Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the probability of identity among genotypes in natural populations: cautions and guidelines

Individual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy‐nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01–0.0001).
Characterization of an early growth response gene, which encodes a zinc finger transcription factor, potentially involved in cell cycle regulation.

Using differential display polymerase chain reaction, early growth response gene alpha (EGR alpha) was first isolated as a 291-base pair 3'-cDNA clone, which was highly expressed in the androgen-independent prostate carcinoma cell lines PC3 and DU145, as compared with the androgen-responsive prostate carcinoma cell line LNCaP. Full length cloning of the EGR alpha coding region revealed that EGR alpha was a new member of an important subfamily of nuclear zinc finger transcription factors (others members e.g. Sp1, EGR-2, and Wilms' tumor gene). Moreover, it was observed that EGR alpha, as with most Sp1 subfamily members, was conserved between mammalian species ranging from human to rabbit. Two hormones important for prostate development and differentiation were found to be potent regulators of EGR alpha mRNA expression. Androgens were observed to induce a down-regulation of EGR alpha mRNA expression (70% in 72 h), while epidermal growth factor induced a rapid transient up-regulation (6-fold in 100 min). The up-regulation was controlled at the transcriptional level and effectively blocked by staurosporine (which suggests the involvement of the protein kinase C pathway). Functional analysis demonstrated that EGR alpha could bind to, and stimulate transcription from, a basic transcription element (BTE) consensus sequence on DNA (BTE is a transcription-modulating sequence in the promoter region of some cytochrome P450 family members). Furthermore, in stage-synchronized prostate cells, EGR alpha mRNA was highly expressed in the early G1 phase of the cell cycle, similar to c-fos mRNA expression. These results indicated that the zinc finger transcription factor EGR alpha seems to play a role in cell cycle regulation.
Breaking the web of needless disability

Background: In 2012 I presented a program to the London IFDM entitled “Breaking the Web of Needless Disability”. The model drew heavily from the latest neuroscientific theory, and was quite well received. This program represents further development of the ideas presented in London to encompass “resilience”. Hypothesis: 1. “Resilience” is a behaviour that is learned and unlearned like any other skill; 2. Understanding how humans think and react in compensation systems will yield valuable insight into the building of resilience to unnecessary disability. Methods: Extension of existing literature and pilot studies examining the differences between those people who suffer injury and recover as expected and those who suffer the same sort of injury and spiral down into despair and dependency. Principal findings: “Resilience” is a specific behaviour beneficially affecting the sense of loss of control that attends injury. There are four specific “styles” of resilience. Each person uses one or more of these styles to a greater or lesser degree. By use of modified psychological inventory tools, the predominant resilience style of an individual can be ascertained, and approaches that enhance their resilience style can be utilised for either prevention or treatment. Discussion: “Habits of thought” are established by repetition. For habits of thinking of one's self as able or disabled, the most significant form of repetition is internal dialog. In resilient people, there are four discrete kinds of dialog that are used to overcome a sense of loss of control. By identifying and bolstering those styles of resilience an injured person can become less susceptible to a sense of loss of control that gives rise to unnecessary disability. Conclusion: The approach is useful in understanding failure to recover as expected, and shows promise for effective individualised treatment for injury management.
Externalities reduction strategies in last mile logistics: A review

In this paper a review of recent contributions in scientific literature on the last mile logistics is presented. The increase in freight transport and the actual growing trends are responsible, in the urban areas, of a critical increase of congestion, air pollution, noise and others externalities that involve the major cities in the world. New technologies and organizational strategies allow handling in a more efficient way the last mile delivery in urban areas. Papers that contribute significantly and with original proposal in reducing externalities in urban logistics are analysed in this work.
LLC resonant converter with variable resonant inductor for wide LED dimming range

In this paper, LLC resonant converter with direct output current controlled variable resonant inductor (VRI) is proposed and studied. The output LED current is directly flowing through the auxiliary windings of VRI as the DC bias current to control the inductance of the VRI and no additional control circuit is needed. The VRI is smallest under rated LED current and increases as LED current decreases. Therefore, the resonant frequency also decreases with LED current and the switching frequency variation range is reduced. In this way, the dimming range of LLC converter with VRI can be extended. Because the same optimized parameters with conventional LLC converter can also be used, the proposed LLC converter with VRI can achieve high efficiency especially under heavy load. Detailed design considerations on this proposed method were presented. Finally, an 110W LLC LED laboratory prototype with 83V/1.32A output was developed. The proposed LLC converter and the conventional LLC converter were tested on the laboratory prototype. Experimental results show that the peak efficiency of the proposed converter is 95.9% and the LED current can be dimmed up to 5% of the rated current.
Oral health literacy levels among a low-income WIC population.

OBJECTIVES To determine oral health literacy (OHL) levels and explore potential racial differences in a low-income population. METHODS This was a cross-sectional study of caregiver/child dyads that completed a structured 30-minute in-person interview conducted by two trained interviewers in seven counties in North Carolina. Sociodemographic, OHL, and dental health-related data were collected. OHL was measured with a dental word recognition test [Rapid Estimate of Adult Literacy in Dentistry (REALD-30)]. Descriptive, bivariate, and multivariate methods were used to examine the distribution of OHL and explore racial differences. RESULTS Of 1658 eligible subjects, 1405 (85 percent) participated and completed the interviews. The analytic sample (N=1280) had mean age 26.5 (standard deviation = 6.9) years with 60 percent having a high school degree or less. OHL varied between racial groups as follows: Whites--mean score = 17.4 (SE = 0.2); African-American (AA)--mean score = 15.3 [standard error (SE) = 0.2]; American Indian (AI)--mean score = 13.7 (SE = 0.3). Multiple linear regression revealed that after controlling for education, county of residence, age, and Hispanic ethnicity, Whites had 2.0 points (95 percent CI = 1.4, 2.6) higher adjusted REALD-30 score versus AA and AI. CONCLUSIONS Differences in OHL levels between racial groups persisted after adjusting for education and sociodemographic characteristics.
Poly(lactic‐co‐glycolic acid) hollow fibre membranes for use as a tissue engineering scaffold

Mass transfer limitations of scaffolds are currently hindering the development of 3‐dimensional, clinically viable, tissue engineered constructs. We have developed a poly(lactide‐co‐glycolide) (PLGA) hollow fibre membrane scaffold that will provide support for cell culture, allow psuedovascularisation in vitro and provide channels for angiogenesis in vivo. We produced PDLLGA flat sheet membranes using 1, 4‐dioxane and 1‐methyl‐2‐pyrrolidinone (NMP) as solvents and water as the nonsolvent, and hollow fibre membranes, using NMP and water, by dry/wet‐ and wet‐spinning. The resulting fibres had an outer diameter of 700 μm and an inner diameter of 250 μm with 0.2–1.0 μm pores on the culture surface. It was shown that varying the air gap and temperature when spinning changed the morphology of the fibres. The introduction of a 50 mm air gap caused a dense skin of 5 μm thick to form, compared to a skin of 0.5 μm thick without an air gap. Spinning at 40°C produced fibres with a more open central section in the wall that contained more, larger macrovoids compared to fibres spun at 20°C. Culture of the immortalised osteogenic cell line 560pZIPv.neo (pZIP) was carried out on the PDLLGA flat sheets in static culture and in a PDLLGA hollow fibre bioreactor under counter‐current flow conditions. Attachment and proliferation was statistically similar to tissue culture polystyrene on the flat sheets and was also successful in the hollow fibre bioreactor. The PDLLGA hollow fibres are a promising scaffold to address the size limitations currently seen in tissue engineered constructs. Biotechnol. Bioeng. 2007;96: 177–187. © 2006 Wiley Periodicals, Inc.
The sea pansy Renilla reniformis luciferase serves as a sensitive bioluminescent reporter for differential gene expression in Candida albicans

The infectious yeast Candida albicans progresses through two developmental programs which involve differential gene expression, the bud-hypha transition and high-frequency phenotypic switching. To understand how differentially expressed genes are regulated in this organism, the promoters of phase-specific genes must be functionally characterized, and a bioluminescent reporter system would facilitate such characterization. However, C. albicans has adopted a nontraditional codon strategy that involves a tRNA with a CAG anticodon to decode the codon CUG as serine rather than leucine. Since the luciferase gene of the sea pansy Renilla reinformis contains no CUGs, we have used it to develop a highly sensitive bioluminescent reporter system for C. albicans. When fused to the galactose-inducible promoter of GAL1, luciferase activity is inducible; when fused to the constitutive EF1 alpha 2 promoter, luciferase activity is constitutive; and when fused to the promoter of the white-phase-specific gene WH11 or the opaque-phase-specific gene OP4, luciferase activity is phase specific. The Renilla luciferase system can, therefore, be used as a bioluminescent reporter to analyze the strength and developmental regulation of C. albicans promoters.
Afferent projections to the rat locus coeruleus as determined by a retrograde tracing technique

Afferent connections to the rat locus coeruleus (LC), which contains exclusively noradrenergic neurons, have been traced using the technique of retrograde transport of horseradish peroxidase (HRP). In order to ensure accurate placement of adequate amounts of HRP in the LC, a microiontophoretic delivery technique coupled with single cell recording was employed. The use of electrophysiological “landmarks” as aids in placing the injections is described. Following HRP injections into the LC, forebrain structures containing labelled neurons included the insular cortex, the central nucleus of the amygdala, the medial, lateral and magnocellular preoptic areas, the bed nucleus of the stria terminalis, and the dorsomedial, paraventricular and lateral hypothalamic areas. In the brainstem reactive neurons were observed in the central grey substance, the reticular formation, the raphe, vestibular, solitary tract and lateral reticular nuclei. In particular, the areas of catecholamine cell groups A1, A2 and A5 appeared to contain many reactive cells. Labelled neurons were also observed in the fastigial nuclei and in the marginal zones of the dorsal horns of the spinal cord. This pattern of afferent innervation supports suggestions for a role for the LC in behavioral arousal mechanisms and autonomic regulation.
Atlas of Wnt and R‐spondin gene expression in the developing male mouse lower urogenital tract

Prostate development is influenced by β‐catenin signaling, but it is unclear which β‐catenin activators are involved, where they are synthesized, and whether their mRNA abundance is influenced by androgens. We identified WNT/β‐catenin‐responsive β‐galactosidase activity in the lower urogenital tract (LUT) of transgenic reporter mice, but β‐galactosidase activity differed among the four mouse strains we examined. We used in situ hybridization to compare patterns of Wnts, r‐spondins (Rspos, co‐activators of β‐catenin signaling), β‐catenin‐responsive mRNAs, and an androgen receptor‐responsive mRNA in wild type fetal male, fetal female, and neonatal male LUT. Most Wnt and Rspo mRNAs were present in LUT during prostate development. Sexually dimorphic expression patterns were observed for WNT/β‐catenin‐responsive genes, and for Wnt2b, Wnt4, Wnt7a, Wnt9b, Wnt10b, Wnt11, Wnt16, and Rspo3 mRNAs. These results reveal sexual differences in WNT/β‐catenin signaling in fetal LUT, supporting the idea that this pathway may be directly or indirectly responsive to androgens during prostate ductal development. Developmental Dynamics 240:2548–2560, 2011. © 2011 Wiley‐Liss, Inc.
Case Studies from Morning Report

Abstract In primary care specialties, Morning Report is a traditional vehicle for expanding medical residents' training in diagnosis and treatment. At one academic medical center, residents and faculty in the Department of Family and Community Medicine use case-based teaching, centered around planning and reviewing patient management, to review intriguing cases from patient encounters in the department's hospital service. Seeking to improve the level of evidence-based information exchanged at Morning Report, department leaders invited reference librarians from the health sciences library to attend weekly Morning Report. The librarians saw this as an opportunity not only to improve residents' information-seeking skills, but also to improve librarians' teaching skills and understanding of the needs of users in clinical settings. This paper describes the evolution of librarians' involvement in Morning Report, examples of the kinds of contributions librarians have made in this setting, and changes made in Morning Report sessions to facilitate this activity.
Interictal spiking during wakefulness and sleep and the localization of foci in temporal lobe epilepsy

We examined variations in interictal spiking during sleep and wakefulness to assess differences in reliability for localizing epileptic foci. Forty patients were studied prospectively. Spikes were assessed for rates, field, and appearance of new foci. Final localization was determined by surgery, electrocorticography, and seizure onset. Comparison of interictal EEG foci with final localization was made. In 39 patients, slow-wave sleep activated spiking compared with wakefulness. Most patients showed maximal spiking in sleep stages 3 or 4. Restriction of field in rapid eye movement (REM) sleep and wakefulness, and extension of field in slow-wave sleep occurred. New foci appeared in non-rapid eye movement sleep in 53% of patients. Similar but not identical spiking rates, foci, and field distributions were seen in wakefulness and REM sleep. All REM foci were unilateral. Our findings suggest that localization of the primary epileptogenic area is more reliable in REM sleep than in wakefulness, and in wakefulness more than in slow-wave sleep.
Joint estimation of contemporary seed and pollen dispersal rates among plant populations

There are few statistical methods for estimating contemporary dispersal among plant populations. A maximum‐likelihood procedure is introduced here that uses pre‐ and post‐dispersal population samples of biparentally inherited genetic markers to jointly estimate contemporary seed and pollen immigration rates from a set of discrete external sources into a target population. Monte Carlo simulations indicate that accurate estimates and reliable confidence intervals can be obtained using this method for both pollen and seed migration rates at modest sample sizes (100 parents/population and 100 offspring) when population differentiation is moderate (FST ≥ 0.1), or by increasing pre‐dispersal samples (to about 500 parents/population) when genetic divergence is weak (FST = 0.01). The method exhibited low sensitivity to the number of source populations and achieved good accuracy at affordable genetic resolution (10 loci with 10 equifrequent alleles each). Unsampled source populations introduced positive biases in migration rate estimates from sampled sources, although they were minor when the proportion of immigration from the latter was comparatively low. A practical application of the method to a metapopulation of the Australian resprouter shrub Banksia attenuata revealed comparable levels of directional seed and pollen migration among dune groups, and the estimate of seed dispersal was higher than a previous estimate based on conservative assignment tests. The method should be of interest to researchers and managers assessing broad‐scale nonequilibrium seed and pollen gene flow dynamics in plants.
Alcohol consumption and mortality among women.

BACKGROUND Studies in men suggest that light-to-moderate alcohol intake is associated with a reduction in overall mortality, due primarily to a reduced risk of coronary heart disease. Among women with similar levels of alcohol consumption, an increased risk of breast cancer has been noted that complicates the balance of risks and benefits. METHODS We conducted a prospective study among 85,709 women, 34 to 59 years of age and without a history of myocardial infarction, angina, stroke, or cancer, who completed a dietary questionnaire in 1980. During the 12-year follow-up period, 2658 deaths were documented. RESULTS The relative risks of death in drinkers as compared with nondrinkers were 0.83 (95 percent confidence interval, 0.74 to 0.93) for women who consumed 1.5 to 4.9 g of alcohol per day (one to three drinks per week), 0.88 (95 percent confidence interval, 0.80 to 0.98) for those who consumed 5.0 to 29.9 g per day, and 1.19 (95 percent confidence interval, 1.02 to 1.38) for those who consumed 30 g or more per day, after adjustment for other predictors of mortality. Light-to-moderate drinking (1.5 to 29.9 g per day) was associated with a decreased risk of death from cardiovascular disease; heavier drinking was associated with an increased risk of death from other causes, particularly breast cancer and cirrhosis. The benefit associated with light-to-moderate drinking was most apparent among women with risk factors for coronary heart disease and those 50 years of age or older. CONCLUSIONS Among women, light-to-moderate alcohol consumption is associated with a reduced mortality rate, but this apparent survival benefit appears largely confined to women at greater risk for coronary heart disease.
Age-related change in contribution of stroke volume to central pulse pressure

ABSTRACT We investigated age-related change in the contribution of stroke volume (SV) to central PP (cPP). Eighty seven adult subjects who were free of vasoactive agents were included. Subjects were divided into three age groups: young (20–39 years, n = 26), middle (40–49 years, n = 29), and old (≥50 years, n = 32). SV was calculated by Doppler echocardiography. Hemodynamic indices were measured using a brachial cuff-based oscillometric method. The brachial and cPP showed a small decline from the young group to the middle group and a greater rise after 50 years old. SV significantly and positively correlated with brachial (r = 0.53, p < 0.01) and cPP (r = 0.57, p < 0.01) in the young group. In the middle group, the association of SV with brachial pulse pressure was significant (r = 0.38, p = 0.04) and that with cPP was bordering significant (r = 0.34, p = 0.07). No significant association was found between SV and PP in the old group. In conclusion, the contribution of SV to cPP decreases with age. Age-related changes in the determinants of cPP should be considered when investigating the clinical value of cPP.
First nuclear DNA amounts in more than 300 angiosperms.

BACKGROUND AND AIMS Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database http://www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. METHODS C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. KEY RESULTS AND CONCLUSIONS The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1.5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see http://www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses.