equations of poroelasticity are used to describe the background porous matrix and the contents of the fractures are inserted into a matrix. Based on the fractured equivalent‐medium theory and Biot's equations of poroelasticity, two sets of porosity are considered in a constitutive equation. The porous matrix permeability and fracture permeability are analysed by using the continuum media seepage theory in equations of motion. We then design a fractured porous equivalent medium and derive the modified effective constants for low‐frequency elastic constants due to the presence of fractures. The expressions of elastic constants are concise and are directly related to the properties of the main porous matrix, the inserted fractures and the pore fluid.The phase velocity and attenuation of the fractured porous equivalent media are investigated based on this model. Numerical simulations are performed. We show that the fractures and pores strongly influence wave propagation, induce anisotropy and cause poroelastic behaviour in the wavefields. We observe that the presence of fractures gives rise to changes in phase velocity and attenuation, especially for the slow P‐wave in the direction parallel to the fracture plane.
High‐resolution esophageal manometry: addressing thermal drift of the manoscan system
Authors: Robertson E. V. , Lee Y. Y. , Derakhshan M. H. , Wirz A. A. , Whiting J. R. H. , Seenan J. P. , Connolly P. , McColl K. E. L. 
Published: December 2011

AbstractBackground  The high resolution esophageal manometry system manufactured by Sierra Scientific Instruments is widely used. The technology is liable to ‘thermal drift’, a change in measured pressure due to change in temperature. This study aims to characterize ‘thermal drift’ and minimize its impact.Methods  Response of the system to immediate temperature change (20 °C to 37 °C) was tested. Accuracy of pressure measurement over two hours at 37 °C was examined. Six repetitions were performed and median pressure change calculated for each sensor. Sensors were compared using Kruskal‐Wallis test. Current correction processes were tested.Key Results  There was a biphasic response of the system to body temperature: an immediate change in recorded pressure, ‘thermal effect’ and an ongoing pressure change with time, ‘baseline drift’. Median thermal effect for all 36 sensors was 7 mmHg (IQR 3.8 mmHg). Median baseline drift was 11.1 mmHg (IQR 9.9 mmHg). Baseline drift varied between sensors but for a given sensor was linear. Interpolated thermal compensation, recommended for prolonged studies, corrects data assuming a linear drift of pressures. When pressures were corrected in this way, baseline pressure was almost restored to zero (Median 0.3 mmHg, IQR 0.3). The standard thermal compensation process did not address the error associated with baseline drift.Conclusions & Inferences  Thermal effect is well compensated in the current operation of the system but baseline drift is not well recognized or addressed. Incorporation of a linear correction into current software would improve accuracy without impact on ease of use.
Intestinal tissue engineering: current concepts and future vision of regenerative medicine in the gut
Authors: Bitar K. N. , Raghavan S. 
Published: December 2011

AbstractBackground and Purpose Functional tissue engineering of the gastrointestinal (GI) tract is a complex process aiming to aid the regeneration of structural layers of smooth muscle, intrinsic enteric neuronal plexuses, specialized mucosa, and epithelial cells as well as interstitial cells. The final tissue‐engineered construct is intended to mimic the native GI tract anatomically and physiologically. Physiological functionality of tissue‐engineered constructs is of utmost importance while considering clinical translation. The construct comprises of cellular components as well as biomaterial scaffolding components. Together, these determine the immune response a tissue‐engineered construct would elicit from a host upon implantation. Over the last decade, significant advances have been made to mitigate adverse host reactions. These include a quest for identifying autologous cell sources like embryonic and adult stem cells, bone marrow‐derived cells, neural crest‐derived cells, and muscle derived‐stem cells. Scaffolding biomaterials have been fabricated with increasing biocompatibility and biodegradability. Manufacturing processes have advanced to allow for precise spatial architecture of scaffolds to mimicin vivomilieu closely and achieve neovascularization. This review will focus on the current concepts and the future vision of functional tissue engineering of the diverse neuromuscular structures of the GI tract from the esophagus to the internal anal sphincter.
‘Idiopathic’ intestinal failure – the importance of identifying and treating primary psychopathology
Authors: Bourke J. , Soldan J. , Silk D. B. A. , Aziz Q. , Libby G. W. 
Published: December 2011

AbstractBackground  Gastrointestinal neuromuscular disorders (GINMD) are an important cause of intestinal failure (IF). We present six cases of IF in whom a diagnosis of GINMD was initially suspected, but in whom psychopathology was discovered to be the primary etiology.Methods  (i) Six consecutive cases referred to our unit with IF, initially presumed to be due to GINMD, were selected. Informed consent was obtained from all patients. Case notes were reviewed for salient clinical information. (ii) A literature search was performed to ascertain the epidemiology of psychopathology in IF and the current evidence for the management of severe functional GI disorders with a multidisciplinary psychiatric approach.Key Results  (i)All six cases required multidisciplinary psychiatric management in a specialized psychiatric unit that included the use of antidepressants, antipsychotics, mood stabilizers, and Electroconvulsive therapy in addition to nutritional support via enteral or parenteral routes. (ii) The evidence base for the treatment of severe FGIDs is sparse.Conclusions & Inferences  There is a need for additional reporting of such cases and further research. Our experience would suggest that a delay in the involvement of a specialist liaison psychiatrist has the potential to be life threatening in such cases. This may be more likely with greater severity, where the apparent predominance of ‘physical’ symptoms generates reluctance in both patient and physician to consider a psychiatric etiology and also appears to occur due to a lengthier investigative process than existed previously. We therefore propose that the provision of a specialist psychiatric assessment for all patients presenting with IF is indicated at the point of initial clinical contact, based upon the substantial clinical benefit it has the potential to confer upon a significant minority. This process need not delay investigation, which can continue as indicated in parallel, but can be life‐saving.
Biological and functional characteristics of a novel low–molecular weight antagonist of glucose‐dependent insulinotropic polypeptide receptor, SKL‐14959, in vitro and in vivo
Authors: Nakamura T. , Tanimoto H. , Mizuno Y. , Tsubamoto Y. , Noda H. 
Published: December 2011

Aim: We recently discovered a glucose‐dependent insulinotropic polypeptide (GIP) receptor antagonist, SKL‐14959. GIP plays a role in the glucose and lipid metabolism, and is associated with obesity and insulin resistance. Therefore, we aimed to ascertain the inhibitory potency and glucose and lipid metabolism of SKL‐14959.Methods: SKL‐14959 was evaluated for its binding affinity to each GIP, glucagon‐like peptide‐1 (GLP‐1) and glucagon receptors by each labelled and non‐labelled ligand; GIP‐stimulated cyclic AMP (cAMP) production in CHO cells expressing human GIP receptor in vitro. Oral and intraperitoneal glucose tolerance tests (OGTT and IPGTT) were performed to examine the insulinotropic effect on endogenous and exogenous GIP. Oil tolerance tests were also conducted to examine the lipid metabolism and the postheparin plasma lipase activity, lipoprotein lipase (LPL) and hepatic lipase (HL).Result: SKL‐14959 selectively bound to GIP receptor and inhibited GIP‐stimulated cAMP production with the Ki value of 55 nM and an IC50 value of 2.9 µM, respectively. SKL‐14959·Na significantly increased blood glucose levels, inhibited insulin secretion in OGTT and inhibited the plasma glucose lowering of exogenous GIP in IPGTT. Furthermore, SKL‐14959 increased plasma triacylglycerol (TG) levels as well as suppressed the postheparin plasma lipase activity in an oil load test.Conclusion: These data indicate that SKL‐14959 is distinguished in the physiological phenotype of GIP following direct binding to the receptor.
The female postabdomen of the enigmatic Nannochoristidae (Insecta: Mecopterida) and its phylogenetic significance
Authors: Hünefeld Frank , Beutel Rolf Georg 
Published: December 2011

AbstractHünefeld, F. and Beutel, R.G. 2011. The female postabdomen of the enigmatic Nannochoristidae (Insecta: Mecopterida) and its phylogenetic significance. —Acta Zoologica (Stockholm) 00: 1–8.External and internal features of the female postabdomen of Nannochorista neotropica are described in detail. The conditions found in females of Nannochoristidae come closest to the ground plan of Mecopterida. This lineage is characterised by telescoping postabdominal segments, a presumptive autapomorphic feature that is modified in some antliophoran groups, but displayed by the nannochoristid species in a typical manner. More potential autapomorphies of Mecopterida, all present in Nannochoristidae, are the neo‐formation of an intersegmental muscle, a transverse muscle spanning between the genital appendages of segment VIII, a muscle connecting these appendages and the genital chamber and the loss of an intersegmental muscle. Plesiomorphic features of Nannochoristidae are the presence of paired genital appendages on segments VIII and IX. Information on the egg‐depositing substrates of the females is not available. The telescoping postabdomen is suitable for oviposition in soft substrates such as moist soil, or rotten plant materials in the riparian zone, and this is possibly a ground‐plan feature of Mecopterida. The results of recent phylogenetic analyses based on morphological data support a placement of Nannochoristidae in Antliophora, whereas the exact position of the group remains ambiguous. No characters of the female postabdomen were found supporting the monophyly of Mecoptera as conventionally circumscribed, that is Nannochoristidae + Boreidae + Pistillifera.
Optimising repeat prostate biopsy decisions and procedures
Authors: Kirby Roger , Fitzpatrick John M. 
Published: December 2011

What's known on the subject? and What does the study add?Due to the fear of missing clinically significant cancer, it is often uncertain whether a repeat biopsy should be performed in men with ≥1 prior negative prostate biopsies but persistent suspicion of prostate cancer. However, the repeat biopsy may again be negative and a biopsy may be associated with anxiety, discomfort and complications (resulting in hospitalisation in 4.1% of men).This review discusses strategies to optimise repeat biopsy procedures in order to better predict the biopsy outcome. Optimising repeat biopsy procedures include adjusting the location and number of cores and the use of MRI to detect suspicious areas. The use of diagnostic markers, e.g. (Prostate CAncer) gene 3, which is predictive of biopsy outcome, can aid in guiding repeat biopsy decisions and reduce the number of unnecessary and uncomfortable biopsies.To review strategies to optimise repeat biopsy procedures and to better predict the biopsy outcome. As it is often uncertain whether a repeat biopsy should be performed in men with ≥1 previous negative prostate biopsies but persistent suspicion of prostate cancer. The repeat biopsy may also be negative and a biopsy may be associated with anxiety, discomfort and occasionally (severe) complications. A search in PubMed was performed to find English language original and review articles related to repeat prostate biopsies. Strategies to optimise repeat biopsy procedures include applying the appropriate indications and adjusting the location and number of biopsy cores. The PROGENSA™ Prostate CAncer gene 3 (PCA3) Assay is a highly prostate cancer‐specific test. A higher PCA3 Score corresponds with an increased probability of a positive repeat biopsy and including the PCA3 Score in multivariate models significantly increased their predictive accuracy for predicting repeat biopsy outcome. The PCA3 Score seems also to be predictive of future biopsy outcome. In clinical practice it is often uncertain whether a prostate biopsy should be repeated or not. Optimising repeat biopsy procedures and the use of diagnostic markers, such as PCA3, can increase the probability of a positive repeat biopsy and reduce the number of unnecessary and uncomfortable biopsies