bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans
Authors: Schott Thomas , Kondadi Pradeep K , Hänninen Marja-Liisa , Rossi Mirko 
Published: December 2011

AbstractBackgroundThe canine Gram-negativeHelicobacter bizzozeroniiis one of seven species inHelicobacter heilmanniisensu lato that are detected in 0.17-2.3% of the gastric biopsies of human patients with gastric symptoms. At the present,H. bizzozeroniiis the only non-pylori gastricHelicobactersp. cultivated from human patients and is therefore a good alternative model of human gastricHelicobacterdisease. We recently sequenced the genome of theH. bizzozeroniihuman strain CIII-1, isolated in 2008 from a 47-year old Finnish woman suffering from severe dyspeptic symptoms. In this study, we performed a detailed comparative genome analysis withH. pylori, providing new insights into non-pyloriHelicobacterinfections and the mechanisms of transmission between the primary animal host and humans.ResultsH. bizzozeroniipossesses all the genes necessary for its specialised life in the stomach. However,H. bizzozeroniidiffers fromH. pyloriby having a wider metabolic flexibility in terms of its energy sources and electron transport chain. Moreover,H. bizzozeroniiharbours a higher number of methyl-accepting chemotaxis proteins, allowing it to respond to a wider spectrum of environmental signals. In this study,H. bizzozeroniihas been shown to have high level of genome plasticity. We were able to identify a total of 43 contingency genes, 5 insertion sequences (ISs), 22 mini-IS elements, 1 genomic island and a putative prophage. AlthoughH. bizzozeroniilacks homologues of some of the majorH. pylorivirulence genes, other candidate virulence factors are present. In particular, we identified a polysaccharide lyase (HBZC1_15820) as a potential new virulence factor ofH. bizzozeronii.ConclusionsThe comparative genome analysis performed in this study increased the knowledge of the biology of gastricHelicobacterspecies. In particular, we propose the hypothesis that the high metabolic versatility and the ability to react to a range of environmental signals, factors which differentiateH. bizzozeroniias well asH. felisandH. suisfromH. pylori, are the molecular basis of the of the zoonotic nature ofH. heilmanniisensu lato infection in humans.
A longitudinal study on BIO14.6 hamsters with dilated cardiomyopathy: micro-echocardiographic evaluation
Authors: Belfiore Maria Paola , Berritto Daniela , Iacobellis Francesca , Rossi Claudia , Nigro Gerardo , Rotundo Ida Luisa , Cozzolino Santolo , Cappabianca Salvatore , Rotondo Antonio , Grassi Roberto 
Published: December 2011

Abstract

Background
In recent years, several new technologies for small-animal imaging have been developed. In particular, the use of ultrasound in animal imaging has focused on the investigation of accessible biological structures such as the heart, of which it provides a morphological and functional assessment. The purpose of this study was to investigate the role of micro-ultrasonography (μ-US) in a longitudinal study on BIO14.6 cardiomyopathic hamsters treated with gene therapy.

Methods
Thirty hamsters were divided into three groups (n = 10): Group I, untreated BIO 14.6 hamsters; Group II, BIO 14.6 hamsters treated with gene therapy; Group III, untreated wild type (WT) hamsters. All hamsters underwent serial μ-US sessions and were sacrificed at predetermined time points.

Results
μ-US revealed: in Group I, progressive dilation of the left ventricle with a change in heart morphology from an elliptical to a more spherical shape, altered configuration of the mitral valve and subvalvular apparatus, and severe reduction in ejection fraction; in Group II, mild decrease in contractile function and ejection fraction; in Group III, normal cardiac chamber morphology and function. There was a negative correlation between the percentage of fibrosis observed at histology and the ejection fraction obtained on μ-echocardiography (Spearman r: -0.839; p < 0.001).

Conclusions
Although histological examination remains indispensable for a conclusive diagnosis, high-frequency μ-echocardiography, thanks to the high spatial and contrast resolution, can be considered sufficient for monitoring therapeutic efficacy and/or the progression of dilated cardiomyopathy, providing an alternative tool for repeatable and noninvasive evaluation.
Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays
Authors: Agbavwe Christy , Kim Changhan , Hong DongGee , Heinrich Kurt , Wang Tao , Somoza Mark M 
Published: December 2011

Abstract

Background
Light-directed in situ synthesis of DNA microarrays using computer-controlled projection from a digital micromirror device--maskless array synthesis (MAS)--has proved to be successful at both commercial and laboratory scales. The chemical synthetic cycle in MAS is quite similar to that of conventional solid-phase synthesis of oligonucleotides, but the complexity of microarrays and unique synthesis kinetics on the glass substrate require a careful tuning of parameters and unique modifications to the synthesis cycle to obtain optimal deprotection and phosphoramidite coupling. In addition, unintended deprotection due to scattering and diffraction introduce insertion errors that contribute significantly to the overall error rate.

Results
Stepwise phosphoramidite coupling yields have been greatly improved and are now comparable to those obtained in solid phase synthesis of oligonucleotides. Extended chemical exposure in the synthesis of complex, long oligonucleotide arrays result in lower--but still high--final average yields which approach 99%. The new synthesis chemistry includes elimination of the standard oxidation until the final step, and improved coupling and light deprotection. Coupling Insertions due to stray light are the limiting factor in sequence quality for oligonucleotide synthesis for gene assembly. Diffraction and local flare are by far the largest contributors to loss of optical contrast.

Conclusions
Maskless array synthesis is an efficient and versatile method for synthesizing high density arrays of long oligonucleotides for hybridization- and other molecular binding-based experiments. For applications requiring high sequence purity, such as gene assembly, diffraction and flare remain significant obstacles, but can be significantly reduced with straightforward experimental strategies.
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
Authors: Rajeev Lara , Luning Eric G , Dehal Paramvir S , Price Morgan N , Arkin Adam P , Mukhopadhyay Aindrila 
Published: December 2011

Abstract
Background
Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems.

Results
We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study.

Conclusions
The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.
Comparison of radiological measures for diagnosing flatfoot
Authors: Lo Huan-Chu , Chu Wen-Cheng , Wu Wei-Kai , Hsieh Hsin , Chou Chieh-Ping , Sun Shao-En , Chou Pin-Ya , Liao Chen-Hui , Guan Xiao-Yun , Li Shu-Chee 
Published: December 2011

BackgroundIn the Taiwanese military, flatfoot is indicated by a calcaneal-fifth metatarsal angle (arch angle) ≥165°. However, the arch angle is not always easily defined.PurposeTo assess correlations between the arch angle and other radiographic measures and thus identify an alternative radiographic measure for diagnosing flatfoot.Material and MethodsEighty-seven male Taiwanese military recruits were studied (median age 22 years, interquartile range 20–23 years). Lateral, weight-bearing radiographs were taken. Five radiographic measurements, including the calcaneal-fifth metatarsal angle (arch angle), medial arch angle (MAA), calcaneal pitch angle (CP), talus angle (TA), and talar-first metatarsal angle (TFM) were made. Correlations between the arch angle and all other measures were determined. A cut-off value for predicting flatfoot (arch angle ≥165°) was determined for each measure using the Youden index and receiver-operating characteristic (ROC) curves were generated for each measure to assess diagnostic accuracy.ResultsAll measures were significantly correlated with arch angle ( P < 0.05); however, the strongest correlation was for CP (ρ = –0.905, P < 0.001). CP was associated with the highest area under the ROC (0.988 vs. 0.711–0.912 for the other measures). Further, CP (cut-off <12.3°) had the highest sensitivity (92.0%), positive predictive value (76.7%), and negative predictive value (96.5%). TFM (>9.5°) had the highest specificity (90.3% vs. 88.75 for CP <12.3°).ConclusionCP is inversely correlated with arch angle in Taiwanese male military recruits. CP < 12.3° is a significant predictor of flatfoot. Assessment of CP may be used as an alternative means of diagnosing flatfoot when the arch angle is not easily defined.
Does Treating Insomnia With Cognitive–Behavioural Therapy Influence Comorbid Anxiety and Depression? An Exploratory Multiple Baseline Design With Four Patients
Authors: Maroti Daniel , Folkeson Pär , Jansson-Fröjmark Markus , Linton Steven J. 
Published: December 2011

AbstractObjectives:Although cognitive–behaviour therapy for insomnia (CBT-I) has been shown to be effective for primary insomnia, the impact of CBT-I on insomnia comorbid with psychiatric conditions is largely unknown.Design:A multiple baseline design with 2–3 weeks of baseline, 6 weeks of CBT-I, and a 3-week follow-up was employed.Methods:Four patients with insomnia comorbid with both anxiety and depressive disorders participated. Sleep onset latency (SOL), wake time after sleep onset (WASO), total sleep time (TST), the Insomnia Severity Index (ISI), the Beck Anxiety Inventory (BAI), and the Beck Depression Inventory (BDI-II) were used as outcome measures.Results:Improvements in SOL, WASO, and TST were observed for all the four patients. Based on ISI, there were reductions for all the patients (32–92%), three patients responded to treatment, and two patients remitted. Based on BAI, reductions on anxiety were observed for all the patients (40–76%), three patients were treatment responders, and two patients remitted. Based on BDI-II, all the patients experienced reductions in depression (36–53%), three patients responded to treatment, and one patient remitted.Conclusions:CBT-I was able to reduce insomnia and co-morbid anxiety and depression, thus providing preliminary evidence for using CBT-I on insomnia co-morbid with psychiatric conditions.
Homework Compliance in a Brief Cognitive-Behavioural and Pharmacological Intervention for Smoking
Authors: Funk Ann P. , Zvolensky Michael J. , Schmidt Norman B. 
Published: December 2011

AbstractHomework assignments have been a key component of cognitive behavioural therapy (CBT) for decades, but very few studies examined the effect of compliance on outcome in regard to smoking behaviour. To fill this gap in the existing literature, the present report evaluated the role of homework compliance on short-term outcome in the context of evidence-based care for smoking cessation. Compliance with out-of-session assignments was assessed in a four-session CBT-nicotine replacement therapy protocol for smoking cessation among adult daily smokers (n= 94). Consistent with expectation, homework compliance was associated with better short-term outcomes, including amount of cigarettes consumed as well as abstinence. Importantly, these effects remained after controlling for a wide range of potentially confounding variables (e.g., motivation to quit, nicotine dependence at intake, attendance problems, and in-session participation). Estimates of quantity versus quality of homework compliance did not differentially predict outcomes. Out-of-session homework assignments incrementally predict short-term smoking abstinence in the context of evidence-based care for smoking cessation.
Dipping Status and Hostility in Newly Diagnosed Essential Hypertension
Authors: Eleni Koroboki , Charalabos Papageorgiou , Efstathios Manios , Vassilios Rotas , Eleftheria Alexaki , Fotis Michas , George Papadimitriou , Nikolaos Zakopoulos 
Published: December 2011

Aim: Personality traits, including hostility, play an important role in the development of cardiovascular disease. Moreover, abnormalities in blood pressure circadian pattern, such as a lack of nocturnal BP fall, are related with target organ damage and increased cardiovascular risk. The aim of this study was to investigate the impact of hostility and its dimensions on dipping status, in newly diagnosed hypertensive patients. Methods: The study population consisted of 114 newly diagnosed untreated essential hypertensives. All participants underwent 24-hour ambulatory blood pressure monitoring (ABPM) in order to assess dipping status. Hostility was assessed by Hostility and Direction of Hostility Questionnaire (HDHQ). The study population was divided in terms of dipping status in two groups, “dippers” and “non-dippers.” Results: The statistical analysis revealed that dippers presented significantly higher score of extrapunitiveness (13.2 + 4.9 vs 11.4 + 3.9, p = 0.032), as well as significantly higher score of the dimension “urge to act out hostility (AH)” (4 + 3 vs 3 + 2, p = 0.025) compared to non-dippers. Multivariate regression analysis revealed extrapunitiveness as the only independent predictor of dipping status. The odds ratio (OR) for dipping status associated with each point increase in extrapunitiveness was 0.912 (95% CI: 0.832–0.992; p = 0.048). Conclusion: The present findings may suggest that hostility and its features affect the circadian variation of blood pressure in hypertensive patients, providing a promising objective for future investigations linking psychological factors and dipping status in essential hypertension.
Global Health Funding at the Crossroads: 2012 and Beyond
Authors: Nicogossian Arnauld , Kloiber Otmar , Stabile Bonnie , Zimmerman Thomas 
Published: December 2011

AbstractSlow global economic recovery is affecting health and access to care by an ever‐increasing number of individuals globally. International health organizations are advocating increased attention to fighting and preventing non‐communicable disorders and equitable access to health. World Bank estimates that an additional annual contribution of 10 billion USD will be required to improve populations' health and minimize disparities. Global health policy was one of the major issues addressed at the November 2011 Group of 20 Presidential Summit. It is hoped that the Summit will also include recommendations for improving the training of additional health care workers necessary to achieve the Millennium Developmental Goals. Rapidly evolving and low cost information technology should provide a temporary solution to the severe global health care workforce shortages.
Monorchiid and aporocotylid cercariae (Digenea) parasitising the purple clam Amiantis purpurata (Bivalvia, Veneridae) from the Southwestern Atlantic coast
Authors: Gilardoni Carmen , Posadas Guadalupe , Kroeck Marina , Cremonte Florencia 
Published: December 2011

AbstractTwo cercariae, one of them ocellate and with well developed tail (Monorchiidae) and another apharyngeate brevifurcocercous (Aporocotylidae), parasite of Amiantis purpurata (Lamarck, 1818) (Bivalvia, Veneridae) from the Patagonian coast on the Southwestern Atlantic Ocean, are described. These reports comprise the second monorchiid intramolluscan infection reported for the Southern Hemisphere and first intramolluscan aporocotylid for the Southern Hemisphere. In addition, this constitutes the first report of aporocotylid intramolluscan stages (parthenita) occupying only the haemocoel of the gills of a marine molluscan host rather than the digestive gland and gonad, the usual site of infection.
Efficacy of Some Organic Amendments for the Control of Ufra Disease of Rice
Authors: Latif M Abdul , Akter Sharmina , Kabir M Shahjahan , Ali M Ansar , Hossain M Anwar , Rahman M Loothfor 
Published: December 2011

Nine organic amendments, namely, Bishkatali leaf dust, mustard cake, sesame cake, jute seed dust, Neem leaf dust, Neem cake, Neem seed dust, Bankalmi leaf dust and rice husk were used in controlling rice ufra disease in three Boro seasons during 1994-1996. The amendments were applied at the rate of 200 kg/ha except for rice husk (500 kg/ha). All the amendments reduced the damaged tiller, ufra 3 and total ufra significantly and gave higher percentage of healthy panicles and increased yield over control (diseased). In all seasons, due to application of Bishkatali leaf dust, mustard cake, sesame cake, jute seed dust, Neem leaf dust, Neem seed dust, Bankalmi leaf dust and rice husk the yield was increased that ranged from 61.60-67.17, 56.07-71.43, 67.98-75.98, 65.78-78.51, 62.25-76.10, 61.79-79.06 and 62.53-80.16, 61.01-71.43% respectively over the control (diseased). The organic amendments could be used as the alternatives of nematicides for the control of ufra disease. Keywords: Organic amendments, Ufra disease, Rice DOI: http://dx.doi.org/10.3329/bjm.v23i2.874Bangladesh J Microbiol, Volume 23, Number 2, December 2006, pp 118-120
Detection of Gamma Radiation-Induced Oxidation in Animal and Bacterial DNA
Authors: Alam M Khorshed 
Published: December 2011

Gamma radiation-induced oxidative DNA damage, in terms of production of 8-hydroxydeoxyguanine (8-OHdG), was studied in the DNA samples from Chinese hamster ovary cell line (CHO-K1), bovine, chicken, Escherichia coli and Deinococcus radiodurans. A radiation dose response with respect to the formation of the 8-OHdG residues from the DNA molecules was observed by employing enzyme-linked immunosorbent assay (ELISA) detection system using monoclonal antibody. At high radiation doses (>5 kGy), the formation or detection of the 8-OHdG residues from bacterial DNA was declined. It was apparent that the oxidative DNA damage was dependent on the base composition of the DNA molecule. However, an inverse relation was observed between the dose limit and nitrogenous base composition especially the guanine residue. Nonetheless, DNA base composition might to be considered in cases of the radiation-induced oxidation of food or other DNA samples. Keywords: Gamma radiation-induced oxidation, 8-Hydroxydeoxyguanine (8-OHdG), ELISA, CHO-K1, Bovine, Chicken, Escherichia coli, Deinococcus radiodurans DOI: http://dx.doi.org/10.3329/bjm.v23i2.877 Bangladesh J Microbiol, Volume 23, Number 2, December 2006, pp 130-132
Optimisation of pH, Temperature and Carbon Nitrogen Ratio for the Degradation of <i>m</i>-Chlorophenol by <i>Pseudomonas putida</i> CP1
Authors: Fakhruddin ANM , Hossain M Alamgir 
Published: December 2011

Aromatic pollutants like m-chlorophenol is toxic to the environment and chlorophenol containing a metachlorine are more persistent under aerobic conditions than compounds lacking a chlorine substituent in positions meta to hydroxyl group. Therefore, it should be removed effectively from the environment. In order to increase the degradative activity, the optimum conditions for m-chlorophenol degradation by Pseudomonas putida CP1, some physicochemical conditions like pH, temperature and carbon nitrogen ratio for the growth and degradation of most persistent monochlorophenol, m-chlorophenol by the organism was optimised. The pH optimum for m-chlorophenol degradation by the bacterium was between pH 6.5 and 7.0 and the temperature optimum was 30°C for removal activity. Carbon : nitrogen (C:N) ratio of 3:1 was found best for effective removal of chemical oxygen demand (COD) and m-chlorophenol by the bacterium. Keywords: m-Chlorophenol degradation, Pseudomonas putida CP1, Chemical oxygen demand (COD)DOI: http://dx.doi.org/10.3329/bjm.v23i2.884 Bangladesh J Microbiol, Volume 23, Number 2, December 2006, pp 159-161
Degradation of Monochlorophenols by <i>Pseudomonas putida</i> CP1 in the Presence of Growth Supplements
Authors: Fakhruddin ANM , Hossain M Alamgir 
Published: December 2011

Influence of readily degradable additional sources of carbon and nitrogen on the degradation of monochlorophenols by Pseudomonas putida CP1 was investigated. The organism grew on all three isomers of monochlorophenols when supplied as the sole source of carbon and energy. Low concentrations (0.01 to 0.5%, w/v) of yeast extract enhanced degradation of monochlorophenols. The order in terms of rate of removal of monochlorophenols was 4-chlorophenol > 2-chlorophenol > 3-chlorophenol, both in the presence and absence of the growth supplements. The rate of removal of monochlorophenols was highest when carbon:nitrogen (C:N) ratio maintained at optimum level (3:1) with monochlorophenols and growth substrates. The organism clumped when grown in the presence of monochlorophenols alone. The degree of clumping decreased with the addition of growth supplements. Keywords: Biodegradation, Growth supplement, Monochlorophenol, Pseudomonas putida CP1DOI: http://dx.doi.org/10.3329/bjm.v24i2.1254 Â Bangladesh J Microbiol, Volume 24, Number 2, December 2007, pp 115-118 Â Â