Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine structure of the cottontail rabbit papillomavirus mRNAs expressed in the transplantable VX2 carcinoma

We analyzed the polyadenylated mRNAs transcribed from the cottontail rabbit papillomavirus genomes present in the domestic rabbit transplantable carcinoma line VX2, employing a combination of S1 nuclease mapping and primer extension techniques with vector M13-based single-stranded DNA probes. Each of the two major mRNA species (1,860 and 1,110 bases long) contained two exons which corresponded to the E6-E7 and E2-E4 open reading frames. The splice donor site for these transcripts was located at position 1371 at the beginning of the E1 open reading frame. Consequently, the splicing event did not lead to the fusion of the E region proximal (E6 and E7) and distal (E2, E4, or E5) open reading frames. The translation of the polycistronic RNA could result in the production of E6 and E7 proteins alone or of an additional E1-E4 fusion product if translation reinitiation can occur after the E7 stop codon. A heterogeneity was detected in the 5' ends of the longer transcript; E6 transcripts could thus yield a full-length or a truncated E6 protein. We also detected a minor subset of mRNAs covering the E2-E4 coding region and including at least three species with estimated sizes of 4.2, 2.8, and 1.8 kilobases. All the viral transcripts detected in the VX2 tumor cells were polyadenylated at the same site (position 4367) 20 base pairs beyond the first AATAAA signal which borders the E region.
Application of pulsed field gel electrophoresis to the 1993 epidemic of whooping cough in the UK

Summary The purpose of this study was to DNA fingerprint the majority (64 %) of isolates received at the Pertussis Reference Laboratory during the 1993 whooping cough epidemic by pulsed field gel electrophoresis of Xba I - generated restriction digests. Two DNA restriction patterns, types 1 and 3, predominated (40% and 23%. respectively, of 180 isolates) but type 2, identified in a previous study was notably absent. Twenty-one new DNA types occurred (24% of isolates), some being atypical as bands 155–230 kb were no longer conserved, but there was no statistically significant difference in their incidence in the upswing (June-September) compared to the downswing (October-December) phase of the epidemic. There was a relatively high proportion of new types, compared to type 1. at the peak (September). About 50% of isolates received were from the North Western Region, where 44% of isolates were DNA type 1. Whereas only 1 out of 10 isolates from Scotland were of this type, suggesting some geographic variation. Statistically significant findings included a higher proportion of isolates from female patients (P < 0·01), most marked in the 12–24 months age group (P < 0·05); a higher proportion of infants under 12 months requiring hospital admission compared to older children (P < 0·05); and a greater number of isolates from unvaccinated children (P < 0·01). Analysis of serotype according to four age groups (under 3 months, 3–12 months, 12–24 months and above 2 years) showed statistically significant differences (P < 0·05) with a noticeably lower proportion (38%) of serotype 1,3 in 3–12 months age group and higher prevalence (74%) of serotype 1,3 in the 12–24 months age group. There was no correlation between DNA type and serotype.
The dynamics of adaptation on correlated fitness landscapes

Evolutionary theory predicts that a population in a new environment will accumulate adaptive substitutions, but precisely how they accumulate is poorly understood. The dynamics of adaptation depend on the underlying fitness landscape. Virtually nothing is known about fitness landscapes in nature, and few methods allow us to infer the landscape from empirical data. With a view toward this inference problem, we have developed a theory that, in the weak-mutation limit, predicts how a population's mean fitness and the number of accumulated substitutions are expected to increase over time, depending on the underlying fitness landscape. We find that fitness and substitution trajectories depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. We introduce a scheme that classifies landscapes in terms of the qualitative evolutionary dynamics they produce. We show that linear substitution trajectories, long considered the hallmark of neutral evolution, can arise even when mutations are strongly selected. Our results provide a basis for understanding the dynamics of adaptation and for inferring properties of an organism's fitness landscape from temporal data. Applying these methods to data from a long-term experiment, we infer the sign and strength of epistasis among beneficial mutations in the Escherichia coli genome.
Genetic epidemiology with a Capital E, ten years after

More than a decade after Duncan Thomas gave his presidential address at the International Society for Genetic Epidemiology entitled “Genetic Epidemiology with a Capital E,” genetic epidemiology has gone mainstream. Epidemiology has taken its place not only in gene discovery studies but also in characterizing genetic effects and gene‐environment interactions in populations. Furthermore, epidemiologic principles are being applied to the evaluation of genetic tests. We used an online informatics tool, the HuGE Navigator, to describe the growth in the field in the past decade. We developed the HuGE Navigator as a means to continuously monitor the evolving information obtained from epidemiologic studies of the human genome. Between 2001 and 2010, the HuGE Navigator included 57,005 articles published in 2,396 journals. During that period, the annual number of publications increased almost four‐fold. The articles included 986 genome‐wide association studies and 1,879 meta‐analyses of gene‐disease associations. The total number of authors of published studies grew from 12,907 in 2001 to 48,389 in 2010. The number of diseases also increased over time, from 697 medical subject headings in 2001 to 1,404 in 2010. Gene‐environment interaction was mentioned explicitly in 17% of published abstracts, almost half of which focused on gene‐drug interactions. Clearly, genetic epidemiology has gone “capital E” in the past decade; however, the ever‐expanding volume and variety of genomic information poses a formidable challenge for developing appropriate methods for analysis, synthesis, and inference on complex genetic and environmental effects. We extend Duncan Thomas' capital E to include “Evaluation” as the tools of epidemiology are increasingly used to assess how genome‐based information can be applied in medicine and public health. Genet. Epidemiol. 35:845–852, 2011. © 2011 Wiley Periodicals, Inc.
Magnetoresistance in LaFe/sub 11.2/Co/sub 0.7/Si/sub 1.1/ compound

Magnetoresistance has been studied in LaFe/sub 11.2/Co/sub 0.7/Si/sub 1.1/ compound. The ferromagnetic ordering at Curie temperature T/sub C/ of 274 K was found being accompanied by a drastic negative lattice expansion due to the strong structural and magnetic interplay. Such a simultaneous magnetic and lattice change would cause changes in transport properties. The measured transport properties indicate that the transition can be induced by temperature or applied magnetic field. The sample shows a metallic character below T/sub C/, whereas the electrical resistance decreases dramatically and then recovers the metal-like behavior above T/sub C/. Application of a magnetic field retains the transitions via increasing the ferromagnetic ordering temperature. An isothermal increase of field leads to an increase of resistance at temperatures near but above T/sub C/, which is a result of the field-induced metamagnetic transition from paramagnetic to ferromagnetic state.
In vitro-in vivo correlations for drugs eliminated by glucuronidation: investigations with the model substrate zidovudine.

AIMS To investigate the effects of incubation conditions on the kinetic constants for zidovudine (AZT) glucuronidation by human liver microsomes, and whether microsomal intrinsic clearance (CLint) derived for the various conditions predicted hepatic AZT clearance by glucuronidation (CLH) in vivo. METHODS The effects of incubation constituents, particularly buffer type (phosphate, Tris) and activators (Brij58, alamethacin, UDP-N-acetylglucosamine (UDP-NAcG)), on the kinetics of AZT glucuronidation by human liver microsomes was investigated. AZT glucuronide (AZTG) formation by microsomal incubations was quantified by h.p.l.c. Microsomal CLint values determined for the various experimental conditions were extrapolated to a whole organ CLint and these data were used to calculate in vivo CLH using the well-stirred, parallel tube and dispersion models. RESULTS Mean CLint values for Brij58 activated microsomes in both phosphate (3.66 +/- 1.40 micro l min-1 mg-1, 95% CI 1.92, 5.39) and Tris (3.79 +/- 0.74 micro l min-1 mg-1, 95% CI 2.87, 4.71) buffers were higher (P < 0.05) than the respective values for native microsomes (1.04 +/- 0.42, 95% CI 0.53, 1.56 and 1.37 +/- 0.30 micro l min-1 mg-1, 95% CI 1.00, 1.73). Extrapolation of the microsomal data to a whole organ CLint and substitution of these values in the expressions for the well-stirred, parallel tube and dispersion models underestimated the known in vivo blood AZT clearance by glucuronidation by 6.5- to 23-fold (3.61-12.71 l h-1vs 82 l h-1). There was no significant difference in the CLH predicted by each of the models for each set of conditions. A wide range of incubation constituents and conditions were subsequently investigated to assess their effects on GAZT formation, including alamethacin, UDP-NAcG, MgCl2, d-saccharic acid 1,4-lactone, ATP, GTP, and buffer pH and ionic strength. Of these, only decreasing the phosphate buffer concentration from 0.1 m to 0.02 m for Brij58 activated microsomes substantially increased the rate of GAZT formation, but the extrapolated CLH determined for this condition still underestimated known AZT glucuronidation clearance by more than 4-fold. AZT was shown not to bind nonspecifically to microsomes. Analysis of published data for other glucuronidated drugs confirmed a trend for microsomal CLint to underestimate in vivo CLH. CONCLUSIONS AZT glucuronidation kinetics by human liver microsomes are markedly dependent on incubation conditions, and there is a need for interlaboratory standardization. Extrapolation of in vitro CLint underestimates in vivo hepatic clearance of drugs eliminated by glucuronidation.
The use of side-mounted loop antennas on platforms to obtain nearly omnidirectional radiation

Antennas mounted to vehicles at VHF frequencies are limited to whip and loop antennas. Often, mechanical constraints force antenna placement to be less than optimal. In this work, we investigate the use of side-mounted loops on rectangular conducting platforms. It will be shown that tall thin platforms radiate similar to a dipole. In addition, as the thickness increases, the loop antennas can radiate in a nearly omnidirectional fashion if the antenna-mounted sides of the platform are not too wide. In effect, a narrow platform width implies return currents for a loop antenna that remain mostly vertical.
Comparison of the Adsorption Capacities of an Activated-Charcoal–Yogurt Mixture Versus Activated-Charcoal–Water Slurry In Vivo and In Vitro

Background. An activated charcoal–yogurt mixture was evaluated in vivo to determine the effect on the gastrointestinal absorption of paracetamol, as compared to activated-charcoal–water slurry. The potential advantage of the activated-charcoal–yogurt mixture is a better palatability and general acceptance by the patients without loss of efficacy. In addition, paracetamol adsorption studies were carried out in vitro to calculate the maximum adsorption capacity of paracetamol to activated-charcoal–yogurt mixture. Methods. In vivo: A randomized crossover study on 15 adult volunteers, using paracetamol 50 mg/kg as a simulated overdose. Each study day volunteers were given a standard meal 1 h before paracetamol, then 50 g activated charcoal 1 h later in either of two preparations: standard water slurry or mixed with 400 mL yogurt. Paracetamol serum concentrations were measured using HPLC. The areas under the concentration-time curve (AUC) of the two preparations were compared and used to estimate the efficacy of each preparation. The palatability of both preparations was evaluated using a visual-analogue scale where the volunteers were asked to evaluate the appearance, smell, flavor, texture, ability to swallow, and overall impression of the mixtures. The time spent to consume the activated charcoal was also registered. In vitro: Activated charcoal, simulated gastric (pH 1.2) or intestinal (pH 7.2) fluid, and paracetamol were mixed with yogurt followed by 1 h incubation. The maximum adsorption capacity of paracetamol to activated charcoal was calculated using Langmuir's adsorption isotherm. Paracetamol concentration was analyzed using HPLC. Results. In vivo there was no significant difference (p > 0.05) in the AUC of paracetamol between the two activated-charcoal preparations. Geometric mean values and 95% CI for the AUCs were (in mg/l · min): 6307 (4932–8065) for the activated charcoal–water slurry and 6525 (5111–8330) for the activated charcoal–yogurt mixture. The palatability study showed significant difference (p < 0.05) only in duration of administration, in favor of the activated charcoal-water slurry. In vitro the maximum adsorption capacity of activated charcoal with added yogurt was 544 mg paracetamol/g activated charcoal (pH 1.2), and 569 mg paracetamol/g activated charcoal (pH 7.2). Conclusion. The two activated-charcoal preparations showed equal (NS) absorption reduction of paracetamol in vivo. Mixing activated charcoal with yogurt rather than water prolonged the ingestion time, but did not improve the palatability in adults. The presence of yogurt reduced the adsorption capacity in vitro by 9–13% (p < 0.05) compared to control without yogurt (previous study with the same setup).
Antidiabetic and antioxidant potency evaluation of different fractions obtained from Cucumis prophetarum fruit

Abstract Context: Cucumis prophetarum Linn. (Cucurbitaceae) fruit is used for inflammatory-related problems and is proved to be possessing anticancer and hepatoprotective effects. Objective: The present investigation was to study the effect of different fractions of C. prophetarum on antidiabetic and antioxidant activity. Materials and methods: Aqueous crude extract (CE) of C. prophetarum fruits was fractionated into water soluble fraction 1 (F1), chloroform fraction 2 (F2), basic fraction 3 (F3), and neutral fraction 4 (F4) by acid–base extraction. CE and its fractions at different doses (0.02–0.1 mg/mL) were subjected to antidiabetic (α-amylase and α-glucosidase inhibition assays) and antioxidant (DPPH, superoxide radical scavenging (SO) and metal chelation) evaluation. Results: F1 exhibited effective antidiabetic activity (p < 0.05) with an IC50 value of 20.6 and 59.9 µg/mL. The activity decreased in the order of CE > F4 >F3 > F2, according to α-amylase assay, which were the same, with the exception of the rank order of F4 and CE, as the α-glucosidase assay. Furthermore, F1 (IC50 = 73 µg/mL) showed better reducing ability than CE >F4 >F2 > F3 (IC50 = 78–272 µg/mL), according to the DPPH assay. In SO and metal chelation assays, F1 showed the highest activity (IC50 = 101 and 147 µg/mL), respectively; the activity decreased in the order of CE >F4 >F3 > F2 (IC50 = 126–469 µg/mL) for SO and 194–944 µg/mL for metal chelation assay. Conclusion: The results indicate that F1 possesses potent in vitro antidiabetic and antioxidant activities.
Creatinine clearance estimation from serum creatinine values: evaluation and comparison of five prediction formulae in Nigerian patients.

Predictability of creatinine clearance (CrCl) from serum creatinine would reduce the cost of renal care and obviate the need for 24-hours urine collection. Correlations have been established between serum creatinine (Scr) and 24-hour urinary creatinine clearance with derivation of various formulae. We have tested the applicability of these formulae in 34 Nigerian patients (22 males, 12 females) aged 18 to 58 years, (mean age 34.97 +/- 11.20 years) with established chronic renal failure (CRF) mean Scr level 742.26 +/- 388.15 mol/L. 32 age and sex matched healthy adults with serum creatinine values below 120 umol/l. , served as controls. Serum creatinine and 24 hour CrCl levels were determined on two consecutive occasions. Creatinine clearance values were also derived from Scr using each of the established prediction formulae: Cockcrof and Gault [1] Gates [2] Hull et al [3]; Jelliffe [4]; and Mawer et al [5]. A relationship was sought between measured CrCl and the predicted values (derived) using the stated formulae. Regression equation were generated and correlation coefficient r, coefficient of determination r2, F-ration, prediction error, all defining the nature and strength of relationship were determined. We observed that good and statistically significant correlations exist between measured CrCl values and those predicated from the formulae (r ranging from 0.908 to 0.968 and r20.82 to 0.93 P = 0.000) and that a linear relationship exists in all cases. Cockcroft and Gault formula gave the highest coefficient of determination r2 = 0.94. It is concluded that the existing formulae are adequate for determining CrCl from Scr and should be frequently used in the long term follow-up of patients with Chronic Renal Failure (CRF) in our setting.
Brain sizes, surfaces, and neuronal sizes of the cortex cerebri: a stereological investigation of man and his variability and a comparison with some mammals (primates, whales, marsupials, insectivores, and one elephant).

This study deals with the stereological estimation of macroscopic sizes of brain and cortex, i.e., volume, surface, and folding, and of microscopic neuronal sizes, i.e., density, mean size, size distribution, and number of neurons. The results show that the degree of variability in man amounts to about 15%. A decrease in volume of the different gray structures can be observed in man after the age of 65 years. The surface, folding index, and length of convolution do not alter with aging. The comparison with mammals of various sizes allows the conclusion that there is a high correlation to brain size for nearly all macroscopic values. Man and elephant, however, have a cortical surface which is, in comparison with whales, relatively small. In contrast, whales have very small cortices compared with man. At the cytoarchitectonic level, the neuronal density has a correlation to brain size. Contrary to other mammals, the primates and man have a high fraction of small granular neurons, especially in layer 4. The assumption that the number of cortical neurons beneath a given surface area of cortex is the same in all mammals cannot be verified, especially in those with large brains. The allometric connection between brain size and parameters is not valid for all measurements (e.g., thickness of cortex, mean size of neurons, perikaryal size distribution, and glial density). Yet some other measurements are well correlated.
Vowel category perception affected by microdurational variations

Vowel quality perception in quantity languages is considered to be unrelated to vowel duration since duration is used to realize quantity oppositions. To test the role of microdurational variations in vowel category perception in Estonian listening experiments with synthetic stimuli were carried out, involving five vowel pairs along the close-open axis. The results show that in the case of high-mid vowel pairs vowel openness correlates positively with stimulus duration; in mid-low vowel pairs no such correlation was found. The discrepancy in the results is explained by the hypothesis that in case of shorter perceptual distances (high-mid area of vowel space) intrinsic duration plays the role of a secondary feature to enhance perceptual contrast between vowels, whereas in case of mid-low oppositions perceptual distance is large enough to guarantee the necessary perceptual contrast by spectral features alone and vowel intrinsic duration as an additional cue is not needed.
Fluctuations in Diffusion Processes in Microgravity

Abstract: It has been shown recently that diffusion processes exhibit giant nonequilibrium fluctuations (NEFs). That is, the diffusing fronts display corrugations whose length scale ranges from the molecular to the macroscopic one. The amplitude of the NEF diverges following a power law behavior ∝ q−4 (where q is the wave vector). However, fluctuations of wave number smaller than a critical “rolloff” wave vector are quenched by the presence of gravity. It is therefore expected that in microgravity conditions, the amplitude of the NEF should be boosted by the absence of the buoyancy‐driven restoring force. This may affect any diffusion process performed in microgravity, such as the crystallization of a protein solution induced by the diffusion of a salt buffer. The aim of GRADFLEX (GRAdient‐Driven FLuctuation EXperiment), a joint project of ESA and NASA, is to investigate the presence of NEFs arising in a diffusion process under microgravity conditions. The project consists of two experiments. One is carried out by UNIMI (University of Milan) and INFM (Istituto Nazionale per la Fisica della Materia) and is focused on NEF in a concentration diffusion process. The other experiment is performed by UCSB (University of California at Santa Barbara) concerning temperature NEF in a simple fluid. In the UNIMI part of the GRADFLEX experimental setup, NEFs are induced in a binary mixture by means of the Soret effect. The diagnostic method is an all‐optical quantitative shadowgraph technique. The power spectrum of the induced NEFs is obtained by the processing of the shadowgraph images. A detailed description of the experimental apparatus as well as the ground‐based experimental results is presented here for the UNIMI‐INFM experiment. The GRADFLEX payload is scheduled to fly on the FOTON M3 capsule in April 2007.