Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating natural language processing systems

A variety of factions may be interested in evaluating natural language processing (NLP) systems, ranging from funding authorities who must choose between competing research projects and justify their choices through the results subsequently obtained, to the end user who needs to choose between competing products. If the product is expensive, or if it implies a major reorganization of workflow, the user may also need to provide post hoc justification. Surprisingly, the literature on evaluation is relatively sparse for several reasons. First, evaluations are often carried out under consultancy arrangements for a particular customer. Not only is the evaluation then tailor-made to suit that customer and therefore not considered to be of general interest, but the customer may be reluctant to have the results of the evaluation made public, either because of an agreement with the manufacturer whose product has been evaluated, or an unwillingness to reveal the results to competitors. Secondly, evaluation of research proposals and of projects in the academic area has traditionally been by peer review. This has changed somewhat in particular areas, under the influence of the DARPA/ARPA series of evaluations, but is still the most common pattern. The only result of a peer review evaluation is a report which is often confidential. Thirdly, evaluation acquired a bad name as a result of the Automatic Language Processing Advisory Committee’s (ALPAC) Evaluating Natural Language Processing Systems Designing customized methods for testing various NLP systems may be costly and
Circular RNA biogenesis can proceed through an exon-containing lariat precursor

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical ‘backsplicing’ event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure. DOI: http://dx.doi. org/10.7554/eLife.07540. 001
Kinesin family in murine central nervous system

In neuronal axons, various kinds of membranous components are transported along microtubules bidirectionally. However, only two kinds of mechanochemical motor proteins, kinesin and brain dynein, had been identified as transporters of membranous organelles in mammalian neurons. Recently, a series of genes that encode proteins closely related to kinesin heavy chain were identified in several organisms including Schizosaccharomyces pombe, Aspergillus niddulans, Saccharomyces cerevisiae, Caenorhabditus elegans, and Drosophila. Most of these members of the kinesin family are implicated in mechanisms of mitosis or meiosis. To address the mechanism of intracellular organelle transport at a molecular level, we have cloned and characterized five different members (KIF1-5), that encode the microtubule-associated motor domain homologous to kinesin heavy chain, in murine brain tissue. Homology analysis of amino acid sequence indicated that KIF1 and KIF5 are murine counterparts of unc104 and kinesin heavy chain, respectively, while KIF2, KIF3, and KIF4 are as yet unidentified new species. Complete amino acid sequence of KIF3 revealed that KIF3 consists of NH2-terminal motor domain, central alpha-helical rod domain, and COOH-terminal globular domain. Complete amino acid sequence of KIF2 revealed that KIF2 consists of NH2-terminal globular domain, central motor domain, and COOH-terminal alpha-helical rod domain. This is the first identification of the kinesin-related protein which has its motor domain at the central part in its primary structure. Northern blot analysis revealed that KIF1, KIF3, and KIF5 are expressed almost exclusively in murine brain, whereas KIF2 and KIF4 are expressed in brain as well as in other tissues. All these members of the kinesin family are expressed in the same type of neurons, and thus each one of them may transport its specific organelle in the murine central nervous system.
Endothelial Nitric Oxide Synthase and Superoxide Mediate Hemodynamic Initiation of Intracranial Aneurysms

Background Hemodynamic insults at arterial bifurcations are believed to play a critical role in initiating intracranial aneurysms. Recent studies in a rabbit model indicate that aneurysmal damage initiates under specific wall shear stress conditions when smooth muscle cells (SMCs) become pro-inflammatory and produce matrix metalloproteinases (MMPs). The mechanisms leading to SMC activation and MMP production during hemodynamic aneurysm initiation are unknown. The goal is to determine if nitric oxide and/or superoxide induce SMC changes, MMP production and aneurysmal remodeling following hemodynamic insult. Methods Bilateral common carotid artery ligation was performed on rabbits (n = 19, plus 5 sham operations) to induce aneurysmal damage at the basilar terminus. Ligated animals were treated with the nitric oxide synthase (NOS) inhibitor LNAME (n = 7) or the superoxide scavenger TEMPOL (n = 5) and compared to untreated animals (n = 7). Aneurysm development was assessed histologically 5 days after ligation. Changes in NOS isoforms, peroxynitrite, reactive oxygen species (ROS), MMP-2, MMP-9, and smooth muscle α-actin were analyzed by immunohistochemistry. Results LNAME attenuated ligation-induced IEL loss, media thinning and bulge formation. In untreated animals, immunofluorescence showed increased endothelial NOS (eNOS) after ligation, but no change in inducible or neuronal NOS. Furthermore, during aneurysm initiation ROS increased in the media, but not the intima, and there was no change in peroxynitrite. In LNAME-treated animals, ROS production did not change. Together, this suggests that eNOS is important for aneurysm initiation but not by producing superoxide. TEMPOL treatment reduced aneurysm development, indicating that the increased medial superoxide is also necessary for aneurysm initiation. LNAME and TEMPOL treatment in ligated animals restored α-actin and decreased MMPs, suggesting that eNOS and superoxide both lead to SMC de-differentiation and MMP production. Conclusion Aneurysm-inducing hemodynamics lead to increased eNOS and superoxide, which both affect SMC phenotype, increasing MMP production and aneurysmal damage.
MULTIPATH EFFECT MITIGATION IN SIGNAL PROPAGATION THROUGH AN INDOOR ENVIRONMENT

�A B S T R A C T Highly accurate positioning of an object is a target that requires measurements performed with devices (mainly Global Navigation Satellite System receivers) able to provide a satellite connection towards minimum four satellites. However, GNSS receivers face low accuracy in areas where the satellite signals are obstructed or even non-existent. In order to obtain location estimate in an Indoor environment, a series of Indoor Positioning Systems based on WLAN technology and pseudolites have been developed. Signal propagation in an Indoor environment is affected by several factors, among them the multipath effect, cause by reflective surfaces around the receiver. This paper aims at analyzing different methods for mitigating the multipath intereference on signal propagation.
Nearest Neighbor Searching in Image Databases

iii Abstract A frequently encountered type of query in image database systems is to nd the k most similar images to a query image with respect to its feature. Processing such queries requires substantially diierent search algorithms than those for the normal k nearest neighbor problem: dimensionality of the feature may be very high and similarity measure may not be as simple as a Euclidean distance. For this problem, low-dimensional transformation techniques were proposed, which map high dimensional feature values into a lower dimensional space and evaluate the original similarity metric only for those within some bound in lower dimension. This reduces the number of the high dimensional matchings. However, to guarantee no false dismissals, the existing methods use a maximal search space, which may be too wider than is practically needed. We propose an incremental ltering algorithm that can reduce the search space. The proposed algorithm rst chooses a minimal search space and incremetally expands it until the target number of results is obtained. This algorithm also guarantees no false dismissals and lower-bounds the existing methods with respect to the number of evaluations of the expensive measure. Abstract iii 1 Introduction 1
Late-Life Risk Factors for All-Cause Dementia and Differential Dementia Diagnoses in Women

AbstractSince the first evidence of a decline in dementia incidence was reported in 2011, the focus on modifiable risk factors has increased. The possibility of risk factor intervention as a prevention strategy has been widely discussed; however, further evidence in relation to risk factors is still needed.The Prospective Epidemiologic Risk Factor (PERF I) study was an observational prospective study of postmenopausal Danish women who were initially examined between 1999 and 2001 (n = 5855). Follow-up data on diagnosis and survival as of December 31, 2014 was retrieved from the National Danish Patient Registry and the National Danish Causes of Death Registry. Cox proportional hazards regression model was applied to calculate adjusted hazard ratios (HR) for selected risk factors for dementia.Of 5512 eligible subjects, 592 developed dementia within the follow-up period of maximum 15 years. The independent factors associated with increased risk of all-cause dementia were depression (HR = 1.75 [95% CI 1.32–2.34]) and impaired fasting glucose levels. A dose–response relationship was observed between fasting glucose level and risk of dementia with HRs of 1.25 [1.05–1.49] and 1.45 [1.03–2.06] for impaired (5.6–6.9 mmol/L) and hyperglycemic (≥7.0 mmol/L) glucose levels, respectively. The factors associated with a decreased risk of dementia were overweight in late-life (HR = 0.75 [0. 62–0.89]) and physical activity at least once weekly (HR = 0.77 [0.61–0.96]). The identified risk factors for dementia in women in late-life are all considered modifiable. This supports the notion that prevention strategies may improve the poor future prospects for dementias in the ageing population.
Tunable 1060nm VCSEL co-packaged with pump and SOA for OCT and LiDAR

A 1060 nm optically pumped tunable VCSEL was formed from an InGaAs/AlGaAs/GaAs half-VCSEL bonded to a MEMS movable mirror on a silicon substrate. The VCSEL was co-packaged in a 14-pin butterfly module with an 825 nm pump laser and a 1060 nm semiconductor optical amplifier. The co-packaged device exhibited shot-noise-limited sensitivity with up to 50 mW output power and 75 nm tunability. Ophthalmic OCT, especially whole-eye imaging and ocular biometry, is considered the primary application of this device. However, we have also investigated LiDAR to greater than 10 meter ranges with non-mechanical beam steering through angular diffraction from a grating. A new generation of photonic integrated circuit LiDARs work this way and we have investigated the depth resolution limitations due to time dispersion from the grating. Distributed fiber temperature sensing was also demonstrated.
Approximate Shortest Descent Path on a Terrain

A path from a point s to a point t on the surface of a polyhedral terrain is said to be descent if for every pair of points p = (x(p);y(p);z(p)) and q = (x(q);y(q);z(q)) on the path, if dist(s;p) < dist(s;q) then z(p) ‚ z(q), where dist(s;p) denotes the distance of p from s along the aforesaid path. Although an ecient algorithm to decide if there is a descending path between two points is known for more than a decade, no ecient algorithm is yet known to find a shortest descending path from s to t in a polyhedral terrain. In this paper we propose an (1 +†)-approximation algorithm running in polynomial time for the same.
Quality of life and aphasia. Multicentric standardization of a questionnaire.

AIM It is important to assess aphasics' quality of life in order to plan a rehabilitation treatment. To date such a tool is still missing for Italian patients. This paper reports normative data of the Italian version of SAQOL-39, a British questionnaire aimed to assess aphasics' quality of life. It consists of 39 items, divided into 4 subdomains (Physical, Communication, Psychosocial and Energy). METHODS Forty-two patients coming from 3 different Speech Therapy Services were enrolled. All patients completed speech therapy before examination. They were submitted to the Italian SAQOL-39 and 2 screening tests for aphasia: 1) Communication Assessment Scale according Goodglass and Kaplan; 2) Franchay Aphasia Screening Test (FAST). A receptive FAST score of 7 out of 15 was used as a cut-off score for SAQOL-39 administration. RESULTS The Italian SAQOL-39 showed good internal consistency (full scale Cronbach's alpha 0.939). Cronbach's alpha for every subdomains ranged from 0.950 (Communication) to 0.720 (Energy). Fluent aphasics gave significantly higher scores than nonfluent ones on full scale, and all out of Energy subdomains. Furthermore gravity of aphasia correlated with both full scale and Communication subdomain scores. CONCLUSIONS In authors' opinion, the Italian SAQOL-39 shares many psychometric features with the English one. This questionnaire seems to be suitable for clinical practice.
Link-based Community Detection with the Commute-Time Kernel

The main purpose of this work is to find communities in a weighted, undirected, graph by using kernel-based clustering methods, directly partitioning the graph according to a well-defined similarity measure between the nodes (a kernel on a graph). The algorithm is based on a two-step procedure. First, the sigmoid commute-time kernel (KCT), providing a meaningful similarity measure between any couple of nodes, is computed from the adjacency matrix of the graph. Then, the nodes of the graph are clustered by performing a kernel clustering on this CT kernel matrix. For this purpose, simple, prototype-based, kernel versions of the k-means, the fuzzy k-means, the entropy-based fuzzy k-means, the gaussian mixtures model, as well as Ward’s hierarchical clustering, are introduced. The joint use of the CT kernel matrix and kernel clustering appears to be quite effective. Indeed, this methodology provides good results, outperforming the spherical k-means and spectral clustering, on a document clustering problem involving the newsgroups database, where the set of documents is viewed as a graph. Finally, the links between the proposed hierarchical kernel clustering and spectral clustering are examined.
Targeted treatment of acute myeloid leukemia in older adults: role of gemtuzumab ozogamicin

As the overall prognosis and treatment response rate to standard chemotherapy for acute myeloid leukemia (AML) remains poor in the older adult population, there is a need for more effective therapeutic agents with lower toxicity profiles that can be offered to these patients. Gemtuzumab ozogamicin (GO) is an anti-CD33 monoclonal antibody that was approved by the US Food and Drug Administration for use as monotherapy in patients 60 years of age and older with relapsed AML. GO consists of a humanized anti-CD33 antibody (hP67.6) which is linked to N-acetyl-γ calicheamicin 1,2-dimethyl hydrazine dichloride. Once the antibody attaches to the surface antigen, it is rapidly internalized. Calicheamicin, a potent enediyne, is subsequently released and acts as a cytotoxic anti-tumor agent. In this population, GO has an acceptable toxicity and yields response rates approaching 30%. The efficacy of GO as monotherapy and in combination therapy for treatment of both de novo and relapsed AML continues to be investigated.
Bubbleworld Builder - 3D Modeling using Two-touch and Sketch Interaction

Commercial 3D modeling applications tend to be difficult and time consuming to use due to complex interfaces and functionality. In this paper we present a simple and intuitive interface for modeling “blobby” 3D objects using touch input. Objects are defined by sketching and modifying contours of cross-sectional slices. Two-touch interactions are used to zoom, rotate and slice the object. The resulting application allows rapid creation of 3D models and looks promising for medical imaging applications. A drawback is that intuitiveness depends on a user’s mental abilities such as 3D vision and the ability to develop a mental model and compare it with visual data.
Electronic Marketplaces and Price Transparency: Strategy, Information Technology, and Success

Electronic marketplaces (EMPs) are widely assumed to increase price transparency and hence lower product prices. Results of empirical studies have been mixed, with several studies showing that product prices have not decreased and others showing that prices have increased in some cases. One explanation is that sellers prefer not to join EMPs with high price transparency, leading highly price transparent EMPs to fail. Therefore, in order to be successful, EMPs might be expected to avoid high price transparency. But that strategy creates a catch-22 for EMPs on the buy side: Why would buyers want to join EMPs in the absence of price transparency and the benefit of lower prices? We argue that successful EMPs must provide compensatory benefits for sellers in the case of high price transparency and for buyers in the case of low price transparency. To understand how EMPs could succeed, regardless of price transparency, we examined the relationships among EMP strategy, price transparency, and performance by analyzing all 19 EMPs that compete by selling a broad range of standard electronics components. We found that all EMPs pursuing a low cost strategy had high price transparency and performed poorly. All EMPs that performed well pursued strategies of differentiation, but, interestingly, not all successful EMPs avoided price transparency: Some EMPs succeeded despite enabling high price transparency. We therefore examined two differentiated EMPs in greater depth-one with high price transparency, the other with low price transparency-to show how they achieved strategic alignment of activities and resources and provided compensatory benefits for their customers.
Pressure wave transmission in the human pulmonary circulation.

In patients without pulmonary hypertension, studied at thoracotomy, pressure oscillations were transmitted with less loss from pulmonary artery to occluded lobar pulmonary vein than from pulmonary vein to occluded lobar pulmonary artery. Theory suggests that the asymmetry is mainly due to inequality of pulmonary arterial and venous compliance. The theory provides a basis for analysing the effects of pulmonary arterial and venous compliance on arterial and “wedge” pressure oscillations.
Adaptive Distributed Resource Allocation in Wireless Sensor Networks

Wireless sensor networks have emerged as a promising technology for a wide range of important applications. A major research challenge in this field is the distributed resource allocation problem, which concerns how the limited resources in a wireless sensor network should be allocated or scheduled to minimize costs and maximize the network capability. In this paper, we propose the Adaptive Distributed Resource Allocation (ADRA) scheme, an adaptive approach for distributed resource allocation in wireless sensor networks. Our scheme specifies relatively simple local actions to be performed by individual sensor nodes in a wireless sensor network for mode management. Each node adapts its operation over time in response to the status and feedback of its neighboring nodes. Desirable global behavior results from the local interactions between nodes. We study the effectiveness of the ADRA scheme for a realistic application scenario; namely, the sensor mode management in an acoustic sensor network to track vehicle movement. We evaluated the scheme via simulations, and also prototyped it using the Crossbow MICA2 motes. Our simulation and hardware implementation results indicate that the ADRA scheme provides a good tradeoff between performance objectives such as coverage area, power consumption, and network lifetime.
Ranking Theory and Conditional Reasoning

Ranking theory is a formal epistemology that has been developed in over 600 pages in Spohn's recent book The Laws of Belief, which aims to provide a normative account of the dynamics of beliefs that presents an alternative to current probabilistic approaches. It has long been received in the AI community, but it has not yet found application in experimental psychology. The purpose of this paper is to derive clear, quantitative predictions by exploiting a parallel between ranking theory and a statistical model called logistic regression. This approach is illustrated by the development of a model for the conditional inference task using Spohn's (2013) ranking theoretic approach to conditionals.
Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge

Entity disambiguation in the biomedical domain is an essential task in any text mining pipeline. Much existing work shares one limitation, in that their model training prerequisite and/or runtime computation are too expensive to be applied to all ambiguous entities in real-time. We propose an automatic, light-weight method that processes MEDLINE abstracts at large-scale and with high-quality output. Our method exploits MeSH terms and knowledge in UMLS to ﬁrst identify unambiguous anchor entities, and then disambiguate remaining entities via heuristics. Experiments showed that our method is 79.6% and 87.7% accurate under strict and re-laxed rating schemes, respectively. When compared to MetaMap’s disambiguation, our method is one order of magnitude faster with a slight advantage in accuracy.