bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fetal and neonatal ovarian cysts: is surgery indicated?
Authors: Monnery‐Noché Marie‐Emmanuelle , Auber Frédéric , Jouannic Jean‐Marie , Bénifla Jean‐Louis , Carbonne Bruno , Dommergues Marc , Lenoir Marion , Lepointe Hubert Ducou , Larroquet Michèle , Grapin Christine , Audry Georges , Hélardot Pierre G. 
Published: January 2008

AbstractObjectivesTo evaluate the frequency of ovarian torsion in neonates with ovarian cysts (OCs) and to analyze the outcome after surgical treatment.MethodsA retrospective review of all infants with OCs managed in our institution during 20 years, was conducted. Our management included a follow‐up (FU) of prenatal serial ultrasound (US) scan without prenatal cyst aspiration and early postnatal US scan. Neonatal surgery was indicated for cysts that appeared complex regardless of size and for simple cysts larger than 20 mm.ResultsSixty‐seven OCs detected through prenatal diagnosis were identified. Cysts were detected at a median gestational age (GA) of 33 weeks. At diagnosis, median size of the OCs was 40 mm, and 18% were complex. On the postnatal US scan, 55% were complex. Neonatal surgery was performed for 64 OCs : 56% were torsed, 6% were hemorrhagic, and 38% were uncomplicated. Proportions of complex‐ and simple‐appearing cysts on prenatal or postnatal US scan were the only significantly different parameters found between infants with torsed or not torsed OC.ConclusionOur study demonstrated that OC bears a high risk of ovarian loss. These findings have implications regarding information and treatment offered to pregnant women bearing an affected fetus. Copyright © 2008 John Wiley & Sons, Ltd.
Rethinking autonomy in the context of prenatal screening decision‐making
Authors: García Elisa , Timmermans Danielle R. M. , van Leeuwen Evert 
Published: January 2008

AbstractObjectivesAnswering the question: Does the offer of prenatal screening impede women in making autonomous choices?MethodsSemi‐structured interviews with 59 women to whom a prenatal screening test was offered and who were in the process of taking a decision.ResultsWomen described the offer as confronting but expressed a positive attitude towards screening and considered the offer as an opportunity for making up their minds about testing. Participants stated that they took decisions freely to follow their individual perspectives. Nevertheless, they preferred to share the responsibility of taking decisions, and its consequences for other family members, with their partner and close persons.ConclusionsThe active offer of an unsolicited prenatal test need not be considered as an impediment for making an autonomous choice. The moral significance of prenatal testing is inseparably bound with the social context in which it is practiced. Influence from other persons and emotional reactions due to the test offer can be interpreted as supportive for making a choice. In clinical practice, testing should be timely offered in order to give women the opportunity of discussing their views with significant others. Caregivers should care for the emotions experienced by women so as to help them decide according to their values. Copyright © 2008 John Wiley & Sons, Ltd.
Screening for trisomy 21 in twin pregnancies in the first trimester: an update of the impact of chorionicity on maternal serum markers
Authors: Spencer Kevin , Kagan Karl O. , Nicolaides Kypros H. 
Published: January 2008

AbstractObjectiveTo examine the distribution of first‐trimester biochemical markers of aneuploidy in twin pregnancies, and to assess whether there are differences in the distributions between monochorionic and dichorionic twins.MethodsMaternal serum‐free β‐hCG and PAPP‐A were measured between 11 + 0 and 13 + 6 weeks as part of a routine first‐trimester screening program in conjunction with fetal nuchal translucency (NT) performed at two sites. Data from twin pregnancies were extracted from the fetal databases along with information on the chorionicty. The individual marker concentrations were expressed as weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM using data from singleton pregnancies as the reference. The overall medians were compared to those in singleton pregnancies and between monochorionic and dichorionic twins.ResultsData was available from 1914 sets of twins. Of these, 1214 had information with respect to chorionicity, with 1024 being dichorionic and 190 being monochorionic. The overall median weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM amongst twin pregnancies were 2.023 for free β‐hCG (sd log10 MoM = 0.2611 and 2.121 for PAPP‐A (sd log10 MoM = 0.2255)—both medians were significantly greater than the medians in singleton pregnancies (1.00 MoM). In the case of monochorionic and dichorionic twins the median weight corrected, ethnicity corrected, smoking corrected and IVF corrected, free β‐hCG MoM's were not significantly different (1.983 v 2.041), however for PAPP‐A the median weight corrected, ethnicity corrected, smoking corrected and IVF corrected MoM in monochorionic twins was significantly lower than in dichorionic twins (1.756 v 2.250) whilst the sd log10 MoM's were not significantly different (0.2185 v 0.2167).ConclusionScreening in twin pregnancies requires adjustment of the calculated MoM to account for the presence of two fetuses. In general, for free β‐hCG, this should be by dividing the observed corrected MoM by 2.023. For PAPP‐A two different factors are required − 2.192 in dichorionic twins and 1.788 in monochorionic twins. Copyright © 2008 John Wiley & Sons, Ltd.
Quality use of medicines: a new method of combining antibiotic consumption and sensitivity data—application in a Russian hospital
Authors: Goryachkina Ksenia , Babak Svetlana , Burbello Aleksandra , Wettemark Björn , Bergman Ulf 
Published: January 2008

AbstractPurposeAntibiotic use and resistance is subject of great concern. There is a need for internationally comparable and locally useful data collection and reporting. We developed a new method to combine and present data on antibiotic use and resistance in a figure in a Russian 1300 bed‐hospital.MethodsWe applied World Health Organization (WHO) Anatomic Therapeutic Chemical (ATC) classification/defined daily doses (DDD) analysis on antibacterials for systemic use (ATC: J01) delivered by the pharmacy for the years 2003–2005. Microbial resistance data were presented within the range of drugs accounting for 90% of the volume in DDD, i.e. drug utilisation 90% (DU90%).ResultsFrom the DU90% profile the following was seen: in 2003, 12 of 25 drugs accounted for 90% of the volume. For six of the most commonly used antibiotics, including the two cheapest (gentamicin, ampicillin), a significant number of the strains tested were resistant. For the remaining antibiotics no resistance data were available. These data were discussed in early 2004. A general decrease of antibiotic use and resistance was seen in 2005 (by 57% from 15.5 to 8.8 DDD/100 bed days) with a concomitant decrease in expenditures (by 64%) and a shift to more potent antibiotics.ConclusionsThe created profile highlighted potential problems in a clear and easy form. Besides being an indicator of the quality of antibiotic use it was a powerful alert and driving force for change. It can be used for external comparisons and for local monitoring of antibiotic use and resistance and can be applied with routinely available data in any hospital. Copyright © 2008 John Wiley & Sons, Ltd.
The impact of diet and micronutrient supplements on the expression of neuroendocrine markers in murine Lady transgenic prostate
Authors: Palmer Jodie , Venkateswaran Vasundara , Fleshner Neil E. , Klotz Laurence H. , Cox Michael E. 
Published: January 2008

AbstractBACKGROUNDNeuroendocrine (NE) differentiation (NED) in prostate cancer (PCa) is associated with morbidity and death; however, the underlying cause(s) promoting NED in PCa have yet to be determined. In this study, we examined the effect of both diet and micronutrient supplementation on the expression of NE markers using the Lady (12T‐10) transgenic model of PCa. Lady (12T‐10) transgenic animals develop advanced adenocarcinoma with NE characteristics that exhibits metastases in approximately 80% of cases. In this model a high fat diet has been shown to increase the severity of disease, while the use of micronutrients can inhibit this progression.METHODSIn this study we used immunohistochemical analysis to determine expression of the NE markers: chromogranin A (CgA), neuron‐specific enolase (NSE), bombesin, parathyroid hormone‐related peptide (PTHrP), neurotensin and serotonin in prostates of PCa‐bearing Lady (12T‐10) mice.RESULTSHigh fat diet was correlated with significantly elevated expression of CgA and serotonin in prostate tissue of Lady (12T‐10) mice. Addition of micronutrients to the control and high fat diet reproducibly elevated PTHrP and bombesin expression and suppressed NSE expression, while prostate tissue from the control diet supplemented with micronutrients exhibited significantly lower numbers of calcitonin‐ and neurotensin‐positive cells.CONCLUSIONSThese results highlight the importance of dietary control in management of disease and identify differential changes in NE marker expression, which may be diagnostically viable in monitoring the impact of therapies on disease status. Prostate 68: 345–353, 2008. © 2008 Wiley‐Liss, Inc.
Water‐mediated interactions between DNA and PhoB DNA‐binding/transactivation domain: NMR‐restrained molecular dynamics in explicit water environment
Authors: Yamane Tsutomu , Okamura Hideyasu , Ikeguchi Mitsunori , Nishimura Yoshifumi , Kidera Akinori 
Published: January 2008

AbstractThe solution structure of the complex between the transcription factor PhoB DNA‐binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB‐DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein‐DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water‐mediated PhoB‐DNA interactions contributed to the molecular recognition between PhoB and DNA. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Differentiation between two‐state and multi‐state folding proteins based on sequence
Authors: Huang Ji‐Tao , Cheng Jin‐Pei 
Published: January 2008

AbstractPrediction of protein‐folding rates follows different rules in two‐state and multi‐state kinetics. The prerequisite for the prediction is to recognize the folding kinetic pathway of proteins. Here, we use the logistic regression and support vector machine to discriminate between two‐state and multi‐state folding proteins. We find that chain length is sufficient to accurately recognize multi‐state proteins. There is a transition boundary between two kinetic models. Protein folds with multi‐state kinetics, if its length is larger than 112 residues. The logistic prediction from amino acid composition shows that the kinetic pathway of folding is closely related to amino acid volume. Small amino acids make two‐state folding easier, and vice versa. However, cysteine, alanine, arginine, lysine, histidine, and methionine do not conform to this rule. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Differentiable, multi‐dimensional, knowledge‐based energy terms for torsion angle probabilities and propensities
Authors: Amir El‐Ad David , Kalisman Nir , Keasar Chen 
Published: January 2008

AbstractRotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force‐driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high‐dimensional and fully‐differentiable energy terms that are derived from high‐resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side‐chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side‐chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native‐like structures within decoy sets. Finally, force‐based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 Å RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Role of the amino acid sequence in domain swapping of the B1 domain of protein G
Authors: Sirota Fernanda L. , Héry‐Huynh Stephanie , Maurer‐Stroh Sebastian , Wodak Shoshana J. 
Published: January 2008

AbstractSubstitution of four amino acid residues (L5V,F30V, Y33F,A34F) in the B1 domain of the immunoglobulin G binding protein (GB1) leads to the formation of a swapped dimer, shown to be in equilibrium with a native‐like monomeric state of the protein (Byeon et al., J Mol Biol 2003;333:141–152). In this study, we employ protein design calculations and molecular dynamics simulations to investigate the role of these substitutions in fostering the swapping reaction. DESIGNER, a fully automatic procedure for computing the amino acid sequences likely to stabilize a given backbone structure is used to investigate the effect of the four substitutions on the stability of the wild type native monomeric conformation. Results indicate that at least three of these substitutions (L5V,F30V, A34F) have a destabilizing effect. The L5V forms destabilizing interactions with surrounding residues, whereas F30V causes local strain due to unfavorable interactions with its own backbone. A dual role in the swapping reaction is played by A34F. It destabilizes the monomer conformation while stabilizing the swapped dimer. Our calculations find an energetically favorable conformation for the 34F side chain in the core of the monomer, but only at the expense of forcing the wild type W43 side chain into a highly strained rotamer, and forming unfavorable interactions with both W43 and V54. Although detailed calculations could not be performed on the swapped dimer, due to the lower accuracy of the model, analysis revealed that the 34F side chain from both subunits are tightly packed against each other in the dimer core, suggesting that their replacement by the smaller Ala, as in the wild type, would be highly destabilizing through the creation of a large internal cavity possibly accompanied by a substantial conformational change. Analysis of room temperature molecular dynamics (MD) simulations of the wild type and the modeled quadruple mutant structures reveals that the latter structure fluctuates more than its wild type counterpart. In addition, its C‐terminal β‐hairpin, which is exchanged in the swapping reaction, undergoes a conformation change, which pushes it further away from the remainder of the protein. Simulations at higher temperature (450 K) show that the quadruple mutant unfolds earlier and more completely than the wild type following a sequence of events that is compatible with the description of the highly fluctuating monomeric state of this mutant observed by NMR. Our findings thus support the notion that domain swapping in GB1 is fostered by three main factors: a decrease in stability and increased flexibility of the monomer conformation, concomitant with stabilization of the swapped dimer conformation through new interactions that have no counterparts in the monomer. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Electron impact K‐shell ionization cross sections of atoms at relativistic energies
Authors: Patoary M. A. R. , Alfaz Uddin M. , Haque A. K. F. , Basak A. K. , Talukder M. R. , Karim K. R. , Saha B. C. 
Published: January 2008

AbstractWe propose an extension of the modified simplified‐improved‐binary‐encounter dipole (MRIBED) model (Uddin et al., Phys Rev A 2005, 72, 032715), incorporating both the ionic and relativistic corrections, to investigate the K‐shell ionization of atomic targets with atomic numbers Z = 1 − 92 for incident energies up to 2 GeV. We also revisit our earlier models, MBELL (Haque et al. Phys Rev A 2006, 73, 012708) and MKLV (Uddin et al. Eur Phys J D 2006, 37, 361), for the K‐shell ionization at these ultra‐relativistic energies. The results from our extended version of MRIBED, MBELL, and MKLV models agree well with the experimental findings. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Simulation for Team Training and Assessment: Case Studies of Online Training with Virtual Worlds
Authors: Heinrichs William LeRoy , Youngblood Patricia , Harter Phillip M. , Dev Parvati 
Published: January 2008

AbstractIndividuals in clinical training programs concerned with critical medical care must learn to manage clinical cases effectively as a member of a team. However, practice on live patients is often unpredictable and frequently repetitive. The widely substituted alternative for real patients—high‐fidelity, manikin‐based simulators (human patient simulator)—are expensive and require trainees to be in the same place at the same time, whereas online computer‐based simulations, or virtual worlds, allow simultaneous participation from different locations. Here we present three virtual world studies for team training and assessment in acute‐care medicine: (1) training emergency department (ED) teams to manage individual trauma cases; (2) prehospital and in‐hospital disaster preparedness training; (3) training ED and hospital staff to manage mass casualties after chemical, biological, radiological, nuclear, or explosive incidents. The research team created realistic virtual victims of trauma (6 cases), nerve toxin exposure (10 cases), and blast trauma (10 cases); the latter two groups were supported by rules‐based, pathophysiologic models of asphyxia and hypovolemia. Evaluation of these virtual world simulation exercises shows that trainees find them to be adequately realistic to “suspend disbelief,” and they quickly learn to use Internet voice communication and user interface to navigate their online character/avatar to work effectively in a critical care team. Our findings demonstrate that these virtual ED environments fulfill their promise of providing repeated practice opportunities in dispersed locations with uncommon, life‐threatening trauma cases in a safe, reproducible, flexible setting.
Using the Internet for scientific publishing: FQS as an example
Authors: Mruck Katja , Mey Günter 
Published: January 2008

Abstract
Since the “Public Library of Science” launched its first open-access journals and the “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities” has been released in 2003 and found enormous attention, the claim for open access—to make publicly funded journal articles available for the public—started to reach German scientists too. But still no experience has been made with electronic publishing in general and more specifically with open-access publishing. One consequence is that the potential capacity of open access—the (inter) national and (trans) disciplinary visibility and accessibility of scientific output—is not sufficiently used by German researchers. Ways to successfully establish an open-access journal are presented in this article by referring to “Forum Qualitative Sozialforschung/Forum:Qualitative Social Research” (FQS) as an example: after introducing the current state of FQS traditional and innovative ways of publishing are being discussed which had been employed while developing FQS and which helped FQS to become the most important electronic journal in the field of qualitative research.
Neonatal screening for medium‐chain acyl‐CoA dehydrogenase (MCAD) deficiency in The Netherlands: The importance of enzyme analysis to ascertain true MCAD deficiency
Authors: Derks T. G. J. , Boer T. S. , van Assen A. , Bos T. , Ruiter J. , Waterham H. R. , Niezen‐Koning K. E. , Wanders R. J. A. , Rondeel J. M. M. , Loeber J. G. , ten Kate L. P. , Smit G. P. A. , Reijngoud D.‐J. 
Published: January 2008

SummaryThe outcome was determined of population‐wide neonatal screening for medium‐chain acyl‐CoA dehydrogenase (MCAD) deficiency using tandem mass spectrometry (MS/MS) in The Netherlands, between October 2003 and September 2005. Prospective population‐wide neonatal screening for MCAD deficiency was performed in the northern part of The Netherlands. In newborns with blood octanoylcarnitine (C8:0) concentrations ≥0.3 μmol/L, clinical and laboratory follow‐up was initiated, including MCAD enzymatic measurements which played a decisive role. In a 2‐year period, 66 216 newborns were investigated for MCAD deficiency and follow‐up was initiated in 28 newborns. True‐positives (n = 14) were identified based upon MCAD enzyme activity <50%, measured with hexanoyl‐CoA as substrate. The observed prevalence of MCAD deficiency was 1/6600 (95% CI: 1/4100–1/17 400). In addition to an elevated C8:0 concentration, a C8:0/C10:0 molar ratio >5.0 turned out to differentiate between false‐positives and true‐positives. Measurement of MCAD activity using phenylpropionyl‐CoA as a substrate further discriminated between newborns with MCAD deficiency and so‐called mild MCAD deficiency. To summarize, neonatal screening for MCAD deficiency in the northern part of The Netherlands resulted in the predicted number of affected newborns. Measurement of MCAD activity in leukocytes or lymphocytes using phenylpropionyl‐CoA as a substrate can be regarded as the gold standard to diagnose MCAD deficiency upon initial positive screening test results.
Comparison of tetrahydrofuran and ethyl acetate as extraction solvents for urinary organic acid analysis
Authors: Wittmann Gy. , Karg E. , Mühl A. , Bodamer O. A. , Túri S. 
Published: January 2008

SummaryThe analysis of urinary organic acids is crucial for the diagnosis of many inborn errors of metabolism. A vital part of the analytical process is the extraction procedure. The sensitivity and linearity of the analysis of 26 diagnostically important urinary metabolites with tetrahydrofuran (THF) and ethyl acetate (EtOAc) as extraction solvents were determined by gas chromatography–mass spectrometry. Good linearity (r2 > 0.90) was observed for all of the compounds in the investigated concentration range (290–900 μmol/L) for both solvents. For less polar compounds, THF extraction yielded lower or similar sensitivities as compared with EtOAc (sensitivity ratio: 0.6–1.3). For more polar compounds, however, much higher sensitivities were observed when THF was used (sensitivity ratio: 1.8–17.2). Our results provide information concerning the use of THF for the sensitive quantitative analysis of polar urinary metabolites which are difficult to quantify using EtOAc.