Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Formal Comparison of Ontology Linking, Mapping and Importing

Multiple distributed and modular ontology representation frameworks have recently appeared. They typically extend Description Logics (DL), with new constructs to represent relations between entities across several ontologies. Three kinds of constructs appear in the liter- ature: link properties, found in E-connections, semantic mapping, found in Distributed Description Logics (DDL), and semantic imports, used in Package-based Description Logics (P-DL). In this work, we aim towards formal comparison of the expressive power of these frameworks, and thus also the ontology combination paradigms that they instantiate. Reduc- tion from DDL to E-connections is already known. We present two new reductions, from P-DL to DDL and vice versa. These results show that there are similarities between these frameworks. However, due to the fact that none of the reductions is unconditional, it cannot be claimed that any of the three approaches is strictly more expressive than another.
Metabolizing enzyme localization and activities in the first trimester human placenta: the effect of maternal and gestational age, smoking and alcohol consumption.

BACKGROUND The rationale for this study was to assess the expression, activity and localization of the enzymes uridine diphosphate glucuronosyltransferase (UGT), beta-glucuronidase, cytochrome P450 1A (CYP1A) and cytochrome P450 2E1 (CYP2E1) in first trimester human placenta and to gauge the effects of maternal variables on placental metabolism. METHODS CYP1A, CYP2E1, UGT and beta-glucuronidase activities were assessed in 25 placentas using ethoxyresorufin, chlorzoxazone, 4-methylumbelliferone and 4-methylumbelliferone glucuronide respectively. Protein expression and localization were detected by immunoblot and immunohistochemistry. All statistics were non-parametric. RESULTS UGT, beta-glucuronidase and CYP1A activities were detected in all placentas sampled; CYP2E1 was undetectable. CYP1A, UGT1A UGT2B proteins were detected in all placentas (n = 6) tested and CYP2E1 in 4/6 placentas sampled and were localized to the syncytium. UGT and CYP1A activities were significantly elevated in the placentas of mothers who smoked (P < 0.05 and P < 0.001 respectively) and were greatest in women who both smoked and drank alcohol (P < 0.05 and P < 0.01 respectively). Enzyme activities were significantly negatively correlated with gestational age (P < 0.05, r = 0.54, UGT) and maternal age respectively (P < 0.001, r = 0.63, CYP1A). beta-Glucuronidase activity did not differ with patient variables. CONCLUSIONS Metabolism of compounds by the human placenta in the first trimester may be affected by maternal and environmental factors altering the activity of constitutive metabolizing enzymes.
BOOTSTRAPPING GMM ESTIMATORS FOR TIME SERIES by Atsushi Inoue and Mototsugu Shintani Working

This paper establishes that the bootstrap provides asymptotic refinements for the generalized method of moments estimator of overidentified linear models when autocorrelation structures of moment functions are unknown. When moment functions are uncorrelated after finite lags, Hall and Horowitz (1996) showed that errors in the rejection probabilities of the t test and the test of overidentifying restrictions based on the bootstrap are o(T−1). In general, however, this rate cannot be obtained with the heteroskedasticity and autocorrelation consistent (HAC) covariance matrix estimator since it converges at a nonparametric rate. By incorporating the HAC covariance matrix estimator in the Edgeworth expansion of the distribution, we show that the bootstrap approximation improves upon the first-order asymptotic approximation when the characteristic exponent of the kernel function is greater than two. The class of such kernels include the trapezoidal kernel and the Parzen (b) kernel as well as the truncated kernel. Monte Carlo evidence and an application to the monetary policy reaction function are also provided. JEL classification: C12; C22; C32
Novel genetic markers improve measures of atrial fibrillation risk prediction

Aims Atrial fibrillation (AF) is associated with adverse outcome. Whether recently discovered genetic risk markers improve AF risk prediction is unknown. Methods and results We derived and validated a novel AF risk prediction model from 32 possible predictors in the Women's Health Study (WHS), a cohort of 20 822 women without cardiovascular disease (CVD) at baseline followed prospectively for incident AF (median: 14.5 years). We then created a genetic risk score (GRS) comprised of 12 risk alleles in nine loci and assessed model performance in the validation cohort with and without the GRS. The newly derived WHS AF risk algorithm included terms for age, weight, height, systolic blood pressure, alcohol use, and smoking (current and past). In the validation cohort, this model was well calibrated with good discrimination [C-index (95% CI) = 0.718 (0.684–0.753)] and improved all reclassification indices when compared with age alone. The addition of the genetic score to the WHS AF risk algorithm model improved the C-index [0.741 (0.709–0.774); P = 0.001], the category-less net reclassification [0.490 (0.301–0.670); P < 0.0001], and the integrated discrimination improvement [0.00526 (0.0033–0.0076); P < 0.0001]. However, there was no improvement in net reclassification into 10-year risk categories of <1, 1–5, and 5+% [0.041 (−0.044–0.12); P = 0.33]. Conclusion Among women without CVD, a simple risk prediction model utilizing readily available risk markers identified women at higher risk for AF. The addition of genetic information resulted in modest improvements in predictive accuracy that did not translate into improved reclassification into discrete AF risk categories.
Fostering Efficiency in Information Systems Support for Product-Service Systems in the Manufacturing Industry

The ongoing shift towards stronger service orientation is leading to a rising number of industrial services offered in the manufacturing industry. In the attempt to fulfill ever-increasing service demands while at the same time reducing operating costs, manufacturing firms search for appropriate information technology (IT) solution for planning and execution. The industry has not yet reached a common understanding of product-service systems and the corresponding processes and IT systems. In order to holistically support such broad design and transformation tasks, we develop a maturity model capturing the key requirements for the information systems (IS) support of product-service systems based on a multiple case study. For a critical reflection on the extant literature, we compared those requirements with scientifically recognized maturity models and standard specifications. Being an integral part of the design science research approach, the model evaluation is organized in accordance with approved evaluation perspectives.
Characterization of the Block in Replication of Nucleocapsid Protein Zinc Finger Mutants from Moloney Murine Leukemia Virus

ABSTRACT Mutagenesis studies have shown that retroviral nucleocapsid (NC) protein Zn2+ fingers (-Cys-X2-Cys-X4-His-X4-Cys- [CCHC]) perform multiple functions in the virus life cycle. Moloney murine leukemia virus mutants His 34→Cys (CCCC) and Cys 39→His (CCHH) were able to package their genomes normally but were replication defective. Thermal dissociation experiments showed that the CCHH mutant was not defective in genomic RNA dimer structure. Primer tRNA placement on the viral genome and the ability of the tRNA to function in reverse transcription initiation in vitro also appear normal. Some “full-length” DNA copies of the viral genome were synthesized in mutant virus-infected cells. The CCCC and CCHH mutants produced these DNA copies at greatly reduced levels. Circle junction fragments, amplified from two-long-terminal-repeat viral DNA (vDNA) by PCR, were cloned and characterized. Remarkably, it was discovered that vDNA isolated from cells infected with mutant virions had a wide variety of abnormalities at the site at which the two ends of the linear precursor had been ligated to form the circle (i.e., the junction between the 5′ end of U3 and the 3′ end of U5). In some molecules, bases were missing from regions corresponding to the U3 and U5 linear vDNA termini; in others, the viral sequences extended either beyond the U5 sequences into the primer-binding site and 5′ leader or beyond the U3 sequences into the polypurine tract into the env coding region. Still other molecules contained nonviral sequences between the linear vDNA termini. Such defective genomes would certainly be unsuitable substrates for integration. Thus, strict conservation of the CCHC structure in NC is required for infection events prior to and possibly including integration.
Coherent-to-Diffuse Power Ratio Estimation for Dereverberation

The estimation of the time- and frequency-dependent coherent-to-diffuse power ratio (CDR) from the measured spatial coherence between two omnidirectional microphones is investigated. Known CDR estimators are formulated in a common framework, illustrated using a geometric interpretation in the complex plane, and investigated with respect to bias and robustness towards model errors. Several novel unbiased CDR estimators are proposed, and it is shown that knowledge of either the direction of arrival (DOA) of the target source or the coherence of the noise field is sufficient for unbiased CDR estimation. The validity of the model for the application of CDR estimates to dereverberation is investigated using measured and simulated impulse responses. A CDR-based dereverberation system is presented and evaluated using signal-based quality measures as well as automatic speech recognition accuracy. The results show that the proposed unbiased estimators have a practical advantage over existing estimators, and that the proposed DOA-independent estimator can be used for effective blind dereverberation.
From prolactin cell to prolactinoma: implications of ontogenic mechanisms in diagnosis and management

Today, most patients with hyperprolactinemia are taken care of by endocrinologists, general internists and gynecologists. With the development of reliable and sensitive hormone assays, the introduction of high definition imaging techniques, and studies of prolactin (PRL) physiology and gene regulation, our understanding of the pathogenesis of prolactinoma in humans has progressed at an astonishing pace over the past 20 years. Clinicians are now relating their clinical findings and therapeutic decisions to this new knowledge of the pathogenesis and biological behavior of human prolactinomas.
Stochastic bounds for randomized load balancing

Randomized load balancing is a cost efficient policy for job scheduling in parallel server queueing systems whereby, with every incoming job, a central dispatcher randomly polls some servers and selects the one with the smallest queue. By exactly deriving the jobsâ delay distribution in such systems, in explicit and closed form, Mitzenmacher [5] proved the socalled â power-of-twoâ result, which states that by randomly polling only two servers yields an exponential improvement in delay over randomly selecting a single server. Such a fundamental result, however, was obtained in an asymptotic regime in the total number of servers, and does do not necessarily provide accurate estimates for practical finite regimes with small or moderate number of servers. In this paper we obtain stochastic lower and upper bounds on the jobsâ average delay in non-asymptotic regimes, by borrowing ideas for analyzing the particular case of the Join-the-Shortest-Queue (JSQ) policy. Numerical illustrations indicate not only that the obtained bounds are remarkably accurate, but also that the existing exact but asymptotic results can be largely misleading in some finite regimes.
Superpure digraph designs

A digraph design is a decomposition of a complete (symmetric) digraph into copies of pre‐specified digraphs. Well‐known examples for digraph designs are Mendelsohn designs, directed designs or orthogonal directed covers. A digraph design is superpure if any two of the subdigraphs in the decomposition have no more than two vertices in common. We give an asymptotic existence theorem for superpure digraph designs, which is a variation of an earlier result of Lamken and Wilson J Combin Theory Ser A 89: 149–200, 2000. As an immediate consequence, we obtain new results for supersimple designs and pure perfect Mendelsohn designs. © 2002 Wiley Periodicals, Inc. J Combin Designs 10: 239–255, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jcd.10013
Neural Dynamics of Single Units in Rat's Agranular Medial and Agranular Lateral Areas during Learning of a Directional Choice Task

Learning by trial-and-error requires retrospective information that whether a past action resulted in a rewarded outcome. Previous outcome in turn may provide information to guide future behavioral adjustment. But the specific contribution of this information to learning a task and the neural representations during the trial-anderror learning process is not well understood. In this dissertation, such learning is analyzed by means of single unit neural recordings in the rats’ motor agranular medial (AGm) and agranular lateral (AGl) while the rats learned to perform a directional choice task. Multichannel chronic recordings using implanted microelectrodes in the rat’s brain were essential to this study. Also for fundamental scientific investigations in general and for some applications such as brain machine interface, the recorded neural waveforms need to be analyzed first to identify neural action potentials as basic computing units. Prior to analyzing and modeling the recorded neural signals, this dissertation proposes an advanced spike sorting system, the M-Sorter, to extract the action potentials from raw neural waveforms. The M-Sorter shows better or comparable performance compared with two other popular spike sorters under automatic mode. With the sorted action potentials in place, neuronal activity in the AGm and AGl areas in rats during learning of a directional choice task is examined. Systematic analyses suggest that rats neural activity in AGm and AGl was modulated by previous trial outcomes during learning. Single unit based neural dynamics during task learning are described in detail in the dissertation. Furthermore, the differences in neural modulation between fast and slow learning rats were compared. The results show that the level of neural modulation of previous trial outcome is different in fast and slow learning rats which may in turn suggest an important role of previous trial outcome encoding in learning.
Computational Identification of Four Spliceosomal snRNAs from the Deep-Branching Eukaryote Giardia intestinalis

RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs) and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5) and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes.
Wiener?s Prefiguring of a Cybernetic Design Theory

Norbert Wiener was not only one of the inventors of cybernetics, but also an early cybernetician of invention (i.e., design). Wiener operated between what is (scientifically describable) and what ought to be (designed). He also reflected theoretically on himself doing so, thereby enacting several concepts of today? s cybernetic design theory ? far ahead of his time.
Introduction to the Special Issue on Computational Linguistics Using Large Corpora

The 1990s have witnessed a resurgence of interest in 1950s-style empirical and statistical methods of language analysis. Empiricism was at its peak in the 1950s, dominat ing a broad set of fields ranging from psychology (behaviorism) to electrical engineering (information theory). At that time, it was common practice in linguistics to classify words not only on the basis of their meanings but also on the basis of their cooccurrence with other words. Firth, a leading figure in British linguistics during the 1950s, summar ized the approach with the memorable line: "You shall know a word by the company it keeps" (Firth 1957). Regrettably, interest in empiricism faded in the late 1950s and early 1960s with a number of significant events including Chomsky 's criticism of n-grams in Syntactic Structures (Chomsky 1957) and Minsky and Papert 's criticism of neural networks in Perceptrons (Minsky and Papert 1969). Perhaps the most immediate reason for this empirical renaissance is the availability of massive quantities of data: more text is available than ever before. Just ten years ago, the one-million word Brown Corpus (Francis and Ku~era, 1982) was considered large, but even then, there were much larger corpora such as the Birmingham Corpus (Sinclair et al. 1987; Sinclair 1987). Today, many locations have samples of text running into the hundreds of millions or even billions of words. Collections of this magni tude are becoming widely available, thanks to data collection efforts such as the Association for Computat ional Linguistics' Data Collection Initiative (ACL/DCI), the European Corpus Initiative (ECI), ICAME, the British National Corpus (BNC), the Linguistic Data Consort ium (LDC), the Consort ium for Lexical Research (CLR), Electronic Dictionary Research (EDR), and standardization efforts such as the Text Encoding Initiative (TEI). 1 The data-intensive approach to language, which is becoming known as Text Analysis, takes a pragmatic approach that is well suited to meet the recent emphasis on numerical evaluations and concrete deliverables. Text Analysis focuses on broad ( though possibly superficial) coverage of unrestricted text, rather than deep analysis of (artificially) restricted domains.
CAOPLE: A Programming Language for Microservices SaaS

The microservices architecture is widely regarded as a promising approach to service-oriented systems. However, developing applications in the microservices architecture presents three main challenges: (a) how to program systems that consists of a large number of services running in parallel and distributed over a cluster of computers, (b) how to reduce the communication overhead caused by executing a large number of small services, (c) how to support the flexible deployment of services to a network to achieve system load balance. This paper presents a programming language called CAOPLE and reports the implementation of the language on a virtual machine called CAVM-2. The paper demonstrates how this approach meets these challenges.
Triage: diagnosing production run failures at the user's site

Diagnosing production run failures is a challenging yet importanttask. Most previous work focuses on offsite diagnosis, i.e.development site diagnosis with the programmers present. This is insufficient for production-run failures as: (1) it is difficult to reproduce failures offsite for diagnosis; (2) offsite diagnosis cannot provide timely guidance for recovery or security purposes; (3)it is infeasible to provide a programmer to diagnose every production run failure; and (4) privacy concerns limit the release of information(e.g. coredumps) to programmers. To address production-run failures, we propose a system, called Triage, that automatically performs onsite software failure diagnosis at the very moment of failure. It provides a detailed diagnosis report, including the failure nature, triggering conditions, related code and variables, the fault propagation chain, and potential fixes. Triage achieves this by leveraging lightweight reexecution support to efficiently capture the failure environment and repeatedly replay the moment of failure, and dynamically--using different diagnosis techniques--analyze an occurring failure. Triage employs afailure diagnosis protocol that mimics the steps a human takes in debugging. This extensible protocol provides a framework to enable the use of various existing and new diagnosis techniques. We also propose a new failure diagnosis technique, delta analysis, to identify failure related conditions, code, and variables. We evaluate these ideas in real system experiments with 10 real software failures from 9 open source applications including four servers. Triage accurately diagnoses the evaluated failures, providing likely root causes and even the fault propagation chain, while keeping normal-run overhead to under 5%. Finally, our user study of the diagnosis and repair of real bugs shows that Triagesaves time (99.99% confidence), reducing the total time to fix by almost half.
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction

MOTIVATION Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases. Closely related organisms are most likely to have common regulatory motifs; however, the recent speciation of such organisms results in the high degree of correlation in their genome sequences, confounding the detection of functional elements. Additionally, alignment algorithms that use optimization techniques are limited to the detection of a single alignment that may not be representative. Comparative-genomics studies must be able to address the phylogenetic correlation in the data and efficiently explore the alignment space, in order to make specific and biologically relevant predictions. RESULTS We describe here a Gibbs sampler that employs a full phylogenetic model and reports an ensemble centroid solution. We describe regulatory motif detection using both simulated and real data, and demonstrate that this approach achieves improved specificity, sensitivity, and positive predictive value over non-phylogenetic algorithms, and over phylogenetic algorithms that report a maximum likelihood solution. AVAILABILITY The software is freely available at http://bayesweb.wadsworth. org/gibbs/gibbs.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.