bluuebunny/crossref_metadata_2025_split huggingface dataset:
Renal expression and serum levels of high mobility group box 1 protein in lupus nephritis
Authors: Zickert Agneta , Palmblad Karin , Sundelin Birgitta , Chavan Sangeeta , Tracey Kevin J , Bruchfeld Annette , Gunnarsson Iva 
Published: February 2012

Abstract
Introduction
High mobility group box 1 protein (HMGB1) is a nuclear DNA binding protein acting as a pro-inflammatory mediator following extracellular release. HMGB1 has been increasingly recognized as a pathogenic mediator in several inflammatory diseases. Elevated serum levels of HMGB1 have been detected in autoimmune diseases including Systemic lupus erythematosus (SLE). However, the local expression of HMGB1 in active lupus nephritis (LN) is not known. Here we aimed to study both tissue expression and serum levels of HMGB1 in LN patients with active disease and after induction therapy.

Methods
Thirty-five patients with active LN were included. Renal biopsies were performed at baseline and after standard induction therapy; corticosteroids combined with immunosuppressive drugs. The biopsies were evaluated according to the World Health Organization (WHO) classification and renal disease activity was estimated using the British Isles lupus assessment group (BILAG) index. Serum levels of HMGB1 were analysed by western blot. HMGB1 expression in renal tissue was assessed by immunohistochemistry at baseline and follow-up biopsies in 25 patients.

Results
Baseline biopsies showed WHO class III, IV or V and all patients had high renal disease activity (BILAG A/B). Follow-up biopsies showed WHO I to II (n = 14), III (n = 6), IV (n = 3) or V (n = 12), and 15/35 patients were regarded as renal responders (BILAG C/D).
At baseline HMGB1 was significantly elevated in serum compared to healthy controls (P < 0.0001). In all patients, serum levels decreased only slightly; however, in patients with baseline WHO class IV a significant decrease was observed (P = 0.03). Immunostaining revealed a pronounced extranuclear HMGB1 expression predominantly outlining the glomerular endothelium and in the mesangium. There was no clear difference in HMGB1 expression comparing baseline and follow-up biopsies or any apparent association to histopathological classification or clinical outcome.

Conclusions
Renal tissue expression and serum levels of HMGB1 were increased in LN. The lack of decrease of HMGB1 in serum and tissue after immunosuppressive therapy in the current study may reflect persistent inflammatory activity. This study clearly indicates a role for HMGB1 in LN.
Autosomal monoallelic expression in the mouse
Authors: Zwemer Lillian M , Zak Alexander , Thompson Benjamin R , Kirby Andrew , Daly Mark J , Chess Andrew , Gimelbrant Alexander A 
Published: February 2012

Abstract
Background
Random monoallelic expression defines an unusual class of genes displaying random choice for expression between the maternal and paternal alleles. Once established, the allele-specific expression pattern is stably maintained and mitotically inherited. Examples of random monoallelic genes include those found on the X-chromosome and a subset of autosomal genes, which have been most extensively studied in humans. Here, we report a genome-wide analysis of random monoallelic expression in the mouse. We used high density mouse genome polymorphism mapping arrays to assess allele-specific expression in clonal cell lines derived from heterozygous mouse strains.

Results
Over 1,300 autosomal genes were assessed for allele-specific expression, and greater than 10% of them showed random monoallelic expression. When comparing mouse and human, the number of autosomal orthologs demonstrating random monoallelic expression in both organisms was greater than would be expected by chance. Random monoallelic expression on the mouse autosomes is broadly similar to that in human cells: it is widespread throughout the genome, lacks chromosome-wide coordination, and varies between cell types. However, for some mouse genes, there appears to be skewing, in some ways resembling skewed X-inactivation, wherein one allele is more frequently active.

Conclusions
These data suggest that autosomal random monoallelic expression was present at least as far back as the last common ancestor of rodents and primates. Random monoallelic expression can lead to phenotypic variation beyond the phenotypic variation dictated by genotypic variation. Thus, it is important to take into account random monoallelic expression when examining genotype-phenotype correlation.
Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
Authors: Siddiqui Najeeb U , Li Xiao , Luo Hua , Karaiskakis Angelo , Hou Huayun , Kislinger Thomas , Westwood J Timothy , Morris Quaid , Lipshitz Howard D 
Published: February 2012

Abstract
Background
During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells.

Results
We purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein Smaug is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding proteins function independently to control transcript elimination.

Conclusions
The scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance.
A Facile and Continuous Fabrication of Polyimide Hollow Nanoparticles Using a Microfluidic System
Authors: Ishizaka Takayuki , Ishigaki Atsushi , Suzuki Akira , Suzuki Toshishige M , Kawanami Hajime 
Published: February 2012

Abstract
A facile and continuous synthesis method of polyimide hollow nanoparticles has been developed by microemulsion reprecipitation method using a microfluidic system within a short reaction time (10 s). The mean particle size and the coefficient of variation were 314 nm and 0.22, respectively. We also successfully demonstrated that the polyimide hollow nanoparticles can be used as a nanocontainer as well as nanoreactor by retracting a chemical dye such as Rhodamine 6G.
Dopamine Detection on Boron-doped Diamond Electrodes Using Fast Cyclic Voltammetry
Authors: Kato Taisuke , Fierro Stéphane , Watanabe Takeshi , Yoshimi Kenji , Einaga Yasuaki 
Published: February 2012

Abstract
A new method is proposed for the accurate and reproducible detection of dopamine using cyclic voltammetry on boron-doped diamond (BDD) electrode. It is shown that reproducible voltammograms can be obtained when applying a relatively high scan rate (100 V s−1) during the detection measurements. For lower scan rates (1 V s−1), it is proven that electrode fouling occurs due do the deposition of a polymer at the electrode surface arising from the oxidation of aminochrome. Cyclic voltammetry measurements of the [Fe(CN)6]3−/[Fe(CN)6]4− couple performed before and after dopamine detection on BDD and glassy carbon electrodes have shown that the electrochemical activity of the electrode decreases only at low scan rates for BDD dopamine (DA) detection, which leads to electrode poisoning whereas the activity remains unchanged for higher scan rates. However, on glassy carbon electrodes, the electrochemical activity of the material decreases after DA detection measurements independently of the scan rate applied. Therefore, this study shows that electrode fouling during the detection of dopamine by cyclic voltammetry can be avoided only when using BDD electrode but also only for high applied scan rates.
The role of lone pairs in the ferroelastic phase transition in the palmierite-type lead phosphate-arsenate solid solution
Authors: Angel Ross J. , Beirau Tobias , Mihailova Boriana , Paulmann C. , Bismayer Ulrich 
Published: February 2012

Abstract
The structural changes associated with the R-3m to C2/c ferroelastic phase transition in the solid solution Pb3(P1–x
As
x
O4)2 have been followed by Raman spectroscopy on samples with x = 0.00, 0.08, 0.37, 0.57, 0.65, 0.80, 1.00 over the temperature range 80–850 K. The high-temperature structural state of four intermediate samples with x = 0.37, 0.57, 0.65 and 0.80 was also studied by synchrotron single-crystal X-ray diffraction. The new results, in combination with previous data, reveal that Pb3(P1–x
As
x
O4)2 undergoes a complex sequence of transformation processes with several characteristic temperatures that can be clearly identified in addition to that of the ferroelastic phase transition at T
c. These structural changes are mainly driven by two phonon modes: vibrations of the Pb2 atoms (stereochemically active in the C2/c phase perpendicular to the layers characteristic of the palmierite-type structure), and rotational modes of the PO4 and AsO4 units within the plane of the layers. The former ensures coupling of the atomic displacements both within and between the layers, while the latter favours the coupling of the monoclinic species within the layers. With decreasing temperature, at T
4 ≫ T
c the Pb2 atoms are displaced from their special positions on the triad axis of the R-3m structure. At T
3 the size of the nanoclusters composed of coupled displacements of Pb2 atoms on the monoclinic pattern is sufficient to produce both macroscopic effects in all compositions (diffuse super-lattice intensities in the diffraction patterns, non-symmetry-breaking strain in the unit-cell parameters, a step in the C

p
curve) and microscopic effects in the broadening of the vibrational modes of the Pb2 atoms. The temperature interval between T
3 and T
4 is considerably smaller for the intermediate compositions than for the end-members indicating that the chemical disorder on the tetrahedral site facilitates the condensation of monoclinic species, probably by smearing the potential barrier between different monoclinic orientational states. At T
2 < T
3, but still above T
c, the AsO4 tetrahedra undergo monoclinic deformation in order to better coordinate the adjacent displaced Pb2 atoms, while the geometry of the PO4 tetrahedra remains unchanged down to T
c (and for As-rich compositions, slightly below T
c). At T
c the ordered Pb2 displacements and rotated tetrahedra drive a displacement of the Pb1 atoms from their trigonal (paraelastic) positions and long-range-ordered ferroelastic domains are formed. However, for all compounds, residual disorder of the Pb2 displacements persists below T
c to a further characteristic temperature T
1 at which the displacements of all types of atoms become completely ordered on all length scales.
Effect of the linear velocity during the melt spinning process on shape memory transformation of Ni-Ti ribbons
Authors: Nuñez-Mendoza E. , López Cuellar E. , Benicio de Castro Walman , López Walle B. 
Published: February 2012

AbstractThe usual process to produce NiTi shape memory alloys is vacuum induction melting (VIM). Currently a new alternative process to produce NiTi shape memory alloys by rapid solidification structures called Melt Spinning has been studied. In this work, results of ribbons with a chemical composition Ti-55.2 Ni (wt %) alloy prepared by this method are presented. The ribbons are prepared at two different linear velocities: 30 m/s and 50 m/s. After that, samples are heat treated at 350 °C during 1 hour. The alloys are characterized by Scanning Electron Microscopy (SEM), Differential Scanning Calorimetry (DSC) and X-Ray Diffraction. According to the cycled DSC test, transformation peaks are associated with the B2→R→B19´ transformation during cooling and B19´→R→B2 during heating, showing transformation in multi-peaks. The martensite B19´ start (Ms) is varying from 35 to 39°C and the martensite finish (Mf) from 15 to 21°C, 42-47°C for austenite B2 start (As) and 65-69°C for austenite finish (Af) approximately. All analyzed ribbons show very similar values of transformation hysteresis temperatures at 50% of transformation of around 28°C. In order to change solidification rate, linear velocity is varied during the melt spinning process. Results indicate that linear velocity affects directly the temperature of transformation. When the linear velocity is increasing, crystallographic Ti-rich precipitates are developed, but dendritic growth disappears, changing the microstructure and decreasing these transformation temperatures. Then changes in linear velocity can dramatically affect shape memory properties, and in this case a velocity of 50 m/s produces a more homogenous alloy.
Mechanical Efficiency Algorithm Solves Drilling Problems in Areas of Limited/Inaccurate Offset Data
Authors: Purwanto Arifin , Ibrahim Hani , Saheta Vishal , Bits Smith 
Published: February 2012

AbstractA well plan is essentially a decision-making roadmap for choosing equipment required for drilling the required wellbore. The operator's ability to properly assess offset drilling data and key lithology factors to match available BHA tools and procedures plays a large role in determining project success. Accordingly, the software support systems utilized to interpret and extrapolate data have a direct impact on the ability of drilling engineers to optimize operations.Historically, most well plans were assembled using data from offset wells and prior experience. However in most cases, a rudimentary analysis could not produce a comprehensive picture of the complex, interdisciplinary downhole dynamics that affect drilling performance, especially in the case of limited or missing offset data. Even when reliable data was available, a one-dimensional analysis has failed to completely exploit the available informational value from offset wells. This has forced engineers to be more conservative when designing wells and include more contingencies. The result is operators are drilling in a reactive manner, which often led to decisions resulting in performance degradation rather than optimization.To solve the problem and improve drilling performance in areas of limited/inaccurate offset data, engineers have developed a Mechanical Efficiency Ratio optimization system (MER) that accurately measures the BHA's use of available energy. The modeling tool was tested in several applications and accurately predicted performance including ROP, footage capabilities and dull bit condition. The tool used data and evaluation of rig capabilities, bit/BHA performance, downhole behavior and formation challenges including high-rock strength and interbedded lithologies.The authors will present three case studies that outline how the software program was used to measure system efficiency to determine which bit would have the highest ROP, total footage capabilities and best dull grade estimate compared to offset runs. The MER will also determine if the system (bit/BHA) or the optimized drilling parameters will improve drilling efficiency.
New Model to Predict Formation Damage due to Sulfur Deposition in Sour Gas Wells
Authors: Mahmoud M. A. , Al-Majed A. A. 
Published: February 2012

AbstractElemental sulfur (S8) is often present in considerable amounts in sour gas reservoirs at the reservoir conditions (pressure and temperature). For the isothermal conditions in the reservoir, the reduction in reservoir pressure below a critical value will cause the elemental sulfur to deposit in the formation. Sulfur deposition can cause severe loss in the pore space available for gas, and in turn it will affect the gas well productivity. Accurate prediction of sulfur deposition in the reservoir will help in better management of sour gas reservoirs with potential sulfur deposition problems.In this paper a new analytical model was developed to predict the formation damage due to sulfur deposition. This model can be used to study the effect of sulfur deposition on gas relative permeability, reservoir porosity, skin damage and reservoir rock wettability. The main objective of this model is to investigate the effect of radial distance on formation damage. Accurate correlations of different rock and fluid properties were used in this model for improved predictions. Accurate correlations of gas viscosity and gas compressibility were used, as the sulfur solubility is a strong function of gas viscosity and gas density. These correlations were used for the calculation of sulfur solubility at reservoir conditions.Model predictions showed that sulfur deposition depends on the radial distance from the well bore. The most damage occurred in the 3 ft around the wellbore. As the radial distance increases the effect of sulfur deposition becomes negligible. Unlike previous models, which neglected the effect of pressure on gas properties, accurate correlations were used in the new model. Also, various sulfur solubility correlations were tested using the new model. A reduction of 2000 psi in the reservoir pressure, causes a 40 % loss of reservoir porosity at a radial distance of 3 ft from the wellbore and almost 85 % loss in the gas relative permeability at the same distance.
A Field Wide Surface Network Modeling and De-bottlenecking of Production Network for Nine Fields of GNPOC
Authors: Kumar Aditya , Omer Omer Mohamed , Sulaiman Abu Bakr 
Published: February 2012

Abstract
Greater Nile Petroleum Operating Company (GNPOC) is facing challenges to sustain their production, which has been declining at the rate of 15% (approximate) annually. Major part of production is sustained by drilling infill wells re-completion. Pipeline network plays important role in delivering the production from wellhead to Field Processing Facility (FPF). Bottlenecks in pipeline can cause rise in wellhead pressure, which can have impact on production substantially. To identify these bottlenecks and reduce backpressure effect on network GNPOC initiated a project for de-bottlenecking of production pipeline network nine fields. A high fidelity Surface Network Model was developed for all field of GNPOC, which have more than 400 producing wells.
This surface network model will help to quickly identify and accurately quantify bottleneck and other opportunity to reduce backpressure on the system and improve production. This model will also help in further field development, pipeline tie-in / lineup, best nearby Oil Gathering Manifold (OGM) to tie-in new wells etc. The approach of building model is kept simple, robust and scalable. Scalable model will helps GNPOC to add-in well model and integrated this production model to reservoir simulator, facility model and real time data easily and quickly. The model would also assist in evaluating field operation and development plan and expedite the engineering decision process. The identified bottleneck has been ranked in order or priority (which needed immediate attention).
A totally new approach was adopted in the study in terms of the location, training and technology transfer in Sudan. The project engineer worked in close association with operation engineers from field and office. Also actual work has been partially carried out in field as well as office. This approach has given more opportunity to field operation engineers to interact with current modeling tool and technology and increase confidence level.
This paper describes the development of the surface network model for nine fields of GNPOC, technical & project management challenges faced and the way ahead. The model includes the production and transportation networks. This paper also includes major de-bottleneck areas in the production network of GPNOC and How to make effective use of this model for engineering analysis.
A New Binary LCM System Helped Cure Losses during Cementing while Minimizing Risk of Plugging for Slim Liners
Authors: Bhaisora Devesh , Paton Nestor , Waheed Arshad , El Nashar Radi , Farouk Mohamed , Soliman Fathy 
Published: February 2012

Abstract
Fibers are commonly used as lost circulation materials (LCMs) during cementing. Their evolution began with 2-in. long natural fibers, and glass fibers 3-mm long are now available to the industry to address lost-circulation issues.
A major operator needed to cement 5-in. production liner in a depleted reservoir in the Gulf of Suez (GOS). The equivalent circulating density (ECD) exceeded the fracture gradient of the formation while circulating more than 1.5 bbl/min of mud. Losses were predicted during the cementing and an effective LCM added to the fluids was necessary to minimize the loss. A higher concentration of conventional fibers was not recommended because they can block the floats or area around liner-hanger slips.
A new spacer and slurry design was formulated using two different types of LCM systems to help minimize losses during cementing. Both types have minimal chances of blocking restricted flow areas inside pipe. These LCMs help minimize risk of plugging floats or liner hangers, particularly in slim liners where the ID of float valves is only a couple of inches. Powdered LCM was used with the spacer only because it can affect cement slurry properties. This LCM can be used in at least two to three times higher concentrations than conventional fibers. The main objective of using it with spacer was to seal any loss zone before cement began entering into that zone. A different type of inert glass-fiber LCM was used with the cement slurry, but in lower concentrations, to provide extra safety measures for curing losses. The combination of these two fibers helped cure losses from a state of complete loss, to minor losses; later, no remedial jobs were required. This paper summarizes job design and lessons learned from this successful job, which can be applied globally, specifically for slim-liner jobs.