bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome analysis of linezolid resistance in Streptococcus pneumoniae reveals resistance and compensatory mutations
Authors: Billal Dewan S , Feng Jie , Leprohon Philippe , Légaré Danielle , Ouellette Marc 
Published: October 2011

Abstract

Background
Several mutations were present in the genome of Streptococcus pneumoniae linezolid-resistant strains but the role of several of these mutations had not been experimentally tested. To analyze the role of these mutations, we reconstituted resistance by serial whole genome transformation of a novel resistant isolate into two strains with sensitive background. We sequenced the parent mutant and two independent transformants exhibiting similar minimum inhibitory concentration to linezolid.

Results
Comparative genomic analyses revealed that transformants acquired G2576T transversions in every gene copy of 23S rRNA and that the number of altered copies correlated with the level of linezolid resistance and cross-resistance to florfenicol and chloramphenicol. One of the transformants also acquired a mutation present in the parent mutant leading to the overexpression of an ABC transporter (spr1021). The acquisition of these mutations conferred a fitness cost however, which was further enhanced by the acquisition of a mutation in a RNA methyltransferase implicated in resistance. Interestingly, the fitness of the transformants could be restored in part by the acquisition of altered copies of the L3 and L16 ribosomal proteins and by mutations leading to the overexpression of the spr1887 ABC transporter that were present in the original linezolid-resistant mutant.

Conclusions
Our results demonstrate the usefulness of whole genome approaches at detecting major determinants of resistance as well as compensatory mutations that alleviate the fitness cost associated with resistance.
Study Protocol: The Behaviour and Pain in Dementia Study (BePAID)
Authors: Scott Sharon , Jones Louise , Blanchard Martin R , Sampson Elizabeth L 
Published: October 2011

Abstract

Background
People with dementia admitted to the acute hospital often receive poor quality care particularly with regards to management of behavioural and psychiatric symptoms of dementia (BPSD) and of pain. There have been no UK studies on the prevalence and type of pain or BPSD in people with dementia in this setting, or on how these may impact on patients, carers, staff and costs of care.

Methods/Design
We shall recruit older people with dementia who have unplanned acute medical admissions and measure the prevalence of BPSD using the Behave-AD (Behaviour in Alzheimer's Disease) and the CMAI (Cohen Mansfield Agitation Inventory). Pain prevalence and severity will be assessed by the PAINAD (Pain Assessment in Advanced Dementia) and the FACES pain scale. We will then analyse how these impact on a variety of outcomes and test the hypothesis that poor management of pain is associated with worsening of BPSD.

Discussion
By demonstrating the costs of BPSD to individuals with dementia and the health service this study will provide important evidence to drive improvements in care. We can then develop effective training for acute hospital staff and alternative treatment strategies for BPSD in this setting.
Amsterdam wrist rules: A clinical decision aid
Authors: Bentohami Abdelali , Walenkamp Monique MJ , Slaar Annelie , Beerekamp M Suzan H , de Groot Joris AH , Verhoog Eva M , Jager L Cara , Maas Mario , Bijlsma Taco S , van Dijkman Bart A , Schep Niels WL , Goslings J C 
Published: October 2011

Abstract

Background
Acute trauma of the wrist is one of the most frequent reasons for visiting the Emergency Department. These patients are routinely referred for radiological examination. Most X-rays however, do not reveal any fractures. A clinical decision rule determining the need for X-rays in patients with acute wrist trauma may help to percolate and select patients with fractures.

Methods/Design
This study will be a multi-center observational diagnostic study in which the data will be collected cross-sectionally. The study population will consist of all consecutive adult patients (≥18 years) presenting with acute wrist trauma at the Emergency Department in the participating hospitals.
This research comprises two components: one study will be conducted to determine which clinical parameters are predictive for the presence of a distal radius fracture in adult patients presenting to the Emergency Department following acute wrist trauma. These clinical parameters are defined by trauma-mechanism, physical examination, and functional testing. This data will be collected in two of the three participating hospitals and will be assessed by using logistic regression modelling to estimate the regression coefficients after which a reduced model will be created by means of a log likelihood ratio test. The accuracy of the model will be estimated by a goodness of fit test and an ROC curve. The final model will be validated internally through bootstrapping and by shrinking it, an adjusted model will be generated.
In the second component of this study, the developed prediction model will be validated in a new dataset consisting of a population of patients from the third hospital. If necessary, the model will be calibrated using the data from the validation study.

Discussion
Wrist trauma is frequently encountered at the Emergency Department. However, to this date, no decision rule regarding this type of trauma has been created. Ideally, radiographs are obtained of all patients entering one of the participating hospitals with trauma to the wrist. However, this is ethically and logistically not feasible and one could argue that patients, for whom no radiography is required according to their physician, are not suspected of having a distal radius fracture and thus are not part of the domain.

Trial registration
This study is registered at the Netherlands Trial Register (NTR 2544) and was granted permission by the Medical Ethical Committee of the Academic Medical Center Amsterdam on 06-01-2011.
Specific knockdown of uPA/uPAR attenuates invasion in glioblastoma cells and xenografts by inhibition of cleavage and trafficking of Notch -1 receptor
Authors: Raghu Hari , Gondi Christopher S , Dinh Dzung H , Gujrati Meena , Rao Jasti S 
Published: October 2011

AbstractBackgrounduPA/uPAR is a multifunctional system that is over expressed in many cancers and plays a critical role in glioblastoma (GBM) invasion. Previous studies from our lab have also shown that uPA/uPAR down regulation inhibits cancer cell invasion in SNB 19 GBM cells.MethodsAs Notch 1 is known to be over expressed and promotes invasion in glioblastoma, we therefore tested our hypothesis of whether down regulation of uPA/uPAR, singly or in tandem, attenuates GBM invasion via Notch 1 receptor. Targeted down regulation of uPA/uPAR, either singly or simultaneously, inhibited the anchorage independent growth of U251MG and GBM xenograft cell lines 4910 and 5310 as assessed by soft agar colony formation assay. Expression of all four Notch receptors was confirmed in GBM tissue array analysis by immunohistochemistry.ResultsDown regulation of uPA/uPAR, either singly or simultaneously, in U251 MG and tumor xenografts inhibited the cleavage of the Notch receptor between the Gly 1743 and Val 1744 positions, thereby suggesting inhibition of activated cytosolic fragment-related Notch gene transcription. Morphological analysis confirmed inhibition of NICD when U251 MG cells were treated with puPA, puPAR or pU2. uPA/uPAR down regulation inhibited Notch 1 mRNA in all three examined cell lines. uPA/uPAR shRNA down regulated nuclear activation of NF-κB subunits and phosphorylation of AKT/mTOR pathway in U251 MG and GBM xenografts. puPA down regulated NICD and HES induced phosphorylation of AKT/ERK and NF-κB. Down regulation of Notch 1 using siRNA inhibited uPA activity as shown by fibrinogen zymography. It also decreased uPA expression levels as shown by western blotting. Exogenous addition of uPA activated Notch 1 in uPAR antisense U251 MG cells and also in uPAR antisense cells transfected with siRNA against Delta and Jagged. The Notch 1 receptor co-localized with LAMP-1, a marker for lysosomes in uPA, uPAR and U2, down regulated U251 MG cells which probably indicates inhibition of Notch 1 receptor trafficking in GBM cells. Notch 1 expression was significantly inhibited in puPA- and pU2-treated pre-established intracranial tumors in mice.ConclusionsOverall our results show that down regulation of uPA/uPAR, either singly or simultaneously, could be an effective approach to attenuate Notch 1 receptor cleavage, signaling and endosomal trafficking in U251MG cells and xenografts, and ultimately inhibiting GBM invasion.
An effective hybrid of hill climbing and genetic algorithm for 2D triangular protein structure prediction
Authors: Su Shih-Chieh , Lin Cheng-Jian , Ting Chuan-Kang 
Published: October 2011

Abstract

Background
Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and embryonic development. It has been a long-standing goal in molecular biology to predict the tertiary structure of a protein from its primary amino acid sequence. From visual comparison, it was found that a 2D triangular lattice model can give a better structure modeling and prediction for proteins with short primary amino acid sequences.

Methods
This paper proposes a hybrid of hill-climbing and genetic algorithm (HHGA) based on elite-based reproduction strategy for protein structure prediction on the 2D triangular lattice.

Results
The simulation results show that the proposed HHGA can successfully deal with the protein structure prediction problems. Specifically, HHGA significantly outperforms conventional genetic algorithms and is comparable to the state-of-the-art method in terms of free energy.

Conclusions
Thanks to the enhancement of local search on the global search, the proposed HHGA achieves promising results on the 2D triangular protein structure prediction problem. The satisfactory simulation results demonstrate the effectiveness of the proposed HHGA and the utility of the 2D triangular lattice model for protein structure prediction.
Cervical adenoid basal carcinoma associated with invasive squamous cell carcinoma: A report of rare co-existence and review of literature
Authors: Viriyapak Boonlert , Park Sung Taek , Lee Ah Won , Park Jong Sup , Lee Chung Won , Song Min Jong , Hur Soo Young 
Published: October 2011

Abstract
Cervical adenoid basal carcinoma (ABC) rarely can harbor associated malignancies like adenoid cystic carcinoma or squamous cell carcinoma (SCC), which express markedly different prognosis from a pure ABC, making an appropriate biopsy essential to provide a clear diagnosis and therapeutic plan. We report a 64-year-old asymptomatic lady with an abnormal cervical cytology, who underwent a conization to reveal an ABC with overlying microinvasive SCC. Doubtful resection margins led us to perform radical hysterectomy with lymph node dissection. Subsequent pathological examination showed a true invasive SCC co-existing with ABC, with invasion of the parametrium. Unlike the indolent course of many pure ABC patients, the prognosis of 11 previously reported co-existing invasive SCC with ABC patients appears to depend on the SCC component. Our case reiterates the importance of adequate biopsy with careful interpretation to cover the possibility of a co-existent malignancy. Besides, it presents an argument in favor of radical surgery for the primary treatment of suspicious associated malignancy, and supports adjuvant treatment according to the unfavorable extent of the co-existent invasive carcinoma.
Effects of nutritional cues on the duration of the winter anovulatory phase and on associated hormone levels in adult female Welsh pony horses (Equus caballus)
Authors: Salazar-Ortiz Juan , Camous Sylvaine , Briant Christine , Lardic Lionel , Chesneau Didier , Guillaume Daniel 
Published: October 2011

Abstract

Background
Mares have an annual reproductive rhythm, with a phase of inactivity in midwinter. The aim of this study was to determine the impact of food restriction on physiological and metabolic hallmarks of this rhythm.

Methods
Over three successive years, 3 groups of 10 mares were kept under natural photoperiod. A 'well-fed' group was fed to maintain the mares in good body condition; a 'restricted' group received a diet calculated to keep the mares thin and a 'variable' group was fed during some periods like the 'restricted' group and during some other periods like the 'well-fed' group, with the aim of mimicking the natural seasonal variation of pasture availability, but a few months in advance of this natural rhythm.

Results
Winter ovarian inactivity always occurred and was long in the restricted group. In contrast, in the 'well-fed' group, 40% of mares showed this inactivity, which was shorter than in the other groups. Re-feeding the 'variable' group in autumn and winter did not advance the first ovulation in spring, compared with the 'restricted' group. Measurements of glucose and insulin concentrations in mares from the 'restricted' group during two 24 h periods of blood sampling, revealed no post-prandial peaks. For GH (Growth hormone), IGF-1 and leptin levels, large differences were found between the 'well-fed' group and the other groups. The glucose, insulin, GH and leptin levels but not melatonin level are highly correlated with the duration of ovulatory activity.

Conclusions
The annual rhythm driven by melatonin secretion is only responsible for the timing of the breeding season. The occurrence and length of winter ovarian inactivity is defined by metabolic hormones.
Synthesis of NaYF4:Yb3+, Er3+ upconversion nanoparticles in normal microemulsions
Authors: Shan Shu-Nan , Wang Xiu-Ying , Jia Neng-Qin 
Published: October 2011

AbstractAn interface-controlled reaction in normal microemulsions (water/ethanol/sodium oleate/oleic acid/n-hexane) was designed to prepare NaYF4:Yb3+, Er3+ upconversion nanoparticles. The phase diagram of the system was first studied to obtain the appropriate oil-in-water microemulsions. Transmission electron microscopy and X-ray powder diffractometer measurements revealed that the as-prepared nanoparticles were spherical, monodisperse with a uniform size of 20 nm, and of cubic phase with good crystallinity. Furthermore, these nanoparticles have good dispersibility in nonpolar organic solvents and exhibit visible upconversion luminescence of orange color under continuous excitation at 980 nm. Then, a thermal treatment for the products was found to enhance the luminescence intensity. In addition, because of its inherent merit in high yielding and being economical, this synthetic method could be utilized for preparation of the UCNPs on a large scale.
Improved characteristics of near-band-edge and deep-level emissions from ZnO nanorod arrays by atomic-layer-deposited Al2O3 and ZnO shell layers
Authors: Sun Wen-Cheng , Yeh Yu-Cheng , Ko Chung-Ting , He Jr-Hau , Chen Miin-Jang 
Published: October 2011

AbstractWe report on the characteristics of near-band-edge (NBE) emission and deep-level band from ZnO/Al2O3 and ZnO/ZnO core-shell nanorod arrays (NRAs). Vertically aligned ZnO NRAs were synthesized by an aqueous chemical method, and the Al2O3 and ZnO shell layers were prepared by the highly conformal atomic layer deposition technique. Photoluminescence measurements revealed that the deep-level band was suppressed and the NBE emission was significantly enhanced after the deposition of Al2O3 and ZnO shells, which are attributed to the decrease in oxygen interstitials at the surface and the reduction in surface band bending of ZnO core, respectively. The shift of deep-level emissions from the ZnO/ZnO core-shell NRAs was observed for the first time. Owing to the presence of the ZnO shell layer, the yellow band associated with the oxygen interstitials inside the ZnO core would be prevailed over by the green luminescence, which originates from the recombination of the electrons in the conduction band with the holes trapped by the oxygen vacancies in the ZnO shell.PACS 68.65.Ac; 71.35.-y; 78.45.+h; 78.55.-m; 78.55.Et; 78.67.Hc; 81.16.Be; 85.60.Jb.
Liposomal doxorubicin improves radiotherapy response in hypoxic prostate cancer xenografts
Authors: Hagtvet Eirik , Røe Kathrine , Olsen Dag R 
Published: October 2011

Abstract

Background
Tumor vasculature frequently fails to supply sufficient levels of oxygen to tumor tissue resulting in radioresistant hypoxic tumors. To improve therapeutic outcome radiotherapy (RT) may be combined with cytotoxic agents.

Methods
In this study we have investigated the combination of RT with the cytotoxic agent doxorubicin (DXR) encapsulated in pegylated liposomes (PL-DXR). The PL-DXR formulation Caelyx® was administered to male mice bearing human, androgen-sensitive CWR22 prostate carcinoma xenografts in a dose of 3.5 mg DXR/kg, in combination with RT (2 Gy/day × 5 days) performed under normoxic and hypoxic conditions. Hypoxic RT was achieved by experimentally inducing tumor hypoxia by clamping the tumor-bearing leg five minutes prior to and during RT. Treatment response evaluation consisted of tumor volume measurements and dynamic contrast-enhanced magnetic resonance imaging (DCE MRI) with subsequent pharmacokinetic analysis using the Brix model. Imaging was performed pre-treatment (baseline) and 8 days later. Further, hypoxic fractions were determined by pimonidazole immunohistochemistry of excised tumor tissue.

Results
As expected, the therapeutic effect of RT was significantly less effective under hypoxic than normoxic conditions. However, concomitant administration of PL-DXR significantly improved the therapeutic outcome following RT in hypoxic tumors. Further, the pharmacokinetic DCE MRI parameters and hypoxic fractions suggest PL-DXR to induce growth-inhibitory effects without interfering with tumor vascular functions.

Conclusions
We found that DXR encapsulated in liposomes improved the therapeutic effect of RT under hypoxic conditions without affecting vascular functions. Thus, we propose that for cytotoxic agents affecting tumor vascular functions liposomes may be a promising drug delivery technology for use in chemoradiotherapy.
Clinical application of CT-guided 125I seed interstitial implantation for local recurrent rectal carcinoma
Authors: Wang Zhongmin , Lu Jian , Liu Lin , Liu Tao , Chen Kemin , Liu Fenju , Huang Gang 
Published: October 2011

Abstract

Purpose
The present study aimed to explore the safety profile and clinical efficacy of CT-guided radioactive seed implantation in treating local recurrent rectal carcinoma.

Materials and methods
CT-guided 125I seed implantation was carried out in 20 patients with locally recurrent rectal carcinoma. 14 of the 20 patient had prior adjuvant external-beam radiation therapy (EBRT). The treatment planning system (TPS) was used preoperatively to reconstruct three dimensional images of the tumor and to calculate the estimated seed number and distribution. The median matched peripheral dose (MPD) was 120 Gy (range, 100-160 Gy).

Results
Of the 20 patients, 12 were male, 8 were female, and ages ranged from 38 to 78, with a median age of 62. Duration of follow-up was 3-34 months. The response rate of pain relief was 85% (17/20). Repeat CT scan 2 months following the procedure revealed complete response (CR) of the tumor in 2 patients, partial response (PR) in 13 patients, stable disease (SD) in 3 patients, and progressive disease (PD) in 2 patients. 75% of patients had either CR or PR. Median survival time was 18.8 months (95% CI: 3.5-22.4 months). 1 and 2 year survival rates were 75% and 25%, respectively. 4 patients died of recurrent tumor; 4 patients died of distant metastases; 9 patients died of recurrent tumor and distant metastases. 3 patients survived after 2 year follow up. Two patients were found to have mild hematochezia, which was reversible with symptomatic management.

Conclusion
CT-guided 125I seed implantation appeared to be a safe, useful and less complicated interventional treatment option for local recurrent rectal carcinoma.
Prognostic factors of atrial fibrillation following elective coronary artery bypass grafting: the impact of quantified intraoperative myocardial ischemia
Authors: Koletsis Efstratios N , Prokakis Christos , Crockett James R , Dedeilias Panagiotis , Panagiotou Matthew , Panagopoulos Nikolaos , Anastasiou Nikolaos , Dougenis Dimitrios , Apostolakis Efstratios 
Published: October 2011

Abstract

Background
Atrial fibrillation (AF) occurs in 28-33% of the patients undergoing coronary artery revascularization (CABG). This study focuses on both pre- and peri-operative factors that may affect the occurrence of AF. The aim is to identify those patients at higher risk to develop AF after CABG.

Patients and methods
Two patient cohorts undergoing CABG were retrospectively studied. The first group (group A) consisted of 157 patients presenting AF after elective CABG. The second group (group B) consisted of 191 patients without AF postoperatively.

Results
Preoperative factors presenting significant correlation with the incidence of post-operative AF included: 1) age > 65 years (p = 0.029), 2) history of AF (p = 0.022), 3) chronic obstructive pulmonary disease (p = 0.008), 4) left ventricular dysfunction with ejection fraction < 40% (p = 0.015) and 5) proximal lesion of the right coronary artery (p = 0.023). The intraoperative factors that appeared to have significant correlation with the occurrence of postoperative AF were: 1) CPB-time > 120 minutes (p = 0.011), 2) myocardial ischemia index < 0.27 ml.m2/Kg.min (p = 0.011), 3) total positive fluid-balance during ICU-stay (p < 0.001), 4) FiO2/PO2 > 0, 4 after extubation and during the ICU-stay (p = 0.021), 5) inotropic support with doses 15-30 μg/Kg/min (p = 0.016), 6) long ICU-stay recovery for any reason (p < 0.001) and perioperative myocardial infarction (p < 0.001).

Conclusions
Our results suggest that the incidence of post-CABG atrial fibrillation can be predicted by specific preoperative and intraoperative measures. The intraoperative myocardial ischemia can be sufficiently quantified by the myocardial ischemia index. For those patients at risk we would suggest an early postoperative precautionary anti-arrhythmic treatment.
Solitary pulmonary nodule of benign metastasizing leiomyoma associated with primary lung cancer: a case report
Authors: Naito Masahiro , Kobayashi Tetsu , Yoshida Masamichi , Fujiwara Kentaro , Onishi Masahiro , Fujiwara Atsushi , Takagi Takehiro , Kobayashi Hiroyasu , Gabazza Esteban C , Takei Yoshiyuki , Taguchi Osamu 
Published: October 2011

Abstract

Introduction
Benign metastasizing leiomyoma in the lung is a very rare disease characterized by the growth of uterine leiomyoma tissue. In most cases there is a previous history of hysterectomy for uterine leiomyoma.

Case presentation
A 50-year-old Asian woman underwent a total abdominal hysterectomy for uterine leiomyoma at the age of 37 years old. She was referred to our hospital because of sudden anterior chest pain. A chest computed tomography scan revealed a ground-glass opacity in her left S10 lung segment and a solitary small nodule in her left bronchial segment, S4. We performed a left lower lobectomy and an upper lung partial resection in order to make a definitive diagnosis and to enable us to determine a further therapeutic strategy. The ground-glass opacity in her left S10 was a primary lung adenocarcinoma, while the small nodule in her left S4 was diagnosed as a benign metastasizing leiomyoma. No additional therapy was done and our patient was followed up with chest computed tomography. Up to date, repetitive evaluation by chest computed tomography has shown no sign of benign metastasizing leiomyoma or lung cancer recurrence.

Conclusion
This is a very rare case of benign metastasizing leiomyoma of the lung associated with primary lung cancer. This comorbid association should be considered in the differential diagnosis when a solitary lung nodule is detected in a patient with a history of uterine leiomyoma.