bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro
Authors: Ahn Jinwoo , Byeon In-Ja L , Dharmasena Sanjeewa , Huber Kelly , Concel Jason , Gronenborn Angela M , Sluis-Cremer Nicolas 
Published: May 2010

AbstractBackgroundLemayet alrecently reported that the RNA binding protein HuR directly interacts with the ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT) and influences the efficiency of viral reverse transcription (Lemayet al., 2008, Retrovirology 5:47). HuR is a member of the embryonic lethal abnormal vision protein family and contains 3 RNA recognition motifs (RRMs) that bind AU-rich elements (AREs). To define the structural determinants of the HuR-RT interaction and to elucidate the mechanism(s) by which HuR influences HIV-1 reverse transcription activityin vitro, we cloned and purified full-length HuR as well as three additional protein constructs that contained the N-terminal and internal RRMs, the internal and C-terminal RRMs, or the C-terminal RRM only.ResultsAll four HuR proteins were purified and characterized by biophysical methods. They are well structured and exist as monomers in solution. No direct protein-protein interaction between HuR and HIV-1 RT was detected using NMR titrations with15N labeled HuR variants or the15N labeled RNase H domain of HIV-1 RT. Furthermore, HuR did not significantly affect the kinetics of HIV-1 reverse transcriptionin vitro, even on RNA templates that contain AREs.ConclusionsOur results suggest that HuR does not impact HIV-1 replication through a direct protein-protein interaction with the viral RT.
Reconstruction of an emergency thoracotomy wound with free rectus abdominis flap: Anatomic and radiologic basis for the surgical technique
Authors: Gilman Kaitlyn , Ipaktchi Kyros , Moore Ernest E , Barnett Carlton , Gurunluoglu Raffi 
Published: May 2010

Abstract
An alcoholic 50-year-old male patient with a history of schizophrenia sustained stab wounds into both ventricles and left lung, and survived following an emergency department thoracotomy. The EDT wound, however became infected requiring serial debridements of soft tissue, rib cartilage and sternum. Regional flap options such as pectoralis major and latissimus dorsi muscle flaps could not be employed due to inadequate reach of these flaps. Additionally, bilateral transection of the internal mammary arteries during emergency thoracotomy eliminated the use of rectus abdominis muscles as pedicled flaps based on the superior epigastric vasculature. Therefore, the EDT wound was reconstructed by using the right rectus abdominis muscle as a free flap. The deep inferior epigastric vessels of the flap were anastomosed to the right internal mammary vessels proximal to their transection level in the third-forth intercostal space. The flap healed with no further wound complications.
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis
Authors: Zhang Yi , Hatch Kim A , Bacon Joanna , Wernisch Lorenz 
Published: May 2010

Abstract

Background
DosR is an important regulator of the response to stress such as limited oxygen availability in Mycobacterium tuberculosis. Time course gene expression data enable us to dissect this response on the gene regulatory level. The mRNA expression profile of a regulator, however, is not necessarily a direct reflection of its activity. Knowing the transcription factor activity (TFA) can be exploited to predict novel target genes regulated by the same transcription factor. Various approaches have been proposed to reconstruct TFAs from gene expression data. Most of them capture only a first-order approximation to the complex transcriptional processes by assuming linear gene responses and linear dynamics in TFA, or ignore the temporal information in data from such systems.

Results
In this paper, we approach the problem of inferring dynamic hidden TFAs using Gaussian processes (GP). We are able to model dynamic TFAs and to account for both linear and nonlinear gene responses. To test the validity of the proposed approach, we reconstruct the hidden TFA of p53, a tumour suppressor activated by DNA damage, using published time course gene expression data. Our reconstructed TFA is closer to the experimentally determined profile of p53 concentration than that from the original study. We then apply the model to time course gene expression data obtained from chemostat cultures of M. tuberculosis under reduced oxygen availability. After estimation of the TFA of DosR based on a number of known target genes using the GP model, we predict novel DosR-regulated genes: the parameters of the model are interpreted as relevance parameters indicating an existing functional relationship between TFA and gene expression. We further improve the prediction by integrating promoter sequence information in a logistic regression model. Apart from the documented DosR-regulated genes, our prediction yields ten novel genes under direct control of DosR.

Conclusions
Chemostat cultures are an ideal experimental system for controlling noise and variability when monitoring the response of bacterial organisms such as M. tuberculosis to finely controlled changes in culture conditions and available metabolites. Nonlinear hidden TFA dynamics of regulators can be reconstructed remarkably well with Gaussian processes from such data. Moreover, estimated parameters of the GP can be used to assess whether a gene is controlled by the reconstructed TFA or not. It is straightforward to combine these parameters with further information, such as the presence of binding motifs, to increase prediction accuracy.
The expression and significance of IDH1 and p53 in osteosarcoma
Authors: Hu Xiang , Yu Ai-Xi , Qi Bai-Wen , Fu Tao , Wu Gang , Zhou Min , Luo Jun , Xu Jun-Hua 
Published: May 2010

Abstract

Background
To detect the expression of isocitrate dehydrogenase 1 (IDH1) and transformation-related protein 53 (p53) in osteosarcoma and analyze the correlation between them and the clinico-pathological features.

Methods
The expressions of IDH1 and p53 were detected in human osteosarcoma cell lines (MG-63 and U2OS) by immunocytochemistry, Real-time PCR and Western Blotting. The expressions of IDH1 and p53 in formalin-fixed paraffin-embedded tissue sections from 44 osteosarcoma patients were determined by immunohistochemistry, and the correlation between them and clinicopagthological features were analyzed. None of these patients received chemotherapy prior to surgery.

Results
IDH1 is detected in osteosarcoma cell lines and biopsies. IDH1 expresses higher in U2OS cells with wild type p53 than in MG-63 cells with mutation p53. IDH1 correlates with histological Rosen grade and metastasis negatively. P53 correlates with histological Rosen grade, metastasis and overall survival in clinical osteosarcoma biopsies. Osteosarcoma patients with High IDH1 expression have a very high p53 expression.

Conclusion
IDH1 may correlate with p53 and be a candidate biomarker for osteosarcoma correlate with histological Rosen grade and metastasis.
Free vs Total Pregnancy-Associated Plasma Protein A (PAPP-A) as a Predictor of 1-Year Outcome in Patients Presenting with Non–ST-Elevation Acute Coronary Syndrome
Authors: Lund Juha , Wittfooth Saara , Qin Qiu-Ping , Ilva Tuomo , Porela Pekka , Pulkki Kari , Pettersson Kim , Voipio-Pulkki Liisa-Maria 
Published: May 2010

AbstractBackground: The free fraction of pregnancy-associated plasma protein A (FPAPP-A) was found to be the PAPP-A form released to the circulation in acute coronary syndrome (ACS). We estimated the prognostic value of FPAPP-A vs total PAPP-A (TPAPP-A) concentrations in forecasting death and nonfatal myocardial infarction (combined endpoint) in patients with non–ST-elevation ACS.Methods: We recruited 267 patients hospitalized for symptoms consistent with non–ST-elevation ACS and followed them for 12 months. FPAPP-A, TPAPP-A, C-reactive protein (CRP), and cardiac troponin I (cTnI) were measured at admission; cTnI was also measured at 6–12 h and 24 h. Because of the recently shown interaction between PAPP-A and heparin, we excluded patients treated with any heparin preparations before the admission blood sampling.Results: During the follow-up, 57 (21.3%) patients met the endpoint (22 deaths and 35 nonfatal myocardial infarctions). According to FPAPP-A (&lt;1.27, 1.27–1.74, &gt;1.74 mIU/L) and TPAPP-A (&lt;1.98, 1.98–2.99, &gt;2.99 mIU/L) tertiles, this endpoint was met by 12 (13.5%), 18 (20.2%), 27 (30.3%) (P = 0.02), and 17 (19.1%), 17 (19.1%), 23 (25.8%) (P = 0.54) patients, respectively. After adjusting for age, sex, diabetes, previous myocardial infarction, and ischemic electrocardiogram (ECG) findings, FPAPP-A &gt;1.74 mIU/L [risk ratio (RR) 2.0; 95% CI 1.0–4.1, P = 0.053), increased cTnI, and CRP ≥2.0 mg/L were independent predictors of an endpoint. The prognostic performance of TPAPP-A was inferior to that of FPAPP-A.Conclusions: FPAPP-A seems to be superior as a prognostic marker compared to TPAPP-A, giving independent and additive prognostic information when measured at the time of admission in patients hospitalized for non–ST-elevation ACS.
The epigenetic regulation of autonomous replicons
Authors: Hagedorn Claudia , Lipps Hans J. , Rupprecht Sina 
Published: May 2010

AbstractThe discovery of autonomous replicating sequences (ARSs) inSaccharomyces cerevisiaein 1979 was considered a milestone in unraveling the regulation of replication in eukaryotic cells. However, shortly afterwards it became obvious that inSaccharomyces pombeand all other higher organisms ARSs were not sufficient to initiate independent replication. Understanding the mechanisms of replication is a major challenge in modern cell biology and is also a prerequisite to developing application-oriented autonomous replicons for gene therapeutic treatments. This review will focus on the development of non-viral episomal vectors, their use in gene therapeutic applications and our current knowledge about their epigenetic regulation.
Leptin and adiponectin levels in pubertal children: relationship with anthropometric variables and body composition
Authors: Schoppen Stefanie , Riestra Pía , García-Anguita Alicia , López-Simón Laura , Cano Beatriz , de Oya Iria , de Oya Manuel , Garcés Carmen 
Published: May 2010

AbstractBackground:Adipocytokines play an important role in controlling energy homeostasis, and in various metabolic processes related to obesity. The aim of this study was to describe serum leptin and adiponectin concentrations in a sample of pubertal Spanish children and to evaluate their association with anthropometric parameters and body composition.Methods:The study included 833 pubertal boys and girls. Serum leptin and adiponectin concentrations were determined by ELISA.Results:Leptin concentrations were significantly higher (p<0.0001) in obese or overweight (OW) children compared with children with normal weight (NW). Adiponectin was significantly lower (p<0.01) in obese or OW girls compared with girls of NW, although these findings were not the same for boys. Weight, body mass index (BMI), waist circumference (WC), hip circumference (HC), and waist to hip ratio were significantly correlated (p<0.01) with leptin concentrations in both genders. Correlation of leptin with fat mass and % fat mass was strong, particularly in boys. The association of adiponectin concentrations with anthropometric variables was weaker in both genders. No significant correlations were found between adiponectin concentrations and fat mass or % fat mass.Conclusions:In summary, our study showed that, in pubertal children, leptin is related to weight, BMI, WC and HC and correlates even more strongly with % fat mass. However, adiponectin was weakly related to anthropometric variables and was not correlated with body fat.Clin Chem Lab Med 2010;48:707–11.
Glycated hemoglobin (HbA1c): old dogmas, a new perspective?
Authors: Lippi Giuseppe , Targher Giovanni 
Published: May 2010

Abstract
The hemoglobin A1c (HbA1c) assay provides a reliable measure of chronic glycemia and correlates well with the risk of long-term diabetes complications, so that it is currently considered the test of choice for monitoring and chronic management of diabetes. Recently, HbA1c testing has been included within the diagnostic criteria recommended for diagnosis of diabetes in nonpregnant individuals by the American Diabetes Association (ADA). The emerging concept that HbA1c can be used rather than blood glucose in the diagnosis of diabetes is highly appealing for a variety of reasons, including less sensitivity to preanalytical variables, lower within subject biological variablity, little to null interference from diurnal variations, acute stress and common drugs which are known to influence glucose metabolism, as well as the fact that one single measurement might provide information for both diagnosing diabetes and tracking glycemic control. On the other hand, the use of HbA1c for screening and diagnosing diabetes also carries some limitations, including the worse diagnostic performance in different populations (i.e., pregnancy, elderly and non-Hispanic blacks), the risk of overdiagnosis in subjects with iron deficiency anemia, in subjects genetically predisposed to hyperglycation, and in those with increased red blood cell turnover. There is also a higher risk of misdiagnosis in patients with end-stage renal disease and heavy alcohol consumption. Finally, HbA1c testing might be biased due to the interference from several hemoglobin variants, is characterized by a higher imprecision than blood glucose measurement, and is more expensive. This paper will critically summarize the potential advantages and limitations of HbA1c as a recommended test for diagnosing diabetes.
Clin Chem Lab Med 2010;48:609–14.
The Influence of the Bucco‐Palatal Distance on Sinus Augmentation Outcomes
Authors: Avila Gustavo , Wang Hom‐Lay , Galindo‐Moreno Pablo , Misch Carl E. , Bagramian Robert A. , Rudek Ivan , Benavides Erika , Moreno‐Riestra Ildefonso , Braun Thomas , Neiva Rodrigo 
Published: May 2010

Background:Maxillary sinus augmentation is one of the most reliable implantsite development options to increase vertical bone height. However,graft consolidation requires adequate angiogenesis and migration ofcells involved in osteogenesis and bone remodeling. It isspeculated that these biologic events are greatly determined by thedimensions of the maxillary sinus cavity. Hence, the purpose ofthis study is to assess the influence of the distance from thelateral to the medial wall of the maxillary sinus on the outcomesof sinus augmentation procedures.Methods:A total of 25 patients in need of sinus augmentation were recruitedfor the study. After initial examination, customized radiographicand surgical guides were fabricated and a cone‐beam computerizedtomography scan was obtained per patient. The bucco‐palataldistance (BPD) was measured at 8, 10, and 12 mm from the alveolarcrest. Sinus grafting was performed by a lateral window approachusing a particulated allograft material. Patients were followed‐upfor 6 months. At the time of implant placement, bone core biopsieswere harvested using the radiographic‐surgical guide. Sections ofthe bone cores at 8, 10, and 12 mm from the alveolar crest werehistomorphometrically analyzed. The proportion of vital bone (%VB)was correlated with the BPD using a statistical model.Results:Twenty‐one patients underwent sinus augmentation for a total of 24sinuses; however, the data analyzed contained only one sinus perpatient. One sinus developed an infection after grafting, resultingin a 96% success rate for the sinus grafting procedure. Twentysinuses were used in the final statistical analysis.Histomorphometric analysis revealed that mean %VB was 22.71 ±19.08, mean percent of remaining allograft was 23.39 ±20.85, and average percent of non‐mineralized connective tissue was53.90 ±13.23. Analysis of the correlation between %VB and BPD by linearregression, using the actual values of BPD showed a strong negativeassociation (R2 =0.141;P<0.001).Conclusion:The findings suggest that the %VB formation after maxillary sinusaugmentation is inversely proportional to the sinus BPD.
Lock-In and the Transition to Hydrogen Cars: Should Governments Intervene?
Authors: Greaker Mads , Heggedal Tom-Reiel 
Published: May 2010

Abstract
The density of fuel filling stations influences consumers' utility of private car transport. We investigate the technology choice of firms and consumers in a formal model of the private transport market. Two competing technologies exist; today's internal combustion engine based on fossil fuels, and tomorrow's hydrogen car. Due to network externalities, several market equilibria may exist, of which one is likely to Pareto dominate the other(s). Thus, a lock-in situation is possible. On the other hand, if either the costs of establishing hydrogen filling stations are too high or the hydrogen car technology is still in its infancy, the only equilibrium is the current internal combustion engine equilibrium. Hence, apart from internalizing the environmental externality on gasoline cars, the government has no reason to intervene before the technology is ripe.
Characterization of granites by 57Fe Mössbauer spectroscopy
Authors: Hassan Kamaledin 
Published: May 2010

Characterization of granites by 57Fe Mössbauer spectroscopyTwo granite complexes in Egypt, a sodic type and an aluminous type are characterized by Mössbauer spectroscopy. Mössbauer spectra (MS) of the sodic granite show a major doublet of ferric (Fe3+) iron that is attributable to octahedral coordination (M1) sites plus/minus a tetrahedron Fe3+ doublet plus/minus a doublet of ferrous (Fe2+) iron on the M1 sites plus/ minus another Fe2+ (M1) doublet and a sextet of Fe3+. The sextet is attributed to α-Fe2O3 (hematite) and the other Fe components are due to NaCaFeSi2O6 (aegirine-augite) plus/minus minor contributions from (Ca2(Mg, Fe)5(Si, Al)8O22(OH)2 (magnesium-hornblende). Changes in the quadrupole splitting and width line of Fe2+ ions are likely composition-related. The MS of the aluminous-type granite, on the other hand, shows evidence only of single doublets containing Fe2+ or Fe3+ in the octahedral M1 sites, with parameters that remain almost constant. This consistency implies that the existing minerals - K(Mg, Fe2+)3 (Al, Fe3+)Si3O10(OH, F)2 (biotite), (Mg, Fe)6(Si, Al)4O10(OH)8 (clinochlore), (Na, K)Ca2(Fe, Mg)5(Al, Si)8O22(OH)2 (ferrohornblende and magnesiohornblende) - have similar iron positions. The intensity of iron oxidized (Fe3+/ΣFe) for the sodic granite is 79.1 to 100% and for the aluminous granite, 28.4 to 38.2%. The observed Fe3+/ΣFe differences between the two granites are source-related and consistent with distributions of other redox-sensitive elements.
Indirect maternal mortality increases in the Netherlands
Authors: SCHUTTE JOKE M. , DE JONGE LAYLA , SCHUITEMAKER NICO W. E. , SANTEMA JOB G. , STEEGERS ERIC A. P. , VAN ROOSMALEN JOS 
Published: May 2010

AbstractObjective. To assess causes, trends, and substandard care in indirect maternal mortality in the Netherlands. Design. Confidential enquiry into causes of maternal death. Setting. Nationwide in the Netherlands. Population. A total of 2,557,208 live births. Methods. Data analysis of indirect maternal deaths in the period 1993–2005. Main outcome measures. Indirect maternal mortality. Results. Of the study subjects, 97 were classified as indirect deaths, representing a maternal mortality ratio of 3.3/100,000 live births, a significant increase compared to the preceding enquiry in the period 1983–1992 (MMR 2.4, OR 1.5, 95%CI 1.0–2.1). The percentage of cases not directly reported to the Maternal Mortality Committee decreased from 15 to 5%. Cardiovascular disorders were the leading cause of indirect maternal mortality, followed by cerebrovascular disorders. Vascular dissection (n = 19) was the most frequent specified cause of death. Risk factors were advanced maternal age, non‐indigenous origin (Surinam and Dutch Antilles), and medical health risks before pregnancy. Substandard care was present in 35%, mainly being misjudgment of the severity of the condition and delay in initiating therapy. Conclusion. The rise of mortality due to indirect causes is considered a reflection of the change in risk profile of women of childbearing age and the result of demographic alterations concerning ethnicity and maternal age. The identification of high risk groups, preferably by programs of preconception care, should lead to improved care for these women, with a multidisciplinary approach when needed.
Self‐reporting compared to motion monitor in the measurement of physical activity during pregnancy
Authors: HAAKSTAD LENE A.H. , GUNDERSEN INGVILD , BØ KARI 
Published: May 2010

AbstractMost pregnancy‐studies have relied on retrospective, cross‐sectional surveys to measure physical activity level. Questionnaires are cost‐effective, but validity of the data may be questionable. Objective. The aim of the present study was to validate a physical activity and pregnancy questionnaire (PAPQ) with a portable activity monitor (ActiReg®). Design. Prospective comparison study. Setting. Healthy pregnant women recruited in a capital area. Population. Seventy‐seven pregnant women wore the ActiReg® sensors during waking hours for seven consecutive days and answered the PAPQ. Main outcome measures. Agreement between the two methods was analyzed by Bland–Altman plots and Spearman correlation coefficients. Results. The results indicated only small differences between the PAPQ and the ActiReg® in cross‐tabulation of total physical activity level and proportion of participants meeting the current exercise guidelines. The correlation between the methods was good (r = 0.59) for time spent in activities with high intensity (METS > 6), moderate for time spent standing/moving (r = 0.36) and fair for sitting/lying (r = 0.29). The Bland–Altman plot of the activity patterns, showed a mean difference near zero with no apparent trends and wide scatter of individual observations. Conclusions. The PAPQ may be considered an acceptable method for assessing habitual physical activity and exercise among pregnant women at group level. However, as questionnaires and portable activity monitors have their strengths in measuring different aspects of physical activity, there may be advantages in combining these two types of instruments for registrations of physical activity level during pregnancy.