Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells

Notch1 regulates gene expression by associating with the DNA-binding factor RBPJ and is oncogenic in murine and human T-cell progenitors. Using ChIP-Seq, we find that in human and murine T-lymphoblastic leukemia (TLL) genomes Notch1 binds preferentially to promoters, to RBPJ binding sites, and near imputed ZNF143, ETS, and RUNX sites. ChIP-Seq confirmed that ZNF143 binds to ∼40% of Notch1 sites. Notch1/ZNF143 sites are characterized by high Notch1 and ZNF143 signals, frequent cobinding of RBPJ (generally through sites embedded within ZNF143 motifs), strong promoter bias, and relatively low mean levels of activating chromatin marks. RBPJ and ZNF143 binding to DNA is mutually exclusive in vitro, suggesting RBPJ/Notch1 and ZNF143 complexes exchange on these sites in cells. K-means clustering of Notch1 binding sites and associated motifs identified conserved Notch1-RUNX, Notch1-ETS, Notch1-RBPJ, Notch1-ZNF143, and Notch1-ZNF143-ETS clusters with different genomic distributions and levels of chromatin marks. Although Notch1 binds mainly to gene promoters, ∼75% of direct target genes lack promoter binding and are presumably regulated by enhancers, which were identified near MYC, DTX1, IGF1R, IL7R, and the GIMAP cluster. Human and murine TLL genomes also have many sites that bind only RBPJ. Murine RBPJ-only sites are highly enriched for imputed REST (a DNA-binding transcriptional repressor) sites, whereas human RPBJ-only sites lack REST motifs and are more highly enriched for imputed CREB sites. Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in TLL cells, as well as unique classes of divergent RBPJ-only sites that also likely regulate transcription.
An effective statistical approach to blog post opinion retrieval

Finding opinionated blog posts is still an open problem in information retrieval, as exemplified by the recent TREC blog tracks. Most of the current solutions involve the use of external resources and manual efforts in identifying subjective features. In this paper, we propose a novel and effective dictionary-based statistical approach, which automatically derives evidence for subjectivity from the blog collection itself, without requiring any manual effort. Our experiments show that the proposed approach is capable of achieving remarkable and statistically significant improvements over robust baselines, including the best TREC baseline run. In addition, with relatively little computational costs, our proposed approach provides an effective performance in retrieving opinionated blog posts, which is as good as a computationally expensive approach using Natural Language Processing techniques.
Fractional quantum Hall effect in suspended graphene: Transport coefficients and electron interaction strength

Strongly correlated electron liquids which occur in quantizing magnetic fields reveal a cornucopia of fascinating quantum phenomena such as fractionally charged quasiparticles, anyonic statistics, topological order, and many others. Probing these effects in GaAs-based systems, where electron interactions are relatively weak, requires sub-kelvin temperatures and record-high electron mobilities, rendering some of the most interesting states too fragile and difficult to access. This prompted a quest for new high-mobility systems with stronger electron interactions. Recently, fractional-quantized Hall effect was observed in suspended graphene (SG), a free-standing monolayer of carbon, where it was found to persist up to T=10 K. The best results in those experiments were obtained on micron-size flakes, on which only two-terminal transport measurements could be performed. Here we pose and solve the problem of extracting transport coefficients of a fractional quantum Hall state from the two-terminal conductance. We develop a method, based on the conformal invariance of two-dimensional magnetotransport, and illustrate its use by analyzing the measurements on SG. From the temperature dependence of longitudinal conductivity, extracted from the measured two-terminal conductance, we estimate the energy gap of quasiparticle excitations in the fractional-quantized nu=1/3 state. The gap is found to be significantly larger than in GaAs-based structures, signaling much stronger electron interactions in suspended graphene. Our approach provides a new tool for the studies of quantum transport in suspended graphene and other nanoscale systems.
‘Similarity breeds liking’ revisited: The moderating role of commitment

The association between perceived similarity and liking for a romantic partner was examined in college students' relationships over the course of one year. Despite substantial evidence that similarity breeds attraction, perceived attribute similarity was positively correlated with liking only in highcommitment relationships. In low-commitment relationships, perceived dissimilarity was associated with greater liking and with maintenance of liking over time, consistent with Aron and Aron's (1997) self-expansion model. Relationship status (ongoing or ended) after one year was primarily explained by commitment at time 1. However, high perceived similarity appeared to buffer couples against destructive accommodation responses; relatively destructive responses were associated with ended status only when perceived similarity was low.
Variance estimates and exploration function in multi-armed bandit

Algorithms based on upper-confidence bounds for balancing exploration and exploitation are gaining popularity since they are easy to implement, efficient and effective. This paper considers a variant of the basic algorithm for the stochastic, multi-armed bandit problem that takes into account the empirical variance of the different arms. In earlier experimental works, such algorithms were found to outperform the competing algorithms. The paper provides a first analysis of the expected regret of such algorithms and of the concentration of the regret of upper confidence bounds algorithm. As expected, these analyses of the regret suggest that the algorithm that use the variance estimates can have a major advantage over its alternatives that do not use such estimates when the variances of the payoffs of the suboptimal arms are low. This work, however, reveals that the regret concentrates only at a polynomial rate. This holds for all the upper confidence bound based algorithms and for all bandit problems except those rare ones where with probability one the payoffs coming from the optimal arm are always larger than the expected payoff for the second best arm. Hence, although upper confidence bound bandit algorithms achieve logarithmic expected regret rates, a risk-averse decision maker may prefer some alternative algorithm. The paper also illustrates some of the results with computer simulations.
Heap bounds protection with low fat pointers

Heap buffer overflow (underflow) errors are a common source of security vulnerabilities. One prevention mechanism is to add object bounds meta information and to instrument the program with explicit bounds checks for all memory access. The so-called "fat pointers" approach is one method for maintaining and propagating the meta information where native machine pointers are replaced with "fat" objects that explicitly store object bounds. Another approach is "low fat pointers", which encodes meta information within a native pointer itself, eliminating space overheads and also code compatibility issues. This paper presents a new low-fat pointer encoding that is fully compatible with existing libraries (e.g. pre-compiled libraries unaware of the encoding) and standard hardware (e.g. x86_64). We show that our approach has very low memory overhead, and competitive with existing state-of-the-art bounds instrumentation solutions.
DEPARTEMENT TOEGEPASTE ECONOMISCHE WETENSCHAPPEN

In this paper we carefully link knowledge flows to and from a firm's innovation process with this firm's investment decisions. Three types of investments are considered: investments in applied research, investments in basic research, and investments in intellectual property protection. Only when basic research is performed, can the firm effectively access incoming knowledge flows and these incoming spillovers serve to increase the efficiency of own applied research. The firm can at the same time influence outgoing knowledge flows, improving appropriability of its innovations, by investing in protection. Our results indicate that firms with small budgets for innovation will not invest in basic research. This occurs in the short run, when the budget for know-how creation is restricted, or in the long-run, when market opportunities are low, when legal protection is not very important, or, when the pool of accessible and relevant external know-how is limited. The ratio of basic to applied research is non-decreasing in the size of the pool of accessible external know-how, the size and opportunity of the market, and, the effectiveness of intellectual property rights protection. This indicates the existence of economies of scale in basic research due to external market related factors. Empirical evidence from a sample of innovative manufacturing firms in Belgium confirms the economies of scale in basic research as a consequence of the firm's capacity to access external knowledge flows and to protect intellectual property, as well as the complementarity between legal and strategic investments.
Use of a process-based model for assessing the methane budgets of global terrestrial ecosystems and evaluation of uncertainty

Abstract. We assessed the global terrestrial budget of methane (CH4) by using a process-based biogeochemical model (VISIT) and inventory data for components of the budget that were not included in the model. Emissions from wetlands, paddy fields, biomass burning, and plants, as well as oxidative consumption by upland soils, were simulated by the model. Emissions from ruminant livestock and termites were evaluated by using an inventory approach. These CH4 flows were estimated for each of the model's 0.5° × 0.5° grid cells from 1901 to 2009, while accounting for atmospheric composition, meteorological factors, and land-use changes. Estimation uncertainties were examined through ensemble simulations using different parameterization schemes and input data (e.g., different wetland maps and emission factors). From 1996 to 2005, the average global terrestrial CH4 budget was estimated on the basis of 1152 simulations, and terrestrial ecosystems were found to be a net source of 308.3 ± 20.7 Tg CH4 yr−1. Wetland and livestock ruminant emissions were the primary sources. The results of our simulations indicate that sources and sinks are distributed highly heterogeneously over the Earth's land surface. Seasonal and interannual variability in the terrestrial budget was also assessed. The trend of increasing net emission from terrestrial sources and its relationship with temperature variability imply that terrestrial CH4 feedbacks will play an increasingly important role as a result of future climatic change.
Pronounced Cell Death in the Absence of NMDA Receptors in the Developing Somatosensory Thalamus

Genetic deletion of NMDA glutamate receptors disrupts development of whisker-related neuronal patterns in the somatosensory system. Independent studies have shown that NMDA receptor antagonists increase cell death among developing neurons. Here, we report that a dramatic feature of the developing somatosensory system in newborn NMDA receptor 1 (NMDAR1) knock-out mice is increased cell death in the ventrobasal nucleus (VB) of the thalamus. Sections were subject to terminal deoxynucleotidyl transferase dUTP nick end labeling staining for apoptotic DNA fragmentation, thionine staining for pyknotic nuclei, silver staining for degenerating cells, and immunostaining for caspase-3. All four methods demonstrated that deletion of NMDAR1 causes a large (on the order of threefold to fivefold) increase in cell death in the VB. The NMDA receptor antagonists dizocilpine maleate (MK-801) and phencyclidine also increase cell death in this structure. The onset of increased cell death in the VB in the absence of NMDA receptor function is approximately the time of birth, overlaps with naturally occurring cell death and synaptogenesis, and displays some anatomical specificity. For example, there was no increase in cell death in the hippocampus or neocortex of NMDAR1 knock-out mice at any of the time points examined: embryonic day 15.5 (E15.5), E17.5, and postnatal day 0. We also report a significant reduction in the size of the VB that is evident starting at E17.5. The results indicate that NMDA receptors play a major role in cell survival during naturally occurring cell death in the VB and demonstrate that cell death is a consideration in NMDA receptor knock-out studies.
Modelling the Time-Temperature dependency of Thermoplastics Used in Solid-Phase Thermoforming Process

Many constitutive theories, hyperelastic and viscoelastic have been proposed for modeling materials used in solid-phase forming processes such as thermoforming and blow molding. The phenomenological hyperelastic models were developed based purely on mathematical interpretation whereas physically base hyperelastic models were established from the formalism of macromolecular conformation as a thermodynamically reversible process. It has been shown earlier that materials being thermoform experienced rate-temperature dependent deformation ranges from constant width (CW) through to equal biaxial (EB). Modeling this complex deformation behavior is widely recognized to be un-feasible with typical hyperelastic model, where the fulfillment of energy conservation would renders these models time independent. In order to account for time-temperature dependency, viscoelastic model that encompass the linking of hyperelastic laws and viscous flow theories have been proposed by numerous researchers. This paper revisited and analyzed a number of the rate-temperature-equivalent viscous flow theories commonly used in material modeling, includes the Williams-Landel-Ferry (WLF), Arrhenius, and Vogel-Fulcher-Tammman (VFT), in term of their effectiveness in interpreting the time-temperature dependent relaxation behavior of polypropylene (PP) and high impact polystyrene (HIPS).
Performance Characteristics of “Spotter,” a Newly Developed Real-Time Wave Measurement Buoy

The Spotter is a low-cost, real-time, solar-powered wave measurement buoy that was recently developed by Spoondrift Technologies, Inc. (Spoondrift). To evaluate the data quality of the Spotter device, we performed a series of validation experiments that included comparisons between Spotter-derived motions and prescribed wave motions (monochromatic and random waves) on a custom-built, motion-controlled validation stand and simultaneous in-water measurements using a conventional wave measurement buoy, the Datawell DWR-G4 (Datawell). Spotter evaluations included time-domain validation (i.e., wave by wave) and comparisons of wave spectra, directional moments, and bulk statistical parameters such as significant wave height, peak period, mean wave direction, and directional spread. Spotter wave measurements show excellent fidelity and lend a high degree of confidence in data quality. Overall, Spotter-derived bulk statistical parameters were within 10% of respective Datawell-derived quantities. The Spotter’s low cost and compact form factor enabled unique field deployments of multiple wave measurement buoys for direct measurements of wave characteristics such as ocean wave decorrelation length scales, wave speed, and directional spread. Wave decorrelation lengths were found to be inversely proportional to the width of the spectrum, and wave speeds compared well against linear wave theory.
Exploring the Relationship Between Initial Mathematics Skill and a Kindergarten Mathematics Intervention

This study examined the role of initial skill in moderating intervention effects of a 50-lesson mathematics intervention program, ROOTS, for at-risk kindergarten students focused on developing whole-number concepts and skills. The study utilized a randomized block design with at-risk students (n = 592) within classrooms (n = 60) randomly assigned to one of two treatment conditions (a small group of two to five students) or control condition. Proximal and distal measures were collected in the fall (pretest), spring (posttest), and winter of first grade (delayed posttest). Analyses examined the moderating effects of initial student achievement level on mathematics outcomes. Results indicated that initial skill moderated student outcomes but the relationship did not differ by group size. Implications for tiered mathematics instruction are discussed.
Dynamic Programming Treatment of the Travelling Salesman Problem

The well-known travelling salesman problem is the following: " A salesman is required ~,o visit once and only once each of n different cities starting from a base city, and returning to this city. What path minimizes the to ta l distance travelled by the salesman? " The problem has been treated by a number of different people using a var ie ty of techniques; el. Dantzig, Fulkerson, Johnson [1], where a combination of ingemtity and linear programming is used, and Miller, Tucker and Zemlin [2], whose experiments using an all-integer program of Gomory did not produce results i~ cases with ten cities although some success was achieved in eases of simply four cities. The purpose of this note is to show tha t this problem can easily be formulated in dynamic programming terms [3], and resolved computationally for up to 17 cities. For larger numbers, the method presented below, combined with various simple manipulations, may be used to obtain quick approximate solutions. Results of this nature were independently obtained by M. Held and R. M. Karp, who are in the process of publishing some extensions and computat ional results.
Evolution & Extinction of the Great Auk: A Palaeogenomic Approach

One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
Probable maximum precipitation in tropical zone (Thailand) as estimated by generalized method and statistical method

The objective of this research was to estimate probable maximum precipitation (PMP) for the duration of 1 to 3 days in Thailand. Rainfall data were collected from 217 meteorological stations. Two methods for estimating PMP were applied: the generalized method which analysed actual storms data using meteorological process, and the Hershfield's statistical method which applied the frequency analysis of the annual maximum rainfall. Both methods were commonly used and were recommended by the World Meteorological Organization (WMO) for estimating PMP. PMP estimation results were presented as isohyetal maps. For the generalized method, most PMP values were found higher in the east and decreased towards the west. However, there was no clear trend with the statistical method in the PMP's spatial distribution. An analysis of the 3‐day PMP averages showed that PMP estimation using the generalized method is 10% higher than that of the statistical method. The study results were then applied to estimate PMP of six large dams in Thailand and compared with the ones used in the design of the spillways. It was found that PMP estimation based on the generalized method was closer to the value used in the spillway design of those dams than PMP estimation based on the statistical method.
The Chemopreventive Agent Myoinositol Inhibits Akt and Extracellular Signal-Regulated Kinase in Bronchial Lesions from Heavy Smokers

Myoinositol is an isomer of glucose that has chemopreventive activity in animal models of cancer. In a recent phase I clinical trial, myoinositol administration correlated with a statistically significant regression of preexisting bronchial dysplastic lesions in heavy smokers. To shed light on the potential mechanisms involved, activation of Akt and extracellular signal-regulated kinase (ERK), two kinases that control cellular proliferation and survival, was assessed in 206 paired bronchial biopsies from 21 patients who participated in this clinical trial. Before myoinositol treatment, strongly positive staining for activation of Akt was detected in 27% of hyperplastic/metaplastic lesions and 58% of dysplastic lesions (P = 0.05, χ2 test). There was also a trend toward increased activation of ERK (28% in regions of hyperplasia/metaplasia to 42% of dysplastic lesions). Following myoinositol treatment, significant decreases in Akt and ERK phosphorylation were observed in dysplastic (P < 0.01 and 0.05, respectively) but not hyperplastic/metaplastic lesions (P > 0.05). In vitro, myoinositol decreased endogenous and tobacco carcinogen–induced activation of Akt and ERK in immortalized human bronchial epithelial cells, which decreased cell proliferation and induced a G1-S cell cycle arrest. These results show that the phenotypic progression of premalignant bronchial lesions from smokers correlates with increased activation of Akt and ERK and that these kinases are targets of myoinositol. Moreover, they suggest that myoinositol might cause regression of bronchial dysplastic lesions through inhibition of active Akt and ERK.
A discriminative parts based model approach for fiducial points free and shape constrained head pose normalisation in the wild

This paper proposes a method for parts-based view-invariant head pose normalisation, which works well even in difficult real-world conditions. Handling pose is a classical problem in facial analysis. Recently, parts-based models have shown promising performance for facial landmark points detection `in the wild'. Leveraging on the success of these models, the proposed data-driven regression framework computes a constrained normalised virtual frontal head pose. The response maps of a discriminatively trained part detector are used as texture information. These sparse texture maps are projected from non-frontal to frontal pose using block-wise structured regression. Finally, a facial kinematic shape constraint is achieved by applying a shape model. The advantages of the proposed approach are: a) no explicit dependence on the outputs of a facial parts detector and, thus, avoiding any error propagation owing to their failure; (b) the application of a shape prior on the reconstructed frontal maps provides an anatomically constrained facial shape; and c) modelling head pose as a mixture-of-parts model allows the framework to work without any prior pose information. Experiments are performed on the Multi-PIE and the `in the wild' SFEW databases. The results demonstrate the effectiveness of the proposed method.
Borg-Marchenko-type Uniqueness Results for CMV Operators

We prove local and global versions of Borg-Marchenko-type uniqueness theorems for half-lattice and full-lattice CMV operators (CMV for Cantero, Moral, and Velazquez \cite{CMV03}). While our half-lattice results are formulated in terms of Weyl-Titchmarsh functions, our full-lattice results involve the diagonal and main off-diagonal Green's functions.