bluuebunny/crossref_metadata_2025_split huggingface dataset:
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
Authors: Price E Magda , Cotton Allison M , Lam Lucia L , Farré Pau , Emberly Eldon , Brown Carolyn J , Robinson Wendy P , Kobor Michael S 
Published: March 2013

Abstract

Background
Measurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potential physiologically-relevant epigenetic changes. Illumina Infinium (Illumina, San Diego, CA, USA) is a commercially available microarray suite used to measure DNAm at many sites throughout the genome. However, it has been suggested that a subset of array probes may give misleading results due to issues related to probe design. To facilitate biologically significant data interpretation, we set out to enhance probe annotation of the newest Infinium array, the HumanMethylation450 BeadChip (450 k), with >485,000 probes covering 99% of Reference Sequence (RefSeq) genes (National Center for Biotechnology Information (NCBI), Bethesda, MD, USA). Annotation that was added or expanded on includes: 1) documented SNPs in the probe target, 2) probe binding specificity, 3) CpG classification of target sites and 4) gene feature classification of target sites.

Results
Probes with documented SNPs at the target CpG (4.3% of probes) were associated with increased within-tissue variation in DNAm. An example of a probe with a SNP at the target CpG demonstrated how sample genotype can confound the measurement of DNAm. Additionally, 8.6% of probes mapped to multiple locations in silico. Measurements from these non-specific probes likely represent a combination of DNAm from multiple genomic sites. The expanded biological annotation demonstrated that based on DNAm, grouping probes by an alternative high-density and intermediate-density CpG island classification provided a distinctive pattern of DNAm. Finally, variable enrichment for differentially methylated probes was noted across CpG classes and gene feature groups, dependant on the tissues that were compared.

Conclusion
DNAm arrays offer a high-throughput approach for which careful consideration of probe content should be utilized to better understand the biological processes affected. Probes containing SNPs and non-specific probes may affect the assessment of DNAm using the 450 k array. Additionally, probe classification by CpG enrichment classes and to a lesser extent gene feature groups resulted in distinct patterns of DNAm. Thus, we recommend that compromised probes be removed from analyses and that the genomic context of DNAm is considered in studies deciphering the biological meaning of Illumina 450 k array data.
Relationship Among Serum and Urine Neopterin, Fibrinogen, and Other Serum Analytes in Atherosclerotic Patients and the Long-term Effect of H.E.L.P. Therapy
Authors: Vrecko Karoline , Walz Manfred , Tafeit Erwin , Reibnegger G. 
Published: March 2013

Summary
In 30 atherosclerotic patients different serum analytes and neopterin concentrations in serum and urine were determined before and after Heparin-Induced Extracorporeal LDL and Fibrinogen Precipitation therapy. Neopterin concentrations in serum of all 30 patients were increased (mean=9.18 nmol/l, SD=3.23) compared to age matched healthy people (mean=5.34 nmol/l, SD=2.70) and were significantly lowered after H.E.L.P therapy (mean=S.22 nmol/l; SD=3.22, p=0.002, t-test) . These results suggest the involvement of the cellular immune system in the occurrence of atherosclerosis. Further neopterin, the macrophagederived immune activation marker, is significantly correlated with fibrinogen (linear correlation coefficient r=0.36, p=0.05). Long-term neopterin concentrations in serum of 4 patients (three with coronary heart disease and one with Papilla edema), from the first up to the 9th, respectively 12th therapy decreased, in contrast to fibrinogen which stayed stable or even increased during long-term treatment.
Modulation of LPS-induced Cell Death by 5,6,7,8-Tetrahydrobiopterin
Authors: Iizuka Hiroyuki , Sagara Hirofumi , Kojima Shuji 
Published: March 2013

Summary
It has been previously reported that 5,6,7,S-tetrahydrobiopterin (BH4) modulates HL-60 cell death induced by a nitric oxide (NO) donor, S-nitroso-N-acetyl-D, L-penicillamine (SNAP). In this study, the role of endogenous BH4 was investigated in lipopolysaccharide (LPS)-induced apoptotic cell death. LPS induced an increase of DNA fragmentation and of nitrite and nitrate content (NOx content) in the macrophage- like RAW 264.7 cell line. 2,4-Diamino-6-hydroxypyrimidine (DAHP) , an inhibitor of BH4 synthesis, suppressed both of them. The NOx content of cells treated with LPS and interferon-y was much higher than that of cells treated with LPS alone. However, the degree of apoptotic cell death induced by LPS and interferon-y did not differ significantly from that induced by LPS alone. Further investigation revealed that LPS-induced cell death of RAW264.7 cells was mainly mediated by reactive oxygen species, such as hydrogen peroxide (H2O2). From these data, it was speculated that BH4 might be a modulator in NO-induced apoptosis, in which BH4 involves LPS-induced cell death by its function asa cofactor of inducible NO synthase and it suppresses the cell death mediated by NO and/or H2O2 via an antioxidative activity.
Correlation of Neopterin Concentrations In Amniotic Fluid and Urine of Pregnant Women at Delivery
Authors: Widner Bernhard , Fuith Lothar C. , Czarnecki Maryan , Fuchs Dietmar 
Published: March 2013

Summary
Median neopterin concentration in amniotic fluid at delivery was 72 nM which is approximately 10-fold the maternal and fetal serum concentration. A strong correlation existed between neopterin concentrations in amniotic fluid and urine, except an unproportionally high level in amniotic fluid in one case with an intrauterine infection.
Cerebrospinal Fluid Levels of α-tocopherol and Neopterin In Patients with Dementia
Authors: Sattler Wolfgang , Leblhuber Friedrich , Walli Johannes , Widner Bernhard , Fuchs Dietmar 
Published: March 2013

Summary
In patients with different forms of dementia we compared serum and cerebrospinal fluid concentrations of α-tocopherol (vitamin-E), the major circulating lipid-soluble antioxidant, and neopterin, a product released from monocytic cells upon stimulation with interferon-γ. A significant inverse correlation was found between the concentrations of both compounds in the cerebrospinal fluid. The data point to a role of oxidative stress to reduce antioxidant levels in elderly demented patients with neurodegenerative diseases.
Soluble Fas ligand and neopterin in patients with systemic and cutaneous discoid lupus erythematosus
Authors: Wirleitner Barbara , Kowald Elisabeth , Widner Bernhard , Ortner Ulrike , Baier-Bitterlich Gabriele , Sepp Norbert , Fuchs Dietmar 
Published: March 2013

Summary
Evidence accumulates suggesting that the pathogenesis in systemic lupus erythematosus (SLE) is associated with modulations in the Fas/FasL system. Serum concentrations of soluble Fas ligand (sFasL) were found to be elevated in patients with SLE. In this study we wanted to determine the levels of sFasL and the status of immune activation - monitored by neopterin secretion - in patients with SLE and cutaneous discoid lupus erythematosus (CDLE). Sixty-five serum samples were assayed. We found elevated concentrations of sFasL in patients with SLE and CDLE. The levels of sFasL in COLE patients were significant lower compared to SLE patients. Neopterin concentrations in serum were found to be slightly increased in patients with CDLE. Compared to patients with SLE, activation of the immune system was significant lower in COLE. Taken together, we found d evated levels of sFasL in patients with SLE as well as CDLE, connected with ar activation of the immune system and thereby increased concentration of neopterin in serum.
Neopterin and kynurenine concentrations in aqueous humour of the anterior chamber of the eye and in serum of cataract patients with pseudoexfoliation
Authors: Laganovska Guna , Martinsons Agris , Pitrans Bronislavs , Widner Bernhard , Fuchs Dietmar 
Published: March 2013

Summary
In 40 cataract patients and in 51 patients without pseudoexfoliation (PES) we determined serum concentrations of neopterin, kynurenine, and selenium and concentrations of neopterin in aqueous humour from the anterior chamber of the eye. In addition, selenium content in lenses was determined. Significantly increased kynurenine and neopterin concentrations in serum and neopterin concentrations in aqueous humour were observed in mature cataract patients with PES compared to those without. These patients also presented with the lowest content of selenium in serum and lens, compared with cataract patients without PES. Increased concentrations of neopterin in serum and aqueous humour of the anterior chamber of eyes suggest an increased degree of oxidative stress in patients with PES. Thus, the results support the role of oxidative stress in the development of PES in cataract patients. The decreased content of selenium may elicit immune system activation via an increased oxidative stress as it is indicated by the increased formation of kynurenine and neopterin.
Neopterin Acting as a Bone Marrow Stem Cell Factor on Early Common Haematopoietic (Myeloid) and Stromal (Dendritic, CD34+) Cell Progenitors in vitro
Authors: Zvetkova E. , Fuchs D. , Katzarova E. , Bakalska M. , Svetoslavova M. , Nikolov B. 
Published: March 2013

Abstract
The in vitro response of early haematopoietic progenitors or stem cells, common for myeloid (granulocyte, eosinophil, megacaryocyte) and marrow stromal (including dendritic CD34+) cells series, to neopterin, exogenously added to the liquid- and semi-liquid (agar-) mouse bone marrow cultures, at doses 12.5 - 25 Jlg/ml culture medium, has been studied. The results obtained show a significant stimulation of common myeloid and stromal dendritic cell (CD34+) progenitors' proliferation and/or differentiation as early as 24h after the in vitro treatment of marrow cultures with neopterin. On day 4 of cultivation the granulocyte/macrophageal proliferation and differentiation has been attenuated giving place to the marrow stromal dendritic cell (probably CD34+) differentiation. The engagement of the nuclear proliferative factor NF-K B may playa role in the light of recent data that neopterin could activate this transcriptionally active nuclear factor. The significance of clonal selective stimulation of healthy (but not of leukaemic) dendritic CD34+ cells in some pathological cases as acute myeloid leukaemia has been also discussed because neopterin could be a more efficient marrow stem cell factor than cytokine cocktails with granulocyte/macrophage-colony stimulating factor. The ex vivo or clinical application of neopterin, alone and/or in specific combinations with other cytokines, in the induction of marrow myeloid and stromal cell proliferation and differentiation towards the dendritic (CD34+) cells merits further investigations ..
Neopterin Concentrations in Colon Dialysate
Authors: Ledjeff E. , Artner-Dworzak E. , Witasek A. , Fuchs D. , Hausen A. 
Published: March 2013

Abstract
Increased production of neopterin in humans is indicative for an activated cellular immune response. The intestinal immune system encounters an enormous amount of infectious agents or injurious substances evoking a cellular immune response. The objective of this pilot study was to measure neopterin levels in colon dialysates of healthy individuals and in comparison with individuals under a starvation diet and with patients. In parallel, urinary and salivary neopterin levels were determined in these subjects. The mean neopterin concentration in colon dialysate was about J 0, times higher than in serum. These high neopterin values agree with a great impact of the cellular immune system within the human colon. Common diseases had a strong and prompt effect on the neopterin levels in colon dialysate, e.g. three individuals with acute gastritis had very high neopterin concentrations. In subjects with a starvation diet according to F.X.Mayr, which is characterized by low fiber and low calorie intake, the neopterin levels in colon dialysate were lower. The data may argue for a regeneration of the cellular immune system during fasting.
Location of CO2 on silicalite-1 zeolite using a single-crystal X-ray method
Authors: Fujiyama Shinjiro , Kamiya Natsumi , Nishi Koji , Yokomori Yoshinobu 
Published: March 2013

Abstract
The location of physisorbed CO2 molecules on silicalite-1 zeolite (MFI-type) is determined using a single-crystal X-ray method. There are four sorption sites for CO2 molecules in the three-dimensional channel system of the silicalite-1. Two of them are in the straight channel in disorder (STR1 and STR2), while the other sites are in the sinusoidal channel (SIN) and at the intersection (INT). Their occupancy factors indicate that a large portion of the CO2 molecules are located in the straight channel. It is also revealed that the straight channel is the most favorable for CO2 molecules as sorption sites.
Effects of Curing Time on Properties of Spin-On Glass as Low-Temperature Insulator
Authors: Dominguez Miguel A. , Rosales Pedro , Torres Alfonso , Moreno Mario 
Published: March 2013

ABSTRACTIn this work, we report the effects of curing time on properties of SiO2 films produced from Spin-On Glass (SOG) diluted with H2O and cured at 200°C. The electrical characterization showed that the insulator breakdown field for the films produced from SOG diluted with H2O with 1 Hr of curing time was approximately 5 MV/cm while for 6.5 Hrs of curing time the breakdown field was 21 MV/cm. Also, the refractive index and surface roughness were improved with longer curing time.
X-ray absorption spectroscopy studies for the determination of adsorption binding modes of selenium oxoanions onto iron and manganese based nanomaterials
Authors: Gonzalez Christina M. , Parsons Jason G. , Hernandez Jeffrey , Gardea-Torresdey Jorge L. 
Published: March 2013

ABSTRACTIncreasing concentrations of selenium oxoanions in the environment are placing many animals at risk for reproduction failure and deformities. The understanding of binding mechanisms of selenium oxoanions to iron and manganese based oxide minerals could lead to enhanced understanding of selenium mobility in the environment. In this study, the binding mechanisms of selenium oxoanions, selenite and selenate, to non microwave-assisted and microwave-assisted synthetic Fe3O4, Mn3O4, and MnFe2O4 nanomaterials were investigated through the use of X-ray absorption spectroscopy. The X-ray absorption near-edge structure (XANES) spectroscopy studies revealed the oxidation state of selenite and selenate remains the same after binding occurs to all nanomaterials in pH 2, 4, or 6 environments. The binding modes of selenite and selenate were determined to be bidentate binuclear through use of Extended x-ray absorption fine structure (EXAFS) and were independent of nanomaterials, synthetic technique, and pH.
Theoretical and experimental advances in Bi2Te3 / Sb2Te3 - based and related superlattice systems
Authors: Winkler M. , Liu X. , Schürmann U. , König J. D. , Kienle L. , Bensch W. , Böttner H. 
Published: March 2013

ABSTRACTRoughly a decade ago an outstanding thermoelectric figure of merit ZT of 2.4 was reported for nanostructured Bi2Te3/Sb2Te3-based thin film superlattice (SL) structures. The published results strongly fueled and renewed the interest in the development of efficient novel nanostructured thermoelectric materials. This review article shall give an overview over the most recent theoretical and experimental advances on Bi2Te3/Sb2Te3 SLs and related superlattice systems. The presented theoretical models are subdivided into electronic and phononic aspects. The experimental results are summarized with regard to the method used. A more detailed elaboration on structural and transport properties is given in the subsequent sections.
Carbon Nanomaterials for Energy Efficient Green Electronics
Authors: Kaul Anupama B. 
Published: March 2013

AbstractDeveloping energy efficient electronics or green electronics is an area that is largely driven by the performance limitations of scaled Si-based CMOS due to the exceptionally high power dissipation and high leakage currents arising in such devices at nanoscale dimensions. It is clear now that Si-based CMOS has been stretched over the past several decades to the point that further miniaturization will make such simple size scaling non-sustainable in the future. New materials and technologies are thus vigorously being explored beyond Si, in order to overcome performance limitations from ultra-miniaturized Si-CMOS. Among these materials, carbon-based nanostructures such as graphene and carbon nanotubes are being considered as viable alternatives to Si-CMOS to enable energy efficient green electronics. Novel architectures for enabling low-power, energy-efficient computation are currently being explored, which include tunneling field-effect-transistors (TFETs), as well as nano-electro-mechanical-systems (NEMS) due to their abrupt ON/OFF transitions, low OFF state currents and high speed operation. In this paper, an overview of carbon nanomaterials is presented and the role they play in enabling energy efficient TFETs and NEMS is also highlighted. Finally, the emergence of a new class of 2D systems beyond graphene is discussed such as MoS2, which may open up new avenues for exploration and enabling applications in electronics.
Electron and Phonon Transport in n- and p-type Skutterudites
Authors: Yang Jiong , Wang S. , Yang Jihui , Zhang W. , Chen L. 
Published: March 2013

ABSTRACTFilled skutterudites are one of the most promising materials for thermoelectric (TE) power generation applications at intermediate temperatures due to their superior TE and thermomechanical performance as compared to other materials. In the past, we have demonstrated that n-type skutterudites can be optimized so that their maximum TE figure of merit reaches 1.7 at 850 K. TE performance of the p-type, however, is lagging behind, which hinders the optimization of skutterudites-based TE module development. In this paper we reveal that the underlying reasons for inferior TE properties of the p-type root in their electronic band structures, which result in higher thermal conductivity at elevated temperatures due to bipolar lattice thermal conduction and lower power factor because of heavy valance bands induced strong electron-phonon interactions. We also identify means of improving the power factor and reducing bipolar effect.
Diffusion barriers for CeFe4Sb12/Cu thermoelectric devices
Authors: Boulat Laetitia , Viennois Romain , Ravot Didier , Fréty Nicole 
Published: March 2013

ABSTRACTThe efficiency of a tantalum nitride interlayer as a diffusion barrier for CeFe4Sb12 thermoelectric material against electrode copper material has been investigated. The thermal stability of CeFe4Sb12/TaN/Cu stackings has been investigated after annealing at 600°C from a microstructural study. CeFe4Sb12 and Cu appear to chemically react through the formation of CeCu2 and Cu2Sb phases whereas no reaction is observed for CeFe4Sb12 with TaN. This study showed that the TaN interlayer cannot inhibit the diffusion of Sb from the skutterudite substrate to the copper electrode but prevents the diffusion of Ce and consequently the formation of the CeCu2 phase.
Water Quality Assessment and Analysis of Spatial Patterns and Temporal Trends
Authors: Gazzaz Nabeel M. , Yusoff Mohd Kamil , Juahir Hafizan , Ramli Mohammad Firuz , Aris Ahmad Zaharin 
Published: March 2013

ABSTRACT: This study investigated relationships of a water quality index (WQI) with multiple water quality variables (WQVs), explored variability in water quality over time and space, and established linear and non‐linear models predictive of WQI from raw WQVs. Data were processed using Spearman's rank correlation analysis, multiple linear regression, and artificial neural network modeling. Correlation analysis indicated that from a temporal perspective, the WQI, temperature, and zinc, arsenic, chemical oxygen demand, sodium, and dissolved oxygen concentrations increased, whereas turbidity and suspended solids, total solids, nitrate nitrogen (NO3‐N), and biochemical oxygen demand concentrations decreased with year. From a spatial perspective, an increase with distance of the sampling station from the headwater was exhibited by 10 WQVs: magnesium, calcium, dissolved solids, electrical conductivity, temperature, NO3‐N, arsenic, chloride, potassium, and sodium. At the same time, the WQI; Escherichia coli bacteria counts; and suspended solids, total solids, and dissolved oxygen concentrations decreased with distance from the headwater. Lastly, regression and artificial neural network models with high prediction powers (81.2% and 91.4%, respectively) were developed and are discussed.
Extreme Estimation Uncertainty and Audit Assurance
Authors: Christensen Brant E. , Glover Steven M. , Wood David A. 
Published: March 2013

SUMMARY
The overall uncertainty inherent in financial statements has increased in recent decades, but the related reports and required level of audit assurance have changed very little. In our study, “Extreme Estimation Uncertainty in Fair Value Estimates: Implications for Audit Assurance” (Christensen et al. 2012a), we examine estimates reported by public companies and find that estimates based on management's subjective models and inputs contain estimation uncertainty that is many times greater than typical audit materiality. We do not question the value that audits provide to the marketplace or the ability of auditors to deploy up-to-date auditing techniques. Rather, we suggest that the convergence of relatively recent events is placing an increasingly difficult and perhaps, in some cases, unrealistic burden on auditors. We discuss potential changes to financial reporting and auditing standards that may improve the information provided to users, and also address the concerns raised in our study.