Miracle-dz/UniFAR-FTUs huggingface dataset:
A Computational Methodology to Screen Activities of Enzyme Variants

We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodology is based on the PM6 and MOZYME methods as implemented in MOPAC2009, and is tested on the first step of the amide hydrolysis reaction catalyzed by the Candida Antarctica lipase B (CalB) enzyme. The barrier heights are estimated using adiabatic mapping and shown to give barrier heights to within 3 kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a small model system. Relatively strict convergence criteria (0.5 kcal/(molÅ)), long NDDO cutoff distances within the MOZYME method (15 Å) and single point evaluations using conventional PM6 are needed for reliable results. The generation of mutant structures and subsequent setup of the semiempirical calculations are automated so that the effect on barrier heights can be estimated for hundreds of mutants in a matter of weeks using high performance computing.
Spherical and Hyperbolic Fractional Brownian Motion

We define a Fractional Brownian Motion indexed by a sphere, or more generally by a compact rank one symmetric space, and prove that it exists if, and only if, $0 < H \leq 1/2$. We then prove that Fractional Brownian Motion indexed by an hyperbolic space exists if, and only if, $0 < H \leq 1/2$. At last, we prove that Fractional Brownian Motion indexed by a real tree exists when $0 < H \leq 1/2$.
The Effect of Cluster Environment on Galaxy Evolution in the Pegasus I Cluster

We present neutral hydrogen observations of 54 galaxies in the Pegasus Cluster. The observations include single-dish H I measurements, obtained with the Arecibo telescope for all 54 galaxies in the sample, as well as H I images obtained with the Very Large Array (VLA) for 10 of these. The Arecibo profiles reveal an overall H I deficiency in the cluster, with ∼40% of the galaxies in the core of the cluster showing modest deficiencies of typically a factor of 2-3. The H I morphology of some galaxies shows that the H I disk is smaller than the optical disk and slightly offset from the stars. We find a correlation between H I deficiency and the ratio of the H I disk size to optical disk size. More H I-deficient galaxies have relatively smaller H I disks, a configuration that is usually attributed to an interaction between the interstellar medium (ISM) of the galaxy and the hot intracluster medium (ICM). Such a result is surprising, since the Pegasus Cluster has a low level of X-ray emission and a low velocity dispersion. The low velocity dispersion, coupled with the lack of a dense hot ICM, indicate that ram pressure stripping should not play a significant role in this environment. In addition, two of the galaxies, NGC 7604 and NGC 7648, are morphologically peculiar. Their peculiarities indicate contradictory scenarios of what is triggering their unusual star formation. Hα imaging, along with long-slit spectroscopy of NGC 7648, reveal morphological features that point to a recent tidal interaction. On the other hand, Hα imaging of NGC 7604 reveals a strong episode of star formation concentrated into an asymmetric arc, preferentially located on one side of the galaxy. VLA H I mapping shows that H I is also highly concentrated into that region, suggestive of a ram pressure event. Our data indicate that ISM-ICM interactions may play a role in a wider variety of environments than suggested by simple ram pressure arguments.
Malignant transformation of immortalized human bronchial epithelial cells by asbestos fibers.

Although asbestos is a well-established lung carcinogen, there currently is no suitable human cell model in which to examine the underlying cellular and molecular changes associated with fiber-mediated bronchial carcinogenesis. Using a recently established transformation model based on a human papillomavirus-immortalized human bronchial epithelial cell line, we successfully transformed these BEP2D cells after a single, 7-day treatment with a 20-microgram/ml (4 micrograms per cm2 area) dose of Union Internationale Contre le Cancer (UICC) Rhodesian chrysotile fibers. Asbestos treatment resulted in a surviving fraction of 0.18 compared to control cells. Transformed cells developed through a series of sequential steps, including altered growth kinetics, resistance to serum-induced terminal differentiation, and anchorage-independent growth, before becoming tumorigenic to form progressively growing tumors in nude mice. Seven tumorigenic cell lines were isolated and determined to be of human epithelial origin based on immunofluorescent staining of keratin and isozyme analysis. Analysis of tumor DNA revealed no mutations at either codon 12 or 13 in any the ras oncogenes. An independent role for K-ras mutation in fiber carcinogenesis, therefore, cannot be confirmed. This model provides a unique opportunity to study the cellular and molecular changes at the various stages in fiber-mediated neoplastic transformation of human bronchial epithelial cells. ImagesFigure 3.Figure 4.
Heat Stress in Wheat during Reproductive and Grain-Filling Phases

Ambient temperatures have increased since the beginning of the century and are predicted to continue rising under climate change. Such increases in temperature can cause heat stress: a severe threat to wheat production in many countries, particularly when it occurs during reproductive and grain-filling phases. Heat stress reduces plant photosynthetic capacity through metabolic limitations and oxidative damage to chloroplasts, with concomitant reductions in dry matter accumulation and grain yield. Genotypes expressing heat shock proteins are better able to withstand heat stress as they protect proteins from heat-induced damage. Heat tolerance can be improved by selecting and developing wheat genotypes with heat resistance. Wheat pre-breeding and breeding may be based on secondary traits like membrane stability, photosynthetic rate and grain weight under heat stress. Nonetheless, improvement in grain yield under heat stress implies selecting genotypes for grain size and rate of grain filling. Integrating physiological and biotechnological tools with conventional breeding techniques will help to develop wheat varieties with better grain yield under heat stress during reproductive and grain-filling phases. This review discusses the impact of heat stress during reproductive and grain-filling stages of wheat on grain yield and suggests strategies to improve heat stress tolerance in wheat.
FSM implementation in embedded memory blocks of programmable logic devices using functional decomposition

Since modern programmable devices contain embedded memory blocks, there exists the possibility of implementing finite state machines (FSM) using such blocks. However, the size of the memory available in programmable devices is limited. The paper presents a general method for the synthesis of sequential circuits using embedded memory blocks. The method is based on the serial decomposition concept and relies on decomposing the memory block into two blocks: a combinational address modifier and a smaller memory block. An appropriately chosen decomposition strategy may allow reducing the required memory size at the cost of additional logic cells for address modifier implementation. This makes possible the implementation of FSMs that exceed available memory by using embedded memory blocks and additional programmable logic.
Antecedents and outcomes of brand love: the mediating role of brand loyalty

Abstract The purpose of this study was to propose and test an integrative conceptual model which incorporates experience-based (i.e. brand experience) and non-experience-based (i.e. self-congruity) antecedents and behavioural outcomes (i.e. brand loyalty and positive word-of-mouth) of brand love. The conceptual model and proposed hypotheses of the study are analysed with a sample of 361 consumers by using a structured survey as a data collection instrument. Structural equation modelling was used to examine the hypothesized linkages among the constructs. The findings of the study demonstrate strong associations between both experience-based and non-experience-based antecedents and brand love, and between brand love and its behavioural outcomes. This study also corroborates the mediating role of brand loyalty on the impact of brand love on positive word-of-mouth. This study is expected to contribute to the field of brand management by investigating the simultaneous impact of experience-based and non-experienced-based antecedents on brand love and the mediating role of brand loyalty on the association between brand love and positive word-of-mouth, which has not been addressed in the previous literature.
The Gaseous Extent of Galaxies and the Origin of Lyα Absorption Systems. III. Hubble Space Telescope Imaging of Lyα-absorbing Galaxies at z < 1

We present initial results of a program to obtain and analyze Hubble Space Telescope (HST) Wide Field Planetary Camera 2 images of galaxies identified in an imaging and spectroscopic survey of faint galaxies in fields of HST spectroscopic target QSOs. We measure properties of 87 galaxies, of which 33 are associated with corresponding Lyα absorption systems and 24 do not produce corresponding Lyα absorption lines to within sensitive upper limits. Considering only galaxy and absorber pairs that are likely to be physically associated and excluding galaxy and absorber pairs within 3000 km s-1 of the background QSOs leaves 26 galaxy and absorber pairs and seven galaxies that do not produce corresponding Lyα absorption lines to within sensitive upper limits. Redshifts of the galaxy and absorber pairs range from 0.0750 to 0.8912 with a median of 0.3718, and impact parameter separations of the galaxy and absorber pairs range from 12.4 to 157.4 h-1 kpc with a median of 62.4 h-1 kpc. The primary result of the analysis is that the amount of gas encountered along the line of sight depends on the galaxy impact parameter and B-band luminosity but does not depend strongly on the galaxy average surface brightness, disk-to-bulge ratio, or redshift. This result confirms and improves upon the anticorrelation between Lyα absorption equivalent width and galaxy impact parameter found previously by Lanzetta et al. in 1995. Spherical halos cannot be distinguished from flattened disks on the basis of the current observations, and there is no evidence that galaxy interactions play an important role in distributing tenuous gas around galaxies in most cases. Galaxies might account for all Lyα absorption systems with W > 0.3 Å, but this depends on the unknown luminosity function and gaseous cross sections of low-luminosity galaxies as well as on the uncertainties of the observed number density of Lyα absorption systems.
Voting-based 3D object cuboid detection robust to partial occlusion from RGB-D images

In this paper, we propose a novel algorithm for 3D object cuboid detection. Contrary to the conventional algorithms based on image segmentation, we propose a part-based voting process to robustly generate cuboids when the object is partially occluded. Our method finds the distinctive parts of RGB-D images and generates the 3D cuboids covering the target objects from the distinctive parts by the proposed probabilistic voting model. To validate the performance of the proposed method, experiments are conducted on the challenging NYU v2 and SUN RGB-D datasets. Experimental results show that our method is computationally efficient and has a competitive performance compared with the state-of-the-art methods. In addition, our method can be combined with the conventional segmentation-based method parallelly, and the combined algorithm is evaluated by experiments to show that it achieves a significant improvement of performance.
Letter to the editor: Comment on "Simultaneous treatment of anterior vaginal wall prolapse and stress urinary incontinence by using transobturator four arms polypropylene mesh"

which was an interesting study that both investigated the safety and efficacy of the four-arm polypropylene mesh (Nazca-Tc, Promedon, Cordoba, Argentina) in the treatment of high-stage cystocele and evaluated clinical outcomes in a subgroup of patients with simultaneous stress urinary incontinence (SUI) via a double transobturator approach. Although the study had strong limitations due to a relatively small number of patients and a single-arm rather than a double-arm study design, the Nazca-Tc system was deemed by the authors to be effective and safe in the treatment of advanced anterior vaginal wall prolapse with a low rate of complications after medium-term followup. Furthermore, the authors suggested that most of the subgroup with concomitant SUI was cured without a second simultaneous procedure. This was a valid and well-conducted study, despite its limitations, and suggests interesting data and conclusions for consideration by urogynecologists. However, the study had a significant structural limitation: the lack of a correct evaluation of pre- and postoperative sexual function. The authors reported that only 29 of 64 patients (45.3%) were
How Robots Persuasion based on Personality Traits May Affect Human Decisions

The use of autonomous agents, such as robots, to perform tasks such as cleaning the floor or washing the car are more frequent in our daily life. Moreover, with the advance of technology the society is in front of a new trend, your devices are connected to each other, for example, the robot that cleans the floor is connected to the cellphone. This trend was named as Smart Interaction. Those connections may be used to persuade the person to do some task in his/her own benefits, e.g., the refrigerator could recommend healthy foods if the bathroom scale informs that the person is overweight. However, the communications and the persuasions made by these autonomous agents should not be performed in an invasive way. In this sense, our motivation is to create a model were the autonomous agents may perform persuasion based on the person's personality traits.
Learning sequential motor tasks

Many real robot applications require the sequential use of multiple distinct motor primitives. This requirement implies the need to learn the individual primitives as well as a strategy to select the primitives sequentially. Such hierarchical learning problems are commonly either treated as one complex monolithic problem which is hard to learn, or as separate tasks learned in isolation. However, there exists a strong link between the robots strategy and its motor primitives. Consequently, a consistent framework is needed that can learn jointly on the level of the individual primitives and the robots strategy. We present a hierarchical learning method which improves individual motor primitives and, simultaneously, learns how to combine these motor primitives sequentially to solve complex motor tasks. We evaluate our method on the game of robot hockey, which is both difficult to learn in terms of the required motor primitives as well as its strategic elements.
Generation of High Resolution Global DSM from ALOS PRISM

Panchromatic Remote-sensing Instrument for Stereo Mapping (PRISM), one of onboard sensors carried on the Advanced Land Observing Satellite (ALOS), was designed to generate worldwide topographic data with its optical stereoscopic observation. The sensor consists of three independent panchromatic radiometers for viewing forward, nadir, and backward in 2.5 m ground resolution producing a triplet stereoscopic image along its track. The sensor had observed huge amount of stereo images all over the world during the mission life of the satellite from 2006 through 2011. We have semi-automatically processed Digital Surface Model (DSM) data with the image archives in some limited areas. The height accuracy of the dataset was estimated at less than 5 m (rms) from the evaluation with ground control points (GCPs) or reference DSMs derived from the Light Detection and Ranging (LiDAR). Then, we decided to process the global DSM datasets from all available archives of PRISM stereo images by the end of March 2016. This paper briefly reports on the latest processing algorithms for the global DSM datasets as well as their preliminary results on some test sites. The accuracies and error characteristics of datasets are analyzed and discussed on various fields by the comparison with existing global datasets such as Ice, Cloud, and land Elevation Satellite (ICESat) data and Shuttle Radar Topography Mission (SRTM) data, as well as the GCPs and the reference airborne LiDAR/DSM.
The Best Choice Problem under Ambiguity Tatjana

We model and solve Best Choice Problems in the multiple prior framework: An ambiguity averse decision maker aims to choose the best among a fixed number of applicants that appear sequentially in a random order. The decision faces ambiguity about the probability that a candidate – a relatively top applicant — is actually best among all applicants. We show that our model covers the classical secretary problem, but also other interesting classes of problems. We provide a closed form solution of the problem for time-consistent priors using minimax backward induction. As in the classical case the derived stopping strategy is simple. Ambiguity can lead to substantial differences to the classical threshold rule.
Padrões de revelação e descoberta do abuso sexual de crianças e adolescentes Patterns of child and adolescent disclosure and discovery of sexual abuse

The study on child and adolescent dis- closure of sexual abuse is related to primary and secondary prevention, in addition to providing in- terventions for this type of violence. This article aims at characterizing the patterns of disclosure and discovery of sexual abuse, verifying its association to individual factors of the victims and perpetrators (age, sex) and relational factors (familiarity between victims and perpetrators, as well as with the recipi- ent of the disclosure). The study analyzed 232 cases of sexual abuse retrieved from records of three specialized services, one service was local- ized in the Brazilian state of Para (PA) and two in the state Rio Grande do Sul (RS). The patterns of disclosure and discovery were significantly associ- ated to the age and sex of the victims, and the place of the sample (PA and RS). Intentional disclosure was more frequent among female victims (33.5%) and accidental detection was more frequent among males (44.7%). In the sample from PA, accidental detection (46.9%) was predominant, whereas among the victims from RS intentional disclosure prevailed (31.1%). The importance of issues such as gender, developmental stage and influence of cultural and structural factors in public policies to prevent sexual abuse is also discussed.
Some Consequences of Demographic Stochasticity in Population Genetics

Much of population genetics is based on the diffusion limit of the Wright–Fisher model, which assumes a fixed population size. This assumption is violated in most natural populations, particularly for microbes. Here we study a more realistic model that decouples birth and death events and allows for a stochastically varying population size. Under this model, classical quantities such as the probability of and time before fixation of a mutant allele can differ dramatically from their Wright–Fisher expectations. Moreover, inferences about natural selection based on Wright–Fisher assumptions can yield erroneous and even contradictory conclusions: at small population densities one allele will appear superior, whereas at large densities the other allele will dominate. Consequently, competition assays in laboratory conditions may not reflect the outcome of long-term evolution in the field. These results highlight the importance of incorporating demographic stochasticity into basic models of population genetics.
Management of Gridded Climate Data for National Scale Integrated Assessment Models

Computer model analyses of climate change impacts are data intensive due to the spatial and temporal dimensions over which climate operates. Data intensity proves a major constraint in the design of such climate models. For policy oriented climate models this constraint proves critical, given the lower specification computer hardware readily available to decision makers. This paper discusses the use of spatial data orderings in combination with run-length encoding to spatially compress climate data. Experiments have been conducted which test the application of various data ordering schemes to the storage of climate data for New Zealand, Australia and Bangladesh. The results of these experiments are presented.
Understanding Semantic Web and Ontologies: Theory and Applications

Semantic Web is actually an extension of the current one in that it represents information more meaningfully for humans and computers alike. It enables the description of contents and services in machine-readable form, and enables annotating, discovering, publishing, advertising and composing services to be automated. It was developed based on Ontology, which is considered as the backbone of the Semantic Web. In other words, the current Web is transformed from being machine-readable to machine-understandable. In fact, Ontology is a key technique with which to annotate semantics and provide a common, comprehensible foundation for resources on the Semantic Web. Moreover, Ontology can provide a common vocabulary, a grammar for publishing data, and can supply a semantic description of data which can be used to preserve the Ontologies and keep them ready for inference. This paper provides basic concepts of web services and the Semantic Web, defines the structure and the main applications of ontology, and provides many relevant terms are explained in order to provide a basic understanding of ontologies.
Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences

The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral‐associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species’ preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.