bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of clostridial glucosylating toxins on the proteome of colonic cells determined by isotope-coded protein labeling and LC-MALDI
Authors: Jochim Nelli , Gerhard Ralf , Just Ingo , Pich Andreas 
Published: August 2011

Abstract

Background
The anaerobe Clostridium difficile produces two major virulence factors toxin A and B that inactivate Rho proteins by glucosylation of a pivotal threonine residue. Purified toxins induce reorganization of the cytoskeleton and cell death in colonic cells. Whether all toxin effects on target cells depend on catalytic glucosyltransferase activity is unclear at present. Thus, we conducted a proteome approach to compare the protein profile of target cells treated either with wild type toxin A (rTcdA wt) or with a catalytically inactive mutant toxin A (mutant rTcdA). Relative protein quantification was feasible using isotope-coded protein labeling techniques (ICPL) and mass spectrometry (LC-MALDI).

Results
Altogether we found a significant differential expression of thirty proteins after treatment with rTcdA wt or mutant rTcdA. Mutant rTcdA caused up-regulation of seven proteins and sixteen proteins were responsive to rTcdA wt after 5 h. Long-term effect of rTcdA wt on protein expression was the down-regulation of eleven proteins. Up- or down-regulation of several proteins was verified by western blot analysis confirming the MS results.

Conclusion
Our results indicate incubation time-dependent effects of the clostridial glucosylating toxin A on colonic cells. The rTcdA wt impact more cellular functions than actin cytoskeleton reorganization and apoptosis. Furthermore, these data give insight into glucosyltransferase independent effects of clostridial glucosylating toxins on target cells after short incubation time. Additionally, our data reveal pro-inflammatory and proliferative effects of mutant rTcdA after short-term incubation.
Early monitoring of the human polyomavirus BK replication and sequencing analysis in a cohort of adult kidney transplant patients treated with basiliximab
Authors: Anzivino Elena , Bellizzi Anna , Mitterhofer Anna Paola , Tinti Francesca , Barile Mario , Colosimo Maria Teresa , Fioriti Daniela , Mischitelli Monica , Chiarini Fernanda , Ferretti Giancarlo , Taliani Gloria , Pietropaolo Valeria 
Published: August 2011

Abstract

Background
Nowadays, better immunosuppressors have decreased the rates of acute rejection in kidney transplantation, but have also led to the emergence of BKV-associated nephropathy (BKVAN). Therefore, we prospectively investigated BKV load in plasma and urine samples in a cohort of kidney transplants, receiving basiliximab combined with a mycophenolate mofetil-based triple immunotherapy, to evaluate the difference between BKV replication during the first 3 months post-transplantation, characterized by the non-depleting action of basiliximab, versus the second 3 months, in which the maintenance therapy acts alone. We also performed sequencing analysis to assess whether a particular BKV subtype/subgroup or transcriptional control region (TCR) variants were present.

Methods
We monitored BK viruria and viremia by quantitative polymerase chain reaction (Q-PCR) at 12 hours (Tx), 1 (T1), 3 (T2) and 6 (T3) months post-transplantation among 60 kidney transplant patients. Sequencing analysis was performed by nested-PCR with specific primers for TCR and VP1 regions. Data were statistically analyzed using χ2 test and Student's t-test.

Results
BKV was detected at Tx in 4/60 urine and in 16/60 plasma, with median viral loads of 3,70 log GEq/mL and 3,79 log GEq/mL, respectively, followed by a significant increase of both BKV-positive transplants (32/60) and median values of viruria (5,78 log GEq/mL) and viremia (4,52 log GEq/mL) at T2. Conversely, a significantly decrease of patients with viruria and viremia (17/60) was observed at T3, together with a reduction of the median urinary and plasma viral loads (4,09 log GEq/mL and 4,00 log GEq/mL, respectively). BKV TCR sequence analysis always showed the presence of archetypal sequences, with a few single-nucleotide substitutions and one nucleotide insertion that, interestingly, were all representative of the particular subtypes/subgroups we identified by VP1 sequencing analysis: I/b-2 and IV/c-2.

Conclusions
Our results confirm previous studies indicating that BKV replication may occur during the early hours after kidney transplantation, reaches the highest incidence in the third post-transplantation month and then decreases within the sixth month, maybe due to induction therapy. Moreover, it might become clinically useful whether specific BKV subtypes or rearrangements could be linked to a particular disease state in order to detect them before BKVAN onset.
Frequency of human immunodeficiency virus type-2 in hiv infected patients in Maputo City, Mozambique
Authors: Maueia Cremildo , Costa Deise , Meggi Bindiya , Ismael Nalia , Walle Carla , Curvo Raphael , Abreu Celina , Bhatt Nilesh , Tanuri Amilcar , Jani Ilesh V , Ferreira Orlando C 
Published: August 2011

Abstract
The HIV/AIDS pandemic is primarily caused by HIV-1. Another virus type, HIV-2, is found mainly in West African countries. We hypothesized that population migration and mobility in Africa may have facilitated the introduction and spreading of HIV-2 in Mozambique. The presence of HIV-2 has important implications for diagnosis and choice of treatment of HIV infection. Hence, the aim of this study was to estimate the prevalence of HIV-2 infection and its genotype in Maputo, Mozambique.
HIV-infected individuals (N = 1,200) were consecutively enrolled and screened for IgG antibodies against HIV-1 gp41 and HIV-2 gp36 using peptide-based enzyme immunoassays (pepEIA). Specimens showing reactivity on the HIV-2 pepEIA were further tested using the INNO-LIA immunoblot assay and HIV-2 PCR targeting RT and PR genes. Subtype analysis of HIV-2 was based on the protease gene.
After screening with HIV-2 pepEIA 1,168 were non-reactive and 32 were reactive to HIV-2 gp36 peptide. Of this total, 30 specimens were simultaneously reactive to gp41 and gp36 pepEIA while two samples reacted solely to gp36 peptide. Only three specimens containing antibodies against gp36 and gp105 on the INNO-LIA immunoblot assay were found to be positive by PCR to HIV-2 subtype A.
The proportion of HIV-2 in Maputo City was 0.25% (90%CI 0.01-0.49). The HIV epidemic in Southern Mozambique is driven by HIV-1, with HIV-2 also circulating at a marginal rate. Surveillance program need to improve HIV-2 diagnosis and consider periodical survey aiming to monitor HIV-2 prevalence in the country.
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
Authors: Milne Caroline B , Eddy James A , Raju Ravali , Ardekani Soroush , Kim Pan-Jun , Senger Ryan S , Jin Yong-Su , Blaschek Hans P , Price Nathan D 
Published: August 2011

Abstract

Background
Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications.

Results
We present the first genome-scale metabolic model (i CM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate i CM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed.

Conclusions
Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. i CM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production.
Effects of atopy and rhinitis on exhaled nitric oxide values ‐ a systematic review
Authors: Linhares Daniela , Jacinto Tiago , Pereira Ana M , Fonseca João A 
Published: August 2011

AbstractBackgroundAtopy and rhinitis are among the factors affecting exhaled nitric oxide (FeNO) values and may contribute to difficulties in the clinical interpretation of FeNO measurements. However, data assessing their effects on FeNO values had never been summarized. This review aims to evaluate the effect of atopy and rhinitis in FeNO values in otherwise healthy individuals.MethodsA systematic review was performed in Pubmed, Scopus and ISI Web of Knowledge. A two‐step selection process was completed, and from 2357 references 19 were included. The inclusion criteria were: participants without known diseases other than rhinitis; atopy assessement by SPT or Specific IgE; and FeNO measurements according to ATS/ERS recommendations.ResultsThe 8 articles measuring FeNO in children showed higher values in both allergic rhinitis and atopic children when compared with healthy children. The 11 articles performed in adults observed higher FeNO in AR patients comparatively with either healthy or atopic individuals. However, adult healthy and atopic individuals had similar FeNO values.ConclusionsFeNO values are higher in individuals with rhinitis and/or atopy without other health problems. These effects are small, seem to be independent and should be further studied using multivariate models. The effect of atopy was observed only in children. The combined effect of atopy and rhinitis produced higher FeNO values in adults. These results support that both atopy and rhinitis should be considered when interpreting or when defining FeNO reference values.
A comparison of 111In- or 64Cu-DOTA-trastuzumab Fab fragments for imaging subcutaneous HER2-positive tumor xenografts in athymic mice using microSPECT/CT or microPET/CT
Authors: Chan Conrad , Scollard Deborah A , McLarty Kristin , Smith Serena , Reilly Raymond M 
Published: August 2011

Abstract

Background
Our objective was to compare 111In- or 64Cu-DOTA-trastuzumab Fab fragments for imaging small or large s.c. tumor xenografts in athymic mice that display a wide range of human epidermal growth factor receptor-2 (HER2) expression using microSPECT/CT or microPET/CT.

Methods
Trastuzumab Fab were labeled with 111In or 64Cu by conjugation to 1,4,7,10-tetraazacyclododecane N, N', N'', N'''-tetraacetic acid (DOTA). The purity of 111In- and 64Cu-DOTA-trastuzumab Fab was measured by SDS-PAGE and HPLC. HER2 binding affinity was determined in saturation radioligand binding assays using SKBR-3 cells (1.3 × 106 HER2/cell). MicroSPECT/CT and microPET/CT were performed in athymic mice bearing s.c. BT-20 and MDA-MB-231 xenografts with low (0.5 to 1.6 × 105 receptors/cell), MDA-MB-361 tumors with intermediate (5.1 × 105 receptors/cell) or SKOV-3 xenografts with high HER2 expression (1.2 × 106 receptors/cell) at 24 h p.i. of 70 MBq (10 μg) of 111In-DOTA-trastuzumab Fab or 22 MBq (10 μg) of 64Cu-DOTA-trastuzumab Fab or irrelevant 111In- or 64Cu-DOTA-rituximab Fab. Tumor and normal tissue uptake were quantified in biodistribution studies.

Results

111In- and 64Cu-DOTA-trastuzumab were > 98% radiochemically pure and bound HER2 with high affinity (K
d = 20.4 ± 2.5 nM and 40.8 ± 3.5 nM, respectively). MDA-MB-361 and SKOV-3 tumors were most clearly imaged using 111In- and 64Cu-DOTA-trastuzumab Fab. Significantly higher tumor/blood (T/B) ratios were found for 111In-DOTA-trastuzumab Fab than 111In-DOTA-rituximab Fab for BT-20, MDA-MB-231 and MDA-MB-361 xenografts, and there was a direct association between T/B ratios and HER2 expression. In contrast, tumor uptake of 64Cu-DOTA-trastuzumab Fab was significantly higher than 64Cu-DOTA-rituximab Fab in MDA-MB-361 tumors but no direct association with HER2 expression was found. Both 111In- and 64Cu-DOTA-trastuzumab Fab imaged small (5 to 10 mm) or larger (10 to 15 mm) MDA-MB-361 tumors. Higher blood, liver, and spleen radioactivity were observed for 64Cu-DOTA-trastuzumab Fab than 111In-DOTA-trastuzumab Fab.

Conclusions
We conclude that 111In-DOTA-trastuzumab Fab was more specific than 64Cu-DOTA-trastuzumab Fab for imaging HER2-positive tumors, especially those with low receptor density. This was due to higher levels of circulating radioactivity for 64Cu-DOTA-trastuzumab Fab which disrupted the relationship between HER2 density and T/B ratios. Use of alternative chelators that more stably bind 64Cu may improve the association between T/B ratios and HER2 density for 64Cu-labeled trastuzumab Fab.
The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Authors: Sandmann Thomas , Vogg Matthias C , Owlarn Suthira , Boutros Michael , Bartscherer Kerstin 
Published: August 2011

Abstract
Background
Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown.

Results
To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning.

Conclusions
Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.
Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites
Authors: Schilling Oliver , dem Keller Ulrich auf , Overall Christopher M. 
Published: August 2011

Abstract
Proteomic identification of protease cleavage site specificity (PICS) is a recent proteomic approach for the easy mapping of protease subsite preferences that determines both the prime- and non-prime side specificity concurrently. Here we greatly facilitate user access by providing an automated and simple web-based data-analysis resource termed WebPics (http://clipserve.clip.ubc.ca/pics/). We demonstrate the utility of WebPics analysis of PICS data by determining the substrate specificity of factor Xa from P6-P6’, an important blood coagulation protease that proteolytically generates thrombin from prothrombin. PICS confirms existing data on non-prime site specificity and refines our knowledge of factor Xa prime-site selectivity.
Musical Communities: Rethinking the Collective in Music
Authors: Shelemay Kay Kaufman 
Published: August 2011

AbstractThis essay discusses the study of musical communities, taking as its point of departure the growing avoidance of the term “community” within much of recent musical scholarship. After exploring factors that have been responsible for the move away from community studies, the paper details both the creation of new nomenclature and the discourse surrounding the introduction of these new terms. Based on insights drawn from musical ethnography with recent African immigrants to the United States, the paper goes on to propose a revised framework for approaching “community.” It suggests that attention to processes of descent, dissent, and affinity both elucidates music's generative role in shaping new collectivities and unsettles the notion of music as a static sonic marker of social groupings. The conclusion touches briefly on new research from the sciences that is beginning to shed new light on music's role in generating social outcomes and the potential it holds for future collaboration with music scholars across disciplinary boundaries.
Palate Dimensions in Six-Year-Old Children with Unilateral Cleft Lip and Palate: A Six-Center Study on Dental Casts
Authors: Koželj Vesna , Vegnuti Miljana , Drevenšek Martina , Hortis-Dzierzbicka Maria , Gonzalez-Landa Gonzalo , Hanstein Siiri , Klimova Irena , Kobus Kazimierz , Kobus-Zaleśna Katarzyna , Semb Gunvor , Shaw Bill 
Published: August 2011

Objective To compare palatal dimensions in 6-year-old children with unilateral cleft lip and palate (UCLP) treated by different protocols with those of noncleft children. Design Retrospective intercenter outcome study. Patients Upper dental casts from 129 children with repaired UCLP and 30 controls were analyzed by the trigonometric method. Setting Six European cleft centers. Main outcome measures Sagittal, transverse, and vertical dimensions of the palate were observed. Statistics Palate variables were analyzed with descriptive methods and nonparametric tests. Regarding several various characteristics measured on a relatively small number of subjects, hierarchical, k-means clustering, and principal component analyses were used. Results Mean values of the observed dimensions for five cleft groups differed significantly from the control (p < .05). The group with one-stage closure of the cleft differed significantly from all other cleft groups in most variables (p < .05). Principal component analysis of all 159 cases identified three clusters with specific morphologic characteristics of the palate. A similar number of treated children were classified into each cluster, while all children without clefts were classified in the same cluster. The percentage of treated children from a particular group that fit this cluster ranged from 0% to 70% and increased with age at palatal closure and number of primary surgical procedures. Conclusion At 6 years of age, children with stepwise repair and hard palate closure after the age of two more frequently result in palatal dimensions of noncleft control than children with earlier palatal closure and one-stage cleft repair.
Nasal Changes after Presurgical Nasoalveolar Molding (PNAM) in the Unilateral Cleft Lip Nose
Authors: Gomez David F. , Donohue Sean T. , Figueroa Alvaro A. , Polley John W. 
Published: August 2011

Purpose Nasal reconstruction for patients with unilateral cleft lip and palate (UCLP) is a challenge for the reconstructive surgeon. Presurgical nasoalveolar molding (PNAM) was introduced to reshape the cleft nasal structures prior to lip repair. This study analyzed two-dimensional nasal changes before and after PNAM in patients with complete UCLP. Methods Thirty UCLP patients (19 males; 11 females) who received PNAM before lip repair were included in this study. PNAM was applied for 100 days. Nasal casts were obtained before and after PNAM. Frontal and 45° standardized digital photographs were taken from all casts, and a photogrammetric analysis (16 linear, six angular, and two area measurements) was performed. Paired Student's t tests were used to search for differences by time, and time versus side (cleft versus noncleft). Results Significant reduction of cleft columella deviation with an increase in columella length, nostril height, and axial inclination on the cleft side were recorded. This resulted in an increase in the projection of the nasal tip. The noncleft measurements remained without significant changes. The cleft nostril area increased significantly more than the noncleft side by 90% with PNAM treatment. Significant normal growth changes were observed in nasal width and nasal height. Conclusion A favorable reshaping of the nose after PNAM was achieved, resulting in an improvement in form before lip surgery. These changes lead to improved nasal symmetry before primary lip and nasal reconstruction in UCLP patients.
Structural Abnormalities of the Central Auditory Pathway in Infants with Nonsyndromic Cleft Lip and/or Palate
Authors: Yang Frank F. , McPherson Bradley , Shu Huang , Xie Na , Xiang Kui 
Published: August 2011

Objective To investigate possible structural abnormalities of the central auditory pathway in infants with nonsyndromic cleft lip and/or palate (NSCL/P). Participants Twenty-seven Chinese infants with NSCL/P, aged from 6 to 24 months. Intervention Morphological magnetic resonance imaging (MRI) measurements of the central auditory nervous system (CANS) in infants with NSCL/P were analyzed and compared with those of age- and sex-matched normal controls. Results No significant group differences were found in general brain measurements, including volumes of the brain stem and right hemisphere. However, infants with NSCL/P had statistically significantly smaller volumes of the left thalamus and left auditory cortex and notably decreased thickness of the left auditory cortex. Conclusion Cortical abnormalities were more marked compared with other MRI measurements. Structural CANS abnormalities in infants with NSCL/P may be located mainly in the left cerebral hemisphere. The development and maturation of the auditory cortex in infants with NSCL/P may be abnormal when compared with those of normal children.