Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracking Transmission of Details in Paintings

In previous articles (di Lenardo et al, 2016; Seguin et al, 2016), we explored how efficient visual search engines operating not on the basis of textual metadata but directly through visual queries, could fundamentally change the navigation in large databases of work of arts. In the present work, we extended our search engine in order to be able to search not only for global similarity between paintings, but also for matching details. This feature is of crucial importance for retrieving the visual genealogy of a painting, as it is often the case that one composition simply reuses a few elements of other works. For instance, some workshops of the 16th century had repertoires of specific characters (a peasant smoking a pipe, a couple of dancing, etc.) and anatomical parts (head poses, hands, etc.) ,that they reused in many compositions (van den Brink, 2001; Tagliaferro et al, 2009). In some cases it is possible to track the circulation of these visual patterns over long spatial and temporal migrations, as they are progressively copied by several generations of painters. Identifying these links permits to reconstruct the production context of a painting, and the connections between workshops and artists. In addition, it permits a fine-grained study of taste evolution in the history of collections, following specific motives successfully reused in a large number of paintings. Tracking these graphical replicators is challenging as they can vary in texture and medium. For instance, a particular character or a head pose of a painting may have been copied from a drawing, an engraving or a tapestry. It is therefore important that the search for matching details still detects visual reuse even across such different media and styles. In the rest of the paper, we describe the matching method and discuss some results obtained using this approach.
Automatic Exploration of Machine Learning Experiments on OpenML

Understanding the influence of hyperparameters on the performance of a machine learning algorithm is an important scientific topic in itself and can help to improve automatic hyperparameter tuning procedures. Unfortunately, experimental meta data for this purpose is still rare. This paper presents a large, free and open dataset addressing this problem, containing results on 38 OpenML data sets, six different machine learning algorithms and many different hyperparameter configurations. Results where generated by an automated random sampling strategy, termed the OpenML Random Bot. Each algorithm was cross-validated up to 20.000 times per dataset with different hyperparameters settings, resulting in a meta dataset of around 2.5 million experiments overall.
The influence of aging on the methylation status of brain‐derived neurotrophic factor gene in blood

Brain‐derived neurotrophic factor (BDNF) is involved in the pathophysiology of psychiatric disorders in adults and elderly individuals, and as a result, the DNA methylation (DNAm) of the BDNF gene in peripheral tissues including blood has been extensively examined to develop a useful biomarker for psychiatric disorders. However, studies to date have not previously investigated the effect of age on DNAm of the BDNF gene in blood. In this context, we measured DNAm of 39 CpG units in the CpG island at the promoter of exon I of the BDNF gene.
An Efficient and Stable Spectral-Element Method for Acoustic Scattering by an Obstacle

A spectral-element method is developed to solve the scattering problem for time-harmonic sound waves due to an obstacle in an homogeneous compressible fluid. The method is based on a boundary perturbation technique coupled with an efficient spectral-element solver. Extensive numerical results are presented, in order to show the accuracy and stability of the method. AMS subject classifications: 78A45, 65N35, 35J05, 41A58
Toward a new arabic question answering system

Question Answering Systems (QAS) aim at returning precise answers to user’s questions that are written in natural language. In this paper, we describe our question processing and document retrieval as two components of Arabic QAS. First, we present Arabic question classification method based on SVM classifier and Li and Roth’s [24] taxonomy. Then, we describe our proposed technique to transform an Arabic question, to a query which is available to get information from the Arabic Wikipedia. In this paper, we use a hybrid Arabic Part-of-Speech (POS) tagging and Arabic WordNet (AWN) for query expansion. We have conducted several experiments using Text Retrieval Conference (TREC) and Cross Lingual Evaluation Forum (CLEF) datasets. The obtained results have shown that the proposed method is more effective as compared with the existing methods.
Comparison of conventional and advanced in vitro models in the toxicity testing of nanoparticles

Abstract Humans are exposed to a wide variety of nanoparticles (NPs) present in the environment, in consumer, health and medical products, and in food. Conventional cytotoxicity testing compared to animal testing is less expensive, faster and avoids ethical problems at the expense of a lower predictive value. New cellular models and exposure conditions have been developed to overcome the limitations of conventional cell culture and obtain more predictive data. The use of three-dimensional culture, co-culture and inclusion of mechanical stimulation can provide physiologically more relevant culture conditions. These systems are particularly relevant for oral, respiratory and intravenous exposure to NPs and it may be assumed that physiologically relevant application of the NPs can improve the predictive value of in vitro testing. Various groups have used advanced culture and exposure systems, but few direct comparisons between data from conventional cultures and from advanced systems exist. In silico models may present another option to predict human health risk by NPs without using animal studies. In the absence of validation, the question whether these alternative models provide more predictive data than conventional testing remains elusive.
Therapeutic Immune Modulation against Solid Cancers with Intratumoral Poly-ICLC: A Pilot Trial

Purpose: Polyinosinic-polycytidylic acid-poly-l-lysine carboxymethylcellulose (poly-ICLC), a synthetic double-stranded RNA complex, is a ligand for toll-like receptor-3 and MDA-5 that can activate immune cells, such as dendritic cells, and trigger natural killer cells to kill tumor cells. Patients and Methods: In this pilot study, eligible patients included those with recurrent metastatic disease in whom prior systemic therapy (head and neck squamous cell cancer and melanoma) failed. Patients received 2 treatment cycles, each cycle consisting of 1 mg poly-ICLC 3× weekly intratumorally (IT) for 2 weeks followed by intramuscular (IM) boosters biweekly for 7 weeks, with a 1-week rest period. Immune response was evaluated by immunohistochemistry (IHC) and RNA sequencing (RNA-seq) in tumor and blood. Results: Two patients completed 2 cycles of IT treatments, and 1 achieved clinical benefit (stable disease, progression-free survival 6 months), whereas the remainder had progressive disease. Poly-ICLC was well tolerated, with principal side effects of fatigue and inflammation at injection site (<grade 2). In the patient with clinical benefit, IHC analysis of tumor showed increased CD4, CD8, PD1, and PD-L1 levels compared with patients with progressive disease. RNA-seq analysis of the same patient's tumor and peripheral blood mononuclear cells showed dramatic changes in response to poly-ICLC treatment, including upregulation of genes associated with chemokine activity, T-cell activation, and antigen presentation. Conclusions: Poly-ICLC was well tolerated in patients with solid cancer and generated local and systemic immune responses, as evident in the patient achieving clinical benefit. These results warrant further investigation and are currently being explored in a multicenter phase II clinical trial (NCT02423863). Clin Cancer Res; 24(20); 4937–48. ©2018 AACR.
Gamification for improving software project: Systematic mapping in project management

Throughout history, software project management issues have been known to negatively affect the software quality and the success of this type of projects. Faced with such issues, some research have proposed solutions to improve the results in software project management in order to contribute significantly to its success. The objective of this paper is to carry out a study of the context of software project management, identifying the management areas that have been intervened with gamification strategies for software process improvement. To this end, this work proposes a systematic mapping as a research method that facilitates the identification of primary studies to analyze information and classify it based on established research criteria. We found 55 primary studies published between 2011 and 2017, on which we performed an information analysis. This analysis highlights the increase in the number of studies that use gamification as an improvement strategy for software project management processes areas. We classified the selected studies by analyzing the type of research method and the type of publication. This analysis shows that it is still an area of research in development and that it is necessary to continue working on the improvement of software project management processes with the aim of contributing to the success of its results.
Therapeutic potential of Pak1 inhibition for pain associated with cutaneous burn injury

Painful burn injuries are among the most debilitating form of trauma, globally ranking in the top 15 leading causes of chronic disease burden. Despite its prevalence, however, chronic pain after burn injury is under-studied. We previously demonstrated the contribution of the Rac1-signaling pathway in several models of neuropathic pain, including burn injury. However, Rac1 belongs to a class of GTPases with low therapeutic utility due to their complex intracellular dynamics. To further understand the mechanistic underpinnings of burn-induced neuropathic pain, we performed a longitudinal study to address the hypothesis that inhibition of the downstream effector of Rac1, Pak1, will improve pain outcome following a second-degree burn injury. Substantial evidence has identified Pak1 as promising a clinical target in cognitive dysfunction and is required for dendritic spine dysgenesis associated with many neurological diseases. In our burn injury model, mice exhibited significant tactile allodynia and heat hyperalgesia and dendritic spine dysgenesis in the dorsal horn. Activity-dependent expression of c-fos also increased in dorsal horn neurons, an indicator of elevated central nociceptive activity. To inhibit Pak1, we repurposed an FDA-approved inhibitor, romidepsin. Treatment with romidepsin decreased dendritic spine dysgenesis, reduced c-fos expression, and rescued pain thresholds. Drug discontinuation resulted in a relapse of cellular correlates of pain and in lower pain thresholds in behavioral tests. Taken together, our findings identify Pak1 signaling as a potential molecular target for therapeutic intervention in traumatic burn-induced neuropathic pain.
Activity Engagement and Everyday Technology Use Among Older Adults in an Urban Area

OBJECTIVE. We investigated associations among activity engagement (AE), number of available and relevant everyday technologies, ability to use everyday technologies, and cognitive status among older adults in an urban area. METHOD. This cross‐sectional study included 110 participants and used three assessments: the Frenchay Activities Index to measure AE, the Everyday Technology Use Questionnaire to measure the number of and ability to use available and relevant everyday technologies, and the Montreal Cognitive Assessment to measure cognitive status. Data analyses used a one‐way analysis of variance and a multiple linear regression model. RESULTS. The number of available and relevant everyday technologies was significantly different (p < .001) among groups that varied in level of AE. Ability to use everyday technologies did not significantly differ among groups. Cognitive status did not explain level of AE when the number of available and relevant everyday technologies was considered. CONCLUSION. Increasing the accessibility of available and relevant everyday technologies among older adults in an urban area may increase AE. &NA; Increasing the accessibility of available and relevant everyday technologies may increase AE among older adults.
Author‐based analysis of conference versus journal publication in computer science

Conference publications in computer science (CS) have attracted scholarly attention due to their unique status as a main research outlet, unlike other science fields where journals are dominantly used for communicating research findings. One frequent research question has been how different conference and journal publications are, considering an article as a unit of analysis. This study takes an author‐based approach to analyze the publishing patterns of 517,763 scholars who have ever published both in CS conferences and journals for the last 57 years, as recorded in DBLP. The analysis shows that the majority of CS scholars tend to make their scholarly debut, publish more articles, and collaborate with more coauthors in conferences than in journals. Importantly, conference articles seem to serve as a distinct channel of scholarly communication, not a mere preceding step to journal publications: coauthors and title words of authors across conferences and journals tend not to overlap much. This study corroborates findings of previous studies on this topic from a distinctive perspective and suggests that conference authorship in CS calls for more special attention from scholars and administrators outside CS who have focused on journal publications to mine authorship data and evaluate scholarly performance.
Maintenance of Mouse Gustatory Terminal Field Organization Is Dependent on BDNF at Adulthood

The rodent peripheral gustatory system is especially plastic during early postnatal development and maintains significant anatomical plasticity into adulthood. Thus, taste information carried from the tongue to the brain is built and maintained on a background of anatomical circuits that have the capacity to change throughout the animal's lifespan. Recently, the neurotrophin brain-derived neurotrophic factor (BDNF) was shown to be required in the tongue to maintain normal levels of innervation in taste buds at adulthood, indicating that BDNF is a key molecule in the maintenance of nerve/target matching in taste buds. Here, we tested whether maintenance of the central process of these gustatory nerves at adulthood also relies on BDNF by using male and female transgenic mice with inducible CreERT2 under the control of the keratin 14 promoter or under control of the ubiquitin promoter to remove Bdnf from the tongue or from all tissues, respectively. We found that the terminal fields of gustatory nerves in the nucleus of the solitary tract were expanded when Bdnf was removed from the tongue at adulthood and with even larger and more widespread changes in mice where Bdnf was removed from all tissues. Removal of Bdnf did not affect numbers of ganglion cells that made up the nerves and did not affect peripheral, whole-nerve taste responses. We conclude that normal expression of Bdnf in gustatory structures is required to maintain normal levels of innervation at adulthood and that the central effects of Bdnf removal are opposite of those in the tongue. SIGNIFICANCE STATEMENT BDNF plays a major role in the development and maintenance of proper innervation of taste buds. However, the importance of BDNF in maintaining innervation patterns of gustatory nerves into central targets has not been assessed. Here, we tested whether Bdnf removal from the tongue or from all structures in adult mice impacts the maintenance of how taste nerves project to the first central relay. Deletion of Bdnf from the tongue and from all tissues led to a progressively greater expansion of terminal fields. This demonstrates, for the first time, that BDNF is necessary for the normal maintenance of central gustatory circuits at adulthood and further highlights a level of plasticity not seen in other sensory system subcortical circuits.
ACUERDO NACIONAL PARA LA SALUD ALIMENTARIA, ESTRATEGIA CONTRA EL SOBREPESO Y LA OBESIDAD; PARTICULARIDADES PARA EL ESTADO DE QUERÉTARO

Overweight and obesity are a burden to public health worldwide, and its prevalence in Mexico is high. In order to address these problems, Mexico joined in 2004 the World Health Organization ́s “Global Strategy on Diet, Physical Activity and Health”, and signed the National Agreement for Food Health: strategy against overweight and obesity in 2010. This “Agreement” was designed under a common objective and a shared responsibility between public and private sectors. Its main goal was to develop action plans for children in elementary schools in order to revert chronic diseases triggered by obesity and overweight. This article describes the “Agreement”, the combined efforts of the stakeholders involved, and the actions taken by Queretaro ́s Ministry of Health, Ministry of Education, the Global Family Development System and the Autonomous University.
STAG2 Is a Biomarker for Prediction of Recurrence and Progression in Papillary Non–Muscle-Invasive Bladder Cancer

Purpose: Most bladder cancers are early-stage tumors known as papillary non–muscle-invasive bladder cancer (NMIBC). After resection, up to 70% of NMIBCs recur locally, and up to 20% of these recurrences progress to muscle invasion. There is an unmet need for additional biomarkers for stratifying tumors based on their risk of recurrence and progression. We previously identified STAG2 as among the most commonly mutated genes in NMIBC and provided initial evidence in a pilot cohort that STAG2-mutant tumors recurred less frequently than STAG2 wild-type tumors. Here, we report a STAG2 biomarker validation study using two independent cohorts of clinically annotated papillary NMIBC tumors from the United States and Europe. Experimental Design: The value of STAG2 immunostaining for prediction of recurrence was initially evaluated in a cohort of 82 patients with papillary NMIBC (“Georgetown cohort”). Next, the value of STAG2 immunostaining for prediction of progression to muscle invasion was evaluated in a progressor-enriched cohort of 253 patients with papillary NMIBC (“Aarhus cohort”). Results: In the Georgetown cohort, 52% of NMIBC tumors with intact STAG2 expression recurred, whereas 25% of STAG2-deficient tumors recurred (P = 0.02). Multivariable analysis identified intact STAG2 expression as an independent predictor of recurrence (HR = 2.4; P = 0.05). In the progressor-enriched Aarhus cohort, 38% of tumors with intact STAG2 expression progressed within 5 years, versus 16% of STAG2-deficient tumors (P < 0.01). Multivariable analysis identified intact STAG2 expression as an independent predictor of progression (HR = 1.86; P = 0.05). Conclusions: STAG2 IHC is a simple, binary, new assay for risk stratification in papillary NMIBC. Clin Cancer Res; 24(17); 4145–53. ©2018 AACR.
Flexible NLP Pipelines for Digital Humanities Research

A lot of Digital Humanities (DH) research involves applying Natural Language Processing (NLP) tasks, such as, sentiment analysis, named entity recognition, or topic modeling. A large amount of NLP software is already available. On the one hand, there are frameworks that bundle software for different tasks and languages (e.g., NLTK [Bird et al, 2009], or xtas1), and on the other hand there are tools that target specific tasks (e.g., gensim, Rehurek and Sojka, 2010). As long as researchers do not need to combine tools from different packages, it is usually relatively easy to write scripts that perform the task. However, for innovative research, combining tools often is required, especially when working with non-English text. This abstract presents work in progress on NLP Pipeline (nlppln), an open source tool that improves access to NLP software by facilitating combining NLP functionality from different software packages2. nlppln is based on Common Workflow Language (CWL), a standard for describing data analysis workflows and tools (Amstutz et al, 2016). The main advantage of using a standard is that any existing NLP tool can be integrated into a workflow, as long as it can be run as a command line tool. This flexibility is missing from existing frameworks for creating NLP pipelines, such as DKPro (Eckart de Castilho, and Gurevych, 2015) using the UIMA framework (Ferrucci, and Lally, 2004). In addition to improved reuse of existing software, CWL increases research reproducibility, as it provides a standardized, formal record of all steps taken in a processing pipeline. Finally, CWL workflows are modular. This means that individual processing steps can easily be swapped in and out. To demonstrate how NLP tools can be combined using nlppln, we show what need to be done to create a pipeline that removes named entities from a directory of text files. This is a common NLP task, that can be used as part of a data anonymization procedure.
Rowmotion and generalized toggle groups

We generalize the notion of the toggle group, as defined in [P. Cameron-D. Fon-der-Flaass '95] and further explored in [J. Striker-N. Williams '12], from the set of order ideals of a poset to any family of subsets of a finite set. We prove structure theorems for certain finite generalized toggle groups, similar to the theorem of Cameron and Fon-der-Flaass in the case of order ideals. We apply these theorems and find other results on generalized toggle groups in the following settings: chains, antichains, and interval-closed sets of a poset; independent sets, vertex covers, acyclic subgraphs, and spanning subgraphs of a graph; matroids and convex geometries. We generalize rowmotion, an action studied on order ideals in [P. Cameron-D. Fon-der-Flaass '95] and [J. Striker-N. Williams '12], to a map we call cover-closure on closed sets of a closure operator. We show that cover-closure is bijective if and only if the set of closed sets is isomorphic to the set of order ideals of a poset, which implies rowmotion is the only bijective cover-closure map.
SOME MODELS OF PHYLOGENETIC TREE SHAPE

As products of diversifying evolution, phylogenetic trees retain signatures of the evolutionary events and mechanisms that gave rise to them. Researchers have used a variety of theoretical models to represent different hypotheses about how diversification might proceed through the evolution of a clade. We outline two widely-used measures of phylogenetic tree shape, review a number of treegenerating models, and set out the predictions they make about tree shapes. The simplest of these models (the “Yule” and “Hey” models) are still used routinely, sometimes as if they provided good representations of diversification in Nature; but in fact, they do rather poorly when confronted with real data. More complex models that incorporate hypothesized macroevolutionary processes can in some cases provide a better fit to real data. We recommend further development of these more complex models for instance, exploration of models that treat species as collections of individuals rather than as simple lineages. Much work remains to be done in estimating trees (especially waiting times), in exploring tree-generating models and in assessing patterns in the shapes of real phylogenies.