bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conditioned media from cell lines: A complementary model to clinical specimens for the discovery of disease‐specific biomarkers
Authors: Dowling Paul , Clynes Martin 
Published: December 2010

AbstractIn the strictest sense, the cell secretome (conditioned media) refers to the collection of proteins that contain a signal peptide and are processed via the endoplasmic reticulum and Golgi apparatus through the classical secretion pathway. More generally, the secretome also encompasses proteins shed from the cell surface and intracellular proteins released through non‐classical secretion pathway or exosomes. These secreted proteins include numerous enzymes, growth factors, cytokines and hormones or other soluble mediators. They are fundamental in the processes of cell growth, differentiation, invasion and angiogenesis by regulating cell‐to‐cell and cell‐to‐extracellular matrix interactions. The main aim of this review is to provide a synopsis of findings from the analysis of the secretome taking diabetes, cancer and neurodegenerative diseases as examples. We will also discuss the preparation of conditioned media and on the main proteomic‐based methodological approaches that have been developed for the study of secreted/shed proteins.
Stimuli‐responsive polymers in the 21st century: Elaborated architecture to achieve high sensitivity, fast response, and robust behavior
Authors: Kirsebom Harald , Galaev Igor Yu. , Mattiasson Bo 
Published: December 2010

AbstractLife is polymeric in its essence. The living cell contains a range of biopolymers such as proteins, carbohydrates, and nucleic acids. The cells are often compartmentalized via membranes that are composed of lipids. These are small molecules, but they spontaneously aggregate into supermolecular structures. The building blocks of these lipids are among others fatty acids, structures built from methylene oligomers. Biopolymers are sensitive to external stimuli. There are examples where the molecules show a highly non‐linear response to external stimuli. This is seen as moderate changes in structural properties in response to changes in an external parameter until a critical point is reached where a dramatic change in molecular properties takes place upon an incremental change in the external conditions. After the transition, the system responds poorly to further changes. Such non‐linear responses contribute to dramatic cooperative conformational changes leading to strong effects in the biological system. The strong response is an integrated effect of many weak interactions, and it is the cooperativity between all these interactions that are the driving forces for processes occurring in such systems. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Effect of Mixing on the Pore Structure of Alumina Extrudates
Authors: Landers John , Devadas Mukundan , Neimark Alexander V. , Timken Hye‐Kyung , Ojo Adeola , Chester Arthur W. 
Published: December 2010

AbstractThe mixing conditions have a direct impact on the pore structure of alumina extrudates. We study the pore structure of samples prepared with two mixers: a standard Eirich mixer and a smaller yet more severe Fukae mixer, which operates at 1500 rpm. We present the development of a bimodal pore size distribution within the range of 25–150 Å produced by using the Fukae mixer. The pore structure consists of larger pores that grow at the expense of the smaller ones and can be tuned as a function of mixing time.
Oxidation of Nanometer‐Sized Titanium Nitride and Micrometer‐Sized Titanium Particles with Titanium Nitride Traces up to 1473 K in Air
Authors: Schulz Olga , Eisenreich Norbert , Fietzek Harald , Juez‐Lorenzo Maria del Mar , Kondratenko Evgenii 
Published: December 2010

AbstractThis study compares the oxidation behaviour of TiN particles (nanometer‐sized to micrometer‐sized) to titanium particles with traces of titanium nitride (micrometer‐sized) regarding the similarities of the formation of the products. These particles were investigated between 323 K and 1473 K in air using high‐temperature X‐ray diffraction, SEM, and the methods of thermal analysis (TG and DSC). The oxidation of the nanometer‐sized TiN particles forms anatase and rutile in two partially overlapping successive steps, whereas the anatase transforms completely to rutile at higher temperatures. The investigated titanium particles directly transform to rutile. Traces of TiN in titanium particles induce the formation of traces of anatase phase which similar to the oxidation of TiN particles transforms to rutile phase. A Jander model for three‐dimensional diffusion was utilized for describing the oxidation kinetics of the both oxidation steps occurring with TiN. A least squares fit procedure gives good agreement of the calculated curves to measured TG and DSC curves and adequate approximation to intensities of X‐ray measurements. The amount of TiN oxidized to anatase was found to be about 46 %. The kinetic parameters were determined: for the first step of TiN oxidation, the pre‐exponential factor was 1.33 · 106 μm2/s and the activation energy was 180.5 kJ/mol as well as for the second step 5.51 · 103 μm2/s and 197.6 kJ/mol, respectively.
Energy‐dependent collision‐induced dissociation study of buprenorphine and its synthetic precursors
Authors: Biri Bernadett , Kalmár József , Nagy Lajos , Sipos Attila , Zsuga Miklós , Kéki Sándor 
Published: December 2010

AbstractThe collision‐induced dissociation (CID) of protonated buprenorphine ([M+H]+) and four related compounds was studied by electrospray quadrupole/time‐of‐flight mass spectrometry (ESI‐QTOF MS). The fragmentation pathways were investigated by using energy‐dependent CID and pseudo‐MS3 (in‐source CID combined with tandem mass spectrometry (MS/MS)) methods. The first steps of the fragmentation are the parallel losses of the substituents from the non‐aromatic ring moieties. Depending on the applied collision energies, a large number of further fragment ions arising from the cross‐ring cleavages of the core‐ring structure were observed. Based on the experimental results, a generalized fragmentation scheme was developed for the five buprenorphine derivatives highlighting the differences for the alternatively substituted compounds. The collision‐energy‐dependent fragmentation profile of buprenorphine is visualized in a two‐dimensional plot to aid its fingerprint identification. Copyright © 2010 John Wiley & Sons, Ltd.
Identification of new minor metabolites of penicillin G in human serum by multiple‐stage tandem mass spectrometry
Authors: Ho Hsin‐Pin , Lee Ren‐Jye , Chen Chung‐Yu , Wang Soo‐Ray , Li Zu‐Guang , Lee Maw‐Rong 
Published: December 2010

AbstractLiquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) were applied to characterize drug metabolites. Although these two methods have overcome the identification and structural characterization of metabolites analysis, they remain time‐consuming processes. In this study, a novel multiple‐stage tandem mass spectrometric method (MSn) was evaluated for identification and characterization of new minor metabolism profiling of penicillin G, one of the β‐lactam antibiotics, in human serum. Seven minor metabolites including five phase I metabolites and two phase II metabolites of penicillin G were identified by using data‐dependent LC/MSn screening in one chromatographic run. The accuracy masses of seven identified metabolites of penicillin G were also confirmed by mass spectral calibration software (MassWorks™). The proposed data‐dependent LC/MSn method is a powerful tool to provide large amounts of the necessary structural information to characterize minor metabolite in metabolism profiling. Copyright © 2010 John Wiley & Sons, Ltd.
Non‐mass‐dependent 17O anomalies generated by a superimposed thermal gradient on a rarefied O2 gas in a closed system
Authors: Sun Tao , Bao Huiming 
Published: December 2010

AbstractCryogenic or heating methods have been widely used in experiments involving gas purification or isolation and in studying phase changes among solids, liquids, or gases for more than a century. Thermal gradients are often present in these routine processes. While stable isotopes of an element are known to fractionate under a thermal gradient, the largely diffusion‐driven fractionation is assumed to be entirely mass‐dependent. We report here, however, that distinct non‐mass‐dependent oxygen isotope fractionation can be generated when subjecting rarefied O2 gas in a closed system to a simple thermal gradient. The Δ17O value, a measure of the 17O anomaly, can be up to −0.51‰ (standard deviation (s.d.) 1σ = 0.03) in one of the temperature compartments. The magnitude of the 17O anomalies decreased with increasing initial gas pressures. The authenticity of this phenomenon is substantiated by a series of blank tests and isotope mass‐balance calculations. The observed anomalies are not the result of H2O contamination in samples or in isotope ratio mass spectrometry. Our finding calls attention to the importance of thermal gradient‐induced isotope fractionation and to its implications in laboratory procedures, stable isotope geochemistry, and the physical chemistry of rarefied gases. Copyright © 2010 John Wiley & Sons, Ltd.
Identification of prenylated pterocarpans and other isoflavonoids in Rhizopus spp. elicited soya bean seedlings by electrospray ionisation mass spectrometry
Authors: Simons Rudy , Vincken Jean‐Paul , Bohin Maxime C. , Kuijpers Tomas F.M. , Verbruggen Marian A. , Gruppen Harry 
Published: December 2010

AbstractPhytoalexins from soya are mainly characterised as prenylated pterocarpans, the glyceollins. Extracts of non‐soaked and soaked soya beans, as well as that of soya seedlings, grown in the presence of Rhizopus microsporus var. oryzae, were screened for the presence of prenylated flavonoids with a liquid chromatography/mass spectrometry (LC/MS)‐based screening method. The glyceollins I–III and glyceollidins I–II, belonging to the isoflavonoid subclass of the pterocarpans, were tentatively assigned. The formation of these prenylated pterocarpans was accompanied by that of other prenylated isoflavonoids of the subclasses of the isoflavones and the coumestans. It was estimated that approx. 40% of the total isoflavonoid content in Rhizopus‐challenged soya bean seedlings were prenylated pterocarpans, whereas 7% comprised prenylated isoflavones and prenylated coumestans. The site of prenylation (A‐ring or B‐ring) of the prenylated isoflavones was tentatively annotated using positive‐ion mode MS by comparing the 1,3A+ retro‐Diels‐Alder (RDA) fragments of prenylated and non‐prenylated isoflavones. Furthermore, the fragmentation pathways of the five pterocarpans in negative‐ion (NI) mode were proposed, which involved the cleavage of the C‐ring and/or D‐ring. The absence of the ring‐closed prenyl (pyran or furan) gave exclusively ‐H2Ox,yRDA fragments, whereas its presence gave predominantly the common RDA fragments. Copyright © 2010 John Wiley & Sons, Ltd.
High‐resolution excitation of ions in a low‐pressure linear ion trap
Authors: Collings B. A. 
Published: December 2010

AbstractAn exploration of the parameters necessary to obtain high‐resolution excitation, using dipolar excitation, of an ion in a linear ion trap has been undertaken in this study. These parameters included ion trap pressure, excitation amplitude, excitation period, drive frequency of the ion trap, Mathieu q value and the mass of the ion of interest. An understanding of how these parameters play a role in high‐resolution excitation is necessary to the development of a method for the targeted tandem mass spectrometric (MS/MS) analysis of ions with the same nominal mass. Resonance excitation profiles with full width half maxima as narrow as 0.015 m/z units could be obtained, under the right conditions, for an ion from a homogenously substituted triazatriphosphorine at m/z 322.049, which translates into a mass resolution of >21 500. In this particular case the requirement for high resolution was a low trap pressure (3.8 × 10−5 Torr), low excitation amplitude (3 mV), long excitation period (100 ms) and a high Mathieu q value(0.8) when using a drive frequency of 1.228 MHz. Similar conditions were used to demonstrate the isolation of individual [M + H]+ component ions from mixtures of bromazepam (m/z 316.008)/chlorprothixene (m/z 316.0921)/fendiline (m/z 316.206) and chlorprothixene (m/z 316.0921)/oxycodone (m/z 316.1543)/fendiline (m/z 316.206) prior to obtaining product ion spectra with excitation at q = 0.236. In the former mixture the individual components were isolated with near 100% efficiency while in the latter mixture the isolation efficiency dropped to near 50% for the oxycodone component and to 80% for the other components. Copyright © 2010 John Wiley & Sons, Ltd.
Pulse labeling of dissolved 13C‐carbonate into tree xylem: developing a new method to determine the fate of recently fixed photosynthate
Authors: Powers Elizabeth M. , Marshall John D. 
Published: December 2010

AbstractStable carbon isotopes are often employed as tracers in plant and soil systems to study the fate and transformations of carbon as is it assimilated by the forest canopies and then translocated into the soil matrix and soil microorganisms. This experiment tested a new method of 13C‐labeling. We dissolved 13C‐carbonate into 12 mL of water and injected it into the xylem of a 6‐cm diameter tree. The isotopic composition of foliage, stem CO2, and phloem contents were measured before the experiment and up to two weeks after the pulse label. Isotopic enrichments of 6.1‰ and 7.7‰ were observed in stem CO2 and phloem contents, respectively. No enrichment in bulk foliage was observed. The pulse came through the phloem five days after the label was injected, consistent with expectations based on transport rates through the tree. The application of this xylem pulse‐labeling method may provide new insights into labile carbon sequestration in trees, perhaps even in much larger trees. Furthermore, the method could be applied under experimental treatments that would elucidate the mechanisms controlling the fate and transformation of recently fixed photosynthate in forests. Copyright © 2010 John Wiley & Sons, Ltd.
A new permutation‐based method for assessing agreement between two observers making replicated binary readings
Authors: Pan Yi , Haber Michael , Barnhart Huiman X. 
Published: December 2010

AbstractA new coefficient for assessing agreement between two observers using a permutation‐based method is introduced in this article. When observations are binary, this coefficient compares the observed disagreement (probability of discordance) between the observers with its expected value under the hypothesis of individual equivalence. This hypothesis states that for each subject, the conditional distributions of the readings of the two observers are identical, and therefore from a statistical viewpoint it does not matter which observer makes the reading on this subject. Let K and L denote the numbers of replicated observations that are available from observers X and Y, respectively, on a given subject. Then the expected disagreement under individual equivalence for a subject is based on the (K + L) choosing K possible assignments of X's and Y's to the K + L observations made on this subject. Simple methods for the estimation of the new coefficient and its standard error are derived. The new coefficient is compared with kappa and the coefficient of individual agreement, which is based on comparing the inter and intra observer disagreements. Simulation studies confirm the validity of the estimated coefficient and its standard error. Data from a study involving the evaluation of mammograms by 10 radiologists are used to illustrate this new approach to the evaluation of observer agreement. Copyright © 2010 John Wiley & Sons, Ltd.
Effect of physicochemical properties of starch on the tendency of potato tuber flesh to darkening and the processed product quality
Authors: Pobereżny Jarosław 
Published: December 2010

AbstractThe aim of the present research was to determine whether, and to what extent, the selected potato starch quality parameters affect the tendency of potato tuber flesh to darkening and the value of thermal processing products. The research was carried out after harvest and after 6 months of tuber storage at the temperature of +8°C and relative air humidity of 95%. The research material was made up of three mid‐early potato cultivars: two Polish cultivars, ‘Lena’ and ‘Mors’, and ‘Agria’, a German cultivar. The research was carried out in three vegetation periods in Poland (the Kujawy and Pomorze region) and in Germany (Lower Saxony). The starch grain size, gel stability after defrosting and raw and cooked tuber flesh tendencies to darkening were significantly modified by the genetic factor, while neither the site nor the year of cultivation affected these characters significantly. As a result of tuber storage, genetic conditions affected the share of large grains (>60 µm) more considerably than the storage conditions and time; unlike the starch gel stability, since a high variation in this character depended on the site of cultivation and place of storage. The potato tuber storage time increases the degree of darkening and the tendency leads to the French fries and chips quality deterioration. The results of the present research clearly show that the fraction of starch grains >60 µm was significantly positively correlated with raw and cooked tuber flesh darkening, whereas fraction <40 µm was significantly negatively correlated with these potato tuber characters.
Granule structural, crystalline, and thermal changes in native Chinese yam starch after hydrolysis with two different enzymes–α‐amylase and gluco‐amylase
Authors: Li Xia , Gao Wenyuan , Wang Yanli , Jiang Qianqian , Huang Luqi 
Published: December 2010

AbstractStarch extracted from Chinese yam was characterized by scanning electron microscope (SEM), X‐ray powder diffractometer (XRD), and differential scanning calorimeter (DSC) in the process of enzymatic hydrolysis. Yam starch was digested by α‐amylase and gluco‐amylase for different lengths of time, respectively, and two different enzymatic hydrolysis results were compared. The most notable phenomenon revealed by SEM after α‐amylase hydrolysis was the formation of the cavum in the center of the starch granules, while after gluco‐amylase hydrolysis, the outer layer of the granules was peeled off and then some granules even broke into pieces. The XRD of the two enzyme hydrolyzed starches revealed the crystal type of the starch changed from typical C‐type XRD pattern to the representative A‐type pattern in the process of enzymatic hydrolysis. The above results also demonstrated that the partially B‐type polymorph was more easily degraded than A‐type. The thermal result showed that the modified yam starches by both enzymes exhibited increased peak gelatinization temperatures (Tp) and decreased gelatinization enthalpy (ΔH).
Item feature effects in evolution assessment
Authors: Nehm Ross H. , Ha Minsu 
Published: December 2010

AbstractDespite concerted efforts by science educators to understand patterns of evolutionary reasoning in science students and teachers, the vast majority of evolution education studies have failed to carefully consider or control for item feature effects in knowledge measurement. Our study explores whether robust contextualization patterns emerge within particular evolutionary reasoning contexts, and the implications of these patterns for instruction, assessment, and models of cognition. We test four hypotheses regarding item feature effects on undergraduate biology majors' evolutionary reasoning using a sample of 1,200 open response explanations of evolutionary change across items differing in context and scale but standardized by taxon and trait. Evolutionary explanations were atomized into a series of scientific and naïve biological elements and tallied among prompts and their features. We documented clear, significant, and predictable item feature effects on evolutionary explanations. Tasks involving evolutionary trait loss elicited a significantly greater number of naïve biological elements than evolutionary trait gain tasks in all contexts, including: within species comparisons, between species comparisons, animal prompts, and plant prompts. Tasks involving between species evolutionary comparisons, regardless of gain or loss, animal or plant, always produced significantly more naïve biological explanatory elements than within species comparisons. For items prompting explanation of trait gain, the use of the core concepts of natural selection were not influenced by the hierarchical level of the task (within or between species). Explanations of trait gain were also the least sensitive to scale and context. Core concepts of natural selection were always deployed less frequently in cases of evolutionary trait loss (within and between species, in animals and plants). We discuss a series of implications of these findings for curriculum, instruction, and assessment. © 2010 Wiley Periodicals, Inc., Inc. J Res Sci Teach 48: 237–256, 2011
Adenomyosis: three‐dimensional sonographic findings of the junctional zone and correlation with histology
Authors: Exacoustos C. , Brienza L. , Di Giovanni A. , Szabolcs B. , Romanini M. E. , Zupi E. , Arduini D. 
Published: December 2010

AbstractObjectiveTo correlate with histopathological features the adenomyosis‐induced morphological alterations of the outer myometrium and the inner myometrium (‘junctional zone’, JZ) detectable on two‐ (2D) and three‐dimensional (3D) transvaginal ultrasound imaging (TVS), and to evaluate their diagnostic accuracy for adenomyosis.MethodsPremenopausal patients scheduled for hysterectomy for benign pathology were enrolled in this prospective study. Before hysterectomy all patients underwent detailed 2D‐TVS and 3D volume acquisition of the entire uterus. The major sonographic signs of adenomyosis were noted. On the multiplanar coronal and longitudinal views obtained by 3D‐TVS we measured the maximum and minimum JZ thickness from the basal endometrium to the internal layer of the outer myometrium (JZmax, JZmin), the difference between them (JZdif = JZmax − JZmin) and the ratio JZmax/total maximum myometrial thickness. Results of these examinations were correlated blindly to the presence of adenomyosis on histological specimens.ResultsA total of 72 premenopausal patients underwent 2D‐ and 3D‐TVS before hysterectomy. The histological prevalence of adenomyosis was 44.4% (32/72 patients). In diagnosing adenomyosis, the presence of myometrial cysts was the most specific 2D‐TVS feature (specificity, 98%; accuracy, 78%) and heterogeneous myometrium was the most sensitive (sensitivity, 88%; accuracy, 75%). The 3D‐TVS markers JZdif ≥ 4 mm and JZ infiltration and distortion had high sensitivity (88%) and the best accuracy (85% and 82%, respectively). For 2D‐TVS and 3D‐TVS, respectively, the overall accuracy for diagnosis of adenomyosis was 83% and 89%, the sensitivity was 75% and 91%, the specificity was 90% and 88%, the positive predictive value was 86% and 85% and the negative predictive value was 82% and 92%.ConclusionsThe coronal section of the uterus obtained by 3D‐TVS permits accurate evaluation and measurement of the JZ, and its alteration has good diagnostic accuracy for adenomyosis. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.