bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR‐1 using LC‐MS based proteomics
Authors: Elias Dwayne A. , Monroe Matthew E. , Marshall Matthew J. , Romine Margaret F. , Belieav Alexander S. , Fredrickson James K. , Anderson Gordon A. , Smith Richard D. , Lipton Mary S. 
Published: July 2005

AbstractThe availability of whole genome sequences has enabled the application of powerful tools for assaying global expression patterns in environmentally relevant bacteria such as Shewanella oneidensis MR‐1. A large number of genes in prokaryote genomes, including MR‐1, have been annotated as hypothetical, indicating that no similar protein has yet been identified in other organisms. Using high‐sensitivity MS coupled with accurate mass and time (AMT) tag methodology, 1078 tryptic peptides were collectively detected in MR‐1 cultures, 671 of which were unique to their parent protein. Using only these unique tryptic peptides and a minimum of two peptides per protein, we identified, with high confidence, the expression of 258 hypothetical proteins. These proteins ranged from 3.5 to 139 kDa, with 47 being 100 amino acid residues or less. Using a combination of information including detection in cells grown under specific culture conditions, presence within a specific cell fraction, and predictive algorithms such as PSORT and PSORT‐B, possible/plausible functions are proposed for some hypothetical proteins. Further, by applying this approach a number of proteins were found not only to be expressed, but only expressed under certain culturing conditions, thereby suggesting function while at the same time isolating several proteins to distinct locales of the cell. These results demonstrate the utility of the AMT tag methodology for comprehensive profiling of the microbial proteome while confirming the expression of a large number of hypothetical genes.
Proteome profiling of interleukin‐12 treated human T helper cells
Authors: Rosengren Arsi T. , Nyman Tuula A. , Lahesmaa Riitta 
Published: July 2005

AbstractSelective activation of T helper subsets 1 (Th1) and 2 (Th2) plays a crucial role in different pathological conditions. Th1 cell response is involved in pathogenesis of autoimmune diseases, such as type II diabetes and multiple sclerosis, and Th2 cell response in pathogenesis of allergy and asthma. Cytokine interleukin‐12 (IL‐12) is one of the key factors in the differentiation of naïve CD4+ T cells into Th1 cells. In this study we used 2‐DE and MS to find and identify IL‐12 regulated proteins in human CD4+ T cells. In total, 42 protein spots were found to be differentially expressed following IL‐12 stimulation, of which 22 were up‐ and 20 down‐regulated. Among the upregulated proteins there are a multifunctional cytokine macrophage migration inhibitory factor and a known IL‐12 target gene Programmed cell death 4. Downregulated proteins include p21‐activated kinase 2 and its upstream GTPase Cdc42. Compared to previous reports our analysis provides a new view on the IL‐12 induced changes on CD4+ T cells underscoring the importance of creating and combining the data generated at various levels to build a comprehensive view of a given biological process of the cell.
Peptidomic analysis of human blood specimens: Comparison between plasma specimens and serum by differential peptide display
Authors: Tammen Harald , Schulte Imke , Hess Rudiger , Menzel Christoph , Kellmann Markus , Mohring Thomas , Schulz‐Knappe Peter 
Published: July 2005

AbstractThe human Plasma Proteome Project pilot phase aims to analyze serum and plasma specimens to elucidate specimen characteristics by various proteomic techniques to ensure sufficient sample quality for the HUPO main phase. We used our proprietary peptidomics technologies to analyze the samples distributed by HUPO. Peptidomics summarizes technologies for visualization, quantitation, and identification of the low‐molecular‐weight proteome (<15 kDa), the “peptidome.” We analyzed all four HUPO specimens (EDTA plasma, citrate plasma, heparin plasma, and serum) from African‐ and Asian‐American donors and compared them to in‐house collected Caucasian specimens. One main finding focuses on the most suitable method of plasma specimen collection. Gentle platelet removal from plasma samples is beneficial for improved specificity. Platelet contamination or activation of platelets by low temperature prior to their removal leads to distinct and multiple peptide signals in plasma samples. Two different specimen collection protocols for platelet‐poor plasma are recommended. Further emphasis is placed on the differences between plasma and serum on a peptidomic level. A large number of peptides, many of them in rather high abundance, are only present in serum and not detectable in plasma. This ex vivo generation of multiple peptides hampers discovery efforts and is caused by a variety of factors: the release of platelet‐derived peptides, other peptides derived from cellular components or the clot, enzymatic activities of coagulation cascades, and other proteases. We conclude that specimen collection is a crucial step for successful peptide biomarker discovery in human blood samples. For analysis of the low‐molecular‐weight proteome, we recommend the use of platelet‐depleted EDTA or citrate plasma.
Plasma Proteome Database as a resource for proteomics research
Authors: Muthusamy Babylakshmi , Hanumanthu G. , Suresh Shubha , Rekha B. , Srinivas D. , Karthick L. , Vrushabendra B. M. , Sharma Salil , Mishra Goparani , Chatterjee Pritam , Mangala K. S. , Shivashankar H. N. , Chandrika K. N. , Deshpande Nandan , Suresh M. , Kannabiran N. , Niranjan Vidya , Nalli Anuradha , Prasad T. S. Keshava , Arun K. S. , Reddy Raghunath , Chandran Sreenath , Jadhav Trafina , Julie D. , Mahesh M. , John S. Lynate , Palvankar Kshitish , Sudhir D. , Bala P. , Rashmi N. S. , Vishnupriya G. , Dhar Kaushik , Reshma S. , Chaerkady Raghothama , Gandhi T. K. B. , Harsha H. C. , Mohan S. Sujatha , Deshpande Krishna S. , Sarker Malabika , Pandey Akhilesh 
Published: July 2005

AbstractPlasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778 distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein‐coding regions were mapped onto the protein sequences. We found a number of examples of isoform‐specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org.
Recent advances in blood‐related proteomics
Authors: Thadikkaran Lynne , Siegenthaler Michèle A. , Crettaz David , Queloz Pierre‐Alain , Schneider Philippe , Tissot Jean‐Daniel 
Published: July 2005

AbstractBlood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.
Toward the development of new medicinal leads with selectivity for protein kinase C isozymes
Authors: Irie Kazuhiro , Nakagawa Yu , Ohigashi Hajime 
Published: July 2005

AbstractTumor promoters such as phorbol esters bind strongly to protein kinase C (PKC) isozymes to induce their activation. Since each PKC isozyme is involved in diverse biological events in addition to tumor promotion, the isozymes serve as promising therapeutic targets. Tumor promoters bind to the C1A and/or C1B domain of conventional (α, βI, βII, and γ) and novel PKC isozymes (δ, ε, η, and θ). As these C1 domains play differential roles in PKC activation and their translocation in cells, the development of agents with binding selectivity for individual C1 domains is a pressing need. For this purpose, we established a synthetic C1 peptide library of all PKC isozymes. The library enabled us to identify indolactam‐V (1) as a promising lead compound. Our diverse structure–activity studies on1indicated that the position of the hydrophobic substituent on the indole ring dominates the PKC isozyme‐ and C1 domain‐selective binding rather than conformation of the nine‐membered lactam. Moreover, we suggested that the indole ring of1could be involved in the CH/π interaction with Pro‐11 of the C1B domain of PKCδ. This invaluable information will lead to the structural optimization of the PKCδ ligand as exemplified by the design and synthesis of naphtholactam‐V8 (21). © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 185–195; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20044
Natural products as tools for studies of ligand‐gated ion channels
Authors: Strømgaard Kristian 
Published: July 2005

AbstractLigand‐gated ion channels, or ionotropic receptors, constitute a group of membrane‐bound proteins that regulate the flux of ions across the cell membrane. In the brain, ligand‐gated ion channels mediate fast neurotransmission. They are crucial for normal brain function and involved in many diseases in the brain. Historically, natural products have been used extensively in biomedical studies and ultimately as drugs or leads for drug design. In studies of ligand‐gated ion channels, natural products have been essential for the understanding of their structure and function. In the following a short survey of natural products and their use in studies of ligand‐gated ion channels is given. © 2005 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 5: 229–239; 2005: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20048
Neonatal outcome of antenatally diagnosed congenital cystic adenomatoid malformations
Authors: Ierullo A. M. , Ganapathy R. , Crowley S. , Craxford L. , Bhide A. , Thilaganathan B. 
Published: July 2005

AbstractObjectiveTo investigate the natural history and outcome of antenatally diagnosed congenital cystic adenomatoid malformation (CCAM) of the lung.MethodsThis was a retrospective study of all cases of fetal CCAM of the lung diagnosed antenatally. All cases were referred to a tertiary center for further management. A computer search identified all referred cases, and the records of these patients were examined to determine the pregnancy outcome.ResultsIn a 4‐year period, 34 cases of fetal CCAM were referred for further management. At presentation, all the cases were noted to be unilateral CCAMs and the majority (79%) were microcystic in nature. The CCAMs were complicated by varying degrees of mediastinal shift (79%) and hydrops fetalis (18%). During the course of the pregnancy, the lung lesion was seen to reduce in size or resolve spontaneously in 76% of cases without any prenatal intervention (including resolution of hydrops in three cases). The overall survival rate into infancy was 88%. One pregnancy was terminated for persisting hydrops fetalis and another resulted in infant death from complications of neonatal cardiac surgery for an associated aortic coarctation.ConclusionThe outcome of antenatally detected CCAM is much better than previously reported even when complicated by hydrops fetalis at presentation. The latter seems to be related to the high spontaneous regression rate of this tumor. Despite the antenatal resolution of CCAMs on ultrasound, postnatal follow‐up is recommended in view of the long‐term complications of this malformation. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
How to identify twins at low risk of spontaneous preterm delivery
Authors: Sperling L. , Kiil C. , Larsen L. U. , Qvist I. , Bach D. , Wøjdemann K. , Bladh A. , Nikkilä A. , Jørgensen C. , Skajaa K. , Bang J. , Tabor A. 
Published: July 2005

AbstractObjectiveThe aim of this study was to evaluate transvaginal sonographic assessment of cervical length at 23 weeks as a screening test for spontaneous preterm delivery in order to define a cut‐off value that could be used to select twin pregnancies at low risk of spontaneous preterm delivery.MethodsIn a prospective multicenter study of 383 twin pregnancies included before 14 + 6 weeks a cervical scan with measurement of the cervical length was performed at 23 weeks' gestation. The results were blinded for the clinicians if the cervical length was ≥ 15 mm. The rates of spontaneous delivery at different cut‐off levels of cervical length were determined.ResultsEighty‐nine percent of the twins had dichorionic placentation and 58% were conceived after assisted reproduction. The rate of spontaneous preterm delivery was 2.3% (1.5% for dichorionic (DC) and 9.1% for (MC) monochorionic twins) before 28 weeks and 18.5% (17.1% for DC and 29.5% for MC twins) before 35 weeks. The screen‐positive rate was 5% for a cervical length ≤ 20, 7–8% at ≤ 25, 16–17% at ≤ 30 and 34–48% at ≤ 35 mm depending on chorionicity. The false‐negative rate (1 − negative predictive value) ranged from 1.2% at 28 weeks to 18.6% at 35 weeks for all twins. Receiver–operating characteristics curves showed that the sensitivity increased with declining gestational age with cut‐off levels of highest accuracy at 21 mm for 28 weeks and 29 mm for 33 weeks.ConclusionsCervical length measurement at 23 weeks of gestation is a good screening test for predicting twins at low risk of preterm and very preterm delivery, especially in DC twins. The present results suggest that a cut‐off of 25 mm should be recommended. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Third‐trimester ultrasound dating algorithms derived from pregnancies conceived with artificial reproductive techniques
Authors: Mongelli M. , Chew S. , Yuxin N. G. , Biswas A. 
Published: July 2005

AbstractObjectiveTo derive an accurate formula for ultrasound estimation of gestational age in late pregnancy.MethodsA database of 123 singleton pregnancies conceived by artificial reproductive techniques with third‐trimester ultrasound measurements was studied. Biometry variables included the fetal head circumference (HC) and femur length (FL). The dataset was equally divided into a derivation sample and a target sample. To derive the equations of best fit, regression analysis was used, with true menstrual age as the dependent variable and fetal biometry measurements as independent variables. The formulae were tested on the target set and the menstrual age estimates were compared with the actual menstrual age. Clinical performance was estimated in terms of systematic and random errors, absolute errors and their 95% CI values.ResultsThe menstrual ages at time of scanning ranged from 26 to 41 weeks, with a mean of 33 weeks. The best performing derived formula was a combination of HC and FL. This had a random error of 7.5 days and prediction errors within a 95% confidence limit of −13 to +17 days. With FL only, the random error was 8.2 days, whereas using the HC only yielded a random error of 9.4 days.ConclusionsUltrasound estimation of gestational age in late pregnancy is better than indicated by older publications. It is more accurately estimated by combining the HC with the FL than by using the FL measurements alone. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Papillary adenofibroma of the cervix: a case report
Authors: Haberal A. , Cil A. P. , Gunes M. , Cavusoglu D. 
Published: July 2005

AbstractAdenofibroma is an extremely rare benign biphasic neoplasm that is classified into the mixed epithelial and mesenchymal tumor group. It typically affects the endometrium, but may occur in the cervix or in an extrauterine location. Preoperative diagnosis of this tumor is usually difficult. We describe the case of a 55‐year‐old woman with papillary cervical adenofibroma, which appeared as a cervical mass containing multiple cystic components on transvaginal ultrasound. This lesion appears to be clinically and histologically benign but must be differentiated from malignant lesions of the uterus, particularly from adenosarcoma, which can be suggestive of adenofibroma. Accurate diagnosis of these benign tumors permits appropriate counseling of patients. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Atypical ductus venosus blood flow pattern in fetuses with severe tricuspid valve regurgitation
Authors: Smrcek J. M. , Krapp M. , Axt‐Fliedner R. , Kohl T. , Geipel A. , Diedrich K. , Gembruch U. , Berg C. 
Published: July 2005

AbstractWe observed seven cases of atypical ductus venosus (DV) blood flow velocity waveform pattern with impairment of systolic forward flow resulting in a notch or a significant reduction in peak velocity during the S‐wave in systole. All affected fetuses had severe tricuspid valve regurgitation associated with congestive heart failure and/or cardiac malformations. The decrease in venous systolic forward flow modulates the venous pulsatility indices towards more favorable values and should be considered when fetuses with tricuspid regurgitation are followed by Doppler assessment of the DV. Detection of these changes in the DV flow profile should prompt detailed color Doppler echocardiography with special emphasis on right atrioventricular valve regurgitation. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Doppler assessment of fetal aortic isthmus blood flow in two different sonographic planes during the second half of gestation
Authors: Del Río M. , Martínez J. M. , Figueras F. , Bennasar M. , Palacio M. , Gómez O. , Coll O. , Puerto B. , Cararach V. 
Published: July 2005

AbstractObjectiveTo compare the reliability of Doppler blood flow measurements of the fetal aortic isthmus (AoI) according to whether the sampling plane is obtained from the traditional longitudinal aortic arch (LAA) view or the more recently described three vessels and trachea (3VT) view of the fetal upper mediastinum.MethodsDoppler blood flow measurements of pulsatility index (PI), resistance index (RI), peak systolic (PSV), end‐diastolic (EDV) and time‐averaged maximum (TAMXV) velocities were performed in the AoI of 40 fetuses between 24 and 36 weeks of gestation. All measurements were sampled in two different sonographic planes of the AoI: the LAA view, at a few millimeters beyond the origin of the left subclavian artery, and the 3VT view, just before the V‐shaped junction of the aortic and ductal arches. All scans were performed by the same observer. The reliability of Doppler blood flow measurements was assessed by calculating intraclass correlation coefficients (ICCs) and limits of agreement between the two different sonographic sites evaluating the AoI.ResultsMean values of PI, RI, PSV, EDV and TAMXV were similar in the LAA and 3VT views. The PI and vascular velocities were reliably measured from both sonographic sites. ICCs for variability of measurements were 0.78, 0.63, 0.63, 0.60 and 0.55 for PI, RI, PSV, EDV and TAMXV, respectively. Limits of agreement revealed minimal disagreement between the two sites of evaluation of the AoI for all measurements.ConclusionsOn the basis of our observations, Doppler blood flow measurements across the fetal AoI can be reliably obtained from both the 3VT and the traditional LAA sonographic views. Since the transverse upper thoracic 3VT plane is achievable in most fetal positions, Doppler study of the AoI appears to be easier than expected. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Ethnic differences in prenatal growth and the association with maternal and fetal characteristics
Authors: Drooger J. C. , Troe J. W. M. , Borsboom G. J. J. M. , Hofman A. , Mackenbach J. P. , Moll H. A. , Snijders R. J. M. , Verhulst F. C. , Witteman J. C. M. , Steegers E. A. P. , Joung I. M. A. 
Published: July 2005

AbstractObjectivesThe objectives of this study were to determine ethnic differences in prenatal growth and to examine their association with differences in maternal and fetal characteristics such as maternal height, weight, age, parity and fetal gender.MethodsA total of 1494 women from Rotterdam, The Netherlands, with a low‐risk pregnancy who participated in a population‐based cohort study, the Generation R Study, were offered three ultrasound examinations during pregnancy. Multilevel modeling was applied to determine ethnic differences in (estimated) fetal weight (including birth weight) and in the separate biometric variables that were used to calculate the estimated fetal weight (abdominal circumference, head circumference and femur length). Additionally the association of ethnic differences with maternal and fetal characteristics (i.e. maternal weight, height, age, parity and fetal gender) was studied.ResultsTurkish, Cape Verdian, Surinamese‐Creole and Surinamese‐Hindustani women had on average smaller fetuses than the native Dutch women. The differences became more pronounced towards term. In the Turkish group the differences were no longer statistically significant when adjusted for maternal weight, height, age, parity and fetal gender. In the Cape Verdian, Surinamese‐Creole and Surinamese‐Hindustani groups the differences decreased after adjustment (31%, 16% and 39%, respectively).ConclusionsThis study shows that there are ethnic differences in fetal growth, which to a large extent may be attributed to differences in maternal weight, height, age and parity. For some ethnic groups, however, additional factors are involved, as differences remain significant after correction for fetal and maternal characteristics. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.