bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics and the respiratory effects of air pollution exposure
Authors: HOLLOWAY JOHN W. , SAVARIMUTHU FRANCIS SANTIYAGU , FONG KWUN M. , YANG IAN A. 
Published: March 2012

ABSTRACTAdverse health effects from air pollutants remain important, despite improvement in air quality in the past few decades. The exact mechanisms of lung injury from exposure to air pollutants are not yet fully understood. Studying the genome (e.g. single‐nucleotide polymorphisms (SNP) ), epigenome (e.g. methylation of genes), transcriptome (mRNA expression) and microRNAome (microRNA expression) has the potential to improve our understanding of the adverse effects of air pollutants. Genome‐wide association studies of SNP have detected SNP associated with respiratory phenotypes; however, to date, only candidate gene studies of air pollution exposure have been performed. Changes in epigenetic processes, such DNA methylation that leads to gene silencing without altering the DNA sequence, occur with air pollutant exposure, especially global and gene‐specific methylation changes. Respiratory cell line and animal models demonstrate distinct gene expression signatures in the transcriptome, arising from exposure to particulate matter or ozone. Particulate matter and other environmental toxins alter expression of microRNA, which are short non‐coding RNA that regulate gene expression. While it is clearly important to contain rising levels of air pollution, strategies also need to be developed to minimize the damaging effects of air pollutant exposure on the lung, especially for patients with chronic lung disease and for people at risk of future lung disease. Careful study of genomic responses will improve our understanding of mechanisms of lung injury from air pollution and enable future clinical testing of interventions against the toxic effects of air pollutants.
Correlation between circulating fibrocytes, and activity and progression of interstitial lung diseases
Authors: FUJIWARA ATSUSHI , KOBAYASHI HIROYASU , MASUYA MASAHIRO , MARUYAMA MITSUKO , NAKAMURA SHIHO , IBATA HIDENORI , FUJIMOTO HAJIME , OHNISHI MASAHIRO , URAWA MASAHITO , NAITO MASAHIRO , TAKAGI TAKEHIRO , KOBAYASHI TETSU , GABAZZA ESTEBAN C. , TAKEI YOSHIYUKI , TAGUCHI OSAMU 
Published: March 2012

ABSTRACTBackground and objective:  Interstitial lung diseases (ILD) are characterized by progressive interstitial pulmonary fibrosis and a decline in lung function. Fibrocytes are bone marrow‐derived mesenchymal progenitor cells that may play a role in the pathogenesis of pulmonary fibrosis. Circulating fibrocyte numbers have been correlated with the prognosis of patients with idiopathic pulmonary fibrosis. The aim of the present study was to evaluate the relationship between circulating fibrocytes, and parameters of disease activity and progression in several groups of patients with ILD.Methods:  The study population comprised 41 patients with ILD and seven healthy control subjects. Circulating CD45+ collagen‐I+ fibrocytes were evaluated by flow cytometry.Results:  The number of circulating fibrocytes was significantly increased in all patients with ILD and particularly in patients with idiopathic interstitial pneumonitis and interstitial pneumonitis associated with collagen vascular disease as compared with healthy control subjects. The numbers of circulating fibrocytes were significantly correlated with pulmonary function test parameters and with serum levels of sialylated carbohydrate antigen, a marker of disease activity. Temporal changes in circulating fibrocyte numbers were evaluated in two patients, and the results suggested that these changes correlated with the activity of ILD.Conclusions:  The results from this study provide further evidence for the role of circulating fibrocytes in fibrotic lung diseases.
Novel posterior reconstruction technique during robot‐assisted laparoscopic prostatectomy: Description and comparative outcomes
Authors: Jeong Chang Wook , Oh Jong Jin , Jeong Seong Jin , Hong Sung Kyu , Byun Seok‐Soo , Choe Gheeyoung , Lee Sang Eun 
Published: March 2012

AbstractThe aim of the present study was to assess the impact of a novel posterior reconstruction technique during robot‐assisted laparoscopic prostatectomy on continence recovery. A total of 116 consecutive patients who received the novel posterior reconstruction (case group) were retrospectively compared with a cohort of 126 patients who did not receive posterior reconstruction (control group). The primary end‐point was the duration of continence recovery (no pad use) after robot‐assisted laparoscopic prostatectomy. The posterior reconstruction was obtained by opposing the median dorsal fibrous raphe to the posterior counterpart of the detrusor apron, rather than the Denonvilliers' fascia. The case group showed higher continence rates at all points of evaluation, which were 2 weeks (30.1% vs 19.8%), 1 month (58.4% vs 45.7%), 3 months (82.7% vs 70.5%) and 6 months postoperatively (95.3% vs 86.4%) (P = 0.007). Application of the novel posterior reconstruction technique, age and length of membranous urethra were significant variables for the complete recovery of continence on multivariable analysis. This study shows that the application of this novel PR technique significantly improves the recovery of continence in patients undergoing robot‐assisted laparoscopic prostatectomy.
Fatigue assessment and failure analysis of shot‐peened leaf springs
Authors: FRAGOUDAKIS R. , SAIGAL A. , SAVAIDIS G. , MALIKOUTSAKIS M. , BAZIOS I. , SAVAIDIS A. , PAPPAS G. , KARDITSAS S. 
Published: March 2012

ABSTRACTThe paper deals with the fatigue and failure analysis of serial shot‐peened leaf springs of heavy trucks emphasizing on the influence of thermal treatment and shot peening on fatigue life. Experimental stress–life curves are determined by investigating smooth specimens subjected to fully reversed rotating bending conditions. These test results are compared to corresponding ones determined from cyclic three‐point bend tests on shot‐peened serial leaf springs in order to reveal the influence of the applied thermal treatment and shot peening process on the fatigue life of the high‐strength steel used for leaf spring manufacturing, dependent on the load level. Microstructure, macro‐ and micro‐hardness analyses are performed to support the analyses and explain the effects resulting from the certain shot peening process on the surface properties of the high‐strength spring steel under investigation. The assessment of the fatigue results reveals nearly no life improvement due to the manufacturing, emphasizing the necessity for mutual adjustment of shot peening and thermal treatment parameters to take account for life improvement.
An energy‐based critical fatigue life prediction method for AL6061‐T6
Authors: LETCHER T. , SHEN M.‐H. H. , SCOTT‐EMUAKPOR O. , GEORGE T. , CROSS C. 
Published: March 2012

ABSTRACTAn energy‐based critical fatigue life prediction method is developed and analysed. The original energy‐based fatigue life prediction theory states that the number of cycles to failure is estimated by dividing the total energy accumulated during a monotonic fracture by the strain energy per cycle. Because the accuracy of this concept is heavily dependent on the cyclic behaviour of the material, a precise understanding of the strain energy behaviour throughout each failure process is necessary. Examination of the stress and strain during fatigue tests shows that the cyclic strain energy behaviour is not perfectly stable as initially presumed. It was discovered that fatigue hysteresis energy always accumulates to the same amount of energy by the end of the stable energy region, which has led to a new ‘critical energy’ material property. Characterization of strain energy throughout the fatigue process has thus improved the understanding of an energy‐based fatigue life prediction method.
Evidence for high‐temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin, Yellowstone National Park
Authors: Loiacono Sara T. , Meyer‐Dombard D'Arcy R. , Havig Jeff R. , Poret‐Peterson Amisha T. , Hartnett Hilairy E. , Shock Everett L. 
Published: March 2012

SummaryGenes encoding nitrogenase (nifH) were amplified from sediment and photosynthetic mat samples collected in the outflow channel of Mound Spring, an alkaline thermal feature in Yellowstone National Park. Results indicate the genetic capacity for nitrogen fixation over the entire range of temperatures sampled (57.2°C to 80.2°C). Amplification of environmental nifH transcripts revealed in situ expression of nifH genes at temperatures up to 72.7°C. However, we were unable to amplify transcripts of nifH at the higher‐temperature locations (> 72.7°C). These results indicate that microbes at the highest temperature sites contain the genetic capacity to fix nitrogen, yet either do not express nifH or do so only transiently. Field measurements of nitrate and ammonium show fixed nitrogen limitation as temperature decreases along the outflow channel, suggesting nifH expression in response to the downstream decrease in bioavailable nitrogen. Nitrogen stable isotope values of Mound Spring sediment communities further support geochemical and genetic data. DNA and cDNA nifH amplicons form several unique phylogenetic clades, some of which appear to represent novel nifH sequences in both photosynthetic and chemosynthetic microbial communities. This is the first report of in situ nifH expression in strictly chemosynthetic zones of terrestrial (non‐marine) hydrothermal systems, and sets a new upper temperature limit (72.7°C) for nitrogen fixation in alkaline, terrestrial hydrothermal environments.
Unclassified renal cell carcinoma: a report of 56 cases
Authors: Lopez‐Beltran Antonio , Kirkali Ziya , Montironi Rodolfo , Blanca Ana , Algaba Ferran , Scarpelli Marina , Yorukoglu Kutsal , Hartmann Arndt , Cheng Liang 
Published: March 2012

Study Type – Therapy (case series)Level of Evidence 4What's known on the subject? and What does the study add?Unclassified RCC represents 0.7–5.7% of renal tumours. Limited reported data from two series suggests that unclassified RCC is an aggressive form of RCC, mainly because most cases are at an advanced stage at presentation, but overall and cancer‐specific survival were not significantly different between unclassified and clear‐cell RCC in an additional series of 38 patients.Our study of 56 cases of unclassified RCC describes the pathological features that can be applied to predict prognosis on a daily basis. In particular nuclear grade, TNM classification, tumour coagulative necrosis, tumour size, microvascular invasion and 2004 WHO histotype are independent predictors of disease‐free and cancer‐specific survival.OBJECTIVE
To evaluate the clinicopathological features and outcomes of 56 patients with unclassified renal cell carcinoma (RCC) meeting 2004 World Health Organization diagnostic criteria.
PATIENTS AND METHODS
Urological pathology files of the participating institutions were reviewed and cases of unclassified RCC that met the inclusion criteria were retrieved.
Nuclear grade, pT status, tumour size, regional lymph node involvement, distant metastases, coagulative tumour necrosis, mucin and sarcomatoid differentiation were evaluated in radical nephrectomy or nephron‐sparing specimens.
Significant factors in univariate analysis were then assessed by a multivariate analysis of independent prognostic factors using Cox proportional hazard regression analysis.
RESULTS
Fifty‐six cases met the histological criteria for unclassified RCC. Thirty‐four (61%) cases were categorized as unrecognizable cell type (mean overall survival 47 months; median 36 months), 20 (36%) as composites of recognized types (mean overall survival 36 months; median 26 months), and two (4%) (mean survival 16 months; median 16 months) as pure sarcomatoid morphology without recognizable epithelial elements.
Cox multivariate analysis showed nuclear grade (P= 0.020), stage (P < 0.001), tumour coagulative necrosis (P= 0.018), tumour size (P < 0.001), microvascular invasion (P < 0.001) and tumour histotype (P= 0.028) to be independent predictors of disease‐free survival, with tumour size being the most significant (hazard ratio [HR] 9.068, 95% confidence interval [CI] 3.231–25.453).
Nuclear grade (P= 0.026), stage (P < 0.001), tumour coagulative necrosis (P < 0.001), tumour size (P= 0.044), microvascular invasion (P < 0.001), tumour recurrence after surgery (P < 0.001) and tumour histotype (P= 0.056) were independent predictors of cancer‐specific survival, with tumour recurrence after surgery being the most significant (HR 14.713, 95% CI 5.329–40.622).
CONCLUSION
The prognosis of patients with unclassified RCC seems to be related to clinicopathological features known to be relevant in common forms of RCC.
An altered redox balance mediates the hypersensitivity of Cockayne syndrome primary fibroblasts to oxidative stress
Authors: Pascucci Barbara , Lemma Tiziana , Iorio Egidio , Giovannini Sara , Vaz Bruno , Iavarone Ivano , Calcagnile Angelo , Narciso Laura , Degan Paolo , Podo Franca , Roginskya Vera , Janjic Bratislav M. , Van Houten Bennett , Stefanini Miria , Dogliotti Eugenia , D’Errico Mariarosaria 
Published: March 2012

SummaryCockayne syndrome (CS) is a rare hereditary multisystem disease characterized by neurological and development impairment, and premature aging. Cockayne syndrome cells are hypersensitive to oxidative stress, but the molecular mechanisms involved remain unresolved. Here we provide the first evidence that primary fibroblasts derived from patients with CS‐A and CS‐B present an altered redox balance with increased steady‐state levels of intracellular reactive oxygen species (ROS) and basal and induced DNA oxidative damage, loss of the mitochondrial membrane potential, and a significant decrease in the rate of basal oxidative phosphorylation. The Na/K‐ATPase, a relevant target of oxidative stress, is also affected with reduced transcription in CS fibroblasts and normal protein levels restored upon complementation with wild‐type genes. High‐resolution magnetic resonance spectroscopy revealed a significantly perturbed metabolic profile in CS‐A and CS‐B primary fibroblasts compared with normal cells in agreement with increased oxidative stress and alterations in cell bioenergetics. The affected processes include oxidative metabolism, glycolysis, choline phospholipid metabolism, and osmoregulation. The alterations in intracellular ROS content, oxidative DNA damage, and metabolic profile were partially rescued by the addition of an antioxidant in the culture medium suggesting that the continuous oxidative stress that characterizes CS cells plays a causative role in the underlying pathophysiology. The changes of oxidative and energy metabolism offer a clue for the clinical features of patients with CS and provide novel tools valuable for both diagnosis and therapy.
Effects of trampling of a wet dairy pasture soil on soil porosity and on mitigation of nitrous oxide emissions by a nitrification inhibitor, dicyandiamide
Authors: Ball B. C. , Cameron K. C. , Di H. J. , Moore S. 
Published: March 2012

AbstractUrine patches in dairy pastures are major sources of nitrous oxide (N2O). Wet winters result in compaction damage to pastures because of animal trampling. The nitrification inhibitor, dicyandiamide (DCD), is effective at reducing N2O emissions from urine patches. Here, we assessed the extent of damage to the physical quality of the soil by trampling and whether this influenced the ability of DCD to mitigate N2O emissions. A field experiment was conducted where a sandy loam soil was trampled by a mechanical hoof just before urine and DCD application. Trampling reduced air permeability and pore continuity, but this had no effect on bulk density. Urine appeared to have contributed to pore collapse and blockage. Trampling increased average cumulative N2O emissions from 1.74 to 4.66% of urine‐N applied. This effect was attributed to increased water‐filled pore space, aggregate destruction and suppression of grass growth. DCD was highly effective in reducing N2O emissions, with the N2O emission factor of the urine‐N being decreased by 58–63%. Trampling did not significantly affect the effectiveness of DCD in reducing N2O emissions.
Predicting the changes in environmentally and agronomically significant phosphorus forms following the cessation of phosphorus fertilizer applications to grassland
Authors: Dodd R. J. , Mcdowell R. W. , Condron L. M. 
Published: March 2012

AbstractPhosphorus (P) loss from soil can impair surface water quality. Losses from soil are related to soil P concentrations, but agronomic measures such as Olsen P do not in many cases predict the potential for P loss. One possible strategy to decrease P loss is to stop applying P fertilizers. We examined the changes in both agronomic (Olsen P) and environmental [water‐extractable P (WEP) and calcium chloride‐extractable P (CaCl2‐P)] P tests, and the potential implications following a halt to P fertilizer application to four long‐term grassland field trials on different soil types. Exponential decreases in Olsen P and WEP concentration over time were observed in three of the four trials, but only in one trial for CaCl2‐P. The rates of decrease in Olsen P (OP) and WEP concentration were best correlated with initial WEP (WEPi) concentration and the quotient of Olsen Pi/P retention (PR, a measure of Al‐ and Fe‐oxides), respectively. The equation t = 1/(−0.035 × ln OPi/PR − 0.0455) × (ln WEPt − ln WEPi) was used to predict the time (t) taken for WEP concentrations at the sites to decrease to 0.02 mg/L (WEPt), which is proposed as a limit for dissolved reactive phosphorus in overland flow, and the result was 23–44 yr. Results from a similar equation for Olsen P predicted a quicker rate of WEP. A significant decline in dry matter (DM) yield was observed at one trial site. For this site, the rate of decline in DM yield was of a similar magnitude to the rate of decline in WEP concentration. This suggests that halting P fertilizer application to decrease P loss as measured by WEP concentration may decrease farm productivity. An alternative, more financially acceptable, strategy is required, such as a negative P balance while maintaining yields with N fertilizer, but further work is required to assess both the agronomic and environmental implications of this strategy.
Carvedilol inhibits the cardiostimulant and thermogenic effects of MDMA in humans
Authors: Hysek CM , Schmid Y , Rickli A , Simmler LD , Donzelli M , Grouzmann E , Liechti ME 
Published: March 2012

BACKGROUND AND PURPOSE The use of ±3,4‐methylenedioxymethamphetamine (MDMA, ‘ecstasy’) is associated with cardiovascular complications and hyperthermia.EXPERIMENTAL APPROACH We assessed the effects of the α1‐ and β‐adrenoceptor antagonist carvedilol on the cardiostimulant, thermogenic and subjective responses to MDMA in 16 healthy subjects. Carvedilol (50 mg) or placebo was administered 1 h before MDMA (125 mg) or placebo using a randomized, double‐blind, placebo‐controlled, four‐period crossover design.KEY RESULTS Carvedilol reduced MDMA‐induced elevations in blood pressure, heart rate and body temperature. Carvedilol did not affect the subjective effects of MDMA including MDMA‐induced good drug effects, drug high, drug liking, stimulation or adverse effects. Carvedilol did not alter the plasma exposure to MDMA.CONCLUSIONS AND IMPLICATIONS α1‐ and β‐Adrenoceptors contribute to the cardiostimulant and thermogenic effects of MDMA in humans but not to its psychotropic effects. Carvedilol could be useful in the treatment of cardiovascular and hyperthermic complications associated with ecstasy use.
Serologic Evidence that Ascaris and Toxoplasma Infections Impact Inflammatory Responses to Helicobacter pylori in Colombians
Authors: Ek Courtney , Whary Mark T. , Ihrig Melanie , Bravo Luis E. , Correa Pelayo , Fox James G. 
Published: March 2012

AbstractBackground:  Helicobacter pylori‐infected children from coastal Tumaco, Colombia, have more parasitism, and adults have lower gastric cancer risk compared with high‐altitude Pasto/Tuquerres residents. Because helminth and Toxoplasma gondii infections alter helicobacter gastritis in rodent models, we determined whether seropositivity to Ascaris lumbricoides or T. gondii was associated with Th2‐IgG1 or Th1‐IgG2 responses to H. pylori.Methods:  Sera (240) from the two populations were evaluated for A. lumbricoides and T. gondii seropositivity and results correlated with IgE and IgG isotype responses to H. pylori.Results:  Most Tumaco children and adults were seropositive for A. lumbricoides (89%, 66%), T. gondii (59%, 98%), or both (45%, 66%). In contrast, seropositivity among Pasto/Tuquerres children was much lower (9%A. lumbricoides, 11%T. gondii, and 2% dual positive) but increased in adults (58%A. lumbricoides, 82%T. gondii, and 41% dual positive). A. lumbricoides seropositivity correlated with elevated IgE and anti‐inflammatory Th2‐IgG1 responses to H. pylori, while T. gondiigondii seropositivity was linked to elevated IgE, pro‐inflammatory Th1‐IgG2, IgG3, and IgG4 responses to H. pylori. Individuals with high T. gondii titers had reduced Th1‐IgG2, IgG3, and IgG4 responses to H. pylori.Conclusions:  Results support regional differences for childhood parasitism and indicate A. lumbricoides and T. gondii infections may impact inflammatory responses to H. pylori and partially explain differences in gastric cancer risk in Colombia.
Effects of Cholesterol on Helicobacter pylori Growth and Virulence Properties In Vitro
Authors: Jiménez‐Soto Luisa F. , Rohrer Stefanie , Jain Utkarsh , Ertl Claudia , Sewald Xaver , Haas Rainer 
Published: March 2012

AbstractBackground:  Colonization of the gastric mucosa by Helicobacter pylori is often associated with chronic gastric pathologies in humans. Development of disease correlates with the presence of distinct bacterial pathogenicity factors, such as the cag type IV secretion system (cag‐T4SS), the vacuolating cytotoxin (VacA), or the ability of the bacteria to acquire and incorporate cholesterol from human tissue.Materials and Methods:  The in vitro growth of H. pylori requires media (Brucella broth) complemented with vitamins and horse serum or cyclodextrins, prepared as blood agar plates or liquid cultures. Liquid cultures usually show a slow growth. Here, we describe the successful growth of H. pylori strains 26695, P217, P12, and 60190 on serum‐free media replacing serum components or cyclodextrins with a commercially available cholesterol solution.Results:  The effects of cholesterol as a substitute for serum or cyclodextrin were rigorously tested for growth of H. pylori on agar plates in vitro, for its general effects on bacterial protein synthesis (the proteome level), for H. pylori’s natural competence and plasmid DNA transfer, for the production of VacA, and the general function of the cag‐pathogenicity island and its encoded cag‐T4SS. Generally, growth of H. pylori with cholesterol instead of serum supplementation did not reveal any restrictions in the physiology and functionality of the bacteria except for strain 26695 showing a reduced growth on cholesterol media, whereas strain 60190 grew more efficient in cholesterol‐ versus serum‐supplemented liquid medium.Conclusions:  The use of cholesterol represents a considerable option to serum complementation of growth media for in vitro growth of H. pylori.