Miracle-dz/UniFAR-FTUs huggingface dataset:
Paramutation-Like Interaction of T-DNA Loci in Arabidopsis

In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best understood in plants. Here we describe an unexpected paramutation-like trans SALK T-DNA interaction in Arabidopsis. Unlike most of the previously described paramutations, which led to gene silencing, the trans SALK T-DNA interaction caused an increase in the transcript levels of the endogenous gene (COBRA) where the T-DNA was inserted. This increased COBRA expression state was stably inherited for several generations and led to the partial suppression of the cobra phenotype. DNA methylation was implicated in this trans SALK T-DNA interaction since mutation of the DNA methyltransferase 1 in the suppressed cobra caused a reversal of the suppression. In addition, null mutants of the DNA demethylase ROS1 caused a similar COBRA transcript increase in the cobra SALK T-DNA mutant as the trans T-DNA interaction. Our results provide a new example of a paramutation-like trans T-DNA interaction in Arabidopsis, and establish a convenient hypocotyl elongation assay to study this phenomenon. The results also alert to the possibility of unexpected endogenous transcript increase when two T-DNAs are combined in the same genetic background.
A proposal for variable selection in the Cox model

We propose a new method for variable selection and estimation in Cox's proportional hazards model. Our proposal minimizes the log partial likelihood subject to the sum of the absolute values of the parameters being bounded by a constant. Because of the nature of this constraint it tends to produce some coeecients that are exactly zero and hence gives interpretable models. The method is a variation of the \lasso" proposal of Tibshirani (1994), designed for the linear regression context. Simulations indicate that the lasso can be more accurate than stepwise selection in this setting.
Parents Knowledge about Early Childhood Sexual Education Based on Level of Education in Krasak Village, Pecangaan Sub-district, Jepara District

The high number of cases of child sexual abuse committed by the nearest children including the family shows the importance of early child sex education. Parents as educators in the family must have knowledge about sexual education for children. This study aims to find out whether there are differences in parental knowledge about early childhood sexual education based on education level in Krasak Village, Pecangaan Sub-district, Jepara Regency and whether parents graduate from Higher Education have knowledge about early child sexual education higher than parent who graduated High school and junior high school. This research type is quantitative with sample of parents who have children aged 4-6 years in Krasak Village, Pecangaan Sub-district, Jepara Regency. Data collection in this research is by using Parents Knowledge Scale of Early Childhood Sexual Education. Method of data analysis in this research is by using F test. The results of the study based on the calculation of statistical values ​​obtained F arithmetic> F table and Pvalue <0.05. Mean value in the group of parents who graduated from junior high school equal to 85.3, for the group of parents who graduated from high school 103.2, for the group of parents who graduated from college of 123.2. The result of research stated that there are differences of knowledge of parents who graduated from college based on education level and parents who graduated from higher education have higher knowledge than parents who graduated from high school.
Observability Analysis for AUV Range-only Localization and Mapping Measures of Unobservability and Experimental Results

Abstract We investigate the observability problem of the Simultaneous Localization and Mapping (SLAM) process of an Autonomous Underwater Vehicle (AUV) equipped with inertial sensors, a depth sensor, and an acoustic ranging device that provides relative range measurements to stationary beacons. For trimming trajectories (that is, when the motion of the AUV is in steady-state with constant linear and angular velocities expressed in the body-frame), we provide conditions under which it is possible to reconstruct the initial state of the resulting SLAM system (and in particular the position of the AUV). We show that the unobservable subspace UO restricted to the assumption that the position of one of the beacons or the initial position of the AUV is known, contains only the zero vector with exception of a distinct case where the UO is composed by a finite set of isolated points. Another problem that we also address in this paper is to understand (independently of the observer scheme) how difficult it is to accurately estimate the state of the system from the pair input/output measured signals. To this end, we compute explicitly the unobservability index and the estimation condition number that provide measures of the degree of unobservability. Simulation and experimental results with the Medusa robotic vehicle are presented and discussed.
Second-Order Method for Occlusion Relationships in Motion Layers

A new method is presented to recover the depth ordering of motion layers in a scene. We derive a measure for determining the occlusion relationship between two layers, by testing whether the support of one motion layer is moving with the predicted local velocity of another motion layer. This is used to construct a graph which represents the depth ordering of all layers. By cascading two rst-order motion models, a second-order model is deened which is sensitive to the motion of motion-deened support regions, which is sometimes called kinetic occlusion. Our algorithm makes few assumptions about the motion and layer models, and can use any motion layer model which provides global hypotheses in the form of velocity elds, and any local motion mechanism which provides the conditional probabilty of a velocity given a local image region.
Activation Transcription Factor-4 Induced by Fibroblast Growth Factor-2 Regulates Vascular Endothelial Growth Factor-A Transcription in Vascular Smooth Muscle Cells and Mediates Intimal Thickening in Rat Arteries Following Balloon Injury

Activation transcription factor (ATF)-4 is a member of the ATF/CREB family of basic leucine zipper transcription factors that regulates cellular responses to a variety of stresses. The role of ATF-4 in smooth muscle cells of the vessel wall is completely unknown. Here, we show that ATF-4 expression is induced in smooth muscle cells in response to injury, both in vitro using a model of mechanical injury and in the media of balloon-injured rat carotid arteries. We demonstrate that ATF-4 is activated by fibroblast growth factor (FGF)-2, an injury-induced mitogen, through the phosphatidylinositol 3-kinase pathway. Injury also activates vascular endothelial growth factor (VEGF)-A, whose expression is stimulated by ATF-4 overexpression and exposure to FGF-2. FGF-2 induces ATF-4 binding to a recognition element located in the VEGF-A gene at +1767 bp and luciferase reporter gene expression dependent on this site. Moreover, ATF-4 knockdown with small interfering RNA or ATF-4 deficiency ameliorates FGF-2–inducible VEGF-A expression. Intraluminal delivery of ATF-4 small interfering RNA in rat carotid arteries blocks balloon injury–inducible ATF-4 and VEGF-A expression after 4 hours and intimal thickening after 14 days. These findings reveal, for the first time, the induction of ATF-4 by both vascular injury and FGF-2. ATF-4 serves as a conduit for the inducible expression of 1 growth factor by another during the process of intimal thickening.
Depression is associated with lower American National Adult Reading Test scores among rural dwellers aged between 50 and 64 years in Texas: A Project FRONTIER Study

Background: Previous studies have shown that depression is associated with cognitive impairment. However, others have shown that there is no significant difference in the scores of the National Adult Reading Test (NART), a screening test for intellectual functioning and general level of education, between those with vs. without depression. This study sought to examine whether depression is associated with the American version of NART (AMNART) in a rural cohort of West Texas. Methods: Participants with IQ and AMNART tests were selected from Project FRONTIER, an ongoing epidemiology study of rural residents in four West Texas counties. Results: AMNART scores were significantly lower in participants with depression (23.3±9.2) vs. those without depression (25.9±9.9) (p<0.05). Analysis by age group showed that AMNART scores were significantly lower in those with depression (22.0±10.1) compared with those without depression (26.2±10.2) in the age group 50 to 64 years (P=0.0322). Although AMNART scores were lower in participants with depression than those without depression in the age groups 40 to 49 years (25.0±8.6 vs. 26.2±10.2) and 65 years or older (23.6±8.2 vs. 25.6±9.5), they were not statistically significantly different. Conclusions: Depression is associated with lower AMNART scores in rural residents aged between 50 and 64 years in West Texas.
Integration of Space Syntax into GIS: New Perspectives for Urban Morphology

The research field of transportation demand forecasting has started to focus on disaggregate travel behavior and micro‐simulation models. To create data infrastructure, disaggregate trip surveys are conducted and large numbers of observations are collected. To efficiently exploit these surveys, the transfer of the individual trip data to a GIS must start with the development of a solid conceptual data model that fully captures the semantic richness of the application domain and emphasizes its spatio‐temporal properties. This paper presents a data modeling process that is based on a combination of complex system theory and the object‐oriented paradigm and produced an object‐oriented spatio‐temporal data model. Main domain entities are modeled as highly structured classes. They encapsulate a memory of their time bound connections and states. Observation data sets are sampled from the origin‐destination survey conducted in the Québec region in 1991. This survey incorporated street networks and activity places. The model was smoothly implemented into a proof‐of‐concept database prototype hosted by an object‐oriented GIS shell. The prototype offers a means to navigate through a nested hierarchy of objects, providing a description of an individual’s travel behavior over space and time. The objects have a solid conceptual basis and can meet the needs of scientific research such as hypothesis formulation, simulation, forecasting and induction.
Image compression using wavelet packet and singular value decomposition

Compression of digital images has been a topic of research for many years and a number of image compression standards have been created for different applications. The role of compression is to reduce bandwidth requirements for transmission and memory requirements for storage of all forms of data. The main objective is to study and implement the operations used in a lossy compression scheme to compress two-dimensional images. Basically, this scheme consists of three operations, which are the transform, quantization and entropy encoding operations. Wavelet Transform and Wavelet Packet Transform are efficient tools to represent the image. Wavelet Packet Transform is a generalization of Wavelet Transform which is more adaptive than the Wavelet Transform because it offers a rich library of bases from which the best one can be chosen for a certain class of images with a specified cost function. Wavelet Packet decomposition yields a redundant representation of the image. In this work, Singular Value Decomposition is used as a tool to select the best basis. After selecting the best tree, the coefficients of the best tree are quantized using dead zone quantization. To reduce the number of bits required to transmit the indexes of the codeword, a lossless Huffman algorithm was implemented as the final stage of the encoding process. To reconstruct the compressed image, the operations are reserved. The simulation result reveals that, the quantity of the image is good even though the compression ratio is increased due to reduction in Wavelet Packet sub-bands.
Secure communication over diverse transports: [short paper]

This paper describes BTP, a protocol that ensures the confidentiality, integrity, authenticity and forward secrecy of communication over diverse underlying transports, from low-latency, bidirectional transports like TCP to high-latency, unidirectional transports like DVDs sent through the mail. BTP is designed for use in censorship-resistant delay-tolerant overlays that operate over heterogeneous mixtures of underlying transports. By providing consistent security properties for a very wide range of transports, BTP simplifies the design and implementation of such overlays. Forward secrecy is achieved by establishing an initial shared secret between each pair of endpoint devices and using a one-way key derivation function to generate a series of temporary shared secrets from the initial shared secret. Once both devices have destroyed a given temporary secret, any keys derived from it cannot be re-derived if the devices are later compromised. BTP is designed to be compatible with traffic analysis prevention techniques such as traffic morphing: the protocol includes optional padding and uses no timeouts, handshakes or plaintext headers, with the goal of making it difficult to distinguish BTP from other protocols. If unlinkability between communicating devices is required, BTP can use anonymity systems such as Tor and Mixminion as underlying transports.
Avoiding bias from weak instruments in Mendelian randomization studies.

BACKGROUND Mendelian randomization is used to test and estimate the magnitude of a causal effect of a phenotype on an outcome by using genetic variants as instrumental variables (IVs). Estimates of association from IV analysis are biased in the direction of the confounded, observational association between phenotype and outcome. The magnitude of the bias depends on the F-statistic for the strength of relationship between IVs and phenotype. We seek to develop guidelines for the design and analysis of Mendelian randomization studies to minimize bias. METHODS IV analysis was performed on simulated and real data to investigate the effect on bias of size of study, number and choice of instruments and method of analysis. RESULTS Bias is shown to increase as the expected F-statistic decreases, and can be reduced by using parsimonious models of genetic association (i.e. not over-parameterized) and by adjusting for measured covariates. Using data from a single study, the causal estimate of a unit increase in log-transformed C-reactive protein on fibrinogen (μmol/l) is shown to increase from -0.005 (P = 0.99) to 0.792 (P = 0.00003) due to injudicious choice of instrument. Moreover, when the observed F-statistic is larger than expected in a particular study, the causal estimate is more biased towards the observational association and its standard error is smaller. This correlation between causal estimate and standard error introduces a second source of bias into meta-analysis of Mendelian randomization studies. Bias can be alleviated in meta-analyses by using individual level data and by pooling genetic effects across studies. CONCLUSIONS Weak instrument bias is of practical importance for the design and analysis of Mendelian randomization studies. Post hoc choice of instruments, genetic models or data based on measured F-statistics can exacerbate bias. In particular, the commonly cited rule of thumb that F > 10 avoids bias in IV analysis is misleading.
Aspect-Oriented Programming with AspectS

AspectS is an approach to general-purpose aspect-oriented programming in the Squeak/Smalltalk environment. Based on concepts of AspectJ it extends the Smalltalk metaobject protocol to accommodate the aspect modularity mechanism. In contrast to systems like AspectJ, weaving and unweaving in AspectS happens dynamically at runtime, on-demand, employing metaobject composition. Instead of introducing new language constructs, AspectS utilizes the expressiveness of Smalltalk itself as a pointcut language.
Representations of All Solutions of Boolean Programming Problems

It is well known that (reduced, ordered) binary decision diagrams (BDDs) can sometimes be compact representations of the full solution set of Boolean optimization problems. Recently they have been suggested to be useful as discrete relaxations in integer and constraint programming (Hoda, van Hoeve, and Hooker 2010). We show that for every independence system there exists a top-down (i.e., single-pass) construction rule for the BDD. Furthermore, for packing and covering problems on n variables whose bandwidth is bounded by O(logn), the maximum width of the BDD is bounded by n. Furthermore, we characterize minimal width of BDDs representing the set of all solutions to a stable set problem for various basic classes of graphs.
THE 6-MINUTE WALK TEST AND OTHER CLINICAL ENDPOINTS IN DUCHENNE MUSCULAR DYSTROPHY: RELIABILITY, CONCURRENT VALIDITY, AND MINIMAL CLINICALLY IMPORTANT DIFFERENCES FROM A MULTICENTER STUDY

Introduction: An international clinical trial enrolled 174 ambulatory males ≥5 years old with nonsense mutation Duchenne muscular dystrophy (nmDMD). Pretreatment data provide insight into reliability, concurrent validity, and minimal clinically important differences (MCIDs) of the 6‐minute walk test (6MWT) and other endpoints. Methods: Screening and baseline evaluations included the 6‐minute walk distance (6MWD), timed function tests (TFTs), quantitative strength by myometry, the PedsQL, heart rate–determined energy expenditure index, and other exploratory endpoints. Results: The 6MWT proved feasible and reliable in a multicenter context. Concurrent validity with other endpoints was excellent. The MCID for 6MWD was 28.5 and 31.7 meters based on 2 statistical distribution methods. Conclusions: The ratio of MCID to baseline mean is lower for 6MWD than for other endpoints. The 6MWD is an optimal primary endpoint for Duchenne muscular dystrophy (DMD) clinical trials that are focused therapeutically on preservation of ambulation and slowing of disease progression. Muscle Nerve 48: 357–368, 2013
BUSTER RESISTANT SUGARCANE SJ SNYMAN ' , NB LEIBBRANDT ' AND FC BOTHA 2 ' south

The aim of this paper is to describe the evaluation of engineered herbicide-resistance in transgenic sugarcane of Herbicide treatment of crops allows economic weed control. To be useful, herbicides must distinguish between crop plant variety NCo3 10 under field conditions. and weed, and this often limits usage. Engineering herbicide resistance into crop plants via genetic transformation techniques is a novel approach to age old problem. A gene construct which confers resistance to the herbicide BusterR (active ingredient glufosinate ammonium), was obtained for research purposes from AgrEvo, Germany. Using the technique of microprojectile bombardment for DNA transfer and embryogenic callus as the recipient material, herbicide resistance was engineered into sugarcane variety NCo310. Young transgenic cane plants grown in the glasshouse were asymptomatic when sprayed with 4 L/ha of the herbicide. Nontransformed NCo3 10 plants showed phytotoxic symptoms within days of being sprayed and plants died after three weeks. Further evaluation at a small scale field trial showed Production of transgenic sugarcane in vitro Sugarcane variety NCo3 10 was transformed by microprojectile bombardment of embryogenic callus (Snyman et al., 1996). The DNA vector used to transform callus contained the synthetic pat gene which confers resistance to the herbicide Buster (active ingredient: 200 g/L, glufosinate ammonium; AgrEvo, Germany). Plants from three independent bombardment events were analysed at the DNA level according to methods described by Gallo-Meagher and Irvine (1996). One of the plants was chosen for further evaluation in the field as it was resistant to 4 L k a herbicide when sprayed the transgenic plants to be resistant to a rate of 7 L/ha Buster in the glasshouse. after repeated applications on a plant crop and two ratoons.
Hybrid Nanotrimers for Dual T1 and T2-Weighted Magnetic Resonance Imaging

Development of multifunctional nanoparticle-based probes for dual T1- and T2-weighted magnetic resonance imaging (MRI) could allow us to image and diagnose the tumors or other abnormalities in an exceptionally accurate and reliable manner. In this study, by fusing distinct nanocrystals via solid-state interfaces, we built hybrid heteronanostructures to combine both T1 and T2- weighted contrast agents together for MRI with high accuracy and reliability. The resultant hybrid heterotrimers showed high stability in physiological conditions and could induce both simultaneous positive and negative contrast enhancements in MR images. Small animal positron emission tomography imaging study revealed that the hybrid heterostructures displayed favorable biodistribution and were suitable for in vivo imaging. Their potential as dual contrast agents for T1 and T2-weighted MRI was further demonstrated by in vitro and in vivo imaging and relaxivity measurements.
Adaptive Artifact Suppression in Ultrasound Image

The aim of this report is to present artifact suppression algorithms for reducing the reverberation artifacts in ultrasonic imaging. These reverberation patterns always occurred as signals among specular reflectors. In ultrasound applications, we need to reduce the artifacts but at the same time to preserve other useful information. Because of the periodic pattern of the artifacts, we will apply a 2D FFT in un-overlap blocks of the image to extract and remove the peaks which are corresponding to artifacts in the frequency domain. The 2D FFT can provide the information in one more dimension compared with the 1D FFT from which we could differentiate the real artifacts and some useful information, for example, the vessel boundary. Test results from several in vivo images show that this new technique can suppress artifact effectively and preserve useful information at the same time.
Distributed multirobot exploration maintaining a mobile network

We present a behaviour-based architecture for multirobot exploration and mapping. The architecture is designed to guide the exploration in a decentralized fashion constrained to maintain local short-range communication in a mobile ad-hoc network. Exploration with multiple robots has been extensively studied but communication constraints have been ignored. We focus on the integration of such constraints and develop a behaviour-based approach. The behaviours are designed to enhance global performance and are triggered based on local information. Robots are encouraged to move together forming a mobile network and sharing relevant information for the team. Up to this date there is no research addressing the effects of communication and sensor constraints on exploration and mapping in structured (office like) environments. Our experimental results show that the increment in time due to the introduction of communication constraints is reasonable and decreases as the size of the team increases.