Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Prp19-Like U-Box Proteins in the MOS4-Associated Complex Play Redundant Roles in Plant Innate Immunity

Plant Resistance (R) proteins play an integral role in defense against pathogen infection. A unique gain-of-function mutation in the R gene SNC1, snc1, results in constitutive activation of plant immune pathways and enhanced resistance against pathogen infection. We previously found that mutations in MOS4 suppress the autoimmune phenotypes of snc1, and that MOS4 is part of a nuclear complex called the MOS4-Associated Complex (MAC) along with the transcription factor AtCDC5 and the WD-40 protein PRL1. Here we report the immuno-affinity purification of the MAC using HA-tagged MOS4 followed by protein sequence analysis by mass spectrometry. A total of 24 MAC proteins were identified, 19 of which have predicted roles in RNA processing based on their homology to proteins in the Prp19-Complex, an evolutionarily conserved spliceosome-associated complex containing homologs of MOS4, AtCDC5, and PRL1. Among these were two highly similar U-box proteins with homology to the yeast and human E3 ubiquitin ligase Prp19, which we named MAC3A and MAC3B. MAC3B was recently shown to exhibit E3 ligase activity in vitro. Through reverse genetics analysis we show that MAC3A and MAC3B are functionally redundant and are required for basal and R protein–mediated resistance in Arabidopsis. Like mos4-1 and Atcdc5-1, mac3a mac3b suppresses snc1-mediated autoimmunity. MAC3 localizes to the nucleus and interacts with AtCDC5 in planta. Our results suggest that MAC3A and MAC3B are members of the MAC that function redundantly in the regulation of plant innate immunity.
A Stateless Cryptographically-Secure Physical Unclonable Function

We present the first stateless construction of a cryptographically-secure Physical Unclonable Function. Our construct requires no non-volatile (permanent) storage, secure or otherwise, and its computational security can be clearly reduced to the hardness of Learning Parity with Noise (LPN) in the random oracle model. The construction is “stateless,” because there is no information stored between subsequent queries, which mitigates attacks against the PUF via tampering. Moreover, our stateless construction corresponds to a PUF whose outputs are free of noise because of internal error-correcting capability, which enables a host of applications beyond authentication. We describe the construction, provide a proof of computational security, and present experimental evidence that this construct is viable.
Hierarchical Reinforcement Learning Using Graphical Models

The graphical models paradigm provides a general framework for automatically learning hierarchical models using ExpectationMaximization, enabling both abstract states and abstract policies to be learned. In this paper we describe a two-phased method for incorporating policies learned with a graphical model to bias the behaviour of an SMDP Q-learning agent. In the first reward-free phase, a graphical model is trained from sample trajectories; in the second phase, policies are extracted from the graphical model and improved by incorporating reward information. We present results from a simulated grid world Taxi task showing that the SMDP Q-learning agent using the learned policies quickly does as well as an SMDP Q-learning agent using hand-coded policies.
Neural Networks and Nonlinear Adaptive Filtering: Unifying Concepts and New Algorithms

The paper proposes a general framework that encompasses the training of neural networks and the adaptation of filters. We show that neural networks can be considered as general nonlinear filters that can be trained adaptively, that is, that can undergo continual training with a possibly infinite number of time-ordered examples. We introduce the canonical form of a neural network. This canonical form permits a unified presentation of network architectures and of gradient-based training algorithms for both feedforward networks (transversal filters) and feedback networks (recursive filters). We show that several algorithms used classically in linear adaptive filtering, and some algorithms suggested by other authors for training neural networks, are special cases in a general classification of training algorithms for feedback networks.
Pogo-like Transposases Have Been Repeatedly Domesticated into CENP-B-Related Proteins

The centromere is a chromatin region that is required for accurate inheritance of eukaryotic chromosomes during cell divisions. Among the different centromere-associated proteins (CENP) identified, CENP-B has been independently domesticated from a pogo-like transposase twice: Once in mammals and once in fission yeast. Recently, a third independent domestication restricted to holocentric lepidoptera has been described. In this work, we take advantage of the high-quality genome sequence and the wealth of functional information available for Drosophila melanogaster to further investigate the possibility of additional independent domestications of pogo-like transposases into host CENP-B related proteins. Our results showed that CENP-B related genes are not restricted to holocentric insects. Furthermore, we showed that at least three independent domestications of pogo-like transposases have occurred in metazoans. Our results highlight the importance of transposable elements as raw material for the recurrent evolution of important cellular functions.
A Universal Self-Stabilizing Mutual Exclusion Algorithm

A distributed system consists of a set of processes and a set of communication links. A distributed system is said to be self-stabilizing if it converges to a correct system state from arbitrary initial system states. A self-stabilizing system is considered to be a fault tolerant system , since it tolerates any kind and any finite number of transient failures. The leader election and mutual exclusion problems are fundamental problems in distributed systems, and they have been investigated extensibly. Study on self-stabilizing leader election and mutual exclusion problems have been focused on the space complexity of processes and convergence time. In this paper, we investigate a class of networks on which the leader election and mutual exclusion problems can be solved. We show graph theoretical characterization of networks on which these problems assuming central and distributed daemons for execution scheduling model and registers for communication model.
Outcomes of Trabeculectomy with 5-Fluorouracil at a Nigerian Tertiary Hospital

Purpose To report the outcomes of trabeculectomy with adjunctive 5-Fluorouracil (5- FU) at a Nigerian tertiary hospital. Methods In this prospective study, all patients with glaucoma undergoing trabeculectomy with 5-FU at the University College Hospital, Ibadan, Nigeria, from June 2009 to May2010 were enrolled. Each patient had a complete ophthalmic evaluation. Intraocular pressure (IOP), visual acuity (VA) and complications post-trabeculectomy were assessed at one year. Success of the procedure was deﬁned as complete when no additional medications were required to achieve an IOP of ≤18mmHg, or qualiﬁed when additional medications were required to achieve the same goal. Results A total of 47 eyes of 31 patients with mean age of 48.9±19.6 (range 14-77; median 52) years including 21 (67.7%) male subjects underwent trabeculectomy with 5-FU. Mean presenting IOP was 31.8±12.2 mmHg. Mean deviation (MD) on Humphrey visual fields was -15.9±9.7dB with the majority of the patients (18 subjects 58.1%) presenting with advanced glaucoma based on MD worse than -12dB and severe glaucomatous optic neuropathy (cup to disc ratio of 0.9-1.0). At 1 year postoperatively, 95.1% achieved qualified success while 83% had complete success. Conclusion This prospective study adds to the existing knowledge that trabeculectomy with 5-FU is effective at controlling IOP in Nigerian patients.
Atypical transcription of microRNA gene fragments

MicroRNAs (miRNAs) are short (∼22 nt) RNAs that impact gene expression by sequence-specific interactions with messenger RNA or promoter sequences of genomic DNA. Ectopic expression of miRNAs can be accomplished by placing fragments of the corresponding miRNA precursor under the control of RNA polymerase II or III (RNAP II/III). Here, we report that, in the absence of exogenous promoters, DNA fragments incorporating miRNA precursors can be delivered directly into a variety of human cells and give rise to the corresponding mature miRNA. Notably, the transcription of these miRNA DNA fragments appears resistant to conventional inhibitors of RNAP I/II/III activity. Taken together, our findings suggest the existence of a previously unrecognized atypical transcription program for miRNA precursor sequences.
Echocardiographic Wall Motion Abnormalities in Hypertensive Patients With Electrocardiographic Left Ventricular Hypertrophy: The LIFE Study

Abstract—There is limited information on correlates of left ventricular wall motion (WM) abnormalities in ambulatory patients with hypertension and ECG left ventricular hypertrophy by Cornell voltage-duration product and/or Sokolow-Lyon voltage criteria. Therefore, we assessed the prevalence and the correlates of echocardiographic global and segmental left ventricular WM abnormalities in 942 hypertensive patients with hypertrophy enrolled in the Losartan Intervention For End-point reduction in hypertension (LIFE) echo substudy. Patients were separated into groups of those with normal WM or those with segmental or global WM abnormalities. Segmental and global WM abnormalities were mostly of mild degree and were detected in 7% and 6% of the study sample. Compared with subjects with normal motion, those with WM abnormalities were mostly men and had higher prevalences of self-reported coronary heart disease, ECG signs of myocardial infarction, ST-strain pattern, and higher Cornell voltage-duration product, echo-left ventricular mass, and albuminuria, but lower total and high-density lipoprotein cholesterol. Blood pressure was similar among groups. No significant differences were found between patients with global or segmental WM abnormalities. Only half of patients with WM abnormalities had a history or ECG signs of coronary heart disease. Independent correlates of WM abnormalities were higher albuminuria and Cornell voltage-duration product, male gender, and echo-left ventricular hypertrophy, but lower cholesterol. In a subanalysis restricted to patients with WM abnormalities, those with evident cardiovascular disease had a higher prevalence of ST-strain pattern than those with subclinical WM abnormalities, but other clinical, ECG, or echocardiographic parameters were indistinguishable between the 2 groups. Thus, in hypertensives with ECG left ventricular hypertrophy, WM abnormalities, mostly of mild degree, occurred in one eighth of the patients and were associated with male gender, left ventricular hypertrophy, and albuminuria. No significant differences were found between patients with global or segmental wall motion abnormalities.
Genes in S and T Subgenomes Are Responsible for Hybrid Lethality in Interspecific Hybrids between Nicotiana tabacum and Nicotiana occidentalis

Background Many species of Nicotiana section Suaveolentes produce inviable F1 hybrids after crossing with Nicotiana tabacum (genome constitution SSTT), a phenomenon that is often called hybrid lethality. Through crosses with monosomic lines of N. tabacum lacking a Q chromosome, we previously determined that hybrid lethality is caused by interaction between gene(s) on the Q chromosome belonging to the S subgenome of N. tabacum and gene(s) in Suaveolentes species. Here, we examined if hybrid seedlings from the cross N. occidentalis (section Suaveolentes)×N. tabacum are inviable despite a lack of the Q chromosome. Methodology/Principal Findings Hybrid lethality in the cross of N. occidentalis×N. tabacum was characterized by shoots with fading color. This symptom differed from what has been previously observed in lethal crosses between many species in section Suaveolentes and N. tabacum. In crosses of monosomic N. tabacum plants lacking the Q chromosome with N. occidentalis, hybrid lethality was observed in hybrid seedlings either lacking or possessing the Q chromosome. N. occidentalis was then crossed with two progenitors of N. tabacum, N. sylvestris (SS) and N. tomentosiformis (TT), to reveal which subgenome of N. tabacum contains gene(s) responsible for hybrid lethality. Hybrid seedlings from the crosses N. occidentalis×N. tomentosiformis and N. occidentalis×N. sylvestris were inviable. Conclusions/Significance Although the specific symptoms of hybrid lethality in the cross N. occidentalis×N. tabacum were similar to those appearing in hybrids from the cross N. occidentalis×N. tomentosiformis, genes in both the S and T subgenomes of N. tabacum appear responsible for hybrid lethality in crosses with N. occidentalis.
Intellectual characteristics of Prader-Willi syndrome: comparison of genetic subtypes.

Advances in genetics have led to an increased understanding of the role of the genotype on behavioural functioning. The purpose of the present study was to examine differences in intellectual functioning in individuals with Prader-Willi syndrome (PWS) with a paternal 15q11-q13 deletion versus maternal uniparental disomy (UPD) of chromosome 15. Measures of intelligence and academic achievement were administered to 38 individuals with PWS (24 with deletion and 14 with UPD). The subjects with UPD had significantly higher verbal IQ scores than those with deletion (P< 0.01). The magnitude of the difference in verbal IQ was 9.1 points (69.9 versus 60.8 for UPD and deletion PWS subjects, respectively). Only 17% of subjects with the 15q11-q13 deletion had a verbal IQ > or = 70, while 50% of those with UPD had a verbal IQ > or = 70. Performance IQ scores did not differ between the two PWS genetic subtype groups. This is the first report to document the difference between verbal and performance IQ score patterns among subjects with PWS of the deletion versus the UPD subtype.
Texture refinement framework for improved video coding

H.264/AVC standard offers an efficient way of reducing the noticeable artefacts of former video coding schemes, but it can be perfectible for the coding of detailed texture areas. This paper presents a conceptual coding framework, utilizing visual perception redundancy, which aims at improving both bit-rate and quality on textured areas. The approach is generic and can be integrated into usual coding scheme. The proposed scheme is divided into three steps: a first algorithm analyses texture regions, with an eye to build a dictionary of the most representative texture sub-regions (RTS). The encoder preserves then them at a higher quality than the rest of the picture, in order to enable a refinement algorithm to finally spread the preserved information over textured areas. In this paper, we present a first solution to validate the framework, detailing then the encoder side in order to define a simple method for dictionary building. The proposed H.264/AVC compliant scheme creates a dictionary of macroblocks
Ovarian Carcinoma Subtypes Are Different Diseases: Implications for Biomarker Studies

Background Although it has long been appreciated that ovarian carcinoma subtypes (serous, clear cell, endometrioid, and mucinous) are associated with different natural histories, most ovarian carcinoma biomarker studies and current treatment protocols for women with this disease are not subtype specific. With the emergence of high-throughput molecular techniques, distinct pathogenetic pathways have been identified in these subtypes. We examined variation in biomarker expression rates between subtypes, and how this influences correlations between biomarker expression and stage at diagnosis or prognosis. Methods and Findings In this retrospective study we assessed the protein expression of 21 candidate tissue-based biomarkers (CA125, CRABP-II, EpCam, ER, F-Spondin, HE4, IGF2, K-Cadherin, Ki-67, KISS1, Matriptase, Mesothelin, MIF, MMP7, p21, p53, PAX8, PR, SLPI, TROP2, WT1) in a population-based cohort of 500 ovarian carcinomas that was collected over the period from 1984 to 2000. The expression of 20 of the 21 biomarkers differs significantly between subtypes, but does not vary across stage within each subtype. Survival analyses show that nine of the 21 biomarkers are prognostic indicators in the entire cohort but when analyzed by subtype only three remain prognostic indicators in the high-grade serous and none in the clear cell subtype. For example, tumor proliferation, as assessed by Ki-67 staining, varies markedly between different subtypes and is an unfavourable prognostic marker in the entire cohort (risk ratio [RR] 1.7, 95% confidence interval [CI] 1.2%–2.4%) but is not of prognostic significance within any subtype. Prognostic associations can even show an inverse correlation within the entire cohort, when compared to a specific subtype. For example, WT1 is more frequently expressed in high-grade serous carcinomas, an aggressive subtype, and is an unfavourable prognostic marker within the entire cohort of ovarian carcinomas (RR 1.7, 95% CI 1.2%–2.3%), but is a favourable prognostic marker within the high-grade serous subtype (RR 0.5, 95% CI 0.3%–0.8%). Conclusions The association of biomarker expression with survival varies substantially between subtypes, and can easily be overlooked in whole cohort analyses. To avoid this effect, each subtype within a cohort should be analyzed discretely. Ovarian carcinoma subtypes are different diseases, and these differences should be reflected in clinical research study design and ultimately in the management of ovarian carcinoma.
SLR-Tool: A Tool for Performing Systematic Literature Reviews

: Systematic literature reviews (SLRs) have been gaining a significant amount of attention from Software Engineering researchers since 2004. SLRs are considered to be a new research methodology in Software Engineering, which allow evidence to be gathered with regard to the usefulness or effectiveness of the technology proposed in Software Engineering for the development and maintenance of software products. This is demonstrated by the growing number of publications related to SLRs that have appeared in recent years. While some tools exist that can support some or all of the activities of the SLR processes defined in (Kitchenham & Charters, 2007), these are not free. The objective of this paper is to present the SLR-Tool, which is a free tool and is available on the following website: http://alarcosj.esi. uclm.es/SLRTool/, to be used by researchers from any discipline, and not only Software Engineering. SLR-Tool not only supports the process of performing SLRs proposed in (Kitchenham & Charters, 2007), but also provides additional functionalities such as: refining searches within the documents by applying text mining techniques; defining a classification schema in order to facilitate data synthesis; exporting the results obtained to the format of tables and charts; and exporting the references from the primary studies to the formats used in bibliographic packages such as EndNote, BibTeX or Ris. This tool has, to date, been used by members of the Alarcos Research Group and PhD students, and their perception of it is that it is both highly necessary and useful. Our purpose now is to circulate the use of SLR-Tool throughout the entire research community in order to obtain feedback from other users.
A geometrical-based trinocular vision system for edges reconstruction

We present a trinocular stereo vision technique that can be used to build a fast, robust description of indoor objects. The proposed technique utilizes the geometrical constraints of the trinocular vision system and considers the uncertainty of image measurements. The technique has been successfully applied to several indoor scenes. The reliability and speed of the proposed system make it particularly suitable for real-time applications such as robot navigation.
Electrospun polymer nanofibers: Mechanical and thermodynamic perspectives

This article reviews and discusses some open problems concerning polymer materials of reduced sizes and dimensions. Such objects exhibit exceptional physical properties when compared with their macroscopic counterparts. More specifically, abrupt increases in polymer nanofiber elastic modulus have been observed when diameters drop below a certain value. In addition, temperature dependence of elastic modulus is highly influenced by fiber diameter. Mechanical (macroscopic) analyses have failed to provide satisfactory explanations for the mechanisms ruling such features, calling for detailed microscopic examination of the systems in question. A hypothesis bridging the current knowledge gaps is presented. The key element of this hypothesis is based on confinement of the supermolecular microstructure of polymer nanofibers and its dominant role in the deformation process. This suggestion challenges the commonly held view suggesting that surface effects are the most significant parameters impacting mechanical and thermodynamic nanofiber behaviors. The review will focus on the mechanical and thermodynamic properties of electrospun polymer nanofibers, selected as representatives of nanoscale polymer objects. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Evaluation of AZD1446 as a Therapeutic in DYT1 Dystonia

DYT1 dystonia is an early-onset, hyperkinetic movement disorder caused by a deletion in the gene TOR1A, which encodes the protein torsinA. Several lines of evidence show that in animal models of DTY1 dystonia, there is impaired basal dopamine (DA) release and enhanced acetylcholine tone. Clinically, anticholinergic drugs are the most effective pharmacological treatment for DYT1 dystonia, but the currently used agents are non-selective muscarinic antagonists and associated with side effects. We used a DYT1 ∆GAG knock-in mouse model (DYT1 KI) to investigate whether nicotine and/or a non-desensitizing nicotinic agonist, AZD1446, would increase DA output in DYT1 dystonia. Using in vivo microdialysis, we found that DYT1 KI mice showed significantly increased DA output and greater sensitivity to nicotine compared to wild type (WT) littermate controls. In contrast, neither systemic injection (0.25–0.75 mg/kg) or intrastriatal infusion (30 μM–1 mM) of AZD1446 had a significant effect on DA efflux in WT or DYT1 KI mice. In vitro, we found that AZD1446 had no effect on the membrane properties of striatal spiny projection neurons (SPNs) and did not alter the spontaneous firing of ChI interneurons in either WT or DYT1 KI mice. We did observe that the firing frequency of dopaminergic neurons was significantly increased by AZD1446 (10 μM), an effect blocked by dihydro-beta-erythroidine (DHβE 3 μM), but the effect was similar in WT and DYT1 KI mice. Our results support the view that DYT1 models are associated with abnormal striatal cholinergic transmission, and that the DYT1 KI animals have enhanced sensitivity to nicotine. We found little effect of AZD1446 in this model, suggesting that other approaches to nicotinic modulation should be explored.