Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual Function for U2AF35 in AG-Dependent Pre-mRNA Splicing

ABSTRACT The splicing factor U2AF is required for the recruitment of U2 small nuclear RNP to pre-mRNAs in higher eukaryotes. The 65-kDa subunit of U2AF (U2AF65) binds to the polypyrimidine (Py) tract preceding the 3′ splice site, while the 35-kDa subunit (U2AF35) contacts the conserved AG dinucleotide at the 3′ end of the intron. It has been shown that the interaction between U2AF35 and the 3′ splice site AG can stabilize U2AF65 binding to weak Py tracts characteristic of so-called AG-dependent pre-mRNAs. U2AF35 has also been implicated in arginine-serine (RS) domain-mediated bridging interactions with splicing factors of the SR protein family bound to exonic splicing enhancers (ESE), and these interactions can also stabilize U2AF65 binding. Complementation of the splicing activity of nuclear extracts depleted of U2AF by chromatography in oligo(dT)-cellulose requires, for some pre-mRNAs, only the presence of U2AF65. In contrast, splicing of a mouse immunoglobulin M (IgM) M1-M2 pre-mRNA requires both U2AF subunits. In this report we have investigated the sequence elements (e.g., Py tract strength, 3′ splice site AG, ESE) responsible for the U2AF35 dependence of IgM. The results indicate that (i) the IgM substrate is an AG-dependent pre-mRNA, (ii) U2AF35dependence correlates with AG dependence, and (iii) the identity of the first nucleotide of exon 2 is important for U2AF35function. In contrast, RS domain-mediated interactions with SR proteins bound to the ESE appear to be dispensable, because the purine-rich ESE present in exon M2 is not essential for U2AF35 activity and because a truncation mutant of U2AF35 consisting only of the pseudo-RNA recognition motif domain and lacking the RS domain is active in our complementation assays. While some of the effects of U2AF35 can be explained in terms of enhanced U2AF65 binding, other activities of U2AF35 do not correlate with increased cross-linking of U2AF65 to the Py tract. Collectively, the results argue that interaction of U2AF35 with a consensus 3′ splice site triggers events in spliceosome assembly in addition to stabilizing U2AF65binding, thus revealing a dual function for U2AF35 in pre-mRNA splicing.
PML-RARα Alleviates the Transcriptional Repression Mediated by Tumor Suppressor Rb*

A fusion between the promyelocytic leukemia (PML) protein and the retinoic acid receptor-α (RARα) results in the transforming protein of acute promyelocytic leukemia, PML-RARα. PML has growth-suppressive properties and is localized within distinct nuclear structures referred to as nuclear bodies. PML participates in numerous cellular functions, including transcriptional activation, apoptosis, and transcriptional repression, whereas PML-RARα blocks these functions. However, the role played by PML-RARα in leukemogenesis remains unclear. Here we report that PML is required for transcriptional repression mediated by the tumor suppressor Rb. Rb interacts with the histone decaetylase (HDAC) complex containing co-repressors and represses the transcription of the E2F target genes. Overexpression of PML enhanced Rb-mediated repression. The degree of Rb-mediated repression was weakened by injecting anti-PML antibodies and was lower in Pml-deficient mouse embryonic fibroblasts. PML-RARα inhibited Rb-mediated repression, and two co-repressor-interacting sites on the PML-RARα molecule were required for this activity. Furthermore, PML-RARα blocked the interaction between Rb and HDAC. Thus, aberrant binding of PML-RARα to co-repressor-HDAC complexes may inhibit their association with Rb, resulting in the abrogation of Rb activity. Thus, the disruption of Rb-mediated repression may be a contributory factor in leukemogenesis.
Fast IR Orbit Feedback at RHIC

Mechanical low-β triplet vibrations lead to horizontal jitter of RHIC beams at frequencies around 10Hz. The resulting beam offsets at the interaction points are considered detrimental to RHIC luminosity performance. To stabilize beam orbits at the interaction points, installation of a fast orbit feedback is foreseen. A prototype of this system is being developed and tested. Recent results will be presented.
Evaluation of Transforming Growth Factor and Vascular Endothelial Growth Factor Polymorphisms in Taiwan Chinese Patients with Pterygium

Purpose Pterygium is an invasive and highly vascularized growth, thought to arise from activated and proliferating limbal epithelial stem cells. Epidemiologic studies have found the increase of active angiogenic and epithelial growth factors in pterygia, and implicated that these molecules could be involved directly or indirectly in the pathogenesis of pterygia as causative factors. The aim of this study was to investigate the association of polymorphisms of transforming growth factor (TGF) and vascular endothelial growth factor (VEGF) with pterygium. Methods A total of 133 pterygium patients and 105 volunteers without pterygium were enrolled in this study. Polymerase chain reaction based restriction fragment length polymorphism analysis was used to resolve the TGF-β1–509 and VEGF-460 genotypes. Results There was no significant difference in the allele frequency or genotype of TGF-β1–509 or VEGF-460 between total pterygium and the control group. No interaction between TGF-β1–509 and VEGF-460 was found either. Conclusions These results indicate that TGF-β1–509 and VEGF-460 polymorphisms were not highly associated with the pathology of pterygium. However, it may still be worthwhile to continue to search for angiogenic gene polymorphisms in order to predict the development of pterygium.
Pj Nonconforming Finite Element Method for the Solution of Radiation Transport Problems

The simulation of radiation transport in the optically thick flux-limited diffusion regime has been identified as one of the most time-consuming tasks within large simulation codes. Due to multimaterial complex geometry, the radiation transport system must often be solved on unstructured grids. In this paper, we investigate the behavior and the benefits of the unstructured Pi nonconforming finite element method, which has proven to be flexible and effective on related transport problems, in solving unsteady implicit nonlinear radiation diffusion problems using Newton and Picard linearization methods. Key words, nonconforming finite elements, radiation transport, inexact Newton linearization, multigrid preconditioning Subject classification. Applied and Numerical Mathematics
Timing of Preference Submissions Under the Boston Mechanism

Exam scores are often the main criteria of students’ priorities in college admissions. Depending on the timing of preference submissions relative to the knowledge of scores, students have various degrees of information about their own priorities. I study three widely used timings under the Boston mechanism. The results suggest first, timing that is associated with less information about priorities yields higher expected utility ex-ante; Second, timing with full information about priorities generates full sorting on scores, whereas timing with less information reduces the tension of such sorting.
Excluded generation: the growing challenges of labor market insertion for Egyptian youth

ABSTRACT Youth in Egypt hold rising aspirations for their adult lives, yet face an increasingly uncertain and protracted transition from school to work and thus into adulthood. This paper investigates how labor market insertion has been evolving over time in Egypt and how the nature of youth transitions relates to gender and social class. The study examines 19,925 respondents from the 2012 wave of the Egypt Labor Market Panel Survey. We demonstrate that recent youth cohorts face poorer chances of transitioning into a good job than previous cohorts, despite large increases in educational attainment. Social class is playing an increasing role in determining the success of the transition from school to work in Egypt. Whether youth successfully make transitions to formal jobs, embark on such transitions and fail, or pursue more traditional careers in informal employment or family businesses or farms depends on a complex and changing interaction between their own educational attainment and the resources of their families. In light of these findings, we discuss the policies that can help facilitate more successful transitions for struggling youth in Egypt.
Normal or High Polyphenol Concentration in Orange Juice Affects Antioxidant Activity, Blood Pressure, and Body Weight in Obese or Overweight Adults.

BACKGROUND The consumption of orange juice may lead to reduced oxidative stress and may enhance the antioxidant defense system. OBJECTIVE The aim was to evaluate the effects of the intake of orange juice containing either normal (NPJ) or high (HPJ) concentrations of polyphenols (299 and 745 mg/d, respectively) on the antioxidant defense system, oxidative stress biomarkers, and clinical signs of metabolic syndrome in 100 nonsmoking subjects who were either overweight or obese. METHODS A randomized, double-blind crossover study was conducted over two 12-wk periods with a 7-wk washout period. The effects on enzymatic and nonenzymatic blood antioxidant defense systems, urinary and plasma oxidative stress biomarkers, and clinical signs of metabolic syndrome were evaluated before and after an intervention with both of the orange juices. Paired t tests and linear mixed-effects models were used to evaluate the effects of juice, time, and interactions. RESULTS The intake of either NPJ or HPJ led to a decrease in urinary 8-hydroxy-2'-deoxyguanosine (NPJ: 935 ± 134 to 298 ± 19 ng/mg creatinine; HPJ: 749 ± 84 to 285 ± 17 ng/mg creatinine), 8-iso-prostaglandin F2α (NPJ: 437 ± 68 to 156 ± 14 ng/mg creatinine; HPJ: 347 ± 43 to 154 ± 13 ng/mg creatinine), erythrocyte catalase, and glutathione reductase activities. A decrease was also observed in body mass index, waist circumference, and leptin (all P < 0.05). The NPJ intervention decreased systolic and diastolic blood pressures (systolic blood pressure: 128 ± 1 to 124 ± 2 mm Hg; diastolic blood pressure: 79 ± 1 to 76 ± 1 mm Hg), whereas the HPJ intervention increased erythrocyte superoxide dismutase (SOD) activity (17.7 ± 1.5 to 23.1 ± 1.7 U/mg hemoglobin). CONCLUSIONS Our results show that the consumption of either NPJ or HPJ protected against DNA damage and lipid peroxidation, modified several antioxidant enzymes, and reduced body weight in overweight or obese nonsmoking adults. Only blood pressure and SOD activity were influenced differently by the different flavanone supplementations. This trial was registered at clinicaltrials.gov as NCT01290250.
Engineering Rapid Industrial Revolutions for Impoverished Agrarian Nations

Being able to emulate the Industrial Revolution has been the dream of many developing countries in the past one hundred plus years. However, the mainstream economics has not been able to preciously figure out what a nation should do to detonate its desired economic takeoff. Based on the recent research development in the area of development economics, this paper presents a detailed procedure on how to engineer the occurrence and evolution of industrial revolutions for an impoverished agrarian nation. This procedure is developed on top of two theorems that are first intuitively seen through the systemic yoyo model and then rigorously proven by using game theory. So, other than its theoretical value to economics, what’s presented in this paper is expected to be able to bring tangible economic benefits for developing nations in the years to come.
Symmetry, degeneracy, and uncoupled modes in two-dimensional photonic lattices.

The photonic bands of two-dimensional triangular and square lattices composed of circular rods were classified by means of the group theory based on the symmetry of the lattice structure. According to this classification, it was shown that the uncoupled mode, or the mode that cannot be excited by an external plane wave, which we previously found for the triangular lattice by the numerical calculation of the transmittance, is an antisymmetric mode under the relevant mirror reflection, and this fact is consistent with the observation by Robertson et al. It was also shown that triangular and square lattices with ${\mathit{C}}_{6\mathit{v}}$ or ${\mathit{C}}_{4\mathit{v}}$ symmetry have many other uncoupled modes with relatively low eigenfrequencies and some of them can be easily identified as the spectral ranges of total reflection in spite of their nonzero state density.
Multi-Agent Simulation of Epidemic Spatio-Temporal Transmission

A new model is proposed based on multi-agent system and geographic information system to simulate spatio-temporal transmission process of infectious diseases. The model consists of following four components: attributes definitions, neighborhood, movement rules and state transition rules. Two new parameters, infection dose decay rate and exponential distance, are introduced in transmission process, and the effect of spatio-temporal is explicitly considered. This model is used to simulate transmission process of infectious diseases in Haizhu district of Guangzhou City. It is found that changes of two parameters have prominent influence upon transmission process. The higher population density there were, the more probability of infection happened.
Combined intravenous treatment with ascorbic acid and desferrioxamine to reduce myocardial reperfusion injury in an experimental model resembling the clinical setting of primary PCI.

INTRODUCTION During reperfusion of ischemic myocardium, oxygen-derived free radicals are produced and can cause deleterious effects, known as reperfusion injury. We aimed to determine if a combination of the antioxidant ascorbic acid and an iron-chelating agent desferrioxamine, which reduces the production of the hydroxyl radical via ferrum-catalyzed reactions, can exert a protective action against reperfusion injury. METHODS Twenty-two young male farm pigs were anesthetized and subjected to 45 mins of ischemia and 3 and a half hours of reperfusion, in the left circumflex coronary artery territory, via the inflation and deflation of an angioplasty balloon. Animals were randomly assigned to receive either an intravenous infusion of 100 mg/ kg ascorbic acid and 60 mg/kg desferrioxamine (treatment group, TG) or an equal amount of normal saline (control group, CG). The I/R ratio, the ratio of the infarcted (necrotic) zone (I) to the myocardial area at risk (R) after 3 and a half hours of reperfusion, was calculated using the tetrazolium staining method. Left ventricular end diastolic pressure (LVEDP), number of episodes of ventricular arrhythmias, TIMI flow in the reperfused vessel, and left ventricular ejection fraction (LVEF) were evaluated within the first hour post reperfusion in order to assess further injury severity. RESULTS There was no significant difference in the I/R between the TG (27.9 ± 2.2%) and the CG (32.9 ± 2.4%) (p=0.15). In both groups there was a significant reduction in LVEF (-11.6 ± 2.28% for TG and -12.0 ± 2.27% for CG, p<0.01 for both groups) and a significant increase in LVEDP (+3.2 ± 0.9 mmHg for TG and +4.6 ± 0.9 mmHg for CG, p<0.01 for both groups) compared to the baseline values. No significant difference was noted between groups (p=0.61 for LVEF and p=0.60 for LVEDP values, at one hour post reperfusion). In all other parameters measured, no significant difference was observed between the study groups. CONCLUSIONS Intravenous treatment with a combination of the antioxidant ascorbic acid and the iron-chelating agent desferrioxamine does not provide significant protection against myocardial reperfusion injury.
Development of a Genetic System for the Denitrifying Bacterium ‘Aromatoleum aromaticum’ Strain EbN1

Members of the betaproteobacterial ‘Aromatoleum’/Azoarcus/Thauera cluster contribute to the biodegradation of aromatic and other recalcitrant compounds in anoxic soils and sediments. The metabolically versatile ‘Aromatoleumaromaticum’ strain EbN1 represents a model organism for this cluster, having already been studied on the physiological, proteogenomic and biochemical level. Here we report the development of a genetic system for ‘A. aromaticum’ strain EbN1 enabling unmarked deletion mutagenesis by heterologous recombination and subsequent complementation. The antibiotic sensitivity of strain EbN1 was characterized and optimal conditions for efficient cultivation on solid medium were established. A procedure for introducing foreign DNA into strain EbN1 by conjugation was developed. The effectiveness of the genetic system was demonstrated by unmarked in-frame deletion of ebdC2, encoding the γ-subunit of a paralogous ethylbenzene dehydrogenase.
No Effect of Acupuncture in the Relief of Delayed-Onset Muscle Soreness: Results of a Randomized Controlled Trial

Background:Delayed-onset muscle soreness (DOMS) is a common symptom in people participating in exercise, sport, or recreational physical activities. Several remedies have been proposed to prevent and alleviate DOMS. Design and Methods:A five-arm randomized controlled study was conducted to examine the effects of acupuncture on eccentric exercise-induced DOMS of the biceps brachii muscle. Participants were recruited through convenience sampling of students and general public. Participants were randomly allocated to needle, laser, sham needle, sham laser acupuncture, and no intervention. Outcome measures included pressure pain threshold (PPT), pain intensity (visual analog scale), and maximum isometric voluntary force. Results:Delayed-onset muscle soreness was induced in 60 participants (22 females, age 23.6 ± 2.8 years, weight 66.1 ± 9.6 kg, and height 171.6 ± 7.9 cm). Neither verum nor sham interventions significantly improved outcomes within 72 hours when compared with no treatment control (P > 0.05). Conclusions:Acupuncture was not effective in the treatment of DOMS. From a mechanistic point of view, these results have implications for further studies: (1) considering the high-threshold mechanosensitive nociceptors of the muscle, the cutoff for PPT (5 kg/cm2) chosen to avoid bruising might have led to ceiling effects; (2) the traditional acupuncture regimen, targeting muscle pain, might have been inappropriate as the DOMS mechanisms seem limited to the muscular unit and its innervation. Therefore, a regionally based regimen including an intensified intramuscular needling (dry needling) should be tested in future studies, using a higher cutoff for PPT to avoid ceiling effects.
Estimation of the Equilibrium Real Exchange Rate for South Africa

Based on the Johansen cointegration estimation methodology, much of the long-run behavior of the real effective exchange rate of South Africa can be explained by real interest rate differentials, GDP per capita (both relative to trading partners), real commodity prices, trade openness, the fiscal balance, and the extent of net foreign assets. On the basis of these fundamentals, the real exchange rate in early 2002 was found to be significantly more depreciated with respect to the estimated equilibrium level. The half-life of the deviation of the real exchange rate from the estimated equilibrium one was found to be somewhat more than two years.
News, Noise and Oil Price Swings

We interpret oil price fluctuations as the result of agents reaction to news about oil market fundamentals. Agents form expectations about future developments in oil production with limited information, and they only observe a noisy signal about its possible changes. We find that a large part of oil price swings is attributable to shocks that do not have any effect on oil production or global demand indexes. The finding is obtained using a VAR with dynamic rotations. We interpret this shock, through the lenses of a simple imperfect information rational expectations framework, as a noise shock in the oil market.
Diabetes and Abdominal Aortic Aneurysm Growth

We performed a systematic literature search and a meta-analysis to assess the association between diabetes mellitus (DM) and abdominal aortic aneurysm (AAA) growth. Databases including MEDLINE and EMBASE were searched through June 2015 using PubMed and OVID. For each study, data regarding AAA growth rates in both the DM and the non-DM groups were used to generate standardized mean differences (SMDs) and 95% confidence intervals (CIs). Our search identified 19 relevant studies including data on 9777 patients with AAA. Pooled analyses demonstrated a statistically significant slower growth rates in DM patients than in non-DM patients (unadjusted SMD, −0.32; 95% CI, −0.40 to −0.24; P < .00001; adjusted SMD, −0.29; 95% CI, −0.417 to −0.18; P < .00001). Despite possible publication bias in favor of DM based on funnel plot asymmetry, even adjustment of the asymmetry did not alter the beneficial effect of DM. In conclusion, on the basis of a meta-analysis of data on a total of 9777 patients (19 studies) identified through a systematic literature search, we confirmed the association of DM with slower growth rates of AAA.
Does sputum eosinophilia predict the response to systemic corticosteroids in children with difficult asthma?

Little evidence exists to guide the management of children with difficult asthma. The aim of this study was to determine whether children with difficult asthma, associated with sputum eosinophilia, are more likely to benefit from further treatment with high‐dose systemic corticosteroids, compared to those without sputum eosinophilia. Induced sputum was obtained from 20 children aged between 8 and 15 years with difficult asthma before and after a systemic corticosteroid trial (prednisolone 40 mg/day for 14 days or a single 80 mg dose of intramuscular triamcinolone). Subjects were defined as “eosinophilic” if the baseline sputum eosinophil percentage was ≥2.5% or “non‐eosinophilic” if <2.5%. Clinical response to the corticosteroid trial was assessed using spirometry and clinical data and defined by an increase in pre‐bronchodilator forced expiratory volume in 1 sec (FEV1) >9% predicted and/or an overall subjective improvement. Seventeen children had evidence of satisfactory adherence to the systemic corticosteroid treatment; eight of these were “eosinophilic” and nine were “non‐eosinophilic” subjects. Following the trial there was a similar clinical improvement in both groups, with FEV1 increasing in both the “eosinophilic” and “non‐eosinophilic” groups (median change in FEV1 16 [range 5–54]% vs. 12.5 [1–29]% predicted). Sputum eosinophils fell in the “eosinophilic” group (median 17.5 [range 3–37]% vs. 0 [0–23]%, P = 0.054), with no change in the “non‐eosinophilic” group (0 [0–2]% vs. 0 [0–1]%, P = 0.12). Sputum neutrophils did not change in either the “eosinophilic” (22.5 [5–50]% vs. 25 [0–91]%) or the “non‐eosinophilic” group (27.5 [0–96] vs. 44 [9–96]%). In conclusion children with difficult asthma may benefit clinically from high‐dose systemic corticosteroids even in the absence of sputum eosinophilia. Pediatr Pulmonol. 2007; 42:298–303. © 2007 Wiley‐Liss, Inc.