bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Randomized Controlled Single-Blinded Comparison of Stretching Versus Stretching and Joint Mobilization for Posterior Shoulder Tightness Measured by Internal Rotation Motion Loss
Authors: Manske Robert C. , Meschke Matt , Porter Andrew , Smith Barbara , Reiman Michael 
Published: December 2009

Background: Posterior shoulder tightness, as demonstrated by limited internal rotation range of motion, is a suggested factor in many shoulder pathologies. Methods to increase posterior shoulder mobility may be beneficial. Hypothesis: Shoulder internal rotation range of motion will not change with either of 2 interventions: cross-body stretch alone and cross-body stretch plus posterior capsule joint mobilization. Study Design: Randomized controlled single-blinded clinical trial. Methods: The study comprised 39 college-age asymptomatic participants (7 men, 32 women) who were randomly assigned to 1 of 2 groups: stretching only (n, 20) and stretching plus posterior joint mobilizations (n, 19). All had a between-shoulder difference of internal rotation of 10° or more. Shoulder internal and external rotation was measured before and after a 4-week intervention period and 4 weeks postintervention. Participants in the stretching-only group performed the cross-body stretch on the limited side. Those in the other group (cross-body stretch plus joint mobilization) were treated with posterior joint mobilization techniques on the limited side. Results: Overall means for internal rotation of the treated shoulders significantly increased over baseline at the end of the intervention period and at 4 weeks postintervention. External rotation in all shoulders remained unchanged. By the end of intervention, total motion increased significantly from baseline but decreased significantly from the end of intervention to 4 weeks postintervention. Although not statistically significant, the second group (cross-body stretch plus joint mobilization) had greater increases in internal rotation. At 4 weeks postintervention, the second group had maintained its internal rotation gains to a greater degree than those of the stretching-only group. Conclusion: Internal rotation increased in both groups. Inclusion of joint mobilization in a rehabilitation program created trends toward increased shoulder internal rotation mobility. Clinical Relevance: Both methods—cross-body stretch and cross-body stretch plus joint mobilization—may be beneficial for those with limited internal rotation range of motion.
Combined effect of total nucleated cell dose and HLA match on transplantation outcome in 1061 cord blood recipients with hematologic malignancies
Authors: Barker Juliet N. , Scaradavou Andromachi , Stevens Cladd E. 
Published: December 2009

AbstractBoth total nucleated cell (TNC) dose and human leukocyte antigen (HLA)–match affect the outcome of cord blood (CB) transplantation. However, how to prioritize these characteristics in unit selection is not established. Therefore, we analyzed the outcomes of 1061 patients who received single-unit myeloablative CB transplantation for leukemia or myelodysplasia. TNC dose and HLA-match each affected survival via their effect on transplant-related mortality (TRM); neither was associated with relapse. Therefore, TRM was the focus of multivariate analyses combining dose and HLA-match. Compared with our 1 HLA-mismatch (MM) reference group with TNC 2.5 to 4.9 × 107/kg, recipients of 0 MM units had the lowest TRM regardless of dose (relative risk [RR] = 0.4, P = .019). TRM for recipients of 1- or 2-MM units with TNC 5.0 × 107/kg or greater was similar to the reference group (RR = 0.8, P = .391 and RR = 1.0, P = .847) despite their greater dose. Recipients of 2 MM units with TNC 2.5 to 4.9 × 107/kg had a greater TRM (RR = 1.5, P = .014), and those with 1 or 2 MM and TNC less than 2.5 × 107/kg or 3 MM did substantially worse. These findings support new unit selection criteria that take into account both TNC dose and HLA-match and have important implications for the size of the global CB inventory needed to find an optimum CB graft.
IRIS: a method for reverse engineering of regulatory relations in gene networks
Authors: Morganella Sandro , Zoppoli Pietro , Ceccarelli Michele 
Published: December 2009

Abstract

Background
The ultimate aim of systems biology is to understand and describe how molecular components interact to manifest collective behaviour that is the sum of the single parts. Building a network of molecular interactions is the basic step in modelling a complex entity such as the cell. Even if gene-gene interactions only partially describe real networks because of post-transcriptional modifications and protein regulation, using microarray technology it is possible to combine measurements for thousands of genes into a single analysis step that provides a picture of the cell's gene expression. Several databases provide information about known molecular interactions and various methods have been developed to infer gene networks from expression data. However, network topology alone is not enough to perform simulations and predictions of how a molecular system will respond to perturbations. Rules for interactions among the single parts are needed for a complete definition of the network behaviour. Another interesting question is how to integrate information carried by the network topology, which can be derived from the literature, with large-scale experimental data.

Results
Here we propose an algorithm, called inference of regulatory interaction schema (IRIS), that uses an iterative approach to map gene expression profile values (both steady-state and time-course) into discrete states and a simple probabilistic method to infer the regulatory functions of the network. These interaction rules are integrated into a factor graph model. We test IRIS on two synthetic networks to determine its accuracy and compare it to other methods. We also apply IRIS to gene expression microarray data for the Saccharomyces cerevisiae cell cycle and for human B-cells and compare the results to literature findings.

Conclusions
IRIS is a rapid and efficient tool for the inference of regulatory relations in gene networks. A topological description of the network and a matrix of gene expression profiles are required as input to the algorithm. IRIS maps gene expression data onto discrete values and then computes regulatory functions as conditional probability tables. The suitability of the method is demonstrated for synthetic data and microarray data. The resulting network can also be embedded in a factor graph model.
Potential impact of stress activated retrotransposons on genome evolution in a marine diatom
Authors: Maumus Florian , Allen Andrew E , Mhiri Corinne , Hu Hanhua , Jabbari Kamel , Vardi Assaf , Grandbastien Marie-Angèle , Bowler Chris 
Published: December 2009

Abstract

Background
Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available.

Results
In the present work, we establish that LTR retrotransposons (LTR-RTs) are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability.

Conclusion
Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.
Effects of temperature on gene expression in embryos of the coral Montastraea faveolata
Authors: Voolstra Christian R , Schnetzer Julia , Peshkin Leonid , Randall Carly J , Szmant Alina M , Medina Mónica 
Published: December 2009

Abstract

Background
Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5°C, 29.0°C, and 31.5°C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours.

Results
Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the long-term regulation upon heat stress.

Conclusions
Embryos responded differently depending on exposure time and temperature level. Embryos showed expression of stress-related genes already at a temperature of 29.0°C, but seemed to be able to counteract the initial response over time. By contrast, embryos at 31.5°C displayed continuous expression of stress genes. The genes that played a role in the response to elevated temperatures consisted of both highly conserved and coral-specific genes. These genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.
The repertoire of equine intestinal α-defensins
Authors: Bruhn Oliver , Paul Sven , Tetens Jens , Thaller Georg 
Published: December 2009

AbstractBackgroundDefensins represent an important class of antimicrobial peptides. These effector molecules of the innate immune system act as endogenous antibiotics to protect the organism against infections with pathogenic microorganisms. Mammalian defensins are classified into three distinct sub-families (α-, β- and θ-defensins) according to their specific intramolecular disulfide-bond pattern. The peptides exhibit an antimicrobial activity against a broad spectrum of microorganisms including bacteria and fungi. Alpha-Defensins are primarily synthesised in neutrophils and intestinal Paneth cells. They play a role in the pathogenesis of intestinal diseases and may regulate the flora of the intestinal tract. An equine intestinal α-defensin (DEFA1), the first characterised in theLaurasiatheria, shows a broad antimicrobial spectrum against human and equine pathogens. Here we report a first investigation of the repertoire of equine intestinal α-defensins. The equine genome was screened for putative α-defensin genes by using known α-defensin sequences as matrices. Based on the obtained sequence information, a set of oligonucleotides specific to the α-defensin gene-family was designed. The products generated by reverse-transcriptase PCR with cDNA from the small intestine as template were sub-cloned and numerous clones were sequenced.ResultsThirty-eight equine intestinal α-defensin transcripts were determined. After translation it became evident that at least 20 of them may code for functional peptides. Ten transcripts lacked matching genomic sequences and for 14 α-defensin genes apparently present in the genome no appropriate transcript could be verified. In other cases the same genomic exons were found in different transcripts.ConclusionsThe large repertoire of equine α-defensins found in this study points to a particular importance of these peptides regarding animal health and protection from infectious diseases. Moreover, these findings make the horse an excellent species to study biological properties of α-defensins. Interestingly, the peptides were not found in other species of theLaurasiatheriato date. Comparison of the obtained transcripts with the genomic sequences in the current assembly of the horse (EquCab2.0) indicates that it is yet not complete and/or to some extent falsely assembled.
BAC array CGH in patients with Velocardiofacial syndrome-like features reveals genomic aberrations on chromosome region 1q21.1
Authors: Brunet Anna , Armengol Lluís , Heine Damià , Rosell Jordi , García-Aragonés Manel , Gabau Elisabeth , Estivill Xavier , Guitart Miriam 
Published: December 2009

Abstract

Background
Microdeletion of the chromosome 22q11.2 region is the most common genetic aberration among patients with velocardiofacial syndrome (VCFS) but a subset of subjects do not show alterations of this chromosome region.

Methods
We analyzed 18 patients with VCFS-like features by comparative genomic hybridisation (aCGH) array and performed a face-to-face slide hybridization with two different arrays: a whole genome and a chromosome 22-specific BAC array. Putative rearrangements were confirmed by FISH and MLPA assays.

Results
One patient carried a combination of rearrangements on 1q21.1, consisting in a microduplication of 212 kb and a close microdeletion of 1.15 Mb, previously reported in patients with variable phenotypes, including mental retardation, congenital heart defects (CHD) and schizophrenia. While 326 control samples were negative for both 1q21.1 rearrangements, one of 73 patients carried the same 212-kb microduplication, reciprocal to TAR microdeletion syndrome. Also, we detected four copy number variants (CNVs) inherited from one parent (a 744-kb duplication on 10q11.22; a 160 kb duplication and deletion on 22q11.21 in two cases; and a gain of 140 kb on 22q13.2), not present in control subjects, raising the potential role of these CNVs in the VCFS-like phenotype.

Conclusions
Our results confirmed aCGH as a successful strategy in order to characterize additional submicroscopic aberrations in patients with VCF-like features that fail to show alterations in 22q11.2 region. We report a 212-kb microduplication on 1q21.1, detected in two patients, which may contribute to CHD.
The requirements and challenges in preventing of road traffic injury in Iran. A qualitative study
Authors: Khorasani-Zavareh Davoud , Mohammadi Reza , Khankeh Hamid Reza , Laflamme Lucie , Bikmoradi Ali , Haglund Bo JA 
Published: December 2009

Abstract

Background
Road traffic injuries (RTIs) are a major public health problem, especially in low- and middle-income countries. Among middle-income countries, Iran has one of the highest mortality rates from RTIs. Action is critical to combat this major public health problem. Stakeholders involved in RTI control are of key importance and their perceptions of barriers and facilitators are a vital source of knowledge. The aim of this study was to explore barriers to the prevention of RTIs and provide appropriate suggestions for prevention, based on the perceptions of stakeholders, victims and road-users as regards RTIs.

Methods
Thirty-eight semi-structured interviews were conducted with informants in the field of RTI prevention including: police officers; public health professionals; experts from the road administrators; representatives from the General Governor, the car industry, firefighters; experts from Emergency Medical Service and the Red Crescent; and some motorcyclists and car drivers as well as victims of RTIs. A qualitative approach using grounded theory method was employed to analyze the material gathered.

Results
The core variable was identified as "The lack of a system approach to road-user safety". The following barriers in relation to RTI prevention were identified as: human factors; transportation system; and organizational coordination. Suggestions for improvement included education (for the general public and targeted group training), more effective legislation, more rigorous law enforcement, improved engineering in road infrastructure, and an integrated organization to supervise and coordinate preventive activities.

Conclusion
The major barriers identified in this study were human factors and efforts to change human behaviour were suggested by means of public education campaigns and stricter law enforcement. However, the lack of a system approach to RTI prevention was also an important concern. There is an urgent need for both an integrated system to coordinate RTI activities and prevention and a major change in stakeholders' attitudes towards RTI prevention. The focus of all activities should take place on road users' safety.
Scale-up from microtiter plate to laboratory fermenter: evaluation by online monitoring techniques of growth and protein expression in Escherichia coli and Hansenula polymorpha fermentations
Authors: Kensy Frank , Engelbrecht Christoph , Büchs Jochen 
Published: December 2009

Abstract

Background
In the past decade, an enormous number of new bioprocesses have evolved in the biotechnology industry. These bioprocesses have to be developed fast and at a maximum productivity. Up to now, only few microbioreactors were developed to fulfill these demands and to facilitate sample processing. One predominant reaction platform is the shaken microtiter plate (MTP), which provides high-throughput at minimal expenses in time, money and work effort. By taking advantage of this simple and efficient microbioreactor array, a new online monitoring technique for biomass and fluorescence, called BioLector, has been recently developed. The combination of high-throughput and high information content makes the BioLector a very powerful tool in bioprocess development. Nevertheless, the scalabilty of results from the micro-scale to laboratory or even larger scales is very important for short development times. Therefore, engineering parameters regarding the reactor design and its operation conditions play an important role even on a micro-scale. In order to evaluate the scale-up from a microtiter plate scale (200 μL) to a stirred tank fermenter scale (1.4 L), two standard microbial expression systems, Escherichia coli and Hansenula polymorpha, were fermented in parallel at both scales and compared with regard to the biomass and protein formation.

Results
Volumetric mass transfer coefficients (kLa) ranging from 100 to 350 1/h were obtained in 96-well microtiter plates. Even with a suboptimal mass transfer condition in the microtiter plate compared to the stirred tank fermenter (kLa = 370-600 1/h), identical growth and protein expression kinetics were attained in bacteria and yeast fermentations. The bioprocess kinetics were evaluated by optical online measurements of biomass and protein concentrations exhibiting the same fermentation times and maximum signal deviations below 10% between the scales. In the experiments, the widely applied green fluorescent protein (GFP) served as an online reporter of protein expression for both strains.

Conclusions
The successful 7000-fold scale-up from a shaken microtiter plate to a stirred tank fermenter was demonstrated in parallel fermentations for standard microbial expression systems. This confirms that the very economical and time efficient platform of microtiter plates can be very easily scaled up to larger stirred tank fermenters under defined engineering conditions. New online monitoring techniques for microtiter plates, such as the BioLector, provide even more real-time kinetic data from fermentations than ever before and at an affordable price. This paves the way for a better understanding of the bioprocess and a more rational process design.
Cooperation of Notch and Ras/MAPK signaling pathways in human breast carcinogenesis
Authors: Mittal Suruchi , Subramanyam Deepa , Dey Devaveena , Kumar Rekha V , Rangarajan Annapoorni 
Published: December 2009

Abstract

Background
Recent studies have implicated aberrant Notch signaling in breast cancers. Yet, relatively little is known about the pattern of expression of various components of the Notch pathway, or its mechanism of action. To better understand the role of the Notch pathway in breast cancer, we have undertaken a detailed expression analysis of various Notch receptors, their ligands, and downstream targets at different stages of breast cancer progression.

Results
We report here that there is a general increase in the expression levels of Notch 1, 2, 4, Jagged1, Jagged2, and Delta-like 4 proteins in breast cancers, with simultaneous upregulation of multiple Notch receptors and ligands in a given cancer tissue. While Notch3 and Delta-like1 were undetectable in normal tissues, moderate to high expression was detected in several cancers. We detected the presence of active, cleaved Notch1, along with downstream targets of the Notch pathway, Hes1/Hes5, in ~75% of breast cancers, clearly indicating that in a large proportion of breast cancers Notch signaling is aberrantly activated. Furthermore, we detected cleaved Notch1 and Hes1/5 in early precursors of breast cancers - hyperplasia and ductal carcinoma in situ - suggesting that aberrant Notch activation may be an early event in breast cancer progression. Mechanistically, while constitutively active Notch1 alone failed to transform immortalized breast cells, it synergized with the Ras/MAPK pathway to mediate transformation. This cooperation is reflected in vivo, as a subset of cleaved Notch positive tumors additionally expressed phopsho-Erk1/2 in the nuclei. Such cases exhibited high node positivity, suggesting that Notch-Ras cooperation may lead to poor prognosis.

Conclusions
High level expression of Notch receptors and ligands, and its increased activation in several breast cancers and early precursors, places Notch signaling as a key player in breast cancer pathogenesis. Its cooperation with the Ras/MAPK pathway in transformation offers combined inhibition of the two pathways as a new modality for breast cancer treatment.
Factors associated with seroprevalence of hepatitis C among dentists at a large Brazilian city
Authors: Resende Vera Lúcia S , Abreu Mauro Henrique G , Paiva Saul M , Teixeira Rosângela , Pordeus Isabela A 
Published: December 2009

AbstractBackgroundThe aim of the present study was to investigate the seroprevalence and sociodemographic data, health-related and occupational factors and other correlates of sero-posivity among dentists in the city of Belo Horizonte, MG, Brazil.MethodsA cross-sectional survey was carried out with 1302 dentists in Belo Horizonte, Brazil. All dentists were tested for anti-HCV using a commercially available enzyme-linked immunosorbent assay (ELISA). Individuals positive for anti-HCV were recalled for further evaluation. The presence of HCV RNA in anti-HCV-positive samples was assessed using reverse transcription-polymerase chain reaction (RT-PCR). Data on demographic, behavioural and occupational exposure aspects were collected through questionnaires.ResultsThe seroprevalence of anti-HCV was 0.9% (95% IC 0.5-1.7%). The factors associated to the prevalence of hepatitis C were history of blood transfusion (p = 0.002) and having undergone a test for hepatitis C (p = 0.015).ConclusionsThe seroprevalence of anti-HCV among dentists is low. Moreover, no occupational exposure was associated to the seroprevalence of hepatitis C.