bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local time‐dependent Pi2 frequencies confirmed by simultaneous observations from THEMIS probes in the inner magnetosphere and at low‐latitude ground stations
Authors: Kwon H.‐J. , Kim K.‐H. , Lee D.‐H. , Takahashi K. , Angelopoulos V. , Lee E. , Jin H. , Park Y.‐D. , Lee J. , Sutcliffe P. R. , Auster H. U. 
Published: December 2011

Using electric and magnetic field data from Time History of Events and Macroscale Interactions during Substorms (THEMIS) fast mode waves away from midnight. probes (TH‐A, TH‐D, and TH‐E) acquired in the inner magnetosphere (L < 4) and low‐latitude ground magnetic field data from Bohyun (BOH, L = 1.35) and Hermanus (HER, L = 1.83) stations, we studied longitudinal variations of Pi2‐associated fast mode waves away from midnight. We selected 48 nightside Pi2 events at BOH identified when THEMIS probes were in the inner magnetosphere for 1 month (February 2008). During that period the probes were located between 4.0 and 20.0 magnetic local time (MLT), i.e., at and on either side of the dayside sector. This choice was motivated by our interest in studying loss of Pi2 wave energy away from its nominal source at the nightside, all the way to the dayside. Between 4.0 and 8.0 MLT the probes often observed poloidal oscillations in space during BOH Pi2 events. The poloidal oscillations had high coherence (>0.6) with BOH Pi2s and radially standing fast mode structures. Thus, these fast mode waves are explained by plasmaspheric resonance. On the duskside, however, few events at THEMIS probes had high coherence with BOH Pi2s. Furthermore, the THEMIS probe data showed no evidence of Pi2 signals at 9.0–18.0 MLT, which is consistent with previous studies. Most of the high‐coherence events were detected when the local time separation between the THEMIS probes and BOH was less than 3 h. These observations suggest that Pi2 wave energy is lost as it propagates azimuthally from a source region localized in longitude. From longitudinally separated simultaneous multipoint observations at THEMIS probes and BOH and HER stations, we found that the Pi2 frequency varies with longitude both in space and on the ground. This implies that although plasmaspheric fast mode waves establish a standing wave structure on a given meridional plane, their frequency changes with longitude if the plasmasphere is not axisymmetric. Finally, we show that a low‐latitude daytime Pi2 is not a fast mode wave propagating to the dayside through the magnetosphere.
Bacterial cis-2-unsaturated fatty acids found in the cystic fibrosis airway modulate virulence and persistence of Pseudomonas aeruginosa
Authors: Twomey Kate B , O'Connell Oisin J , McCarthy Yvonne , Dow J Maxwell , O'Toole George A , Plant Barry J , Ryan Robert P 
Published: December 2011

Abstract
There is an increasing appreciation of the polymicrobial nature of many bacterial infections such as those associated with cystic fibrosis (CF) and of the potentially important role for interspecies interactions in influencing both bacterial virulence and response to therapy. Patients with CF are often co-infected with Pseudomonas aeruginosa and other pathogens including Burkholderia cenocepacia and Stenotrophomonas maltophilia. These latter bacteria produce signal molecules of the diffusible signal factor (DSF) family, which are cis-2-unsaturated fatty acids. We have previously shown by in vitro studies that DSF from S. maltophilia leads to altered biofilm formation and increased resistance to antibiotics by P. aeruginosa; these responses of P. aeruginosa require the sensor kinase PA1396. Here we show that DSF signals are present in sputum taken from patients with CF. Presence of these DSF signals was correlated with patient colonization by S. maltophilia and/or B. cenocepacia. Analysis of 50 clinical isolates of P. aeruginosa showed that each responded to the presence of synthetic DSF by increased antibiotic resistance and these strains demonstrated little sequence variation in the PA1396 gene. In animal experiments using CF transmembrane conductance regulator knockout mice, the presence of DSF promoted P. aeruginosa persistence. Furthermore, antibiotic resistance of P. aeruginosa biofilms grown on human airway epithelial cells was enhanced in the presence of DSF. Taken together, these data provide substantial evidence that interspecies DSF-mediated bacterial interactions occur in the CF lung and may influence the efficacy of antibiotic treatment, particularly for chronic infections involving persistence of bacteria.
Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils
Authors: Zhang Li-Mei , Hu Hang-Wei , Shen Ju-Pei , He Ji-Zheng 
Published: December 2011

Abstract
Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH&lt;4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. 13CO2-DNA-stable isotope probing results showed significant assimilation of 13C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO2 fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active 13CO2-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices
Authors: Harmston Nathan , Filsell Wendy , Stumpf Michael P. H. 
Published: December 2011

AbstractMotivation: The scientific literature contains a wealth of information about biological systems. Manual curation lacks the scalability to extract this information due to the ever-increasing numbers of papers being published. The development and application of text mining technologies has been proposed as a way of dealing with this problem. However, the inter-species ambiguity of the genomic nomenclature makes mapping of gene mentions identified in text to their corresponding Entrez gene identifiers an extremely difficult task. We propose a novel method, which transforms a MEDLINE record into a mixture of adjacency matrices; by performing a random walkover the resulting graph, we can perform multi-class supervised classification allowing the assignment of taxonomy identifiers to individual gene mentions. The ability to achieve good performance at this task has a direct impact on the performance of normalizing gene mentions to Entrez gene identifiers. Such graph mixtures add flexibility and allow us to generate probabilistic classification schemes that naturally reflect the uncertainties inherent, even in literature-derived data.Results: Our method performs well in terms of both micro- and macro-averaged performance, achieving micro-F1 of 0.76 and macro-F1 of 0.36 on the publicly available DECA corpus. Re-curation of the DECA corpus was performed, with our method achieving 0.88 micro-F1 and 0.51 macro−F1. Our method improves over standard classification techniques [such as support vector machines (SVMs)] in a number of ways: flexibility, interpretability and its resistance to the effects of class bias in the training data. Good performance is achieved without the need for computationally expensive parse tree generation or ‘bag of words classification’.Contact: m.stumpf@imperial.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Expression of Microbiota, Toll‐like Receptors, and Their Regulators in the Small Intestinal Mucosa in Celiac Disease
Authors: Kalliomäki Marko , Satokari Reetta , Lähteenoja Hannu , Vähämiko Sanna , Grönlund Juhani , Routi Taina , Salminen Seppo 
Published: December 2011

ABSTRACTObjectives:Less than one‐tenth of the carriers of the risk genes HLA‐DQ2 or HLA‐DQ8 develop celiac disease, suggesting that other genetic and environmental factors are important in the pathogenesis. The role of gut microbiota has been addressed previously with inconsistent findings. Our aim was to evaluate microbiota, its receptors (Toll‐like receptors [TLRs]), and regulators of the TLRs in the small intestinal mucosa in celiac disease.Methods:Microbiota was analyzed by quantitative polymerase chain reaction (total bacteria and 10 bacterial group‐ and species‐specific primers) and gene expression of interleukin‐8 (IL‐8), TLR2, TLR3, TLR4, TLR5, TLR9, and regulators of TLRs, Toll‐interacting protein (TOLLIP), and single immunoglobulin IL‐1R–related molecule, by relative quantitative reverse transcription‐polymerase chain reaction in 10 children with celiac disease (untreated celiacs), 9 children with normal small intestinal mucosa (controls), and 6 adults with celiac disease with normal small intestinal mucosa after following a gluten‐free diet (treated celiacs).Results:Small intestinal microbiota was comparable among controls, untreated celiacs, and treated celiacs. Expression of IL‐8 mRNA, a marker of intestinal inflammation, was significantly increased in untreated celiacs as compared with treated celiacs (P = 0.002) and controls (P = 0.001). Expression of TLR‐2 mRNA was significantly decreased in untreated (P = 0.001) and treated (P = 0.03) celiacs, whereas expression of TLR‐9 mRNA was increased in untreated celiacs (P = 0.001) as compared with controls. Expression of TOLLIP mRNA was downregulated in untreated celiacs as compared with controls (P = 0.02).Conclusions:Altered gene expression of TLR2, TLR9, and TOLLIP in small intestinal biopsies in celiac disease suggests that microbiota‐associated factors may be important in the development of the disease.
A case series of thermal scald injuries in dogs exposed to hot water from garden hoses (garden hose scalding syndrome)
Authors: Quist Erin M. , Tanabe Mika , Mansell Joanne E. K. L. , Edwards Jeffrey L. 
Published: December 2011

AbstractIn this report, we present a series of cases of thermal burns (scalds) in dogs resulting from exposure to hot water from a garden hose that had been lying in the sun. These dogs typically inhabited the southern and western regions of the USA, where the recorded high temperatures often exceed 32°C (90°F) during the warm summer months. Dogs with thermal scald injury in these cases presented with linear thermal burns along the dorsum, in addition to a variety of other macroscopic lesions that were dependent upon the degree of burn exposure and ranged from local erythema to ulcerated, necrotic and sloughing skin. Chronic, healed wounds were often alopecic, with markedly thickened skin and characteristically smooth and glassy scar tissue formation. Histologically, the lesions of thermal scald injury in these dogs were indistinguishable from any other second or third degree burn, and consisted of full‐thickness dermal and epidermal necrosis with occasional fibrinoid necrosis of vessel walls, vasculitis and intravascular thrombosis. Here, we closely examine 10 cases of dogs with dorsal thermal burns collected from Texas, Arizona, California, Utah, Nevada, Indiana, Michigan and North Carolina and propose the term ‘garden hose scalding syndrome (GHS)’ to describe this unique type of scald injury.
A child with BK virus infection: Inadequacy of current therapeutic strategies
Authors: Pereira Tanya , Rojas Claudia P. , Garcia‐Buitrago Monica T. , Chandar Jayanthi , Abitbol Carolyn , Seeherunvong Wacharee , Rusconi Paolo , Bruce Jocelyn H. , Zilleruelò Gaston 
Published: December 2011

Pereira T, Rojas CP, Garcia‐Buitrago MT, Chandar J, Abitbol C, Seeherunvong W, Rusconi P, Bruce JH, Zilleruelò G. A child with BK virus infection: Inadequacy of current therapeutic strategies.  Pediatr Transplantation 2011. © 2011 John Wiley & Sons A/S.Abstract:  In this report, we describe the development of BKVN in the native kidneys of a child with a cardiac transplant. Elevated BK viral DNA load by PCR necessitated a prolonged course of treatment with escalating doses of cidofovir. Despite a reduction in plasma BK viral load, the infection evolved into an invasive CNS disease, resulting in rhomboencephalitis. This case highlights the need for awareness of the possibility of developing multiorgan complications from BKV infection. The current treatment options for BKV tissue invasive disease are inadequate and need to be improved.
Topical application of 0.005% latanoprost increases episcleral venous pressure in normal dogs
Authors: Tsai Susan , Miller Paul E. , Struble Craig , Howard Susan , Almazan Alexandra , Burke James A. , Hughes Patrick M. , Li Huajiang , Conforti Paul , Lee Susan S. , Robinson Michael R. 
Published: December 2011

AbstractIntroduction  Episcleral venous pressure (EVP) has an important role in intraocular pressure (IOP) homeostasis and accounts for more than 70% of the IOP in the normal dog. A frequently used species in glaucoma research is the normotensive dog especially when evaluating the efficacy of prostaglandin analogues and prostamides; however, aqueous humor dynamic studies in normal dogs are lacking, and the effect of 0.005% latanoprost on canine EVP is not known. We sought to determine the effects to the EVP of topically applied 0.005% latanoprost in the normotensive beagle dog.Methods  Female beagle dogs (n = 14) were used and each had a normal ophthalmic examination on study entry. EVP was determined using a standard episcleral venomanometer. Animals were dosed in one eye with 0.005% latanoprost, and the effects on EVP were compared with the averaged baseline EVP’s determined in the predosing phase and the fellow nondosed eye. The Mixed Model Repeated Measures method was used to analyze the EVP data.Results  During the dosing phase of the study with topical 0.005% latanoprost, the mean EVPs of dosed eyes were significantly higher than that of nondosed eyes (P < 0.0001).Conclusions  The increase in EVP in the dog with exposure to topical 0.005% latanoprost has not been observed in other species that have been studied, such as in the mouse and in humans, where the drug had no significant effect on the EVP. This response may be unique to dogs and suggests that dogs may not fully mimic human aqueous humor dynamics with topical 0.005% latanoprost. Although frequently performed in human studies, EVP should not be regarded to be a constant value in aqueous humor dynamic studies in the normal beagle dog.
Importance of metabolic changes induced by chemotherapy on prognosis of early‐stage breast cancer patients: a review of potential mechanisms
Authors: Gadéa E. , Thivat E. , Planchat E. , Morio B. , Durando X. 
Published: December 2011

SummaryWeight variation has been reported as a side effect of chemotherapy treatment in early breast cancer patients and has been identified as a factor of poor prognosis. Causes of weight variation during chemotherapy and mechanisms involved in the poor prognosis have been little studied. Here is reviewed the current knowledge about the main causes and mechanisms involved in body weight change. Special emphasis is placed on factors associated with weight variation which could potentially be involved in the risk of relapse in breast cancer survivors. In recent decades, some studies have investigated the causes of weight variation by studying energy balance of breast cancer patients during chemotherapy. Weight gain or loss may be the consequence of energy imbalance through different factors linked with chemotherapy, such as poor treatment tolerance, decreased muscle mass and function, or hormonal alterations. This results in body composition modifications in favour of fat gain and/or lean body mass loss. Increased adipose tissue, especially in the abdominal region, could induce metabolic disturbances such as insulin resistance, through various pathways involving adipokines. These molecules have growth properties and could therefore play a role in cancer relapse. Understanding such mechanisms is key to developing preventive strategies for improving the prognosis of early‐stage breast cancer patients.
The differential effect of illicit drug use on cognitive function in first‐episode psychosis and healthy controls
Authors: Donoghue K. , Mazzoncini R. , Hart J. , Zanelli J. , Morgan C. , Dazzan P. , Morgan K. D. , Murray R. M. , Jones P. B. , Doody G. A. 
Published: December 2011

Donoghue K, Mazzoncini R, Hart J, Zanelli J, Morgan C, Dazzan P, Morgan KD, Murray RM, Jones PB, Doody GA. The differential effect of illicit drug use on cognitive function in first‐episode psychosis and healthy controls.Objective::  Illicit drug use can result in impairment in cognitive function in healthy individuals. Individuals with a psychotic disorder also show a deficit in cognitive function. Drug use may simply contribute to the characteristic cognitive deficit found in psychosis or alternatively result in a ‘double deficit’. This study aims to investigate the association between drug use and cognitive function at the first‐episode of psychosis and in community‐matched controls.Method::  One hundred and seventy‐seven patients at the first episode of psychosis completed a battery of neuropsychological tests. Those that had used drugs in the previous year (n = 80) were compared with those who had not used drugs in the previous year (n = 97). A subsample of the first‐episode psychosis patients were compared with community‐matched controls (n = 110) according to drug‐use status.Results::  Patients with a first episode of psychosis who had used drugs performed equally to those who had not used drugs on neuropsychological tests. In contrast, healthy controls who had used drugs in the previous year performed worse on tests of executive function and working memory compared with those controls that had not used drugs.Conclusion::  There are differential associations of illicit drug misuse with cognitive function for first‐episode psychosis patients and healthy controls.
Causal theory and the etiology of periodontal diseases
Authors: Heaton Brenda , Dietrich Thomas 
Published: December 2011

AbstractCausal theory and causal models have proven to be helpful in understanding the multi‐factorial causation of many diseases, including periodontitis. The design and application of causal models is essential to the appropriate design, conduct and analysis of studies on periodontal disease causation. This review discusses the principles of causation and causal theory, both in general and as they pertain to studies of the etiology of periodontitis. Specifically, we present an overview of models of causation, including the potential outcomes model, the sufficient component cause model, and directed acyclic graphical models. More thorough explanations and accompanying illustrations are provided for the sufficient component cause model and the directed acyclic graphical model. Topics related to the study of periodontitis, as illustrated by such models, include the principles of confounding and effect measure modification (interaction). Existing models of periodontitis etiology are critically reviewed in this context.
Using administrative data for epidemiological research: case study to identify persons with periodontitis
Authors: Spangler Leslie , Chaudhari Monica , Barlow William E. , Newton Katherine M. , Inge Ronald , Hujoel Philippe , Genco Robert J. , Reid Robert J. 
Published: December 2011

AbstractThe availability of automated administrative databases in medical and dental healthcare, combined with modern computing power, allows sophisticated multi‐layered analyses of the causes and consequences of care delivered to large populations. These automated databases are now also commonly linked to data extracted from electronic medical records, and are used to measure health system performance, adjust payments, assess providers for quality improvement purposes, and inform policy decisions. Use of health insurance databases can be particularly powerful when linked through common unique identifiers to allow examination of the influences of dental care on medical outcomes and costs, and vice versa. This review describes the growing use of these databases for epidemiological and health services research, their advantages and limitations, and presents a case study in which dental claims data are used to identify persons with periodontitis in order to enable critical assessment of the relationship between periodontal interventions and systemic health outcomes/medical costs.
Association study of CARD8 (p.C10X) and NLRP3 (p.Q705K) variants with rheumatoid arthritis in French and Tunisian populations
Authors: Ben Hamad M. , Cornelis F. , Marzouk S. , Chabchoub G. , Bahloul Z. , Rebai A. , Fakhfakh F. , Ayadi H. , Petit‐Teixeira E. , Maalej A. 
Published: December 2011

SummaryThe objective of the study was to investigate the association of caspase activating and recruitment domain 8 (CARD8) and nucleotide‐binding oligomerization domain, leucine‐rich repeat and pyrin domain containing 3 (NLRP3) polymorphisms with rheumatoid arthritis (RA) in Tunisian and French populations. CARD8 (c.30T>A, rs2043211) and NLRP3 (c.2113C>A, rs35829419) single nucleotide polymorphisms (SNPs) were genotyped in 100 French RA trio families and 141 Tunisian patients with RA and 191 unrelated healthy controls, using TaqMan® allelic discrimination assay. The genetic analyses for the association and linkage in French families were performed using the comparison of allelic frequencies (AFBAC), the genotype relative risk (GRR) and the transmission disequilibrium test (TDT). Data for case and control samples were analysed by chi‐square‐test, GRR and odds ratio (OR). No significant differences between alleles and genotypes frequencies were detected in French trio and Tunisian patients with RA and controls, either with CARD8 or with NLRP3 SNPs both in French and in Tunisian populations. Moreover, stratifying patients according to the presence of rheumatoid factor (RF), anti‐cyclic peptides antibodies (ACPA), erosion, nodules, other autoimmune disease or HLA‐DRB1*04‐positive subgroups did not show any significant association with CARD8 or NLRP3 (P ≥ 0.05). This study suggests that variations in the innate immunity genes CARD8 (p.C10X) and NLRP3 (p.Q705K) have no effect on RA susceptibility either in the Tunisian or in the French population.