Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect

Macromolecular crowding extends the range of ionic conditions supporting high DNA polymerase reaction rates. Reactions tested were nick-translation and gap-filling by DNA polymerase I of Escherichia coli, nuclease and polymerase activities of the large fragment of that polymerase, and polymerization by the T4 DNA polymerase. For all of these reactions, high concentrations of nonspecific polymers increased enzymatic activity under otherwise inhibitory conditions resulting from relatively high ionic strength. The primary mechanism of the polymer effect seems to be to increase the binding of polymerase to DNA. We suggest that this effect on protein-DNA complexes is only one example of a general "metabolic buffering" action of crowded solutions on a variety of macromolecular interactions.

Estimating the incidence of rheumatoid arthritis: trying to hit a moving target?

OBJECTIVE

To examine the effect of delay between symptom onset and notification to an arthritis register and the effect of application of the American College of Rheumatology (ACR; formerly, the American Rheumatism Association) 1987 criteria in a cumulative manner on estimates of the incidence of rheumatoid arthritis (RA).

METHODS

General practitioners and/or hospital consultants in the Norwich Health Authority, Norfolk, UK, notified the Norfolk Arthritis Register (NOAR) of all patients who had onset of inflammatory polyarthritis (swelling of > or =2 joints) during 1990. The patients were assessed within 2 weeks of notification and annually thereafter. The ACR 1987 criteria for RA were applied at each assessment. Age- and sex-specific incidence rates were calculated.

RESULTS

If up to 12 months elapsed from symptom onset to notification to NOAR and the ACR criteria were applied at the baseline assessment, RA incidence estimates, age-adjusted to the population of England and Wales, were 30.8/100,000 for women and 12.7/100,000 for men. If up to 5 years elapsed from symptom onset to notification, these estimates rose by 45% for women and 36% for men. If up to 5 years elapsed between symptom onset and notification and the criteria were applied cumulatively, the estimates rose by 75% and 93% for women and men, respectively, compared with the 1-year data, reaching 54.0/100,000 for women and 24.5 per 100,000 for men.

CONCLUSION

Accurate estimation of the incidence of RA requires long-term followup of patients who present with undifferentiated inflammatory polyarthritis. The highest age-adjusted estimates from this study are probably the best that are available.

Identifying male college students' perceived health needs, barriers to seeking help, and recommendations to help men adopt healthier lifestyles

Seven focus groups at a university campus were formed to identify college men's health concerns, barriers to seeking help, and recommendations to help college men adopt healthier lifestyles. Content analysis was used to identify and organize primary patterns in the focus-group data. Results of the study revealed that the college men were aware that they had important health needs but took little action to address them. The participants identified both physical and emotional health concerns. Alcohol and substance abuse were rated as the most important issues for men. The greatest barrier to seeking services was the men's socialization to be independent and conceal vulnerability. The most frequently mentioned suggestions for helping men adopt healthier lifestyles were offering health classes, providing health information call-in service, and developing a men's center. Implications of the results are discussed.

The meaning and experience of being a stroke survivor: an interpretative phenomenological analysis

PURPOSE

To investigate the meaning and experience of being a stroke survivor.

METHOD

Qualitative in-depth semi-structured interviews were conducted with 10 stroke survivors (five face-to-face and five e-mail interviews). The interview data were transcribed verbatim (these were pre-transcribed in e-mail exchange) and analysed using Interpretative Phenomenological Analysis.

RESULTS

Four themes emerged from the analysis: Disrupted embodiment and the loss of self; Invisibility of emotional difficulties; Gender, romance and sexuality; and Social interaction. These themes, respectively, revealed that participants often had difficulties with psychological adaptation to the physically disabling aspects of their stroke; they experienced enduring and disabling emotional difficulties; they had a particular concern for the viability and maintenance of romantic and sexual relationships; and they often became socially withdrawn, resulting in an increased pressure on familial caregivers.

CONCLUSION

The findings of the present work suggest the need for post-stroke counselling regarding romantic and sexual relationships, as well as promoting acceptance of some of the physical disabilities that come with having a stroke and encouraging positive self-regard. There would also appear to be a need to address the issue of social withdrawal and familial relationships, perhaps when health professionals convey information regarding the person's stroke, and in counselling targeted specifically at family caregivers.

Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10(-4) ). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.

Quantifying the exact role of HLA-DRB1 alleles in susceptibility to inflammatory polyarthritis: results from a large, population-based study

OBJECTIVE

To accurately determine the contributions of HLA-DRB1 alleles in explaining susceptibility to inflammatory polyarthritis in a large, true population-based cohort of new-onset cases.

METHODS

A cohort of 680 consecutive patients with inflammatory polyarthritis, of whom 404 satisfied the American College of Rheumatology (ACR) criteria for rheumatoid arthritis (RA), was recruited from the population-based Norfolk Arthritis Register. All cases were compared with 286 local population controls. A standardized clinical assessment was performed on all patients. HLA-DRB1 phenotypes, including DR4 subtypes, were determined using a semiautomated, reverse dot-blot method. Results were expressed as odds ratios (OR) and 95% confidence intervals (95% CI).

RESULTS

There was only a modest association (OR 1.8, 95% CI 1.4-2.4) between inflammatory polyarthritis and the presence of any shared epitope (SE) allele; the strongest individual risk was with DRB1*0404 (OR 3.5, 95% CI 1.8-6.8). Comparison of the genotypes demonstrated that the effect of being SE homozygous (OR 2.1, 95% CI 1.5-3.0) was only moderately greater than the effect of being SE heterozygous (OR 1.3, 95% CI 1.1-1.6). The exception to this was genotypic combinations that included HLA-DRB1*0404, which exhibited ORs ranging up to 18.0. There were no differences between either the phenotype or genotype data when the patients were stratified by RA status (defined by the ACR criteria). In contrast, the associations were substantially stronger in patients who were positive for rheumatoid factor.

CONCLUSION

Previous studies had not been able to clarify whether the influence of HLA-DRB1 on RA was related to disease susceptibility or to disease severity and progression. These data on a unique population-based incident cohort suggest only weak effects on susceptibility, with the exception of the clearly distinct influence of HLA-DRB1*0404.

A simple algorithm to predict the development of radiological erosions in patients with early rheumatoid arthritis: prospective cohort study

OBJECTIVE

To produce a practical algorithm to predict which patients with early rheumatoid arthritis will develop radiological erosions.

DESIGN

Primary care based prospective cohort study.

SETTING

All general practices in the Norwich Health Authority, Norfolk.

SUBJECTS

175 patients notified to the Norfolk Arthritis Register were visited by a metrologist soon after they had presented to their general practitioners with inflammatory polyarthritis, and again after a further 12 months. All the patients satisfied the American Rheumatism Association's 1987 criteria for rheumatoid arthritis and were seen by a metrologist within six months of the onset of symptoms. The study population was randomly split into a prediction sample (n = 105) for generating the algorithm and a validation sample (n = 70) for testing it.

MAIN OUTCOME MEASURES

Predictor variables measured at baseline included rheumatoid factor status, swelling of specific joint areas, duration of morning stiffness, nodules, disability score, age, sex, and disease duration when the patient first presented. The outcome variable was the presence of radiological erosions in the hands or feet, or both, after 12 months.

RESULTS

A simple algorithm based on a combination of three variables--a positive rheumatoid factor test, swelling of at least two large joints, and a disease duration of more than three months--was best able to predict erosions. When the accuracy of this algorithm was tested with the validation sample, the erosion status of 79% of patients was predicted correctly.

CONCLUSIONS

A simple algorithm based on three easily measured items of information can predict which patients are at high risk and which are at low risk of developing radiological erosions.

Additive effect of pretransplant obesity, diabetes, and cardiovascular risk factors on outcomes after liver transplantation

The effects of pretransplant obesity, diabetes mellitus (DM), coronary artery disease (CAD), and hypertension (HTN) on outcomes after liver transplantation (LT) are controversial. Questions have also been raised about the appropriateness of the body mass index (BMI) for assessing obesity in patients with end-stage liver disease. Both issues have implications for organ allocation in LT. To address these questions, we undertook a cohort study of 202 consecutive patients (2000-2010) undergoing LT at a national center in New Zealand. BMI and body fat percentage (%BF) values (dual-energy X-ray absorptiometry) were measured before transplantation, and the methods were compared. The influence of pretransplant risk variables (including obesity, DM, CAD, and HTN) on the 30-day postoperative event rate, length of hospital stay, and survival were analyzed. There was agreement between the calculated BMI and the measured %BF for 86.0% of the study population (κ coefficient = 0.73, 95% confidence interval = 0.61-0.85), and this was maintained across increasing Model for End-Stage Liver Disease scores. Obesity was an independent risk factor for the postoperative event rate [count ratio (CR) = 1.03, P < 0.001], as was DM (CR = 1.4, P < 0.001). Obesity with concomitant DM was the strongest predictor of the postoperative event rate (CR = 1.75, P < 0.001) and a longer hospital stay (5.81 days, P < 0.01). Independent metabolic risk factors had no effect on 30-day, 1-year, or 5-year patient survival. In conclusion, BMI is an adequate tool for assessing obesity-associated risk in LT. Early post-LT morbidity is highest for patients with concomitant obesity and DM, although these factors do not appear to influence recipient survival.

The influence of HLA-DRB1 alleles and rheumatoid factor on disease outcome in an inception cohort of patients with early inflammatory arthritis

OBJECTIVE

There are conflicting data concerning the role of HLA-DRB1 alleles in disease outcome in early rheumatoid arthritis. The exact role of these alleles in short-term outcome is determined in this large, prospective, population-based study.

METHODS

We recruited 532 patients with inflammatory polyarthritis from the Norfolk Arthritis Register and typed their sera for HLA-DRB1 alleles using polymerase chain reaction-based methods. Disease outcome was assessed at 2 years in terms of persistent joint inflammation, functional disability, and radiologic erosions. Results are expressed as risk ratios (RR) with 95% confidence intervals (95% CI).

RESULTS

There was no influence of HLA-DRB1 alleles, in any combination, on the likelihood of disease persistence, and only a modest effect on functional disability (Health Assessment Questionnaire score > or = 1). The most obvious effect was on the development of erosions (RR 1.9, 95% CI 1.4-2.6 for those who carried at least 1 DRB1 shared epitope [SE] allele), with slightly greater effects for those who were homozygous for SE-bearing alleles (RR 2.5, 95% CI 1.8-3.6). This effect of HLA-DRB1 was restricted to patients whose sera were negative for rheumatoid factor. Among patients with erosions, HLA-DRB1 had no influence on the severity of radiologic damage (defined as the number of eroded joints, or total Larsen score).

CONCLUSION

These data do not support routine HLA-DRB1 screening of patients with early arthritis to identify those at risk for subsequent severe disease.

Multiphase Flow Metering: Current Trends and Future Developments

Distinguished Author Series articles are general, descriptive representations that summarize the state of the art in an area of technology by describing recent developments for readers who are not specialists in the topics discussed. Written by individuals recognized as experts in the area, these articles provide key references to more definitive work and present specific details only to illustrate the technology. Purpose: to inform the general readership of recent advances in various areas of petroleum engineering.

Abstract

Over the last decade, the development, evaluation, and use of multiphase-flow-metering (MFM) systems have been a major focus for the oil and gas industry worldwide. Many alternative metering systems have been developed, but none can be referred to as generally applicable or universally accurate. Both established and novel technologies suitable to measure the flow rates of gas, oil, and water in three-phase flow are reviewed and assessed within this framework. Technologies already implemented in various commercial meters then are evaluated in terms of operational and economical advantages or shortcomings from an operator's point of view. The lessons learned about the practical reliability, accuracy, and use of available technology are discussed. As operators now realize, use of MFM systems (MFMSs) is essential in exploiting marginal fields. A new approach to flow assurance, deepwater developments, downhole/seabed separation systems, and wet-gas fields is foreseen. The authors suggest where additional research to develop the next generation MFM devices will be focused to meet the as yet unsolved problems.

Brief History

The first commercial MFMSs appeared approximately 10 years ago, as a result of several multiphase metering research projects in the early 1980s. The driving force to develop MFM technology was the forecast decline of production from the major North Sea fields, accompanied by the necessity to tie backfuture smaller discoveries to existing infrastructure. Increasing gas and waterfractions, inherent in a mature producing province, would create more-unstable flow conditions in existing production facilities and require more-flexible multiphase solutions.

In less than a decade, MFM has become accepted in the field and is beginning to be considered as a primary metering solution for new field developments.

MFM Applications

Within the oil and gas industry, it is generally recognized that MFM could lead to great benefits in terms of the following.1,2,3

Layout of Production Facilities.

The use of MFMs reduces the hardware needed for onshore, offshore topside, and offshore subsea applications. Of primary importance is the removal of a dedicated test separator for well-testing applications. Use of MFM (with its smaller footprint) for topside applications minimizes platform space and load requirements for well-testing operations. Finally, costly well-testing lines can be stripped from the production facilities, which may be of vital importance for unmanned locations, deepwater developments, and satellite fields.

Well Testing.

Conventional test separators are expensive and require much time to monitor each well's performance because of the time required to reach stabilized flow conditions. It is particularly important in deepwater developments, because of the exceptional length of the flowlines. In such cases, production from individual wells connected to the same manifold may be monitored by use of a dedicated test line to avoid shutting down all the wells, then testing them one by one (with considerable production loss). However, the expense of a separate flowline may be prohibitive, hence the advantages of MFM installed in the subsea manifold. Test separators have an accuracy between approximately 5 and10% (currently achievable with MFMSs) but require regular intervention by trained personnel and cannot provide continuous well monitoring. Another disadvantage of conventional well testing with conventional separators is that well performance suffers after shutdown cycles related to well testing. Often, wells tested on a regular basis require more-frequent workovers to maintain their production rates.

Use of MFMSs for exploration-well testing4 provides satisfactory flow measurements without separation of the phases. It is claimed that they can be used to monitor the well during its cleanup flow (traditionally, this flow information is lost because the well stream is not directed through the test separator). Added value is represented by improved control of the drawdown applied to the formation, the pressure transient, and shortened flow periods.

Reservoir Management.

MFMSs provide real-time, continuous data to enable operators to characterize field and reservoir performance better and react faster. Changes in gas/oil ratio or water cut can be detected and quantified immediately, where as traditional test separators provide information about only cumulative volumes at discrete points in time.

Mechanical induction of osteogenesis: the importance of pin rigidity

Eight dogs, divided into two groups of four by varying pin rigidity, underwent 15% left tibial lengthening by the Ilizarov method. In group I, "tensioned" 1.6-mm wires maintained a rigidity approaching that of 4.0-mm pins. In group II, the wires, maintained at half the tension, averaged 45% of the rigidity measured in group I. All dogs in group I filled the experimental gap with de novo osteogenesis, whereas all of the dogs in group II prematurely bridged the gap, arresting the process of osteogenesis. From these experimental results, clinical trials have been started using commercially available external fixation devices utilizing pins with equivalent rigidity.

Polymer-stimulated ligation: enhanced ligation of oligo- and polynucleotides by T4 RNA ligase in polymer solutions

The effects of macromolecular crowding were tested on several reactions catalyzed by T4 RNA ligase. The rate of cyclization of oligoriboadenylates was stimulated up to 10-fold by relatively high concentrations of several polymers (polyethylene glycol (PEG) 8000 or 20,000; bovine plasma albumin; Ficoll 70). In addition, higher concentrations of PEG 8000 or PEG 20,000 allowed the novel formation of large linear products from the oligoriboadenylates. Also stimulated by high concentrations of PEG 8000 were the rate at which T4 RNA ligase joined p(dT)10 to oligoriboadenylates and the rate at which the enzyme activated p(dT)n by transfer of an adenylyl moiety from ATP to the oligonucleotides. These results with T4 RNA ligase are compared to earlier studies on the effects of crowding on DNA ligases.

Prognostic factors and survival after resection of colorectal liver metastasis in the era of preoperative chemotherapy: an 11-year single-centre study

INTRODUCTION

A variety of factors have been identified in the literature which influence survival following resection of colorectal liver metastases (CRLM). Much of this literature is historical, and its relevance to contemporary practice is not known. The aim of this study was to identify those factors which influence survival during the era of preoperative chemotherapy in patients undergoing resection of CRLM in a UK centre.

METHODS

All patients having liver resection for CRLM during an 11-year period up to 2011 were identified from a prospectively maintained database. Prognostic factors analysed included tumour size (≥5 or <5 cm), lymph node status of the primary tumour, margin positivity (R1; <1 mm), neo-adjuvant chemotherapy (for liver), tumour differentiation, number of liver metastases (≥4), preoperative carcinoembryonic antigen (CEA; ≥200 ng/ml) and whether metastases were synchronous (i.e. diagnosed within 12 months of colorectal resection) or metachronous to the primary tumour. Overall survival (OS) was compared using Kaplan-Meier plots and a log rank test for significance. Multivariate analysis was performed using a Cox regression model. Statistical analysis was performed in SPSS v19, and p < 0.05 was considered to be significant.

RESULTS

432 patients underwent resection of CRLM during this period (67% male; mean age 64.5 years), and of these, 54 (13.5%) had re-resections. The overall 5-year survival in this series was 43% with an actuarial 10-year survival of 40%. A preoperative CEA ≥200 ng/ml was present in 10% of patients and was associated with a poorer 5-year OS (24 vs. 45%; p < 0.001). A positive resection margin <1 mm was present in 16% of patients, and this had a negative impact on 5-year OS (15 vs. 47%; p < 0.001). Tumour differentiation, number, biliary or vascular invasion, size, relationship to primary disease, nodal status of the primary disease or the use of neo-adjuvant chemotherapy had no impact on OS. Multivariate analysis identified only the presence of a positive resection margin (OR 1.75; p < 0.05) and a preoperative CEA ≥200 ng/ml (OR 1.88; p < 0.01) as independent predictors of poor OS.

CONCLUSION

Despite the wide variety of prognostic factors reported in the literature, this study was only able to identify a preoperative CEA ≥200 ng/ml and the presence of tumour within 1 mm of the resection margin as being of value in predicting survival. These variables are likely to identify patients who may benefit from intensive follow-up to enable early aggressive treatment of recurrent disease.

Time to first occurrence of erosions in inflammatory polyarthritis: results from a prospective community-based study

OBJECTIVE

To examine the time of occurrence of first radiographic erosions in a cohort of patients with inflammatory polyarthritis.

METHODS

Patients were recruited through the Norfolk Arthritis Register, which follows up patients annually. Patients with features of rheumatoid arthritis (other than erosions) sufficient, together with erosions, to meet the American College of Rheumatology (formerly, the American Rheumatism Association) 1987 revised criteria were requested to undergo radiographic examinations of the hands and feet at the first and/or second annual followup visits. All patients were requested to undergo radiographic examinations at the fifth annual followup visit. The most recent erosion-free radiograph was identified for 416 eligible patients, and these data were used to derive the duration of disease since the recalled date of onset of first symptoms. The rate of occurrence of first erosions was then determined (as a cumulative prevalence and as an incidence rate using Poisson regression) from analysis of followup films. Patients were assumed to be free of erosions at symptom onset.

RESULTS

The cumulative prevalence of erosions in patients whose first film was obtained 12-24 months after disease onset was 36%, equivalent to an incidence rate of 24.5/1,000 patient-months. We identified 3 analysis groups of patients who were free of erosions based on films obtained 12-24 months, 24-36 months, and 36-60 months since the recalled date of onset of first symptoms. New erosions were observed in all 3 groups, with cumulative prevalences of 23%, 28%, and 47%, respectively. These were equivalent to first-erosion incidence rates/1,000 patient-months of 5.4 (95% confidence interval [95% CI] 3.8-83), 6.8 (95% CI 4.7-10.0), and 13.0 (95% CI 8.9-19.2), respectively.

CONCLUSION

Many patients with erosive disease first develop their erosions >2 years from disease onset.

T4 polynucleotide kinase: macromolecular crowding increases the efficiency of reaction at DNA termini

The amount of reaction catalyzed by T4 polynucleotide kinase on a variety of its substrates is greatly increased in the presence of polyethylene glycol 8000 (PEG 8000). Both the forward and reverse reactions as well as the exchange reaction can be stimulated. The stimulation is a general effect on T4 polynucleotide kinase reactions involving high molecular weight DNA substrates. The use of PEG 8000 is particularly advantageous for labeling or removing terminal 5'-phosphate groups which are only slowly or incompletely labeled or removed under ordinary conditions, such as those at recessed termini or at "nicks" in duplex DNA, although the reaction on blunt-ended or protruding termini is also increased. It is further advantageous for labeling very low concentrations of substrates.