Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective degradation of early-response-gene mRNAs: functional analyses of sequence features of the AU-rich elements

The metabolic lifetime of mRNA can be specified by specific cis-acting elements within mRNA. One type of element is an adenylate- and uridylate-rich element (ARE) found in the 3' untranslated region of many highly unstable mRNAs for mammalian early-response genes (ERGs). Among the better-characterized members of the ERG family are certain genes encoding nuclear transcription factors. Of particular significance was the finding that their mRNAs decay rapidly with kinetics similar to those of c-fos mRNA. Our previous studies of the c-fos ARE-directed mRNA decay have revealed the existence in this ARE of two structurally distinct and functionally interdependent domains, termed domain I and domain II. We proposed that the c-fos ARE-directed decay is a two-step mechanism in which rapid shortening of the poly(A) tail leads to the decay of the mRNA body and further hypothesized that this is a general mechanism by which the ERG AREs mediate rapid mRNA degradation. To test this hypothesis and to further address the generality of the critical structural characteristics within the c-fos ARE, the RNA-destabilizing functions of more than 10 different AU-rich sequences from various nuclear transcription factor mRNAs have been tested. Consistent with the above-mentioned hypothesis is the observation that mRNAs carrying the functional AREs display a biphasic decay, which is characteristic of the proposed two-step mechanism. Our results indicated that the presence of AUUUA pentanucleotides in an AU-rich region does not always guarantee an RNA-destabilizing function for this region. Our results also led to the identification of a novel class of AU-rich destabilizing elements which contains no AUUUA pentanucleotide. The results of sequence comparison and functional tests revealed that a continuous U-rich sequence is a unique feature among the functional AREs. Finally, our experiments further showed that the c-fos ARE domain II has an RNA decay-enhancing ability upon its fusion to heterologous AU-rich regions and defined for the first time an RNA decay-enhancing element, which we termed the RDE element.
Comparison between Semen Parameters of Ejaculates Collected Via Masturbation Versus Coitus Interruptus

Proper collections of human ejaculates are necessary for semen analysis and infertility treatment purposes. The objective of this study was to assess the seminal characteristics of ejaculates collected by patients via masturbation and coitus interruptus. Thirty individuals produced one sample via masturbation and one via incomplete coitus during a 3-days interval. The semen parameters were compared and analyzed with student t-test and Nemar test. The results showed that mean values for progressive motility of spermatozoa were increased from 46.81+15.7% to 58.76+13.5% in coitus interruptus and masturbation, respectively (Pl0.01). Also, the mean values for normal sperm morphology was 54.03+25.1% in coitus interruptus and 63.36+13.4% in samples collected via masturbation (Pl0.01). In addition, sperm concentration was significantly improved in ejaculates collected with masturbation (Pl0.05). Although, insignificant, the concentration of round cells were lower in specimens collected via masturbation than coitus interruptus. Therefore, via masturbation method, better semen characteristics were yielded which subsequently may improve the infertility treatment outcome.
Interpolation theorems, lower bounds for proof systems, and independence results for bounded arithmetic

Abstract A proof of the (propositional) Craig interpolation theorem for cut-free sequent calculus yields that a sequent with a cut-free proof (or with a proof with cut-formulas of restricted form; in particular, with only analytic cuts) with k inferences has an interpolant whose circuit-size is at most k. We give a new proof of the interpolation theorem based on a communication complexity approach which allows a similar estimate for a larger class of proofs. We derive from it several corollaries: (1) Feasible interpolation theorems for the following proof systems:(a) resolution(b) a subsystem of LK corresponding to the bounded arithmetic theory (α)(c) linear equational calculus(d) cutting planes. (2) New proofs of the exponential lower bounds (for new formulas)(a) for resolution ([15])(b) for the cutting planes proof system with coefficients written in unary ([4]). (3) An alternative proof of the independence result of [43] concerning the provability of circuit-size lower bounds in the bounded arithmetic theory (α). In the other direction we show that a depth 2 subsystem of LK does not admit feasible monotone interpolation theorem (the so called Lyndon theorem), and that a feasible monotone interpolation theorem for the depth 1 subsystem of LK would yield new exponential lower bounds for resolution proofs of the weak pigeonhole principle.
Imidazoquinoxaline anticancer derivatives and imiquimod interact with tubulin: Characterization of molecular microtubule inhibiting mechanisms in correlation with cytotoxicity

Displaying a strong antiproliferative activity on a wide variety of cancer cells, EAPB0203 and EAPB0503 belong to the imidazo[1,2-a]quinoxalines family of imiquimod structural analogues. EAPB0503 has been shown to inhibit tubulin polymerization. The aim of the present study is to characterize the interaction of EAPB0203 and EAPB0503 with tubulin. We combine experimental approaches at the cellular and the molecular level both in vitro and in silico in order to evaluate the interaction of EAPB0203 and EAPB0503 with tubulin. We examine the influence of EAPB0203 and EAPB0503 on the cell cycle and fate, explore the binding interaction with purified tubulin, and use a computational molecular docking model to determine the binding modes to the microtubule. We then use a drug combination study with other anti-microtubule agents to compare the binding site of EAPB0203 and EAPB0503 to known potent tubulin inhibitors. We demonstrate that EAPB0203 and EAPB0503 are capable of blocking human melanoma cells in G2 and M phases and inducing cell death and apoptosis. Second, we show that EAPB0203 and EAPB0503, but also unexpectedly imiquimod, bind directly to purified tubulin and inhibit tubulin polymerization. As suggested by molecular docking and binding competition studies, we identify the colchicine binding site on β-tubulin as the interaction pocket. Furthermore, we find that EAPB0203, EAPB0503 and imiquimod display antagonistic cytotoxic effect when combined with colchicine, and disrupt tubulin network in human melanoma cells. We conclude that EAPB0203, EAPB0503, as well as imiquimod, interact with tubulin through the colchicine binding site, and that the cytotoxic activity of EAPB0203, EAPB0503 and imiquimod is correlated to their tubulin inhibiting effect. These compounds appear as interesting anticancer drug candidates as suggested by their activity and mechanism of action, and deserve further investigation for their use in the clinic.
C‐terminal CTII motif of 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase undergoes carboxylmethylation

Eukaryotic proteins with a carboxyl‐terminal CaaX motif are modified by isoprenylation and subsequently processed by proteolysis of the three terminal amino acids and carboxylmethylation of the exposed cysteine residue. The myelination‐associated 2′,3′‐Cyclic Nucleotide 3′‐Phosphodiesterase (CNP) has a C‐terminal CTII sequence and is isoprenylated; however, no examples of subsequent processing exist when threonine, a polar residue, is located adjacent to the cysteine. Here we show that CNP is capable of being carboxylmethylated in both insect cells and glioma cells. This processing is dependent upon isoprenylation of the cysteine and can be inhibited with the isoprenylated cysteine derivative, N‐acetyl‐S‐farnesyl‐L‐cysteine. Although the role of the methyl group at the C‐terminus of other isoprenylated proteins is not fully understood, modulation of signal transduction pathways is strongly indicated. This modification of CNP may similarly regulate cell biological processes in myelinogenesis. © 1994 Wiley‐Liss, Inc.
Perceptual Judgment of Voice Pitch during Pitch-Matching Tasks

This study investigated the perceptual judgment of voice pitch. 24 individuals were assigned to two groups to assess whether there is a difference in perceptual judgment of voice during pitch-matching tasks. Group I, Naïve listeners, had no previous experience in anatomy, physiology, or voice pitch-evaluation methods. Group II, Experienced listeners, were master's level speech-language pathologists having completed academic training in evaluation of voice. Both groups listened to identical stimuli, which required matching audiotaped voice-pitch samples of a male and female voice to a note on an electronic keyboard. The experiment included two tasks. The first task assessed pitch range, which required marching of the lowest and highest voice pitch of both a male and female speaker singing /a/ to a note on a keyboard. The second task assessed habitual pitch, which required matching of the voice pitch of a word spoken by a male and female speaker to a note on a keyboard. A one-way analysis of variance indicated a significant difference between groups occurred for only one of four conditions measured, perceptual judgment of the female pitch range. No differences between groups were found in the perceptual judgments of the male pitch range or during perceptual judgment of the female or male habitual pitch, suggesting that the skill possessed by speech-language pathology students is no different from that of inexperienced listeners.
Conjugated linoleic acid content of beef from cattle fed diets containing high grain , CLA , or raised on forages

Twenty Angus crossbred steers were assigned to one of four treatments and followed from weaning to slaughter to study the effect of diet on the conjugated linoleic acid (C18:2 cis-9, trans-11 and C18:2 trans-10, cis-12 CLA isomers) content and quality of beef. During the adaptation period, treatments 1 (CTL), 2 (CLA), and 3 (GPS) received a diet consisting of 520 g corn silage, 213 g alfalfa hay, 250 g rolled barley, and 17 g mineral–vitamin premix/kg of dry matter (DM). Treatment 4 (PS) received alfalfa hay only. During the finishing period, CTL and CLA steers received a diet consisting of 123 g corn silage, 67 g alfalfa hay, 764 g rolled barley, and 46 g mineral–vitamin premix/kg of diet dry matter. In addition to the basal diet, CLA steers received 84 g/head/day of a synthetic mixture of partially rumen protected CLA isomers. The GPS and PS treatments were finished solely on pasture. Subcutaneous adipose tissue samples were collected from the M. longissimus dorsi at the end of the adaptation period, and both adipose and muscle tissues were collected from the longissimus and M. semitendinosus of each carcass at slaughter for fatty acid analysis. Beef tissues from PS and GPS steers had 466% and 218% more CLA (C18:2 cis-9, trans-11 isomer) at slaughter compared with beef tissues from CTL steers, respectively. Supplementing synthetic CLA did not increase C18:2 cis-9, trans-11 CLA content of beef, but increased trans-10, cis-12 CLA by 380% compare to beef from CTL animals. A trained taste panel detected no differences in tenderness or juiciness among treatments. However, beef from PS received higher off-flavor scores than other treatments. Raising cattle on forage and pasture with no grain supplementation enhances beef CLA content. Additionally, finishing cattle on pasture increased the vitamin E content of beef by 300% compared to beef from animals finished on a traditional high-grain diet. D 2004 Elsevier B.V. All rights reserved.
q-Extensions of Erdélyi ’ s Fractional Integral Representations for Hypergeometric Functions and Some Summation Formulas for Double q-Kampé de Fériet Series

q-Analogues of Erdélyi’s fractional integral representations of hypergeometric functions are derived and extended to expansion formulas for certain 3φ2 and 4φ3 basic hypergeometric series. Special cases of some of the derived formulas are used to derive new summation formulas for double hypergeometric and basic hypergeometric Kampé de Fériet series, including a summation formula for a double basic hypergeometric Kampé de Fériet series that was conjectured in work of J. Van der Jeugt, S.N. Pitre, and K. Srinivasa Rao on the evaluation of the 9-j recoupling coefficients appearing in the quantum theory of angular momentum.
Viral R plasmid Rphi6P: properties of the penicillinase plasmid prophage and the supercoiled, circular encapsidated genome

Properties of the viral R plasmid Rphi6P are described. As a temperate bacteriophage, it plaques on the facultative phototroph Rhodopseudomonas sphaeroides. Under aerobic conditions the phage had a latent period of 180 min, a burst time of 200 min, and a burst size of 15 to 20 particles per infective center. The encapsidated viral genome occurred as a supercoiled, circular DNA duplex with a mean contour length of 16.5 +/- 10 micron. Percent guanine plus cytosine, as calculated from thermal denaturation profiles, was 63.5. Mitomycin C-induced loss of the prophage suggested an extrachromosomal location in the host cell. Use of this curing agent enabled the isolation of a plasmid-free strain of R. sphaeroides. Biophysical analysis of the plasmid-free strain lysogenized with Rphi6P confirmed that the prophage occurred as a plasmid in the host cell.
Computational Evaluation of Effects of Motivation Reinforcement on Player Retention

: We study how virtual incentive mechanisms (such as leaderboards) help motivate players to extend the game playing time. We have designed a multiplayer strategy game, called OilTrader, which is set in a game-theoretic framework of a Minority Game, to verify the effect of motivation reinforcement on the sustainability of game playing process. We have conducted an experiment with 114 players and evaluated their psychological types using the HEXAD player type model. Players were divided into a main experimental group (who used the user interface enhanced with motivation-increasing factors) and a control group (who used a simpler game interface). Results indicate that game players, who have used the motivation-enhancing interface, have had stronger motivation to play the game longer. Using statistical analysis, we have discovered that Free Spirits, Disruptors and Players (according to the HEXAD questionnaire player types) are more motivated by a progress leaderboard rather than an achievement leaderboard.
Microsatellite frequency and size variation in the parthenogenetic parasitic wasp Venturia canescens (Gravenhorst) (Hymenoptera: Ichneumonidae)

Nine genomic libraries of the parthenogenetic wasp Venturia canescens were screened for microsatellite loci. In contrast to other Hymenoptera (GT)n and not (CT)n, was the predominant repeat category found with 14 kb and 28 kb genomic DNA between loci, respectively. Mono‐ and trinucleotide microsatellites were rarer, occurring at frequencies between 231 kb and 589 kb of genome, whilst tetranucleotide repeats are scarce, with (ATTC)n and (CCGG)n loci occurring every 692 kb and 983 kb, respectively, and only one small imperfect (GATA)n locus and no (GACA)n loci were revealed. Over 70% of the dinucleotide, and all the trinucleotide microsatellites were small (less than eleven repeats), whilst 60% to 80% of loci were imperfect. Moreover, very few compound microsatellites and only a single association between different microsatellites were observed.
Multi stage adaptive filter for identification of the systems with variable sparsity

Adaptive identification of sparse systems is one of the popular adaptive signal processing topics due to its application in acoustic and network echo cancellation, adaptive channel estimation and several other areas. It has been observed that sometimes the amount of sparseness in the identifiable system impulse response can vary greatly depending on the nonstationary nature of the system. The compressive sensing based sparsity-aware adaptive algorithm performs satisfactorily in strongly sparse environment, but is shown to perform worse than the conventional ones when sparseness of the impulse response decreases. We propose an algorithm which works well both in sparse and non-sparse circumstances, and adapts dynamically to the level of sparseness using a dual stage adaptive filtering approach using an affine combination of the outputs of two single stage adaptive filters using two different algorithms. The proposed algorithm is supported by simulation results that show its robustness against variable sparsity.
Tailor‐Made Fructooligosaccharides by a Combination of Substrate and Genetic Engineering

The combination of sucrose analogues as novel substrates (substrate engineering) and highly active recombinant β‐fructofuranosidase from A. niger (genetic engineering) provides a new powerful tool for the efficient preparative synthesis of tailor‐made saccharides of the important 1‐kestose and 1‐nystose type headed with different monosaccharides of interest. These novel compounds have been isolated. They did not display toxic effects or suppress cell growth in initial studies, making these new compounds potential candidates for prebiotics.
Genotypic Characterization of Staphylococcus aureus Obtained from Humans and Bovine Mastitis Samples in India

Aim and Background: Staphylococcus aureus is a major human pathogen that also causes important infections in cattle and sheep. The present study aimed to test genetic diversity among strains of S. aureus isolated from cattle (n=34) and humans (n=22) by DNA typing. Materials and Methods: Fluorescent amplified fragment length polymorphism (FAFLP) is the genotyping tool used in the study. The presence of the mecA and Panton-Valentine leukocidin (PVL) genes among these strain groups was also checked. Results: A dendrogram deduced from FAFLP showed that all the strains clustered into 10 groups (A–J) with a relative genetic divergence of less than 8%. Sixty-seven percent of the isolates from bovine sources clustered together in two clades (A and H), while another major cluster with 13 isolates (59%) (Cluster G) had all strains from a human host. The remaining strains from both the hosts clustered independently into smaller clusters with the exception of two strains of human origin, which clustered along with a bovine cluster. Thirteen strains belonging to cluster G were highly clonal. About 77% of strains obtained from human infections were methicillin-resistant S. aureus (MRSA), whereas only 29% of strains from bovine origin were MRSA. Only three strains from human origin showed PVL positive, while no strain from cattle had PVL genes. The complete absence of PVL genes in all the bovine strains in the study appears to be significant. Conclusions: FAFLP can be successfully applied to assess the genetic relationship of S. aureus isolates from different hosts. The study also provided the valuable epidemiological data on S. aureus from bovine sources in India, which is lacking.
A novel mutation in PRDM5 in brittle cornea syndrome

To the Editor : Brittle cornea syndrome (BCS) (MIM229200) is an autosomal recessive disorder characterized by abnormally fragile cornea that can easily rupture. It was debated whether BCS is a distinct disorder or a subtype of Ehler-Danlos syndrome (EDS VI specifically) (1). However, the demonstration of normal lysylpyridinoline to total hydroxylysylpyridinoline (typically abnormal in EDS VI) provided an early clue and the finding of ZNF469 mutations in BCS proved that BCS is indeed a distinct disorder albeit with overlapping phenotype (1–3). In this communication, we report the results of the molecular characterization of a BCS patient which led to the identification of a new genetic lesion. Patient 1 is a 2-year-old Saudi girl with blue sclerae and keratoconus. Her parents are healthy first cousins and she has a healthy brother. Her development has been appropriate and her past medical history was negative for fractures or delayed healing. She had normal growth parameters, Stickler-like flat face, blue sclerae and Beighton score of 4 (Fig. 1). Skin displayed
Contrast enhanced phototrichogram pinpoints scalp hair changes in androgen sensitive areas of male androgenetic alopecia

In male androgenetic alopecia (AGA), global changes of scalp hair observed on many years are the cumulative result of discrete changes. Such changes reflect structural and/or functional modifications occurring at the level of individual hair follicles. The patterning of scalp hair loss is the phenotypic expression of clusters of hormone sensitive follicles located in specific scalp areas.The aim of this study was to evaluate, in 21 untreated male subjects with AGA, the relation between various hair measurements using a new validated photographic method with clinical staging (modified Norwood‐Hamilton scale) as compared with five controls.
Medical student participation in surface anatomy classes

Surface anatomy is an integral part of medical education and enables medical students to learn skills for future medical practice. In the past decade, there has been a decline in the teaching of anatomy in the medical curriculum, and this study seeks to assess the attitudes of medical students to participation in surface anatomy classes. Consequently, all first year medical students at the Guy's, King's and St Thomas's Medical School, London, were asked to fill in an anonymous questionnaire at the end of their last surface anatomy session of the year. A total of 290 medical students completed the questionnaires, resulting in an 81.6% response rate. The students had a mean age of 19.6 years (range 18–32) and 104 (35.9%) of them were male. Seventy‐six students (26.2%) were subjects in surface anatomy tutorials (60.5% male). Students generally volunteered because no one else did. Of the volunteers, 38.2% would rather not have been subjects, because of embarrassment, inability to make notes, or to see clearly the material being taught. Female medical students from ethnic minority groups were especially reluctant to volunteer to be subjects. Single‐sex classes improved the volunteer rate to some extent, but not dramatically. Students appreciate the importance of surface anatomy to cadaveric study and to future clinical practice. Computer models, lectures, and videos are complementary but cannot be a substitute for peer group models, artists' models being the only alternative. Clin. Anat. 19:627–631, 2006. © 2005 Wiley‐Liss, Inc.
Dynamic nanoindentation testing: is there an influence on a material’s hardness?

ABSTRACT Modern nanoindentation devices are capable of dynamic experimentations, which allow us to exploit instrumented hardness tests extensively. Beside the assets of recording mechanical properties continuously over displacement, there are ongoing debates whether the superimposed force alters the material’s hardness. We will show for a broad range of materials that significant hardness differences are noted between dynamic and static tests, even for large displacements. Those mainly result from a changing indentation strain-rate during the hold segment at peak load. This fact must be implicitly considered in studies using static indentation tests to guarantee comparability of obtained nanoindentation hardness values and derived quantities. GRAPHICAL ABSTRACT IMPACT STATEMENT A mismatch between static and dynamic nanoindentation hardness has been identified to result from strain-rate deviations during hold segments in static nanoindentation tests, in particular affecting rate-sensitive materials.