bluuebunny/crossref_metadata_2025_split huggingface dataset:
The detection, correlation, and comparison of peptide precursor and product ions from data independent LC‐MS with data dependant LC‐MS/MS
Authors: Geromanos Scott J. , Vissers Johannes P. C. , Silva Jeffrey C. , Dorschel Craig A. , Li Guo‐Zhong , Gorenstein Marc V. , Bateman Robert H. , Langridge James I. 
Published: March 2009

AbstractThe detection, correlation, and comparison of peptide and product ions from a data independent LC‐MS acquisition strategy with data dependent LC‐MS/MS is described. The data independent mode of acquisition differs from an LC‐MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan‐to‐scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge‐state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC‐MS/MS and data‐independent, alternate scanning LC‐MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data‐independent LC‐MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC‐MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC‐MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC‐MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time‐aligned data from data‐independent alternate scanning LC‐MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor‐product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.
Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures
Authors: Li Guo‐Zhong , Vissers Johannes P. C. , Silva Jeffrey C. , Golick Dan , Gorenstein Marc V. , Geromanos Scott J. 
Published: March 2009

AbstractA novel database search algorithm is presented for the qualitative identification of proteins over a wide dynamic range, both in simple and complex biological samples. The algorithm has been designed for the analysis of data originating from data independent acquisitions, whereby multiple precursor ions are fragmented simultaneously. Measurements used by the algorithm include retention time, ion intensities, charge state, and accurate masses on both precursor and product ions from LC‐MS data. The search algorithm uses an iterative process whereby each iteration incrementally increases the selectivity, specificity, and sensitivity of the overall strategy. Increased specificity is obtained by utilizing a subset database search approach, whereby for each subsequent stage of the search, only those peptides from securely identified proteins are queried. Tentative peptide and protein identifications are ranked and scored by their relative correlation to a number of models of known and empirically derived physicochemical attributes of proteins and peptides. In addition, the algorithm utilizes decoy database techniques for automatically determining the false positive identification rates. The search algorithm has been tested by comparing the search results from a four‐protein mixture, the same four‐protein mixture spiked into a complex biological background, and a variety of other “system” type protein digest mixtures. The method was validated independently by data dependent methods, while concurrently relying on replication and selectivity. Comparisons were also performed with other commercially and publicly available peptide fragmentation search algorithms. The presented results demonstrate the ability to correctly identify peptides and proteins from data independent acquisition strategies with high sensitivity and specificity. They also illustrate a more comprehensive analysis of the samples studied; providing approximately 20% more protein identifications, compared to a more conventional data directed approach using the same identification criteria, with a concurrent increase in both sequence coverage and the number of modified peptides.
Proteome wide screening using peptide affinity capture
Authors: Poetz Oliver , Hoeppe Sibylle , Templin Markus F. , Stoll Dieter , Joos Thomas O. 
Published: March 2009

AbstractMS‐based strategies are key technologies for identifying proteins in proteomic research. Despite significant improvements in recent years efficient fractionation processes of target analytes remain major bottlenecks in MS‐based protein analysis. Immunoaffinity‐based sample fractionation strategies have shown their potential for the enrichment of analyte peptides of interest, but only small numbers of analytes can be quantified in one experiment. The lack of appropriate capture reagents limits the application of immunoaffinity‐based approaches and only biased biomarker discovery approaches are possible. This perspective discusses the current status of immunoaffinity MS‐based approaches and introduces a novel concept that uses group specific anti‐peptide antibodies – Triple X Proteomics Antibodies – for the enrichment of signature peptides. Classes of peptides with identical termini can be fractionated based on TXP immunoaffinity enrichment steps and can subsequently be identified using established tandem MS procedures. Based on bioinformatic algorithms minimal sets of TXP epitopes can be specified, that cover a wide range of given proteome landscapes of one or even several different species. This opens the possibility to use a minimal number of TXP antibodies as a universal toolbox for general immunoaffinity‐based approaches in proteome analysis.
Structure Retention and Water Stability of Microwave Plasma Polymerized Films From Allylamine and Acrylic Acid
Authors: Finke Birgit , Schröder Karsten , Ohl Andreas 
Published: March 2009

AbstractLow‐pressure downstream microwave plasma was used to deposit thin water resistant PPAAm and PPAAc films on titanium substrates. Film stability against dissolution was tested under sonication in ultrapure water. Variation of duty cycle on mean power was applied to evaluate the sensitivity of film properties on plasma conditions. Strong cross‐linked and therewith water resistant PPAAm and PPAAc films correlate with a relatively low but for biomedical applications sufficient density of functional groups. Furthermore, some similarity exists between process parameter and dissolution stability of deposited plasma polymer films prepared by microwave and reported for radio frequency plasmas.
Non‐invasive biomarker sampling and analysis of the exhaled breath proteome
Authors: Bloemen Karolien , Hooyberghs Jef , Desager Kristine , Witters Erwin , Schoeters Greet 
Published: March 2009

AbstractExhaled breath condensate (EBC) is a biological fluid that contains trace amounts of secreted pulmonary proteins, and is emerging as a potentially valuable and non‐invasively obtained source of disease biomarkers. Proteome analysis of these samples could lead to the identification of prognostic indicators of airway diseases. The objective of this study was to develop a protocol for proteome analysis of EBC samples. In this report, an improved procedure for EBC sample preparation and concentration is presented, together with a method for comparison of the protein profiles between two groups. The presented approach enabled to study the condensed exhaled breath proteome for biomarker analysis, and revealed proteins not previously identified in an EBC proteomics approach. In a comparative pilot study, EBC protein profiles obtained from smokers and non‐smokers showed distinct differences and are illustrative for its potential in clinical studies. EBC from smokers contained higher concentrations of the more abundant proteins, such as cytokeratins, compared to non‐smokers, and calgranulin B was identified uniquely in EBC samples from smokers.
Molecular beam epitaxial growth of ZnCrO films by using RF plasma source
Authors: Yoneta Minoru , Satou Yuichi , Shintani Motoyuki , Ii Masakazu , Yoshino Kenji , Honda Makoto , Ohishi Masakazu 
Published: March 2009

AbstractThe transition‐metal chromium‐doped zinc oxide, ZnCrO, was successfully grown on an a ‐sapphire (11$ \bar 2 $0) substrate by radio frequency‐plasma‐assisted molecular beam epitaxy. The growth and optical property of ZnCrO were investigated. The growth mode changed from a 2‐dimensional one to a 3‐dimensional one with Cr doping. The ZnCrO films showed a textured morphology and the surface roughness of each was clearly reduced by increasing the amount of Cr doping.The X‐ray diffraction peak intensity from ZnO (0002) became smaller as the Cr cell temperature was increased. A photoluminescence spectrum of ZnCrO was dominated by an excitonic peak around 3.36 eV. The transmission spectra showed that light wavelength shorter than 3.26 eV was removed. This was caused by Cr doping, and its losses caused by Cr doping. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Safety of ultrasonography in pregnancy: WHO systematic review of the literature and meta‐analysis
Authors: Torloni M. R. , Vedmedovska N. , Merialdi M. , Betrán A. P. , Allen T. , González R. , Platt L. D. 
Published: March 2009

AbstractObjectiveIn the context of the planned International Society of Ultrasound in Obstetrics and Gynecology–World Health Organization multicenter study for the development of fetal growth standards for international application, we conducted a systematic review and meta‐analysis to evaluate the safety of human exposure to ultrasonography in pregnancy.MethodsA systematic search of electronic databases, reference lists and unpublished literature was conducted for trials and observational studies that assessed short‐ and long‐term effects of exposure to ultrasonography, involving women and their fetuses exposed to ultrasonography, using B‐mode or Doppler sonography during any period of pregnancy, for any number of times. The outcome measures were: (1) adverse maternal outcome; (2) adverse perinatal outcome; (3) abnormal childhood growth and neurological development; (4) non‐right handedness; (5) childhood malignancy; and (6) intellectual performance and mental disease.ResultsThe electronic search identified 6716 citations, and 19 were identified from secondary sources. A total of 61 publications reporting data from 41 different studies were included: 16 controlled trials, 13 cohort and 12 case–control studies. Ultrasonography in pregnancy was not associated with adverse maternal or perinatal outcome, impaired physical or neurological development, increased risk for malignancy in childhood, subnormal intellectual performance or mental diseases. According to the available clinical trials, there was a weak association between exposure to ultrasonography and non‐right handedness in boys (odds ratio 1.26; 95% CI, 1.03–1.54).ConclusionAccording to the available evidence, exposure to diagnostic ultrasonography during pregnancy appears to be safe. Copyright © World Health Organization (2009).
The First Structure with Isolated Carbon‐Centered Tetrahedra of Rare‐Earth Metals – the New Compound Ce4CCl8
Authors: Schaloske Manuel C. , Kienle Lorenz , Hoch Constantin , Mattausch Hansjürgen , Kremer Reinhard K. , Simon Arndt 
Published: March 2009

AbstractCe4CCl8 is prepared by heating stoichiometric mixtures of cerium, CeCl3 and carbon in sealed tantalum capsules at 820 °C. It forms black polyhedral, in fragments transparent orange to red and moisture‐sensitive crystals [space group Pc, a = 13.538(1) Å, b = 10.487(1) Å, c = 22.845(1) Å, β = 126.31(1)°]. The crystal structure contains C‐centered Ce4C single tetrahedra, linked by chlorine atoms above edges and corners in different ways. The compound is further characterized by HRTEM, electron‐diffraction investigations and magnetic measurements.
Clinical Improvement After Duodenojejunal Bypass for Nonobese Type 2 Diabetes Despite Minimal Improvement in Glycemic Homeostasis
Authors: Ferzli G. S. , Dominique E. , Ciaglia M. , Bluth M. H. , Gonzalez A. , Fingerhut A. 
Published: March 2009

AbstractBackgroundGlycemic control of type 2 diabetes mellitus (T2DM) remains a dilemma to physicians. Although gastric bypass surgery undertaken for morbid obesity has been shown to resolve this disease well, data on the effectiveness of duodenojejunal bypass in improving or resolving T2DM and the metabolic syndrome (MS), especially in nonobese patients are scarce. This study was intended to evaluate the clinical effects of laparoscopic duodenojejunal bypass (LDJB) in patients with T2DM and a body mass index of <35 kg/m2.MethodsWe conducted a 12‐month prospective study on the changes in glucose homeostasis and the MS in seven T2DM subjects undergoing LDJB with similar DM duration, type of DM treatment, and glycemic control. Laboratory values including glycosylated hemoglobin A (HbA1c), fasting blood glucose, cholesterol, triglyceride, and C‐peptide were followed throughout the 12 months. Serum levels of gastric inhibitory peptide and ghrelin were followed for 1 month. Serum levels of gastrin and glucagon‐like peptide were followed for 3 months.ResultsAt 12 months after surgery, all subjects consistently felt relief from fatigue, pain and/or numbness in the extremities, polyuria, and polydypsia. Clinical resolution was obtained for one patient, and the preoperative diabetic medication requirements decreased for most of the other patients. The subjects demonstrated an overall improved HbA1c (from 9.4% to 8.5%) and fasting blood glucose level (from 209 to 154 mg/dl). Although the change in fasting blood glucose approached statistical significance, these measures of glucose homeostasis did not achieve significance. Cholesterol and triglycerides increased slightly, and C‐peptide decreased slightly over 1 year. These changes were not statistically significant.ConclusionsAlthough this is a small series, our data show that at 12 months after surgery, clinical improvement was obvious in all of our seven patients, but LDJB may not be effective at inducing remission of T2DM and the MS in certain patients undergoing this operation. This suggests that larger patient studies should be conducted, before concluding that surgery may offer clinical and biochemical resolution to a disease once treated only medically. Longer follow‐up is required for better evaluation.
Effects of Land Mines and Unexploded Ordnance on the Pediatric Population and Comparison with Adults in Rural Cambodia
Authors: Bendinelli Cino 
Published: March 2009

AbstractBackgroundThis paper was designed to evaluate and compare the impact of explosive war remnants on children versus adults in rural Cambodia.MethodsA prospective review of trauma database from November 2003 to January 2006 of the Civilian War Victims Surgical Centre in Battambang, Cambodia, run by an Italian NGO called “EMERGENCY” was performed. Age, female ratio, time of evacuation, type of ordnance, pattern of injury, number of operations, transfused patients, hospitalization, mortality, and residual disability were registered and compared.ResultsA total of 356 patients acutely wounded by antipersonnel land mines, antitank land mines, or unexploded ordnances (UXO) were admitted. Among these, 94 (26.4%) were children (younger than aged 16 years). Females were more common among children than adults (31.9% vs. 11.8%); 61.7% of children were injured by UXO, whereas 72.1% of adults were victims of antipersonnel land mines. Antitank mines victims were uncommon in both groups. The majority of adults (49.2%) were injured to lower limbs, whereas 50% of children were injured to upper limbs, face, and torso. Random wounds, typical of an explosion in vicinity, were observed in 32.9% of children and 18.7% of adults. All differences were statistically significant (P < 0.005). Time of evacuation, number of operations, and hospitalization did not statistically differ among groups. Number of transfused patients (23% vs. 7.2%), mortality (6.3% vs. 1.5%), incidence of blindness (21.2% vs. 9.5%), and maimed upper limbs (23.3% vs. 8.8%) were significantly higher in children compared with adults (P < 0.05).ConclusionsLong after ceasefire, antitank mines, antipersonnel land mines, and UXO continue to injure and kill civilians. Children are commonly injured and sustain more severe injuries.
The Combined Role of Ultrasound and Frozen Section in Surgical Management of Thyroid Nodules Read as Suspicious for Papillary Thyroid Carcinoma on Fine Needle Aspiration Biopsy: A Retrospective Study
Authors: Moon Hee Jung , Kwak Jin Young , Kim Eun‐Kyung , Kim Min Jung , Park Cheong Soo , Chung Woung Youn , Son Eun Ju 
Published: March 2009

AbstractBackgroundThe purpose of this study was to evaluate the combined role of ultrasound (US) and frozen section (FS) in the surgical management of thyroid nodules that are suspicious for papillary thyroid carcinoma (PTC) on US‐guided fine‐needle aspiration biopsy (US‐FNAB).MethodsBetween 2006 and 2008, 217 patients with thyroid nodules classified as suspicious for PTC on US‐FNAB underwent intraoperative FS and surgery. A thyroid nodule with any suspicious US findings of marked hypoechogenicity, microlobulated or irregular margins, microcalcifications, or taller than wider in shape was defined as positive and that without was defined as negative. FSs were classified as malignant, indeterminate, defer, and benign. We compared the results of US groupings, FS, and final histopathologic diagnosis.ResultsTwenty‐one (52.5%) of 40 patients with a negative US revealed malignancy. In contrast, 168 (94.9%) of 177 patients with a positive US had malignancy. Fourteen (50%) of 28 patients with benign pathology on FS had malignancy, and 166 (97.6%) of 170 patients with malignancy on FS proved malignancy on histopathology. Of 40 patients with negative US, 13 (92.9%) of 14 with malignancy on FS proved malignancy.ConclusionsThe malignancy rate of thyroid nodules read as “suspicious for PTC” on US‐FNAB was 87.1%. When a thyroid nodule with “suspicious for PTC” on US‐FNAB has suspicious malignant US features, FS may be unnecessary due to a very high risk of malignancy (94.9%). In contrast, when a thyroid nodule read as “suspicious for PTC” on US‐FNAB has no suspicious malignant US features, FS can help surgeons determine the extent of surgery.
Investigation of the Lymphatic Stream of the Stomach in Gastric Cancer with Solitary Lymph Node Metastasis
Authors: Tokunaga Masanori , Ohyama Shigekazu , Hiki Naoki , Fukunaga Tetsu , Yamada Kazuhiko , Sano Takeshi , Yamaguchi Toshiharu 
Published: March 2009

AbstractBackgroundUnderstanding the lymphatic drainage route in gastric cancer is crucial for complete lymph node retrieval from sites susceptible to metastasis. However, the lymphatic stream of the stomach is complex and remains incompletely characterized.MethodsPatients with small (<4 cm) serosa‐negative gastric cancer with solitary lymph node metastasis treated at the Cancer Institute Hospital were included in this study. A total of 135 patients were classified according to the location of the solitary lymph node metastasis into the left gastric artery (LGA) group, the right gastroepiploic artery (RGEA) group, the right gastric artery (RGA) group, or the splenic artery (SA) group. The location of the primary tumors was investigated to aid the mapping of the lymphatic stream of the stomach.ResultsLymphatic flow in LGA (65 patients) and in RGEA (57 patients) are main lymphatic drainage routes of the stomach. The lymphatic area overlapped in the lower third of the stomach in LGA and RGEA, and the lymphatic flow associated with gastric cancer located within this overlapped area can be multidirectional. Skip metastases were observed in 13 patients (10%), and all skip metastases were observed in the suprapancreatic area (station 7, 8a, 9, or 11p).ConclusionsThe lymphatic stream of the stomach is complicated and multidirectional. Understanding and mapping the complex lymphatic streams of the stomach will allow surgeons to perform more effective lymph node dissection during gastric cancer surgery.
Using the Identity Processing Style Q‐Sort to examine identity styles of Turkish young adults
Authors: Eryigit Suna , Kerpelman Jennifer 
Published: March 2009

ABSTRACTThis paper reports on two studies with Turkish young adults that used the Turkish version of the Identity Processing Style Q‐Sort (IPSQ). The IPSQ is based on Berzonsky's informational, normative, and diffused identity styles. Participants sort descriptors of the styles into columns ranging from most to least like them. Patterns in Turkish young adults’ identity styles were examined in the first study. The construct validity of the IPSQ‐Turkish version based on associations between the IPSQ and measures of cultural orientation, self‐definitions, self‐concept clarity, self‐esteem, and coping was tested in the second study. Results of the first study were consistent with the current literature in terms of a negative correlation between informational and diffuse/avoidant styles, and a relatively weaker relationship between informational and normative styles. Support for the construct validity of the Turkish version of the IPSQ was found in the second study, with results consistent with other IPSQ research.
Overexpression of E2F‐1 inhibits progression of gastric cancer in vitro
Authors: Xie Yubo , Wang Changqing , Li Lei , Ma Yulin , Yin Yongshuo , Xiao Qiang 
Published: March 2009

AbstractE2F‐1 plays a critical role in cell cycle regulation and other biological processes in cells. E2F‐1 mediates apoptosis and suppresses tumorigenesis in many tissue types, but there are few data available on E2F‐1 expression and its relationship to tumor kinetics in gastric cancer. To gain better insight into the involvement of E2F‐1 in the biological characteristics of gastric tumors, we investigated the effect of E2F‐1 overexpression on the progression of gastric carcinoma cells. A gastric cancer cell line stably overexpressing E2F‐1 (MGC‐803/E2F‐1) was established. The influence of E2F‐1 overexpression on in vitro cell growth was assessed by measuring cell survival, colony formation, and cell cycle progression. The results clearly show that overexpression of E2F‐1 significantly inhibits cell growth and proliferation, blocking entry into the S‐phase of the cell cycle. MGC‐803/E2F‐1 cells also had a higher apoptotic rate than control cells. In addition, E2F‐1 reduced the motility and invasion of gastric cancer cells.