Miracle-dz/UniFAR-FTUs huggingface dataset:
Top-k Spatio-Textual Similarity Join

With the development of location-based services (LBS), LBS users are generating more and more spatio-textual data, e.g., checkins and attraction reviews. Since a spatio-textual entity may have different representations, possibly due to GPS deviations or typographical errors, it calls for effective methods to integrate the spatio-textual data from different data sources. In this paper, we study the problem of top-<inline-formula><tex-math>$k$</tex-math> <alternatives><inline-graphic xlink:type="simple" xlink:href="li-ieq1-2485213.gif"/></alternatives></inline-formula> spatio-textual similarity join (<sc>Topk-STJoin</sc>), which identifies the <inline-formula><tex-math>$k$</tex-math><alternatives> <inline-graphic xlink:type="simple" xlink:href="li-ieq2-2485213.gif"/></alternatives></inline-formula> most similar pairs from two spatio-textual data sets. One big challenge in <sc>Topk-STJoin</sc> is to efficiently identify the top-<inline-formula> <tex-math>$k$</tex-math><alternatives><inline-graphic xlink:type="simple" xlink:href="li-ieq3-2485213.gif"/></alternatives></inline-formula> similar pairs by considering both textual relevancy and spatial proximity. Traditional join algorithms that consider only one dimension (textual or spatial) are inefficient because they cannot utilize the pruning ability on the other dimension. To address this challenge, we propose a signature-based top-<inline-formula><tex-math>$k$</tex-math> <alternatives><inline-graphic xlink:type="simple" xlink:href="li-ieq4-2485213.gif"/></alternatives></inline-formula> join framework. We first generate a spatio-textual signature set for each object such that if two objects are in the top-<inline-formula> <tex-math>$k$</tex-math><alternatives><inline-graphic xlink:type="simple" xlink:href="li-ieq5-2485213.gif"/></alternatives></inline-formula> similar pairs, their signature sets must overlap. With this property, we can prune large numbers of dissimilar pairs without common signatures. We find that the order of accessing the signatures has a significant effect on the performance. So, we compute an upper bound for each signature and propose a best-first accessing method that preferentially accesses signatures with large upper bounds while those pairs with small upper bounds can be pruned. We prove the optimality of our best-first accessing method. Next, we optimize the spatio-textual signatures and propose progressive signatures to further improve the pruning power. Experimental results on real-world datasets show that our algorithm achieves high performance and good scalability, and significantly outperforms baseline approaches.
Learning nonsingular phylogenies and hidden Markov models

In this paper, we study the problem of learning phylogenies and hidden Markov models. We call a Markov model nonsingular if all transition matrices have determinants bounded away from 0 (and 1). We highlight the role of the nonsingularity condition for the learning problem. Learning hidden Markov models without the nonsingularity condition is at least as hard as learning parity with noise. On the other hand, we give a polynomial-time algorithm for learning nonsingular phylogenies and hidden Markov models.
Leukoencephalopathy with spheroids (HDLS) and pigmentary leukodystrophy (POLD)

Hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) and familial pigmentary orthochromatic leukodystrophy (POLD) present as adult-onset dementia with motor impairment and epilepsy. They are regarded as distinct diseases. We review data from the literature that support their being a single entity. Apart from a slightly older age at onset, a more rapid course, and more prominent pyramidal tract involvement, familial POLD is clinically similar to HDLS. Moreover, the pathologic hallmarks of the two diseases, axonal spheroids in HDLS and pigmented macrophages in POLD, can be identified in both conditions. This supports HDLS and POLD being referred collectively as adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP).
Knowledge-intensive Processes: An Overview of Contemporary Approaches

Engineering of knowledge-intensive processes is far from being mastered. Processes are defined knowledge-intensive when people/agents carry them out in a fair degree of “uncertainty”, where the uncertainty depends on different factors, such as the high number of tasks to be represented, their unpredictable nature, or their dependency on the scenario. In the worst case, there is no pre-defined view of the knowledge-intensive process, and tasks are mainly discovered as the process unfolds. In this work, starting from three different real scenarios, we present a critical comparative analysis of the existing approaches used for supporting knowledge-intensive processes, and we discuss some recent research techniques that may complement or extend the existing state of
The IWSLT 2011 Evaluation Campaign on Automatic Talk Translation

We report here on the eighth evaluation campaign organized in 2011 by the IWSLT workshop series. That IWSLT 2011 evaluation focused on the automatic translation of public talks and included tracks for speech recognition, speech translation, text translation, and system combination. Unlike in previous years, all data supplied for the evaluation has been publicly released on the workshop website, and is at the disposal of researchers interested in working on our benchmarks and in comparing their results with those published at the workshop. This paper provides an overview of the IWSLT 2011 evaluation campaign, and describes the data supplied, the evaluation infrastructure made available to participants, and the subjective evaluation carried out.
Engineering Multiversion Neural-Net Systems

In this paper we address the problem of constructing reliable neural-net implementations, given the assumption that any particular implementation will not be totally correct. The approach taken in this paper is to organize the inevitable errors so as to minimize their impact in the context of a multiversion system, i.e., the system functionality is reproduced in multiple versions, which together will constitute the neural-net system. The unique characteristics of neural computing are exploited in order to engineer reliable systems in the form of diverse, multiversion systems that are used together with a "decision strategy" (such as majority vote). Theoretical notions of "methodological diversity" contributing to the improvement of system performance are implemented and tested. An important aspect of the engineering of an optimal system is to overproduce the components and then choose an optimal subset. Three general techniques for choosing final system components are implemented and evaluated. Several different approaches to the effective engineering of complex multiversion systems designs are realized and evaluated to determine overall reliability as well as reliability of the overall system in comparison to the lesser reliability of component substructures.
Priority Union and Generalization in Discourse Grammars

We describe an implementation in Carpenter's typed feature formalism, ALE, of a discourse grammar of the kind proposed by Scha, Polanyi, et al. We examine their method for resolving parallelism-dependent anaphora and show that there is a coherent feature-structural rendition of this type of grammar which uses the operations of priority union and generalization. We describe an augmentation of the ALE system to encompass these operations and we show that an appropriate choice of definition for priority union gives the desired multiple output for examples of VP-ellipsis which exhibit a strict/sloppy ambiguity.
A needed narrowing strategy

The narrowing relation over terms constitutes the basis of the most important operational semantics of languages that integrate functional and logic programming paradigms. It also plays an important role in the definition of some algorithms of unification modulo equational theories that are defined by confluent term rewriting systems. Due to the inefficiency of simple narrowing, many refined narrowing strategies have been proposed in the last decade. This paper presents a new narrowing strategy that is optimal in several respects. For this purpose, we propose a notion of a needed narrowing step that, for inductively sequential rewrite systems, extends the Huet and Lévy notion of a needed reduction step. We define a strategy, based on this notion, that computes only needed narrowing steps. Our strategy is sound and complete for a large class of rewrite systems, is optimal with respect to the cost measure that counts the number of distinct steps of a derivation, computes only incomparable and disjoint unifiers, and is efficiently implemented by unification.
Do Strength‐Related Attitude Properties Determine Susceptibility to Response Effects? New Evidence From Response Latency, Attitude Extremity, and Aggregate Indices

A great deal of research has shown that small changes in question wording, format, orordering can sometimes substantially alter people's reports of their attitudes. Althoughmany scholars have presumed that these so-called response effects are likely to be morepronounced when the attitudes being measured are weak, a number of studies have disconfirmedthis notion. This paper presents several new tests of this hypothesis using a variety of measuresand analytic techniques. The findings largely replicated previously documented effects andnon-effects but also uncovered new effects not previously tested. No single strength-relatedattitude attribute emerged as a consistent moderator of all response effects. Rather, differentindividual attributes moderated different effects, and a conglomeration of strength-relateddimensions did not emerge as a reliable moderator. Taken together, these results support theconclusions that different response effects occur as the result of different cognitive processes,and that various strength-related attitude attributes reflect distinct latent constructs rather than asingle one.
Bed sediment entrainment by streamflow: State of the science

In fluvial sedimentology, bed sediment entrainment by streamflow has a decisive role in controlling several fluvial processes. Owing to its huge practical importance, the subject has been painstakingly explored for over a century. However, a detailed understanding of the mechanism of the bed sediment entrainment phenomenon achieved hitherto is far from complete. The central theme of bed sediment entrainment is occupied by the sediment entrainment threshold, which varies enormously in its qualitative definition, identification and quantification encompassing a broad range of spatiotemporal scales. This article presents the state of the science of the entrainment of non‐cohesive bed sediments under a steady‐unidirectional streamflow. It begins with the diverse definitions and representations of the entrainment threshold criterion from both qualitative and quantitative perspectives, scrutinising its suitability and ambit of applicability. Then, the effects of energetic factors that drive the entrainment threshold criterion are critically appraised. The indispensable mechanisms of bed sediment entrainment, including the theoretical background and modelling strategies, the role of turbulent bursting phenomenon and the phenomenological perspective into the origin of the scaling laws of sediment entrainment, are explained. Throughout the article, special emphasis is given to the strengths and weaknesses of the current state of the science. In addition, a deliberate attempt is made to invoke the thought‐provoking ideas on the multifarious features of bed sediment entrainment. Finally, the innovative perspectives on the bed sediment entrainment are provided and the concluding remarks are made, elucidating the major challenges and suggesting the prospective ways to resolve them as a future scope of research.
Responses of Dorsal Cochlear Nucleus Neurons to Signals in the Presence of Modulated Maskers

The detection of a signal in noise is enhanced when the masking noise is coherently modulated over a wide range of frequencies. This phenomenon, known as comodulation masking release (CMR), has been attributed to across-channel processing; however, the relative contribution of different stages in the auditory system to such across-channel processing is unknown. It has been hypothesized that wideband or lateral inhibition may underlie a physiological correlate of CMR. To further test this hypothesis, we have measured the responses of single units from the dorsal cochlear nucleus in which wideband inhibition is particularly pronounced. Using a sinusoidally amplitude-modulated tone at the best frequency of each unit as a masker, a pure-tone signal was added in the dips of the masker modulation. Flanking bands (FBs, also amplitude-modulated pure tones) were positioned to fall within the inhibitory sidebands of the receptive field of the unit. The FBs were either in phase (comodulated) or out of phase (codeviant) with the on-frequency masker. For the majority of units, the addition of the comodulated FBs produced a strong reduction in the response to the masker modulation, making the signal more salient in the post stimulus time histograms. The change in spike rate in response to the signal between the masker and signal-plus-masker conditions was greatest for the comodulated condition for 29 of 45 units. These results are consistent with the hypothesis that wideband inhibition may play a role in across-channel processing at an early stage in the auditory pathway.
Long–term genetic shifts in a microcrustacean egg bank associated with anthropogenic changes in the Lake Constance ecosystem

Diapausing egg banks of aquatic zooplankton have the potential to remain viable for decades or even centuries, and can thus harbour potentially high levels of genetic variation. Diapausing (ephippial) eggs from the Daphnia galeata–hyalina complex (Crustacea: Anomopoda) in Lake Constance (Bodensee), Germany, were isolated from sections of dated sediment cores, hatched in the laboratory, and established as a clone bank. We used cellulose acetate electrophoresis at four polymorphic enzyme loci (Pgm, Pgi, Ao, and Got) to examine long–term temporal changes in the genetic composition of the hatchling pool. Our results indicate that significant shifts have occurred in the genetic structure of this population, which parallel concomitant shifts in the trophic state of Lake Constance during the past 25–35 years. Here we discuss the utility of egg bank propagules as good model organisms to study microevolution, as related to past environmental change.
Escherichia coli O157:H7 Strain Origin, Lineage, and Shiga Toxin 2 Expression Affect Colonization of Cattle

ABSTRACT Enterohemorrhagic Escherichia coli O157:H7 has evolved into an important human pathogen with cattle as the main reservoir. The recent discovery of E. coli O157:H7-induced pathologies in challenged cattle has suggested that previously discounted bacterial virulence factors may contribute to the colonization of cattle. The objective of the present study was to examine the impact of lineage type, cytotoxin activity, and cytotoxin expression on the amount of E. coli O157:H7 colonization of cattle tissue and cells in vitro. Using selected bovine- and human-origin strains, we determined that lineage type predicted the amount of E. coli O157:H7 strain colonization: lineage I > intermediate lineages > lineage II. All E. coli O157:H7 strain colonization was dose dependent, with threshold colonization at 103 to 105 CFU and maximum colonization at 107 CFU. We also determined that an as-yet-unknown factor of strain origin was the most dominant predictor of the amount of strain colonization in vitro. The amount of E. coli O157:H7 colonization was also influenced by strain cytotoxin activity and the inclusion of cytotoxins from lineage I or intermediate lineage strains increased colonization of a lineage II strain. There was a higher level of expression of the Shiga toxin 1 gene (stx1) in human-origin strains than in bovine-origin strains. In addition, lineage I strains expressed higher levels of the Shiga toxin 2 gene (stx2). The present study supports a role for strain origin, lineage type, cytotoxin activity, and stx2 expression in modulating the amount of E. coli O157:H7 colonization of cattle.
Atypical Chikungunya virus infections: clinical manifestations, mortality and risk factors for severe disease during the 2005–2006 outbreak on Réunion

SUMMARY In April 2005, an outbreak of Chikungunya fever occurred on the island of Réunion in the Indian Ocean. During winter 2005, six patients developed meningoencephalitis and acute hepatitis due to Chikungunya virus. Our objectives were to determine the incidence and mortality of atypical Chikungunya viral infections and to identify risk factors for severe disease. A hospital-based surveillance system was established to collect data on atypical Chikungunya cases. Case reports, medical records and laboratory results were reviewed and analysed. We defined an atypical case as one in which a patient with laboratory-confirmed Chikungunya virus infection developed symptoms other than fever and arthralgia. We defined a severe atypical case as one which required maintenance of at least one vital function. We recorded 610 atypical cases of Chikungunya fever: 222 were severe cases, 65 affected patients died. Five hundred and forty-six cases had underlying medical conditions (of which 226 suffered from cardiovascular, 147 from neurological and 150 from respiratory disorders). Clinical features that had never been associated with Chikungunya fever were recorded, such as bullous dermatosis, pneumonia, and diabetes mellitus. Hypertension, and underlying respiratory or cardiological conditions were independent risk factors for disease severity. The overall mortality rate was 10·6% and it increased with age. This is the first time that severe cases and deaths due to Chikungunya fever have been documented. The information presented in this article may assist clinicians in identifying the disease, selecting the treatment strategy, and anticipating the course of illness.
Chemotherapy increases long-term survival in patients with adult medulloblastoma--a literature-based meta-analysis.

BACKGROUND Adult medulloblastoma is a potentially curable malignant entity with an incidence of 0.5-1 per million. Valid data on prognosis, treatment, and demographics are lacking, as most current knowledge stems from retrospective studies. Surgical resection followed by radiotherapy are accepted parts of treatment regimes; however, established prognostic factors and data clarifying the role of chemotherapy are missing. METHODS We investigated 227 publications from 1969-2013, with 907 identifiable, individual patients being available for meta-analysis. Demographic data, risk stratification, and treatment of these patients were similar to previous cohorts. RESULTS The median overall survival (mOS) was 65 months (95% CI: 54.6-75.3) , the 5-year overall survival was 50.9% with 16% of the patients dying more than 5 years after diagnosis. Incomplete resection, clinical and radiological signs for brainstem infiltration, and abstinence from radiotherapy were predictive of worse outcome. Metastatic disease at tumor recurrence was identified as a new prognostic factor, while neither metastasis at initial diagnosis nor desmoplastic/classic histology was correlated with survival. Patients receiving chemotherapy first-line survived significantly longer (mOS: 108 mo, 95% CI: 68.6-148.4) than patients treated with radiation alone (mOS: 57 mo, 95% CI: 39.6-74.4) or patients who received chemotherapy at tumor recurrence. This effect was not biased by tumor stage or decade of treatment. Importantly, (neo)adjuvant chemotherapy also significantly increased the chance for long-term survival (>5 y) compared with radiotherapy alone or chemotherapy at tumor recurrence. CONCLUSIONS This meta-analysis clarifies relevant prognostic factors and suggests that chemotherapy as part of first-line therapy improves overall survival and increases the proportion of patients with long-term survival.
Human Papillomavirus and Long-term Oral Contraceptive Use Increase the Risk of Adenocarcinoma in Situ of the Cervix 1

We examined United States Surveillance, Epidemiology, and End Results incidence data and conducted a population-based case-control study to examine the role of human papillomavirus (HPV) and oral contraceptive (OC) use in the etiology of adenocarcinomain situ of the cervix (ACIS). One hundred and fifty women diagnosed with ACIS and 651 randomly selected control women completed in-person interviews. The presence of HPV DNA in archival ACIS specimens was determined by E6 and L1 consensus PCR. Serum samples from case and control subjects were collected at interview, and antibodies to HPV-16 L1 and HPV-18 L1 were detected by virus-like particle capture assays. The overall prevalence of HPV DNA was 86.6%, with 39.0% positive for HPV-16 DNA, 52.4% positive for HPV-18 DNA, and 13.4% positive for more than one HPV type. The ageadjusted relative risk of ACIS associated with HPV-18 seropositivity was 3.3 (95% confidence interval 2.2–4.9). No increased risk was associated with antibodies to HPV16 L1. Among women born after 1945, the relative risk increased with duration of OC use, with the highest risk for 12 or more years of use (odds ratio, 5.5; 95% confidence interval, 2.1–14.6) relative to nonusers. The detection of HPV DNA in 86.6% of ACIS and the strong association of ACIS with HPV-18 L1 seropositivity underscore the importance of HPV, particularly HPV-18, in the etiology of ACIS. In addition, long-term OC use may contribute to the pathogenesis of these tumors in some women.
Integrated gene and species phylogenies from unaligned whole genome protein sequences

MOTIVATION Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments. In this work, the singular value decomposition of a sparse tetrapeptide frequency matrix is used to represent the proteins of organisms uniquely and precisely as vectors in a high-dimensional space. Vectors of this kind can be used to calculate pairwise distance values based on the angle separating the vectors, and the resulting distance values can be used to generate phylogenetic trees. Protein trees so derived can be examined directly for homologous sequences. Alternatively, vectors defining each of the proteins within an organism can be summed to provide a vector representation of the organism, which is then used to generate species trees. RESULTS Using a large mitochondrial genome dataset, we have produced species trees that are largely in agreement with previously published trees based on the analysis of identical datasets using different methods. These trees also agree well with currently accepted phylogenetic theory. In principle, our method could be used to compare much larger bacterial or nuclear genomes in full molecular detail, ultimately allowing accurate gene and species relationships to be derived from a comprehensive comparison of complete genomes. In contrast to phylogenetic methods based on alignments, sequences that evolve by relative insertion or deletion would tend to remain recognizably similar.