Miracle-dz/UniFAR-FTUs huggingface dataset:
Toponym resolution in text: annotation, evaluation and applications of spatial grounding

In Information Extraction (IE), processing of named entities in text has traditionally been seen as a two-step process comprising a flat text span recognition sub-task and an atomic classification sub-task; relating the text span to a model of the world has been ignored by evaluations such as DARPA/NIST's MUC or ACE. However, spatial and temporal expressions refer to events in space-time, and the grounding of events is a precondition for accurate reasoning. Thus, automatic grounding can improve many applications such as automatic map drawing (e.g. for choosing a focus) and question answering (e.g., for questions like How far is London from Edinburgh, given a story in which both occur and can be resolved). Whereas temporal grounding has received considerable attention in the recent Past [2, 3], robust spatial grounding has long been neglected. Concentrating on geographic names for populated places, I define the task of automatic Toponym Resolution (TR) as computing the mapping from occurrences of names for places as found in a text to a representation of the extensional semantics of the location referred to (its referent), such as a geographic latitude/longitude footprint. The task of mapping from names to locations is hard due to insufficient and noisy databases, and a large degree of ambiguity: common words need to be distinguished from proper names (geo/non-geo ambiguity), and the mapping between names and locations is ambiguous London can refer to the capital of the UK or to London, Ontario, Canada, or to about forty other Londons on earth). In addition, names of places and the boundaries referred to change over time, and databases are incomplete.
Temperature distributions measurement of high intensity focused ultrasound using a thin-film thermocouple array and estimation of thermal error caused by viscous heating

To improve the throughput of high intensity focused ultrasound (HIFU) treatment, we have considered a focus switching method at two points. For this method, it is necessary to evaluate the thermal distribution under exposure to ultrasound. The thermal distribution was measured using a prototype thin-film thermocouple array, which has the advantage of minimizing the influence of the thermocouple on the acoustic and temperature fields. Focus switching was employed to enlarge the area of temperature increase and evaluate the proposed evaluation parameters with respect to safety and uniformity. The results indicate that focus switching can effectively expand the thermal lesion while maintaining a steep thermal boundary. In addition, the influence caused by the thin-film thermocouple array was estimated experimentally. This thermocouple was demonstrated to be an effective tool for the measurement of temperature distributions induced by HIFU.
MQDF Retrained on Selected Sample Set

SUMMARY This letter has retrained an MQDF classiﬁer on the retraining set, which is constructed by samples locating near classiﬁcation boundary. The method is evaluated on HCL2000 and HCD Chinese handwriting sets. The results show that the retrained MQDF outperforms MQDF and cascade MQDF on all test sets. key words: MQDF retraining, sample selection, sample number regularization
A Semantically Annotated Corpus from MEDLINE Abstracts

Automatic information extraction is a key technology to help researchers access the information contained in research papers and to extend databases on substances and biological processes. We aim to build information extraction databases [2] from biochemical papers and their abstracts available from the MEDLINE [3] database. To objectively measure the performance of our systems, we built a corpus of expert-tagged abstracts from MEDLINE that can be used as the judgment set. This paper outlines the features of this corpus. An annotated corpus has several other uses. For example, a large corpus can be a learning data set for statistical programs for information extraction (e.g., [1]). Also, computational linguists can explore semantic processing methods, or get insight into the linguistic patterns of how the relationship between the entities are represented in the texts, using the corpus explicitly marked with such entities.
Cisplatin-induced injury of the renal distal convoluted tubule is associated with hypomagnesaemia in mice.

BACKGROUND Cisplatin is an effective anti-neoplastic drug, but its clinical use is limited due to dose-dependent nephrotoxicity. The majority of cisplatin-treated patients develop hypomagnesaemia, often associated with a reduced glomerular filtration rate (GFR), polyuria and other electrolyte disturbances. The aim of this study is to unravel the molecular mechanism responsible for these particular electrolyte disturbances. METHODS Two groups of 10 mice were injected intraperitoneally three times, once every 4 days, with cisplatin (5 mg/kg body weight,) or vehicle. Serum and urine electrolyte concentrations were determined. Next, renal mRNA levels of distal convoluted tubule (DCT) genes epithelial Mg(2+) channel TRPM6, the Na(+)-Cl(-) cotransporter (NCC), and parvalbumin (PV), as well as marker genes for other tubular segments were measured by real-time qPCR. Subsequently, renal protein levels of NCC, PV, aquaporin 1 and aquaporin 2 were determined using immunoblotting and immunohistochemistry (IHC). RESULTS The cisplatin-treated mice developed significant polyuria (2.5 ± 0.3 and 0.9 ± 0.1 mL/24 h, cisplatin versus control, P < 0.05), reduced creatinine clearance rate (CCr) (0.18 ± 0.02 and 0.26 ± 0.02 mL/min, cisplatin versus control, P < 0.05) and a substantially reduced serum level of Mg(2+) (1.23 ± 0.03 and 1.58 ± 0.03 mmol/L, cisplatin versus control, P < 0.05), whereas serum Ca(2+), Na(+) and K(+) values were not altered. Measurements of 24 h urinary excretion demonstrated markedly increased Mg(2+), Ca(2+), Na(+) and K(+) levels in the cisplatin-treated group, whereas Pi levels were not changed. The mRNA levels of TRPM6, NCC and PV were significantly reduced in the cisplatin group. The expression levels of the marker genes for other tubular segments were unaltered, except for claudin-16, which was significantly up-regulated by the cisplatin treatment. The observed DCT-specific down-regulation was confirmed at the protein level. CONCLUSIONS The present study identified the DCT as an important cisplatin-affected renal segment, explaining the high prevalence of hypomagnesaemia following treatment.
A Practical Double-Parameter Steady Voltage Stability Boundary Tracing Method

The interaction and nonlinear relationship between different parameters or groups of parameters always are interested by the operators in control center of power grid. A practical tracing method of two parameter stability boundary for voltage stability assessment is proposed. In the traditional tracing method of two parameter bifurcation boundary a second order Hessian matrix of power flow equations has to be computed and factorized, which is a difficulty for on-line application of a large scale power system. By using the single parameter trajectory tracing and the bifurcation point seeking and identification alternately, with the computational expenses of some additional points, the proposed method handles the Jacobin matrix and overcomes this difficulty. The preposition of the proposed method is that the interested part of two parameter stability boundary is composed of both the saddle node bifurcation points and the limit induced bifurcation points, without double saddle node bifurcation points. It is satisfied since the interested part of the boundary is limited. The numerical results about a 3187 bus actual system show that the proposed method is very efficient for on-line application.
Graph reductions to speed up importance sampling-based static reliability estimation

We speed up the Monte Carlo simulation of static graph reliability models by adding graph reductions to zero-variance importance sampling (ZVIS) approximation techniques. ZVIS approximation samples the status of links sequentially, and at each step we check if series-parallel reductions can be performed. We present two variants of the algorithm and describe their respective advantages. We show that the method satisfies robustness properties as the reliability of links increases. We illustrate theoretically on small examples and numerically on large ones the gains that can be obtained, both in terms of variance and computational time.
Dense View Interpolation on Mobile Devices Using Focal Stacks

Light field rendering is a widely used technique to generate novel views of a scene from novel viewpoints. Interpolative methods for light field rendering require a dense description of the scene in the form of closely spaced images. In this work, we present a simple method for dense view interpolation over general static scenes, using commonly available mobile devices. We capture an approximate focal stack of the scene from adjacent camera locations and interpolate intermediate images by shifting each focal region according to appropriate disparities. We do not rely on focus distance control to capture focal stacks and describe an automatic method of estimating the focal textures and the blur and disparity parameters required for view interpolation.
Software Patterns

Software patterns are attempts to describe successful solutions to common software problems [26]. Software patterns reflect common conceptual structures of these solutions, and can be applied over and over again when analyzing, designing, and producing applications in a particular context. The purpose of this chapter is to gradually introduce the concept of software patterns and describe most frequently used classes of patterns. Key ideas are first presented by describing some practical needs and experiences of software designers. Then a commonly used classification of software patterns is shown, followed by an informal example that illustrates the presence of patterns in different fields of software engineering and knowledge engineering. The introductory part of the chapter closes with a brief history of software patterns. The central part begins with a discussion of how the information and the knowledge of patterns are organized in practice and how designers should use that information/knowledge. Then the chapter dedicates one entire section to each one of the frequently used classes of patterns. Within any such a section, the objectives and the scope of the corresponding class of patterns are stated, and an example pattern is described in detail. The remainder of the chapter discusses the concept of pattern languages and some important research issues.
FBK-TR: Applying SVM with Multiple Linguistic Features for Cross-Level Semantic Similarity

Recently, the task of measuring semantic similarity between given texts has drawn much attention from the Natural Language Processing community. Especially, the task becomes more interesting when it comes to measuring the semantic similarity between different-sized texts, e.g paragraph-sentence, sentence-phrase, phrase-word, etc. In this paper, we, the FBK-TR team, describe our system participating in Task 3 "Cross-Level Semantic Similarity", at SemEval 2014. We also report the results obtained by our system, compared to the baseline and other participating systems in this task.
A Framework for the Recognition of Nonmanual Markers in Segmented Sequences of American Sign Language

Despite the fact that there is critical grammatical information expressed through facial expressions and head gestures, most research in the field of sign language recognition has primarily focused on the manual component of signing. We propose a novel framework for robust tracking and analysis of non-manual behaviours, with an application to sign language recognition. The novelty of our method is threefold. First, we propose a dynamic feature representation. Instead of using only the features available in the current frame (e.g., head pose), we additionally aggregate and encode the feature values in neighbouring frames to better encode the dynamics of expressions and gestures (e.g., head shakes). Second, we use Multiple Instance Learning [12] to handle feature misalignment resulting from drifting of the face tracker and partial occlusions. Third, we utilize a discriminative Hidden Markov Support Vector Machine (HMSVM) [1] to learn finer temporal dependencies between the features of interest. We apply our signerindependent framework to segmented recognition of five classes of grammatical constructions conveyed through facial expressions and head gestures: wh-questions, negation, conditional/when clauses, yes/no questions and topics, and show improvement over previous methods.
Adiponectin levels measured in dried blood spot samples from neonates born small and appropriate for gestational age.

OBJECTIVE Adiponectin levels measured in neonatal dried blood spot samples (DBSS) might be affected by both prematurity and being born small for gestational age (SGA). The aim of the study was to measure adiponectin levels in routinely collected neonatal DBSS taken on day 5 (range 3-12) postnatal from infants. DESIGN A retrospective case-control study. SUBJECTS AND METHODS One hundred and twenty-two infants: 62 very premature (34 SGA) and 60 mature infants (27 SGA). Adiponectin concentrations were determined in stored neonatal DBSS using a sandwich immunoassay based on flow metric Luminex xMap technology. RESULTS Adiponectin was measurable in all samples, and repeated measurements correlated significantly (r = 0.94). Adiponectin concentrations were negatively associated with both SGA (B = -0.283, P = 0.04) and prematurity (B = -2.194, P < 0.001), independently of each other. In the premature but not the mature group, adiponectin levels increased with increasing postnatal age at blood sampling (B = 0.175, P < 0.001). CONCLUSIONS Reliable quantification of adiponectin in stored DBSS is feasible and may be used to study large populations of routinely collected samples. Low levels of adiponectin in neonatal DBSS are associated with SGA as well as prematurity. Blood adiponectin levels increase with postnatal age in premature infants, suggesting a rapid yet unexplained metabolic adaptation to premature extrauterine life.
From Modular to Centralized Organization of Synchronization in Functional Areas of the Cat Cerebral Cortex

Recent studies have pointed out the importance of transient synchronization between widely distributed neural assemblies to understand conscious perception. These neural assemblies form intricate networks of neurons and synapses whose detailed map for mammals is still unknown and far from our experimental capabilities. Only in a few cases, for example the C. elegans, we know the complete mapping of the neuronal tissue or its mesoscopic level of description provided by cortical areas. Here we study the process of transient and global synchronization using a simple model of phase-coupled oscillators assigned to cortical areas in the cerebral cat cortex. Our results highlight the impact of the topological connectivity in the developing of synchronization, revealing a transition in the synchronization organization that goes from a modular decentralized coherence to a centralized synchronized regime controlled by a few cortical areas forming a Rich-Club connectivity pattern.
Immune Responses to AAV-Vectors, the Glybera Example from Bench to Bedside

Alipogene tiparvovec (Glybera®) is an adeno-associated virus serotype 1 (AAV1)-based gene therapy that has been developed for the treatment of patients with lipoprotein lipase (LPL) deficiency. Alipogene tiparvovec contains the human LPL naturally occurring gene variant LPLS447X in a non-replicating viral vector based on AAV1. Such virus-derived vectors administered to humans elicit immune responses against the viral capsid protein and immune responses, especially cellular, mounted against the protein expressed from the administered gene have been linked to attenuated transgene expression and loss of efficacy. Therefore, a potential concern about the use of AAV-based vectors for gene therapy is that they may induce humoral and cellular immune responses in the recipient that may impact on efficacy and safety. In this paper, we review the current understanding of immune responses against AAV-based vectors and their impact on clinical efficacy and safety. In particular, the immunogenicity findings from the clinical development of alipogene tiparvovec up to licensing in Europe will be discussed demonstrating that systemic and local immune responses induced by intra-muscular injection of alipogene tiparvovec have no deleterious effects on clinical efficacy and safety. These findings show that muscle-directed AAV-based gene therapy remains a promising approach for the treatment of human diseases.
Simple learning algorithm for the traveling salesman problem

We propose a learning algorithm for solving the traveling salesman problem based on a simple strategy of trial and adaptation. (i) A tour is selected by choosing cities probabilistically according to the ``synaptic'' strengths between cities. ii) The ``synaptic'' strengths of the links that form the tour are then enhanced (reduced) if the tour length is shorter (longer) than the average result of the previous trials. We perform extensive simulations of the random distance traveling salesman problem. For sufficiently slow learning rates, near-optimal tours can be obtained with the average tour lengths close to the lower bounds for the shortest tour lengths.
Iron overload: accuracy of in-phase and out-of-phase MRI as a quick method to evaluate liver iron load in haematological malignancies and chronic liver disease.

OBJECTIVES The purpose of this prospective study was to evaluate the accuracy of in-phase and out-of-phase imaging to assess hepatic iron concentration in patients with haematological malignancies and chronic liver disease. METHODS MRI-based hepatic iron concentration (M-HIC, μmol g(-1)) was used as a reference standard. 42 patients suspected of having iron overload and 12 control subjects underwent 1.5 T in- and out-of-phase and M-HIC liver imaging. Two methods, semi-quantitative visual grading made by two independent readers and quantitative relative signal intensity (rSI) grading from the signal intensity differences of in-phase and out-of-phase images, were used. Statistical analyses were performed using the Spearman and Kruskal-Wallis tests, receiver operator curves and κ coefficients. RESULTS The correlations between M-HIC and visual gradings of Reader 1 (r = 0.9534, p < 0.0001) and Reader 2 (r = 0.9456, p < 0.0001) were higher than the correlations of the rSI method (r = 0.7719, p < 0.0001). There was excellent agreement between the readers (weighted κ = 0.9619). Both visual grading and rSI were similar in detecting liver iron overload: rSI had 84.85% sensitivity and 100% specificity; visual grading had 85% sensitivity and 100% specificity. The differences between the grades of visual grading were significant (p < 0.0001) and the method was able to distinguish different degrees of iron overload at the threshold of 151 μmol g(-1) with 100% positive predictive value and negative predictive value. CONCLUSION Detection and grading of liver iron can be performed reliably with in-phase and out-of-phase imaging. Liver fat is a potential pitfall, which limits the use of rSI.
Relay Location Optimization for Full-Duplex Decode-and-Forward Relaying

In this paper, we investigate the optimum relay location for full-duplex decode-and-forward (DF) relaying systems. The outage probability is adopted as the optimization criterion and a relay location optimization problem is formulated. Analytical and numerical results are provided to show the advantages of the location optimization. The intriguing effect of residual self-interference (RSI) introduced by full-duplex transmission is examined in terms of the optimal relay location, outage probability improvement and power saving benefits.
Stress-Specific Activation and Repression of Heat Shock Factors 1 and 2

ABSTRACT Vertebrate cells express a family of heat shock transcription factors (HSF1 to HSF4) that coordinate the inducible regulation of heat shock genes in response to diverse signals. HSF1 is potent and activated rapidly though transiently by heat shock, whereas HSF2 is a less active transcriptional regulator but can retain its DNA binding properties for extended periods. Consequently, the differential activation of HSF1 and HSF2 by various stresses may be critical for cells to survive repeated and diverse stress challenges and to provide a mechanism for more precise regulation of heat shock gene expression. Here we show, using a novel DNA binding and detection assay, that HSF1 and HSF2 are coactivated to different levels in response to a range of conditions that cause cell stress. Above a low basal activity of both HSFs, heat shock preferentially activates HSF1, whereas the amino acid analogue azetidine or the proteasome inhibitor MG132 coactivates both HSFs to different levels and hemin preferentially induces HSF2. Unexpectedly, we also found that heat shock has dramatic adverse effects on HSF2 that lead to its reversible inactivation coincident with relocalization from the nucleus. The reversible inactivation of HSF2 is specific to heat shock and does not occur with other stressors or in cells expressing high levels of heat shock proteins. These results reveal that HSF2 activity is negatively regulated by heat and suggest a role for heat shock proteins in the positive regulation of HSF2.
Nanosecond Pulsed Electric Field Suppresses Development of Eyes and Germ Cells through Blocking Synthesis of Retinoic Acid in Medaka (Oryzias latipes)

Application of nanosecond pulsed electric fields (nsPEFs) has attracted rising attention in various scientific fields including medical, pharmacological, and biological sciences, although its effects and molecular mechanisms leading to the effects remain poorly understood. Here, we show that a single, high-intensity (10–30 kV/cm), 60-ns PEF exposure affects gene expression and impairs development of eyes and germ cells in medaka (Oryzias latipes). Exposure of early blastula stage embryos to nsPEF down-regulated the expression of several transcription factors which are essential for eye development, causing abnormal eye formation. Moreover, the majority of the exposed genetic female embryos showed a fewer number of germ cells similar to that of the control (unexposed) genetic male at 9 days post-fertilization (dpf). However, all-trans retinoic acid (atRA) treatment following the exposure rescued proliferation of germ cells and resumption of normal eye development, suggesting that the phenotypes induced by nsPEF are caused by a decrease of retinoic acid levels. These results confirm that nsPEFs induce novel effects during embryogenesis in medaka.