bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns and influencing factor of synonymous codon usage in porcine circovirus
Authors: LIU Xin-sheng , Zhang Yong-guang , Fang Yu-zhen , Wang Yong-lu 
Published: March 2012

Abstract

Background
Analysis of codon usage can reveal much about the molecular evolution of the viruses. Nevertheless, little information about synonymous codon usage pattern of porcine circovirus (PCV) genome in the process of its evolution is available. In this study, to give a new understanding on the evolutionary characteristics of PCV and the effects of natural selection from its host on the codon usage pattern of the virus, Patterns and the key determinants of codon usage in PCV were examined.

Methods
We carried out comprehensive analysis on codon usage pattern in the PCV genome, by calculating relative synonymous codon usage (RSCU), effective number of codons (ENC), dinucleotides and nucleic acid content of the PCV genome.

Results
PCV genomes have relatively much lower content of GC and codon preference, this result shows that nucleotide constraints have a major impact on its synonymous codon usage. The results of the correspondence analysis indicate codon usage patterns of PCV of various genotypes, various subgenotypes changed greatly, and significant differences in codon usage patterns of Each virus of Circoviridae.There is much comparability between PCV and its host in their synonymous codon usage, suggesting that the natural selection pressure from the host factor also affect the codon usage patterns of PCV. In particular, PCV genotype II is in synonymous codon usage more similar to pig than to PCV genotype I, which may be one of the most important molecular mechanisms of PCV genotype II to cause disease. The calculations results of the relative abundance of dinucleotides indicate that the composition of dinucleotides also plays a key role in the variation found in synonymous codon usage in PCV. Furthermore, geographic factors, the general average hydrophobicity and the aromaticity may be related to the formation of codon usage patterns of PCV.

Conclusion
The results of these studies suggest that synonymous codon usage pattern of PCV genome are the result of interaction between mutation pressure and natural selection from its host. The information from this study may not only have theoretical value in understanding the characteristics of synonymous codon usage in PCV genomes, but also have significant value for the molecular evolution of PCV.
Exploiting the inter-strain divergence of Fusarium oxysporum for microbial bioprocessing of lignocellulose to bioethanol
Authors: Ali Shahin S , Khan Mojibur , Fagan Brian , Mullins Ewen , Doohan Fiona M 
Published: March 2012

AbstractMicrobial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. A targeted evolution-based study was undertaken to determine if inter-strain microbial variability could be exploited for bioprocessing of lignocellulose to bioethanol. The microorganism studied wasFusarium oxysporumbecause of its capacity to both saccharify and ferment lignocellulose. Strains ofF. oxysporumwere isolated and assessed for their genetic variability. Using optimised solid-state straw culture conditions, experiments were conducted that compared fungal strains in terms of their growth, enzyme activities (cellulases, xylanase and alcohol dehydrogenase) and yield of bioethanol and the undesirable by-products acetic acid and xylitol. Significant inter-strain divergence was recorded in regards to the capacity of studiedF. oxysporumstrains to produce alcohol from untreated straw. No correlation was observed between bioethanol synthesis and either the biomass production or microbial enzyme activity. A strong correlation was observed between both acetic acid and xylitol production and bioethanol yield. The level of diversity recorded in the alcohol production capacity among closely-related microorganism means that a targeted screening of populations of selected microbial species could greatly improve bioprocessing yields, in terms of providing both new host strains and candidate genes for the bioethanol industry.
Implications of E-learning systems and self-efficiency on students outcomes: a model approach
Authors: Saba Tanzila 
Published: March 2012

Abstract
Background
This paper presents a model approach to examine the relationships among e-learning systems, self-efficacy, and students' apparent learning results for university online courses.

Methods
Independent variables included in this study are e-learning system quality, information quality, computer self-efficacy, system-use, self-regulated learning behavior and user satisfaction as prospective determinants of online learning results. An aggregate of 674 responses of students completing at least one online course from Wawasan Open University (WOU) Malaysia were used to fit the path analysis model.

Results
The results indicated that system quality, information quality, and computer self-efficacy all affected system use, user satisfaction, and self-managed learning behavior of students.

Conclusion
Proposed path analytical model suggests that hypothesized variables are useful to forecast e-learning results
Effects of mechanical insufflation-exsufflation in preventing respiratory failure after extubation: a randomized controlled trial
Authors: Gonçalves Miguel R , Honrado Teresa , Winck João Carlos , Paiva José Artur 
Published: March 2012

Abstract
Introduction
Weaning protocols that include noninvasive ventilation (NIV) decrease re-intubation rates and ICU length of stay. However, impaired airway clearance is associated with NIV failure. Mechanical insufflation-exsufflation (MI-E) has been proven to be very effective in patients receiving NIV. We aimed to assess the efficacy of MI-E as part of an extubation protocol.

Method
Patients with mechanical ventilation (MV) for more than 48 hours with specific inclusion criteria, who successfully tolerated a spontaneous breathing trial (SBT), were randomly allocated before extubation, either for (A) a conventional extubation protocol (control group), or (B) the MI-E extubation protocol (study group). During the postextubation period (48 hours), group A patients received standard medical treatment (SMT), including NIV in case of specific indications, whereas group B received the same postextubation approach plus three daily sessions of mechanical in-exsufflation (MI-E). Reintubation rates, ICU length of stay, and NIV failure rates were analyzed.

Results
Seventy-five patients (26 women) with a mean age of 61.8 ± 17.3 years were randomized to a control group (n = 40; mean SAPS II, 47.8 ± 17.7) and to a study group (n = 35; mean SAPS II, 45.0 ± 15.0). MV time before enrollment was 9.4 ± 4.8 and 10.5 ± 4.1 days for the control and the study group, respectively. In the 48 hours after extubation, 20 control patients (50%) and 14 study patients (40%) used NIV. Study group patients had a significant lower reintubation rate than did controls; six patients (17%) versus 19 patients (48%), P < 0.05; respectively, and a significantly lower time under MV; 17.8 ± 6.4 versus 11.7 ± 3.5 days; P < 0.05; respectively. Considering only the subgroup of patients that used NIV, the reintubation rates related to NIV failure were significantly lower in the study group when compared with controls; two patients (6%) versus 13 (33%); P < 0.05, respectively. Mean ICU length of stay after extubation was significantly lower in the study group when compared with controls (3.1 ± 2.5 versus 9.8 ± 6.7 days; P < 0.05). No differences were found in the total ICU length of stay.

Conclusion
Inclusion of MI-E may reduce reintubation rates with consequent reduction in postextubation ICU length of stay. This technique seems to be efficient in improving the efficacy of NIV in this patient population.
Replacement of fentanyl infusion by enteral methadone decreases the weaning time from mechanical ventilation: a randomized controlled trial
Authors: Wanzuita Raquel , Poli-de-Figueiredo Luiz F , Pfuetzenreiter Felipe , Cavalcanti Alexandre Biasi , Westphal Glauco Adrieno 
Published: March 2012

Abstract
Introduction
Patients undergoing mechanical ventilation (MV) are frequently administered prolonged and/or high doses of opioids which when removed can cause a withdrawal syndrome and difficulty in weaning from MV. We tested the hypothesis that the introduction of enteral methadone during weaning from sedation and analgesia in critically ill adult patients on MV would decrease the weaning time from MV.

Methods
A double-blind randomized controlled trial was conducted in the adult intensive care units (ICUs) of four general hospitals in Brazil. The 75 patients, who met the criteria for weaning from MV and had been using fentanyl for more than five consecutive days, were randomized to the methadone (MG) or control group (CG). Within the first 24 hours after study enrollment, both groups received 80% of the original dose of fentanyl, the MG received enteral methadone and the CG received an enteral placebo. After the first 24 hours, the MG received an intravenous (IV) saline solution (placebo), while the CG received IV fentanyl. For both groups, the IV solution was reduced by 20% every 24 hours. The groups were compared by evaluating the MV weaning time and the duration of MV, as well as the ICU stay and the hospital stay.

Results
Of the 75 patients randomized, seven were excluded and 68 were analyzed: 37 from the MG and 31 from the CG. There was a higher probability of early extubation in the MG, but the difference was not significant (hazard ratio: 1.52 (95% confidence interval (CI) 0.87 to 2.64; P = 0.11). The probability of successful weaning by the fifth day was significantly higher in the MG (hazard ratio: 2.64 (95% CI: 1.22 to 5.69; P < 0.02). Among the 54 patients who were successfully weaned (29 from the MG and 25 from the CG), the MV weaning time was significantly lower in the MG (hazard ratio: 2.06; 95% CI 1.17 to 3.63; P < 0.004).

Conclusions
The introduction of enteral methadone during weaning from sedation and analgesia in mechanically ventilated patients resulted in a decrease in the weaning time from MV.
Effects of Intravenous Zoledronate on Bone Turnover and Bone Density Persist for at Least Five Years in HIV-Infected Men
Authors: Bolland Mark J. , Grey Andrew , Horne Anne M. , Briggs Simon E. , Thomas Mark G. , Ellis-Pegler Rod B. , Gamble Greg D. , Reid Ian R. 
Published: March 2012

Context:
In HIV-infected men, the antiresorptive effects of zoledronate persist for at least 2 yr after the second annual dose.

Objective:
Our objective was to determine the duration of action of zoledronate in men.

Design and Setting:
This was 4-yr extension of a 2-yr, double-blind, randomized, placebo-controlled trial at an academic research center.

Participants:
Participants included 43 HIV-infected men with bone mineral density (BMD) T score below −0.5, 35 of whom entered the extension study.

Intervention:
Intervention was annual administration of 4 mg iv zoledronate or placebo at baseline and 1 yr and no intervention subsequently.

Main Outcome Measures:
We evaluated changes in the bone turnover markers, serum osteocalcin and serum C-telopeptide (CTx), and changes in BMD at the lumbar spine, total hip, and total body.

Results:
There was no time × treatment interaction between 1 and 5 yr after the second zoledronate dose for osteocalcin or CTx (P &gt; 0.4) or any BMD site (P &gt; 0.7). Between 1 and 5 yr after the second dose, on average, osteocalcin was 41% lower (95% confidence interval = 19–62%; P &lt; 0.001), CTx 52% lower (33–71%; P &lt; 0.001), lumbar spine BMD 3.7% greater (0.3–7.0%; P = 0.03), total hip BMD 2.3% greater (0.3–4.3%; P = 0.02), and total body BMD 2.5% greater (0.8–4.1%; P = 0.004) in the zoledronate group than the placebo group. Five years after the second dose, the between-groups differences were 38% (13–62%) for osteocalcin, 49% (20–77%) for CTx, 3.5% (0.7–6.7%) for lumbar spine BMD, 3.4% (1.4–5.4%) for total hip BMD, and 1.6% (0.2–3.1%) for total body BMD.

Conclusion:
The effects of two annual 4-mg doses of zoledronate in men persist for at least 5 yr after the second dose. Larger trials assessing the antifracture efficacy of less frequent dosing of zoledronate are justified.
Pitfalls in Diagnostic Gastrin Measurements
Authors: Rehfeld Jens F , Bardram Linda , Hilsted Linda , Poitras Pierre , Goetze Jens P 
Published: March 2012

AbstractBACKGROUNDGastrin measurements are performed primarily for the diagnosis of gastrin-producing tumors, gastrinomas, which cause the Zollinger–Ellison syndrome (ZES). Gastrin circulates as several bioactive peptides, however, and the peptide pattern in gastrinoma patients often deviates from normal. Therefore, it is necessary to measure all forms of gastrin.CONTENTOnly immunoassays are useful for measurement of gastrin in plasma. The original assays were RIAs developed in research laboratories that used antibodies directed against the C terminus of gastrin peptides. Because the C-terminal tetrapeptide amide sequence constitutes the active site of gastrin peptides, these assays were well suited for gastrinoma diagnosis. More recently, however, most clinical chemistry laboratories have switched to commercial kits. Because of recent cases of kit-measured normogastrinemia in patients with ZES symptoms, the diagnostic sensitivity and analytical specificity of the available kits have been examined. The results show that gastrin kits frequently measure falsely low concentrations because they measure only a single gastrin form. Falsely high concentrations were also encountered, owing to overreactivity with O-sulfated gastrins or plasma proteins. Thus, more than half of the gastrin kits on the market are unsuited for diagnostics.SUMMARYGastrinomas are neuroendocrine tumors, some of which become malignant. A delay in diagnosis leads to fulminant ZES, with major, even lethal, complications. Consequently, it is necessary that the diagnostic sensitivity of gastrin kits be adequate. This diagnostic sensitivity requires antibodies that bind the C-terminal epitope of bioactive gastrins without the influence of O-sulfation.
Variation in rhodolith morphology and biogenic potential of newly discovered rhodolith beds in Newfoundland and Labrador (Canada)
Authors: Gagnon Patrick , Matheson Kyle , Stapleton Maria 
Published: March 2012

Abstract
For the first time the subarctic northwestern Atlantic, we examined variation in rhodolith (Lithothamnion glaciale) morphology and biogenic potential in two large (>500 m2) rhodolith beds we discovered recently between the depths of 5–25 m off St. Philip’s and Holyrood, Newfoundland and Labrador. Rhodoliths at St. Philip’s were >50% larger and contained 7% more internal space in deep (15–17 m) than shallow (8–10 m) water, whereas shallow rhodoliths were >180% larger at Holyrood than at St. Philip’s. Rhodoliths were predominantly spheroidal and compact at St. Philip’s and platy or bladed at Holyrood. Shallow rhodoliths varied in length from 41.1–114.6 mm at St. Philip’s and 61.3–189.1 mm at Holyrood. Rhodolith density was similar between beds (858.1–938.9 individuals m-2) although biomass was significantly higher at Holyrood than St. Philip’s (25.3 versus 19.4 kg m-2). There was a strong positive relationship (R2>0.93) between rhodolith volume and dry weight in both beds. Invertebrates associated with shallow rhodoliths belonging to the taxonomic groups Asteroidea, Echinoidea, Ophiuroidea, Bivalvia, Gastropoda, Polyplacophora, Crustacea, and Annelida were present at both sites, although they varied in terms of size, density, and biomass. Brittle stars (Ophiopholis aculeata) and chitons (Tonicella marmorea) accounted for at least 82% (up to 2026.7 individuals m-2) of total numbers of invertebrates in each bed. Larger rhodoliths appeared to facilitate reproduction and feeding in dominant fish and invertebrate species. Differences in hydrodynamic conditions within and between beds may have contributed to these patterns.
Experiences and Perceptions of Medical Discrimination Among a Multiethnic Sample of Breast Cancer Patients in the Greater San Francisco Bay Area, California
Authors: Quach Thu , Nuru-Jeter Amani , Morris Pagan , Allen Laura , Shema Sarah J. , Winters June K. , Le Gem M. , Gomez Scarlett Lin 
Published: March 2012

Objectives. We conducted qualitative interviews with breast cancer survivors to identify themes related to institutional, personally mediated, and internalized discrimination in the medical setting. Methods. We conducted 7 focus groups and 23 one-on-one interviews with a multiethnic sample of breast cancer survivors randomly selected from a population-based registry covering the Greater San Francisco Bay Area, California. Results. Participants reported experiencing different forms of medical discrimination related to class, race, and language. Among African Americans, participants reported experiencing internalized discrimination and personal or group discrimination discrepancy—perceiving discrimination against them as a racial/ethnic group, yet not perceiving or discussing personal experiences of discrimination. Among Asian immigrants, participants reported experiencing institutional and personally mediated overt types of discrimination, including lack of access to quality and readily available translation services. Our results also indicated well-established coping mechanisms in response to discrimination experiences in both groups. Conclusions. Participants reported experiencing medical discrimination at all 3 levels, which may have deleterious health effects through the biopsychosocial stress pathway and through active coping mechanisms that could lead to delayed- or underutilization of the health care system to avoid discrimination.
Pharmaceutical Companies’ Role in State Vaccination Policymaking: The Case of Human Papillomavirus Vaccination
Authors: Mello Michelle M. , Abiola Sara , Colgrove James 
Published: March 2012

Objectives. We sought to investigate roles that Merck & Co Inc played in state human papillomavirus (HPV) immunization policymaking, to elicit key stakeholders’ perceptions of the appropriateness of these activities, and to explore implications for relationships between health policymakers and industry. Methods. We used a series of state case studies combining data from key informant interviews with analysis of media reports and archival materials. We interviewed 73 key informants in 6 states that were actively engaged in HPV vaccine policy deliberations. Results. Merck promoted school-entry mandate legislation by serving as an information resource, lobbying legislators, drafting legislation, mobilizing female legislators and physician organizations, conducting consumer marketing campaigns, and filling gaps in access to the vaccine. Legislators relied heavily on Merck for scientific information. Most stakeholders found lobbying by vaccine manufacturers acceptable in principle, but perceived that Merck had acted too aggressively and nontransparently in this case. Conclusions. Although policymakers acknowledge the utility of manufacturers’ involvement in vaccination policymaking, industry lobbying that is overly aggressive, not fully transparent, or not divorced from financial contributions to lawmakers risks undermining the prospects for legislation to foster uptake of new vaccines.
Discrimination and the Stress Response: Psychological and Physiological Consequences of Anticipating Prejudice in Interethnic Interactions
Authors: Sawyer Pamela J. , Major Brenda , Casad Bettina J. , Townsend Sarah S. M. , Mendes Wendy Berry 
Published: March 2012

Objectives. We sought to demonstrate that individuals who anticipate interacting with a prejudiced cross-race/ethnicity partner show an exacerbated stress response, as measured through both self-report and hemodynamic and vascular responses, compared with individuals anticipating interacting with a nonprejudiced cross-race/ethnicity partner. Methods. Through a questionnaire exchange with a White interaction partner (a confederate) Latina participants learned that their partner had racial/ethnic biased or egalitarian attitudes. Latina participants reported their cognitive and emotional states, and cardiovascular responses were measured while participants prepared and delivered a speech to the White confederate. Results. Participants who believed that their interaction partner held prejudiced attitudes reported greater concern and more threat emotions before the interaction, and more stress after the interaction, and showed greater cardiovascular response than did participants who believed that their partner had egalitarian attitudes. Conclusions. This study shows that merely anticipating prejudice leads to both psychological and cardiovascular stress responses. These results are consistent with the conceptualization of anticipated discrimination as a stressor and suggest that vigilance for prejudice may be a contributing factor to racial/ethnic health disparities in the United States.
The Lived Experience of Race and Its Health Consequences
Authors: Smedley Brian D. 
Published: March 2012

A growing body of research illuminates the mechanisms through which racism and discrimination influence the health status of people of color. Much of the focus of this research, however, has been on individually mediated racism (i.e., acts of discrimination and racial bias committed by White individuals against people of color). Yet research literature provides numerous examples of how racism operates not just at individual levels, but also at internalized, institutional, and structural levels. A more comprehensive model of the lived experience of race is needed that considers the cumulative, interactive effects of different forms of racism on health over the lifespan. Such a model must facilitate an intersectional analysis to better understand the interaction of race with gender, socioeconomic status, geography, and other factors, and should consider the negative consequences of racism for Whites.