bluuebunny/crossref_metadata_2025_split huggingface dataset:
EGFRmutation testing in lung cancer: a review of available methods and their use for analysis of tumour tissue and cytology samples
Authors: Ellison Gillian , Zhu Guanshan , Moulis Alexandros , Dearden Simon , Speake Georgina , McCormack Rose 
Published: November 2012

AimsActivating mutations in the gene encoding epidermal growth factor receptor (EGFR) can confer sensitivity to EGFR tyrosine kinase inhibitors such as gefitinib in patients with advanced non-small-cell lung cancer. Testing for mutations inEGFRis therefore an important step in the treatment-decision pathway. We reviewed reported methods forEGFRmutation testing in patients with lung cancer, initially focusing on studies involving standard tumour tissue samples. We also evaluated data on the use of cytology samples in order to determine their suitability forEGFRmutation analysis.MethodsWe searched the MEDLINE database for studies reporting onEGFRmutation testing methods in patients with lung cancer.ResultsVarious methods have been investigated as potential alternatives to the historical standard forEGFRmutation testing, direct DNA sequencing. Many of these are targeted methods that specifically detect the most commonEGFRmutations. The development of targeted mutation testing methods and commercially available test kits has enabled sensitive, rapid and robust analysis of clinical samples. The use of screening methods, subsequent to sample micro dissection, has also ensured that identification of more rare, uncommon mutations is now feasible. Cytology samples including fine needle aspirate and pleural effusion can be used successfully to determineEGFRmutation status provided that sensitive testing methods are employed.ConclusionsSeveral different testing methods offer a more sensitive alternative to direct sequencing for the detection of commonEGFRmutations. Evidence published to date suggests cytology samples are viable alternatives for mutation testing when tumour tissue samples are not available.
The Frontal Assessment Battery in the Differential Diagnosis of Dementia
Authors: Boban Marina , Malojčić Branko , Mimica Ninoslav , Vuković Sunčica , Zrilić Ivan 
Published: November 2012

Aim: The Frontal Assessment Battery (FAB) has been used in different clinical settings as a valuable quick bedside test for executive dysfunction. The aim of the study was to evaluate clinical utility of the FAB for differential diagnosis of Alzheimer disease (AD), subcortical vascular cognitive impairment (scVCI), and frontotemporal lobar degeneration (FTLD). Methods: Scores of the total FAB test and subtests were compared between consecutive series of 37 patients with AD, 31 patients with scVCI, 13 patients with FTLD, and 29 cognitively healthy individuals. Results: There was no statistically significant difference in the total FAB scores among the groups of patients with dementia. When comparing subtest scores, patients with FTLD had significantly lower scores on the lexical fluency subtest compared to the patients with AD ( P < .001) or scVCI ( P < .001); patients with scVCI had significantly lower scores on the motor series subtest compared to patients with FTLD ( P = .02) and AD ( P = .035) and on conflicting instructions subtest compared to patients with AD ( P = .033). Conclusion: Some FAB subtests might enhance diagnostic accuracy taking into account clinical history and other tests of executive function.
Nuclear genomic control of naturally occurring variation in mitochondrial function in Drosophila melanogaster
Authors: Jumbo-Lucioni Patricia , Bu Su , Harbison Susan T , Slaughter Juanita C , Mackay Trudy FC , Moellering Douglas R , De Luca Maria 
Published: November 2012

AbstractBackgroundMitochondria are organelles found in nearly all eukaryotic cells that play a crucial role in cellular survival and function. Mitochondrial function is under the control of nuclear and mitochondrial genomes. While the latter has been the focus of most genetic research, we remain largely ignorant about the nuclear-encoded genomic control of inter-individual variability in mitochondrial function. Here, we usedDrosophila melanogasteras our model organism to address this question.ResultsWe quantified mitochondrial state 3 and state 4 respiration rates and P:O ratio in mitochondria isolated from the thoraces of 40 sequenced inbred lines of the Drosophila Genetic Reference Panel. We found significant within-population genetic variability for all mitochondrial traits. Hence, we performed genome-wide association mapping and identified 141 single nucleotide polymorphisms (SNPs) associated with differences in mitochondrial respiration and efficiency (P≤1 × 10-5). Gene-centered regression models showed that 2–3 SNPs can explain 31, 13, and 18% of the phenotypic variation in state 3, state 4, and P:O ratio, respectively. Most of the genes tagged by the SNPs are involved in organ development, second messenger-mediated signaling pathways, and cytoskeleton remodeling. One of these genes,sallimus(sls), encodes a component of the muscle sarcomere. We confirmed the direct effect ofslson mitochondrial respiration using two viable mutants and their coisogenic wild-type strain. Furthermore, correlation network analysis revealed thatslsfunctions as a transcriptional hub in a co-regulated module associated with mitochondrial respiration and is connected toCG7834, which is predicted to encode a protein with mitochondrial electron transfer flavoprotein activity. This latter finding was also verified in theslsmutants.ConclusionsOur results provide novel insights into the genetic factors regulating natural variation in mitochondrial function inD. melanogaster. The integrative genomic approach used in our study allowed us to identifyslsas a novel hub gene responsible for the regulation of mitochondrial respiration in muscle sarcomere and to provide evidence thatslsmight act via the electron transfer flavoprotein/ubiquinone oxidoreductase complex.
The retention of health human resources in primary healthcare centers in Lebanon: a national survey
Authors: Alameddine Mohamad , Saleh Shadi , El-Jardali Fadi , Dimassi Hani , Mourad Yara 
Published: November 2012

Abstract

Background
Critical shortages of health human resources (HHR), associated with high turnover rates, have been a concern in many countries around the globe. Of particular interest is the effect of such a trend on the primary healthcare (PHC) sector; considered a cornerstone in any effective healthcare system. This study is a rare attempt to investigate PHC HHR work characteristics, level of burnout and likelihood to quit as well as the factors significantly associated with staff retention at PHC centers in Lebanon.

Methods
A cross-sectional design was utilized to survey all health providers at 81 PHC centers dispersed in all districts of Lebanon. The questionnaire consisted of four sections: socio-demographic/ professional background, organizational/institutional characteristics, likelihood to quit and level of professional burnout (using the Maslach-Burnout Inventory). A total of 755 providers completed the questionnaire (60.5% response rate). Bivariate analyses and multinomial logistic regression were used to determine factors associated with likelihood to quit.

Results
Two out of five respondents indicated likelihood to quit their jobs within the next 1–3 years and an additional 13.4% were not sure about quitting. The top three reasons behind likelihood to quit were poor salary (54.4%), better job opportunities outside the country (35.1%) and lack of professional development (33.7%). A U-shaped relationship was observed between age and likelihood to quit. Regression analysis revealed that high levels of burnout, lower level of education and low tenure were all associated with increased likelihood to quit.

Conclusions
The study findings reflect an unstable workforce and are not conducive to supporting an expanded role for PHC in the Lebanese healthcare system. While strategies aiming at improving staff retention would be important to develop and implement for all PHC HHR; targeted retention initiatives should focus on the young-new recruits and allied health professionals. Particular attention should be dedicated to enhancing providers’ role satisfaction and sense of job security. Such initiatives are of pivotal importance to stabilize the workforce and ensure its longevity.
Validation of an enzyme-linked immunosorbent assay for the quantification of human IgG directed against the repeat region of the circumsporozoite protein of the parasite Plasmodium falciparum
Authors: Clement Frederic , Dewar Vincent , Van Braeckel Eva , Desombere Isabelle , Dewerchin Marianne , Swysen Christine , Demoitié Marie-Ange , Jongert Erik , Cohen Joe , Leroux-Roels Geert , Cambron Pierre 
Published: November 2012

AbstractBackgroundSeveral pre-erythrocytic malaria vaccines based on the circumsporozoite protein (CSP) antigen ofPlasmodium falciparumare in clinical development. Vaccine immunogenicity is commonly evaluated by the determination of anti-CSP antibody levels using IgG-based assays, but no standard assay is available to allow comparison of the different vaccines.MethodsThe validation of an anti-CSP repeat region enzyme-linked immunosorbent assay (ELISA) is described. This assay is based on the binding of serum antibodies to R32LR, a recombinant protein composed of the repeat region ofP. falciparumCSP. In addition to the original recombinant R32LR, an easy to purify recombinant His-tagged R32LR protein has been constructed to be used as solid phase antigen in the assay. Also, hybridoma cell lines have been generated producing human anti-R32LR monoclonal antibodies to be used as a potential inexhaustible source of anti-CSP repeats standard, instead of a reference serum.ResultsThe anti-CSP repeats ELISA was shown to be robust, specific and linear within the analytical range, and adequately fulfilled all validation criteria as defined in the ICH guidelines. Furthermore, the coefficient of variation for repeatability and intermediate precision did not exceed 23%. Non-interference was demonstrated for R32LR-binding sera, and the assay was shown to be stable over time.ConclusionsThis ELISA, specific for antibodies directed against the CSP repeat region, can be used as a standard assay for the determination of humoral immunogenicity in the development of any CSP-basedP. falciparummalaria vaccine.
Near-infrared quantum cutting in Ho3+, Yb3+-codoped BaGdF5 nanoparticles via first-and second-order energy transfers
Authors: Guo Linna , Wang Yuhua , Zhang Jia , Wang Yanzhao , Dong Pengyu 
Published: November 2012

Abstract
Infrared quantum cutting involving Yb3+ 950–1,000 nm (2 F5/2 → 2 F7/2) and Ho3+ 1,007 nm (5S2,5F4 → 5I6) as well as 1,180 nm (5I6 → 5I8) emissions is achieved in BaGdF5: Ho3+, Yb3+ nanoparticles which are synthesized by a facile hydrothermal route. The mechanisms through first- and second-order energy transfers were analyzed by the dependence of Yb3+ doping concentration on the visible and infrared emissions, decay lifetime curves of the 5 F5 → 5I8, 5S2/5F4 → 5I8, and 5 F3 → 5I8 of Ho3+, in which a back energy transfer from Yb3+ to Ho3+ is first proposed to interpret the spectral characteristics. A modified calculation equation for quantum efficiency of Yb3+-Ho3+ couple by exciting at 450 nm was presented according to the quantum cutting mechanism. Overall, the excellent luminescence properties of BaGdF5: Ho3+, Yb3+ near-infrared quantum cutting nanoparticles could explore an interesting approach to maximize the performance of solar cells.
Statistical analysis of immuno-functionalized tumor-cell behaviors on nanopatterned substrates
Authors: Kim Dong-Joo , Lee Geehee , Kim Gil-Sung , Lee Sang-Kwon 
Published: November 2012

Abstract
Laser scanning cytometry has been proven as a powerful technology for high-content, high-throughput quantitative analysis of cellular functions in a fully automated manner. It utilizes a large-area fluorescence imaging scheme and rigorous image quantitation algorithms to enable informative analysis of cell samples attached to solid substrates. While this technology represents a powerful approach for high-content screening using cell lines, it has not been applied to the study of tumor-cell behaviors on these solid nanopatterned substrates after several hours of incubation. Herein, we statistically demonstrated functional cellular morphology information, including size, shape, and distribution of the captured cells after 0.5 to 45 h of incubation on nanopatterned substrates, such as silicon nanowires and quartz nanopillars, along with planar glass substrates. With increasing incubation time up to 45 h, we observed that the nanopatterned substrates could have not only increased adhesion and traction forces between cells and nanopatterned substrates, but also limited cell spreading on the substrates compared to the planar glass substrates. On the basis of our results, we suggest that the most important factors to influence the cell behaviors on the three solid substrates are the degree of dimension on cell behaviors and cell traction force.
Defective lysosomal proteolysis and axonal transport are early pathogenic events that worsen with age leading to increased APP metabolism and synaptic Abeta in transgenic APP/PS1 hippocampus
Authors: Torres Manuel , Jimenez Sebastian , Sanchez-Varo Raquel , Navarro Victoria , Trujillo-Estrada Laura , Sanchez-Mejias Elisabeth , Carmona Irene , Davila Jose Carlos , Vizuete Marisa , Gutierrez Antonia , Vitorica Javier 
Published: November 2012

Abstract

Background
Axonal pathology might constitute one of the earliest manifestations of Alzheimer disease. Axonal dystrophies were observed in Alzheimer’s patients and transgenic models at early ages. These axonal dystrophies could reflect the disruption of axonal transport and the accumulation of multiple vesicles at local points. It has been also proposed that dystrophies might interfere with normal intracellular proteolysis. In this work, we have investigated the progression of the hippocampal pathology and the possible implication in Abeta production in young (6 months) and aged (18 months) PS1(M146L)/APP(751sl) transgenic mice.

Results
Our data demonstrated the existence of a progressive, age-dependent, formation of axonal dystrophies, mainly located in contact with congophilic Abeta deposition, which exhibited tau and neurofilament hyperphosphorylation. This progressive pathology was paralleled with decreased expression of the motor proteins kinesin and dynein. Furthermore, we also observed an early decrease in the activity of cathepsins B and D, progressing to a deep inhibition of these lysosomal proteases at late ages. This lysosomal impairment could be responsible for the accumulation of LC3-II and ubiquitinated proteins within axonal dystrophies. We have also investigated the repercussion of these deficiencies on the APP metabolism. Our data demonstrated the existence of an increase in the amyloidogenic pathway, which was reflected by the accumulation of hAPPfl, C99 fragment, intracellular Abeta in parallel with an increase in BACE and gamma-secretase activities. In vitro experiments, using APPswe transfected N2a cells, demonstrated that any imbalance on the proteolytic systems reproduced the in vivo alterations in APP metabolism. Finally, our data also demonstrated that Abeta peptides were preferentially accumulated in isolated synaptosomes.

Conclusion
A progressive age-dependent cytoskeletal pathology along with a reduction of lysosomal and, in minor extent, proteasomal activity could be directly implicated in the progressive accumulation of APP derived fragments (and Abeta peptides) in parallel with the increase of BACE-1 and gamma-secretase activities. This retard in the APP metabolism seemed to be directly implicated in the synaptic Abeta accumulation and, in consequence, in the pathology progression between synaptically connected regions.
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection
Authors: Haury Anne-Claire , Mordelet Fantine , Vera-Licona Paola , Vert Jean-Philippe 
Published: November 2012

AbstractBackgroundInferring the structure of gene regulatory networks (GRN) from a collection of gene expression data has many potential applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy.ResultsIn this paper, we formulate GRN inference as a sparse regression problem and investigate the performance of a popular feature selection method, least angle regression (LARS) combined with stability selection, for that purpose. We introduce a novel, robust and accurate scoring technique for stability selection, which improves the performance of feature selection with LARS. The resulting method, which we call TIGRESS (for Trustful Inference of Gene REgulation with Stability Selection), was ranked among the top GRN inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated to be the best linear regression-based method in the challenge. We investigate in depth the influence of the various parameters of the method, and show that a fine parameter tuning can lead to significant improvements and state-of-the-art performance for GRN inference, in both directed and undirected settings.ConclusionsTIGRESS reaches state-of-the-art performance on benchmark data, including bothin silicoandin vivo(E. coliandS. cerevisiae) networks. This study confirms the potential of feature selection techniques for GRN inference. Code and data are available onhttp://cbio.ensmp.fr/tigress. Moreover, TIGRESS can be run online through the GenePattern platform (GP-DREAM,http://dream.broadinstitute.org).
Rapid resolution of an acute subdural hematoma by increasing the shunt valve pressure in a 63-year-old man with normal-pressure hydrocephalus with a ventriculoperitoneal shunt: a case report and literature review
Authors: Hayes Jackson , Roguski Marie , Riesenburger Ron I 
Published: November 2012

Abstract

Introduction
Symptomatic subdural hematoma development is a constant concern for patients who have undergone cerebrospinal fluid shunting procedures to relieve symptoms related to normal-pressure hydrocephalus. Acute subdural hematomas are of particular concern in these patients as even minor head trauma may result in subdural hematoma formation. The presence of a ventricular shunt facilitates further expansion of the subdural hematoma and often necessitates surgical treatment, including subdural hematoma evacuation and shunt ligation.

Case presentation
We present the case of a 63-year-old North American Caucasian man with normal-pressure hydrocephalus with an adjustable valve ventriculoperitoneal shunt who developed an acute subdural hematoma after sustaining head trauma. Conservative treatment was favored over operative evacuation because our patient was neurologically intact, but simple observation was considered to be too high risk in the setting of a low-pressure ventriculoperitoneal shunt. Thus, the valve setting on the ventriculoperitoneal shunt was increased to its maximum pressure setting in order to reduce flow through the shunt and to mildly increase intracranial pressure in an attempt to tamponade any active bleeding and limit hematoma expansion. A repeat computed tomography scan of the head six days after the valve adjustment revealed complete resolution of the acute subdural hematoma. At this time, the valve pressure was reduced to its original setting to treat symptoms of normal-pressure hydrocephalus.

Conclusions
Programmable shunt valves afford the option for non-operative management of acute subdural hematoma in patients with ventricular shunts for normal-pressure hydrocephalus. As illustrated in this case report, increasing the shunt valve pressure may result in rapid resolution of the acute subdural hematoma in some patients.
Stability of the splay state in networks of pulse-coupled neurons
Authors: Olmi Simona , Politi Antonio , Torcini Alessandro 
Published: November 2012

Abstract
We analytically investigate the stability of splay states in the networks of N globally pulse-coupled phase-like models of neurons. We develop a perturbative technique which allows determining the Floquet exponents for a generic velocity field and implement the method for a given pulse shape. We find that in the case of discontinuous velocity fields, the Floquet spectrum scales as

1
/

N
2

and the stability is determined by the sign of the jump at the discontinuity. Altogether, the form of the spectrum depends on the pulse shape, but it is independent of the velocity field.

PACS:05.45.Xt, 84.35.+i, 87.19.lj.
Combinatorial bases of modules for affine Lie algebra B
2(1)
Authors: Primc Mirko 
Published: November 2012

Abstract
We construct bases of standard (i.e. integrable highest weight) modules L(Λ) for affine Lie algebra of type B
2(1) consisting of semi-infinite monomials. The main technical ingredient is a construction of monomial bases for Feigin-Stoyanovsky type subspaces W(Λ) of L(Λ) by using simple currents and intertwining operators in vertex operator algebra theory. By coincidence W(kΛ0) for B
2(1) and the integrable highest weight module L(kΛ0) for A
1(1) have the same parametrization of combinatorial bases and the same presentation P/I.
Effect of thermal annealing in air on scintillation properties of LuAG and LuAG:Pr
Authors: Brylew Kamil , Drozdowski Winicjusz , Witkowski Marcin , Kamada Kei , Yanagida Takayuki , Yoshikawa Akira 
Published: November 2012

AbstractPure and Pr-activated Lu3Al5O12 (LuAG) crystals have been grown by the Czochralski method. In order to improve the scintillation properties, several samples have been annealed in air. Various annealing temperatures and periods of time have been tested to determine optimal conditions in the way of scintillation yield and energy resolution enhancement. The largest increase of yield of LuAG:Pr (17%), accompanied by a distinct decrease of resolution, has been observed after annealing at 1100°C for 48 h. On the contrary, in case of undoped LuAG no significant changes following thermal annealing have been noticed.
Zooplankton communities of inter-connected sections of lower River Oder (NW Poland)
Authors: Czerniawski Robert , Pilecka-Rapacz Małgorzata , Domagała Józef 
Published: November 2012

AbstractThe aim of this study was the determination and comparative analysis of the zooplankton communities between the inter-connected sections of the lower Oder river in relation to physicochemical factors. The study was performed at five sites of Oder. Two sites were localized in the main channel of Oder (East Oder), other sites were localized in the west arm of Oder and at the beginning of the canal carrying the post-cooling water from the power plant, and the last site was below at the shallow channel joining the Western Oder with the Eastern Oder. At the channel site in which the two arms of the river are connected a significantly higher taxa number, abundance and biomass of crustaceans was observed than at the other sites. The taxonomic similarity index between all sites was at a rather low level. The Pearson’s coefficient, multiple regression analysis and CCA showed that temperature, conductivity and content of nitrates had the strongest impact on the abundance of zooplankton. Thus, in lower, slowly flowing section of River Oder the physico-chemical variables influenced zooplankton density. Post-cooling water from the power plant influenced the zooplankton communities only in the channel discharging the waters into the river, while its influence on the zooplankton in the Oder is insignificant.