Miracle-dz/UniFAR-FTUs huggingface dataset:
LRP 6 exerts non-canonical effects on Wnt signaling during neural tube closure

Low-density lipoprotein receptor related protein 6 (Lrp6) mutational effects on neurulation were examined using gain (Crooked tail, Lrp6) and loss (Lrp6) of function mouse lines. Two features often associated with canonical Wnt signaling, dorsal–ventral patterning and proliferation, were no different from wild-type (WT) in the Lrp6 neural tube. Lrp6 embryos showed reduced proliferation and subtle patterning changes in the neural folds.Cellpolarity defects inbothLrp6 andLrp6 cranial foldswere indicatedbycell shape,centrosome displacement and failure of F-actin and GTP-RhoA accumulation at the apical surface. Mouse embryonic fibroblasts (MEFs) derived from Lrp6 or Lrp6 embryos exhibited elevated and decreased RhoA basal activity levels, respectively. While ligand-independent activation of canonical Wnt signaling, bypassing LrpFrizzled receptors, did not activate RhoA, non-canonical Wnt5a stimulation of RhoA activity was impaired in Lrp6 MEFs. RhoA inhibition exacerbated NTDs in cultured Lrp6 knockout embryos compared with WT littermates. In contrast, a ROCK inhibitor rescued Lrp6 embryos from NTDs. Lrp6 co-immunoprecipitated with Disheveled-associated activator of morphogenesis 1 (DAAM1), a formin promoting GEF activity in Wnt signaling. Biochemical and cell biological data revealed intracellular accumulation of Lrp6 protein where interaction with DAAM1 could account for observed elevated RhoA activity. Conversely, null mutation that eliminates Lrp6 interaction with DAAM1 led to lower basal RhoA activity in Lrp6 embryos. These results indicate that Lrp6 mediates not only canonical Wnt signaling, but can also modulate non-canonical pathways involving RhoA-dependent mechanisms to impact neurulation, possibly through intracellular complexes with DAAM1.
Intellectual Property Protection Legal Protection Technical Protection Software Protection Watermarking Cryptographic Methods Obfuscation Hadware Protection

Software is more and more frequently distributed in form of source code. Unprotected code is easy to alter and build in others projects. The answer for such attacks is obfuscation. Transformation of software source code which preserves its semantical functionality but analizability is made very dificult. We focus in our research on Very High Speed Integrated Circuits Hardware Description Language (VHDL). In previous articles we presented transformats assimilated from other high level languages for needs of hardware designs and we showed a set of new transformants which do not appear in different languages than VHDL. The next step we have to do is to establish a set of criterias through which we can rate quality of analyzed transformats. In article we present current bacground of software quality measure and we rate their usage for protecting intellectual property on digital designs. After that we propose a new way of obfuscation quality measure taking into account requirements of hardware designs.
Sculpture for the Q uantified S elf – A study into physical ambient data visualisation and time-based activity tracking Jordi Casanueva

The Quantified Self refers to individuals that collect data about themselves to improve health, aspects of their life and finding new life experiences. Time tracking of activities is a common data-collection habit Quantified Selfers engage for improving aspects of their life, however, they struggle engaging and understanding their data due to ineffective tools for visualisation. Studies have identified that Physical Ambient Data Visualisations are effective for this, specially Data Sculptures, which are data embedded objects with functional and aesthetic qualities that allow awareness, engagement, exploration and data sense-making for a wide range of users. This thesis explores the experience of nonexpert Quantified Selfers utilising Data Sculptures for awareness of their daily activities, their usage patterns and how they appropriate them. The Data Sculptures displayed information utilising light, colours and allowed exploration and comparison of data. A one-week In The Wild study was conducted in a household in London with two non-expert Quantified Selfers using two Data Sculptures and activity trackers for collection of time-based activities. The participants collected more than 60 hours of data, 50% productivity related, the Data Sculptures were integrated into the environment, utilised individually as daily decision taking and data awareness tools. Yet, participants preferred self-comparison of data and had opposite views regarding time-based data visualisation and more importantly, concerns regarding Data Sculptures’ appropriation, as they could become invasive in households. Author
A Theory on Formatting Sensory Input for Cognition.

Over the last few decades, a lot of progress has been made in understanding different aspects of the brain's ability to form abstract representations, but a specific mechanism for how they are created and used remains to emerge. Here, we review recent findings on the subject and we propose a mechanism for the dynamics of forming abstract representations, where the formation of local connectivity in neural networks determines the of search terms between the prefrontal cortex and the hippocampus, as well as the amount of detail that is transcribed into abstract representations.
Simulation Study and Analysis of Diffusive Molecular Communications With an Apertured Plane

Molecular communication via diffusion (MCvD) is a method of achieving nano- and micro-scale connectivity by utilizing the free diffusion mechanism of information molecules. The randomness in diffusive propagation is the main cause of inter-symbol interfe-rence (ISI) and the limiting factor of high data rate MCvD applications. In this paper, an apertured plane is considered between the transmitter and the receiver of an MCvD link. Either after being artificially placed or occurring naturally, surfaces or volumes that resemble an apertured plane only allow a fraction of the molecules to pass. Contrary to intuition, it is observed that such topology may improve communication performance, given the molecules that can pass through the aperture are the ones that take more directed paths towards the receiver. Furthermore, through both computer simulations and a theoretical signal evaluation metric named signal-to-interference and noise amplitude ratio (SINAR), it is found that the size of the aperture imposes a trade-off between the received signal power and the ISI combating capability of an MCvD system, hinting to an optimal aperture size that minimizes the bit error rate (BER). It is observed that the trend of BER is accurately mirrored by SINAR, suggesting the proposed metric’s applicability to optimization tasks in MCvD systems, including finding the optimal aperture size of an apertured plane. In addition, computer simulations and SINAR show that said optimal aperture size is affected by the location of the aperture and the bit rate. Lastly, the paper analyzes the effects of radial and angular offsets in the placement of the apertured plane, and finds that a reduction in BER is still in effect up to certain offset values. Overall, our results imply that apertured plane-like surfaces may actually help communication efficiency, even though they reduce the received signal power.
Heterogeneity of MGMT gene promoter methylation and protein expression in serial specimens in newly diagnosed glioblastoma

O6-methylguanine-DNA methyltransferase (MGMT) is known as a predictive marker, which has been associated with longer survival in glioblastoma patients who were treated with alkylating agents. However, little is known about heterogeneity of MGMT gene promoter methylation and its protein expression across different regions within the same tumor. This study was aimed to compare the status of MGMT gene promoter methylation and protein expression in different sites’ specimens of newly diagnosed glioblastoma. Two to four specimens were obtained from different regions in the same tumor during surgical procedure in 20 newly diagnosed glioblastoma patients guided by neuronavigation system(overall number of specimens: 60, all of which were prepared for the following analysis except one specimen showed necrotic obiviously). MGMT promoter profile was analyzed by Methylation-specific polymerase-Chain-reaction analysis (MSP). The MGMT protein expression was assessed by immunohistochemistry (IHC) and western blotting (WB). MGMT promoter Methylation was detected in 45.76% (27/59) specimens. IHC and WB analysis exhibited high concordant findings (r=0.93, P<0.001). There was no significant correlation between MGMT promoter methylation and protein expression (IHC and MSP, x2=3.18 P=0.074; WB and MSP, Z=-1.712 P=0.087), and this study also demonstrated the regional heterogeneity of MGMT status of methylation in 10.00% (2/20) patients and MGMT protein expression in 40.00% (8/20) patients. MGMT promoter methylation is probably not the only modulating factor in MGMT protein expression. Our research questions the guiding significance of MGMT promoter methylation or its protein expression to the therapeutic scheme, which detected only in a small piece of specimen in clinical practice.
Interactive comment on “ Effects of climate variability and functional changes on the interannual variation of the carbon balance in a temperate deciduous forest ” by J .

Reviewer #2 concluded that the simple empirical model applied in this study has led to a flawed analysis as it lacks a detailed description of the processes which could be incorporated in a more ideal mechanistic model. Undoubtedly, we agree that mechanistic modeling is important for both process learning and future prediction. However, we also believe that models of lower complexity (e.g. empirical models) can be equally useful, depending on the scope and objective of the study.
Lund University Predicting Corporate Defaults : Evaluating Moody ’ s Credit Rating Institute by A . Baltaev and

The ability of the Merton model and the logistic regression to accurately forecast corporate defaults is evaluated. Additionally, the probability-of-default (PD) estimates obtained from these two models are compared with the corresponding rating class historic default rates presented by Moody’s. Data for 56 defaulted and 272 healthy US publicly traded organizations serves as the basis for this study. Results reveal that: (i) the logistic regression is more accurate in distinguishing between defaulted and healthy companies, but provides overly conservative PD estimates; (ii) the Merton model struggles to correctly identify true defaults and true non-defaults, while providing default probabilities that are in line with historic default rates (iii) no framework was deemed superior in this context, ascertaining the difficulty associated with identifying the precise timing of a corporate default.
Uncomplicated Procedure for Thesaurus Mapping : Use of Stemming , Edit Distance and Vector Matching

This paper reports the results of an experiment on methods for finding similar terms in another thesaurus when a descriptor in one thesaurus is given, which is usually called thesaurus matching. The experiment used two well-known thesauri in the field of social science, the ICPSR Thesaurus (as the source) and the ERIC Thesaurus (as the target). First, 232 pairs of descriptors found by stem-based matching were examined by a human assessor. As a result, about 51% of them were categorized as ‘equivalent’ and 40% were judged as ‘nearly equivalent’. The other 8.6% were mismatches. Next, by using two measures, an ERIC descriptor that was most similar with a given ICPSR descriptor was selected and evaluated. The measures were the edit distance (Levenshtein Distance) between names of descriptors and the cosine similarity between vectors constructed specially for the descriptors. The vectors consisted of terms extracted from the descriptor and its non-descriptors, broader terms, narrower terms, and related terms. When two descriptors had different stems, the vector matching by cosine similarity specified similar ERIC descriptors more successfully than the edit distance. The experiment thus suggested a three-stage procedure for thesaurus matching: 1) string matching in a case-insensitive manner, 2) stem-based matching, and 3) vector matching based on cosine similarity.
Title An efficient algorithm for the extended ( l , d )-motif problem withunknown number of binding sites

Finding common patterns, or motifs, from a set of DNA sequences is an important problem in molecular biology. Most motif-discovering algorithms/software require the length of the motif as input. Motivated by the fact that the motif’s length is usually unknown in practice, Styczynski et al. introduced the Extended (l,d)-Motif Problem (EMP), where the motif’s length is not an input parameter. Unfortunately, the algorithm given by Styczynski et al. to solve EMP can take an unacceptably long time to run, e.g. over 3 months to discover a length14 motif. This paper makes two main contributions. First, we eliminate another input parameter from EMP: the minimum number of binding sites in the DNA sequences. Fewer input parameters not only reduces the burden of the user, but also may give more realistic/robust results since restrictions on length or on the number of binding sites make little sense when the best motif may not be the longest nor have the largest number of binding sites. Second, we develop an efficient algorithm to solve our redefined problem. The algorithm is also a fast solution for EMP (without any sacrifice to accuracy) making EMP practical.
An HPSG Approach to Synchronous Deixis and Speech Katya

The usage of deixis is highly pervasive in everyday communication. Through definite referring expressions, pronouns and pointing gestures with the head and hand, people engage the context of the communicative event in the utterance interpretation. In this paper, we concentrate on deictic (pointing) gestures performed by the hand, and we demonstrate that deixis, along with speech, can be described in terms of standardly used formal methods in linguistics, namely constraint-based formal grammars and compositional semantics. In particular, we use the form of the deictic gesture, the form of the synchronous speech and the utterance-specific time and space to combine speech and gesture into a single tree and to map them them to an underspecified meaning representation. As a grammar formalism we choose hpsg because of its mechanisms to construct structured phonology in parallel with syntax (Klein, 2000), and also because the semantic composition is expressed in Robust Minimal Recursion Semantics (r)mrs (Copestake et al., 2005). rmrs overcomes the shortcomings of λ-calculus in that the composition is constrained, i.e., it does not allow a functor to pick arguments that are arbitrarily embedded in the ulf; also, rmrs produces underspecified logical formulae (ulf): whereas with operations such as functional application or β-reduction, one imposes scope constraints and embeddings driven from the syntactic tree, (r)mrs produces a flat description of the possible readings without having to access the distinct readings themselves. This property is particularly useful for composing gestural meaning since even through discourse processing the semantic predications yielded by gestural form may remain unresolved. Deictic gestures demarcate spatial reference by projecting the hand to a region that is proximal or distal in relation to the speaker’s origo. The pointing does not necessarily identify a concrete referent that is present in the communicative situation. It can identify an abstract individual or object placed by the speaker on a virtually created map—also known as abstract pointing (McNeill, 2005)—or it can highlight a word or phrase from the simultaneously produced speech—known as nomination pointing (Kendon, 2004). Since these distinct types of deictic gestures might have distinct semantic effects, we can represent them in a typed hierarchy, thereby allowing a type to share by inheritance information with its supertypes (Pollard and Sag, 1994).
Statistical phylogeography: Migrate-N, IMa, and ABC

Nested clade analysis [15, 16, 17] represented the earliest attempt to develop a formal approach to using an estimate of phylogenetic relationships among haplotypes to infer something both about the biogeographic history of the populations in which they are contained and the evolutionary processes associated with the pattern of diversification implied by the phylogenetic relationships among haplotypes and their geographic distribution. The statistical parsimony part of NCA depends heavily on coalescent theory for calculating the “limits” of parsimony. As a result, NCA combines aspects of pure phylogenetic inference — parsimony — with aspects of pure population genetics — coalescent theory — to develop a set of inferences about the phylogeographic history of populations within species. NCA is now of primarily historical interest. So far as I am aware, no one uses it any more. Instead everyone uses methods based directly on coalescent theory or similar approaches. Before we get to that, though, I need to describe one complication that is taken for granted now that first became widely recognized in the late 1980s. Pekka Pamilo and Mashatoshi Nei [13] pointed out that the phylogenetic relationships of a single gene might be different from those of the populations from which the samples were collected.
Politis Patients with Neural Transplants Serotonergic Neurons Mediate Dyskinesia Side Effects in Parkinson ' s

bioengineered or stem cells. here, is important in that it will inform future treatments with grafts that consist of cells from other sources, such as reported the long-term consequences of such replacement tissue, such as the atypical movements and their inhibition replace the function of the diseased dopamine cells, forming connections with the existing brain cells. Exploration of ago. In some patients, the grafted cells survived, possibly as a result of stem cells within the graft, and were able to The patients described here are only two of a larger number who received fetal neural tissue implants years excess serotonergic neurons had in fact been pumping out dopamine, causing the dyskinesias. responded by a sudden and almost complete resolution of the troublesome abnormal movements, suggesting that the tested this idea by giving the patients low doses of a serotonin receptor agonist called buspirone. Both patients case, then desensitizing these serotonin neurons, and so inhibiting their activity, would reduce the dyskinesias. They neurotransmitter to adopt dopamine as a so-called false transmitter, releasing it to cause dyskinesias. If this were the The authors hypothesized that the explanation lies in the ability of the serotonin neurons to switch to a different dopamine, not serotonin, stimulation. usual. This presented a conundrum because dyskinesias in Parkinson s disease are thought to be a result of that binds to the serotonin transporter showed an abnormality; there seemed to be more serotonin neurons than the dopamine neurons that decay during Parkinson s disease were restored by the grafts. Another scan with an agent tomography, radioactive tracers that tag dopaminergic neurons and that bind to the dopamine receptor showed that Brain imaging exposed what was happening in these patients brains. When imaged by positron emission serotonin agonist eliminates these dyskinesias. have determined are a result of an overabundance of serotonin-using neurons that developed from the graft. A Recently, however, both have started to experience abnormal uncontrolled movements, which Politis and colleagues several years, the patients showed mild improvement but eventually were able to function well with no drugs. received grafts, one in the putamen and the other in both the caudate and the putamen, of fetal midbrain tissue. For Parkinson s disease proved that the diseased brain could be repaired, at least for a while. Two of these patients Before stem cells, there were fetal grafts. Pioneering treatments performed in the 1990s in patients with
A high-quality video denoising algorithm based on reliable motion estimation

Although the recent advances in the sparse representations of images have achieved outstanding denosing results, removing real, structured noise in digital videos remains a challenging problem. We show the utility of reliable motion estimation to establish temporal correspondence across frames in order to achieve high-quality video denoising. In this paper, we propose an adaptive video denosing framework that integrates robust optical flow into a non-local means (NLM) framework with noise level estimation. The spatial regularization in optical flow is the key to ensure temporal coherence in removing structured noise. Furthermore, we introduce approximate K-nearest neighbor matching to significantly reduce the complexity of classical NLM methods. Experimental results show that our system is comparable with the state of the art in removing AWGN, and significantly outperforms the state of the art in removing real, structured noise.
E ffi cient Search on the Job and the Business Cycle

We develop a model of search on the job where match-specific productivity induces workers to move between jobs and where workers can direct search toward particular jobs. After characterizing the social planner’s allocation, we prove that there exists a unique equilibrium in the market economy and it decentralizes the social planner’s allocation. We calibrate the model to the US economy to measure the contribution of aggregate productivity shocks to the cyclical volatility of labor market variables. Aggregate productivity shocks account for a sizable fraction of the cyclical volatility of the labor market if match quality is observed after the match is created, but only for a small fraction of the cyclical volatility if match quality is observed before the match is created. However, we argue that the version of the model in which matches are experience goods provides an unambiguously better description of the US labor market and, hence, deserves more confidence in its predictions about the effect of aggregate productivity shocks. ∗We are grateful to an editor and two referees for comments. We have also received comments from participants at the Search Theory conference at the University of Quebec in Montreal (April 2007), the Society for Economic Dynamics Meetings (New Orleans, January 2008, and Cambridge, July 2008), the Econometric Society Meeting in Pittsburgh (June 2008), the Vienna Macroeconomic Workshop (October, 2008), the NBER Summer Institute in Cambridge (July, 2008), the Canadian Macro Study Group Meeting (November, 2009) and at the seminars at Michigan, Stanford, Princeton, Columbia, Wisconsin, Boston University, Bank of Canada and Hoover Institution. Discussions with Rudi Bachmann, Gadi Barlevy, Mike Elsby, Martin Gervais, Marcus Hagedorn, Bob Hall, Nir Jaimovich, Nobuhiro Kiyotaki, Dale Mortensen, Giuseppe Moscarini, Thijs van Rens and Ludo Visschers led to significant improvements in the paper. We thank Frank Diebold, Jason Faberman, Giuseppe Moscarini, Eva Nagypál, David Neumark and Daniel Polsky for generously sharing their data with us. Menzio gratefully acknowledges the financial support and the hospitality of the Hoover Institution. Shi gratefully acknowledges the financial support from the Social Sciences and Humanities Research Council of Canada and from the Bank of Canada Fellowship. The usual disclaimer applies.