bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche
Authors: de Muinck Eric J , Lagesen Karin , Afset Jan Egil , Didelot Xavier , Rønningen Kjersti S , Rudi Knut , Stenseth Nils Chr , Trosvik Pål 
Published: February 2013

Abstract

Background
Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche.

Results
Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles.

Conclusions
Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.
DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development
Authors: Hirabayashi Keiji , Shiota Kunio , Yagi Shintaro 
Published: February 2013

Abstract

Background
Tissues and their component cells have unique DNA methylation profiles comprising DNA methylation patterns of tissue-dependent and differentially methylated regions (T-DMRs). Previous studies reported that DNA methylation plays crucial roles in cell differentiation and development. Here, we investigated the genome-wide DNA methylation profiles of mouse neural progenitors derived from different developmental stages using HpyCH4IV, a methylation-sensitive restriction enzyme that recognizes ACGT residues, which are uniformly distributed across the genome.

Results
Using a microarray-based genome-wide DNA methylation analysis system focusing on 8.5-kb regions around transcription start sites (TSSs), we analyzed the DNA methylation profiles of mouse neurospheres derived from telencephalons at embryonic days 11.5 (E11.5NSph) and 14.5 (E14.5NSph) and the adult brain (AdBr). We identified T-DMRs with different DNA methylation statuses between E11.5NSph and E14.5NSph at genes involved in neural development and/or associated with neurological disorders in humans, such as Dclk1, Nrcam, Nfia, and Ntng1. These T-DMRs were located not only within 2 kb but also distal (several kbs) from the TSSs, and those hypomethylated in E11.5NSph tended to be in CpG island (CGI-) associated genes. Most T-DMRs that were hypomethylated in neurospheres were also hypomethylated in the AdBr. Interestingly, among the T-DMRs hypomethylated in the progenitors, there were T-DMRs that were hypermethylated in the AdBr. Although certain genes, including Ntng1, had hypermethylated T-DMRs 5′ upstream, we identified hypomethylated T-DMRs in the AdBr, 3′ downstream from their TSSs. This observation could explain why Ntng1 was highly expressed in the AdBr despite upstream hypermethylation.

Conclusion
Mouse adult brain DNA methylation and gene expression profiles could be attributed to developmental dynamics of T-DMRs in neural-related genes.
Transcriptional analysis of ftsZ within the dcw cluster in Bacillus mycoides
Authors: Santini Tiziana , Turchi Luana , Ceccarelli Giulia , Di Franco Carmen , Beccari Elena 
Published: February 2013

Abstract

Background
In Bacillus mycoides, as well as in other members of the B. cereus group, the tubulin-like protein of the division septum FtsZ is encoded by the distal gene of the cluster division and cell wall (dcw). Along the cluster the genes coding for structural proteins of the division apparatus are intermingled with those coding for enzymes of peptidoglycan biosynthesis, raising the possibility that genes with this different function might be coexpressed. Transcription of ftsZ in two model bacteria had been reported to differ: in B. subtilis, the ftsZ gene was found transcribed as a bigenic mRNA in the AZ operon; in E. coli, the transcripts of ftsZ were monogenic, expressed by specific promoters. Here we analyzed the size and the initiation sites of RNAs transcribed from ftsZ and from other cluster genes in two B. mycoides strains, DX and SIN, characterized by colonies of different chirality and density, to explore the correlation of the different morphotypes with transcription of the dcw genes.

Results
In both strains, during vegetative growth, the ftsZ-specific RNAs were composed mainly of ftsZ, ftsA-ftsZ and ftsQ-ftsA-ftsZ transcripts. A low number of RNA molecules included the sequences of the upstream murG and murB genes, which are involved in peptidoglycan synthesis. No cotranscription was detected between ftsZ and the downstream genes of the SpoIIG cluster. The monogenic ftsZ RNA was found in both strains, with the main initiation site located inside the ftsA coding sequence. To confirm the promoter property of the site, a B. mycoides construct carrying the ftsA region in front of the shortened ftsZ gene was inserted into the AmyE locus of B. subtilis 168. The promoter site in the ftsA region was recognized in the heterologous cellular context and expressed as in B. mycoides.

Conclusions
The DX and SIN strains of B. mycoides display very similar RNA transcription specificity. The ftsZ messenger RNA can be found either as an independent transcript or expressed together with ftsA and ftsQ and, in low amounts, with genes that are specific to peptidoglycan biosynthesis.
Developing longitudinal qualitative designs: lessons learned and recommendations for health services research
Authors: Calman Lynn , Brunton Lisa , Molassiotis Alex 
Published: February 2013

Abstract

Background
Longitudinal qualitative methods are becoming increasingly used in the health service research, but the method and challenges particular to health care settings are not well described in the literature.We reflect on the strategies used in a longitudinal qualitative study to explore the experience of symptoms in cancer patients and their carers, following participants from diagnosis for twelve months; we highlight ethical, practical, theoretical and methodological issues that need to be considered and addressed from the outset of a longitudinal qualitative study.

Results
Key considerations in undertaking longitudinal qualitative projects in health research, include the use of theory, utilizing multiple methods of analysis and giving consideration to the practical and ethical issues at an early stage. These can include issues of time and timing; data collection processes; changing the topic guide over time; recruitment considerations; retention of staff; issues around confidentiality; effects of project on staff and patients, and analyzing data within and across time.

Conclusions
As longitudinal qualitative methods are becoming increasingly used in health services research, the methodological and practical challenges particular to health care settings need more robust approaches and conceptual improvement. We provide recommendations for the use of such designs. We have a particular focus on cancer patients, so this paper will have particular relevance for researchers interested in chronic and life limiting conditions.
Recurrent symptomatic intraocular pressure spikes during hemodialysis in a patient with unilateral anterior uveitis
Authors: Lim Su-Ho , Son Junhyuk , Cha Soon Cheol 
Published: February 2013

Abstract

Background
The relationship between intraocular pressure (IOP) changes and hemodialysis has been evaluated for several decades. However, no report on an IOP rise in uveitis patients during hemodialysis has been previously documented. This report describes the case of an uveitis patient with repetitive IOP spikes associated with severe ocular pain during hemodialysis sessions, which resolved after glaucoma filtering surgery.

Case presentation
A 47-year-old male with diabetes and hypertension had complained of recurrent ocular pain in the left eye during hemodialysis sessions. A slit-lamp examination showed diffuse corneal epithelial edema with several white keratic precipitates and inflammatory cells (Grade 3+) in the anterior chamber of the left eye. No visible neovascularization or synechiae were visible on the iris or angle. Topical glaucoma eye-drops and intravenous mannitol before hemodialysis did not prevent subsequent painful IOP spikes in the left eye. At the end of hemodialysis, IOP averaged ~40 mmHg. After trabeculectomy with mitomycin C in the left eye, his IOP stabilized in the low-teens (range, 10–14 mmHg) and no painful IOP spikes occurred during hemodialysis over the first postoperative year.

Conclusion
We present a case of recurrent painful IOP spikes during hemodialysis in a patient with unilateral anterior uveitis unresponsive to conventional medical treatment prior to hemodialysis. To our knowledge, this is the first case report of repetitive symptomatic IOP rise during hemodialysis in an uveitic glaucoma patient. This case highlights the importance of the awareness of the possibility that IOP may rise intolerably during hemodialysis in uveitis patients with a compromised outflow facility.
The novel application of artificial neural network on bioelectrical impedance analysis to assess the body composition in elderly
Authors: Hsieh Kuen-Chang , Chen Yu-Jen , Lu Hsueh-Kuan , Lee Ling-Chun , Huang Yong-Cheng , Chen Yu-Yawn 
Published: February 2013

AbstractBackgroundThis study aims to improve accuracy of Bioelectrical Impedance Analysis (BIA) prediction equations for estimating fat free mass (FFM) of the elderly by using non-linear Back Propagation Artificial Neural Network (BP-ANN) model and to compare the predictive accuracy with the linear regression model by using energy dual X-ray absorptiometry (DXA) as reference method.MethodsA total of 88 Taiwanese elderly adults were recruited in this study as subjects. Linear regression equations and BP-ANN prediction equation were developed using impedances and other anthropometrics for predicting the reference FFM measured by DXA (FFMDXA) in 36 male and 26 female Taiwanese elderly adults. The FFM estimated by BIA prediction equations using traditional linear regression model (FFMLR) and BP-ANN model (FFMANN) were compared to the FFMDXA. The measuring results of an additional 26 elderly adults were used to validate than accuracy of the predictive models.ResultsThe results showed the significant predictors were impedance, gender, age, height and weight in developed FFMLRlinear model (LR) for predicting FFM (coefficient of determination, r2= 0.940; standard error of estimate (SEE) = 2.729 kg; root mean square error (RMSE) = 2.571kg,P< 0.001). The above predictors were set as the variables of the input layer by using five neurons in the BP-ANN model (r2= 0.987 with a SD = 1.192 kg and relatively lower RMSE = 1.183 kg), which had greater (improved) accuracy for estimating FFM when compared with linear model. The results showed a better agreement existed between FFMANNand FFMDXAthan that between FFMLRand FFMDXA.ConclusionWhen compared the performance of developed prediction equations for estimating reference FFMDXA, the linear model has lower r2with a larger SD in predictive results than that of BP-ANN model, which indicated ANN model is more suitable for estimating FFM.
Clinicopathologic features and surgical outcome of solid pseudopapillary tumor of the pancreas: analysis of 17 cases
Authors: Wang Xiao-Guang , Ni Quan-Fa , Fei Jian-Guo , Zhong Zheng-Xiang , Yu Peng-Fei 
Published: February 2013

Abstract

Background
We summarize our experience of the diagnosis, surgical treatment, and prognosis of solid pseudopapillary tumors (SPTs).

Methods
We carried out a retrospective study of clinical data from a series of 17 patients with SPT managed in two hospitals between October 2001 and November 2011.

Results
All of the 17 patients were female and the average age at diagnosis was 26.6 years (range 11 years to 55 years). The tumor was located in the body or tail in ten patients, the head in five patients, and the neck in two patients. The median tumor size was 5.5 cm (range 2 cm to 10 cm). All 17 patients had curative resections, including seven distal pancreatectomies, five local resections, four pancreaticoduodenectomies, and one central pancreatectomy. Two patients required concomitant splenic vein resection due to local tumor invasion. All patients were alive and disease-free at a median follow-up of 48.2 months (range 2 to 90 months). There were no significant associations between clinicopathologic factors and malignant potential of SPT. Ki-67 was detected in three patients with pancreatic parenchyma invasion.

Conclusions
The SPT is an infrequent tumor, typically affecting young women without notable symptoms. Surgical resection is justified even in the presence of local invasion or metastases, as patients demonstrate excellent long-term survival. Positive immunoreactivity for Ki-67 may predict the malignant potential of SPTs.
Synthesis of (cinnamate-zinc layered hydroxide) intercalation compound for sunscreen application
Authors: Mohsin Sumaiyah Megat Nabil , Hussein Mohd Zobir , Sarijo Siti Halimah , Fakurazi Sharida , Arulselvan Palanisamy , Hin Taufiq-Yap Yun 
Published: February 2013

Abstract

Background
Zinc layered hydroxide (ZLH) intercalated with cinnamate, an anionic form of cinnamic acid (CA), an efficient UVA and UVB absorber, have been synthesized by direct method using zinc oxide (ZnO) and cinnamic acid as the precursor.

Results
The resulting obtained intercalation compound, ZCA, showed a basal spacing of 23.9 Å as a result of cinnamate intercalated in a bilayer arrangement between the interlayer spaces of ZLH with estimated percentage loading of cinnamate of about 40.4 % w/w. The UV–vis absorption spectrum of the intercalation compound showed excellent UVA and UVB absorption ability. Retention of cinnamate in ZLH interlayers was tested against media usually came across with sunscreen usage to show low release over an extended period of time. MTT assay of the intercalation compound on human dermal fibroblast (HDF) cells showed cytotoxicity of ZCA to be concentration dependent and is overall less toxic than its precursor, ZnO.

Conclusions
(Cinnamate-zinc layered hydroxide) intercalation compound is suitable to be used as a safe and effective sunscreen with long UV protection effect.
Primary signet-ring cell carcinoma of the urinary bladder successfully managed with cisplatin and gemcitabine: a case report
Authors: El Ammari Jalal Eddine , Ahsaini Mustapha , Riyach Omar , El Fassi Mohammed Jamal , Farih My Hassan , Hammas Nawal , Elfatmi Hind , Amarti Afaf 
Published: February 2013

Abstract

Introduction
Primary signet-ring cell carcinoma of the urinary bladder is a rare variant of mucus-producing adenocarcinoma constituting approximately 0.5% to 2.0% of all primary carcinomas of the bladder. This tumor initially presents as a high-grade, high-stage lesion and diffusely invades the bladder wall without forming intraluminal growth. The patients have no specific symptoms, which leads to delayed diagnosis and poor prognosis.

Case presentation
We report the case of a 51-year-old Moroccan Berber man consulting for gross hematuria. Ultrasonography and a computed tomography scan found a bladder tumor diffusely invading the bladder wall. A histopathological examination of the tumor chips from a transurethral resection of the bladder revealed signet-ring cell adenocarcinoma. The gastrointestinal tract exploration did not reveal any other tumor localization. A radical cystectomy and adjuvant cisplatin and gemcitabine chemotherapy were therefore performed resulting in 18 months of survival without metastasis and a good quality of life within that time.

Conclusion
The rarity and the successful management with carboplatin and gemcitabine as adjuvant chemotherapy of this entity, which is rarely reported in the literature, are two remarkable characteristics described in this case report.
Identification of antifungal principle in the solvent extract of an endophytic fungus Chaetomium globosum from Withania somnifera
Authors: Kumar Susheel , Kaushik Nutan , Proksch Peter 
Published: February 2013

Abstract
Extracts of Chaetomium globosum EF18, isolated as endophytic fungus from Withania somnifera, were found effective against Sclerotinia sclerotiorum. Ethyl acetate and methanol extracts were more effective than hexane extract showing >80% growth inhibition. Bioactive compound (antibiotic Sch 210971, m/z 445 and λmax 290) having antifungal activity against S. sclerotiorum has been isolated in pure form from the ethyl acetate extract following bioassay guided fractionation. Apart from this compound other fractions of polar to medium polarity were also found effective. Fraction no. VIII from VLC (Vacuum liquid chromatography) column of ethyl acetate extract was most active having IC50 value 35.4 μg/ml.
Inhibition of PI3K/AKT/mTOR Pathway Enhances Temozolomide-Induced Cytotoxicity in Pituitary Adenoma Cell Lines in Vitro and Xenografted Pituitary Adenoma in Female Nude Mice
Authors: Dai Congxin , Zhang Bo , Liu Xiaohai , Ma Sihai , Yang Yakun , Yao Yong , Feng Ming , Bao Xinjie , Li Guilin , Wang Janxin , Guo Kai , Ma Wenbin , Xing Bing , Lian Wei , Xiao Jianqi , Cai Feng , Zhang Hongbin , Wang Renzhi 
Published: February 2013

Abstract
Invasive pituitary adenomas (PAs) are often refractory to standard therapy and salvage treatment with temozolomide (TMZ). Hyperactivation of the phosphoinositide 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway contributes to chemotherapy resistance in many cancers. XL765, a novel dual-PI3K/mTOR inhibitor, has recently shown its efficacy as a monotherapy and in combination with conventional therapeutics in many cancers. The hyperactive PI3K/AKT/mTOR pathway frequently occurs in invasive PAs. In this study, we investigated whether XL765 sensitizes PA cells to TMZ in vitro and in vivo. Experiments were carried out to evaluate the effect of XL765 and TMZ alone or in combination on cell proliferation and apoptosis of PA cell lines (αT3-1, GH3, and MMQ) in vitro as well as the tumor growth and serum GH and prolactin secretions in a GH3 xenograft tumor model of female nude mice. XL765 and TMZ synergistically inhibited the growth of PA cell lines and induced apoptosis. Combination of XL765 and TMZ synergistically inhibited tumor growth, decreased serum GH and prolactin levels, and reduced the sacrifice rate of GH3 xenograft tumor models without increased systemic side effects. In addition, XL765 in combination with TMZ dramatically decreased phosphorylation of AKT and mTOR as well as the expression of Bcl-2. The increased expression of cleaved poly (ADP-ribose) polymerase and Bcl-2-associated X protein along with elevated caspase-3/7 activity were also observed in the combination group. Therefore, dual inhibitors of PI3K and mTOR may enhance alkylating agent-mediated cytotoxicity and provide a novel regimen in the treatment of invasive PAs.
Insulin Degludec: A Novel Basal Insulin Analogue
Authors: Goldman-Levine Jennifer D , Patel Dhiren K , Schnee David M 
Published: February 2013

OBJECTIVE: To review the pharmacology, pharmacokinetics, clinical trial data, adverse effects, and potential role in therapy of insulin degludec. DATA SOURCES: Articles were identified using the MEDLINE database (January 1996-December 2012). Abstracts and posters were identified from respective congressional websites and published supplements of the American Diabetes Association, the European Association for the Study of Diabetes, and the American Association of Clinical Endocrinologists (January 2008-December 2012). Clinicaltrials.gov was used to identify any ongoing clinical trials or completed trials whose results had not been presented or published. STUDY SELECTION AND DATA EXTRACTION: All available studies were reviewed for inclusion; pharmacokinetic studies were limited to those reporting human data. DATA SYNTHESIS: Insulin degludec is a novel, ultra-long-acting basal insulin analogue that has a similar safety and efficacy profile when compared with insulin glargine in patients with type 1 or type 2 diabetes. Clinical trials have indicated that there is less hypoglycemia, particularly nocturnal hypoglycemia, associated with this agent. CONCLUSIONS: If insulin degludec is approved, it may offer an alternative basal insulin for patients needing more flexible dosing, having a history of nocturnal hypoglycemia, or those with severe insulin resistance needing a higher concentration of basal insulin.
Visual Hallucinations Treated with the Reinitiation of Memantine in a Patient with Lewy Body Dementia
Authors: Mathys Monica L , McCarrell Jamie , Sleeper Rebecca B , Blaszczyk Amie Taggart 
Published: February 2013

OBJECTIVE: To report on a patient with Lewy body dementia who developed worsening of hallucinations with memantine withdrawal and significant improvement with reinitiation of the drug. CASE SUMMARY: A 78-year-old man presented to a geriatric psychiatry clinic in March 2011. The patient had experienced gradual memory loss since 2007 and was diagnosed with dementia with Lewy bodies (DLB) in 2009. His medication regimen included donepezil and memantine; his cognitive and functional status appeared stable. Occasional mild visual hallucinations occurred but were not concerning to the patient or his wife. The patient did well to July 2011, when memantine became restricted within the health care institution; memantine was therefore tapered to discontinuation. From July to September 2011, the patient's cognition and function appeared to decline significantly. He also began experiencing severe visual hallucinations daily. Memantine was reinitiated in September 2011 and, within days, the patient was free of hallucinations. By November 2011, his cognition and function were noted to have improved to previous status, and hallucinations were rare. DISCUSSION: Three small randomized studies and 4 case reports were found addressing the use of memantine for DLB. Both improvement and worsening of hallucinations were noted with memantine use in the case reports, but the studies showed only a small benefit in cognition. However, cognitive and psychiatric symptoms worsened when memantine was discontinued. One study found that Neuropsychiatric-Inventory scores and hallucination scores improved significantly for patients taking memantine. CONCLUSIONS: The literature investigating the use of memantine for the psychiatric symptoms of DLB is limited but there are data noting results similar to what we observed in our patient when his memantine was discontinued and reinitiated.