Miracle-dz/UniFAR-FTUs huggingface dataset:
The buckeye corpus of speech: updates and enhancements

This paper describes recent progress in the development of the Buckeye Corpus of Speech, a phonetically labeled corpus of conversational American English speech, first described in [1]. With the publication of the second phase of transcription, the corpus has nearly doubled in size from the first release. We briefly give an overview of the corpus, report on additional studies of inter-labeler agreement, and describe a new GUI designed to facilitate searching the annotated speech files.
Mixed Bruhat Operators and Yang-Baxter Equations for Weyl Groups

We introduce and study a family of operators which act in the group algebra of a Weyl group W and provide a multiparameter solution to the quantum Yang-Baxter equations of the corresponding type. These operators are then used to derive new combinatorial properties of W and to obtain new proofs of known results concerning the Bruhat order of W. The paper is organized as follows. Section 2 is devoted to preliminaries on Coxeter groups and associated Yang-Baxter equations. In Theorem 3.1 of Section 3, we describe our solution of these equations. In Section 4, we consider a certain limiting case of our solution, which leads to the quantum Bruhat operators. These operators play an important role in the explicit description of the (small) quantum cohomology ring of G/B. Section 5 contains the proof of Theorem 3.1. Section 6 is devoted to combinatorial applications of our operators. For an arbitrary element u ∈W,we define a graded partial order onW called the tilted Bruhat order; this partial order has unique minimal element u. (The usual Bruhat order corresponds to the special case where u = e, the identity element.) We then prove that tilted Bruhat orders are lexicographically shellable graded posets whose every interval is Eulerian. This generalizes the well-known results of D. -N. Verma, A. Bjorner, M. Wachs, and M. Dyer.
Characteristics of binding of Escherichia coli serotype O157:H7 strain CL-49 to purified intestinal mucin

Purified rat intestinal mucin was used as a model mucin to study the binding of Escherichia coli serotype O157:H7, a human pathogen associated with outbreaks of hemorrhagic colitis and hemolytic uremic syndrome. Of six O157:H7 strains, only one strain (designated CL-49) bound to rat (and other) intestinal mucins by a specific and saturable process. Binding was observed only after the bacteria were serially passaged to promote the expression of type 1 pili (fimbriae). Several other type 1-piliated E. coli strains, however, did not bind to mucin. Binding of E. coli CL-49 was inhibited by D-mannose and short oligomannosyl derivatives, particularly Man-alpha-1,3-Man, Man-alpha-1,2-Man, and Man-alpha-1,3-Man-beta-1,4-N-acetylglucosamine. Other inhibitors of binding included p-nitrophenol (10(-4) M), heating at 60 degrees C (to remove pili), an antibody to type 1 pili, and purified type 1 pili of E. coli CL-49 used as hapten inhibitors. A comparison of the hydrophobicity of piliated E. coli CL-49 with other type 1-piliated E. coli strains indicated that the former strain was much more hydrophobic than the others. These findings indicate that highly purified intestinal mucins possess specific mannosyl receptor sites for bacterial type 1 pili on E. coli CL-49, but that strong hydrophobic interactions between the mucin and the pili stabilize the mannose-dependent binding process. We speculate that the mucin receptors for type 1 pili reside in oligosaccharides of the 118-kilodalton "link" glycopeptide, since this is the only mucin component known to contain mannose.
Uncovering Many Views of Biological Networks Using Ensembles of Near-Optimal Partitions

Densely interacting regions of biological networks often correspond to functional modules such as protein complexes. Most algorithms proposed to uncover modules, however, produce one clustering that only reveals a single view of how the cell is organized. We describe two new methods to find ensembles of provably near-optimal modularity partitions that lie within a heuristically constrained search space. We also show how to count the number of solutions in this space that exist within a bounded modularity range. We apply our algorithms to a protein interaction network for S. cerevisiae and show how fine-grained differences between near-optimal partitions can be used to define robust communities. We also propose a technique to find structurally diverse nearoptimal solutions and show that these different partitions are enriched for different biological functions. Our results indicate that near-optimal solutions can represent alternative and complementary views of the network’s structure.
Improving Word Sense Induction by Exploiting Semantic Relevance

Word Sense Induction (WSI) is the task of automatically inducing the different senses of a target word from unannotated text. Traditional approaches based on the vector space model (VSM) represent each context of a target word as a vector of selected features (e.g. the words occurring in the context). These approaches assume that the words occurring in the context are independent and do not exploit semantic relevance between words. In this paper we propose a WSI method which can exploit semantic relevance between words by incorporating a word graph into the framework of clustering of context vectors. The method is evaluated on the testing data of the Chinese Word Sense Induction task of the first CIPSSIGHAN Joint Conference on Chinese Language Processing (CLP2010). Experimental results show that our method significantly outperforms the baseline methods.
Computing and verifying depth orders

A depth order on a set of objects is an order such that object <italic>a</italic> comes before object <italic>a′</italic> in the order when <italic>a′</italic> lies behind <italic>a′</italic>, or, in other words, when <italic>a</italic> is (partially) hidden by <italic>a′</italic> by <italic>a′</italic>. We present efficient algorithms for the computation and verification of depth orders of sets of <italic>n</italic> rods in 3–space. Our algorithms run in time <italic>O</italic>(<italic>n</italic><supscrpt>4/3+ε</supscrpt>), for any fixed ε > 0). If all rods are axis-parallel, or, more generally, have only a constant number of different orientations, then the sorting algorithm runs in <italic>O</italic>(<italic>n</italic> log<supscrpt>2</supscrpt> <italic>n</italic>) time. The algorithms can be generalized to handle triangles and other polygons instead of rods. They are based on a general framework for computing and verifying linear extensions of implicitly defined binary relations.
On Graphical Modeling of Preference and Importance

In recent years, CP-nets have emerged as a useful tool for supporting preference elicitation, reasoning, and representation. CP-nets capture and support reasoning with qualitative conditional preference statements, statements that are relatively natural for users to express. In this paper, we extend the CP-nets formalism to handle another class of very natural qualitative statements one often uses in expressing preferences in daily life - statements of relative importance of attributes. The resulting formalism, TCP-nets, maintains the spirit of CP-nets, in that it remains focused on using only simple and natural preference statements, uses the ceteris paribus semantics, and utilizes a graphical representation of this information to reason about its consistency and to perform, possibly constrained, optimization using it. The extra expressiveness it provides allows us to better model tradeoffs users would like to make, more faithfully representing their preferences.
Randomized Assessment of Ticagrelor Versus Prasugrel Antiplatelet Effects in Patients With Diabetes

OBJECTIVE It has been postulated that prasugrel might be the preferred treatment option in diabetes mellitus (DM) patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI). We aimed to compare the pharmacodynamic action of ticagrelor versus prasugrel. RESEARCH DESIGN AND METHODS In a prospective, single-center, single-blind, crossover study, 30 consecutive ACS patients with DM who had been pretreated with clopidogrel were randomized to either 90 mg ticagrelor twice daily or 10 mg prasugrel once daily with a 15-day treatment period. Platelet reactivity (PR) was assessed with the VerifyNow P2Y12 function assay, measured in P2Y12 reaction units (PRU). RESULTS PR was significantly lower after ticagrelor (45.2 PRU [95% CI 27.4–63.1]) compared with prasugrel (80.8 PRU [63.0–98.7]), with a least squares mean difference of –35.6 PRU (−55.2 to −15.9, P = 0.001). High PR rate was 0% for ticagrelor and 3.3% for prasugrel (P = 1.0). CONCLUSIONS In DM patients with ACS who had been pretreated with clopidogrel and who undergo PCI, ticagrelor achieves a significantly higher platelet inhibition than prasugrel. Both antiplatelet agents effectively treat high PR. The relevance of these findings to the clinical efficacy and safety of ticagrelor and prasugrel in DM patients needs further elucidation.
Functional and structural properties of immobilized subunits of Escherichia coli alkaline phosphatase.

Alkaline phosphatase from Escherichia coli has been immobilized on Sepharose CL-4B using low levels of cyanogen bromide activation in order to favor the attachment of the dimer to the support through a single covalent linkage. The matrix-bound subunits obtained after dissociation of the immobilized dimer were shown to be catalytically inactive by three different criteria: 1) The level of phosphatase activity in the matrix-bound subunit population ,was dependent on the extent of cyanogen bromide activation of the support. 2) After cross-linking reversibly immobilized subunit preparations, sodium dodecyl sulfate gel electrophoresis of protein released from the Sepharose demonstrated the presence of sufficient amounts of dimeric structures to account for the phosphatase activity in these populations. 3) The protein in the matrix-bound subunits was more susceptible to proteolytic digestion than that in the matrix-bound dimer, while the catalytic activity in both immobilized derivatives remained constant. These results indicate that the subunits of alkaline phosphatase are catalytically inactive, and that the low levels of phosphatase activity observed are due to the presence of trace amounts of contaminating dimers. Titration of matrix-bound ‘261-labeled subunits with soluble nascent ‘311-labeled subunits restored 60% of the original phosphatase activity. The isotope ratio of I3’I- to “%protein reached a final value of 1.06 and provided a very sensitive indication of the extent of dimerization throughout the titration. When the immobilized apodimer and apomonomer were titrated with ssZnz+, the matrix-bound monomer bound 0.9 eq of Zn2+ while the matrix-bound dimer bound 4.1 eq of Zn2+; the Zn2+ binding sites in both immobilized derivatives had dissociation constants of 2 X M or lower. The preparation and characterization of immobilized subunits of alkaline phosphatase under solvent conditions optimal for renaturation should provide a valuable approach for studying the role of subunit interactions in this enzyme. Moreover, the techniques used in this investigation are generally applicable for the characterization of other immobilized enzyme derivatives. Although many proteins form oligomeric structures, the importance of subunit interactions for enzymatic function, regulation, or conformational stability has not yet been established. The major reason for this difficulty is that the contributions of secondary and tertiary structures to the properties
Tabletop sharing of digital photographs for the elderly

We have recently begun to see hardware support for the tabletop user interface, offering a number of new ways for humans to interact with computers. Tabletops offer great potential for face-to-face social interaction; advances in touch technology and computer graphics provide natural ways to directly manipulate virtual objects, which we can display on the tabletop surface. Such an interface has the potential to benefit a wide range of the population and it is important that we design for usability and learnability with diverse groups of people.This paper describes the design of SharePic -- a multiuser, multi-touch, gestural, collaborative digital photograph sharing application for a tabletop -- and our evaluation with both young adult and elderly user groups. We describe the guidelines we have developed for the design of tabletop interfaces for a range of adult users, including elders, and the user interface we have built based on them. Novel aspects of the interface include a design strongly influenced by the metaphor of physical photographs placed on the table with interaction techniques designed to be easy to learn and easy to remember. In our evaluation, we gave users the final task of creating a digital postcard from a collage of photographs and performed a realistic think-aloud with pairs of novice participants learning together, from a tutorial script.
Higher-order term indexing using substitution trees

We present a higher-order term indexing strategy based on substitution trees for simply typed lambda-terms. There are mainly two problems in adapting first-order indexing techniques. First, many operations used in building an efficient term index and retrieving a set of candidate terms from a large collection are undecidable in general for higher-order terms. Second, the scoping of variables and binders in the higher-order case presents challenges. The approach taken in this article is to reduce the problem to indexing linear higher-order patterns, a decidable fragment of higher-order terms, and delay solving terms outside of this fragment. We present insertion of terms into the index based on computing the most specific linear generalization of two linear higher-order patterns, and retrieval based on matching two linear higher-order patterns. Our theoretical framework maintains that terms are in βη-normal form, thereby eliminating the need to renormalize and raise terms during insertion and retrieval. Finally, we prove correctness of our presented algorithms. This indexing structure is implemented as part of the Twelf system to speed up the execution of the tabled higher-logic programming interpreter.
Image-based collision detection and response between arbitrary volume objects

We present a new image-based method to process contacts between objects bounded by triangular surfaces. Unlike previous methods, it relies on image-based volume minimization, which eliminates complex geometrical computations and robustly handles deep intersections. The surfaces are rasterized in three orthogonal directions, and intersections are detected based on pixel depth and normal orientation. Per-pixel contact forces are computed and accumulated at the vertices. We show how to compute pressure forces which serve to minimize the intersection volume, as well as friction forces. No geometrical precomputation is required, which makes the method efficient for both deformable and rigid objects. We demonstrate it on rigid, skinned, and particle-based physical models with detailed surfaces in contacts at interactive frame rates.
Rare Type of Quadricuspid Aortic Valve Requiring Surgical Replacement

Quadricuspid aortic valve, a rare congenital anomaly, is often related to severe aortic regurgitation and has a significant morbidity. The first described case was reported in 1862. Quadricuspid aortic valve is, in most cases, an isolated malformation, but it can be associated with other concomitant anomalies. We present here the case of a quadricuspid aortic valve discovered by intraoperative transesophageal echocardiography and successfully replaced with a mechanical aortic valve.
Sequence and spatial expression of zebrafish (Danio rerio) alphaA-crystallin.

PURPOSE To determine the nucleotide sequence, amino acid sequence and tissue specificity of zebrafish alphaA-crystallin. METHODS RACE, both 3' and 5', was used to clone the zebrafish alphaA-crystallin gene. The peptide sequence of the encoded protein was deduced and compared to cavefish, shark, amphibian, bird and human orthologues using the CLUSTAL W algorithm. alphaA-crystallin transcript was evaluated in brain, heart, lens, liver, skeletal muscle/skin, and spleen by semi-quantitative RT-PCR. RESULTS The 173 amino acid sequence of zebrafish alphaA-crystallin was determined to be 73% and 86% similar to its human and cavefish orthologues, respectively. We detected high expression of zebrafish alphaA-crystallin in the lens and very low expression in liver and spleen. CONCLUSIONS Few amino acids identified as being functionally important to chaperone function differ between zebrafish and mammalian alphaA-crystallin. The expression of alphaA-crystallin is mainly confined to the lens in both taxa. These data suggest that zebrafish alphaA-crystallin plays a physiologically limited role outside of the zebrafish lens, similar to its mammalian orthologues.
Three-Dimensional Atlas System for Mouse and Rat Brain Imaging Data

Tomographic neuroimaging techniques allow visualization of functionally and structurally specific signals in the mouse and rat brain. The interpretation of the image data relies on accurate determination of anatomical location, which is frequently obstructed by the lack of structural information in the data sets. Positron emission tomography (PET) generally yields images with low spatial resolution and little structural contrast, and many experimental magnetic resonance imaging (MRI) paradigms give specific signal enhancements but often limited anatomical information. Side-by-side comparison of image data with conventional atlas diagram is hampered by the 2-D format of the atlases, and by the lack of an analytical environment for accumulation of data and integrative analyses. We here present a method for reconstructing 3-D atlases from digital 2-D atlas diagrams, and exemplify 3-D atlas-based analysis of PET and MRI data. The reconstruction procedure is based on two seminal mouse and brain atlases, but is applicable to any stereotaxic atlas. Currently, 30 mouse brain structures and 60 rat brain structures have been reconstructed. To exploit the 3-D atlas models, we have developed a multi-platform atlas tool (available via The Rodent Workbench, http://rbwb.org) which allows combined visualization of experimental image data within the 3-D atlas space together with 3-D viewing and user-defined slicing of selected atlas structures. The tool presented facilitates assignment of location and comparative analysis of signal location in tomographic images with low structural contrast.
Tuning pathological brain oscillations with neurofeedback: a systems neuroscience framework

Neurofeedback (NFB) is emerging as a promising technique that enables self-regulation of ongoing brain oscillations. However, despite a rise in empirical evidence attesting to its clinical benefits, a solid theoretical basis is still lacking on the manner in which NFB is able to achieve these outcomes. The present work attempts to bring together various concepts from neurobiology, engineering, and dynamical systems so as to propose a contemporary theoretical framework for the mechanistic effects of NFB. The objective is to provide a firmly neurophysiological account of NFB, which goes beyond traditional behaviorist interpretations that attempt to explain psychological processes solely from a descriptive standpoint whilst treating the brain as a “black box”. To this end, we interlink evidence from experimental findings that encompass a broad range of intrinsic brain phenomena: starting from “bottom-up” mechanisms of neural synchronization, followed by “top-down” regulation of internal brain states, moving to dynamical systems plus control-theoretic principles, and concluding with activity-dependent as well as homeostatic forms of brain plasticity. In support of our framework, we examine the effects of NFB in several brain disorders, including attention-deficit hyperactivity (ADHD) and post-traumatic stress disorder (PTSD). In sum, it is argued that pathological oscillations emerge from an abnormal formation of brain-state attractor landscape(s). The central thesis put forward is that NFB tunes brain oscillations toward a homeostatic set-point which affords an optimal balance between network flexibility and stability (i.e., self-organised criticality (SOC)).
On the robustness of the OLSR protocol under unwanted interference

Optimized Link State Routing (OLSR) is a popular protocol for proactively establishing peer-to-peer links in mobile ad hoc networks (MANETs). Protocol ‘hello’ messages between neighbouring nodes establish link connections that are used to route information from a source via multiple relays to ultimately reach destinations that would not otherwise be directly connected to that source. The ‘hello’ messages are sent periodically with a random timing jitter in order to avoid collisions with messages of other neighbouring nodes such that the connection integrity of the MANET, and thus network availability, remain high. In this paper we explore the robustness of the OLSR protocol under unwanted interference that causes a denial of service. We simulate the denial of service with a statistical method, targeting the ‘hello’ messages with unwanted interference, and measure the mean time between failure and percent ‘connectedness’ of a network link. Our results show that the commercial off-the-shelf implementations of the OLSR protocol are not resilient to unwanted interference leading a MANET to potential denial or degradation if its routing protocol were targeted. We conclude that a randomized jitter in OLSR ‘hello’ message periodicity is an important element in avoiding this unwanted interference.
Comparison of methods to assess energy expenditure and physical activity in people with spinal cord injury

Abstract Objective To compare different methods of assessing energy expenditure (EE) and physical activity (PA) in people with spinal cord injury (SCI) under community-dwelling conditions. Methods A reference standard encompassing the doubly labelled water (DLW) technique, heart rate monitoring (FLEX-HR), a multi-sensor armband (SenseWear Armband (SWA)), and two PA recall questionnaires were employed in 14 people with SCI to estimate EE and leisure-time PA. Results Mean total daily energy expenditure (TDEE) assessed by DLW, FLEX-HR, and SWA were 9817 ± 2491 kJ/day, 8498 ± 1516 kJ/day, and 11414 ± 3242 kJ/day, respectively. Physical activity energy expenditure (PAEE) quantified by DLW was 2841 ± 1626 kJ/day, 2935 ± 1732 kJ/day estimated from FLEX-HR, and 2773 ± 2966 kJ/day derived from SWA. After converting the PA recall questionnaire data to EE in kJ/day, PAEE for the Physical Activity Recall Assessment for People with Spinal Cord Injury (PARA-SCI) was 2339 ± 1171 kJ/day and for Physical Activity Scale for Individuals with Physical Disabilities (PASIPD) 749 ± 1026 kJ/day. DLW-quantified PAEE was moderately associated with PARA-SCI (R2 = 0.62, P < 0.05), but not with the other estimates of PAEE (R2 ranged between 0.13 and 0.30, P > 0.05). Conclusion Our findings revealed that the PARA-SCI recall questionnaire was the best estimate of PAEE compared to the reference standard DLW approach. Although the between-method variability for SWA, FLEX-HR, and PASIPD-derived PAEE was small, there was a weak association between these methods and the criterion DLW technique. The best estimate of DLW-quantified TDEE was by FLEX-HR. SWA significantly overestimated TDEE in this population.