bluuebunny/crossref_metadata_2025_split huggingface dataset:
PCR enrichment techniques to identify the diet of predators
Authors: O’RORKE R. , LAVERY S. , JEFFS A. 
Published: December 2011

AbstractThe increasing sensitivity of PCR has meant that in the last two decades PCR has emerged as a major tool in diet studies, enabling us to refine our understanding of trophic links and to elucidate the diets of predators whose prey is as yet uncharacterized. The achievements and methods of PCR‐based diet studies have been reviewed several times, but here we review an important development in the field: the use of PCR enrichment techniques to promote the amplification of prey DNA over that of the predator. We first discuss the success of using group‐specific primers either in parallel single reactions or in multiplex reactions. We then concentrate on the more recent use of PCR enrichment techniques such as restriction enzyme digests, peptide nucleic acid clamping, DNA blocking and laser capture microdissection. We also survey the vast literature on enrichment techniques in clinical biology, to ascertain the pitfalls of enrichment techniques and what refinements have yielded some highly sensitive methods. We find that while there are several new approaches to enrichment, peptide nucleic acid clamping and DNA blocking are generally sufficient techniques for the characterization of diets of predators and highlight the most important considerations of the approach.
Multiplexed microsatellite markers for genetic studies of beech
Authors: LEFÈVRE S. , WAGNER S. , PETIT R. J. , De LAFONTAINE G. 
Published: December 2011

AbstractEuropean beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects on forests. Multiplex PCR of microsatellites is a fast and cost‐effective technique allowing high‐throughput genotyping. Here we present the procedure used to develop two multiplex kits (8‐plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the 16 amplified loci are largely devoid of null alleles and allow rapid and cost‐effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.
Aliskiren as a novel therapeutic agent for hypertension and cardio-renal diseases
Authors: Rashikh Azhar , Ahmad Shibli Jameel , Pillai Krishna Kolappa , Najmi Abul Kalam 
Published: December 2011

Abstract

Objectives
High blood pressure (BP) is a major risk factor for cardiovascular and renal complications. A majority of treated hypertensive patients still complain of high BP. The renin-angiotensin aldosterone system (RAAS) has been a centre-stage target for all the cardiovascular and cardio-renal complications. Aliskiren, is the first direct renin inhibitor (DRI) to be approved by the US FDA. Renin controls the rate-limiting step in the RAAS cascade and hence is the most favorable target for RAAS suppression.

Key findings
This review article strives to summarize the pharmacokinetic, preclinical and clinical studies done so far pertaining to the efficacy of aliskiren. Further, the pharmacology of aliskiren has been comprehensively dealt with to enhance understanding so as to further research in this unfathomed area in the multitude of cardiovascular disorders and renal diseases.

Summary
Aliskiren has been shown to have comparable BP-lowering effects to other RAAS inhibitors. Recent clinical trials have indicated that it might contribute significantly in combination with other agents for the protection of end-organ diseases.
Single injection of ONO-1301-loaded PLGA microspheres directly after ischaemia reduces ischaemic damage in rats subjected to middle cerebral artery occlusion
Authors: Hazekawa Mai , Sakai Yoshiki , Yoshida Miyako , Haraguchi Tamami , Uchida Takahiro 
Published: December 2011

Abstract

Objectives
ONO-1301 was developed as a novel long-acting prostacyclin agonist with thromboxane synthase inhibitory activity. In this study, we investigated the therapeutic time window of oral ONO-1301 and the effect of a single subcutaneous injection of ONO-1301-loaded poly(lactide-co-glycolide) (PLGA) microspheres (ONO-1301 PLGA MS) on infarction volume, functional deficits and plasma ONO-1301 levels following a 1 h middle cerebral artery occlusion (MCAO) in rats.

Methods
Rats were treated with ONO-1301 (3 mg/kg) orally twice-daily starting 1 (directly), 6 or 24 h after MCAO. Rats received a single subcutaneous injection of ONO-1301 PLGA MS (10 mg/kg) directly after MCAO. Neurological scores were evaluated directly after, 1 and 6 h, 1, 2, and 3 days after MCAO. Infarct volume, oedema and plasma ONO-1301 levels were measured three days after MCAO.

Key findings
Neurological scores, oedema and infarct volume were all significantly improved in rats repeatedly treated with oral ONO-1301 and subcutaneous ONO-1301 PLGA MS directly after MCAO. Plasma ONO-1301 levels were significantly lower in rats treated directly after MCAO (either with ONO-1301 or ONO-1301 PLGA MS) than in rats treated 6 h or 24 h after MCAO.

Conclusions
ONO-1301 PLGA MS subcutaneous treatment directly after MCAO showed a neuroprotective effect as well as oral ONO-1301. This treatment should be clinically more convenient than ONO-1301 oral administration since it is delivered as a single treatment after MCAO.
Pharmacokinetic profile of Oncofid-S after intraperitoneal and intravenous administration in the rat
Authors: Tringali Giuseppe , Bettella Fabio , Greco Maria Cristina , Campisi Monica , Renier Davide , Navarra Pierluigi 
Published: December 2011

Abstract

Objectives
Oncofid-S is a bio-conjugate molecule obtained from the binding of campthotecin, SN-38, to hyaluronic acid. In view of a possible clinical development for loco-regional treatment of peritoneal carcinomatosis, this study aimed to establish the pharmacokinetic profile of Oncofid-S after single intraperitoneal or intravenous administration in the rat.

Methods
Single-dose intraperitoneal or intravenous administrations of Oncofid-S were performed. Groups of six rats were sacrificed at various times (up to 24 and 72 h in i.p. and i.v. study, respectively) after drug injection. Trunk blood, livers and spleens were collected for subsequent analysis. Total SN-38 was assayed by HPLC.

Key findings
We found that Oncofid-S was poorly absorbed after intraperitoneal injection, the estimated AUC0–72 being less than2%. The drug was distributed in liver, but not spleen, and was eliminated with a terminal half-life of 16 h. After intravenous dosing, Oncofid-S was found in liver as well as in spleen.

Conclusions
Here we have demonstrated that Oncofid-S administered intraperitoneally in the rat was poorly absorbed into the systemic circulation, even after the administration of an extremely high dose. This finding reinforces the rationale for developing Oncofid-S in the loco-regional intraperitoneal treatment of peritoneal carcinomatosis in man.
Introductory Biology Textbooks Under-Represent Scientific Process
Authors: Duncan Dara B. , Lubman Alexandra , Hoskins Sally G. 
Published: December 2011

Attrition of undergraduates from Biology majors is a long-standing problem. Introductory courses that fail to engage students or spark their curiosity by emphasizing the open-ended and creative nature of biological investigation and discovery could contribute to student detachment from the field. Our hypothesis was that introductory biology books devote relatively few figures to illustration of the design and interpretation of experiments or field studies, thereby de-emphasizing the scientific process.
To investigate this possibility, we examined figures in six Introductory Biology textbooks published in 2008. On average, multistep scientific investigations were presented in fewer than 5% of the hundreds of figures in each book. Devoting such a small percentage of figures to the processes by which discoveries are made discourages an emphasis on scientific thinking. We suggest that by increasing significantly the illustration of scientific investigations, textbooks could support undergraduates’ early interest in biology, stimulate the development of design and analytical skills, and inspire some students to participate in investigations of their own.
Outer Membrane Targeting of Pseudomonas aeruginosa Proteins Shows Variable Dependence on the Components of Bam and Lol Machineries
Authors: Hoang Hanh H. , Nickerson Nicholas N. , Lee Vincent T. , Kazimirova Anastasia , Chami Mohamed , Pugsley Anthony P. , Lory Stephen 
Published: December 2011

ABSTRACT

In Gram-negative bacteria, the Lol and Bam machineries direct the targeting of lipidated and nonlipidated proteins, respectively, to the outer membrane (OM). Using
Pseudomonas aeruginosa
strains with depleted levels of specific Bam and Lol proteins, we demonstrated a variable dependence of different OM proteins on these targeting pathways. Reduction in the level of BamA significantly affected the ability of the β-barrel membrane protein OprF to localize to the OM, while the targeting of three secretins that are functionally related OM proteins was less affected (PilQ and PscC) or not at all affected (XcpQ). Depletion of LolB affected all lipoproteins examined and had a variable effect on the nonlipidated proteins. While the levels of OprF, PilQ, and PscC were significantly reduced by LolB depletion, XcpQ was unaffected and was correctly localized to the OM. These results suggest that certain β-barrel proteins such as OprF primarily utilize the complete Bam machinery. The Lol machinery participates in the OM targeting of secretins to variable degrees, likely through its involvement in the assembly of lipidated Bam components. XcpQ, but not PilQ or PscC, was shown to assemble spontaneously into liposomes as multimers. This work raises the possibility that there is a gradient of utilization of Bam and Lol insertion and targeting machineries. Structural features of individual proteins, including their β-barrel content, may determine the propensity of these proteins for folding (or misfolding) during periplasmic transit and OM insertion, thereby influencing the extent of utilization of the Bam targeting machinery, respectively.

IMPORTANCE
Targeting of lipidated and nonlipidated proteins to the outer membrane (OM) compartment in Gram-negative bacteria involves the transfer across the periplasm utilizing the Lol and Bam machineries, respectively. We show that depletion of Bam and Lol components in
Pseudomonas aeruginosa
does not lead to a general OM protein translocation defect, but the severity (and therefore, Lol and Bam dependence), varies with individual proteins. XcpQ, the secretin component of the type II secretion apparatus, is translocated into the OM without the assistance of Bam or Lol machineries. The hypothesis that XcpQ, after secretion across the cytoplasmic membrane, does not utilize the OM targeting machineries was supported by demonstrating that
in vitro
-synthesized XcpQ (but not the other
P. aeruginosa
secretins) can spontaneously incorporate into lipid vesicles. Therefore, the requirement for ancillary factors appears to be, in certain instances, dictated by the intrinsic properties of individual OM proteins, conceivably reflecting their propensities to misfold during periplasmic transit.
The value of intervening for intimate partner violence in South African primary care: project evaluation
Authors: Joyner Kate , Mash Robert James 
Published: December 2011

ObjectivesIntimate partner violence (IPV) is an important contributor to the burden of disease in South Africa. Evidence-based approaches to IPV in primary care are lacking. This study evaluated a project that implemented a South African protocol for screening and managing IPV. This article reports primarily on the benefits of this intervention from the perspective of women IPV survivors.DesignThis was a project evaluation involving two urban and three rural primary care facilities. Over 4–8 weeks primary care providers screened adult women for a history of IPV within the previous 24 months and offered referral to the study nurse. The study nurse assessed and managed the women according to the protocol. Researchers interviewed the participants 1 month later to ascertain adherence to their care plan and their views on the intervention.ResultsIn total, 168 women were assisted and 124 (73.8%) returned for follow-up. Emotional (139, 82.7%), physical (115, 68.5%), sexual (72, 42.9%) and financial abuse (72, 42.9%) was common and 114 (67.9%) were at high/severe risk of harm. Adherence to the management plan ranged from testing for syphilis 10/25 (40.0%) to consulting a psychiatric nurse 28/58 (48.3%) to obtaining a protection order 28/28 (100.0%). Over 75% perceived all aspects of their care as helpful, except for legal advice from a non-profit organisation. Women reported significant benefits to their mental health, reduced alcohol abuse, improved relationships, increased self-efficacy and reduced abusive behaviour. Two characteristics seemed particularly important: the style of interaction with the nurse and the comprehensive nature of the assessment.ConclusionFemale IPV survivors in primary care experience benefit from an empathic, comprehensive approach to assessing and assisting with the clinical, mental, social and legal aspects. Primary care managers should find ways to integrate this into primary care services and evaluate it further.
Selection bias and patterns of confounding in cohort studies: the case of the NINFEA web-based birth cohort
Authors: Pizzi Costanza , De Stavola Bianca L , Pearce Neil , Lazzarato Fulvio , Ghiotti Paola , Merletti Franco , Richiardi Lorenzo 
Published: December 2011

BackgroundSeveral studies have examined the effects of sample selection on the exposure–outcome association estimates in cohort studies, but the reasons why this selection may induce bias have not been fully explored.AimsTo investigate how sample selection of the web-based NINFEA birth cohort may change the confounding patterns present in the source population.MethodsThe characteristics of the NINFEA participants (n=1105) were compared with those of the wider source population—the Piedmont Birth Registry (PBR)—(n=36 092), and the association of two exposures (parity and educational level) with two outcomes (low birth weight and birth by caesarean section), while controlling for other risk factors, was studied. Specifically the associations among measured risk factors within each dataset were examined and the exposure–outcome estimates compared in terms of relative ORs.ResultsThe associations of educational level with the other risk factors (alcohol consumption, folic acid intake, maternal age, pregnancy weight gain, previous miscarriages) partly differed between PBR and NINFEA. This was not observed for parity. Overall, the exposure–outcome estimates derived from NINFEA only differed moderately from those obtained in PBR, with relative ORs ranging between 0.74 and 1.03.ConclusionsSample selection in cohort studies may alter the confounding patterns originally present in the general population. However, this does not necessarily introduce selection bias in the exposure–outcome estimates, as sample selection may reduce some of the residual confounding present in the general population.
Identification of putative migratory pheromones from Pacific lamprey (Lampetra tridentata)
Authors: Yun Sang-Seon , Wildbill Andrew J. , Siefkes Michael J. , Moser Mary L. , Dittman Andrew H. , Corbett Stephen C. , Li Weiming , Close David A. 
Published: December 2011

Pacific lamprey, Lampetra tridentata , has declined precipitously throughout their range in the Columbia River basin of North America. Tribal Nations and Federal and State agencies are engaged in efforts to restore these fish. Understanding whether Pacific lamprey emit and detect migratory pheromones is particularly important for these restoration efforts. Using behavioural assays, we demonstrated that migratory adult Pacific lamprey are attracted to odors emanating from their larval conspecifics. We then identified putative pheromones released by larval Pacific lamprey. Chemical analysis of the conditioned water from larval lamprey using liquid chromatography – mass spectrometry (LC–MS) revealed that the Pacific lamprey can release petromyzonamine disulfate (PADS), petromyzosterol disulfate (PSDS), and petromyzonol sulfate (PZS). Electro-olfactogram studies further demonstrated that adult Pacific lamprey can smell those bile acid compounds. Our data strongly indicate that the Pacific lamprey employ a chemical communication system mediated by a mixture of bile acids, as evidenced by pheromonal functions of the bile acid compounds in guiding migratory adult sea lamprey to the spawning streams. Comprehensive understanding of the chemical communications involved in lamprey migratory behavior may lead to improved scientific approaches for restoration efforts.
Impact ofEGFRGenetic Variants on Glioma Risk and Patient Outcome
Authors: Costa Bruno Marques , Viana-Pereira Marta , Fernandes Ricardo , Costa Sandra , Linhares Paulo , Vaz Rui , Pinheiro Céline , Lima Jorge , Soares Paula , Silva Ana , Pardal Fernando , Amorim Júlia , Nabiço Rui , Almeida Rui , Alegria Carlos , Pires Manuel Melo , Pinheiro Célia , Carvalho Ernesto , Oliveira Pedro , Lopes José M. , Reis Rui M. 
Published: December 2011

AbstractBackground: The epidermal growth factor receptor (EGFR) regulates important cellular processes and is frequently implicated in human tumors. Three EGFR polymorphisms have been described as having a transcriptional regulatory function: two single-nucleotide polymorphisms in the essential promoter region, −216G/T and −191C/A, and a polymorphic (CA)n microsatellite sequence in intron 1. We aimed to elucidate the roles of these EGFR polymorphisms in glioma susceptibility and prognosis.Methods: We conducted a case–control study with 196 patients with glioma and 168 cancer-free controls. Unconditional multivariate logistic regression models were used to calculate ORs and 95% confidence intervals. A Cox regression model was used to evaluate associations with patient survival. False-positive report probabilities were also assessed.Results: None of the EGFR −216G/T variants was significantly associated with glioma risk. The −191C/A genotype was associated with higher risk for glioma when the (CA)n alleles were classified as short for ≤16 or ≤17 repeats. Independently of the (CA)n repeat cutoff point used, shorter (CA)n repeat variants were significantly associated with increased risk for glioma, particularly glioblastoma and oligodendroglioma. In all tested models with different (CA)n cutoff points, only −191C/A genotype was consistently associated with improved survival of patients with glioblastoma.Conclusions: Our findings implicate EGFR −191C/A and the (CA)n repeat polymorphisms as risk factors for gliomas, and suggest −191C/A as a prognostic marker in glioblastoma.Impact: Our data support a role of these EGFR polymorphisms in determining glioma susceptibility, with potential relevance for molecularly based stratification of patients with glioblastoma for individualized therapies. Cancer Epidemiol Biomarkers Prev; 20(12); 2610–7. ©2011 AACR.
Tumor and Salivary Matrix Metalloproteinase Levels Are Strong Diagnostic Markers of Oral Squamous Cell Carcinoma
Authors: Stott-Miller Marni , Houck John R. , Lohavanichbutr Pawadee , Méndez Eduardo , Upton Melissa P. , Futran Neal D. , Schwartz Stephen M. , Chen Chu 
Published: December 2011

Abstract
Background: The matrix metalloproteinases (MMP) cause degradation of the extracellular matrix and basement membranes, and thus may play a key role in cancer development.
Methods: In our search for biomarkers for oral squamous cell carcinomas (OSCC), we compared primary OSCC, oral dysplasia and control subjects with respect to: (i) expression of MMP1, MMP3, MMP10, and MMP12 in oral epithelial tissue using Affymetrix U133 2.0 Plus GeneChip arrays, followed by quantitative reverse transcription-PCR (qRT-PCR) for MMP1, and (ii) determination of MMP1 and MMP3 concentrations in saliva.
Results: MMP1 expression in primary OSCC (n = 119) was &gt;200-fold higher (P = 7.16 × 10−40) compared with expression levels in nonneoplastic oral epithelium from controls (n = 35). qRT-PCR results on 30 cases and 22 controls confirmed this substantial differential expression. The exceptional discriminatory power to separate OSCC from controls was validated in two independent testing sets (AUC% = 100; 95% CI: 100–100 and AUC% = 98.4; 95% CI: 95.6–100). Salivary concentrations of MMP1 and MMP3 in OSCC patients (33 stage I/II, 26 stage III/IV) were 6.2 times (95% CI: 3.32–11.73) and 14.8 times (95% CI: 6.75–32.56) higher, respectively, than in controls, and displayed an increasing trend with higher stage disease.
Conclusion: Tumor and salivary MMPs are robust diagnostic biomarkers of OSCC.
Impact: The capacity of MMP gene expression to identify OSCC provides support for further investigation into MMPs as potential markers for OSCC development. Detection of MMP proteins in saliva in particular may provide a promising means to detect and monitor OSCC noninvasively. Cancer Epidemiol Biomarkers Prev; 20(12); 2628–36. ©2011 AACR.
A Case–Control Study of a Sex-Specific Association between a 15q25 Variant and Lung Cancer Risk
Authors: Wei Chongjuan , Han Younghun , Spitz Margaret R. , Wu Xifeng , Chancoco Haidee , Akiva Pinchas , Rechavi Gideon , Brand Hadar , Wun Issac , Frazier Marsha L. , Amos Christopher I. 
Published: December 2011

Abstract
Background: Genetic variants located at 15q25, including those in the cholinergic receptor nicotinic cluster (CHRNA5) have been implicated in both lung cancer risk and nicotine dependence in recent genome-wide association studies. Among these variants, a 22-bp insertion/deletion, rs3841324 showed the strongest association with CHRNA5 mRNA expression levels. However the influence of rs3841324 on lung cancer risk has not been studied in depth.
Methods: We have, therefore, evaluated the association of rs3841324 genotypes with lung cancer risk in a case–control study of 624 Caucasian subjects with lung cancer and 766 age- and sex-matched cancer-free Caucasian controls. We also evaluated the joint effects of rs3841324 with single-nucleotide polymorphisms (SNP) rs16969968 and rs8034191 in the 15q25 region that have been consistently implicated in lung cancer risk.
Results: We found that the homozygous genotype with both short alleles (SS) of rs3841324 was associated with a decreased lung cancer risk in female ever smokers relative to the homozygous wild-type (LL) and heterozygous (LS) genotypes combined in a recessive model [ORadjusted = 0.55, 95% confidence interval (CI), 0.31–0.89, P = 0.0168]. There was no evidence for a sex difference in the association between this variant and cigarettes smoked per day (CPD). Diplotype analysis of rs3841324 with either rs16969968 or rs8034191 showed that these polymorphisms influenced the lung cancer risk independently.
Conclusions and Impact: This study has shown a sex difference in the association between the 15q25 variant rs3841324 and lung cancers. Further research is warranted to elucidate the mechanisms underlying these observations. Cancer Epidemiol Biomarkers Prev; 20(12); 2603–9. ©2011 AACR.