Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehension-Driven Generation of Meta-Technical Utterances in Math Tutoring

A technical discussion often contains conversational expressions like "however," "as I have stated before," "next," etc. These expressions, denoted Meta-technical Utterances (MTUs) carry important information which the listener uses to speed up the comprehension process. In this research we model the meaning of MTUs in terms of their anticipated effect on the listener comprehension, and use these predictions to select MTUs and weave them into a computer generated discourse. This paradigm was implemented in a system called FIGMENT, which generates commentaries on the solution of algebraic equations.
Structured document segmentation and representation by the modified X-Y tree

We describe a top-down approach to the segmentation and representation of documents containing tabular structures. Examples of these documents are invoices and technical papers with tables. The segmentation is based on an extension of X-Y trees, where the regions are split by means of cuts along separators (e.g. lines), in addition to cuts along white spaces. The leaves describe regions containing homogeneous information and cutting separators. Adjacency links among leaves of the tree describe local relationships between corresponding regions.
Molecular Pathways: A Novel Approach to Targeting Hypoxia and Improving Radiotherapy Efficacy via Reduction in Oxygen Demand

Tumor hypoxia presents a unique therapeutic challenge in the treatment of solid malignancies. Its presence has been established to be a poor prognostic factor in multiple cancer types, and past hypoxia-directed approaches have yielded generally disappointing results. Previous approaches have centered on either increasing oxygen delivery or administering agents that preferentially radiosensitize or kill hypoxic cells. However, a novel and potentially more effective method may be to increase therapeutic benefit by decreasing tumor oxygen consumption via agents such as metformin or nelfinavir in a patient population that is enriched for tumor hypoxia. This promising approach is currently being investigated in clinical trials and the subject of this article. Clin Cancer Res; 21(9); 1995–2000. ©2015 AACR.
Childhood asthma prevalence: cross-sectional record linkage study comparing parent-reported wheeze with general practitioner-recorded asthma diagnoses from primary care electronic health records in Wales

Introduction Electronic health records (EHRs) are increasingly used to estimate the prevalence of childhood asthma. The relation of these estimates to those obtained from parent-reported wheezing suggestive of asthma is unclear. We hypothesised that parent-reported wheezing would be more prevalent than general practitioner (GP)-recorded asthma diagnoses in preschool-aged children. Methods 1529 of 1840 (83%) Millennium Cohort Study children registered with GPs in the Welsh Secure Anonymised Information Linkage databank were linked. Prevalences of parent-reported wheezing and GP-recorded asthma diagnoses in the previous 12 months were estimated, respectively, from parent report at ages 3, 5, 7 and 11 years, and from Read codes for asthma diagnoses and prescriptions based on GP EHRs over the same time period. Prevalences were weighted to account for clustered survey design and non-response. Cohen’s kappa statistics were used to assess agreement. Results Parent-reported wheezing was more prevalent than GP-recorded asthma diagnoses at 3 and 5 years. Both diminished with age: by age 11, prevalences of parent-reported wheezing and GP-recorded asthma diagnosis were 12.9% (95% CI 10.6 to 15.4) and 10.9% (8.8 to 13.3), respectively (difference: 2% (−0.5 to 4.5)). Other GP-recorded respiratory diagnoses accounted for 45.7% (95% CI 37.7 to 53.9) and 44.8% (33.9 to 56.2) of the excess in parent-reported wheezing at ages 3 and 5 years, respectively. Conclusion Parent-reported wheezing is more prevalent than GP-recorded asthma diagnoses in the preschool years, and this difference diminishes in primary school-aged children. Further research is needed to evaluate the implications of these differences for the characterisation of longitudinal childhood asthma phenotypes from EHRs.
Probing the role of nonmuscle tropomyosin isoforms in intracellular granule movement by microinjection of monoclonal antibodies

Chicken embryo fibroblast (CEF) cells were microinjected with several different monoclonal antibodies that recognize certain nonmuscle isoforms of tropomyosin. Immediately after injection, cells were recorded with a time-lapse video imaging system; later analysis of the tapes revealed that particles in cells injected with one of these antibodies (CG1, specific for CEF tropomyosin isoforms 1 and 3) showed a dramatic decrease in instantaneous speed while moving, distance moved per saltation, and proportion of time spent in motion. Injection of Fab fragments of CG1 resulted in similar changes in the pattern of granule movement. This inhibition of granule movement by CG1 antibody was reversible; at 2.5 h after injection, granules in injected cells had already reached three-fourths of normal speed. The speed of granule movement in cells injected either with antibody specific for tropomyosin isoforms not present in CEF cells, or with CG1 antibody preabsorbed with tropomyosin, was not significantly different from the speed of granules in uninjected cells. When cells were injected with CG1 or Fab fragments of CG1, fixed, and counter-stained with rabbit antibodies to reveal the microtubule, microfilament, and intermediate filament systems, no obvious differences from the patterns normally seen in uninjected cells were observed. Examination of the ultrastructure of injected cells by EM confirmed the presence of apparently intact and normal microtubule, actin, and intermediate filament networks. These experiments suggest that tropomyosin may play an important role in the movement of vesicles and organelles in the cell cytoplasm. Also, we have shown previously that the CG1 determinant can undergo a motility-dependent change in reactivity, that may be important for the regulatory function of nonmuscle tropomyosin (Hegmann, T. E., J. L.-C. Lin, and J. J.-C. Lin. 1988. J. Cell Biol. 106:385-393). Therefore, in addition to postulated microtubule-based motors, microfilaments may play a critical role in regulating granule movement in nonmuscle cells.
The ‘regulated death’: a documentary analysis of the regulation and inspection of dying and death in English care homes for older people

In England, processes of regulation and inspection have been established to ensure that older people living in long-term care settings receive quality care. This paper describes how dying and death in care homes for older people is regulated and inspected. A documentary analysis was undertaken of the standard that addresses dying and death in the 2001 Care Homes for Older People: National Minimum Standards. Present in the standard is a ‘good death’ template drawn from constructions of best practice in palliative care. The way in which this national standard is enacted in the inspection process is described using a content analysis of the inspection reports from 226 care homes for older people. These present a narrow focus on dying and death, one that emphasises the older person's wishes and the degree of adherence to policies and procedures concerned with the dying and death event. A regulated death attenuates the ‘good death’ template and reflects both the inspection process and capabilities of the residents of care homes. If the regulation and inspection process is to integrate dying with living, a broader conception and regime of inspection is required. Only then will end-of-life care be provided that meets the diverse needs of older people who live in care homes.
Prominence Ranking in Graphs with Community Structure

We consider prominence ranking in graphs involving actors, their artifacts and the artifact groups. When multiple actors contributing to an artifact constitutes a social tie, associations between the artifacts can be used to infer prominence among actors. This is because prominent actors will tend to collaborate on prominent artifacts, and prominent artifacts will be associated with other prominent artifacts. Our testbed example is the DBLP co-authorship graph: multiple authors (the actors) collaborate to publish research papers (the artifacts); collaboration is the social tie. Papers have prominence themselves (eg. quality and impact of the work) and the prominence of the venues are tied to the prominence of the papers in them. We use our methods to infer prominence based on the venue-based associations of papers, and compare our rankings with external citation based measures of prominence. We compare with numerous other ranking algorithms, and show that the ranking performance gain from using the venues is statistically significant. What if there are no natural artifact groups like venues? We develop a new algorithm which uses discovered artifact groups. Our approach consists of two steps. First, we find artifact groups by linking artifacts with common contributors. Note that instead of finding communities of actors, we consider communities of artifacts. We then use these grouped artifacts in the prominence ranking algorithm. We consider different methods for obtaining the artifact groups, in particular a very efficient embedding based algorithm for graph clustering and show the effectiveness of our method in improving the ranking of actors. The inferred groups are as good as or better than the natural conference venues for DBLP.
A Classical Adaptive Filtering Blind Signal Separation

A classical adaptive filtering view of the problem of instantaneous blind signal separation is presented. This classical form enables an easy understanding of the natural gradient algorithm. A new RLS-based algorithm is developed using this classical interpretation. The algorithm provides improved on-line separation speed under the same steady state error compared to the natural gradient algorithm without requiring pre-whitening
Crystal isomorphisms for irreducible highest weight U_{v}{\hat{sl}}_{e})-modules of higher level

We study the crystal graphs of irreducible $U_{v}(\hat{sl}}_{e})$-modules of higher level l. Generalizing works of the first author, we obtain a simple description of the bijections between the classes of multipartitions which naturally label these graphs: the Uglov multipartitions. This is achieved by expliciting an embedding of the $U_{v}(\hat{sl}}_{e})$-crystals of level l into $U_{v}(\hat{sl}_{\infty})$-crystals associated to highest weight modules.
Statistical Fault Localization via Semi-dynamic Program Slicing

Fault localization is a critical step of software debugging. We present a statistical fault localization approach via semi-dynamic slicing in this paper. In our technique, we first conduct the execution flow graph based on both the coverage information and static control-flow-graph to model the executions approximately. Second, we use the backward slicing to analyze the dependence relationships between execution statements and execution results, obtain sliced statements and calculate the coverage statistics. At last, we calculate the fault suspiciousness according to Tarantula, a classic approach of statistical fault localization. Controlled experiments are setup on the Siemens subjects, and the results are promising.
Evolutionary biology Did true frogs ‘ dispersify ’ ?

The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene–Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date in order to: (i) characterize tempo and patterns of diversification; (ii) assess the impact of the EOEE; and (iii) test the hypothesis that range expansion was followed by increased net diversification. We show that late Eocene colonization of novel biogeographic regions was not affected by the EOEE and surprisingly, global expansion was not followed by increased net diversification. On the contrary, the diversification rate declined or did not shift following geographical expansion. Thus, the diversification history of true frogs contradicts the prevailing expectation that amphibian net diversification accelerated towards the present or increased following range expansion. Rather, our results demonstrate that despite their dynamic biogeographic history, true frogs diversified at a relatively constantly rate, even as they colonized the major land masses of Earth.
Modeling TCP Reno performance: a simple model and its empirical validation

The steady-state performance of a bulk transfer TCP flow (i.e., a flow with a large amount of data to send, such as FTP transfers) may be characterized by the send rate, which is the amount of data sent by the sender in unit time. In this paper we develop a simple analytic characterization of the steady-state send rate as a function of loss rate and round trip time (RTT) for a bulk transfer TCP flow. Unlike the models of Lakshman and Madhow (see IEE/ACM Trans. Networking, vol.5, p.336-50, 1997), Mahdavi and Floyd (1997), Mathis, Semke, Mahdavi and Ott (see Comput. Commun. Rev., vol.27, no.3, 1997) and by by Ott et al., our model captures not only the behavior of the fast retransmit mechanism but also the effect of the time-out mechanism. Our measurements suggest that this latter behavior is important from a modeling perspective, as almost all of our TCP traces contained more time-out events than fast retransmit events. Our measurements demonstrate that our model is able to more accurately predict TCP send rate and is accurate over a wider range of loss rates. We also present a simple extension of our model to compute the throughput of a bulk transfer TCP flow, which is defined as the amount of data received by the receiver in unit time.
Trustworthy numerical computation in Scala

Modern computing has adopted the floating point type as a default way to describe computations with real numbers. Thanks to dedicated hardware support, such computations are efficient on modern architectures, even in double precision. However, rigorous reasoning about the resulting programs remains difficult. This is in part due to a large gap between the finite floating point representation and the infinite-precision real-number semantics that serves as the developers' mental model. Because programming languages do not provide support for estimating errors, some computations in practice are performed more and some less precisely than needed. We present a library solution for rigorous arithmetic computation. Our numerical data type library tracks a (double) floating point value, but also a guaranteed upper bound on the error between this value and the ideal value that would be computed in the real-value semantics. Our implementation involves a set of linear approximations based on an extension of affine arithmetic. The derived approximations cover most of the standard mathematical operations, including trigonometric functions, and are more comprehensive than any publicly available ones. Moreover, while interval arithmetic rapidly yields overly pessimistic estimates, our approach remains precise for several computational tasks of interest. We evaluate the library on a number of examples from numerical analysis and physical simulations. We found it to be a useful tool for gaining confidence in the correctness of the computation.
Multiple bandwidth volumetric optoacoustic tomography using conventional ultrasound linear arrays

In optoacoustic imaging absorbing structures excited with short laser pulses generate broadband ultrasound waves, which tomographically detected outside the sample enable reconstruction of initial pressure distribution. As light scatters in biological tissues, the excitation has a three-dimensional (3D) pattern allocation. Accurate reconstruction of the 3D distribution of optical absorption requires a large solid angle of detection of the ultrasonic field. Moreover, the center frequency and bandwidth of a given detector define the range of structure sizes it is able to resolve. Therefore, detectors with different frequency bandwidths record different subsets of information. A volumetric optoacoustic system using linear ultrasound arrays with different central frequencies, 6MHz and 24MHz, is introduced. By employing a novel scanning geometry that takes advantage of the high sensitivity on the transversal dimension of these linear probes, high resolution optoacoustic signals are being recorded. Resolution performance and biological capabilities are demonstrated with a 20um crossed-suture phantom and an excised mouse liver lobe.
Considerations for Improving the Accuracy of Permittivity Measurement using Time Domain Reflectometry

In a paper presented by Heimovaara (1993) a method of calibrating TDR sensors was presented using air and water. Time has moved on but time domain reflectometry (TDR) sensors are still calibrated in a number of different ways. In this article we present a rigorous investigation of the method proposed by Heimovaara and demonstrate its accuracy. We demonstrate that the placement of a starting point in any place other than the one determined using Heimovaara's method results in erroneous permittivity measurement. This will be most significant at low values of permittivity. We propose that Heimovaara's method be adopted as a standard method for calibrating TDR sensors for measuring permittivity. The discussion centers on the placement of the first time marker used to measure the signal travel time from which permittivity is measured. Our modeling results suggest that this point is slightly forward of the apex of the bump on the waveform which corresponds to the impedance increase as the wave travels from the cable into the TDR sensor head. We also demonstrate that using the apex of this bump as a starting point reference can lead to erroneous measurements of travel time in layered dielectric media. Finally we examine the use of long cables to connect sensors to the TDR. We demonstrate that the travel time in the cable changes as a function of temperature and that fixed travel time markers based on cable length cause error in the measurement of travel time. For a 2.6-m cable the error was 1.6% at 50°C, and 4.7% for a 10.3-m cable, relative to calibration at 25°C. Software that tracks the sensor head either through the impedance mismatch caused by the head or using an electrical marker eliminates this source of error.
The Relative Pruning Power of Strong Stubborn Sets and Expansion Core

In the last years, pruning techniques based on partial order reduction have found increasing attention in the planning community. One recent result is that the expansion core method is a special case of the strong stubborn sets method proposed in model checking. However, it is still an open question if there exist efficiently computable strong stubborn sets with strictly higher pruning power than expansion core. In this paper, we prove that the pruning power of strong stubborn sets is strictly higher than the pruning power of expansion core even for a straight-forward instantiation of strong stubborn sets. This instantiation is as efficiently computable as expansion core. Hence, our theoretical results suggest that strong stubborn sets should be preferred to expansion core. Our empirical evaluation on all optimal benchmarks from the international planning competitions up to 2011 supports the theoretical results.
Using DNA microarrays to study gene expression in closely related species

MOTIVATION Comparisons of gene expression levels within and between species have become a central tool in the study of the genetic basis for phenotypic variation, as well as in the study of the evolution of gene regulation. DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. Thus, in order to study gene expression levels in species for which microarrays are not available, researchers face three sets of choices: (i) use a microarray designed for another species, but only compare gene expression levels within species, (ii) construct a new microarray for every species whose gene expression profiles will be compared or (iii) build a multi-species microarray with probes from each species of interest. Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach. RESULTS We find that, for inter-species comparisons, estimates of expression differences based on multi-species microarrays are more accurate than those based on multiple species-specific arrays. We also demonstrate that within-species expression differences can be estimated using a microarray for a closely related species, without discernible loss of information. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Interconnect-Efficient LDPC Code Design

In this paper, we present a new, hardware-oriented technique for designing Low Density Parity Check (LDPC) codes. The technique targets to achieve an interconnect- efficient architecture that reduces the area and delay of the decoder implementation while maintaining good error correction performance. With a fully parallel implementation of the LDPC decoder, the proposed design assumes a constraint on the interconnect wire length which has a direct impact on the maximum signal delay and power dissipation. Furthermore, this design approach is shown to lower interconnect routing congestion, and hence reduce the chip area and maximize chip utilization.
End-to-End Optimization of High-Throughput DNA Sequencing

At the core of Illumina's high-throughput DNA sequencing platforms lies a biophysical surface process that results in a random geometry of clusters of homogeneous short DNA fragments typically hundreds of base pairs long-bridge amplification. The statistical properties of this random process and the lengths of the fragments are critical as they affect the information that can be subsequently extracted, that is, density of successfully inferred DNA fragment reads. The ensembles of overlapping DNA fragment reads are then used to computationally reconstruct the much longer target genome sequence. The success of the reconstruction in turn depends on having a sufficiently large ensemble of DNA fragments that are sufficiently long. In this article using stochastic geometry, we model and optimize the end-to-end flow cell synthesis and target genome sequencing process, linking and partially controlling the statistics of the physical processes to the success of the final computational step. Based on a rough calibration of our model, we provide, for the first time, a mathematical framework capturing the salient features of the sequencing platform that serves as a basis for optimizing cost, performance, and/or sensitivity analysis to various parameters.