bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor β-chain repertoire
Authors: Di Tommaso Silvia , Antonacci Rachele , Ciccarese Salvatrice , Massari Serafina 
Published: January 2010

AbstractBackgroundIn most species of mammals, theTRBlocus has the common feature of a library ofTRBVgenes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a singleTRBDgene, 6-7TRBJgenes and oneTRBCgene. An enhancer located at the 3'end of the lastTRBCand a well-defined promoter situated at the 5'end of theTRBDgene and/or a undefined promoter situated at the 5'end of theTRBD2are sufficient to generate the full recombinase accessibility at the locus. In ruminant species, the 3'end of theTRBlocus is characterized by the presence of three D-J-C clusters, each constituted by a singleTRBD, 5-7TRBJand oneTRBCgenes with the center cluster showing a structure combined with the clusters upstream and downstream, suggesting that a unequal crossover occurred in the duplication. An enhancer downstream the lastTRBC, and a promoter at the 5'-end of eachTRBDgene are also present.ResultsIn this paper we focused our attention on the analysis of a large number of sheep TR β-chain transcripts derived from four different lymphoid tissues of three diverse sheep breed animals to certify the use and frequency of the three gene clusters in the β-chain repertoire. As the sheepTRBlocus genomic organization is known, the exact interpretation of the V-D-J rearrangements was fully determined. Our results clearly demonstrate that sheep β-chain constitutes a level of variability that is substantially larger than that described in other mammalian species. This is due not only to the increase of the number of D and J genes available to the somatic recombination, but also to the presence of the trans-rearrangement process. Moreover, the functional complexity of β-chain repertoire is resolved by other mechanisms such as alternative cis- and trans-splicing and recombinational diversification that seems to affect the variety of the constant region.ConclusionAll together our data demonstrate that a disparate set of molecular mechanisms operate to perform a diversified repertoire in the sheep β-chain and this could confer some special biological properties to the corresponding αβ T cells in the ruminant lineage.
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species
Authors: Lescat Mathilde , Hoede Claire , Clermont Olivier , Garry Louis , Darlu Pierre , Tuffery Pierre , Denamur Erick , Picard Bertrand 
Published: January 2010

AbstractBackgroundPrevious studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny ofEscherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.ResultsWe identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis ofaesnucleotide sequences in a panel of 78 reference strains, including theE. colireference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed fromaessequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1and B2by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link betweenaesand extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region ofaesto be associated with virulence.ConclusionOur findings suggest thataesdoes not play a direct role in the virulence ofE. coliextraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaeaL.)
Authors: Zhao Chuan-Zhi , Xia Han , Frazier Taylor Price , Yao Ying-Yin , Bi Yu-Ping , Li Ai-Qin , Li Meng-Jun , Li Chang-Sheng , Zhang Bao-Hong , Wang Xing-Jun 
Published: January 2010

Abstract

Background
MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy.

Results
In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts.

Conclusions
This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.
Apyrase treatment of myocardial infarction according to a clinically applicable protocol fails to reduce myocardial injury in a porcine model
Authors: van der Pals Jesper , Koul Sasha , Götberg Michael I , Olivecrona Göran K , Ugander Martin , Kanski Mikael , Otto Andreas , Götberg Matthias , Arheden Håkan , Erlinge David 
Published: January 2010

AbstractBackgroundEctonucleotidase dependent adenosine generation has been implicated in preconditioning related cardioprotection against ischemia-reperfusion injury, and treatment with a soluble ectonucleotidase has been shown to reduce myocardial infarct size (IS) when applied prior to induction of ischemia. However, ectonucleotidase treatment according to a clinically applicable protocol, with administration only after induction of ischemia, has not previously been evaluated. We therefore investigated if treatment with the ectonucleotidase apyrase, according to a clinically applicable protocol, would reduce IS and microvascular obstruction (MO) in a large animal model.MethodsA percutaneous coronary intervention balloon was inflated in the left anterior descending artery for 40 min, in 16 anesthetized pigs (40-50 kg). The pigs were randomized to 40 min of 1 ml/min intracoronary infusion of apyrase (10 U/ml, n = 8) or saline (0.9 mg/ml, n = 8), twenty minutes after balloon inflation. Area at risk (AAR) was evaluated byex vivoSPECT. IS and MO were evaluated byex vivoMRI.ResultsNo differences were observed between the apyrase group and saline group with respect to IS/AAR (75.7 ± 4.2% vs 69.4 ± 5.0%, p = NS) or MO (10.7 ± 4.8% vs 11.4 ± 4.8%, p = NS), but apyrase prolonged the post-ischemic reactive hyperemia.ConclusionApyrase treatment according to a clinically applicable protocol, with administration of apyrase after induction of ischemia, does not reduce myocardial infarct size or microvascular obstruction.
Predictors of health decline in older adults with pneumonia: findings from the Community Acquired Pneumonia Impact Study
Authors: Fernandez Eduardo , Krueger Paul , Loeb Mark 
Published: January 2010

AbstractBackgroundThe purpose of this study was to identify predictors of health decline among older adults with clinically diagnosed community acquired pneumonia (CAP). It was hypothesized that older adults with CAP who had lower levels of social support would be more likely to report a decline in health.MethodsA telephone survey was used to collect detailed information from older adults about their experiences with CAP. A broader determinants of health framework was used to guide data collection. This was a community wide study with participants being recruited from all radiology clinics in one Ontario community.ResultsThe most important predictors of a health decline included: two symptoms (no energy; diaphoresis), two lifestyle variables (being very active; allowing people to smoke in their home), one quality of life variable (little difficulty in doing usual daily activities) and one social support variable (having siblings).ConclusionsA multiplicity of factors was found to be associated with a decline in health among older adults with clinically diagnosed CAP. These findings may be useful to physicians, family caregivers and others for screening older adults and providing interventions to help ensure positive health outcomes.
A randomised controlled trial and cost-effectiveness evaluation of "booster" interventions to sustain increases in physical activity in middle-aged adults in deprived urban neighbourhoods
Authors: Hind Daniel , Scott Emma J , Copeland Robert , Breckon Jeff D , Crank Helen , Walters Stephen J , Brazier John E , Nicholl Jon , Cooper Cindy , Goyder Elizabeth 
Published: January 2010

Abstract

Background
Systematic reviews have identified a range of brief interventions which increase physical activity in previously sedentary people. There is an absence of evidence about whether follow up beyond three months can maintain long term physical activity. This study assesses whether it is worth providing motivational interviews, three months after giving initial advice, to those who have become more active.

Methods/Design
Study candidates (n = 1500) will initially be given an interactive DVD and receive two telephone follow ups at monthly intervals checking on receipt and use of the DVD. Only those that have increased their physical activity after three months (n = 600) will be randomised into the study. These participants will receive either a "mini booster" (n = 200), "full booster" (n = 200) or no booster (n = 200). The "mini booster" consists of two telephone calls one month apart to discuss physical activity and maintenance strategies. The "full booster" consists of a face-to-face meeting with the facilitator at the same intervals. The purpose of these booster sessions is to help the individual maintain their increase in physical activity. Differences in physical activity, quality of life and costs associated with the booster interventions, will be measured three and nine months from randomisation. The research will be conducted in 20 of the most deprived neighbourhoods in Sheffield, which have large, ethnically diverse populations, high levels of economic deprivation, low levels of physical activity, poorer health and shorter life expectancy. Participants will be recruited through general practices and community groups, as well as by postal invitation, to ensure the participation of minority ethnic groups and those with lower levels of literacy. Sheffield City Council and Primary Care Trust fund a range of facilities and activities to promote physical activity and variations in access to these between neighbourhoods will make it possible to examine whether the effectiveness of the intervention is modified by access to community facilities. A one-year integrated feasibility study will confirm that recruitment targets are achievable based on a 10% sample.

Discussion
The choice of study population, study interventions, brief intervention preceding the study, and outcome measure are discussed.

Trial Registration
Current Controlled Trials: ISRCTN56495859; ClinicalTrials.gov: NCT00836459.
Health-related quality of life among individuals with long-standing spinal cord injury: a comparative study of veterans and non-veterans
Authors: Saadat Soheil , Javadi Masoud , Divshali Baharak Sabet , Tavakoli Amir Hussein , Ghodsi Seyed Mohammad , Montazeri Ali , Rahimi-Movaghar Vafa 
Published: January 2010

Abstract

Background
Spinal cord-injured (SCI) patients experience poor health-related quality of life (HRQOL) and they usually report lower HRQOL than the general population or population subgroups in Iran and elsewhere. The aim of this study was to compare HRQOL between veterans and non-veterans with SCI in Iran.

Methods
This was a cross-sectional study. HRQOL was measured using the 36-item Short Form Health Survey (SF-36). Thirty-nine male veterans and 63 non-veteran males with SCI were included in the study. Regression analyses were applied to determine the variables affecting physical and mental health-related quality of life among the patients.

Results
The male veterans had a lower HRQOL than the non-veterans with SCI. The differences were significant for all measures except for physical and social functioning. The greatest difference was observed for bodily pain (P = 0.001). The regression analysis results indicated that a longer time since injury was associated (P = 0.01) with better physical health-related quality of life (PCS), while being a veteran (P < 0.001) and having a spinal lesion in the cervical region (P = 0.001) were associated with poorer PCS. Older age (P < 0.001) and higher education (P = 0.01) were associated with better mental health-related quality of life (MCS), while being a veteran and having a spinal lesion in the cervical region (P = 0.02) were associated with poorer MCS.

Conclusion
The study findings showed that veterans with SCI experienced lower HRQOL than their non-veteran counterparts. A qualitative study is recommended to evaluate why HRQOL was lower in veterans than in non-veterans with SCI although veterans had higher incomes as a result of their pensions and increased access to equipment, and medications. To improve quality of life in both veterans and non-veterans with spinal cord injuries, policy changes or implementation of new interventions may be essential so that veterans could receive additional support (e.g. counseling, recreation therapy, vocational therapy, etc.) and non-veterans could meet their basic needs.
Assessing a risk tailored intervention to prevent disabling low back pain - protocol of a cluster randomized controlled trial
Authors: Schmidt Carsten Oliver , Chenot Jean-François , Pfingsten Michael , Fahland Ruth Anja , Lindena Gabriele , Marnitz Ulf , Pfeifer Klaus , Kohlmann Thomas 
Published: January 2010

Abstract

Background
Although most patients with low back pain (LBP) recover within a few weeks a significant proportion has recurrent episodes or will develop chronic low back pain. Several mainly psychosocial risk factors for developing chronic LBP have been identified. However, effects of preventive interventions aiming at behavioural risk factors and unfavourable cognitions have yielded inconsistent results. Risk tailored interventions may provide a cost efficient and effective means to take systematic account of the individual risk factors but evidence is lacking.

Methods/Design
This study will be a cluster-randomised controlled trial comparing screening and a subsequent risk tailored intervention for patients with low back pain to prevent chronic low back pain compared to treatment as usual in primary care. A total of 600 patients from 20 practices in each study arm will be recruited in Berlin and Goettingen. The intervention comprises the following elements: Patients will be assigned to one of four risk groups based on a screening questionnaire. Subsequently they receive an educational intervention including information and counselling tailored to the risk group. A telephone/email consulting service for back pain related problems are offered independent of risk group assignment. The primary outcomes will be functional capacity and sick leave.

Discussion
This trial will evaluate the effectiveness of screening for risk factors for chronic low back pain followed by a risk tailored intervention to prevent chronic low back pain. This trial will contribute new evidence regarding the flexible use of individual physical and psychosocial risk factors in general practice.

Trial registration
ISRCTN 68205910
Plexin-B1, glycodelin and MMP7 expression in the human fallopian tube and in the endometrium
Authors: Amir Michal , Romano Shabtai , Goldman Shlomit , Shalev Eliezer 
Published: January 2010

Abstract

Background
To study the expression of Plexin-B1, Glycodelin, and MMP7 during the menstrual cycle in the endometrium and in the fallopian tube.

Methods
The research included women undergoing hysterectomy, tubal sterilization or salpingo-oophoerectomy. Total RNA from endometrial and fallopian tube tissues was extracted using a total RNA isolation kit. Semi-quantitative RT-PCR was performed to examine mRNA relative expression.

Results
Plexin-B1 expression in the endometrium was significantly higher on days 19 - 23 compared to days 12 - 14 (1.166 +/- 0.42 versus 0.523 +/- 0.299), P < 0.005. In the fallopian tube the level of plexin-B1 did not change significantly throughout the menstrual cycle. Glycodelin expression was significantly higher on days 19 - 23 compared with days 12-14, both in the endometrium (0.819 +/- 0.564 versus 0.072 +/- 0.343, P < 0.05) and the fallopian tube (0.796 +/- 0.196 versus 0.329 +/- 0.398, P < 0.05). Although the level of MMP7 secretion was the highest in the secretory phase the difference from the proliferative phase did not reach statistical significance, neither in the endometrium nor in the fallopian tube. This could result from a lack of power.

Conclusions
In the endometrium, both Glycodelin and Plexin-B1 are exhibiting a cyclic pattern suggesting a possible steroid regulation and a role in endometrial receptivity.
Evaluation of ammonia fibre expansion (AFEX) pretreatment for enzymatic hydrolysis of switchgrass harvested in different seasons and locations
Authors: Bals Bryan , Rogers Chad , Jin Mingjie , Balan Venkatesh , Dale Bruce 
Published: January 2010

Abstract

Background
When producing biofuels from dedicated feedstock, agronomic factors such as harvest time and location can impact the downstream production. Thus, this paper studies the effectiveness of ammonia fibre expansion (AFEX) pretreatment on two harvest times (July and October) and ecotypes/locations (Cave-in-Rock (CIR) harvested in Michigan and Alamo harvested in Alabama) for switchgrass (Panicum virgatum).

Results
Both harvest date and ecotype/location determine the pretreatment conditions that produce maximum sugar yields. There was a high degree of correlation between glucose and xylose released regardless of the harvest, pretreatment conditions, or enzyme formulation. Enzyme formulation that produced maximum sugar yields was the same across all harvests except for the CIR October harvest. The least mature sample, the July harvest of CIR switchgrass, released the most sugars (520 g/kg biomass) during enzymatic hydrolysis while requiring the least severe pretreatment conditions. In contrast, the most mature harvest released the least amount of sugars (410 g/kg biomass). All hydrolysates were highly fermentable, although xylose utilisation in the July CIR hydrolysate was poor.

Conclusions
Each harvest type and location responded differently to AFEX pretreatment, although all harvests successfully produced fermentable sugars. Thus, it is necessary to consider an integrated approach between agricultural production and biochemical processing in order to insure optimal productivity.
The Pin 1 inhibitor juglone attenuates kidney fibrogenesis via Pin 1-independent mechanisms in the unilateral ureteral occlusion model
Authors: Reese Shannon , Vidyasagar Aparna , Jacobson Lynn , Acun Zeki , Esnault Stephane , Hullett Debra , Malter James S , Djamali Arjang 
Published: January 2010

Abstract

Background
Pin 1 is a peptidyl-prolyl isomerase inhibitor related to cyclophilin A and FK506 binding protein (FKBP). Juglone (5-hydroxy-1,4-naphthoquinone) is a natural inhibitor of Pin 1 with anti-inflammatory and antifibrotic properties. We evaluated the role of Pin 1 in renal fibrogenesis by evaluating the effects of juglone on epithelial to mesenchymal transition (EMT) and fibrogenesis in the rat unilateral ureteral obstruction (UUO) model and normal rat tubular epithelial cells (NRK52E).

Results
After 2 weeks of UUO, immunoblot analyses demonstrated that juglone (0.25 and 1 mg/kg/24 h) inhibited the deposition of matrix (α-smooth muscle actin (SMA), collagen type III and vimentin) and the activation of signaling pathways involved in fibrogenesis (phospho-smad2) and stress response (phospho-heat shock protein (HSP)27). Juglone also reduced EMT (α-SMA and E-cadherin dual staining) and oxidative stress (Mn superoxide dismutase (SOD) and NAPDH oxidase 2 (Nox-2) dual staining) in the obstructed kidney. There was no difference in Pin 1 levels between treatment and control groups. Pin 1 activity was significantly decreased in obstructed kidneys regardless of treatment status. In vitro, juglone (1 μM) significantly decreased α-SMA and p-smad levels compared to vehicle.

Conclusions
Juglone attenuates fibrogenesis via Pin 1-independent mechanisms in the UUO model. The antifibrotic effects of juglone may result from the inhibition of smad2 and oxidative stress.
Effectiveness of group-based cognitive–behavioural therapy in patients with obsessive–compulsive disorder
Authors: Kearns Colette , Tone Yvonne , Rush Gavin , Lucey James V. 
Published: January 2010

Aims and methodTo establish whether cognitive-behavioural therapy (CBT) with response and exposure prevention (ERP) is effective in individuals with obsessive–compulsive disorder (OCD). Twenty-four patients with OCD, divided into four groups, participated in ten sessions of group CBT. All patients completed the Yale–Brown Obsessive–Compulsive Scale (Y-BOCS), the Maudsley Obsessive–Compulsive Inventory (MOCI), the Beck Depression Inventory (BDI) and the Beck Anxiety Inventory (BAI) pre- and post-treatment.ResultsThe mean (s.d.) YBOC score post-treatment was 17.1 (5.8). This was significantly lower than the mean (s.d.) YBOC pre-treatment (24.7 (6.1); t = 8.4, d.f. = 23, P < 0.005). A significant reduction was also observed in relation to all other rating scales.Clinical implicationsCognitive–behavioural therapy for OCD delivered in a group setting is a clinically effective and acceptable treatment for patients. The use of group-based CBT is an effective means to improve access to psychotherapy.