Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased expression of telomere length regulating factors TRF1, TRF2 and TIN2 in patients with adult T‐cell leukemia

Here, we report that freshly isolated unstimulated adult T‐cell leukemia (ATL) cells present high telomerase activity compared to asymptomatic carriers or normal donors. In spite of this high telomerase activity, ATL cells retained shorter telomeres compared to those of uninfected cells isolated from the same patients. Because the safeguarding of telomere length is critical to the unlimited proliferation of tumor cells, we investigated the underlying mechanism for short telomere maintenance in ATL cells. Transcriptional and posttranscriptional expression of telomere‐binding proteins TRF1, TRF2, TIN2 and POT1, known to regulate telomere homeostasis and protection, were evaluated. We found that TRF1 and TRF2 are overexpressed in in vivo patient's samples from ATL but not asymptomatic carriers, while levels of POT1 expression did not specifically increase in ATL. To gain insights into the regulation of TRF genes in HTLV‐I infected cells, we investigated the expression of TIN2, a regulator of these genes, and found an increase in TIN2 expression in ATL patients. Together our results underscore the importance of telomerase and telomere length regulating factors as novel markers for ATL disease progression and as potential therapeutic targets for the treatment of HTLV‐I‐associated malignancies. © 2006 Wiley‐Liss, Inc.
The Grapevine R2R3-MYB Transcription Factor VvMYBF1 Regulates Flavonol Synthesis in Developing Grape Berries1[W][OA]

Flavonols are important ultraviolet light protectants in many plants and contribute substantially to the quality and health-promoting effects of fruits and derived plant products. To study the regulation of flavonol synthesis in fruit, we isolated and characterized the grapevine (Vitis vinifera ‘Shiraz’) R2R3-MYB transcription factor VvMYBF1. Transient reporter assays established VvMYBF1 to be a specific activator of flavonol synthase1 (VvFLS1) and several other promoters of grapevine and Arabidopsis (Arabidopsis thaliana) genes involved in flavonol synthesis. Expression of VvMYBF1 in the Arabidopsis mutant myb12 resulted in complementation of its flavonol-deficient phenotype and confirmed the function of VvMYBF1 as a transcriptional regulator of flavonol synthesis. Transcript analysis of VvMYBF1 throughout grape berry development revealed its expression during flowering and in skins of ripening berries, which correlates with the accumulation of flavonols and expression of VvFLS1. In addition to its developmental regulation, VvMYBF1 expression was light inducible, implicating VvMYBF1 in the control of VvFLS1 transcription. Sequence analysis of VvMYBF1 and VvFLS1 indicated conserved putative light regulatory units in promoters of both genes from different cultivars. By analysis of the VvMYBF1 amino acid sequence, we identified the previously described SG7 domain and an additional sequence motif conserved in several plant MYB factors. The described motifs have been used to identify MYB transcription factors from other plant species putatively involved in the regulation of flavonol biosynthesis. To our knowledge, this is the first functional characterization of a light-inducible MYB transcription factor controlling flavonol synthesis in fruit.
Histone Deacetylase Inhibitor, Trichostatin A, Affects Gene Expression Patterns during Morphogenesis of Chicken Limb Buds in vivo

Acetylation is one of the key chromatin modifications that control gene transcription during embryonic development and tumorigenesis. The types of genes sensitive to such modifications in vivo are not known to date. We investigated the expression of a number of genes involved in embryonic development after treatment with trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor, in the limbs of chicken embryos. Our results show that TSA affects the expression profiles of some genes that play important roles during limb development. The expression of BMP4, SF/HGF and Twist1 increased, whereas the expression of BMP2, FGF8, Shh, Scleraxis, Myf5 and MyoD was decreased or even inhibited. In contrast, the expression of Pax3, Paraxis, Msx1, CREB, and PCNA was not affected. Our results indicate that the chicken embryo can serve as an effective in vivo model for studying the effect of HDAC inhibitors on gene expression and can be helpful for understanding the role of chromatin remodeling and epigenetic control of gene expression.
A 6‐Year Exercise Program Improves Skeletal Traits Without Affecting Fracture Risk: A Prospective Controlled Study in 2621 Children

Most pediatric exercise intervention studies that evaluate the effect on skeletal traits include volunteers and follow bone mass for less than 3 years. We present a population‐based 6‐year controlled exercise intervention study in children with bone structure and incident fractures as endpoints. Fractures were registered in 417 girls and 500 boys in the intervention group (3969 person‐years) and 835 girls and 869 boys in the control group (8245 person‐years), all aged 6 to 9 years at study start, during the 6‐year study period. Children in the intervention group had 40 minutes daily school physical education (PE) and the control group 60 minutes per week. In a subcohort with 78 girls and 111 boys in the intervention group and 52 girls and 54 boys in the control group, bone mineral density (BMD; g/cm2) and bone area (mm2) were measured repeatedly by dual‐energy X‐ray absorptiometry (DXA). Peripheral quantitative computed tomography (pQCT) measured bone mass and bone structure at follow‐up. There were 21.7 low and moderate energy‐related fractures per 1000 person‐years in the intervention group and 19.3 fractures in the control group, leading to a rate ratio (RR) of 1.12 (0.85, 1.46). Girls in the intervention group, compared with girls in the control group, had 0.009 g/cm2 (0.003, 0.015) larger gain annually in spine BMD, 0.07 g (0.014, 0.123) larger gain in femoral neck bone mineral content (BMC), and 4.1 mm2 (0.5, 7.8) larger gain in femoral neck area, and at follow‐up 24.1 g (7.6, 40.6) higher tibial cortical BMC (g) and 23.9 mm2 (5.27, 42.6) larger tibial cross‐sectional area. Boys with daily PE had 0.006 g/cm2 (0.002, 0.010) larger gain annually in spine BMD than control boys but at follow‐up no higher pQCT values than boys in the control group. Daily PE for 6 years in at study start 6‐ to 9‐year‐olds improves bone mass and bone size in girls and bone mass in boys, without affecting the fracture risk. © 2014 American Society for Bone and Mineral Research.
An efficient mechanism of generating call graph for JavaScript using dynamic analysis in web application

Web applications are replacing traditional native applications in recent years. For web applications, JavaScript is the most extensively used client side programming languages. The large JavaScript codebase often makes applications hard to understand, maintain and extend. Call graph is a human understandable program representation that can be used as a basis for maintenance and further extension of the application. In maintenance phase call graph can play a vital role by facilitating developers to easily trace the code that implements a particular feature. There is insufficient tool support for generating call graph for JavaScript. For its dynamic nature, JavaScript call graph generation becomes challenging. We present a dynamic analysis based mechanism to construct the call graph of JavaScript of a client side web application. Our evaluation on web applications demonstrates that the technique is precise and the rate of unidentified nodes in call graph is acceptable.
Trend Detection and Data Mining via Wavelet and

This paper presents the formulation and evaluation of effective algorithms of reliable data analysis for real-time monitoring of incipient faults and anomalies, data fusion and event classification. The objective is to alleviate the shortcomings of the existing techniques for data mining by taking advantage of nonlinear filtering to handle non-Gaussian and non-stationary multiplicative noise and uncertainties. New concepts have been developed toward characterization of the data features and behavior interpretation of the underlying processes to evaluate their performance. In particular, the techniques of wavelet transform, Hilbert-Huang transform, and symbolic encoding are investigated to explore their effectiveness and relative simplicity to interpret and implement data mining tasks.
RESPIRATORY QUOTIENT AND METABOLIC RATE IN NORMAL FULL‐TERM AND SMALL‐FOR‐DATE NEWBORN INFANTS 1

Respiratory quotient and gaseous metabolism were measured in normal full‐term and small‐for‐date infants during the first week of life. In both groups RQ dropped during the first day and rose again during the next few days. However, the RQ was lower during the first 5 days in small‐for‐date infants. The O2 uptake of the small‐for‐date babies is initially lower but rises during the first 5 days.
The importance of the A-rich loop in human immunodeficiency virus type 1 reverse transcription and infectivity

Nucleotide segment (+169)AAAA(+172) constitutes an A-rich loop within human immunodeficiency virus type 1 (HIV-1) (HXB2D) RNA and is able to interact with the anticodon loop (33)/USUU(36) of primer tRNA3(Lys). We have shown that the deletion of this A-rich loop resulted in diminished levels of infectivity and reduced synthesis of viral DNA in MT-2 cells and cord blood mononuclear cells. Endogenous reverse transcriptase (RT) assays revealed that the mutated viruses, termed HIV/del-A, generated fewer cDNA products than did wild-type virus, designated HIV/WT. We also employed in vitro RT assays with in vitro-synthesized viral RNA templates, recombinant HIV-1 RT(p66/51), and natural tRNA3(Lys) as primers to show that the mutated RNA templates, designated PBS/del-A, generated less minus-strand strong-stop DNA product than did the wild-type RNA template, designated PBS/WT. The initiation efficiency of reverse transcription from the mutated RNA template was significantly impaired compared with that from the wild-type RNA template when a single-base extension assay from the tRNA3(Lys) primer was employed. However, RT reactions performed with DNA oligonucleotides complementary to the primer binding site (PBS) as primers did not yield differences between the mutated PBS/del-A and wild-type RNA templates. Long-term culture of HIV/del-A in MT-2 cells resulted in the replacement of two G's at nucleotide positions 167 and 168 by two A's that possessed the same relationship to the 5' end of the PBS as did the wild-type A's at positions 171 and 172. In vitro RT assays performed with recombinant enzyme with tRNA3(Lys) as the primer showed that the RNA template thus generated, termed PBS/A2, yielded levels of minus-strand strong-stop DNA product similar to those yielded by the wild-type RNA template. Coincidentally, viruses containing A's at positions 167 and 168 were able to replicate with efficiencies similar to those of the wild-type viruses. Thus, the (+169)AAAA(+172) A-rich loop plays a key role in the synthesis of viral DNA.
A compact multiband hybrid meander-Koch Fractal antenna for WLAN USB dongle

There is a current upsurge for the high data rate and wide bandwidth in the communication technologies. This has posed several challenges for the researchers. These challenges include but are not limited to size reduction, high efficiency, and low-cost. The prevailing fashion in the communication system is to integrate several WLAN standards in small user equipment. The emergence of the USB dongle for WLAN has attracted the antenna design engineers to design multi band antennas. The antenna size is restricted to the small size of the USB dongle. The main challenge is to reduce the antenna size without compromising on the performance related characteristics such as; wide bandwidth, low VSWR, high gain and high radiation efficiency. In this paper a novel Koch-meander Fractal antenna has been proposed for the application of WLAN USB dongle. The proposed compact antenna is simulated in CST microwave studio. The simulation results depicts that the antenna has a −10 dB return loss bandwidth of 2.2909–2.553 GHz and 5.1406–5.8737 GHz. The minimum return loss of −28.9 dB is achieved at the lower band of 2.41 GHz. While the upper band depicts a return loss of −20.8 dB at 5.36 GHz. The proposed antenna is capable of covering the whole band required for the WLAN 802.11 a/b/g standards.
Serum amino acid responses to three different exercise sessions in male power athletes.

BACKGROUND The purpose of this study was to investigate serum amino acid responses to 3 different exercise sessions in male power athletes (sprinters and jumpers; n=11). METHODS All subjects performed 2 running exercise sessions: a short run session (SRS) of 3 x 4 x 60 m with recoveries of 120 and 360 sec, and a long run session (LRS) of 20 sec runs with recoveries of 100 sec until exhaustion. Ten subjects performed a strength exercise session (SES) of 90 min. Serum amino acids (n=21) were assayed 10 min before and 10 min after the sessions. Peak blood lactate was analyzed from fingertip blood samples taken 1 and 5 min after the sessions. RESULTS The before-after comparisons showed that the essential amino acids (EAAs) decreased by 8.7% (p<0.01) and alanine increased by 26.7% (p<0.001) after SRS. Following LRS the EAAs decreased also by 8.7% (p<0.01) and alanine increased by 25.3% (p<0.001). In the sum of all amino acids there were no changes after SRS and LRS but a significant decrease (14.8%; p<0.01) was observed after SES. Also the EAAs decreased (20.6%; p<0.001) but alanine, taurine and citrulline were the only single amino acids with no changes after SES. The peak blood lactate concentrations after SRS, LRS and SES were 13.8+/-1.9, 16.4+/-1.3 and 2.5+/-0.4 mmol/L, respectively. The lactate value after SES differed (p<0.001) from the values observed after SRS and LRS. The comparison of the changes in the serum amino acid concentrations following the 3 exercise sessions revealed that SRS and LRS were very similar but SES differed from SRS and LRS strongly (p<0.01) in the sum of all amino acids. CONCLUSIONS The current data indicate that the sum concentrations of all amino acids in serum decrease after the strength exercise session but not after the lactic anaerobic running exercises.
Manic/Hypomanic Switch During Acute Antidepressant Treatment for Unipolar Depression

Abstract: A significant proportion of patients with unipolar depression clinically develop manic or hypomanic switch during acute antidepressant treatment. Elucidation of its prevalence and predicting factors is of clinical relevance during acute antidepressant treatment of such patients. We retrospectively studied patients with unipolar depression who were admitted to our department during the 6-year period from 1997 to 2002 and who had fewer than 3 previous episodes before admission. The clinical background of the consecutive patients with manic/hypomanic switch (n = 37) who met Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria was compared with that of patients without manic/hypomanic switch (n = 245). The prevalence rate of manic/hypomanic switch was 13.1%. The switch group was composed of 23 men and 14 women, whose average age was 48.8 ± 12.3 years (range, 26-78 years). Manic/hypomanic switch was most frequently observed between 2 and 3 weeks after the antidepressant was increased to the ongoing dose. Antidepressants were decreased in 13 patients and discontinued in 23. Manic/hypomanic episodes lasted from 1 to 8 weeks. The patients in the switch group included a greater proportion of male subjects and had a higher frequency of family history of bipolar disorders than those in the nonswitch group. The mean doses of antidepressants were not significantly different between these groups. The higher frequency of manic/hypomanic switch occurring around the period when antidepressants begin to show clinical effects and the higher frequency of family history of bipolar disorders might suggest a biological susceptibility to antidepressants in patients of the switch group.
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans

Caloric restriction (CR), a reduction in calorie intake without malnutrition, retards aging in several animal models from worms to mammals. Developing CR mimetics, compounds that reproduce the longevity benefits of CR without its side effects, is of widespread interest. Here, we employed the Connectivity Map to identify drugs with overlapping gene expression profiles with CR. Eleven statistically significant compounds were predicted as CR mimetics using this bioinformatics approach. We then tested rapamycin, allantoin, trichostatin A, LY‐294002 and geldanamycin in Caenorhabditis elegans. An increase in lifespan and healthspan was observed for all drugs except geldanamycin when fed to wild‐type worms, but no lifespan effects were observed in eat‐2 mutant worms, a genetic model of CR, suggesting that life‐extending effects may be acting via CR‐related mechanisms. We also treated daf‐16 worms with rapamycin, allantoin or trichostatin A, and a lifespan extension was observed, suggesting that these drugs act via DAF‐16‐independent mechanisms, as would be expected from CR mimetics. Supporting this idea, an analysis of predictive targets of the drugs extending lifespan indicates various genes within CR and longevity networks. We also assessed the transcriptional profile of worms treated with either rapamycin or allantoin and found that both drugs use several specific pathways that do not overlap, indicating different modes of action for each compound. The current work validates the capabilities of this bioinformatic drug repositioning method in the context of longevity and reveals new putative CR mimetics that warrant further studies.
[Use of liquid perfluorocarbons in vitrectomy for difficult cases of proliferative diabetic retinopathy].

PURPOSE Thanks to their physical properties, could perfluorocarbon liquids (PFCL) be useful during vitrectomy for severe cases of proliferative diabetic vitreo-retinopathy (PDVR)? METHODS Among 120 vitrectomies for PDVR performed in a period of time from August 1992 to July 1993, we reviewed 24 cases with a minimal follow-up of six months for which we have used PFCL as intraoperative tool. Among these eyes, three (12%) were preoperatively attached, seven (29%) presented with a tractional retinal detachment sparing the macular area and 14 (59%) with a retinal detachment involving the macula. The indication for PFCL injection was either to flatten the retina in case of iatrogenic tear or retinotomy (15/24 eyes) or to stop a bleeding coming from the optic disc (9/24). The aim was to allow a good laser endophotocoagulation in all the cases and to inject an intraocular tamponade on a reattached retina if needed. As final tamponade, silicone oil was used in 10 eyes, gas in nine eyes and none in five eyes. RESULTS At the end of the study, 20 (83%) eyes had a totally reattached retina and four (17%) a detached retina. The postoperative compared to the preoperative visual acuity was improved in 13 eyes (54%), unchanged in seven eyes (30%) and decreased in four eyes (16%). In one case (4%), some droplets of PFCL were noticed in the vitreous cavity, under the silicone oil bubble, with a good clinical tolerance. No specific complication of PFCL injection could be found in the 23 other eyes. CONCLUSION In some selected cases of severe PDVR, the use of PFCL may help to flatten the retina, to stop bleeding from the optic disc and to perform a good endolaser photocoagulation. This allows to achieve good anatomical and visual results with few specific complications.
Impact of age, redundancy, and perceptual noise on visual search.

We examined adult age differences in the impact of redundancy and perceptual noise during visual search. Using a two-choice, visual search task, subjects responded to letters presented in one to four corners of an imaginary display square. On each trial, one, two, or three instances of a given target letter were presented. In the target-plus-noise condition, all nontarget corners of the imaginary square were filled with distractor (i.e., noise) letters. In the target-only condition, all nontarget corners were left blank. The results indicated that older adults showed relatively greater redundancy benefits than the young adults for the target-plus-noise trials than for the target-only trials. These results are interpreted within an internal noise framework.
BIOCHEMICAL AND IMMUNOLOGICAL MARKERS OF OVERTRAINING

Athletes fail to perform to the best of their ability if they become infected, stale, sore or malnourished. Excessive training with insufficient recovery can lead to a debilitating syndrome in which performance and well being can be affected for months. Eliminating or minimizing these problems by providing advice and guidelines on training loads, recovery times, nutrition or pharmacological intervention and regular monitoring of athletes using an appropriate battery of markers can help prevent the development of an overtraining syndrome in athletes. The potential usefulness of objective physiological, biochemical and immunological markers of overtraining has received much attention in recent years. Practical markers would be ones that could be measured routinely in the laboratory and offered to athletes as part of their sports science and medical support. The identification of common factors among overtrained athletes in comparison with well-trained athletes not suffering from underperformance could permit appropriate intervention to prevent athletes from progressing to a more serious stage of the overtraining syndrome. To date, no single reliable objective marker of impending overtraining has been identified. Some lines of research do, however, show promise and are based on findings that overtrained athletes appear to exhibit an altered hormonal response to stress. For example, in response to a standardized bout (or repeated bouts) of high intensity exercise, overtrained athletes show a lower heart rate, blood lactate and plasma cortisol response. Several immune measures that can be obtained from a resting blood sample (e.g. the expression of specific cell surface proteins such as CD45RO+ on T-lymphocytes) also seem to offer some hope of identifying impending overtraining. If an athlete is suspected of suffering from overtraining syndrome, other measures will also required, if only to exclude other possible causes of underperformance including post-viral fatigue, glandular fever, clinical depression, poor diet, anaemia, asthma, allergies, thyroid disorders, myocarditis and other medical problems interfering with recovery.