bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site‐specific characterisation of densely O‐glycosylated mucin‐type peptides using electron transfer dissociation ESI‐MS/MS
Authors: Thaysen‐Andersen Morten , Wilkinson Brendan L. , Payne Richard J. , Packer Nicolle H. 
Published: December 2011

AbstractSite‐specific characterisation of mucin‐type O‐linked glycosylation is an analytical challenge due to glycan heterogeneity, lack of glycosylation site consensus sequence and high density of occupied glycosylation sites. Here, we report the use of electron transfer dissociation (ETD) for the site‐specific characterisation of densely glycosylated mucin‐type O‐linked glycopeptides using ESI‐IT‐MS/MS. Synthetic glycopeptides from the human mucin‐1 (MUC‐1) tandem repeat region containing a range of O‐linked, tumour‐associated carbohydrate antigens, namely Tn, T and sialyl T, with different glycosylation site occupancies and an increasing number of tandem repeats were studied. In addition, a glycopeptide from the anti‐freeze glycoprotein of Antarctic and Arctic notothenoids, bearing four O‐linked, per‐acetylated T antigens was characterised. ETD MS/MS of infused or capillary LC‐separated glycopeptides provided broad peptide sequence coverage (c/z·‐type fragment ions) with intact glycans still attached to the Ser/Thr residues. Thus, the glycosylation sites were unambiguously determined, while simultaneously obtaining information about the attached glycan mass and peptide identity. Highly sialylated O‐glycopeptides showed less efficient peptide fragmentation, but some sequence and glycosylation site information was still obtained. This study demonstrates the capabilities of ETD MS/MS for site‐specific characterisation of mucin‐type glycopeptides containing high‐density O‐linked glycan clusters, using accessible and relative low‐resolution/low‐mass accuracy IT MS instrumentation.
Plasma proteomics for biomarker discovery: A study in blue
Authors: Di Girolamo Francesco , Righetti Pier Giorgio 
Published: December 2011

AbstractThe performance of Cibacron Blue dye (HiTrapBlue or Affigel Blue) in depleting albumin from plasma, as a pre‐treatment for biomarker searching in the low‐abundance proteome, is here assessed. It is shown that (i) co‐depletion of non‐albumin species is an ever‐present hazard; (ii) the only proper eluant able to release quantitatively the proteins bound to the dye is boiling 4% SDS‐25 mM DTT, an ion shock (2 M NaCl) being quite ineffective in releasing the low‐abundance species tightly bound to the dye moiety; (iii) the mechanism of dye–protein interaction, after an initial ion–ion docking, is a robust hydrophobic interaction, which progressively augments at lower and lower pH values; (iv) at pH 2.2 in the presence of 0.1% TFA, the blue resin behaves, for all practical purposes, just as a reverse‐phase chromatography column, since all residual proteins present in plasma are completely harvested. However Cibacron Blue technology should not necessarily be discarded: As long as also the plasma fraction adsorbed is properly released and analyzed, together with the flow through, one should be able to perform a viable analysis of the low‐abundance proteome.
Alternate fuels: Calculating the value of rooftop solar
Authors: Powers Bill 
Published: December 2011

AbstractIn California, the price paid for renewable energy resources has historically been linked to the cost of energy from new natural gas—fired baseload plants, ostensibly to protect utility ratepayers from paying too much for renewable energy resources. Numerous new natural gas—fired plants have been authorized by the California Public Utilities Commission (CPUC) in recent years.
Outlook—natural gas prices: FERC anticipates continued low natural gas prices
Authors:   Federal Energy Regulatory Commission
Published: December 2011

AbstractMarket conditions going into the winter are generally positive. Despite a 2.6 percent increase in natural gas demand this year, prices remain among the lowest in the past decade, due to continued production growth and new pipelines transporting gas from the producing areas to consumers. Gas‐fired electric generation is benefiting from the lower gas prices, raising expectations for continued demand growth from this sector in the upcoming winter. As has been the case in past years, we can expect localized pipeline constraints in the Northeast during extreme cold weather periods, as growing gas power generation adds to peak gas demand for space heating.
NERC matters: Should NERC impose winter preparedness requirements on generators?
Authors: Carpentier Deborah 
Published: December 2011

AbstractDuring February 2011, the southwestern United States experienced unusually severe cold and windy weather, with many cities experiencing a 50‐degree drop in temperature over an 18‐hour period, with sustained winds of 30 to 40 miles an hour. During this period, generating units in the Southwest experienced an outage, a derate, or a failure to start, leading to controlled load shedding of about 5,300 megawatts.
Electric regulation: Future of the electric vehicle
Authors: Bowden Nicholas S. 
Published: December 2011

AbstractA 1997 article in Business and Economic History written by David Kirsch of UCLA suggests that alternatives to the internal combustion engine existed “but only for a brief period of time before 1902.”1 He asserts that growth in the scale and scope of the gasoline‐based automobile industry over time resulted in a decreased probability that electric vehicles would reenter the marketplace.
Single‐arm phase II study of multiagent concurrent chemoradiotherapy and gefitinib in locoregionally advanced squamous cell carcinoma of the head and neck
Authors: Rodriguez Cristina P. , Adelstein David J. , Rybicki Lisa A. , Saxton Jerrold P. , Lorenz Robert R. , Wood Benjamin G. , Scharpf Joseph , Ives Denise I. 
Published: December 2011

AbstractBackgroundThis phase II study tested the addition of the oral epidermal growth factor receptor gefitinib to multiagent concurrent chemoradiotherapy regimen in head and neck squamous cell cancer (HNSCC).MethodsPatients with stage III–IV HNSCC received hyperfractionated radiation (72–74.4 Gy at 120 cGy twice daily), with concurrent 96‐hour infusions of cisplatin 20 mg/m2/day and fluorouracil 1000 mg/m2/day given during weeks 1 and 4. Daily gefitinib 250 mg was started on day 1 of radiation and continued for 2 years. Results were retrospectively compared with our previous study using identical chemoradiotherapy without gefitinib.ResultsSixty patients were enrolled in the study; 80% had stage IV disease and 68% had oropharyngeal primary tumors. The full course of gefitinib was not tolerated by 42%; there were 5 treatment‐related deaths (8%). With a median follow‐up of 54 months, 2‐ and 3‐year overall survival estimates were 80% and 71%, respectively. Projected distant metastatic control at 2 and 3 years was 88%. When compared with our historical cohort, acute toxicities including renal dysfunction and unplanned rehospitalization were worse in the study patients. Projected outcome estimates did not differ between the 2 cohorts.ConclusionsAddition of gefitinib to concurrent chemoradiotherapy was difficult to complete, did not improve outcomes, and increased toxicity. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Thyroid gland involvement in advanced laryngeal cancer: Association with clinical and pathologic characteristics
Authors: Hilly Ohad , Raz Raanan , Vaisbuch Yona , Strenov Yulia , Segal Karl , Koren Rumelia , Shvero Jacob 
Published: December 2011

AbstractBackgroundIndications for thyroidectomy during laryngectomy are controversial. We examined whether clinicopathologic features can predict thyroid gland involvement, and the prognostic effect of thyroid gland involvement in patients undergoing total laryngectomy.MethodsThe study set out to review preoperative assessment, operation findings, pathologic findings, and follow‐up data.ResultsThyroid gland involvement was found in 11 of 53 patients (21%) undergoing total laryngectomy and thyroidectomy. Preoperative work‐up failed to predict thyroid gland involvement. Thyroid gland involvement was associated with salvage procedures (p = .025), paratracheal metastases (p = .003), and poor overall survival (hazard ratio = 2.74, p = .008).ConclusionsThyroid gland involvement in patients undergoing total laryngectomy is frequent and is associated with poor prognosis. Preoperative assessment failed to predict thyroid gland involvement. We believe that thyroidectomy should be considered in cases with paratracheal lymphatic spread irrespective of tumor location within the larynx. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Prospective randomized trial of high versus low negative pressure suction in management of chyle fistula after neck dissection for metastatic thyroid carcinoma
Authors: Wu Gaosong , Chang Xiaofei , Xia Yun , Huang Wei , Koch Wayne M. 
Published: December 2011

AbstractBackgroundNegative pressure drainage has been shown to be an effective treatment of chyle fistula. However, the optimal level of negative pressure has not been determined. We therefore conducted a prospective randomized trial to address this issue.MethodsIn all, 21 patients with chyle fistula were randomly assigned to a high negative pressure suction (HNPS) group (−600 mmHg, n = 10) or low negative pressure suction (LNPS) group (−125 mmHg, n = 11). The duration of drain leakage and hospital stay, and the incidence of complications were compared between the 2 groups.ResultsAll patients were successfully treated with conservative management without surgical intervention. The median durations of chyle leakage and hospital stay were significantly shorter in the HNPS group compared with the LNPS group: 4 versus 7 days (p = .0048) and 5 versus 11 days (p = .0107), respectively.ConclusionsNegative suction was demonstrated to be highly effective in the management of chyle fistula, and HNPS appeared to be more efficient than LNPS. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Integrating multiple microarray datasets on oral squamous cell carcinoma to reveal dysregulated networks
Authors: Liu Zhongyu , Niu Yulong , Li Chao , Yang Yi , Gao Chunfang 
Published: December 2011

AbstractBackgroundOral squamous cell carcinoma (OSCC) is the sixth most common type of carcinoma worldwide. The pathogenic pathways involved in this cancer are mostly unknown; therefore, a better characterization of the OSCC gene expression profile would represent a considerable advance. The public availability of gene expression datasets was meant to obtain new insights on biological processes.MethodsWe integrated 4 public microarray datasets on OSCC to evaluate the degree of consistency among the biological results obtained in these different studies and to identify common regulatory pathways that could be responsible for tumor growth.ResultsTwelve altered cellular pathways implicated in OSCC and 4 genes altered in the extracellular matrix (ECM) receptor pathway were validated by quantitative real‐time polymerase chain reaction (qRT‐PCR).ConclusionUsing 4 expression array datasets, we have developed a robust method for analyzing pathways altered in OSCC. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
The bergman cyclizations of the enediyne and its N‐substituted analogs using multiconfigurational second‐order perturbation theory
Authors: Dong Hua , Chen Bo‐Zhen , Huang Ming‐Bao , Lindh Roland 
Published: December 2011

AbstractThe Bergman cyclizations of the enediyne and its four N‐substituted analogs [(Z)‐pent‐2‐en‐4‐ynenitrile, 3‐azahex‐3‐en‐1,5‐diyne, malenotrile, and 3,4‐azahex‐3‐en‐1,5‐diyne] have been studied using the complete active space self‐consistent field and multiconfigurational second‐order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S0 (the ground state) and T1 (the lowest‐lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data. The distance between two terminal carbons in enediyne, which was considered as an important parameter governing the Bergman cyclization, was predicted to be 4.319 Å, in agreement with the experimental value of 4.321 Å. Our calculations indicate that the replacements of the terminal C atom(s) or the middle C atom(s) in the CC bond by the N atom(s) increase or decrease the energy barrier values, respectively. There exist stable ring biradical products on the T1 PESs for the five reactions. However, on the S0 PESs the ring biradical products exist only for the reactions of enediyne, (Z)‐pent‐2‐en‐4‐ynenitrile, and 3‐azahex‐3‐en‐1,5‐diyne. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Latin squares with restricted transversals
Authors: Egan Judith , Wanless Ian M. 
Published: December 2011

AbstractWe prove that for all odd m≥3 there exists a latin square of order 3 m that contains an (m−1) × m latin subrectangle consisting of entries not in any transversal. We prove that for all even n≥10 there exists a latin square of order n in which there is at least one transversal, but all transversals coincide on a single entry. A corollary is a new proof of the existence of a latin square without an orthogonal mate, for all odd orders n≥11. Finally, we report on an extensive computational study of transversal‐free entries and sets of disjoint transversals in the latin squares of order n⩽9. In particular, we count the number of species of each order that possess an orthogonal mate. © 2011 Wiley Periodicals, Inc. J Combin Designs 20:124‐141, 2012
Regulation of articular chondrocyte aggrecan and collagen gene expression by multiple growth factor gene transfer
Authors: Shi Shuiliang , Mercer Scott , Eckert George J. , Trippel Stephen B. 
Published: December 2011

AbstractGene transfer is a promising approach to the delivery of chondrotrophic growth factors to promote cartilage repair. It is unlikely that a single growth factor transgene will optimally regulate these cells. The aim of this study was to identify those growth factor transgene combinations that optimally regulate aggrecan, collagen type II and collagen type I gene expression by articular chondrocytes. We delivered combinations of the transgenes encoding fibroblast growth factor‐2, insulin‐like growth factor I, transforming growth factor beta1, bone morphogenetic protein‐2, and/or bone morphogenetic protein‐7 and assessed chondrocyte responses by measuring changes in the expression of aggrecan, type II collagen and type I collagen genes. These growth factor transgenes differentially regulated the magnitude and time course of all three‐matrix protein genes. In concert, the transgenes regulated matrix gene expression in an interactive fashion that ranged from synergistic to inhibitory. Maximum stimulation of aggrecan (16‐fold) and type II collagen (35‐fold) expression was with the combination of IGF‐I, BMP‐2, and BMP‐7 transgenes. The results indicate that the optimal choice of growth factor genes for cell‐based cartilage repair cannot be predicted from observations of individual transgenes. Rather, such gene therapy will require an empirically based selection of growth factor gene combinations. 2011 Orthopaedic Research Society. This article is a US Government work and as such is in the public domain in the United States of America. Published by Wiley Periodicals, Inc. J Orthop Res 30:1026–1031, 2012
Sensitivity of gait parameters to the effects of anti‐inflammatory and opioid treatments in knee osteoarthritis patients
Authors: Boyer Katherine A. , Angst Martin S. , Asay Jessica , Giori Nicholas J. , Andriacchi Thomas P. 
Published: December 2011

AbstractThe study aim was to address the need for objective markers of pain‐modifying interventions by testing the hypothesis that selective gait measures of knee joint loading can distinguish differences between non‐steroidal anti‐inflammatory (NSAID), analgesic treatment (opioid‐receptor agonist), and placebo in patients medial knee osteoarthritis (OA). A randomized, single‐blind washout, double‐blind treatment, double‐dummy cross‐over trial using three treatment arms placebo, opioid (Oxycodone), and NSAID (Celecoxib) in medial compartment knee OA patients. Six patients with Kellgren–Lawrence radiographic severity grades of 2 or 3 completed six testing sessions (gait and pain assessment) at 2‐week intervals. A significant increase was found in the knee total reaction moment and vertical ground reaction force (GRF) for Celecoxib compared to placebo (p = 0.005, p = 0.003), but not for Oxycodone compared to placebo (p = 0.20, p = 0.27) treatments. Walking speed was significantly higher for the Celecoxib and Oxycodone compared to placebo treatment (p = 0.041 and p = 0.031, respectively). Self‐reported function (WOMAC scores) was not different among treatments (p > 0.05). The changes in total reaction moments and GRFs for only the NSAID suggest that greater increases in joint loading occurs when joint inflammation is treated in addition to pain. The total knee reaction moment, representing the magnitude of the extrinsic moment, appears to be a sensitive marker, more so than self‐reported metrics, for evaluating knee OA treatment effects. © 2011 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1118–1124, 2012
Availability of exchangeable and non‐exchangeable K in Argentine soils with different mineralogy
Authors: Zubillaga María M. , Conti Marta E. 
Published: December 2011

AbstractThere were two objectives in the study: 1) To determine exchangeable K and non‐exchangeable K in soils with different potassium depletion levels and mineralogy as plant sources 2) To establish a relationship between the mineralogy vs exchangeable K (Ke) and non‐exchangeable K (Kne) mobilization. An extraction experiment of soils was carried out in a greenhouse, with a total of 6 consecutive crops of ryegrass.Different supply rates for plant K were determined by Ke and Kne mobilization according to the soil intensity of use. The contribution of the Ke was greater and generated higher amount of K uptake during maximum availability period (from 0 to the 1st harvest) than in the later period when soil K was already depleted. For this the initial exchangeable K and the illite concentration of soils accounted for almost 100% (R2 = 0.981 P=0.01) of the K taken up by ryegrass. For the following period (from the 2nd harvest to the 6th), Kne forms became more important. Plant K supply was not only a result of initial exchangeable K and illite concentration but presumably also of primary K‐bearing minerals.
Gas diffusivity in soils compared to ideal isotropic porous media
Authors: Kühne Anke , Schack‐Kirchner Helmer , Hildebrand Ernst E. 
Published: December 2011

AbstractEvidence of anisotropy is reported for advective air and water permeabilities in soils. Thus, anisotropy is likely to exist also for diffusive gas fluxes. Information about direction‐dependent soil gas diffusivity is scarce and most modeling approaches assume isotropy. At hundreds of closely lying positions in a compacted and adjacent undisturbed forest soil, gas diffusivity (Ds/D0) was measured either in vertical or horizontal direction. The volume‐independent diffusion efficiency (i.e., diffusivity divided by air‐filled porosity) was fitted by a generalized additive model (GAM). Significant regressors were air‐filled porosity (ϵ), soil depth, and the discrete diffusion direction. The model yields in all cases higher vertical diffusion efficiencies. The compaction factor did not yield a significant regressor of its own, i.e., the reduction of diffusivity in the compacted soil was the same as in low‐porosity samples of the undisturbed profile. To elucidate the role of sharing vertically and horizontally orientated pore space and a potential competition between diffusivity in different spatial directions, simple geometric models consisting of 3‐dimensionally crossed pores have been parameterized. These models provided a good explanation of the typical nonlinear Ds/D0(ϵ) relationship. By simple one‐parameter correction (linear or power function), this mechanistic model could be fitted to the data. The one‐parameter correction of the geometric model could be a straightforward approach to consider direction dependence of measured diffusivities. However, by applying this approach to the observations the anisotropy effect was not clearly evident, which could be attributed to a changing Ds/D0(ϵ) relationship with depth. As a reason for the preference of the vertical gas diffusion the dominance of vertical stresses and the activity of anecic earthworms are discussed. Direction dependency of gas diffusivity seems to be a basic feature of natural pore systems and has to be considered for modeling gas fluxes in soils. Generally, a preferential vertical diffusion direction reduces horizontal balancing and increases the heterogeneity of gas concentrations in the soil air.
Christian G. Ehrenberg and the birth of soil microbiology in the middle of the 19th century
Authors: Blume Hans‐Peter , Bölter Manfred , Kusber Wolf‐Henning 
Published: December 2011

AbstractEarly in the 19th century, the German doctor and natural scientist Christian G. Ehrenberg (1795–1876) determined and classified through microscopic investigation the species and contents of microorganisms (bacteria, algae, diatoms, protozoa) of more than 1000 soil samples from all over the world. He identified phytoliths and minerals using a polarization microscope and described the morphology of the organic particles. Two of his soil descriptions were a Chernozem from Russia and an Ornithogenic Cryosol of the Maritime Antarctic. He further identified several soil‐forming processes like the formation and decomposition of organic matter, mineral weathering, and new formation of carbonates, Fe oxides, and silicate under the influence of microorganisms long before other investigators. Although this was criticized during his time, it is still fully accepted today. Therefore, Ehrenberg can be regarded as the main founder of soil microbiology and as a pioneer in soil micromorphology.
Physiological changes, phenolic content and antioxidant activity of Salvia officinalis L. grown under saline conditions
Authors: Taârit Mouna Ben , Msaada Kamel , Hosni Karim , Marzouk Brahim 
Published: December 2011

AbstractBACKGROUND: Hydroponic culture was used to investigate the effect of NaCl concentrations on the growth, nutrient uptake, phenolic content and antioxidant activity of Salvia officinalis L. leaves. The antioxidant capacity of the methanolic extract of S. officinalis was evaluated by using 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) radical scavenging test and β‐carotene‐linoleic acid bleaching assay. Physiological and biochemical parameters of S. officinalis were assessed after 4 weeks of salt treatment with 0, 25, 50, 75 and 100 mmol L−1 NaCl.RESULTS: Plant growth exhibited a reduction of 61% at 100 mmol L−1 NaCl. Assessment of Na+, K+ and Ca2+ and water contents of shoots and roots showed that S. officinalis is able to regulate Na+ concentration by active compartmentation in vacuoles. Salvia officinalis phenolics were increased in response to salinity at the threshold of 75 mmol L−1 NaCl. This herb was also found to be able to achieve important DPPH• quenching activity and to inhibit the β‐carotene‐linoleic acid bleaching notably enhanced by salt treatment. It is interesting to highlight the correlation between the phenolic and antioxidant activity, suggesting the involvement of these compounds in this activity.CONCLUSION: Salvia officinalis treated with 75 mmol L−1 NaCl constitutes a potential source for production of secondary metabolites useful in several applications. Copyright © 2011 Society of Chemical Industry