Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Topoisomerase Iα Affects the Floral Transition1[OPEN]

The Arabidopsis DNA topoisomerase Iα modulates the expression of FLC, MAF4, and MAF5 to control flowering time. DNA topoisomerases modulate DNA topology to maintain chromosome superstructure and genome integrity, which is indispensable for DNA replication and RNA transcription. Their function in plant development still remains largely unknown. Here, we report a hitherto unidentified role of Topoisomerase Iα (TOP1α) in controlling flowering time in Arabidopsis (Arabidopsis thaliana). Loss of function of TOP1α results in early flowering under both long and short days. This is attributed mainly to a decrease in the expression of a central flowering repressor, FLOWERING LOCUS C (FLC), and its close homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, during the floral transition. TOP1α physically binds to the genomic regions of FLC, MAF4, and MAF5 and promotes the association of RNA polymerase II complexes to their transcriptional start sites. These correlate with the changes in histone modifications but do not directly affect nucleosome occupancy at these loci. Our results suggest that TOP1α mediates DNA topology to facilitate the recruitment of RNA polymerase II at FLC, MAF4, and MAF5 in conjunction with histone modifications, thus facilitating the expression of these key flowering repressors to prevent precocious flowering in Arabidopsis.
Loss of 18q22.3 Involving the Carboxypeptidase of Glutamate-like Gene Is Associated with Poor Prognosis in Resected Pancreatic Cancer

Purposes: Pancreatic cancer is the fourth leading cause of cancer-related death, and studies on the clinical relevance of its genomic imbalances are warranted. Experimental Design: Recurrent copy number alterations of cytobands and genes were analyzed by array comparative genomic hybridization (aCGH) in 44 resected pancreatic cancer specimens. Prognostic markers identified by aCGH were validated by PCR gene copy number assay in an independent validation cohort of 61 resected pancreatic cancers. The functions of gene identified were evaluated by proliferation, cell cycle, and migration assays in pancreatic cancer cells. Results: We showed recurrent copy number gains and losses in the first cohort. Loss of 18q22.3 was significantly associated with short-term overall survival in the first cohort (P = 0.019). This cytoband includes the carboxypeptidase of glutamate-like (CPGL) gene. CPGL gene deletion was associated with shorter overall survival in the validation cohort (P = 0.003). CPGL deletion and mutations of TP53 or Kras seem to be independent events. A Cox model analysis of the two cohorts combined showed that loss of 18q22.3/deletion of the CPGL gene was an independent poor prognostic factor for overall survival (HR = 2.72, P = 0.0007). Reconstitution of CPGL or its splicing variant CPGL-B into CPGL-negative pancreatic cancer cells attenuated cell growth, migration, and induced G1 accumulation. Conclusion: Loss of 18q22.3/deletion of the CPGL gene is a poor prognostic marker in resected pancreatic cancer, and functional studies suggest the CPGL gene as growth suppressor gene in pancreatic cancer. Clin Cancer Res; 18(2); 524–33. ©2011 AACR.
Vigilance against predators induced by eavesdropping on heterospecific alarm calls in a non-vocal lizard Oplurus cuvieri cuvieri (Reptilia: Iguania)

Prey animals can reduce their risk of predation by detecting potential predators before encounters occur. Some animals gain information about nearby predators by eavesdropping on heterospecific alarm calls. Despite having well-developed ears, most lizards do not use vocal information for intraspecific communication, and few studies have shown practical use of the ears in wild lizards. Here, we show that the Madagascan spiny-tailed iguana (Oplurus cuvieri cuvieri) obtains auditory signals for predator detection. The Madagascan spiny-tailed iguana and the Madagascar paradise flycatcher (Terpsiphone mutata) are syntopic inhabitants of the Ampijoroa dry deciduous forest of Madagascar. The iguana and the flycatcher have neither a predator–prey relationship nor resource competition, but they have shared predators such as raptors and snakes. Using playback experiments, we demonstrated that the iguana discriminates mobbing alarm calls of the flycatcher from its songs and then enhances its vigilance behaviour. Our results demonstrate the occurrence of an asymmetrical ecological relationship between the Madagascan spiny-tailed iguana and the paradise flycatcher through eavesdropping on information about the presence of predators. This implies that indirect interspecific interactions through information recognition may be more common than generally thought in an animal community.
On the Fair Resource-Sharing in Large Peer-to-Peer Systems 1

Accountability is becoming a major concern for the Internet. Wide spread of misconduct by profit driven hackers makes trust (faith)-based applications vulnerable to malicious attacks. An evidence based resource management system can guarantee that collaborative parties will share their resources based un-deniable evidence, so that community members cannot abuse their privileges without being caught. In this paper we propose fair resource sharing scheme for peer to peer (P2P) networks based on modified e-coin algorithms. A computing node joins a resource sharing community through the initial brokerage of a credential authority, which issues unforgeable yet anonymous transaction tokens, so that it can use the token to generate evidences of resource sharing with other nodes. We study offline fair sharing of resources in P2P systems, in which fraudulent activities can be detected based on the undeniable evidences generated in the transactions. These evidences can be used for unveiling the identity of a participant attempting to forge the evidences in transactions.
Comparison of PCR, Culture, and Direct Fluorescent-Antibody Testing for Detection of Bordetella pertussis

ABSTRACT We prospectively compared the performance of culture, direct fluorescent-antibody testing (DFA), and an in-house-developed PCR test targeting the repeated insertion sequence IS481 for the detection of Bordetella pertussis in nasopharyngeal swab specimens. We tested 319 consecutive paired specimens on which all three tests were performed. A total of 59 specimens were positive by one or more tests. Of these, 5 were positive by all three tests, 2 were positive by culture and PCR, 16 were positive by PCR and DFA, 28 were positive by PCR only, and 8 were positive by DFA only. Any specimen positive by culture was considered to be a true positive, as were specimens positive by both PCR and DFA. Specimens positive only by PCR or DFA were considered discrepant, and their status was resolved by review of patient histories. Patients with symptoms meeting the Centers for Disease Control and Prevention clinical case definition for pertussis and who had a specimen positive by PCR or DFA were considered to have true B. pertussis infections. Of the 28 patients positive by PCR only, 20 met the clinical case definition for pertussis, while 3 of the 8 patients positive by DFA only met the clinical case definition. After resolution of the status of discrepant specimens, the sensitivity, specificity, positive predictive value, and negative predictive value were 15.2, 100, 100, and 87.5%, respectively, for culture; 93.5, 97.1, 84.3, and 98.9%, respectively, for PCR; and 52.2, 98.2, 82.8, and 92.4%, respectively, for DFA. The actual positive predictive value of PCR was probably greater, as several PCR-positive patients who did not meet the clinical case definition had symptoms consistent with typical or atypical pertussis. PCR is a sensitive and specific method for the detection of B. pertussis.
New Strategies for Selecting Reuse Candidates on Automated Program Repair

Automated program repair (in short, APR) is a truly desired technique because it can reduce debugging costs drastically. A well-known technique in APR is a reuse-based approach, which inserts existing program statements in a given program to suspicious code for an exposed bug. Some reports show the reuse-based approach was able to fix many bugs in open source software. However, the existing approach often takes very long time to fix bugs. Its main factor is that so many variant programs are generated by insertions and so many test cases are executed for the variant programs before a fixed program is generated. In order to shorten fixing time with the reuse-based approach, a fixed program must be generated much more efficiently. In this paper, we propose two strategies to generate a fixed program more efficiently. We also implement the two strategies and confirm that there are real bugs which the two strategies contribute to shortening fixing time.
An exponential FISTAR model applied to the US real effective exchange rate

The aim of this paper is to study the dynamics of the US real effective exchange rate by capturing nonlinearity and long memory features. In this context, we used the family of fractionally integrated STAR (FISTAR) models proposed by van Dijk, Franses and Paap (2002) to the case when the transition function is an exponential function and we develop an estimation procedure. Indeed, these models can take into account processes characterized by several distinct dynamic regimes and persistence phenomena.
Genomic and Coexpression Analyses Predict Multiple Genes Involved in Triterpene Saponin Biosynthesis in Medicago truncatula[C][W]

This study sought to identify genes involved in the biosynthesis of the triterpene skeleton in Medicago truncatula using a comprehensive gene expression clustering analysis. The UGT73F3 gene was shown to function as a uridine diphosphate glycosyltransferase in the biosynthesis of triterpene saponins. Saponins, an important group of bioactive plant natural products, are glycosides of triterpenoid or steroidal aglycones (sapogenins). Saponins possess many biological activities, including conferring potential health benefits for humans. However, most of the steps specific for the biosynthesis of triterpene saponins remain uncharacterized at the molecular level. Here, we use comprehensive gene expression clustering analysis to identify candidate genes involved in the elaboration, hydroxylation, and glycosylation of the triterpene skeleton in the model legume Medicago truncatula. Four candidate uridine diphosphate glycosyltransferases were expressed in Escherichia coli, one of which (UGT73F3) showed specificity for multiple sapogenins and was confirmed to glucosylate hederagenin at the C28 position. Genetic loss-of-function studies in M. truncatula confirmed the in vivo function of UGT73F3 in saponin biosynthesis. This report provides a basis for future studies to define genetically the roles of multiple cytochromes P450 and glycosyltransferases in triterpene saponin biosynthesis in Medicago.
Constituency to Dependency Translation with Forests

Tree-to-string systems (and their forest-based extensions) have gained steady popularity thanks to their simplicity and efficiency, but there is a major limitation: they are unable to guarantee the grammaticality of the output, which is explicitly modeled in string-to-tree systems via target-side syntax. We thus propose to combine the advantages of both, and present a novel constituency-to-dependency translation model, which uses constituency forests on the source side to direct the translation, and dependency trees on the target side (as a language model) to ensure grammaticality. Medium-scale experiments show an absolute and statistically significant improvement of +0.7 BLEU points over a state-of-the-art forest-based tree-to-string system even with fewer rules. This is also the first time that a tree-to-tree model can surpass tree-to-string counterparts.
Asparagine biosynthesis in soybean nodules.

Asparagine biosynthesis in soybean (Glycine max [L.] Merr.) nodules has been difficult to demonstrate due to the poor conversion of suspected immediate precursors to asparagine and the instability of the key enzyme asparagine synthetase. The present study was designed to explore the effects of two ammonium assimilation inhibitors on the metabolism of (14)CO(2) to [(14)C]asparagine and to demonstrate the existence in nodules of the enzyme asparagine synthetase. When detached nodules were incubated in (14)CO(2), radioactivity in asparagine (as a percentage of amino acid cpm) increased 10-fold over 4 hours. Vacuum infiltration of 10 mm methionine sulfoximine or 10 mm azaserine prior to (14)CO(2) incubations decreased both the rate of dark fixation and the radioactivity in the amino acid fraction. These inhibitors also decreased the recovery of label in aspartate and asparagine. These results, plus the sequence of labeling of metabolites from (14)CO(2), are consistent with a glutamine-dependent synthesis of asparagine from aspartate with oxalacetate as a precursor to aspartate.An enzyme catalyzing the ATP- and glutamine-dependent amidation of aspartic acid to form asparagine was isolated from soybean nodules. High levels of sulfhydryl protectants were required and the inclusion of glycerol and substrates in the extraction buffer helped to stabilize the enzyme. Enzyme activity in taproot nodules increased between 38 and 41 days after planting and peaked soon after flower initiation (45 days). The activity then declined to basal levels by 70 days. On a total enzyme activity basis, there was 170-fold more asparagine synthetase activity in the infected zone of the nodule than in the cortex, and 205-fold more activity in the cytosol than the bacteroid fraction. The enzyme has a broad pH maximum around pH 8.25, and the apparent K(m) values for the substrates aspartate, MgATP, and glutamine are 1.24 mm, 0.076 mm, and 0.16 mm, respectively. Ammonium ion can replace glutamine as the nitrogen donor, but the K(m) value of the enzyme for ammonium ion is 40-fold higher than that for glutamine.
Novel clusters of receptors for sphingosine‐1‐phosphate, sphingosylphosphorylcholine, and (lyso)‐phosphatidic acid: New receptors for “Old” ligands

The (lyso)phospholipid mediators sphingosine‐1‐phosphate (S1P), lysophosphatidic acid (LPA), sphingosylphosphorylcholine (SPC), and phosphatidic acid (PA) regulate diverse cellular responses such as proliferation, survival and death, cytoskeletal rearrangements, cell motility, and differentiation among many others. Signaling is complex and many signaling events are mediated through the activation of cell surface seven transmembrane (7TM) G protein coupled receptors. Five high affinity receptors for S1P have been identified so far and named S1P1, 2 ,3 ,4 ,5 (formerly referred to as endothelial differentiation gene (edg)1, 5, 3, 6, 8). Recently, the orphan receptor GPR63 was identified a low affinity S1P receptor structurally distant from the S1P1–5 family. The orphan GPR3, 6, 12 cluster, phylogenetically related to the edg and melanocortin receptors appears to be subject to modulation by S1P and SPC although all three receptors are strong constitutive stimulators of the Gαs‐adenylyl cyclase (AC) pathway and would not require additional ligand stimulation but rather inverse agonism to control activity. Ovarian cancer G protein coupled receptor 1 (OGR1) and GPR4, two structurally closely related receptors were assigned in functional and binding studies as high affinity molecular targets for SPC. Very recently, however, both OGR1 and GPR4 were described as receptors endowed with the ability to signal cells in response to protons. LPA exerts its biological effects through the activation of G protein coupled LPA1–3 receptors (formerly referred to as edg2, 4, 7). A fourth high affinity LPA receptor has been identified: P2Y9 (GPR23) structurally related to nucleotide receptors and phylogenetically quite distant from the high affinity LPA1–3 cluster. This review attempts to give an overview about the existing families of lysophosholipid receptors and the spectrum of lipid agonists they use as high or low affinity ligands to relay extracellular signals into intracellular responses. Recently deorphaned lipid receptors, within and outside the known lipid receptor clusters will receive particular attention. © 2004 Wiley‐Liss, Inc.
Antibiotic Prophylaxis for Urinary Tract Infections in Antenatal Hydronephrosis

BACKGROUND AND OBJECTIVE: Continuous antibiotic prophylaxis (CAP) is recommended to prevent urinary tract infections (UTIs) in newborns with antenatal hydronephrosis (HN). However, there is a paucity of high-level evidence supporting this practice. The goal of this study was to conduct a systematic evaluation to determine the value of CAP in reducing the rate of UTIs in this patient population. METHODS: Pertinent articles and abstracts from 4 electronic databases and gray literature, spanning publication dates between 1990 and 2010, were included. Eligibility criteria included studies of children <2 years old with antenatal HN, receiving either CAP or not, and reporting on development of UTIs, capturing information on voiding cystourethrogram (VCUG) result and HN grade. Full-text screening and quality appraisal were conducted by 2 independent reviewers. RESULTS: Of 1681 citations, 21 were included in the final analysis (N = 3876 infants). Of these, 76% were of moderate or low quality. Pooled UTI rates in patients with low-grade HN were similar regardless of CAP status: 2.2% on prophylaxis versus 2.8% not receiving prophylaxis. In children with high-grade HN, patients receiving CAP had a significantly lower UTI rate versus those not receiving CAP (14.6% [95% confidence interval: 9.3–22.0] vs 28.9% [95% confidence interval: 24.6–33.6], P < .01). The estimated number needed to treat to prevent 1 UTI in patients with high-grade HN was 7. CONCLUSIONS: This systematic review suggests value in offering CAP to infants with high-grade HN, however the impact of important variables (eg, gender, reflux, circumcision status) could not be assessed. The overall level of evidence of available data is unfortunately moderate to low.
The unified theory of pseudorandomness

Pseudorandomness is the theory of efficiently generating objects that "look ran- dom" despite being constructed with little or no randomness. One of the achieve- ments of this research area has been the realization that a number of funda- mental and widely studied "pseudorandom" objects are all almost equivalent when viewed appropriately. These objects include pseudorandom generators, expander graphs, list-decodable error-correcting codes, averaging samplers, and hardness amplifiers. In this survey, we describe the connections between all of these objects, showing how they can all be cast within a single "list-decoding framework" that brings out both their similarities and differences.
An indexing approach for speeding-up image classification

One of the most common computer vision tasks is that of recognizing the category of objects present in a given image. Previous work has mostly focused on building accurate classifiers based on carefully selected features. Classification is often carried on individual test images, while most of the practical situations, such as webscale image indexing, demand the simultaneous classification of a large collection of images. This is especially true for real-world datasets, that already contain numerous un-indexed images and videos. In this paper, we work towards developing a computationally efficient approach towards object recognition, that is inspired by retrieval schemes. We perform an offline indexing of the features from the collection, so that the classifier only needs to work on a small subset of the entire feature set. Over a set of 2 Million features extracted from 7000 images, classification against 5 object categories using a standard SVM would require more than 260 hours. Over the same test case, the classification time using our indexing based approach is reduced to less than 13 hours. The compromise on the accuracy is less than 7% for the 20X speedup achieved.
Distributed interference control in OFDMA-based femtocells

This paper proposes a decentralized interference control scheme for an OFDMA (Orthogonal Frequency Division Multiple Access) cellular scenario where multiple macrocells and femtocells are deployed. In particular, we model the distributed resource allocation problem by means of a potential game, which is demonstrated to converge to a unique and pure Nash equilibrum. In this game, the femto base stations are the players, their actions are the resource blocks and the corresponding power levels to be allocated for downlink transmission, and the utility is designed to guarantee coexistence with the macro system, guaranteeing a fair tradeoff between femto and macro systems' performances. To do that, the utility function does not only consider the capacity of the femtocells, but also the different sources of inter-system interference: macrocell to femtocell, femtocell to femtocell, and femtocell to macrocell. The game is solved by applying a better response dynamic, which first selects the best resource blocks allocation policy for the femtousers, and then selects the most appropriate power levels for each resource block, through the solution of the corresponding convex optimization problem. Simulation results show that the introduction of femtocells in the scenario increases the total system capacity, and that the considered utility function provides an improvement in macro system performance of up to 40%, while reducing the femto capacity only up to 7%, with respect to the well known iterative waterfilling game.
Premature ovarian failure

Premature ovarian failure (POF) is the occurrence of amenorrhoea, elevated gonadotrophins and hypoestrogenism in women under 40 years of age. It has important physical and psychological consequences and is increasingly common due to improved survival following treatment for malignancy. Despite this, it remains a poorly understood condition. Here we review the presentation and investigation of POF, discuss recent advances in the management of affected women, and suggest how our knowledge of the condition could be improved.
Design and implementation of a hard disk drive servo system using robust and perfect tracking approach

We tackle the problem of a servo system design for a conventional hard disk drive with a single voice-coil-motor (VCM) actuator using the so-called robust and perfect tracking (RPT) approach. We first model the physical system and then formulate it into a robust and perfect tracking problem, in which a measurement feedback controller can be obtained to achieve a robust and perfect tracking for any step reference in the presence of external disturbances and arbitrarily initial conditions. Some trade-offs are then made in order for the RPT controller to be implementable using existing hardware setup. The implementation results of the RPT controller are compared with those of a PID controller. The results show that the servo system with our RPT controller has much better performances than the PID one has. It has faster settling time, lower overshoots and higher accuracy.