Miracle-dz/UniFAR-FTUs huggingface dataset:
Short‐term time step convergence in a climate model

This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities.
On the use of participatory sensing to better understand city dynamics

In this position paper we argue that certain types of social media systems, such as Instagram and Foursquare, can act as valuable source of sensing, providing access to important characteristics of urban locations and urban social behavior. We discuss some of our previous studies and present our thoughts about the future of this field based insights obtained from them.
Increasing social engagement in children with high-functioning autism spectrum disorder using collaborative technologies in the school environment

This study examined the effectiveness of a school-based, collaborative technology intervention combined with cognitive behavioral therapy to teach the concepts of social collaboration and social conversation to children with high-functioning autism spectrum disorders (n = 22) as well as to enhance their actual social engagement behaviors (collaboration and social conversation) with peers. Two computer programs were included in the intervention: “Join-In” to teach collaboration and “No-Problem” to teach conversation. Assessment in the socio-cognitive area included concept perception measures, problem solving, Theory of Mind, and a dyadic drawing collaborative task to examine change in children’s social engagement. Results demonstrated improvement in the socio-cognitive area with children providing more active social solutions to social problems and revealing more appropriate understanding of collaboration and social conversation after intervention, with some improvement in Theory of Mind. Improvement in actual social engagement was more scattered.
Pore pressure prediction in carbonates using pore and matrix compressibilities

Es de gran importancia obtener dato de gran calidad referentes a la presion de poro, con el objetivo de alcanzar el exito en las tareas de perforacion, asi como para realizar una simulacion de yacimientos mas exacta. La mayoria de los metodos de presion de poro realizan una comparacion entre una tendencia normal y con medidos del registro sonico, registro de resistividad o del exponente d. Las formaciones de lutita muestran una respuesta directa en la porosidad y la presion de poro en funcion de la profundidad; la mayoria de los metodos para prediccion de presion de poro estan basados en el comportamiento de las lutitas. Sin embargo, los carbonatos presentan un origen sedimentario totalmente diferente; son rigidos y pueden no presentar respuesta en porosidad, pero si sobrepresion. Este trabajo esta basado y presenta algunos resultados de una tesis de Maestria presentada en la Universidad Nacional Autonoma de Mexico, (UNAM). Este trabajo trata la teoria del nuevo metodo para la prediccion de poro en carbonatos desarrollado por Vahid Atashbari et al., publicado por la Sociedad de Ingenieros Petroleros (SPE por sus siglas en Ingles). El nuevo metodo para el calculo del esfuerzo efectivo se obtuvo utilizando datos de las compresibilidades del yacimiento y de las formaciones rocosas. En el caso de bajo compactacion, la presion de poro depende del cambio del espacio poroso. De igual manera se presenta una solucion propuesta al nuevo metodo para la prediccion de la presion de poro. Adicionalmente, se muestran tres aplicaciones del nuevo metodo en formaciones de carbonatos en Mexico
Degrees of freedom of SIMO X channel

In this study, the authors mainly study the degrees of freedom (DoFs) of M × N user single input multiple output (SIMO) (or multiple input single output (MISO)) X channels, in which the channel coefficients are drawn from a continuous distribution and data-sharing among users are unavailable. First, the authors establish an outer bound of DoFs for multiple-in multiple-out (MIMO) X channel, which is tighter than those in previous work. For SIMO X channel with R antennas at each user, the authors prove that the DoFs is [ MNR /( M + NR − R )], which is achieved by symbol extension and interference alignment. As the transmitters and receivers are interchangeable in the network considered, the authors obtain corresponding results for MISO X channel. Finally, the authors generalise our result to MIMO X channel with R antennas at each user, and show that its DoFs is [ MNR /( M + N − 1)].
Future of nanoindentation in archaeometry

This review aims to consolidate scarce literature on the use of modern nanomechanical testing technique like instrumented nanoindentation in the field of archaeometry materials research. The review showcase on how can the nanoindentation tests provide valuable data about mechanical properties which, in turn, relate to the evolution of ancient biomaterials as well as human history and production methods. This is particularly useful when the testing is limited by confined volumes and small material samples (since the contact size is in the order of few microns). As an emerging novel application, some special considerations are warranted for characterization of archaeometry materials. In this review, potential research areas relating to how nanoindentation is expected to benefit and help improve existing practices in archaeometry are identified. It is expected that these insights will raise awareness for use of nanoindentation at various world heritage sites as well as various museums.
Editorial: 2008 year in review

2008 was an eventful inaugural year for Evolutionary Applications. We published four issues comprising 45 papers in total, including the special issue: Evolutionary Perspectives on Salmonid Conservation and Management. Wiley-Blackwell sponsored an Evolutionary Applications symposium at the Canadian Society of Ecology and Evolution annual meeting in Vancouver (May), and hosted an official Evolutionary Applications launch reception at the SSE annual meeting in Minneapolis (June). The journal received much press coverage, and was featured in both Nature and New Scientist. The year was successfully capped with the acceptance of the journal for full indexing in ISI. The Editorial team would like to thank the scientific community for their overwhelming support of this new and unique journal. Undoubtedly this support, as well as the official endorsement of the journal by both the Society for the Study of Evolution, and the European Society for Evolutionary Biology (ESEB), contributed to the exceptionally rapid acceptance of the journal into ISI. In 2008, Evolutionary Applications published papers in most of the fields listed on our website (http://www.evolutionaryapplications.org; see Table 1). Published papers also focused on a wide diversity of organisms of applied importance, including plants, animals and microbes (Table 2). Clearly, the journal is fulfilling its primary goal of being the principal outlet for the increasing number of high-quality papers using evolutionary concepts to address issues of economic, medical and social relevance. Table 1 Subjects covered in 2008 in Evolutionary Applications Table 2 Examples of organisms of applied significance featured in Evolutionary Applications In 2009, we are again publishing four issues, including this current special issue on evolutionary medicine, and an upcoming special issue on the impact of harvesting on fish evolution and Darwinian fishery science. Among other events, in August, Wiley-Blackwell will be sponsoring a full-day symposium on evolutionary applications at the 12th ESEB Congress in Turin, Italy. Despite being in our first year of operation, we succeeded in maintaining a very short time from submission to first decision (34 days). Also, our transparent online review and production system allows authors to track the progress of their manuscripts from submission to publication. We will continue striving both to publish the highest quality research on applied evolution, and to make the importance and broad relevance of evolutionary biology more accessible to all interested readers.
LMI CONDITIONS FOR GLOBAL ASYMPTOTIC STABILITY OF NEURAL NETWORKS WITH DISCRETE AND DISTRIBUTED DELAYS

In recently years, the stability of Cellular Neural networks has attracted many researchers, and many different types of neural networks have been widely investi- gated. In this paper, sufficient conditions of stability for a class of neural networks with time-varying delay are developed, which are in terms of linear matrix inequalities (LMIs). An example is given to illustrate the applicability of the theoretic results obtained.
Effects of in vitro exposure to autologous blood and serum on expression of interleukin-8, interleukin-1β, and chemokine (C-X-C motif) ligand 2 in equine primary bronchial epithelial cell cultures.

OBJECTIVE To examine the effects of in vitro exposure to solutions of autologous horse blood (AHB) and autologous horse serum (AHS) on expressions of selected cytokine genes in equine primary bronchial epithelial cell (BEC) cultures and to contrast these responses to those induced in BEC cultures by endotoxin and hay dust. SAMPLE BEC cultures established from bronchi of 6 healthy horses. PROCEDURES 5-day-old BEC cultures were treated with PBS solution, AHB (2 concentrations), AHS, hay dust solution, and lipopolysaccharide solution for 24 hours. Gene expressions of interleukin (IL)-8, IL-1β, chemokine (C-X-C motif) ligand 2 (CXCL2), and glyceralde-hyde-3-phosphate dehydrogenase were subsequently measured with a kinetic PCR assay. RESULTS With the exception of AHS, all treatments of the BECs resulted in upregulation of each target gene expression relative to its expression in cultures exposed to PBS solution. Treatment with AHB induced a dose-dependent increase of each target gene, with IL-1β expression increasing the most (> 1,200-fold increase). Lipopolysaccharide and hay dust solution treatments each resulted in 20-fold increases in IL-8 and IL-1β gene expressions. Lipopolysaccharide and hay dust solution treatments also resulted in a 7- and 8-fold increase in CXCL2 gene expression, respectively. The increases in IL-8 and CXCL2 gene expressions following treatment with the higher concentration of blood were equivalent to those associated with hay dust solution or lipopolysaccharide. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that chemokine expression by cultured equine BECs following exposure to pulmonary hemorrhage conditions may contribute to the development of inflammatory airway disease in horses.
Pleiotrophin inhibits melanogenesis via Erk1/2‐MITF signaling in normal human melanocytes

Pleiotrophin (PTN) is a secreted heparin‐binding protein that is involved in various biological functions of cell growth and differentiation. Little is known about the effects of PTN on the melanocyte function and skin pigmentation. In this study, we investigated whether PTN would affect melanogenesis. PTN was expressed in melanocytes and fibroblasts of human skin. Transfection studies revealed that PTN decreased melanogenesis, probably through MITF degradation via Erk1/2 activation in melanocytes. The inhibitory action of PTN in pigmentation was further confirmed in ex vivo cultured skin and in the melanocytes cocultured with fibroblasts. These findings suggest that PTN is a crucial factor for the regulation of melanogenesis in the skin.
Ultrasound measurement of the corpus callosum and neural development of premature infants

Length and thickness of 152 corpus callosa were measured in neonates within 24 hours of birth. Using ultrasonic diagnostic equipment with a neonatal brain-specific probe, corpus callosum length and thickness of the genu, body, and splenium were measured on the standard mid-sagittal plane, and the anteroposterior diameter of the genu was measured in the coronal plane. Results showed that corpus callosum length as well as thickness of the genu and splenium increased with tional age and birth weight, while other measures did not. These three factors on the standard mid-sagittal plane are therefore likely to be suitable for real-time evaluation of corpus callosum velopment in premature infants using cranial ultrasound. Further analysis revealed that thickness of the body and splenium and the anteroposterior diameter of the genu were greater in male infants than in female infants, suggesting that there are sex differences in corpus callosum size during the neonatal period. A second set of measurements were taken from 40 premature infants whose gestational age was 34 weeks or less. Corpus callosum measurements were corrected to a gestational age of 40 weeks, and infants were grouped for analysis depending on the outcome of a neonatal behavioral neurological assessment. Compared with infants with a normal neurological assessment, corpus callosum length and genu and splenium thicknesses were less in those with abnormalities, indicating that corpus callosum growth in premature infants is associated with neurobehavioral development during the early extrauterine stage.
The Genus Aeromonas: Biochemical Characteristics, Atypical Reactions, and Phenotypic Identification Schemes

ABSTRACT A total of 193 strains representing 14 different Aeromonas genomospecies were evaluated for 63 phenotypic properties to create useful tables for the reference identification of mesophilic aeromonads. Only 9 of 62 biochemical tests (14%) yielded uniform results, and the fermentation of certain carbohydrates was found to be linked to specific species. A number of unusual or aberrant properties for the genus Aeromonas were also detected in the collection of 428 strains (193 in the phenotypic study, 235 in a retrospective review). These tests included susceptibility to the vibriostatic agent, fermentation of m-inositol and d-xylose, hydrolysis of urea, and the lack of cytochrome oxidase activity. Fermentation of melibiose was linked to raffinose fermentation in all Aeromonas species except A. jandaei. Keys are provided for clinical laboratories choosing to identify aeromonads to species level based upon initial Møeller decarboxylase and dihydrolase reactions. In addition, several new tests were identified that help to separate members of the A. caviae complex (A. caviae, A. media, and A. eucreonophila).
Tenascins in Retinal and Optic Nerve Neurodegeneration

Tenascins represent key constituents of the extracellular matrix (ECM) with major impact on central nervous system (CNS) development. In this regard, several studies indicate that they play a crucial role in axonal growth and guidance, synaptogenesis and boundary formation. These functions are not only important during development, but also for regeneration under several pathological conditions. Additionally, tenascin-C (Tnc) represents a key modulator of the immune system and inflammatory processes. In the present review article, we focus on the function of Tnc and tenascin-R (Tnr) in the diseased CNS, specifically after retinal and optic nerve damage and degeneration. We summarize the current view on both tenascins in diseases such as glaucoma, retinal ischemia, age-related macular degeneration (AMD) or diabetic retinopathy. In this context, we discuss their expression profile, possible functional relevance, remodeling of the interacting matrisome and tenascin receptors, especially under pathological conditions.
Visual Methods for Examining Support Vector Machine Results, with Applications to Gene Expression Data Analysis

Support vector machines (SVM) oer a theoretically well-founded approach to automated learning of pattern classifiers. They have been proven to give highly accurate results in complex classification problems, for example, gene expression analysis. The SVM algorithm is also quite intuitive with a few inputs to vary in the fitting process and several outputs that are interesting to study. For many data mining tasks (e.g., cancer prediction) finding classifiers with good predictive accuracy is important, but understanding the classifier is equally important. By studying the classifier outputs we may be able to produce a simpler classifier, learn which variables are the important discriminators between classes, and find the samples that are problematic to the classification. Visual methods for exploratory data analysis can help us to study the outputs and complement automated classification algorithms in data mining. We present the use of tour-based methods to plot aspects of the SVM classifier. This approach provides insights about the cluster structure in the data, the nature of boundaries between clusters, and problematic outliers. Furthermore, tours can be used to assess the variable importance. We show how visual methods can be used as a complement to cross-validation methods in order to find good SVM input parameters for a particular data set.
Spermatozoal RNAs: What about their functions?

The profound architectural changes that transform spermatids into spermatozoa result in a high degree of DNA packaging within the sperm head. However, the mature sperm chromatin that harbors imprinted genes exhibits a dual nucleoprotamine/nucleohistone structure with DNase‐sensitive regions, which could be implicated in the establishment of efficient epigenetic information in the developing embryo. Despite its apparent transcriptionally inert state, the sperm nucleus contains diverse RNA populations, mRNAs, antisense and miRNAs, that have been transcribed throughout spermatogenesis. There is also an endogenous reverse transcriptase that may be activated under certain circumstances. It is now commonly accepted that sperm can deliver some RNAs to the ovocyte at fertilization. This review presents potential links between male‐specific genomic imprinting, chromatin organization, and the presence of diverse RNA populations within the sperm nucleus and discusses the functional significance of these RNAs in the spermatozoon itself and in the early embryo following fertilization. Some recent data are provided, supporting the view that analyzing the profile of spermatozoal RNAs could be useful for assessment of male fertility. Microsc. Res. Tech. 2009. © 2009 Wiley‐Liss, Inc.
Economic-Environmental Indicators to Support Investment Decisions: A Focus on the Buildings’ End-of-Life Stage

The aim of this paper is to propose a methodology for supporting decision making in design activities; in case of new projects or retrofitting of existing buildings. A multidisciplinary approach is adopted; involving Real Estate Appraisal and Economic Evaluation of Project and Building Environmental Design. It is proposed a methodology for selecting the preferable solutions among technological options; considering both economic and environmental aspects; in terms of global performance. Assuming the principles of Life Cycle Thinking and Circular Economy focus is posed at the end-of-life stage. Attention is paid on disposal costs and residual value as relevant items enable to orient investment decisions. This is done through an approach for quantifying environmental indicators related to Life Cycle Assessment (Standard ISO 14040:2006); and economic indicators adopting the Life Cycle Costing (Standard ISO 15686:2008). The paper proposes a conjoint “economic-environmental indicator”. An application of Global Cost calculation is illustrated; including monetized environmental impacts (Embodied energy and Embodied carbon); disposal/dismantling costs and residual value. The result of the Global Cost calculation is expressed through a “synthetic economic-environmental indicator” in order to select; between two different technologies; the most viable solution for a multifunctional building glass facade project; in Northern Italy. The study demonstrates that the initial investment decisions depend on the design solutions; since the early stages; related to the whole building life cycle considering conjointly the construction-management phases and the end-of-life stage.
Book Reviews: Lexical Acquisition: Exploiting On-Line Resources to Build a Lexicon

It's taken a good three years to squeeze this collection of workshop papers through the publishing pipeline. No great matter: the state of the art in lexical acquisition is still much as it was. Editor Zernik has used the time to impose some coherence on the multi-disciplinary material by adding a substantial introduction, and at least some of the authors have cross-referenced their papers to other contributions. The effort has succeeded up to a point. But, as with most such proceedings, it is still up to the reader to fit the bits and pieces into a common frame of reference. The papers are as follows:
School of Informatics, University of Edinburgh

: This paper summarizes a series of recent research results made at Edinburgh University based on projects that apply domain knowledge of standard shapes and relationships to solve or improve reverse engineering problems. The problems considered are how to enforce known relationships when data ﬁtting, how to extract features even in very noisy data, how to get better shape parameter estimates and how to infer data about unseen features.