bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMR spectroscopic and analytical ultracentrifuge analysis of membrane protein detergent complexes
Authors: Maslennikov Innokentiy , Kefala Georgia , Johnson Casey , Riek Roland , Choe Senyon , Kwiatkowski Witek 
Published: November 2007

Abstract

Background
Structural studies of integral membrane proteins (IMPs) are hampered by inherent difficulties in their heterologous expression and in the purification of solubilized protein-detergent complexes (PDCs). The choice and concentrations of detergents used in an IMP preparation play a critical role in protein homogeneity and are thus important for successful crystallization.

Results
Seeking an effective and standardized means applicable to genomic approaches for the characterization of PDCs, we chose 1D-NMR spectroscopic analysis to monitor the detergent content throughout their purification: protein extraction, detergent exchange, and sample concentration. We demonstrate that a single NMR measurement combined with a SDS-PAGE of a detergent extracted sample provides a useful gauge of the detergent's extraction potential for a given protein. Furthermore, careful monitoring of the detergent content during the process of IMP production allows for a high level of reproducibility. We also show that in many cases a simple sedimentation velocity measurement provides sufficient data to estimate both the oligomeric state and the detergent-to-protein ratio in PDCs, as well as to evaluate the homogeneity of the samples prior to crystallization screening.

Conclusion
The techniques presented here facilitate the screening and selection of the extraction detergent, as well as help to maintain reproducibility in the detergent exchange and PDC concentration procedures. Such reproducibility is particularly important for the optimization of initial crystallization conditions, for which multiple purifications are routinely required.
Self-assembly of human latexin into amyloid-like oligomers
Authors: Pallarés Irantzu , Berenguer Clara , Avilés Francesc X , Vendrell Josep , Ventura Salvador 
Published: November 2007

Abstract

Background
In conformational disorders, it is not evident which amyloid aggregates affect specific molecular mechanisms or cellular pathways, which cause disease because of their quantity and mechanical features and which states in aggregate formation are pathogenic. Due to the increasing consensus that prefibrillar oligomers play a major role in conformational diseases, there is a growing interest in understanding the characteristics of metastable polypeptide associations.

Results
Here, we show that human latexin, a protein that shares the same fold with cystatin C, assembles into stable spherical amyloid-like oligomers that bind thioflavin-T and congo red similarly to common amyloid structures but do not evolve into fibrils. Latexin self-assembly correlates with the formation of a mostly denaturated state rather than with the population of partially structured intermediates during the unfolding process. The results suggest that unfolding of α-helix 3 might be involved in the transition of latexin toward amyloidotic species, supporting the notion of the protective role of the native protein structure against polymerization.

Conclusion
Overall the data herein indicate that latexin could be a good model for the study of the structural and sequential determinants of oligomeric assemblies in protein aggregation processes.
Decline of placental malaria in southern Ghana after the implementation of intermittent preventive treatment in pregnancy
Authors: Hommerich Lena , von Oertzen Christa , Bedu-Addo George , Holmberg Ville , Acquah Patrick A , Eggelte Teunis A , Bienzle Ulrich , Mockenhaupt Frank P 
Published: November 2007

AbstractBackgroundIntermittent preventive treatment in pregnancy with sulphadoxine-pyrimethamine (IPTp-SP) has been adopted as policy by many countries in sub-Saharan Africa. However, data on the post-implementation effectiveness of this measure are scarce.MethodsClinical and parasitological parameters were assessed among women delivering at a district hospital in rural southern Ghana in the year 2000 when pyrimethamine chemoprophylaxis was recommended (n= 839) and in 2006 (n= 226), approximately one year after the implementation of IPTp-SP. Examinations were performed in an identical manner in 2000 and 2006 including the detection of placentalPlasmodium falciparuminfection by microscopy, histidine-rich protein 2, and PCR.ResultsIn 2006, 77% of the women reported to have taken IPTp-SP at least once (26%, twice; 24%, thrice). In 2006 as compared to 2000, placentalP. falciparuminfection was reduced by 43–57% (P< 0.0001) and maternal anaemia by 33% (P= 0.0009), and median birth weight was 130 g higher (P= 0.02). In 2006, likewise, women who had taken ≥ 1 dose of IPTp-SP revealed less infection and anaemia and their children tended to have higher birth weights as compared to women who had not used IPTp-SP. However, placentalP. falciparuminfection was still observed in 11% (microscopy) to 26% (PCR) of those women who had taken three doses of IPTp-SP.ConclusionIn southern Ghana, placental malaria and maternal anaemia have declined substantially and birth weight has increased after the implementation of IPTp-SP. Likely, these effects can further be increased by improving IPTp-SP coverage and adherence. However, the remnant prevalence of infection in women having taken three doses of IPTp-SP suggests that additional antimalarial measures are needed to prevent malaria in pregnancy in this region.
Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?
Authors: Klebanov Lev , Chen Linlin , Yakovlev Andrei 
Published: November 2007

Abstract

Background.
This work was undertaken in response to a recently published paper by Okoniewski and Miller (BMC Bioinformatics 2006, 7: Article 276). The authors of that paper came to the conclusion that the process of multiple targeting in short oligonucleotide microarrays induces spurious correlations and this effect may deteriorate the inference on correlation coefficients. The design of their study and supporting simulations cast serious doubt upon the validity of this conclusion. The work by Okoniewski and Miller drove us to revisit the issue by means of experimentation with biological data and probabilistic modeling of cross-hybridization effects.

Results.
We have identified two serious flaws in the study by Okoniewski and Miller: (1) The data used in their paper are not amenable to correlation analysis; (2) The proposed simulation model is inadequate for studying the effects of cross-hybridization. Using two other data sets, we have shown that removing multiply targeted probe sets does not lead to a shift in the histogram of sample correlation coefficients towards smaller values. A more realistic approach to mathematical modeling of cross-hybridization demonstrates that this process is by far more complex than the simplistic model considered by the authors. A diversity of correlation effects (such as the induction of positive or negative correlations) caused by cross-hybridization can be expected in theory but there are natural limitations on the ability to provide quantitative insights into such effects due to the fact that they are not directly observable.

Conclusion.
The proposed stochastic model is instrumental in studying general regularities in hybridization interaction between probe sets in microarray data. As the problem stands now, there is no compelling reason to believe that multiple targeting causes a large-scale effect on the correlation structure of Affymetrix gene expression data. Our analysis suggests that the observed long-range correlations in microarray data are of a biological nature rather than a technological flaw.

Reviewers:
The paper was reviewed by I. K. Jordan, D. P. Gaile (nominated by E. Koonin), and W. Huber (nominated by S. Dudoit).
Medicinal plants in an urban environment: the medicinal flora of Banares Hindu University, Varanasi, Uttar Pradesh
Authors: Verma Archana K , Kumar Munesh , Bussmann Rainer W 
Published: November 2007

Abstract
Varanasi is one of the oldest continuously inhabited cities of the world, and one of the most important Hindu pilgrimage sites. Despite this importance, very little information exits on the cities flora in general, and medicinal species found within its limit in particular. Traditional medicine plays a large role in Indian society. The presented study attempted to investigate if traditional plant use and availability of important common medicinal plants are maintained in urban environments. The paper presents information on the traditional uses of seventy-two plant species collected form the campus of Banares Hindu University, Varanasi, Uttar Pradesh, and highlights the uses of these plants by the local inhabitants.
Clinical relevance of and risk factors for HSV-related tracheobronchitis or pneumonia: results of an outbreak investigation
Authors: Engelmann Ilka , Gottlieb Jens , Meier Astrid , Sohr Dorit , Ruhparwar Arjang , Henke-Gendo Cornelia , Gastmeier Petra , Welte Tobias , Schulz Thomas Friedrich , Mattner Frauke 
Published: November 2007

Abstract
Introduction
Herpes simplex virus (HSV) type 1 was identified in respiratory specimens from a cluster of eight patients on a surgical intensive care unit within 8 weeks. Six of these patients suffered from HSV-related tracheobronchitis and one from HSV-related pneumonia only. Our outbreak investigation aimed to determine the clinical relevance of and risk factors associated with HSV-related tracheobronchitis or pneumonia in critically ill patients, and to investigate whether the cluster was caused by nosocomial transmission.

Methods
A retrospective cohort study was performed to identify risk factors for the outcomes of HSV-related tracheobronchitis or pneumonia and death using univariable analysis as well as logistic regression analysis. Viruses were typed by molecular analysis of a fragment of the HSV type 1 glycoprotein G.

Results
The cohort of patients covering the outbreak period comprised 53 patients, including six patients with HSV-related tracheobronchitis and one patient with pneumonia only. HSV-related tracheobronchitis or pneumonia was associated with increased mortality (100% in patients with versus 17.8% in patients without HSV-related tracheobronchitis or pneumonia; P < 0.0001). The interaction of longer duration of ventilation and tracheotomy was associated with HSV-related tracheobronchitis or pneumonia in multivariable analysis.
Identical HSV type 1 glycoprotein G sequences were found in three patients and in two patients. The group of three identical viral sequences belonged to a widely circulating strain. The two identical viral sequences were recovered from bronchoalveolar lavages of one patient with HSV-related tracheobronchitis and of one patient without clinical symptoms. These viral sequences showed unique polymorphisms, indicating probable nosocomial transmission.

Conclusion
HSV-related tracheobronchitis or pneumonia is associated with increased mortality in critically ill patients. Care should be taken to avoid nosocomial transmission and early diagnosis should be attempted.
Sequence and functional analyses of Haemophilusspp. genomic islands
Authors: Juhas Mario , Power Peter M , Harding Rosalind M , Ferguson David JP , Dimopoulou Ioanna D , Elamin Abdel RE , Mohd-Zain Zaini , Hood Derek W , Adegbola Richard , Erwin Alice , Smith Arnold , Munson Robert S , Harrison Alistair , Mansfield Lucielle , Bentley Stephen , Crook Derrick W 
Published: November 2007

Abstract
Background
A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results
These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion
Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.
Reviews
Authors: Govil Nitin , Tracy James F , Mosdell Nick , Housley William 
Published: November 2007

Gandhi Meets Primetime: Globalization and Nationalism in Indian Television, Shanti Kumar (2005)Champaign, IL: University of Illinois Press, 284 pp., ISBN 025203001X (hbk), $45.00; ISBN 0252072448 (pbk), 25.00Waves of Opposition: Labour and the Struggle for Democratic Radio, Elizabeth Fones-Wolf (2006)Urbana, IL: University of Illinois Press, 256 pp., ISBN 0252031199 (hbk), 60.00; ISBN 0252073649 (pbk), 25.00Leading to the 2003 Iraq War: The Global Media Debate, Alexander Nikolaev and Ernest Hakanen (eds.) (2006)New York: Palgrave MacMillan, 283 pp., ISBN 1-4039-7113-7 (hbk), 42.00Media and Conflict in the Twenty-First Century, Philip Seib (ed.) (2005)New York: Palgrave MacMillan, 242 pp., ISBN 1-4039-6833-0 (hbk), 42.00Hypercapitalism: New Media, Language and Social Perceptions of Value, Phil Graham, 2005New York, Peter Lang, 202 pp., ISBN 0-8204-6217-9 (pbk), 17.42
Differential expression of γ-aminobutyric acid receptor A (GABAA) and effects of homocysteine
Authors: Tyagi Neetu , Lominadze David , Gillespie William , Moshal Karni S. , Sen Utpal , Rosenberger Dorothea S. , Steed Mesia , Tyagi Suresh C. 
Published: November 2007

AbstractClin Chem Lab Med 2007;45:1777–84.
Hyperhomocysteinemia – association with renal transsulfuration and redox signaling in rats
Authors: Pin-Lan Li , Fan Yi , Ningjun Li 
Published: November 2007

AbstractDespite substantial evidence indicating the association of hyperhomocysteinemia (hHcys) and end-stage renal disease (ESRD), the pathogenic role of increased plasma homocysteine (Hcys) levels in the progression of ESRD remains unclear. This review will briefly summarize recent findings regarding the role of hHcys in the development of glomerulosclerosis, the association of hHcys with reduced renal transsulfuration and Hcys-induced changes of redox signaling in the development of glomerulosclerosis in rat kidneys. Based on these results, it is concluded that hHcys is implicated in glomerular sclerosis in hypertension, elevated plasma Hcys in Dahl salt-sensitive (SS) hypertensive rats is due to downregulation of cystathionine β-synthase (CBS) expression and consequent abnormality of transsulfuration in the kidney compared with normotensive rats. Hcys-induced superoxide (OClin Chem Lab Med 2007;45:1688–93.
Association between homocysteine, vitamin B6 concentrations and inflammation
Authors: Gori Anna Maria , Sofi Francesco , Marcucci Rossella , Giusti Betti , Franco Gensini Gian , Abbate Rosanna 
Published: November 2007

AbstractDuring the last years, a growing body of evidence has been accumulated on the role of hyperhomocysteinemia in the occurrence of coronary artery disease and other arterial occlusive diseases. The mechanism by which high circulating homocysteine concentrations are a risk factor for atherothrombosis is incompletely understood. The present review is aimed to evaluate the role of inflammation in influencing homocysteine (Hcy) and vitamin BClin Chem Lab Med 2007;45:1728–36.
Homocysteine, left ventricular dysfunction and coronary artery disease: is there a link?
Authors: Rossi Gian Paolo , Seccia Teresa Maria , Pessina Achille Cesare 
Published: November 2007

AbstractExperimental and observational studies support a role of plasma homocysteine levels (tHcy) in coronary artery disease (CAD). In the GENICA (Genetic and Environmental factors In Coronary Atherosclerosis) study, we found that high tHcy predicted cardiovascular mortality in hypertensive, but not in normotensive, patients independently of CAD and history of myocardial infarction. Moreover, despite not being associated with the coronary atherosclerotic burden, tHcy was inversely associated with left ventricular (LV) ejection fraction. This inverse relationship between LV systolic function and tHcy, which has been independently confirmed, might explain the association of tHcy with the risk of incident heart failure documented in the Framingham Heart Study. Thus, additional mechanistic investigation taking into consideration the effects of tHcy on LV function is necessary to further explore the potential therapeutic usefulness of tHcy lowering treatment in CAD.Clin Chem Lab Med 2007;45:1645–51.
Effects of background substraction on differential kidney function measured by static scintigraphy with DMSA and dynamic scintigraphy with MAG 3
Authors: Smokvina A. , Grbac Ivanković S. , Licul V. , Girotto N. 
Published: November 2007

SummaryThe aim of this study was to assess the influence of background subtraction (BS) on estimation of differential kidney function (DF) on the static scintigraphy with 99mTc dimercaptosuccinic acid (DMSA) and dynamic scintigraphy with 99mTc mercaptoacetyltriglicine (MAG3) and to establish possible differences between DF values estimated with these methods. Patients, methods: Patients (n = 106) were selected among those scheduled to static and dynamic scintigraphies within 3 months, with no interim clinical and laboratory changes, regardless the kidney pathology. DF was estimated according to the uptake ratio method. Four background regions of interest (ROIs) were applied, identical for both studies, and DF values were recalculated after BS. The corrected values were compared to the values before correction, separately for DMSA and MAG3, and between the studies. The results showed that ROIs used introduce variable results for the same patients, predominantly when noncorrected DF values were <45%. There were no significant differences between DF values (corrected and noncorrected) obtained from static and dynamic scintigraphy in all groups of patients. Since numerous reasons can bring to the errors in DF estimation when BS is used, the conclusions are that it would probably be more accurate to avoid BS, particularly when DF values are compared in a patient follow-up, and when kidney function is normal. BS should be used, but always in the same way, only when there is a significant difference in kidney size, or when DF is <25%, since background activity is then considerable. MAG3 and DMSA can be equally used for DF estimation and their results compared in patient follow-up.
99mTc-MIBI SPECT in primary hyperparathyroidism
Authors: Thoma N. , Dietlein M. , Moka D. , Eschner W. , Faust M. , Schröder W. , von Hülst-Schlabrendorff M. , Ehses W. , Schicha H. , Schmidt M. 
Published: November 2007

SummaryAim of the study was to analyse the influence of a concomitant vitamin D deficiency on the results of 99mTc-MIBI studies in patients (pts) with primary hyperparathyroidism (pHPT). Patients, methods: Between January 1998 and May 2004, 71 pts with pHPT had undergone operation after a 99mTc-MIBI study of whom 54 pts (76%) had normal values of 25-OH-vitamin D3 and 17 pts (24%) had vitamin D deficiency. Results of a dual-phase 99mTc-MIBI protocol with SPECT were compared with histopathology. Results: In 54 pts with normal vitamin D values late SPECT images identified more lesions (n = 51, sensitivity 91%) than early planar (n = 45, sensitivity 82%) or late planar images (n = 50, sensitivity 88%). In 17 pts with vitamin D deficiency late SPECT images identified more lesions (n = 13, sensitivity 72%) than early planar (n = 10, sensitivity 56%) or late planar images (n = 10, sensitivity 56%) too. In pts with vitamin D deficiency the sensitivity of a 99mTc-MIBI SPECT study was lower than in those with normal vitamin D status (72% vs. 91%) and dependent on the value for PTH. However, the results did not reach statistical significance: early planar: p = 0.1625; late planar: p = 0.0039; 99mTc-MIBI SPECT: p = 0.1180. Conclusion: The likelihood of a pathological 99mTc-MIBI study being obtained in pts with pHPT is dependent on the parathyroid hormone level. However, a negative influence of a low vitamin D level on the scintigraphic detection rate of a parathyroid adenoma could not be proven which may be due to the low number of pts with vitamin D deficiency.
Is radioiodine therapy conducted too late in patients suffering from thyroid autonomy?
Authors: Happel C. , Döbert N. , Grünwald F. , Spilker L. 
Published: November 2007

SummaryAim: The effectiveness of radioiodine therapy (RIT) is proven. The aim of this study was to determine, how much time passes between diagnosis of thyroid autonomy or occurrence of functional and/or local symptoms on one hand and RIT on the other hand. Patients, methods: This retrospective study comprises 196 patients, who were treated with radioiodine for thyroid autonomy between 2002 and 2005. Evaluated parameters are begin of functional and/ or local symptoms, first scintigraphy with relevant Tc-Uptake as time point of primary diagnosis of thyroid autonomy and time point of implementation of RIT. Results: Between first scintigraphy with relevant Tc-Uptake and implementation of RIT 0–72 months passed (median: 3 months). 160 patients (81.6%) had a prior diagnosis of goitre by their general practitioner and 163 patients (83.3%) had a prior diagnosis of TSH suppression. The time period between first recommendation of RIT and implementation of RIT was 0–89 months (median: 2 months). In 142 patients (71.4%) functional and/or local symptoms were present over 73 months (median; range: 0–180 months) before the first scintigraphy with therapy relevant Tc-Uptake was conducted. Conclusion: Despite clear recommendations in corresponding guidelines too much time passes between first symptoms (median: 73 months), primary diagnosis of therapy relevant thyroid autonomy (median: 2 months) and implementation of RIT. Patients with functional and/or local symptoms should be examined for thyroid autonomy early. If thyroid autonomy is proven, RIT should be planned immediately, especially in high-risk patients.