bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross
Authors: Samarakoon Upeka , Gonzales Joseph M , Patel Jigar J , Tan Asako , Checkley Lisa , Ferdig Michael T 
Published: September 2011

Abstract

Background
Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs.

Results
We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.

Conclusions
CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.
Roles of RpoN in the resistance of Campylobacter jejuni under various stress conditions
Authors: Hwang Sunyoung , Jeon Byeonghwa , Yun Jiae , Ryu Sangryeol 
Published: September 2011

Abstract

Background

Campylobacter jejuni is a leading foodborne pathogen worldwide. Despite the fastidious nature of C. jejuni growth, increasing numbers of human campylobacteriosis suggest that C. jejuni may possess unique mechanisms to survive under various stress conditions. C. jejuni possesses only three sigma factors (FliA, RpoD, and RpoN) and lacks stress-defense sigma factors. Since FliA and RpoD are dedicated to flagella synthesis and housekeeping, respectively, in this study, we investigated the role of RpoN in C. jejuni's defense against various stresses.

Results
Survivability of an rpoN mutant was compared with the wild-type C. jejuni under various stress conditions. While the growth of the rpoN mutant was as comparably as that of the wild type in shaking cultures, the rpoN mutant exhibited significant survival defects when cultured statically. The rpoN mutant was more sensitive to osmotic stress (0.8% NaCl) with abnormally-elongated cell morphology. Compared to the wile type, the rpoN mutant was more susceptible to acid stress (pH 5) and more resistant to hydrogen peroxide. However, the rpoN mutation had little effect on the resistance of C. jejuni to alkaline pH, heat, cold and antimicrobials.

Conclusions
The results demonstrate that RpoN plays an important role in C. jejuni's defense against various stresses which this bacterial pathogen may encounter during transmission to and infection of humans.
Prognostic and predictive value of clinical and biochemical factors in breast cancer patients with bone metastases receiving "metronomic" zoledronic acid
Authors: Zhao Xinmin , Xu Xiaofeng , Zhang Qunling , Jia Zhen , Sun Si , Zhang Jian , Wang Biyun , Wang Zhonghua , Hu Xichun 
Published: September 2011

Abstract

Background
To assess prognostic and predictive effects of clinical and biochemical factors in our published randomized study of a weekly low dose (metronomic arm) versus a conventional dosage of zoledronic acid (conventional arm) in breast cancer patients with bone metastases.

Methods
Treatment outcome of 60 patients with bone metastases were used to assess impacts of following potential prognostic factors, estrogen receptor status, lymph node status, 2 year-disease free interval (DFI), numbers of chemotherapy regimens administered, interventions, and serum levels of VEGF, N-telopeptide of type I collagen (NTx), CEA, and CA 15-3.

Results
In univariate analyses, patients pretreated with 2 or fewer chemotherapy regimens, ER-positive tumors, 3 or fewer lymph nodes, DFI of more than 2 years, serum VEGF of less than 500 pg/mL after 3 months of intervention, serum CEA and CA 15-3 of less than ULN, and baseline serum NTx of less than 18 nM BCE had significantly longer progression free survival (PFS). The multivariate analysis showed that ER positivity (hazard ratio [HR], 0.295; 95% confidence interval [CI], 0.141-0.618; P = 0.001), serum VEGF of less than 500 pg/mL after 3 months of intervention (HR, 2.220; 95% CI, 1.136-4.338; P = 0.020), baseline serum NTx of less than 18 nM BCE (HR, 2.842; 95% CI, 1.458-5.539; P = 0.001), and 2 or fewer chemotherapy regimens received (HR, 7.803; 95% CI, 2.884-21.112; P = 0.000) were associated with a better PFS. When evaluating the predictive effect of the biochemical factors, an interaction between NTx and zoledronic acid intervention was shown (P = 0.005). The HR of weekly low dose versus a conventional dosage of zoledronic acid was estimated to be 2.309 (99% CI, 1.067-5.012) in patients with baseline serum NTx of more than 18 nM BCE, indicating a superiority of weekly low dose of zoledronic acid.

Conclusions
ER, serum VEGF level after intervention, and numbers of chemotherapy regimens administered are prognostic but not predictive factors in breast cancer patients with bone metastases. Patients with baseline serum NTx of more than 18 nM BCE might benefit more from weekly low-dose of zoledronic acid.

Trial registration
ClinicalTrials.gov unique identifier: ClinicalTrials.gov: NCT00524849
Identification of clinically significant psychological distress and psychiatric morbidity by examining quality of life in subjects with occupational asthma
Authors: Miedinger David , Lavoie Kim L , L'Archeveque Jocelyne , Ghezzo Heberto , Malo Jean-Luc 
Published: September 2011

Abstract

Background
The Juniper Asthma Specific Quality of Life Questionnaire (AQLQ(S)) is a questionnaire that allows measurement of disease specific quality of life. We wanted to examine correlations between the (AQLQ(S)) general and different subscale scores and both psychiatric morbidity and levels of psychological distress in individuals with occupational asthma (OA) and to determine if results in the emotional function subscale allow identification of individuals with clinically significant psychological distress or current psychiatric disorders.

Methods
This was a cross-sectional study of individuals with OA who were assessed during a re-evaluation for permanent disability, after they were no longer exposed to the sensitizing agent. Patients underwent a general sociodemographic and medical history evaluation, a brief psychiatric interview (Primary Care Evaluation of Mental Disorders, PRIME-MD) and completed a battery of questionnaires including the AQLQ(S), the St-Georges Respiratory Questionnaire (SGRQ), and the Psychiatric Symptom Index (PSI).

Results
There was good internal consistency (Cronbach alpha = 0.936 for the AQLQ(S) total score) and construct validity for the AQLQ(S) (Spearman rho = -0.693 for the SGRQ symptom score and rho = -0.650 for the asthma severity score). There were medium to large correlations between the total score of the AQLQ(S) and the SGRQ symptom score (r = -.693), and PSI total (r = -.619) and subscale scores (including depression, r = -.419; anxiety, r = -.664; anger, r = -.367; cognitive disturbances, r = -.419). A cut-off of 5.1 on the AQLQ(S) emotional function subscale (where 0 = high impairment and 7 = no impairment) had the best discriminative value to distinguish individuals with or without clinically significant psychiatric distress according to the PSI, and a cut-off of 4.7 best distinguished individuals with or without a current psychiatric disorder according to the PRIME-MD.

Conclusions
Impaired quality of life is associated with psychological distress and psychiatric disorders in individuals with OA. Findings suggest that the AQLQ(S) questionnaire may be used to identify patients with potentially clinically significant levels of psychological distress.
A network model for biofilm development in Escherichia coli K-12
Authors: Shalá Andrew A , Restrepo Silvia , González Barrios Andrés F 
Published: September 2011

Abstract

Background
In nature, bacteria often exist as biofilms. Biofilms are communities of microorganisms attached to a surface. It is clear that biofilm-grown cells harbor properties remarkably distinct from planktonic cells. Biofilms frequently complicate treatments of infections by protecting bacteria from the immune system, decreasing antibiotic efficacy and dispersing planktonic cells to distant body sites. In this work, we employed enhanced Boolean algebra to model biofilm formation.

Results
The network obtained describes biofilm formation successfully, assuming - in accordance with the literature - that when the negative regulators (RscCD and EnvZ/OmpR) are off, the positive regulator (FlhDC) is on. The network was modeled under three different conditions through time with satisfactory outcomes. Each cluster was constructed using the K-means/medians Clustering Support algorithm on the basis of published Affymetrix microarray gene expression data from biofilm-forming bacteria and the planktonic state over four time points for Escherichia coli K-12.

Conclusions
The different phenotypes obtained demonstrate that the network model of biofilm formation can simulate the formation or repression of biofilm efficiently in E. coli K-12.
Amyloid beta protein-induced zinc sequestration leads to synaptic loss via dysregulation of the ProSAP2/Shank3 scaffold
Authors: Grabrucker Andreas M , Schmeisser Michael J , Udvardi Patrick T , Arons Magali , Schoen Michael , Woodling Nathaniel S , Andreasson Katrin I , Hof Patrick R , Buxbaum Joseph D , Garner Craig C , Boeckers Tobias M 
Published: September 2011

Abstract

Background
Memory deficits in Alzheimer's disease (AD) manifest together with the loss of synapses caused by the disruption of the postsynaptic density (PSD), a network of scaffold proteins located in dendritic spines. However, the underlying molecular mechanisms remain elusive. Since it was shown that ProSAP2/Shank3 scaffold assembly within the PSD is Zn2+-dependent and that the amyloid beta protein (Aβ) is able to bind Zn2+, we hypothesize that sequestration of Zn2+ ions by Aβ contributes to ProSAP/Shank platform malformation.

Results
To test this hypothesis, we designed multiple in vitro and in vivo assays demonstrating ProSAP/Shank dysregulation in rat hippocampal cultures following Aβ oligomer accumulation. These changes were independent from alterations on ProSAP/Shank transcriptional level. However, application of soluble Aβ prevented association of Zn2+ ions with ProSAP2/Shank3 in a cell-based assay and decreased the concentration of Zn2+ clusters within dendrites. Zn2+ supplementation or saturation of Aβ with Zn2+ ions prior to cell treatment was able to counter the effects induced by Aβ on synapse density and ProSAP2/Shank3 levels at the PSD. Interestingly, intracellular Zn2+ levels in APP-PS1 mice and human AD hippocampus are reduced along with a reduction in synapse density and synaptic ProSAP2/Shank3 and Shank1 protein levels.

Conclusions
We conclude that sequestration of Zn2+ ions by Aβ significantly contributes to changes in ProSAP2/Shank3 platforms. These changes in turn lead to less consolidated (mature) synapses reflected by a decrease in Shank1 protein levels at the PSD and decreased synapse density in hippocampal neurons.
Mycobacterium chimaera pulmonary infection complicating cystic fibrosis: a case report
Authors: Cohen-Bacrie Stéphan , David Marion , Stremler Nathalie , Dubus Jean-Christophe , Rolain Jean-Marc , Drancourt Michel 
Published: September 2011

Abstract

Background

Mycobacterium chimaera is a recently described species within the Mycobacterium avium complex. Its pathogenicity in respiratory tract infection remains disputed. It has never been isolated during cystic fibrosis respiratory tract infection.

Case presentation
An 11-year-old boy of Asian ethnicity who was born on Réunion Island presented to our hospital with cystic fibrosis after a decline in his respiratory function over the course of seven years. We found that the decline in his respiratory function was correlated with the persistent presence of a Mycobacterium avium complex organism further identified as M. chimaera.

Conclusion
Using sequencing-based methods of identification, we observed that M. chimaera organisms contributed equally to respiratory tract infections in patients with cystic fibrosis when compared with M. avium subsp. hominissuis isolates. We believe that M. chimaera should be regarded as an emerging opportunistic respiratory pathogen in patients with cystic fibrosis, including young children, and that its detection warrants long-lasting appropriate anti-mycobacterial treatment to eradicate it.
Suppressing miRNA-15a/-16 expression by interleukin-6 enhances drug-resistance in myeloma cells
Authors: Hao Mu , Zhang Li , An Gang , Sui Weiwei , Yu Zhen , Zou Dehui , Xu Yan , Chang Hong , Qiu Lugui 
Published: September 2011

Abstract
The bone marrow microenvironment facilitates the survival, differentiation, and proliferation of myeloma (MM) cells. This study identified that microRNA-15a and -16 expressions tightly correlated with proliferation and drug sensitivity of MM cells. miRNA-15a/-16 expression in MM cells was significantly increased after treatment with cytotoxic agents. The interaction of bone marrow stromal cells (BMSC) with MM cells resulted in decreased miRNA-15a/-16 expression and promoted the survival of the MM cells. Interleukin-6 (IL-6) produced by BMSCs suppressed the expression of miRNA-15a and 16 in a time- and dose- dependent pattern, with the suppression on miRNA-15a being more significant than on miRNA-16. miRNA-15a-transfected MM cells were found to be arrested in G1/S checkpoint, and the transfected MM cells had decreased growth and survival. In conclusion, our data suggest that via suppressing miRNA-15a and -16 expressions, IL-6 secreted by BMSCs promotes drug-resistance in myeloma cells.
A Transient Water Release and Imbibitions Method for Rapidly Measuring Wetting and Drying Soil Water Retention and Hydraulic Conductivity Functions
Authors: Wayllace Alexandra , Lu Ning 
Published: September 2011

Abstract
A transient water release and imbibitions (TWRI) method for measuring the soil water retention curve (SWRC) and hydraulic conductivity function (HCF) under drying and wetting states is presented. The intellectual merit of the TWRI method is its integration of physical and numerical experiments: it employs the simple and reliable measurement of transient water content by electronic balance to record the signature of transient unsaturated flow in soil sample, and it takes advantage of the robust inverse modeling capability to simulate the physical process. The TWRI method; therefore, has two integrated components: testing and modeling. The testing consists of water release upon two-steps increase in matric suction and water imbibitions upon one-step decrease in matric suction. Each process lasts sufficient time in order to obtain transient water content. The data is then used as an objective function in an inverse numerical modeling process to obtain the unsaturated hydrologic parameters that fully define the SWRC and HCF of the soil. A novel feature of the TWRI method is its capability to measure SWRC and HCF under wetting state. The apparatus can accommodate both undisturbed and remolded samples. The testing time required for completing a full drying and wetting loop is approximately one week for most soils. Validation of the technique has been performed both experimentally and numerically. Comparisons between data obtained with the TWRI method and the independent Tempe cell method verify the reliability, applicability, and accuracy of the TWRI method. Results from three different soils are presented to illustrate the procedure and performance of the TWRI method for different soils from fine sand to clayey silt. The TWRI method provides a fast, accurate, and simple testing tool for obtaining SWRC and HCF of various types of soils under both wetting and drying states with high range of matric suction several orders of magnitude above the air-entry pressure of the ceramic stone used in the experimental setup.
A New Method for Soil Water Characteristic Curve Measurement Based on Similarities Between Soil Freezing and Drying
Authors: Liu Zhen , Zhang Bin , (Bill) Yu Xiong , Zhang Bin , Tao Junliang 
Published: September 2011

Abstract
The soil water characteristic curve (SWCC) is the basis to explain a variety of processes in unsaturated soils, ranging from transport phenomena to mechanical behaviors. In this paper, a new method is developed for SWCC estimation based on the similarity between the freezing/thawing process and drying/wetting process in soils. The theoretical basis for this method is first reviewed. The concept of the soil freezing characteristic curve (SFCC) is introduced to describe the relationship between the unfrozen water content and matric suction in frozen soils. SFCC is analogous to SWCC in that both of them describe the energy status of liquid water associated with liquid water content. Relationships between SWCC and SFCC are discussed. To measure the SFCC, a thermo-time domain reflectometry (TDR) sensor was developed which combines both temperature sensors and conventional TDR sensor. The TDR module and algorithm measured the bulk free water content of soils during the freezing/thawing processes, while the built-in thermocouples measured the internal temperature distribution. SFCCs were obtained from the simultaneously measured TDR and temperature data. Experiments were conducted on a few types of soils to validate this new procedure. The SFCC was obtained from thermo-TDR data collected in specimens subjected to a controlled thawing process, while the SWCC was directly measured by ASTM D5298, the filter paper method. Reasonable agreements were found between SWCC and SFCC. The experimental results implied that the SWCC could be estimated from SFCC, which also provided more evidence of the similarity of freezing/thawing processes and desorption/sorption processes.
Roofing Assembly Simulated Heat and Light Test
Authors: Burns Robert S. 
Published: September 2011

Abstract
The goal of this project is to search for a testing procedure for roof covering products that will radiate both heat and light onto a roof covering and then measure the impact that a given roof covering product has on heat transfer through the entire roofing assembly. Identical roof assemblies were built with ethylene propylene diene terpolymer (EPDM) rubber roof membrane over a wood deck. Sixteen heat lamps were positioned 1.14 m [45 in.] above the roof covering product to provide both heat and light. Thermocouples were placed on the underside of the wood deck and were insulated from outside air. The roofing assembly and the roof covering temperatures were brought to 18°C to 21°C prior to testing. Heat and light were radiated onto the roof coverings for 360 min and the under deck temperature was recorded at 1 min intervals for 600 min. Tested roof coverings included gravel, growing media, coatings, and panels in the form of concrete, ceramic foam, and rubber. The results of the tests have shown data similar to that which were recorded during warm, sunny days. As expected, the highest temperatures were achieved by the uncovered and uncoated black EPDM roof assembly. The temperature of this assembly diminished almost immediately upon the removal of the heat and light source. Thicker layers of growing media and ceramic foam block did not reach the peak temperature until several hours after the heat lamps were turned off. The roof assembly covered with reflective coating showed realistic resistance to the heat and light source. This is a significant advancement in the effort to provide equitable data for all roof coverings. The test provides a standard method of collecting data for traditional roof coverings as well as emerging technology roof covering materials to evaluate a roofing assemblies’ thermal performance from solar heat gain.
Development of ZnO/Ta2O5 heterojunction using low-temperature technological processes
Authors: Baca R. , Andraca J. A. , Arellano M. G. , Paredes G. R. , Sierra R. P. 
Published: September 2011

ABSTRACTZnO/Ta2O5 heterojunctions were formed on glass substrates using low temperature processes. Formerly insulating Ta2O5 films were deposited on glass substrates by vacuum evaporation using Ta2O5 powder, Afterwards transparent and conductive ZnO films were formed on the Ta2O5 films by thermal oxidation at 3200C in air atmosphere of zinc (Zn) films deposited by dc sputtering process. Structural and optical properties of ZnO were investigated by X-ray diffraction (XRD) and photoluminescence (PL). The Ta2O5 insulating films were characterized by Raman scattering. The ZnO/Ta2O5 heterojunction was characterized by current-voltage measurements at room temperature as well as transient response under a rectangular-pulse voltage source. The electrical and the transient response suggest that the ZnO/Ta2O5 heterojunction is a potential alternative for the fabrication of alternating-current-driven thin film electroluminescent (ACTFEL) devices.
The origin of predominance of cementite among iron carbides in steel at elevated temperature
Authors: Fang C.M. , Sluiter M.H.F. , van Huis M.A. , Ande C.K. , Zandbergen H.W. 
Published: September 2011

ABSTRACTA systematic first-principles study was conducted on the stability of binary iron carbides. The calculations showed that all the binary iron carbides are unstable relative to the elemental solids (α-Fe and graphite). Apart from a cubic Fe23C6phase, the energetically most favorable carbides exhibit hexagonal close-packed (hcp) Fesublattices. Structural relaxation of the hcp iron carbides was analyzed and discussed together with their relative thermodynamically stability. Finite-temperature analysis showed that contributions from lattice vibration and anomalous magnetic ordering (Curie-Weiss behavior), rather than from the conventional lattice mismatch with the matrix, are the origin of the high stability and predominance of cementite among the iron carbides in steels.
Thermal diffusivity measurement of insulating material using infrared thermography
Authors: Chudzik S. 
Published: September 2011

AbstractThe article presents the results of research developing methods for determining the coefficient of thermal diffusivity of thermal insulating material. This method applies a periodic heating as an excitation and an infrared camera is used to measure the temperature distribution on the surface of tested material. In simulation study, the usefulness of known analytical solution of the inverse problem was examined using a three-dimensional model of the phenomenon of heat diffusion in the sample of tested material. To solve the coefficient inverse problem, an approach using artificial neural network is proposed. The measurements were performed on an experimental setup equipped with a ThermaCAM PM 595 infrared camera and frame grabber. The experiment allowed to verify the chosen 3D model of heat diffusion phenomenon and to determine suitability of the proposed test method.