bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epitope mapping by random peptide phage display reveals essential residues for vaccinia extracellular enveloped virion spread
Authors: He Yong , Wang Yonggang , Struble Evi B , Zhang Pei , Chowdhury Soma , Reed Jennifer L , Kennedy Michael , Scott Dorothy E , Fisher Robert W 
Published: September 2012

AbstractBackgroundA33 is a type II integral membrane protein expressed on the extracellular enveloped form of vaccinia virus (VACV). Passive transfer of A33-directed monoclonal antibodies or vaccination with an A33 subunit vaccine confers protection against lethal poxvirus challenge in animal models. Homologs of A33 are highly conserved among members of theOrthopoxvirusgenus and are potential candidates for inclusion in vaccines or assays targeting extracellular enveloped virus activity. One monoclonal antibody directed against VACV A33, MAb-1G10, has been shown to target a conformation-dependent epitope. Interestingly, while it recognizes VACV A33 as well as the corresponding variola homolog, it does not bind to the monkeypox homolog. In this study, we utilized a random phage display library to investigate the epitope recognized by MAb-1G10 that is critical for facilitating cell-to-cell spread of the vaccinia virus.ResultsBy screening with linear or conformational random phage libraries, we found that phages binding to MAb-1G10 display the consensus motif CEPLC, with a disulfide bond formed between two cysteine residues required for MAb-1G10 binding. Although the phage motif contained no linear sequences homologous to VACV A33, structure modeling and analysis suggested that residue D115 is important to form the minimal epitope core. A panel of point mutants expressing the ectodomain of A33 protein was generated and analyzed by either binding assays such as ELISA and immunoprecipitation or a functional assessment by blocking MAb-1G10 mediated comet inhibition in cell culture.ConclusionsThese results confirm L118 as a component of the MAb-1G10 binding epitope, and further identify D115 as an essential residue. By defining the minimum conformational structure, as well as the conformational arrangement of a short peptide sequence recognized by MAb-1G10, these results introduce the possibility of designing small molecule mimetics that may interfere with the function of A33in vivo. This information will also be useful for designing improved assays to evaluate the potency of monoclonal and polyclonal products that target A33 or A33-modulated EV dissemination.
The Cytochrome P450 Inhibitor, Ketoconazole, Inhibits Oxidized Linoleic Acid Metabolite-Mediated Peripheral Inflammatory Pain
Authors: Ruparel Shivani , Green Dustin , Chen Paul , Hargreaves Kenneth M 
Published: September 2012

Background: Oxidized linoleic acid metabolites (OLAMs) are a class of endogenous agonists to the transient receptor potential V1 (TRPV1) receptor. Although TRPV1 mediates inflammatory heat hyperalgesia, it is not known if the OLAMs contribute to the peripheral activation of this receptor during tissue inflammation. In the present study, we evaluated whether the OLAM system is activated during inflammation and whether cytochrome P450 enzymes mediate OLAM contributions to heat hyperalgesia using the complete Freund's adjuvant (CFA) model of inflammation. Results: Our results demonstrate that the intraplantar (ipl) injection of anti-OLAM antibodies significantly reversed CFA-induced heat hyperalgesia. Moreover, application of lipid extracts from inflamed rat skin to cultured sensory neurons triggered a significant release of iCGRP that is blocked by co-treatment with I-RTX, a TRPV1 antagonist. To determine the role of CYP enzymes in mediating OLAM effects, we used a broad spectrum CYP inhibitor, ketoconazole. Pretreatment with ketoconazole inhibited the release of TRPV1 agonists in lipid extracts from inflamed skin and significantly reversed CFA-induced heat hyperalgesia by a peripheral mechanism of action. Moreover, the ipl injection of linoleic acid to rats 24 hr after CFA evoked spontaneous nocifensive behaviors that were significantly reduced by capsazepine, by knockout of the TRPV1 gene, or by pretreatment with either anti-OLAM antibodies or ketoconazole. Conclusions: Taken together, our data suggests that OLAMs contribute to inflammatory nociception in the periphery and that cytochrome P450 enzymes play a crucial role in mediating OLAM contributions to inflammatory heat hyperalgesia.
Fire ignition during laser surgery in pet rodents
Authors: Collarile Tommaso , Di Girolamo Nicola , Nardini Giordano , Ciraci Ivano Antonio , Selleri Paolo 
Published: September 2012

AbstractBackgroundLaser surgery is an attractive alternative to other means of section device in terms of tissue inflammation and interaction, which has been extensively used in human and veterinary medicine. Although accidental ignition during laser surgeries is sporadically reported in human medical literature, to the authors’ knowledge this is the first report regarding laser-dependent fire ignition during surgery in veterinary medicine.Case presentationTwo rodents, a 13-month old, 27-gram, male pet mouse (Mus musculus) and a 1-year old, female Russian hamster (Phodopus sungorus), underwent surgical removal of masses with diode laser. During the surgical procedures fires ignited from the face masks. The mouse presented severe burns on the head and both forelimbs, it was hospitalized and approximately 2 months after surgery burns were resolved. The hamster presented severe burns on the face and the proximal regions of the body. At 72 hours from the accident the hamster was euthanized.ConclusionThe present report suggests that fire ignition is a potential life-threatening complication of laser surgery in non-intubated rodents maintained under volatile anesthesia. High oxygen concentrations, the presence of combustible, and the narrowness of the surgical field with the face mask during laser surgery on rodents are risk factors for fire ignition.
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
Authors: Birtwistle Marc R , Rauch Jens , Kiyatkin Anatoly , Aksamitiene Edita , Dobrzyński Maciej , Hoek Jan B , Kolch Walter , Ogunnaike Babatunde A , Kholodenko Boris N 
Published: September 2012

Abstract

Background
Cell-to-cell variability in protein expression can be large, and its propagation through signaling networks affects biological outcomes. Here, we apply deterministic and probabilistic models and biochemical measurements to study how network topologies and cell-to-cell protein abundance variations interact to shape signaling responses.

Results
We observe bimodal distributions of extracellular signal-regulated kinase (ERK) responses to epidermal growth factor (EGF) stimulation, which are generally thought to indicate bistable or ultrasensitive signaling behavior in single cells. Surprisingly, we find that a simple MAPK/ERK-cascade model with negative feedback that displays graded, analog ERK responses at a single cell level can explain the experimentally observed bimodality at the cell population level. Model analysis suggests that a conversion of graded input–output responses in single cells to digital responses at the population level is caused by a broad distribution of ERK pathway activation thresholds brought about by cell-to-cell variability in protein expression.

Conclusions
Our results show that bimodal signaling response distributions do not necessarily imply digital (ultrasensitive or bistable) single cell signaling, and the interplay between protein expression noise and network topologies can bring about digital population responses from analog single cell dose responses. Thus, cells can retain the benefits of robustness arising from negative feedback, while simultaneously generating population-level on/off responses that are thought to be critical for regulating cell fate decisions.
Synthesis, structure and solvatochromic properties of some novel 5-arylazo-6-hydroxy-4-phenyl-3-cyano-2-pyridone dyes
Authors: Alimmari Adel , Mijin Dušan , Vukićević Radovan , Božić Bojan , Valentić Nataša , Vitnik Vesna , Vitnik Željko , Ušćumlić Gordana 
Published: September 2012

Abstract

Background
A series of some novel arylazo pyridone dyes was synthesized from the corresponding diazonium salt and 6-hydroxy-4-phenyl-3-cyano-2-pyridone using a classical reaction for the synthesis of the azo compounds.

Results
The structure of the dyes was confirmed by UV-vis, FT-IR, 1H NMR and 13C NMR spectroscopic techniques and elemental analysis. The solvatochromic behavior of the dyes was evaluated with respect to their visible absorption properties in various solvents.

Conclusions
The azo-hydrazone tautomeric equilibration was found to depend on the substituents as well as on the solvent. The geometry data of the investigated dyes were obtained using DFT quantum-chemical calculations. The obtained calculational results are in very good agreement with the experimental data.
Chloramine-induced anaphylaxis while showering: a case report
Authors: D’Alò Simona , De Pasquale Tiziana , Incorvaia Cristoforo , Illuminati Ilenia , Mistrello Gianni , Roncarolo Daniela , Pucci Stefano 
Published: September 2012

Abstract

Introduction
Sodium-N-chlorine-p-toluene sulfonamide, commonly known as chloramine-T, is a derivative of chlorine which is widely used as a disinfectant. For many years, chloramine-T has been described as a cause of immediate-type hypersensitivity, especially with regard to asthma and rhinitis, and as a cause of occupational dermatoses in cleaning personnel in hospitals, although no anaphylactic reaction has yet been reported. Hence, to the best of our knowledge we present the first case of anaphylaxis to chloramine-T with evidence of specific immunoglobulin E antibodies.

Case presentation
We describe the case of a 25-year-old Caucasian woman who was in good health and with a negative history for atopy, including no respiratory symptoms of rhinitis or asthma, and with no professional exposure to chloramine-T. She, while showering, applied a chloramine-T solution to a skin area with folliculitis on her leg, and within a few minutes developed generalized urticaria and angioedema, followed by vomiting and collapse with loss of consciousness. A skin prick test with a chloramine-T solution at 10mg/mL concentration was positive, and specific immunoglobulin E to chloramine-T was quantified at a value of 2.9 optical density as measured by the enzyme allergosorbent test technique.

Conclusion
The strict cause-effect relationship and the results of the skin test and the in vitro test make certain the causative role of chloramine-T in this case of anaphylaxis. This suggests that chloramine-T, based on its wide use as a disinfectant, should be considered a possible cause in anaphylaxis of unknown origin.
A role for low-abundance miRNAs in colon cancer: the miR-206/Krüppel-like factor 4 (KLF4) axis
Authors: Parasramka Mansi A , Dashwood W Mohaiza , Wang Rong , Saeed Hassaan H , Williams David E , Ho Emily , Dashwood Roderick H 
Published: September 2012

Abstract

Background
MicroRNAs (miRNAs or miRs) are short non-coding RNAs that affect the expression of genes involved in normal physiology, but that also become dysregulated in cancer development. In the latter context, studies to date have focused on high-abundance miRNAs and their targets. We hypothesized that among the pool of low-abundance miRNAs are some with the potential to impact crucial oncogenic signaling networks in colon cancer.

Results
Unbiased screening of over 650 miRNAs identified miR-206, a low-abundance miRNA, as the most significantly altered miRNA in carcinogen-induced rat colon tumors. Computational modeling highlighted the stem-cell marker Krüppel-like factor 4 (KLF4) as a potential target of miR-206. In a panel of primary human colon cancers, target validation at the mRNA and protein level confirmed a significant inverse relationship between miR-206 and KLF4, which was further supported by miR-206 knockdown and ectopic upregulation in human colon cancer cells. Forced expression of miR-206 resulted in significantly increased cell proliferation kinetics, as revealed by real-time monitoring using HCT116 cells.

Conclusions
Evolutionarily conserved high-abundance miRNAs are becoming established as key players in the etiology of human cancers. However, low-abundance miRNAs, such as miR-206, are often among the most significantly upregulated miRNAs relative to their expression in normal non-transformed tissues. Low-abundance miRNAs are worthy of further investigation, because their targets include KLF4 and other pluripotency and cancer stem-cell factors.
Measuring Direct Thrombin Inhibitors With Routine and Dedicated Coagulation Assays
Authors: Curvers Joyce , van de Kerkhof Daan , Stroobants An K. , van den Dool Erik-Jan , Scharnhorst Volkher 
Published: September 2012

Abstract
The use of direct thrombin inhibitors (DTIs) for prophylactic or therapeutic anticoagulation is increasing because of the predictable bioavailability and short half-life of these DTIs. However, in certain situations, indication of the concentration is warranted. We investigated the effects of 3 DTIs (lepirudin, argatroban, and bivalirudin) in 6 pooled plasma specimens on routine coagulation assays (activated partial thromboplastin time [aPTT], prothrombin time [PT], and thrombin time [TT]) and dedicated DTI assays (Hemoclot, HemosIL, the ecarin clotting time, and a chromogenic ecarin clotting time) on 2 coagulation analyzers. We found routine tests to be nondiscriminative between concentrations of different DTIs in the aPTT. Moreover, for PT and TT, the responses for different DTIs differed. This was similar for ecarin clotting assays. The Hemoclot and HemosIL assays showed identical linear increases for all 3 DTIs. We conclude that dedicated calibrated assays based on a diluted TT (Hemoclot and HemosIL) appear to be the most suitable for monitoring purposes.
DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms
Authors: Ramsey David M. , Futschik Andreas 
Published: September 2012

Abstract
The development of next generation genome sequencers gives the opportunity of learning more about the genetic make-up of human and other populations. One important question involves the location of sites at which variation occurs within a population. Our focus will be on the detection of rare variants. Such variants will often not be present in smaller samples and are hard to distinguish from sequencing errors in larger samples. This is particularly true for pooled samples which are often used as part of a cost saving strategy. The focus of this article is on experiments that involve DNA pooling. We derive experimental designs that optimize the power of statistical tests for detecting single nucleotide polymorphisms (SNPs, sites at which there is variation within a population). We also present a new simple test that calls a SNP, if the maximum number of reads of a prospective variant across lanes exceeds a certain threshold. The value of this threshold is defined according to the number of available lanes, the parameters of the genome sequencer and a specified probability of accepting that there is variation at a site when no variation is present. On the basis of this test, we derive pool sizes which are optimal for the detection of rare variants. This test is compared with a likelihood ratio test, which takes into account the number of reads of a prospective variant from all the lanes. It is shown that the threshold based rule achieves a comparable power to this likelihood ratio test and may well be a useful tool in determining near optimal pool sizes for the detection of rare alleles in practical applications.
Hepatoprotective and in vivo antioxidant activities of ethanolic extract of whole fruit of Lagenaria breviflora
Authors: Saba Adebowale B. , Onakoya Omowumi M. , Oyagbemi Ademola A. 
Published: September 2012

Abstract

Background: This study was designed to investigate the hepatoprotective and in vivo antioxidant effects of the ethanol extract of whole fruit of Lagenaria breviflora (LB) in experimental animals.

Methods: Forty nine Wistar albino rats were divided into seven groups of seven. Group I served as the control group; rats in Group II were given i.p. carbon tetrachloride (CCL4) (1.5 mL/kg) alone; Groups III–VI received different concentrations of plant extract (100, 250 and 500 mg/kg) with CCL4 and Group VII received kolaviron (KV) at 200 mg/kg as a reference hepatoprotective agent.

Results: There was a significant (p<0.05) increase in malondialdehyde (MDA) and hydrogen peroxide (H202) generation in the serum of CCL4 treated rats (Group II) while the serum glutathione (GSH) level decreased significantly. Pretreatment with LB extract led to a significant (p<0.05) increase in serum GSH and a significant (p<0.05) reduction in MDA and H2O2generation. The activities of marker enzymes, such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), bilirubin, creatinine and blood urea nitrogen (BUN) increased (p<0.05) significantly in CCL4 treated rats (Group II).

Conclusions: The present study suggested that treatment with LB extract enhances the recovery from CCL4 induced hepatic damage and oxidative stress via its antioxidant and hepatoprotective properties.
Implementation of Collaborative Software in Enterprises: A Thematic Analysis
Authors: Schubert Petra , Williams Susan P. 
Published: September 2012

Abstract
The article investigates 16 implementation projects (cases) of collaborative systems to identify structures, processes and activities associated with implementing change. Using an interpretive research process we apply thematic content analysis to the case documents to identify key themes in the introduction of collaborative technologies. The coding process yielded 184 individual codes which were grouped into 28 themes. These themes are discussed and the findings presented using the 8C Framework. The findings indicate a complex array of methods, processes and strategies for the management of change.
Vorhersage des Phasenrauschens in optischen Messsystemen mit strukturierter Beleuchtung
Authors: Fischer Marc , Petz Marcus , Tutsch Rainer 
Published: September 2012

Zusammenfassung
In dieser Arbeit wird eine Methode vorgestellt, mit der sich ein Schätzwert für das Phasenrauschen in optischen Messsystemen mit strukturierter Beleuchtung direkt aus den aufgezeichneten Grauwerten berechnen lässt. Das verwendete Rauschmodell basiert auf einer Richtlinie zur Charakterisierung von Bildsensoren (EMVA 1288), so dass die benötigten Parameter direkt einem konformen Datenblatt entnommen werden können. Alternativ wird in dieser Arbeit auch eine Methode beschrieben, mit der die Parameter ohne zusätzlichen Geräteaufwand experimentell ermittelt werden können.
Fundamental Investigation of the HER on a Pt(111) Surface at Temperatures down to 120K
Authors: Brülle Tine , Schneider Oliver , Stimming Ulrich 
Published: September 2012

Abstract
The hydrogen evolution reaction (HER) is of fundamental importance in electrochemistry, and despite the large number of theoretical and experimental investigations, it is still far from being completely understood. In the present work, the HER is studied on a Pt(111) surface in a wide range of temperatures down to 120 K. The overall reaction and the first reaction step, the Volmer reaction, were evaluated separately using potentiostatic pulses in order to obtain a detailed understanding of the different reaction steps. At room temperature, the Volmer reaction exhibits a Tafel slope of 120 mV/dec, which is the expected value for a single electron transfer. For the overall reaction a change in Tafel slope at -η ≈ 50 mV is found. While the Tafel slope is ≈ 30 mV/dec for small overpotentials, it is 120 mV/dec for larger overpotentials. For both the overall reaction and the Volmer reaction, a strong dependence of the apparent transfer coefficient on temperature is found. This temperature dependence cannot be explained using classical electron transfer theory.
The Bakken: Utilizing a Petroleum System Based Analysis to Optimally Exploit One of the World's Largest Oil Deposits
Authors: Alcoser L. , Ovalle A. , Parsons M. 
Published: September 2012

Abstract
This paper is a comprehensive literature survey and analysis of the Bakken Oil play, Williston Basin, which is one of the largest known oil accumulations in the world. This analysis includes; examining reservoir characterization and resource assessments, and evaluating project economics as well as current operators activities. These characteristics and assessments are then used to better understand and put context around the current drilling and completion best practices as well as water handling and operational constraints. The paper thoroughly analyzes the prolific Bakken petroleum system and describes the successful application of technologies and efficient operating practices that have enabled current Bakken production to increase to the cusp of the 500,000 BOPD mark.
The hydrocarbon charge comes from two very organic-rich shales, which have matured and expelled oil both into the fractured clastic layer that separates them and the fractured mixed clastics and carbonates that bound them above and below. Where the upper and lower Bakken shale members are both thick and mature, the middle member has high residual oil saturation and high fracture density. Although the natural fractures are well interconnected over large portions of the basin, the highest resource density occurs in areas with the highest fracture densities. Through rapid dynamic evolution and application of new horizontal drilling and multistage fracturing technologies, this prolific play has experienced a recent resurgence in activity. Today, operators are able to produce the Bakken at reported rates of up to 7,000 bopd, utilizing (typical) well designs consisting of horizontal wells with 10,000’ nominal lateral lengths, stimulated with 18–36+ fracture stimulation stages. Since 2000, Bakken activity has surged, with 1,946 horizontal wells completed between January 2000 and July 2010. Operators, from small private firms to large public multinationals, are continuing to invest heavily in the Bakken.
The continuation of this rapid pace of development has led to many challenges, including; water supply and handling challenges, increased infrastructure and human resource demands, and environmental sustainability. Nevertheless, the industry continues to rise to meet these challenges and is betting on continued Bakken success.
Rapid Work Flows for Accurately Determining Optimal Horizontal Well Spacing and Fracture Cluster Spacing
Authors: Buchwalter James L , Craig Mark , Wardlow Richard 
Published: September 2012

Abstract
This paper will discuss how accurate infill well development strategies for horizontal wells are efficiently developed using production and pressures from vertical discovery wells.
The work flow requires developing pattern* models for the vertical wells using best engineering assumptions for parameters, and then improving the reservoir description in the models using computer assisted history matching. The resulting rock properties are mapped between wells using a Kriging geostatistic algorithm. In the final step, different horizontal well locations and completion strategies are investigated to create an optimal well spacing and completion strategy. Close agreement between model production forecasts and recent horizontal well production and pressure records validates the accuracy of the approach.