Miracle-dz/UniFAR-FTUs huggingface dataset:
The Leukemia Inhibitory Factor Receptor Gene Is a Direct Target of RUNX1

Activation of cytokine signaling via the leukemia inhibitory factor receptor (LIFR) plays an integral role in hematopoiesis, osteogenesis, and placental development, along with mediating neurotrophic mechanisms. However, the regulatory control of the LIFR gene has remained largely unexplored. Here, we characterize the LIFR gene as a novel target of the RUNX1 transcription factor. The RUNX1 transcription factor is an essential regulator of hematopoiesis and is a frequent target of point mutations and chromosomal alterations in leukemia. RUNX1 regulates hematopoiesis through its control of genes important for hematopoietic cell growth, proliferation, and differentiation, including a number of cytokines and cytokine receptors. LIFR is regulated by two alternate promoters: a placental‐specific and a ubiquitously active general promoter. We show that both of these promoters are regulated by RUNX1. However, in myeloid cells LIFR expression is driven solely by the general LIFR promoter with our data indicating that the placental promoter is epigenetically silenced in these cells. While RUNX1 activates the LIFR general promoter, the oncogenic RUNX1‐ETO fusion protein generated by the t(8;21) translocation commonly associated with acute myeloid leukemia represses promoter activity. The data presented here establish LIFR as a transcriptional target of RUNX1 and suggest that disruption of RUNX1 activity in myeloid cells may result in altered LIFR signaling in these cells. J. Cell. Biochem. 117: 49–58, 2016. © 2015 Wiley Periodicals, Inc.
The Maastricht Convergence Criteria and Optimal Monetary Policy for the EMU Accession Countries

The EMU accession countries are obliged to fulfill the Maastricht convergence criteria prior to entering the EMU. What should be the optimal monetary policy satisfying these criteria? To answer this question, the paper proposes a DSGE model of a two-sector small open economy. First, I derive the micro founded loss function that represents the objective function of the optimal monetary policy not constrained to satisfy the criteria. I find that the optimal monetary policy should not only target inflation rates in the domestic sectors and aggregate output fluctuations but also domestic and international terms of trade. Second, I show how the loss function changes when the monetary policy is constrained to satisfy the Maastricht criteria. The loss function of such a constrained policy is characterized by additional elements penalizing fluctuations of the CPI inflation rate, the nominal interest rate and the nominal exchange rate around the new targets which are different from the steady state of the unconstrained optimal monetary policy. Under the chosen parameterization, the optimal monetary policy violates two criteria: concerning the CPI inflation rate and the nominal interest rate. The constrained optimal policy is characterized by a deflationary bias. This results in targeting the CPI inflation rate and the nominal interest rate that are 0.7% lower (in annual terms) than the CPI inflation rate and the nominal interest rate in the countries taken as a reference. Such a policy leads to additional welfare costs amounting to 30% of the optimal monetary policy loss.
Speech recognition with auxiliary information

State-of-the-art automatic speech recognition (ASR) systems are usually based on hidden Markov models (HMMs) that emit cepstral-based features which are assumed to be piecewise stationary. While not really robust to noise, these features are also known to be very sensitive to "auxiliary" information, such as pitch, energy, rate-of-speech (ROS), etc. Attempts so far to include such auxiliary information in state-of-the-art ASR systems have often been based on simply appending these auxiliary features to the standard acoustic feature vectors. In the present paper, we investigate different approaches to incorporating this auxiliary information using dynamic Bayesian networks (DBNs) or hybrid HMM/ANNs (HMMs with artificial neural networks). These approaches are motivated by the fact that the auxiliary information is not necessarily (directly) emitted by the HMM states but, rather, carries higher-level information (e.g., speaker characteristics) that is correlated with the standard features. As implicitly done for gender modeling elsewhere, this auxiliary information then appears as a conditional variable in the emission distributions and can be hidden (except in the case of some HMM/ANNs) as its estimates become too noisy. Based on recognition experiments carried out on the OGI Numbers database (free format numbers spoken over the telephone), we show that auxiliary information that conditions the distribution of the standard features can, in certain conditions, provide more robust recognition than using auxiliary information that is appended to the standard features; this is most evident in the case of energy as an auxiliary variable in noisy speech.
Endovascular repair of giant traumatic pseudo-aneurysm of the common carotid artery.

BACKGROUND Delayed presentation of carotid artery pseudoaneurysm following many years after self-inflicted penetrating injury of the neck is extremely rare. Open surgical carotid repair may involve sternotomy for proximal vascular control. Endovascular treatment is evolving as a less-invasive treatment option. METHODS We report a 55-year-old man with a history of paranoid schizophrenia who presented with a progressively enlarging left sided neck mass many years after attempted suicide. CT scan confirmed a 6 cm pseudoaneurysm arising from the common carotid artery. RESULTS Through an open retrograde puncture of the distal common carotid artery, the common carotid pseudoaneurysm was successfully repaired with a BARD fluency carotid stentgraft of 8 mm×80 mm (BARD, Tempe, AZ). The patient recovered well with no neurological deficits and was discharged on postoperative day 4. Dual antiplatelet agents of aspirin and clopidogrel were given for six months and then clopidogrel was administered lifelong. The neck mass decreased in size gradually and became non pulsatile upon follow-up. CONCLUSION Endovascular stenting of giant carotid pseudoaneurysm is an acceptable less invasive treatment option for giant carotid pseudoaneurysm. Long-term follow-up and a greater number of cases are mandatory to establish the safety of this strategy.
Designing the Market Game for a Trading Agent Competition

The authors discuss the design and operation of a trading agent competition, focusing on the game structure and some of the key technical issues in running and playing the game. They also describe the competition's genesis, its technical infrastructure, and its organization. The article by A. Greenwald and P. Stone (2001), describes the competition from a participant's perspective and describes the strategies of some of the top-placing agents. A visualization of the competition and a description of the preliminary and final rounds of the TAC are available in IC Online (http://computer.org/internet/tac.htm).
Filter Preferential Entailment for the Logic of Action in Almost Continuous Worlds

Mechanical systems, of the kinds which are of interest for qualitative reasoning, are characterized by a set of real-valued parameters, each of which is a piecewise continuous function of real-valued time. A temporal logic is introduced which allows the description of parameters, both in their continuous intervals and around their breakpoints, and which also allows the description of actions being performed in sequence or in parallel. If axioms are given which characterize physical laws, conditions and effects of actions, and observations or goals at specific points in time, one wishes to identify sets of actions ("plans") which account for the observations or obtain the goals. The paper proposes preference criteria which should determine the model set for such axioms. It is shown that conventional preferential entailment is not sufficient. A modified condition, filter preferential entailment is defined where preference conditions and axiom satisfaction conditions are interleaved.
Their Phagocytic Capacity Produce Nonclassical Retinoids To Enhance Macrophages Engulfing Apoptotic Cells

Christopher D. Gregory and Zsuzsa SzondyZsolt Sarang, Gergely Joos, Eva Garabuczi, Ralph Ruhl,http://www.jimmunol.org/content/192/12/5730doi: 10.4049/jimmunol.1400284May 2014;J Immunol€2014; 192:5730-5738; Prepublished online 21Referenceshttp://www.jimmunol.org/content/192/12/5730.full#ref-list-1This article cites 53 articles, 20 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai. org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis

Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway.
RBE of 10 kV X Rays Determined for the Human Mammary Epithelial Cell Line MCF-12A

Abstract Lehnert, A. , Dörr, W. , Lessmann, E. and Pawelke, J. RBE of 10 kV X Rays Determined for the Human Mammary Epithelial Cell Line MCF-12A. Radiat. Res. 169, 330–336 (2008). The dependence of relative biological effectiveness (RBE) on photon energy is a topic of extensive discussions. The increasing amount of in vitro data in the low-energy region indicates this to be a complex dependence that is influenced by the end point and cell line studied. In the present investigation, the RBE of 10 kV X rays (W anode) was determined relative to 200 kV X rays (W anode, 0.5 mm copper filter) for cell survival in the dose range 1–10 Gy and for induction of micronuclei in the range 0.5–3.6 Gy for MCF-12A human mammary epithelial cells. The RBE for cell survival was found to increase with decreasing dose, being 1.21 ± 0.03 at 10% survival. Considerably higher values were obtained for micronucleus induction, where the RBEM obtained from the ratio of the linear coefficients of the dose–effect curves was 2.6 ± 0.4 for the fraction of binucleated cells with micronuclei and 4.1 ± 1.0 for the number of micronuclei per binucleated cell. These values, together with our previous data, support a monotonic increase in RBE with decreasing photon energy down to the mean energy of 7.3 keV used in the present study.
BRDF Slices: Accurate Adaptive Anisotropic Appearance Acquisition

In this paper we introduce unique publicly available dense an isotropic BRDF data measurements. We use this dense data as a reference for performance evaluation of the proposed BRDF sparse angular sampling and interpolation approach. The method is based on sampling of BRDF subspaces at fixed elevations by means of several adaptively-represented, uniformly distributed, perpendicular slices. Although this proposed method requires only a sparse sampling of material, the interpolation provides a very accurate reconstruction, visually and computationally comparable to densely measured reference. Due to the simple slices measurement and method's robustness it allows for a highly accurate acquisition of BRDFs. This in comparison with standard uniform angular sampling, is considerably faster yet uses far less samples.
Combining Feature Norms and Text Data with Topic Models

Many psychological theories of semantic cognition assume that concepts are represented by features. The empirical procedures used to elicit features from humans rely on explicit human judgments which limit the scope of such representations. An alternative computational framework for semantic cognition that does not rely on explicit human judgment is based on the statistical analysis of large text collections. In the topic modeling approach, documents are represented as a mixture of learned topics where each topic is represented as a probability distribution over words. We propose feature-topic models, where each document is represented by a mixture of learned topics as well as predefined topics that are derived from feature norms. Results indicate that this model leads to systematic improvements in generalization tasks. We show that the learned topics in the model play in an important role in the generalization performance by including words that are not part of current feature norms.
The Rectal Cancer microRNAome – microRNA Expression in Rectal Cancer and Matched Normal Mucosa

Purpose: miRNAs play a prominent role in a variety of physiologic and pathologic biologic processes, including cancer. For rectal cancers, only limited data are available on miRNA expression profiles, whereas the underlying genomic and transcriptomic aberrations have been firmly established. We therefore, aimed to comprehensively map the miRNA expression patterns of this disease. Experimental Design: Tumor biopsies and corresponding matched mucosa samples were prospectively collected from 57 patients with locally advanced rectal cancers. Total RNA was extracted, and tumor and mucosa miRNA expression profiles were subsequently established for all patients. The expression of selected miRNAs was validated using semi-quantitative real-time PCR. Results: Forty-nine miRNAs were significantly differentially expressed (log2-fold difference >0.5 and P < 0.001) between rectal cancer and normal rectal mucosa. The predicted targets for these miRNAs were enriched for the following pathways: Wnt, TGF-beta, mTOR, insulin, mitogen-activated protein kinase, and ErbB signaling. Thirteen of these 49 miRNAs seem to be rectal cancer-specific, and have not been previously reported for colon cancers: miR-492, miR-542-5p, miR-584, miR-483-5p, miR-144, miR-2110, miR-652, miR-375, miR-147b, miR-148a, miR-190, miR-26a/b, and miR-338-3p. Of clinical impact, miR-135b expression correlated significantly with disease-free and cancer-specific survival in an independent multicenter cohort of 116 patients. Conclusion: This comprehensive analysis of the rectal cancer miRNAome uncovered novel miRNAs and pathways associated with rectal cancer. This information contributes to a detailed view of this disease. Moreover, the identification and validation of miR-135b may help to identify novel molecular targets and pathways for therapeutic exploitation. Clin Cancer Res; 18(18); 4919–30. ©2012 AACR.
Biogeographic histories and genetic diversity of western North American tree species: implications for climate change

Over the last two million years, the evolution of North American tree species, subspecies, and genetic varieties has taken place in a constantly changing landscape often dominated by extensive ice sheets and restricted temperate climate environments. Here, I approximately reconstruct post-glacial vegetation histories and glacial refugia of western North American trees using species distribution models to test biogeographic hypotheses regarding the existence of glacial refugia in Beringia, the evolution of subspecies in widespread conifers, the origin of Pacific Northwest inland rainforests, and levels of modern genetic diversity. The first two chapters have a methodological emphasis, where I select and test a variety of species distribution models for their accuracy and robustness. Validations against 3,571 pollen and fossil records from 835 study sites indicated fair accuracy for most techniques (AUCs around 0.75). Ecosystem-based modelling approaches outperformed in specificity statistics and robustness against extrapolations far beyond training data, suggesting that they are well suited to reconstruct historical biogeographies. Evaluations at the biome level indicated that species distribution models could approximately reconstruct biomes for the midto late-Holocene but became unreliable in the Late Pleistocene due to the emergence of no-analogue climates. However, the limitation applied primarily to non-forested biomes. Using a set of three robust species distribution modelling techniques, I investigate how modern genetic diversity and genetic structure was shaped by refugial history, using published estimates of allelic richness and expected heterozygosity for 473 populations of 22 tree species. Species with strong genetic differentiation into subspecies and varieties had widespread and large glacial refugia, while species with restricted refugia showed no differentiation and little genetic diversity. In a regression tree analysis, 66% of allelic richness could be explained by the total size of glacial refugia, while expected heterozygosity was best explained by the number of glacial refugia. A comparison of projected past and future habitats showed that future migration requirements were much faster than, but highly correlated with, past migration requirements across 24 tree species. Populations in certain localities may be at risk of maladaptation due to the inability of gene flow to keep pace with the migration of climate habitats.
Rad50 Is Dispensable for the Maintenance and Viability of Postmitotic Tissues

ABSTRACT The majority of spontaneous chromosome breakage occurs during the process of DNA replication. Homologous recombination is the primary mechanism of repair of such damage, which probably accounts for the fact that it is essential for genome integrity and viability in mammalian cells. The Mre11 complex plays diverse roles in the maintenance of genomic integrity, influencing homologous recombination, checkpoint activation, and telomere maintenance. The complex is essential for cellular viability, but given its myriad influences on genomic integrity, the mechanistic basis for the nonviability of Mre11 complex-deficient cells has not been defined. In this study we generated mice carrying a conditional allele of Rad50 and examined the effects of Rad50 deficiency in proliferative and nonproliferative settings. Depletion of Rad50 in cultured cells caused extensive DNA damage and death within 3 to 5 days of Rad50 deletion. This was not associated with gross telomere dysfunction, suggesting that the telomeric functions of the Mre11 complex are not required for viability. Rad50 was also dispensable for the viability of quiescent liver and postmitotic Purkinje cells of the cerebellum. These findings support the idea that the essential functions of the Mre11 complex are associated with DNA replication and further suggest that homologous recombination is not essential in nondividing cells.
Independent Factor Analysis

We introduce the independent factor analysis (IFA) method for recovering independent hidden sources from their observed mixtures. IFA generalizes and unifies ordinary factor analysis (FA), principal component analysis (PCA), and independent component analysis (ICA), and can handle not only square noiseless mixing but also the general case where the number of mixtures differs from the number of sources and the data are noisy. IFA is a two-step procedure. In the first step, the source densities, mixing matrix, and noise covariance are estimated from the observed data by maximum likelihood. For this purpose we present an expectation-maximization (EM) algorithm, which performs unsupervised learning of an associated probabilistic model of the mixing situation. Each source in our model is described by a mixture of gaussians; thus, all the probabilistic calculations can be performed analytically. In the second step, the sources are reconstructed from the observed data by an optimal nonlinear estimator. A variational approximation of this algorithm is derived for cases with a large number of sources, where the exact algorithm becomes intractable. Our IFA algorithm reduces to the one for ordinary FA when the sources become gaussian, and to an EM algorithm for PCA in the zero-noise limit. We derive an additional EM algorithm specifically for noiseless IFA. This algorithm is shown to be superior to ICA since it can learn arbitrary source densities from the data. Beyond blind separation, IFA can be used for modeling multidimensional data by a highly constrained mixture of gaussians and as a tool for nonlinear signal encoding.
Camera Calibration via Stereo Vision Using Tsai's Method

To enable a mobile robot to navigate in an unknown environment, vision is used as a primary navigation tool. The paper focuses on studying camera calibration via stereo vision. Tsai’s camera calibration technique will be introduced and tested with our miniature CCD color cameras to get intrinsic and extrinsic parameters of them. The results demonstrate that Tsai’s method is a feasible and accurate technique for camera calibration.
What's the difference?: efficient set reconciliation without prior context

We describe a synopsis structure, the Difference Digest, that allows two nodes to compute the elements belonging to the set difference in a single round with communication overhead proportional to the size of the difference times the logarithm of the keyspace. While set reconciliation can be done efficiently using logs, logs require overhead for every update and scale poorly when multiple users are to be reconciled. By contrast, our abstraction assumes no prior context and is useful in networking and distributed systems applications such as trading blocks in a peer-to-peer network, and synchronizing link-state databases after a partition. Our basic set-reconciliation method has a similarity with the peeling algorithm used in Tornado codes [6], which is not surprising, as there is an intimate connection between set difference and coding. Beyond set reconciliation, an essential component in our Difference Digest is a new estimator for the size of the set difference that outperforms min-wise sketches [3] for small set differences. Our experiments show that the Difference Digest is more efficient than prior approaches such as Approximate Reconciliation Trees [5] and Characteristic Polynomial Interpolation [17]. We use Difference Digests to implement a generic KeyDiff service in Linux that runs over TCP and returns the sets of keys that differ between machines.