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11.
The murid rodent subfamily Sigmodontinae contains 79 genera which are
distributed throughout the New World. The time of arrival of the first
sigmodontines in South America and the estimated divergence time(s) of the
different lineages of South American sigmodontines have been controversial
due to the lack of a good fossil record and the immense number of extant
species. The "early-arrival hypothesis" states that the sigmodontines must
have arrived in South America no later than the early Miocene, at least 20
MYA, in order to account for their vast present-day diversity, whereas the
"late-arrival hypothesis" includes the sigmodontines as part of the
Plio-Pleistocene Great American Interchange, which occurred approximately
3.5 MYA. The phylogenetic relationships among 33 of these genera were
reconstructed using mitochondrial DNA (mtDNA) sequence data from the ND3,
ND4L, arginine tRNA, and ND4 genes, which we show to be evolving at the
same rate. A molecular clock was calibrated for these genes using published
fossil dates, and the genetic distances were estimated from the DNA
sequences in this study. The molecular clock was used to estimate the dates
of the South American sigmodontine origin and the main sigmodontine
radiation in order to evaluate the "early-" and "late-arrival" scenarios.
We estimate the time of the sigmodontine invasion of South America as
between approximately 5 and 9 MYA, supporting neither of the scenarios but
suggesting two possible models in which the invading lineage was either (1)
ancestral to the oryzomyines, akodonts, and phyllotines or (2) ancestral to
the akodonts and phyllotines and accompanied by the oryzomyines. The
sigmodontine invasion of South America provides an example of the advantage
afforded to a lineage by the fortuitous invasion of a previously
unexploited habitat, in this case an entire continent.
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12.
Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment 总被引:11,自引:2,他引:9
When microbes evolve in a continuous, nutrient-limited environment, natural
selection can be predicted to favor genetic changes that give cells greater
access to limiting substrate. We analyzed a population of baker's yeast
that underwent 450 generations of glucose-limited growth. Relative to the
strain used as the inoculum, the predominant cell type at the end of this
experiment sustains growth at significantly lower steady-state glucose
concentrations and demonstrates markedly enhanced cell yield per mole
glucose, significantly enhanced high-affinity glucose transport, and
greater relative fitness in pairwise competition. These changes are
correlated with increased levels of mRNA hybridizing to probe generated
from the hexose transport locus HXT6. Further analysis of the evolved
strain reveals the existence of multiple tandem duplications involving two
highly similar, high- affinity hexose transport loci, HXT6 and HXT7.
Selection appears to have favored changes that result in the formation of
more than three chimeric genes derived from the upstream promoter of the
HXT7 gene and the coding sequence of HXT6. We propose a genetic mechanism
to account for these changes and speculate as to their adaptive
significance in the context of gene duplication as a common response of
microorganisms to nutrient limitation.
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13.
Background
The importance of effective clinical teaching for the quality of future patient care is globally understood. Due to recent changes in graduate medical education, new tools are needed to provide faculty with reliable and individualized feedback on their teaching qualities. This study validates two instruments underlying the System for Evaluation of Teaching Qualities (SETQ) aimed at measuring and improving the teaching qualities of obstetrics and gynecology faculty.Methods and Findings
This cross-sectional multi-center questionnaire study was set in seven general teaching hospitals and two academic medical centers in the Netherlands. Seventy-seven residents and 114 faculty were invited to complete the SETQ instruments in the duration of one month from September 2008 to September 2009. To assess reliability and validity of the instruments, we used exploratory factor analysis, inter-item correlation, reliability coefficient alpha and inter-scale correlations. We also compared composite scales from factor analysis to global ratings. Finally, the number of residents'' evaluations needed per faculty for reliable assessments was calculated. A total of 613 evaluations were completed by 66 residents (85.7% response rate). 99 faculty (86.8% response rate) participated in self-evaluation. Factor analysis yielded five scales with high reliability (Cronbach''s alpha for residents'' and faculty): learning climate (0.86 and 0.75), professional attitude (0.89 and 0.81), communication of learning goals (0.89 and 0.82), evaluation of residents (0.87 and 0.79) and feedback (0.87 and 0.86). Item-total, inter-scale and scale-global rating correlation coefficients were significant (P<0.01). Four to six residents'' evaluations are needed per faculty (reliability coefficient 0.60–0.80).Conclusions
Both SETQ instruments were found reliable and valid for evaluating teaching qualities of obstetrics and gynecology faculty. Future research should examine improvement of teaching qualities when using SETQ. 相似文献14.
Background
Current management of asplenic patients is not in compliance with best practice standards, such as defined by the British Committee for Standards in Haematology. To improve quality of care, factors inhibiting best practice care delivery need to be identified first. With this study, we aimed to identify and quantify physicians'' barriers to adhere to best practice management of asplenic patients in the Netherlands.Methods and Principal Findings
A cross-sectional survey, preceded by multiple focus group discussions, was performed among Dutch physicians responsible for prevention of infections in asplenic patients, including specialists (of Internal medicine and Surgery) and general practitioners (GPs). Forty seven GPs and seventy three hospital specialists returned the questionnaire, yielding response rates of 47% and 36,5% respectively. Physicians reported several barriers to deliver best practice. For both GPs and specialists, the most frequently listed barriers were: poor patient knowledge (>80% of hospital specialists and GPs) and lack of clarity about which physician is responsible for the management of asplenic patients (50% of Internists, 46% of Surgeons, 55% of GPs). Both GPs and hospital specialists expressed to experience a lack of mutual trust: specialists were uncertain whether the GP would follow their advice given on patient discharge (33–59%), whereas half of GPs was not convinced that specialists'' discharge letters contained the correct recommendations. Almost all physicians (>90%) indicated that availability of a national guideline would improve adherence to best practice, especially if accessible online.Conclusion
This study showed that, in accordance with reports on international performance, care delivery for asplenic patients in the Netherlands is suboptimal. We identified and quantified perceived barriers by physicians that prevent adherence to post-splenectomy guidelines for the first time. Better transmural collaboration and better informed patients are likely to improve the quality of care of the asplenic patient population. A national, online-available guideline is urgently required. 相似文献15.
Translocations for conservation often involve species limited to relict distributions. However, uncertainty can exist regarding the ability of source individuals to acclimatise following a shift to a distant location. We investigated the ability of captive-reared juvenile tuatara (Sphenodon punctatus) of Cook Strait stock (41°S) to adjust to outdoor, predator-protected pens within Orokonui Ecosanctuary (45 °S). We examined potential basking and within burrow temperatures, the influence of temperature on emergence, and growth rates in comparison with other locations. Tuatara at Orokonui reached their preferred temperature when basking over summer, and burrows provided protection from freezing over winter. Emergence was temperature-dependent and essentially ceased during winter. Growth rates of Orokonui-held juveniles were within the range for four other captive-rearing facilities and faster than for wild juveniles from a Cook Strait population. As all Orokonui-held juveniles have survived and grown we conclude that the climate at this southern location is suitable to consider a free-release. 相似文献
16.
Background
Digital polymerase chain reaction (dPCR) is an increasingly popular technology for detecting and quantifying target nucleic acids. Its advertised strength is high precision absolute quantification without needing reference curves. The standard data analytic approach follows a seemingly straightforward theoretical framework but ignores sources of variation in the data generating process. These stem from both technical and biological factors, where we distinguish features that are 1) hard-wired in the equipment, 2) user-dependent and 3) provided by manufacturers but may be adapted by the user. The impact of the corresponding variance components on the accuracy and precision of target concentration estimators presented in the literature is studied through simulation.Results
We reveal how system-specific technical factors influence accuracy as well as precision of concentration estimates. We find that a well-chosen sample dilution level and modifiable settings such as the fluorescence cut-off for target copy detection have a substantial impact on reliability and can be adapted to the sample analysed in ways that matter. User-dependent technical variation, including pipette inaccuracy and specific sources of sample heterogeneity, leads to a steep increase in uncertainty of estimated concentrations. Users can discover this through replicate experiments and derived variance estimation. Finally, the detection performance can be improved by optimizing the fluorescence intensity cut point as suboptimal thresholds reduce the accuracy of concentration estimates considerably.Conclusions
Like any other technology, dPCR is subject to variation induced by natural perturbations, systematic settings as well as user-dependent protocols. Corresponding uncertainty may be controlled with an adapted experimental design. Our findings point to modifiable key sources of uncertainty that form an important starting point for the development of guidelines on dPCR design and data analysis with correct precision bounds. Besides clever choices of sample dilution levels, experiment-specific tuning of machine settings can greatly improve results. Well-chosen data-driven fluorescence intensity thresholds in particular result in major improvements in target presence detection. We call on manufacturers to provide sufficiently detailed output data that allows users to maximize the potential of the method in their setting and obtain high precision and accuracy for their experiments.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-283) contains supplementary material, which is available to authorized users. 相似文献17.
Kiki M. J. M. H. Lombarts Maas Jan Heineman Albert J. J. A. Scherpbier Onyebuchi A. Arah 《PloS one》2014,9(1)
Background
To understand teaching performance of individual faculty, the climate in which residents’ learning takes place, the learning climate, may be important. There is emerging evidence that specific climates do predict specific outcomes. Until now, the effect of learning climate on the performance of the individual faculty who actually do the teaching was unknown.Objectives
This study: (i) tested the hypothesis that a positive learning climate was associated with better teaching performance of individual faculty as evaluated by residents, and (ii) explored which dimensions of learning climate were associated with faculty’s teaching performance.Methods and Materials
We conducted two cross-sectional questionnaire surveys amongst residents from 45 residency training programs and multiple specialties in 17 hospitals in the Netherlands. Residents evaluated the teaching performance of individual faculty using the robust System for Evaluating Teaching Qualities (SETQ) and evaluated the learning climate of residency programs using the Dutch Residency Educational Climate Test (D-RECT). The validated D-RECT questionnaire consisted of 11 subscales of learning climate. Main outcome measure was faculty’s overall teaching (SETQ) score. We used multivariable adjusted linear mixed models to estimate the separate associations of overall learning climate and each of its subscales with faculty’s teaching performance.Results
In total 451 residents completed 3569 SETQ evaluations of 502 faculty. Residents also evaluated the learning climate of 45 residency programs in 17 hospitals in the Netherlands. Overall learning climate was positively associated with faculty’s teaching performance (regression coefficient 0.54, 95% confidence interval: 0.37 to 0.71; P<0.001). Three out of 11 learning climate subscales were substantially associated with better teaching performance: ‘coaching and assessment’, ‘work is adapted to residents’ competence’, and ‘formal education’.Conclusions
Individual faculty’s teaching performance evaluations are positively affected by better learning climate of residency programs. 相似文献18.
Y Deng J Zhao D Sakurai KM Kaufman JC Edberg RP Kimberly DL Kamen GS Gilkeson CO Jacob RH Scofield CD Langefeld JA Kelly ME Alarcón-Riquelme BIOLUPUS GENLES Networks JB Harley TJ Vyse BI Freedman PM Gaffney KM Sivils JA James TB Niewold RM Cantor W Chen BH Hahn EE Brown PROFILE BP Tsao 《Arthritis research & therapy》2012,14(Z3):A5
19.
20.
A mouse genomic clone containing a lactate dehydrogenase-A (LDH-A)
processed pseudogene and a B1 repetitive element was isolated, and a
nucleotide sequence of approximately 3 kb was determined. The pseudogene
and B1 element are flanked by perfect 13-bp repeats, and the B1 sequence
starts at 14 nucleotides 3' to the presumptive polyadenylation signal of
the pseudogene. The nucleotide sequences of the LDH-A genes and processed
pseudogenes from mouse, rat, and human were compared, and a phylogenetic
tree was constructed. The rate and pattern of nucleotide substitutions in
the LDH-A pseudogenes are similar to previously reported results (Li et al.
1984). The average rate of nucleotide substitutions in the LDH-A
pseudogenes is 4.3 X 10(- 9)/site/year. The substitutions of C----T and
G----A are most frequent, and A----G substitutions are relatively high. The
rate of synonymous substitutions in the LDH-A genes is 5.3 X 10(-9), which
is not significantly higher than the average rate of 4.7 X 10(-9) for 35
mammalian genes. The rate of nonsynonymous substitutions in the LDH-A genes
is 0.20 X 10(-9), which is considerably lower than the average rate of 0.88
X 10(-9) for 35 mammalian genes. Thus, the mammalian LDH-A gene appears to
be highly conserved in evolution.
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