Miracle-dz/UniFAR-FTUs huggingface dataset:
Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes

Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity are frequently unreliable. On the other hand, comprehensive experimental validation is difficult and time consuming. We introduce a simple strategy that dramatically improves robustness and accuracy of computational binding site prediction. First, we evaluate the rate of recurrence of computational TFBS predictions by commonly used sampling procedures. We find that the vast majority of results are biologically meaningless. However clustering results based on nucleotide position improves predictive power. Additionally, we find that positional clustering increases robustness to long or imperfectly selected input sequences. Positional clustering can also be used as a mechanism to integrate results from multiple sampling approaches for improvements in accuracy over each one alone. Finally, we predict and validate regulatory sequences partially responsible for transcriptional control of the mammalian type A γ-aminobutyric acid receptor (GABAAR) subunit genes. Positional clustering is useful for improving computational binding site predictions, with potential application to improving our understanding of mammalian gene expression. In particular, predicted regulatory mechanisms in the mammalian GABAAR subunit gene family may open new avenues of research towards understanding this pharmacologically important neurotransmitter receptor system.
An experimental investigation of the phenomenology of delusional beliefs in people with Asperger syndrome

There is evidence that Asperger syndrome is associated with delusional beliefs. Cognitive theories of delusions in psychosis literature propose a central role for impaired theory of mind ability in the development of delusions. The present study investigates the phenomenology of delusional ideation in Asperger syndrome. Fortysix individuals with Asperger syndrome participated and were found to have relatively high levels of delusional ideation, primarily grandiose or persecutory. Factors associated with delusional belief were anxiety, social anxiety and self-consciousness, but not theory of mind ability or autobiographical memory. The findings indicate that delusional belief is a prominent feature in Asperger syndrome, but do not support a mentalization based account. A preliminary cognitive model of delusions in Asperger syndrome is proposed and the theoretical and clinical implications of the findings are discussed.
Annexin II in exocytosis: catecholamine secretion requires the translocation of p36 to the subplasmalemmal region in chromaffin cells

Annexin II is a Ca(2+)-dependent membrane-binding protein present in a wide variety of cells and tissues. Within cells, annexin II is found either as a 36-kD monomer (p36) or as a heterotetrameric complex (p90) coupled with the S-100-related protein, p11. Annexin II has been suggested to be involved in exocytosis as it can restore the secretory responsiveness of permeabilized chromaffin cells. By quantitative confocal immunofluorescence, immunoreplica analysis and immunoprecipitation, we show here the translocation of p36 from the cytosol to a subplasmalemmal Triton X-100 insoluble fraction in chromaffin cells following nicotinic stimulation. A synthetic peptide corresponding to the NH2-terminal domain of p36 which contains the phosphorylation sites was microinjected into individual chromaffin cells and catecholamine secretion was monitored by amperometry. This peptide blocked completely the nicotine-induced recruitment of p36 to the cell periphery and strongly inhibited exocytosis evoked by either nicotine or high K+. The light chain of annexin II, p11, was selectively expressed by adrenergic chromaffin cells, and was only present in the subplasmalemmal Triton X-100 insoluble protein fraction of both resting and stimulated cells. p11 can modify the Ca(2+)- and/or the phospholipid-binding properties of p36. We found that loss Ca2+ was required to stimulate the translocation of p36 and to trigger exocytosis in adrenergic chromaffin cells. Our findings suggest that the translocation of p36 to the subplasmalemmal region is an essential event in regulated exocytosis and support the idea that the presence of p11 in adrenergic cells may confer a higher Ca2+ affinity to the exocytotic pathway in these cells.
National survey of doctor‐reported secondary preventive treatment for patients with acute coronary syndrome in China

Background Long‐term use of antiplatelet agents, statins, beta‐blockers and angiotensin‐converting enzyme inhibitors are proven therapies for secondary prevention in acute coronary syndrome. However, little is known of physicians’ opinion about their use in China. Methods In 2010, standard questionnaires were posted to chief cardiologists in 1397 geographically diverse and representative sample of tertiary and secondary hospitals in China, collecting information about their opinions on the recommended treatments for acute coronary syndrome. Results A total of 1009 (72%) cardiologists responded with a valid questionnaire. Of them, 77% reported routine use of all the four main secondary preventive treatments, with little difference between secondary and tertiary hospitals (75% vs. 79%, P=0.16). Of the cardiologists reporting routine or selective use of aspirin, beta‐blockers, statins and angiotensin‐converting enzyme inhibitors, 94%, 85%, 73% and 86% would recommend indefinite use respectively. For all the 4 treatments combined, only 63.5% reported indefinite use at the same time, with no significant difference between secondary and tertiary hospitals (62% vs. 65%, P=0.17), nor between hospitals with or without fast track for primary percutaneous coronary intervention (66% vs. 61%, P=0.50). Conclusions Although Chinese cardiologists seem well informed about the value of main secondary preventive treatments for acute coronary syndrome, there is still gap in their understanding of the need for combined and prolonged use of these treatments.
The prostaglandin synthase 2/cyclooxygenase 2 (PTGS2/ COX2) rs5277 polymorphism does not influence risk of colorectal cancer in an Iranian population.

BACKGROUND The prostaglandin-endoperoxide synthase 2 [PTGS2, commonly known as cyclooxygenase-2 (COX-2)] is an enzyme induced by proinflammatory stimuli that is often overexpressed in malignant tissue and involved in the synthesis of prostaglandins and thromboxanes, regulators of processes such as inflammation, cell proliferation, and angiogenesis, all relevant for cancer development. We investigated whether a functional genetic polymorphism, rs5277, in COX-2 may have a risk-modifying effect on sporadic colorectal cancer in an Iranian population. MATERIALS AND METHODS We conducted a case-control study on 167 patients with colorectal cancer and 197 cancer-free controls in Taleghani Hospital in Tehran, Iran, between 2007 and 2011. Peripheral blood samples of both groups were processed for DNA extraction and genotyping of the COX-2 gene polymorphism (rs5277) using PCR-RFLP. RFLP results were confirmed by direct sequencing. Logistic regression analysis was performed to calculate the adjusted odds ratio (OR) and 95% confidence interval (95% CI). RESULTS There was no significant difference in the distribution of COX-2 gene rs5277 polymorphism genotype and the allelic form, among CRC patients compared with the healthy control group (p: 0.867). CONCLUSIONS Our results suggest that rs5277 polymorphism in COX2 could not be a good prognostic indicator for patients with CRC.
Tracking Seed Fates of Tropical Tree Species: Evidence for Seed Caching in a Tropical Forest in North-East India

Rodents affect the post-dispersal fate of seeds by acting either as on-site seed predators or as secondary dispersers when they scatter-hoard seeds. The tropical forests of north-east India harbour a high diversity of little-studied terrestrial murid and hystricid rodents. We examined the role played by these rodents in determining the seed fates of tropical evergreen tree species in a forest site in north-east India. We selected ten tree species (3 mammal-dispersed and 7 bird-dispersed) that varied in seed size and followed the fates of 10,777 tagged seeds. We used camera traps to determine the identity of rodent visitors, visitation rates and their seed-handling behavior. Seeds of all tree species were handled by at least one rodent taxon. Overall rates of seed removal (44.5%) were much higher than direct on-site seed predation (9.9%), but seed-handling behavior differed between the terrestrial rodent groups: two species of murid rodents removed and cached seeds, and two species of porcupines were on-site seed predators. In addition, a true cricket, Brachytrupes sp. , cached seeds of three species underground. We found 309 caches formed by the rodents and the cricket; most were single-seeded (79%) and seeds were moved up to 19 m. Over 40% of seeds were re-cached from primary cache locations, while about 12% germinated in the primary caches. Seed removal rates varied widely amongst tree species, from 3% in Beilschmiedia assamica to 97% in Actinodaphne obovata. Seed predation was observed in nine species. Chisocheton cumingianus (57%) and Prunus ceylanica (25%) had moderate levels of seed predation while the remaining species had less than 10% seed predation. We hypothesized that seed traits that provide information on resource quantity would influence rodent choice of a seed, while traits that determine resource accessibility would influence whether seeds are removed or eaten. Removal rates significantly decreased (p < 0.001) while predation rates increased (p = 0.06) with seed size. Removal rates were significantly lower for soft seeds (p = 0.002), whereas predation rates were significantly higher on soft seeds (p = 0.01). Our results show that murid rodents play a very important role in affecting the seed fates of tropical trees in the Eastern Himalayas. We also found that the different rodent groups differed in their seed handling behavior and responses to changes in seed characteristics.
Fast Modular Composition in any Characteristic

We give an algorithm for modular composition of degree n univariate polynomials over a finite field F<sub>q</sub> requiring n <sup>1</sup> <sup>+</sup> <sup>o(1)</sup> log<sup>1</sup> <sup>+</sup> <sup>o(1)</sup> q bit operations; this had earlier been achieved in characteristic n<sup>o(1)</sup> by Umans (2008). As an application, we obtain a randomized algorithm for factoring degree n polynomials over F<sub>q</sub> requiring (n<sup>1.5</sup> <sup>+</sup> <sup>o(1)</sup> + n <sup>1</sup> <sup>+</sup> <sup>o(1)</sup> log q) log<sup>1</sup> <sup>+</sup> <sup>o(1)</sup> q bit operations, improving upon the methods of von zur Gathen & Shoup (1992) and Kaltofen & Shoup (1998). Our results also imply algorithms for irreducibility testing and computing minimal polynomials whose running times are best-possible, up to lower order terms.As in Umans (2008), we reduce modular composition to certain instances of multipoint evaluation of multivariate polynomials. We then give an algorithm that solves this problem optimally (up to lower order terms), in arbitrary characteristic. The main idea is to lift to characteristic 0, apply a small number of rounds of multimodular reduction, and finish with a small number of multidimensional FFTs. The final evaluations are then reconstructed using the Chinese Remainder Theorem. As a bonus, we obtain a very efficient data structure supporting polynomial evaluation queries, which is of independent interest. Our algorithm uses techniques which are commonly employed in practice, so it may be competitive for real problem sizes. This contrasts with previous asymptotically fast methods relying on fast matrix multiplication.
Characteristics and prognosis of myocardial infarction in patients with normal coronary arteries.

STUDY OBJECTIVES Myocardial infarction with angiographically normal coronary arteries (MINC) is a life-threatening event with many open questions for physicians and patients. There are little data concerning the prognosis for patients with MINC. DESIGN Retrospective follow-up study. SETTING Tertiary referral center. PATIENTS Patients with MINC were investigated and compared to age- and sex-matched control subjects with myocardial infarction due to coronary artery disease (CAD). The patients were examined clinically using stress exercise and hyperventilation tests. Migraine and Raynaud's symptoms were determined by means of a standardized questionnaire. Serum lipoproteins; the seroprevalence of cytomegalovirus, Helicobacter pylori, and Chlamydia pneumoniae infections; and the most frequent causes of thrombophilia were assessed. MEASUREMENTS AND RESULTS From > 4,300 angiographies that were performed between 1989 and 1996, 21 patients with MINC were identified. The mean +/- SD patient age at the time of myocardial infarction was 42 +/- 7.5 years. When compared to control subjects (n = 21), patients with MINC had fewer risk factors for CAD. In contrast, MINC patients had more frequent febrile reactions prior to myocardial infarction (six patients vs zero patients; p < 0.05), and the migraine score was significantly higher (7.1 +/- 6.3 vs 2.2 +/- 4.1; p < 0.01). The seroprevalence of antibodies against cytomegalovirus, C pneumoniae, and H pylori tended to be higher in patients with MINC and CAD as compared to matched healthy control subjects. Three patients with MINC vs none with CAD had coagulopathy. During follow-up (53 +/- 37 months), no major cardiac event occurred in the MINC group; no patients with MINC vs nine with CAD (p = 0.0001) underwent repeated angiography. CONCLUSION High migraine score and prior febrile infection together with a lower cardiovascular risk profile are compatible with an inflammatory and a vasomotor component in the pathophysiology of the acute coronary event in MINC patients. The prognosis for these patients is excellent.
Nucleotide specificity of the enzymatic and motile activities of dynein, kinesin, and heavy meromyosin

The substrate specificities of dynein, kinesin, and myosin substrate turnover activity and cytoskeletal filament-driven translocation were examined using 15 ATP analogues. The dyneins were more selective in their substrate utilization than bovine brain kinesin or muscle heavy meromyosin, and even different types of dyneins, such as 14S and 22S dynein from Tetrahymena cilia and the beta-heavy chain-containing particle from the outer-arm dynein of sea urchin flagella, could be distinguished by their substrate specificities. Although bovine brain kinesin and muscle heavy meromyosin both exhibited broad substrate specificities, kinesin-induced microtubule translocation varied over a 50-fold range in speed among the various substrates, whereas heavy meromyosin-induced actin translocation varied only by fourfold. With both kinesin and heavy meromyosin, the relative velocities of filament translocation did not correlate well with the relative filament- activated substrate turnover rates. Furthermore, some ATP analogues that did not support the filament translocation exhibited filament- activated substrate turnover rates. Filament-activated substrate turnover and power production, therefore, appear to become uncoupled with certain substrates. In conclusion, the substrate specificities and coupling to motility are distinct for different types of molecular motor proteins. Such nucleotide "fingerprints" of enzymatic activities of motor proteins may prove useful as a tool for identifying what type of motor is involved in powering a motility-related event that can be reconstituted in vitro.
Sensor Placement for Minimum Exposure in Distributed Active Sensing Networks

Distributed active sensing is a new sensing paradigm, where active sensors and passive sensors are distributed in a field, and collaboratively detect and track the objects. "Exposure" of distributed active sensing networks (DASNs) quantifies the dimension limitations in detectability. It is important to deploy the sensors such that the exposure is minimized. Exposure minimization is shown to be NP-hard, and thus efficient heuristic algorithms are needed. In this paper, we propose a Genetic Algorithm (GA)-based solution that aims at achieving low exposure, scalability, and fast convergence. A novel flat binary chromosome encoding scheme and corresponding crossover and mutation operators are devised. Geometric knowledge is incorporated to significantly improve the convergence rate. Through extensive simulations, we demonstrate that the proposed algorithm outperforms a simple heuristic algorithm by up to 75%. The simulation results show that this algorithm is robust, self-adaptive and efficient under irregular boundary conditions.
Metabolic Effects of Chronic Cannabis Smoking

OBJECTIVE We examined if chronic cannabis smoking is associated with hepatic steatosis, insulin resistance, reduced β-cell function, or dyslipidemia in healthy individuals. RESEARCH DESIGN AND METHODS In a cross-sectional, case-control study, we studied cannabis smokers (n = 30; women, 12; men, 18; 27 ± 8 years) and control subjects (n = 30) matched for age, sex, ethnicity, and BMI (27 ± 6). Abdominal fat depots and intrahepatic fat content were quantified by magnetic resonance imaging and proton magnetic resonance spectroscopy, respectively. Insulin-sensitivity indices and various aspects of β-cell function were derived from oral glucose tolerance tests (OGTT). RESULTS Self-reported cannabis use was: 9.5 (2–38) years; joints/day: 6 (3–30) [median (range)]. Carbohydrate intake and percent calories from carbohydrates, but not total energy intake, were significantly higher in cannabis smokers. There were no group differences in percent total body fat, or hepatic fat, but cannabis smokers had a higher percent abdominal visceral fat (18 ± 9 vs. 12 ± 5%; P = 0.004). Cannabis smokers had lower plasma HDL cholesterol (49 ± 14 vs. 55 ± 13 mg/dL; P = 0.02), but fasting levels of glucose, insulin, total cholesterol, LDL cholesterol, triglycerides, or free fatty acids (FFA) were not different. Adipocyte insulin resistance index and percent FFA suppression during an OGTT was lower (P < 0.05) in cannabis smokers. However, oral glucose insulin sensitivity index, measures of β-cell function, or incretin concentrations did not differ between the groups. CONCLUSIONS Chronic cannabis smoking was associated with visceral adiposity and adipose tissue insulin resistance but not with hepatic steatosis, insulin insensitivity, impaired pancreatic β-cell function, or glucose intolerance.
Anticancer Potential of Plants and Natural Products: A Review

Cancer is one of the leading causes of death and globally the numbers of cases of cancer are increasing gradually. There are several medicines available in the market to treat the various types of cancer but no drug is found to be fully effective and safe. The major problem in the cancer chemotherapy is the toxicity of the established drugs. However plants and plant derived products have proved effective and safe in the treatment and management of cancers. These days most of the research work on cancer drugs is targeted on plants and plants derived natural products. Many natural products and their analogues have been identified as potent anti-cancer agents and day by day the anti-cancer property of various plants is being identified. Here an attempt is being made through this review to highlights the natural products and their analogues established as anti-cancer agents and the new plant species identified with anti-cancer properties either in vivo or in vitro.
Design of Lyapunov based controllers as TCP AQM

The paper considers the design of robust AQM for the congestion problem of a router. Using a state space representation of a linearized fluid model of TCP, we provide an AQM which stabilises the queue length of the buffer for any delay less than a prescribed upper bound. Our results rely on the use of recently developed Lyapunov-Krasovskii functio nal and have been expressed in terms of Linear Matrix Inequaliti es which can be solved easily. Finally, an example extracted fr om the literature and simulations support our study.
Efficient Inference of Continuous Markov Random Fields with Polynomial Potentials

In this paper, we prove that every multivariate polynomial with even degree can be decomposed into a sum of convex and concave polynomials. Motivated by this property, we exploit the concave-convex procedure to perform inference on continuous Markov random fields with polynomial potentials. In particular, we show that the concave-convex decomposition of polynomials can be expressed as a sum-of-squares optimization, which can be efficiently solved via semidefinite programing. We demonstrate the effectiveness of our approach in the context of 3D reconstruction, shape from shading and image denoising, and show that our method significantly outperforms existing techniques in terms of efficiency as well as quality of the retrieved solution.
A situation-aware action selection based on individual's preference using emotion estimation

Long-term relationships between humans and robots will expand in the future. We therefore consider that an affinity to robots is one of the important components of a stable relationship. In this paper, we propose an action selection system for robots. We expect the system to select an appropriate action that matches human's individual preference. We used an emotion estimation system to achieve this. This is an approach to create an affinity to robots. As a human's preference will be affected by their emotions, we used emotion estimation to learn these preferences. In this paper, we outline the proposed system, experiments, and evaluation of its efficacy. We performed two types of experiments using a simulated robot over one week and four weeks. In each of the experiments, the robot was varying its behaviors, based on learning of individual's preferences.
RACK 1 Functions in Rice Innate Immunity by Interacting with the Rac 1 Immune Complex

Ayako Nakashima,a,1 Letian Chen,a,1 Nguyen Phuong Thao,a Masayuki Fujiwara,a Hann Ling Wong,a Masayoshi Kuwano,b Kenji Umemura,c Ken Shirasu,d,2 Tsutomu Kawasaki,a and Ko Shimamotoa,3 a Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan b Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan c Agricultural and Veterinary Laboratories, Meiji Seika Kaisha, Kohoku-ku, Yokohama 222-8567, Japan d Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, United Kingdom
Magma system recharge of Mount St. Helens from precise relative hypocenter location of microearthquakes

[1] Four hundred forty-seven well-recorded earthquakes at Mount St. Helens during the late 1990s are relocated with high precision using a combination of a cross-correlation technique and then a procedure to obtain a one-dimensional velocity structure solution together with station corrections. The resulting high-resolution pattern of the spatial-temporal evolution of the earthquake activity, along with focal mechanisms of events provide additional evidence for the presence of a magma reservoir in the depth range 5.5–10 km, connected to the surface by a thin vertical conduit. Moreover, the distribution of the events below 5.5 km yielded a much clearer view of the structures that generate the seismicity at that depth. Some of the deeper events occur along a sequence of faults under the influence of a radial stress field; however, a large number of the events occur on a NNE-SSW striking steeply dipping fault with slip consistent with magma being periodically injected into a truncated dike on the northwest side of this fault.