Science Gateways and AI/ML: How Can Gateway Concepts and Solutions Meet the Needs in Data Science?

Science gateways are a crucial component of critical infrastructure as they provide the means for users to focus on their topics and methods instead of the technical details of the infrastructure. They are defined as end-to-end solutions for accessing data, software, computing services, sensors, and equipment specific to the needs of a science or engineering discipline and their goal is to hide the complexity of the underlying infrastructure. Science gateways are often called Virtual Research Environments in Europe and Virtual Labs in Australasia; we consider these two terms to be synonymous with science gateways. Over the past decade, artificial intelligence (AI) and machine learning (ML) have found applications in many different fields in private industry, and private industry has reaped the benefits. Likewise, in the academic realm, large-scale data science applications have also learned to apply public high-performance computing resources to make use of this technology. However, academic and research science gateways have yet to fully adopt the tools of AI. There is an opportunity in the gateways space, both to increase the visibility and accessibility to AI/ML applications and to enable researchers and developers to advance the field of science gateway cyberinfrastructure itself. Harnessing AI/ML is recognized as a high priority by the science gateway community. It is, therefore, critical for the next generation of science gateways to adapt to support the AI/ML that is already transforming many scientific fields. The goal is to increase collaborations between the two fields and to ensure that gateway services are used and are valuable to the AI/ML community. This chapter presents state-of-the-art examples and areas of opportunity for the science gateways community to pursue in relation to AI/ML and some vision of where these new capabilities might impact science gateways and support scientific research

Evidence of spatial clustering of childhood acute lymphoblastic leukemia cases in Greater Mexico City: report from the Mexican Inter-Institutional Group for the identification of the causes of childhood leukemia

BackgroundA heterogeneous geographic distribution of childhood acute lymphoblastic leukemia (ALL) cases has been described, possibly, related to the presence of different environmental factors. The aim of the present study was to explore the geographical distribution of childhood ALL cases in Greater Mexico City (GMC).MethodsA population-based case-control study was conducted. Children <18 years old, newly diagnosed with ALL and residents of GMC were included. Controls were patients without leukemia recruited from second-level public hospitals, frequency-matched by sex, age, and health institution with the cases. The residence address where the patients lived during the last year before diagnosis (cases) or the interview (controls) was used for geolocation. Kulldorff’s spatial scan statistic was used to detect spatial clusters (SCs). Relative risks (RR), associated p-value and number of cases included for each cluster were obtained.ResultsA total of 1054 cases with ALL were analyzed. Of these, 408 (38.7%) were distributed across eight SCs detected. A relative risk of 1.61 (p<0.0001) was observed for the main cluster. Similar results were noted for the remaining seven ones. Additionally, a proximity between SCs, electrical installations and petrochemical facilities was observed.ConclusionsThe identification of SCs in certain regions of GMC suggest the possible role of environmental factors in the etiology of childhood ALL

Highly Sensitive Liquid Core Temperature Sensor Based On Multimode Interference Effects

A novel fiber optic temperature sensor based on a liquid-core multimode interference device is demonstrated. The advantage of such structure is that the thermo-optic coefficient (TOC) of the liquid is at least one order of magnitude larger than that of silica and this, combined with the fact that the TOC of silica and the liquid have opposite signs, provides a liquid-core multimode fiber (MMF) highly sensitive to temperature. Since the refractive index of the liquid can be easily modified, this allows us to control the modal properties of the liquid-core MMF at will and the sensor sensitivity can be easily tuned by selecting the refractive index of the liquid in the core of the device. The maximum sensitivity measured in our experiments is 20 nm/°C in the low-temperature regime up to 60 °C. To the best of our knowledge, to date, this is the largest sensitivity reported for fiber-based MMI temperature sensors

Motivational enhancement treatment in outpatient addiction centers: A multisite randomized trial

Background/Objectives: Motivational Enhancement Treatment in Spanish (METS) is a brief intervention aimed at resolving patient ambivalence towards behavior change that has demonstrated efficacy in substance use disorder treatment to reduce use and increase treatment engagement in different populations. In order to have evidence for its implementation in Mexico, a multi-site, randomized, two-arm, controlled clinical trial was conducted at three outpatient addiction treatment centers in the country to compare the effect of METS with Counseling as Usual (CAU). Method: One hundred and twenty patients were randomized to receive three sessions of METS ( n  = 54) or CAU ( n  = 66) during the first four weeks of treatment and were assessed during the following 12 weeks. Primary outcome measures were self-reported days of substance use and of treatment services utilization, which were tested using Generalized Estimating Equations. Results: Results associated both conditions with significant changes in substance use over, whereas there were no differences between conditions in substance use or in service utilization. Conclusions: Findings do not support the hypothesis that METS is more effective than CAU, but suggest that brief interventions at treatment initiation may improve patient outcomes

Intervención de incremento motivacional en centros ambulatorios para las adicciones: un ensayo aleatorizado multi-céntrico

Antecedentes/Objetivos: La Intervención de Incremento Motivacional (METS) es una intervención breve para resolver la ambivalencia del paciente con respecto a su comportamiento y ha demostrado eficacia en distintas poblaciones para reducir el consumo de sustancias e incrementar la asistencia al tratamiento en adicciones. Con el objetivo de generar evidencia para su implementación en México, se desarrolló un ensayo clínico controlado, multi-sede, aleatorizado, de dos brazos en tres centros de tratamiento ambulatorio para adicciones, para comparar el efecto de METS con el del tratamiento usual (CAU). Método: Ciento veinte pacientes fueron aleatorizados a tres sesiones de METS (n=54) o CAU (n=66) durante las primeras cuatro semanas de tratamiento y evaluados durante las siguientes doce. Se midieron resultados mediante autoinforme de días con consumo de sustancias y días de utilización de servicios, los cuales fueron analizados mediante ecuaciones de estimación generalizadas. Resultados: Los resultados asociaron ambas condiciones a cambios significativos en uso de sustancias a lo largo del tiempo, pero no demostraron diferencias entre condiciones en el uso de sustancias o en la utilización de servicios. Conclusiones: Los hallazgos contradicen la hipótesis de superioridad de METS sobre CAU, pero sugieren que las intervenciones breves al inicio del tratamiento pudieran mejorar la respuesta del paciente. © 2017 Asociación Española de Psicología Conductual. Published by Elsevier España, S.L.U. This is an open access article under the CC BY−NC−ND license (http://creativecommons. org/licenses/by−nc−nd/4.0/)

Antiprotozoan lead discovery by aligning dry and wet screening: Prediction, synthesis, and biological assay of novel quinoxalinones

Protozoan parasites have been one of the most significant public health problems for centuries and several human infections caused by them have massive global impact. Most of the current drugs used to treat these illnesses have been used for decades and have many limitations such as the emergence of drug resistance, severe side-effects, low-to-medium drug efficacy, administration routes, cost, etc. These drugs have been largely neglected as models for drug development because they are majorly used in countries with limited resources and as a consequence with scarce marketing possibilities. Nowadays, there is a pressing need to identify and develop new drug-based antiprotozoan therapies. In an effort to overcome this problem, the main purpose of this study is to develop a QSARs-based ensemble classifier for antiprotozoan drug-like entities from a heterogeneous compounds collection. Here, we use some of the TOMOCOMD-CARDD molecular descriptors and linear discriminant analysis (LDA) to derive individual linear classification functions in order to discriminate between antiprotozoan and non-antiprotozoan compounds as a way to enable the computational screening of virtual combinatorial datasets and/or drugs already approved. Firstly, we construct a wide-spectrum benchmark database comprising of 680 organic chemicals with great structural variability (254 of them antiprotozoan agents and 426 to drugs having other clinical uses). This series of compounds was processed by a k-means cluster analysis in order to design training and predicting sets. In total, seven discriminant functions were obtained, by using the whole set of atom-based linear indices. All the LDA-based QSAR models show accuracies above 85% in the training set and values of Matthews correlation coefficients (C) vary from 0.70 to 0.86. The external validation set shows rather-good global classifications of around 80% (92.05% for best equation). Later, we developed a multi-agent QSAR classification system, in which the individual QSAR outputs are the inputs of the aforementioned fusion approach. Finally, the fusion model was used for the identification of a novel generation of lead-like antiprotozoan compounds by using ligand-based virtual screening of 'available' small molecules (with synthetic feasibility) in our 'in-house' library. A new molecular subsystem (quinoxalinones) was then theoretically selected as a promising lead series, and its derivatives subsequently synthesized, structurally characterized, and experimentally assayed by using in vitro screening that took into consideration a battery of five parasite-based assays. The chemicals 11(12) and 16 are the most active (hits) against apicomplexa (sporozoa) and mastigophora (flagellata) subphylum parasites, respectively. Both compounds depicted good activity in every protozoan in vitro panel and they did not show unspecific cytotoxicity on the host cells. The described technical framework seems to be a promising QSAR-classifier tool for the molecular discovery and development of novel classes of broad - antiprotozoan - spectrum drugs, which may meet the dual challenges posed by drug-resistant parasites and the rapid progression of protozoan illnesses. © 2014 Elsevier Ltd. All rights reserved.Peer Reviewe

Polygala reinii Franch. et Savat.

原著和名: カキノハグサ科名: ヒメハギ科 = Polygalaceae採集地: 静岡県 引佐郡 引佐町 渋川 (遠江 引佐郡 引佐町 渋川)採集日: 1966/6/4採集者: 萩庭丈壽整理番号: JH036052国立科学博物館整理番号: TNS-VS-98605

Table_1_Evidence of spatial clustering of childhood acute lymphoblastic leukemia cases in Greater Mexico City: report from the Mexican Inter-Institutional Group for the identification of the causes of childhood leukemia.xlsx

BackgroundA heterogeneous geographic distribution of childhood acute lymphoblastic leukemia (ALL) cases has been described, possibly, related to the presence of different environmental factors. The aim of the present study was to explore the geographical distribution of childhood ALL cases in Greater Mexico City (GMC).MethodsA population-based case-control study was conducted. Children ResultsA total of 1054 cases with ALL were analyzed. Of these, 408 (38.7%) were distributed across eight SCs detected. A relative risk of 1.61 (pConclusionsThe identification of SCs in certain regions of GMC suggest the possible role of environmental factors in the etiology of childhood ALL.</p

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data