bluuebunny/crossref_metadata_2025_split huggingface dataset:
The need for continued monitoring of antibiotic resistance patterns in clinical isolates of Staphylococcus aureus from London and Malta
Authors: Gould Simon WJ , Cuschieri Paul , Rollason Jess , Hilton Anthony C , Easmon Sue , Fielder Mark D 
Published: July 2010

Abstract

Background
Antibiotic resistance is an increasing problem in isolates of Staphylococcus aureus (S. aureus) worldwide. In 2001 The National Health Service in the UK introduced a mandatory bacteraemia surveillance scheme for the reporting of S. aureus and methicillin-resistant S. aureus (MRSA). This surveillance initiative reports on the percentage of isolates that are methicillin resistant. However, resistance to other antibiotics is not currently reported and therefore the scale of emerging resistance is currently unclear in the UK. In this study, multiple antibiotic resistance (MAR) profiles against fourteen antimicrobial drugs were investigated for 705 isolates of S. aureus collected from two European study sites in the UK (London) and Malta.

Results
All isolates were susceptible to linezolid, teicoplanin and vancomycin. Multiple antibiotic resistance profiles from both countries were determined, a total of forty-two and forty-five profiles were seen in the UK cohort (MRSA and MSSA respectively) and comparatively, sixty-two and fifty-two profiles were shown in the Maltese group. The largest MAR profile contained six antibiotics (penicillin G, methicillin, erythromycin, ciprofloxacin, clindamycin and clarithromycin) and was observed in the MRSA isolates in both the UK and Maltese cohorts.

Conclusion
The data presented here suggests that the monitoring of changing resistance profiles locally in maintaining treatment efficacy to resistant pathogens.
Evaluation of normalization methods for two-channel microRNA microarrays
Authors: Zhao Yingdong , Wang Ena , Liu Hui , Rotunno Melissa , Koshiol Jill , Marincola Francesco M , Landi Maria Teresa , McShane Lisa M 
Published: July 2010

Abstract

Background
MiR arrays distinguish themselves from gene expression arrays by their more limited number of probes, and the shorter and less flexible sequence in probe design. Robust data processing and analysis methods tailored to the unique characteristics of miR arrays are greatly needed. Assumptions underlying commonly used normalization methods for gene expression microarrays containing tens of thousands or more probes may not hold for miR microarrays. Findings from previous studies have sometimes been inconclusive or contradictory. Further studies to determine optimal normalization methods for miR microarrays are needed.

Methods
We evaluated many different normalization methods for data generated with a custom-made two channel miR microarray using two data sets that have technical replicates from several different cell lines. The impact of each normalization method was examined on both within miR error variance (between replicate arrays) and between miR variance to determine which normalization methods minimized differences between replicate samples while preserving differences between biologically distinct miRs.

Results
Lowess normalization generally did not perform as well as the other methods, and quantile normalization based on an invariant set showed the best performance in many cases unless restricted to a very small invariant set. Global median and global mean methods performed reasonably well in both data sets and have the advantage of computational simplicity.

Conclusions
Researchers need to consider carefully which assumptions underlying the different normalization methods appear most reasonable for their experimental setting and possibly consider more than one normalization approach to determine the sensitivity of their results to normalization method used.
Self-assembly of virus-like particles of porcine circovirus type 2 capsid protein expressed from Escherichia coli
Authors: Yin Shuanghui , Sun Shiqi , Yang Shunli , Shang Youjun , Cai Xuepeng , Liu Xiangtao 
Published: July 2010

Abstract

Background
Porcine circovirus 2 (PCV2) is a serious problem to the swine industry and can lead to significant negative impacts on profitability of pork production. Syndrome associated with PCV2 is known as porcine circovirus closely associated with post-weaning multisystemic wasting syndrome (PMWS). The capsid (Cap) protein of PCV2 is a major candidate antigen for development of recombinant vaccine and serological diagnostic method. The recombinant Cap protein has the ability to self-assemble into virus-like particles (VLPs) in vitro, it is particularly opportunity to develop the PV2 VLPs vaccine in Escherichia coli,(E.coli ), because where the cost of the vaccine must be weighed against the value of the vaccinated pig, when it was to extend use the VLPs vaccine of PCV2.

Results
In this report, a highly soluble Cap-tag protein expressed in E.coli was constructed with a p-SMK expression vector with a fusion tag of small ubiquitin-like modifiers (SUMO). The recombinant Cap was purified using Ni2+ affinity resins, whereas the tag was used to remove the SUMO protease. Simultaneously, the whole native Cap protein was able to self-assemble into VLPs in vitro when viewed under an electron microscope. The Cap-like particles had a size and shape that resembled the authentic Cap. The result could also be applied in the large-scale production of VLPs of PCV2 and could be used as a diagnostic antigen or a potential VLP vaccine against PCV2 infection in pigs.

Conclusion
we have, for the first time, utilized the SUMO fusion motif to successfully express the entire authentic Cap protein of PCV2 in E. coli. After the cleavage of the fusion motif, the nCap protein has the ability to self-assemble into VLPs, which can be used as as a potential vaccine to protect pigs from PCV2-infection.
Polycyclic aromatic hydrocarbon components contribute to the mitochondria-antiapoptotic effect of fine particulate matter on human bronchial epithelial cells via the aryl hydrocarbon receptor
Authors: Ferecatu Ioana , Borot Marie-Caroline , Bossard Camille , Leroux Melanie , Boggetto Nicole , Marano Francelyne , Baeza-Squiban Armelle , Andreau Karine 
Published: July 2010

AbstractBackgroundNowadays, effects of fine particulate matter (PM2.5) are well-documented and related to oxidative stress and pro-inflammatory response. Nevertheless, epidemiological studies show that PM2.5exposure is correlated with an increase of pulmonary cancers and the remodeling of the airway epithelium involving the regulation of cell death processes. Here, we investigated the components of Parisian PM2.5involved in either the induction or the inhibition of cell death quantified by different parameters of apoptosis and delineated the mechanism underlying this effect.ResultsIn this study, we showed that low levels of Parisian PM2.5are not cytotoxic for three different cell lines and primary cultures of human bronchial epithelial cells. Conversely, a 4 hour-pretreatment with PM2.5prevent mitochondria-driven apoptosis triggered by broad spectrum inducers (A23187, staurosporine and oligomycin) by reducing the mitochondrial transmembrane potential loss, the subsequent ROS production, phosphatidylserine externalization, plasma membrane permeabilization and typical morphological outcomes (cell size decrease, massive chromatin and nuclear condensation, formation of apoptotic bodies). The use of recombinant EGF and specific inhibitor led us to rule out the involvement of the classical EGFR signaling pathway as well as the proinflammatory cytokines secretion. Experiments performed with different compounds of PM2.5suggest that endotoxins as well as carbon black do not participate to the antiapoptotic effect of PM2.5. Instead, the water-soluble fraction, washed particles and organic compounds such as polycyclic aromatic hydrocarbons (PAH) could mimic this antiapoptotic activity. Finally, the activation or silencing of the aryl hydrocarbon receptor (AhR) showed that it is involved into the molecular mechanism of the antiapoptotic effect of PM2.5at the mitochondrial checkpoint of apoptosis.ConclusionsThe PM2.5-antiapoptotic effect in addition to the well-documented inflammatory response might explain the maintenance of a prolonged inflammation state induced after pollution exposure and might delay repair processes of injured tissues.
Inflammatory myofibroblastic tumor of the lung- a case report
Authors: Chen Chien-Kuang , Jan Chia-Ing , Tsai Jian-Shun , Huang Hsu-Chih , Chen Pin-Ru , Lin Yu-Sen , Chen Chih-Yi , Fang Hsin-Yuan 
Published: July 2010

Abstract
A 45-year-old man presented with a six-month history of progressive dyspnea with productive cough and wheezing. The patient was a heavy smoker and had a history of tongue cancer, hypertension, and asthma. Chest X-ray and computed tomography showed a mass lesion in the left hilar region and total collapse of the upper left lobe of the lung. Bronchoscopy revealed a whitish solid tumor obstructing the left upper lobe bronchus. Positron emission tomography showed increased tracer uptake in the lesion. A thoracoscopic lobectomy of the left upper lobe of the lung was performed. The final pathologic diagnosis was inflammatory myofibroblastic tumor.
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent
Authors: Wang Yuanfeng , Christley Scott , Mjolsness Eric , Xie Xiaohui 
Published: July 2010

Abstract

Background
Stochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species.

Results
We propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD). We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC), and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models.

Conclusions
The SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is computationally efficient and is effective for both partially and fully observed systems. Automatic construction of reversible jump samplers and general formulation of the likelihood gradient function makes our method applicable to a wide range of stochastic models. Furthermore our derivations can be useful for other purposes such as using the gradient information for parametric sensitivity analysis or using the reversible jump samplers for full Bayesian inference. The software implementing the algorithms is publicly available at http://cbcl.ics.uci.edu/sgd
Parkinsonism secondary to metastatic lesions within the central nervous system: a case report
Authors: Hortelano Eduardo , Perea Christian , Uña Esther , Cebayos Amelia , Diezhandino Patricia , González Montserrat 
Published: July 2010

Abstract

Introduction
Colorectal cancer is one of the most common human diseases worldwide, and metastases are detected in approximately 20% of patients at diagnosis. Brain metastases occur in only 4% of cases, however, and usually present with hemiparesis or other motor or sensory symptoms. There have been only a few reports of parkinsonism secondary to a brain tumor-related mass effect.

Case presentation
We present an unusual case of parkinsonism secondary to multiple brain metastases. A 57-year-old Caucasian man had recently been diagnosed with primary carcinoma of the colon and had multiple metastases in the lungs and liver. He subsequently developed bilateral symmetrical parkinsonism, and multiple brain tumors were detected by computed tomography scanning. The condition of our patient deteriorated rapidly, and he became akinetic and dependent for all activities of daily living. He was followed up and treated at home by our palliative care unit team and died two weeks after the onset of his neurologic symptoms.

Conclusion
Although primary and secondary brain tumors are uncommon causes of parkinsonism, their clinical presentation may resemble that of idiopathic Parkinson's disease. An awareness of this rare differential diagnosis is therefore important in ensuring early diagnosis and treatment, thus improving prognosis and quality of life. A rapid progression in neurologic symptoms was observed in our patient, and clinicians should be alert to this atypical presentation of secondary parkinsonism.
A synthetic three-color scaffold for monitoring genetic regulation and noise
Authors: Cox Robert Sidney , Dunlop Mary J , Elowitz Michael B 
Published: July 2010

Abstract

Background
Current methods for analyzing the dynamics of natural regulatory networks, and quantifying synthetic circuit function, are limited by the lack of well-characterized genetic measurement tools. Fluorescent reporters have been used to measure dynamic gene expression, but recent attempts to monitor multiple genes simultaneously in single cells have not focused on independent, isolated measurements. Multiple reporters can be used to observe interactions between natural genes, or to facilitate the 'debugging' of biologically engineered genetic networks. Using three distinguishable reporter genes in a single cell can reveal information not obtainable from only one or two reporters. One application of multiple reporters is the use of genetic noise to reveal regulatory connections between genes. Experiments in both natural and synthetic systems would benefit from a well-characterized platform for expressing multiple reporter genes and synthetic network components.

Results
We describe such a plasmid-based platform for the design and optimization of synthetic gene networks, and for analysis of endogenous gene networks. This network scaffold consists of three distinguishable fluorescent reporter genes controlled by inducible promoters, with conveniently placed restriction sites to make modifications straightforward. We quantitatively characterize the scaffold in Escherichia coli with single-cell fluorescence imaging and time-lapse microscopy. The three spectrally distinct reporters allow independent monitoring of genetic regulation and analysis of genetic noise. As a novel application of this tool we show that the presence of genetic noise can reveal transcriptional co-regulation due to a hidden factor, and can distinguish constitutive from regulated gene expression.

Conclusion
We have constructed a general chassis where three promoters from natural genes or components of synthetic networks can be easily inserted and independently monitored on a single construct using optimized fluorescent protein reporters. We have quantitatively characterized the baseline behavior of the chassis so that it can be used to measure dynamic gene regulation and noise. Overall, the system will be useful both for analyzing natural genetic networks and assembling synthetic ones.
Positive end-expiratory pressure affects the value of intra-abdominal pressure in acute lung injury/acute respiratory distress syndrome patients: a pilot study
Authors: Verzilli Daniel , Constantin Jean-Michel , Sebbane Mustapha , Chanques Gérald , Jung Boris , Perrigault Pierre-François , Malbrain Manu , Jaber Samir 
Published: July 2010

Abstract
Introduction
To examine the effects of positive end-expiratory pressure (PEEP) on intra-abdominal pressure (IAP) in patients with acute lung injury (ALI).

Methods
Thirty sedated and mechanically ventilated patients with ALI or acute respiratory distress syndrome (ARDS) admitted to a sixteen-bed surgical medical ICU were included. All patients were studied with sequentially increasing PEEP (0, 6 and 12 cmH2O) during a PEEP-trial.

Results
Age was 55 ± 17 years, weight was 70 ± 17 kg, SAPS II was 44 ± 14 and PaO2/FIO2 was 192 ± 53 mmHg. The IAP was 12 ± 5 mmHg at PEEP 0 (zero end-expiratory pressure, ZEEP), 13 ± 5 mmHg at PEEP 6 and 15 ± 6 mmHg at PEEP 12 (P < 0.05 vs ZEEP). In the patients with intra-abdominal hypertension defined as IAP ≥ 12 mmHg (n = 15), IAP significantly increased from 15 ± 3 mmHg at ZEEP to 20 ± 3 mmHg at PEEP 12 (P < 0.01). Whereas in the patients with IAP < 12 mmHg (n = 15), IAP did not significantly change from ZEEP to PEEP 12 (8 ± 2 vs 10 ± 3 mmHg). In the 13 patients in whom cardiac output was measured, increase in PEEP from 0 to 12 cmH2O did not significantly change cardiac output, nor in the 8 out of 15 patients of the high-IAP group. The observed effects were similar in both ALI (n = 17) and ARDS (n = 13) patients.

Conclusions
PEEP is a contributing factor that impacts IAP values. It seems necessary to take into account the level of PEEP whilst interpreting IAP values in patients under mechanical ventilation.
Risk of Invasive Cervical Cancer and Cervical Intraepithelial Neoplasia Grade Iii in Central Italy by Area of Birth
Authors: Crocetti Emanuele , Manneschi Gianfranco , Visioli Carmen Beatriz , Zappa Marco 
Published: July 2010

Objective To evaluate cervical cancer incidence among women born in different countries but residing in Italy. Setting Women aged 25-59 from a central Italian population-based cancer registry. Methods Invasive and in situ cervical cancer incidence rates from 2000-2004 were calculated. Standardized incidence rates were based on the European standard population. Places of birth were categorized by nine different areas. Results Within the resident population aged 25-59, there were 148 invasive cervical cancers (17.6% in women born outside Italy) and 501 (14.2% in women born outside Italy) cervical intraepithelial neoplasia grade III (CIN III) diagnoses. The incidence of invasive cervical cancer for women born in ‘Central & South America and the Caribbean’ was 60.5 per 100,000 and in ‘Central and Eastern Europe’ it was 38.3, statistically significantly higher than for women born in Italy (9.5 per 100,000). The CIN III rate was 35.0 per 100,000 for women born in Italy. The ratio between standardized rates for CIN III and invasive cancers was around 4 for women born in Italy and the ‘extended European Union’, and around 6 for those born in ‘Asia’. It was 1.64 for women born in ‘Africa’, 1.31 in ‘Central & South America and the Caribbean’ and 0.69 for those born in ‘Eastern Europe’. Conclusions Women who reside in Italy but were born in ‘Central & South America and the Caribbean’ or in ‘Central and Eastern Europe’ are at high risk for invasive cervical cancer. These groups are less inclined to participate in screening, and appropriate preventive strategies should be planned accordingly.
A Fall-off in Cervical Screening Coverage of Younger Women in Developed Countries
Authors: Lancucki L , Fender M , Koukari A , Lynge E , Mai V , Mancini E , Onysko J , Ronco G , Tornberg S , Vessey M , Patnick J 
Published: July 2010

Objectives To analyse cervical screening coverage data by age over time in a number of developed countries throughout the world, with specific emphasis on trends for younger women and on age differentials between younger and older women. Methods Routinely collected cervical screening statistics and survey data were collected on the proportion of women who have undergone cervical screening with cytology in seven countries in the period 1995 to 2005. Results Data for the 25-29 age group were examined. Coverage fell in most countries, in three by more than 5 percentage points. In two countries while overall coverage rose in the period, the rise was not as steep in the youngest group of women. Data for each available 5-year age group for the different countries shows a similar gradient in most, regardless of the absolute level of coverage. Although the trend is not uniform in every country, it appears that generally the gap between coverage of younger women and coverage of older women increased, sometimes dramatically, between the mid-1990s and the mid-2000s. Conclusions There is a general trend in developed countries towards lower coverage in young women (25-29 years old). No common underlying cause has been clearly identified and there is a need for further studies to investigate the possible reasons for this phenomenon.
Relationship Between Serum Heparanase and Microscopic Venous Invasion in Patients With Hepatocellular Carcinoma
Authors: Wang Gui-Bo , Zhou Xin-Yu , Wang Xiao-Qin 
Published: July 2010

Abstract
The serum heparanase level of 92 patients with hepatocellular carcinoma (HCC) measured by enzyme-linked immunosorbent assay (median, 91.4 U/mL) was higher than that of 19 healthy control subjects. Serum heparanase levels were higher in patients with HCC characterized by large tumors (&gt;5 cm), advanced pTNM stage (III and IV), tumor capsule absence, and portal vein invasion. Positive correlations between serum heparanase and tumor heparanase expression were observed in 92 patients with HCC, 53 among them treated with tumor resection. In these 53 patients, the rate of microscopic venous invasion was significantly higher in 18 cases with high serum heparanase levels (&gt;91.4 U/mL) than in the other 35 cases with low heparanase levels (14/18 vs 10/35; P = .001). Serum heparanase and vascular endothelial growth factor were identified as independent predictive factors for HCC microscopic venous invasion. The postoperative recurrence-free time (median, 8.7 months; range, 4.1–22.9 months), recurrence rate (72% [13/18]), 1.5-year disease-free survival rate (29.7%) were significantly worse in these 18 patients.
Detection of SYT and EWS Gene Rearrangements by Dual-Color Break-Apart CISH in Liquid-Based Cytology Samples of Synovial Sarcoma and Ewing Sarcoma/Primitive Neuroectodermal Tumor
Authors: Kumagai Arisa , Motoi Toru , Tsuji Kaori , Imamura Tetsuo , Fukusato Toshio 
Published: July 2010

Abstract
To improve cytologic diagnostic accuracy for translocation-associated sarcomas, we explored dual-color break-apart (dc) chromogenic in situ hybridization (CISH) on liquid-based cytology (LBC) samples of 2 prototypic sarcomas: synovial sarcoma (SS) and Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET). LBC samples of 10 cases of SS and 9 cases of ES/PNET were subjected to dc-CISH using probes for the specifically rearranged genes in each tumor entity: SYT in SS and EWS in ES/PNET.
Rearranged SYT was successfully detected in all SSs but not in any ES/PNETs. In contrast, EWS rearrangement was identified in all ES/PNETs but not in any SSs. These results were validated by dc-fluorescence in situ hybridization and reverse transcription–polymerase chain reaction.
dc-CISH on LBC samples is a reliable modality to detect gene rearrangements in sarcomas. This system has a clear advantage over other methods, enabling simultaneous visualization of the genetic abnormality and well-preserved, nonoverlapping cytomorphologic features with clear background under bright-field microscope.