Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Analysis Arabidopsis FHY 3 / FAR 1 Gene Family and Distinct Roles of Its Members in Light Control of Arabidopsis Development 1

FHY3 (far-red elongated hypocotyls 3) and FAR1 (far-red-impaired response) are two homologous proteins essential for phytochrome A controlled far-red responses in Arabidopsis (Arabidopsis thaliana). There are 12 additional FHY3/FAR1-related genes in the Arabidopsis genome. The predicted sizes of this family of proteins range from 531 amino acids to 851 amino acids, and they share 12.0% to 82.4% amino acid identities over their entire lengths. In addition, most FRS proteins contain one to three coiled-coil domains and one or two putative nuclear localization signals. Semiquantitative reverse transcriptionpolymerase chain reaction analyses revealed that all FRS genes except FRS10 are expressed in all tissues examined, including rosette leaves, cauline leaves, inflorescence stems, flowers, and siliques. Analyses of gene specific promoter::GUS fusion reporter gene expression revealed that all FRS genes except FRS1 are expressed in hypocotyls, and their expression in hypocotyl is induced by far-red light treatment. Transient expression of green fluorescent protein tagged FRS fusion proteins in onion (Allium cepa) epidermal cells revealed that all FRS proteins are targeted into the nucleus. T-DNA knockout frs6 and frs8mutants flowered early under both long-day and short-day conditions (with much more drastic effects under short-day conditions), suggesting that FRS6 and FRS8 regulate flowering time. In addition, FRS9 RNAi transgenic plants showed a specific hypersensitivity to red light inhibition of hypocotyl elongation and light-regulated gene expression, indicating that FRS9 is a specific negative regulator of phyB signaling mediating seedling deetiolation. In summary, our results support the notion that FRS family members play distinct roles in light control of Arabidopsis development, most likely by regulating nuclear gene expression.
Surface reconstruction of noisy and defective data sets

We present a novel surface reconstruction algorithm that can recover high-quality surfaces from noisy and defective data sets without any normal or orientation information. A set of new techniques is introduced to afford extra noise tolerability, robust orientation alignment, reliable outlier removal, and satisfactory feature recovery. In our algorithm, sample points are first organized by an octree. The points are then clustered into a set of monolithically singly-oriented groups. The inside/outside orientation of each group is determined through a robust voting algorithm. We locally fit an implicit quadric surface in each octree cell. The locally fitted implicit surfaces are then blended to produce a signed distance field using the modified Shepard's method. We develop sophisticated iterative fitting algorithms to afford improved noise tolerance both in topology recognition and geometry accuracy. Furthermore, this iterative fitting algorithm, coupled with a local model selection scheme, provides a reliable sharp feature recovery mechanism even in the presence of bad input.
A Novel Interaction between Procaspase 8 and SPARC Enhances Apoptosis and Potentiates Chemotherapy Sensitivity in Colorectal Cancers*

Chemotherapy resistance accounts for the high mortality rates in patients with advanced cancers. We previously used a genomics approach to determine novel genes associated with this phenomenon and identified secreted protein acidic and rich in cysteine (SPARC) as a chemosensitizer capable of reversing therapy resistance in colorectal cancer cells by enhancing apoptosis in vitro and tumor regression in vivo. Here, we examined the mechanisms by which SPARC enhances apoptosis in the presence of chemotherapy. We show that SPARC potentiates apoptosis by augmenting the signaling cascade in a caspase-8-dependent manner, because apoptosis can be abolished by caspase 8 small interfering RNA in the presence of SPARC. This occurs independently of death receptor activation and leads to downstream involvement of Bid and subsequent apoptosis. Interestingly, this results from an interaction between SPARC and the N terminus of the procaspase-8 DED-containing domain. These exciting findings provide an initial map of the apoptosis signaling events mediated by SPARC and how this can ultimately result in the reversal of chemotherapy resistance and enhanced tumor regression. This signaling cascade can be exploited therapeutically and may have potential clinical implications for patients with advanced and therapy-refractory cancers.
Generalization Error Bounds for Collaborative Prediction with Low-Rank Matrices

We prove generalization error bounds for predicting entries in a partially observed matrix by fitting the observed entries with a low-rank matrix. In justifying the analysis approach we take to obtain the bounds, we present an example of a class of functions of finite pseudodimension such that the sums of functions from this class have unbounded pseudodimension.
Modeling Uncertainty for a Vision System Applied to Vibration Measurements

In this paper, a new analytical model is proposed to describe the behavior of uncertainty for a generic vision-based measurement system applied to mechanical vibration measurement. In particular, this paper proposes a novel way to evaluate the effects of motion blur. The theoretical framework presented here takes into account the camera acquisition parameters, the dynamics of the measurand (in terms of instantaneous speed), and the image scaling factor to develop a physical model of uncertainty when measuring a mainly monomodal vibration. Uncertainty is evaluated starting from the normalized discrepancy between a measured position and the actual one. The analytical model proposed here has been validated extensively with the help of a test stand that can generate biaxial monomodal vibrations. The motion of a target mounted on the test stand has been simultaneously monitored by a stereo vision rig and a set of triangulation lasers. Model validation has been carried out using two measurement techniques: stereo vision blob analysis and digital image correlation. The experimental results show that the proposed model is able to represent the behavior of uncertainty for both the techniques. After the model has been validated, it is shown how it is possible to exploit it to estimate the uncertainty of a vision rig starting from the nominal characteristics of both the vision system and the target. This can be a tool to facilitate the design of vision-based measurement systems.
Thermochronological Evidence of Early Orogenesis, Eastern Pyrenees, France

In collisional orogens, distinguishing the thermal signature of early orogenesis from the preceding rift or from subsequent thermal events is a major challenge. We present an integrated geological and low‐temperature thermochronology study of the Paleozoic Agly‐Salvezines crustal block in the retrowedge of the eastern Pyrenees (France). The northern Pyrenees preserves one of the best geological records of a rift‐to‐collision transition. The Agly‐Salvezines block represents the inverted distal European margin of an Aptian–Cenomanian rift system. Seventeen samples were collected throughout the external orogenic massif and analyzed for low‐temperature thermochronology: zircon (U‐Th)/He dating documents the cooling history of the massif during the initiation and early phase of Pyrenean convergence, while apatite (U‐Th)/He dating completes the record of plate collision. Using inverse and forward modeling of new low‐temperature thermochronology data, we show that the Pyrenean retrowedge records two clear phases of orogenic cooling, Late Campanian–Maastrichtian and Ypresian–Bartonian, which we relate to early inversion of the distal rifted margin and main collision, respectively. An earlier, late Aptian–Turonian cooling history is detected, possibly related to rifting and/or postrift. No cooling is evidenced during the Paleocene during which tectonic quiescence is recorded in the adjacent Aquitaine retroforeland basin. Using our low‐temperature thermochronology data and geological constraints, we propose a crustal‐scale sequentially restored model for the tectonic and thermal transition from extension to peak orogenesis in the eastern Pyrenees, which suggests that both thrusting and underplating processes contributed to early inversion of the Aptian–Cenomanian rift system.
Baseline Requirements and Architecture for Cloud Computing Services

Government initiatives such as the “Cloud First” policy are bringing the cloud computing services into Federal Agencies. Further, many of the sectors in the Critical Infrastructure of the nation already use cloud computing. Although cloud computing services are slowly coming to age, many issues remain. This paper therefore takes a closer look at the cloud computing services. First it establishes a baseline by specifying high level requirements for cloud computing services. Next it improves upon the current architecture for the cloud computing services by adding new modules to the current architecture. The new modules are gleaned from an analysis of the telecommunications cloud and security in distributed systems. The new modules include a management and control network, a set of trust domains, and a set of proxies. The improved architecture is more ready for primetime use and supports a richer operational model.
Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets

Streptomycetes produce a wealth of natural products, including over half of all known antibiotics. It was previously demonstrated that N-acetylglucosamine and secondary metabolism are closely entwined in streptomycetes. Here we show that DNA recognition by the N-acetylglucosamine-responsive regulator DasR is growth-phase dependent, and that DasR can bind to sites in the S. coelicolor genome that have no obvious resemblance to previously identified DasR-responsive elements. Thus, the regulon of DasR extends well beyond what was previously predicted and includes a large number of genes with functions far removed from N-acetylglucosamine metabolism, such as genes for small RNAs and DNA transposases. Conversely, the DasR regulon during vegetative growth largely correlates to the presence of canonical DasR-responsive elements. The changes in DasR binding in vivo following N-acetylglucosamine induction were studied in detail and a possible molecular mechanism by which the influence of DasR is extended is discussed. Discussion of DasR binding was further informed by a parallel transcriptome analysis of the respective cultures. Evidence is provided that DasR binds directly to the promoters of all genes encoding pathway-specific regulators of antibiotic production in S. coelicolor, thereby providing an exquisitely simple link between nutritional control and secondary metabolism.
Simplex and Diamond Hierarchies: Models and Applications

Hierarchical spatial decompositions are a basic modelling tool in a variety of application domains. Several papers on this subject deal with hierarchical simplicial decompositions generated through regular simplex bisection. Such decompositions, originally developed for finite elements, are extensively used as the basis for multi‐resolution models of scalar fields, such as terrains, and static or time‐varying volume data. They have also been used as an alternative to quadtrees and octrees as spatial access structures. The primary distinction among all such approaches is whether they treat the simplex or clusters of simplices, called diamonds, as the modelling primitive. This leads to two classes of data structures and to different query approaches. We present the hierarchical models in a dimension‐independent manner, and organize the description of the various applications, primarily interactive terrain rendering and isosurface extraction, according to the dimension of the domain.
Cyclic association rules

We study the problem of discovering association rules that display regular cyclic variation over time. For example, if we compute association rules over monthly sales data, we may observe seasonal variation where certain rules are true at approximately the same month each year. Similarly, association rules can also display regular hourly, daily, weekly, etc., variation that is cyclical in nature. We demonstrate that existing methods cannot be naively extended to solve this problem of cyclic association rules. We then present two new algorithms for discovering such rules. The first one, which we call the sequential algorithm, treats association rules and cycles more or less independently. By studying the interaction between association rules and time, we devise a new technique called cycle pruning, which reduces the amount of time needed to find cyclic association rules. The second algorithm, which we call the interleaved algorithm, uses cycle pruning and other optimization techniques for discovering cyclic association rules. We demonstrate the effectiveness of the interleaved algorithm through a series of experiments. These experiments show that the interleaved algorithm can yield significant performance benefits when compared to the sequential algorithm. Performance improvements range from 5% to several hundred percent.
Plasma vitamin D metabolites and risk of colorectal cancer in women.

OBJECTIVE Experimental evidence suggests that 1,25-dihydroxyvitamin D and its precursor, 25-hydroxyvitamin D [25(OH)D], may aid in the prevention of colorectal cancer. We therefore examined risk in relation to plasma concentrations of these vitamin D metabolites. METHODS In a nested case-control study among women in the Nurses' Health Study, we identified 193 colorectal cancer cases, ages 46 to 78 years, diagnosed up to 11 years after blood collection. Two controls were matched per case on year of birth and month of blood draw. Odds ratios (OR) for risk of colorectal cancer were calculated using conditional logistic regression adjusted for body mass index, physical activity, smoking, family history, use of hormone replacement therapy, aspirin use, and dietary intakes. RESULTS We found a significant inverse linear association between plasma 25(OH)D and risk of colorectal cancer (P = 0.02). Among women in the highest quintile, the OR (95% confidence interval) was 0.53 (0.27-1.04). This inverse association remained strong when limited to women > or =60 years at blood collection (P = 0.006) but was not apparent among the younger women (P = 0.70). Benefit from higher 25(OH)D concentrations was observed for cancers at the distal colon and rectum (P = 0.02) but was not evident for those at the proximal colon (P = 0.81). In contrast to 25(OH)D, we did not observe an association between 1,25-dihydroxyvitamin D and colorectal cancer, although risk was elevated among the women in the highest quintile if they were also in the lower half of the 25(OH)D distribution (OR, 2.52; 95% confidence interval, 1.04-6.11). CONCLUSION From these results and supporting evidence from previous studies, we conclude that higher plasma levels of 25(OH)D are associated with a lower risk of colorectal cancer in older women, particularly for cancers at the distal colon and rectum.
Stromal architecture and periductal decorin are potential prognostic markers for ipsilateral locoregional recurrence in ductal carcinoma in situ of the breast

The incidence of ductal carcinoma in situ (DCIS) has increased since the introduction of screening mammography. Recurrence prediction is still not accurate, and could be improved by identifying additional prognostic markers. Periductal stroma actively participates in early breast cancer progression. Therefore, the aim of this study was to explore the prognostic potential of stromal characteristics in DCIS.
Direct Gradient-Based Reinforcement Learning: I. Gradient Estimation Algorithms

Despite their many empirical successes, approximate value -function based approaches to reinforcement learning suffer from a paucity of theoretical guarantees on the performance of the policy generated by the value-func tio . In this paper we pursue an alternative approach: first compute the gradien t of the average reward with respect to the parameters controlling the state transi tio in a Markov chain (be they parameters of a class of approximate value fun ctions generating a policy by some form of look-ahead, or parameters directly pa rameterizing a set of policies), and then use gradient ascent to generate a new set of parameters with increased average reward. We call this method “direct” rein forcement learning because we are not attempting to first find an accurate value-fun ction from which to generate a policy, we are instead adjusting the parameters t o directly improve the average reward. We present an algorithm for computing approximations to the gradient of the average reward from a single sample path of the underlying Ma rkov chain. We show that the accuracy of these approximations depends on th e relationship between the discount factor used by the algorithm and the mixin g time of the Markov chain, and that the error can be made arbitrarily small by set ting he discount factor suitably close to1. We extend this algorithm to the case of partially observabl e Markov decision processes controlled by stochastic polici es. We prove that both algorithms converge with probability 1.
3D tracking in unknown environments using on-line keypoint learning for mobile augmented reality

In this paper we present a natural feature tracking algorithm based on on-line boosting used for localizing a mobile computer. Mobile augmented reality requires highly accurate and fast six degrees of freedom tracking in order to provide registered graphical overlays to a mobile user. With advances in mobile computer hardware, vision-based tracking approaches have the potential to provide efficient solutions that are non-invasive in contrast to the currently dominating marker-based approaches. We propose to use a tracking approach which can use in an unknown environment, i.e. the target has not be known beforehand. The core of the tracker is an on-line learning algorithm, which updates the tracker as new data becomes available. This is suitable in many mobile augmented reality applications. We demonstrate the applicability of our approach on tasks where the target objects are not known beforehand, i.e. interactive planing.
The influence of temporal and spatial features on the performance of next-place prediction algorithms

Several algorithms to predict the next place visited by a user have been proposed in the literature. The accuracy of these algorithms -- measured as the ratio of the number of correct predictions and the number of all computed predictions -- is typically very high. In this paper, we show that this good performance is due to the high predictability intrinsic in human mobility. We also show that most algorithms fail to correctly predict transitions, i.e. situations in which users move between different places. To this end, we analyze the performance of 18 prediction algorithms focusing on their ability to predict transitions. We run our analysis on a data set of mobility traces of 37 users collected over a period of 1.5 years. Our results show that even algorithms achieving an overall high accuracy are unable to reliably predict the next location of the user if this is different from the current one. Building upon our analysis we then present a novel next-place prediction algorithm that can both achieve high overall accuracy and reliably predict transitions. Our approach combines all the 18 algorithms considered in our analysis and achieves its good performance at the cost of a higher computational and memory overhead.
The Extracellular Matrix and Cell Migration

As we know all too well, pancreatic cancer has a very poor prognosis largely due to its early tendency to invade, locally and distantly. Recently, scientists in the field have increasingly focused on the desmoplastic reaction, which is characteristic of most pancreatic cancers. This reaction is associated with proliferation of fibroblastic cells, sometimes outnumbering local tumor cells, and consists of abundant extracellular matrix (ECM) proteins. Importantly, the processes of invasion and metastasis take place within this tumor microenvironment. Stroma and tumor cells exchange signals to modify the local ECM, which subsequently stimulates cell migration and promotes proliferation and survival. Even though recognition of the significance of these microenvironment interactions exists, knowledge on the mechanisms of the interplay among pancreatic cells, myofibroblasts, and the ECM is lacking. Therefore, this ‘Pancreatology and the Web’ focuses on websites that provide information on the ECM and cell migration.
[Prevalence of dyspepsia and associated sociodemographic factors].

OBJECTIVE To assess prevalence of dyspepsia and distribution of dyspepsia and frequent dyspepsia in subgroups of adults (20 years and older) according to their demographic and socioeconomic characteristics. METHODS A cross-sectional population-based study was carried out comprising 3,934 subjects living in Pelotas, Southern Brazil, from October 1999 to January 2000. Data was collected through household interviews. Dyspepsia was defined as epigastric pain or discomfort associated or not with nausea in the previous year, according to Rome I and Rome II criteria. Frequent dyspepsia was defined as more than six dyspepsia episodes in the previous year and/or nausea, at least once a month. These outcomes were analyzed according to age, gender, skin color, educational level, per capita income and marital status. Data analysis was carried out through Pearson Chi-square test for categorical variables and linear trend test, when applicable. RESULTS The prevalence of dyspepsia was 44.4% and frequent dyspepsia, 27.4%. The prevalences of reflux-like, ulcer-like, dysmotility-like and unspecific dyspepsia subtypes were 19.4%, 6.3%, 13.9%, and 16.6%, respectively. The prevalences of these subtypes of frequent dyspepsia were 14.7%, 4.9%, 11.2% and 6.8%, respectively. Prevalences among women were 50% higher. Low-income young people seemed to be more affected by dyspeptic symptoms. The analysis according to Rome II criteria showed prevalences of 15.9% and 7.5% for dyspepsia and frequent dyspepsia, respectively. CONCLUSIONS Dyspepsia and frequent dyspepsia were prevalent problems in the studied population. Most people could be classified in more than one subgroup of dyspepsia.
Rapid Genetic Engineering of Human Cytomegalovirus by Using a Lambda Phage Linear Recombination System: Demonstration that pp28 (UL99) Is Essential for Production of Infectious Virus

ABSTRACT A highly efficient lambda phage recombination system previously utilized for studies of bacterial artificial chromosome (BAC)-maintained mouse chromosomal DNA was adapted for the study of the role of human cytomegalovirus (HCMV)-encoded pp28 (UL99) in virus replication. Incorporating a two-step mutagenesis strategy with blue/white selection in Escherichia coli containing a HCMV AD169 BAC, we have shown that we can rapidly introduce point mutations into the HCMV BAC using linear PCR fragments. All manipulations were carried out in bacteria, which greatly accelerated the introduction and analysis of mutations in the viral genome. Our results indicated that HCMV pp28 was essential for the production of infectious virus and that introduction of a single base change that resulted in loss of the myristylation site on pp28 was also associated with the lack of production of infectious virus. Although the block in the viral morphogenesis cannot be determined from these studies, the latter finding suggested that authentic intracellular localization of pp28, not only the expression of the protein, is required for virus assembly.