Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization , modeling and docking of CYP 107 CB 2 from Bacillus lehensis G 1 , an alkaliphile Swi

Cytochrome P450s are a superfamily of heme monooxygenases which catalyze a wide range of biochemical reactions. The reactions involve the introduction of an oxygen atom into an inactivated carbon of a compound which is essential to produce an intermediate of a hydroxylated product. The diversity of chemical reactions catalyzed by cytochrome P450s has led to their increased demand in numerous industrial and biotechnology applications. A recent study showed that a gene sequence encoding a CYP was found in the genome of Bacillus lehensis G1, and this gene shared structural similarity with the bacterial vitamin D hydroxylase (Vdh) from Pseudonocardia autotrophica. The objectives of present study was to mine, for a novel CYP from a new isolate B. lehensis G1 alkaliphile and determine the biological properties and functionalities of CYP in this bacterium. Our study employed the usage of computational methods to search for the novel CYP from CYP structural databases to identify the conserved pattern, functional domain and sequence properties of the uncharacterized CYP from B. lehensis G1. A computational homology model of the protein’s structure was generated and a docking analysis was performed to provide useful structural knowledge on the enzyme’s possible substrate and their interaction. Sequence analysis indicated that the newly identified CYP, termed CYP107CB2, contained the fingerprint heme binding sequence motif FxxGxxxCxG at position 336-345 as well as other highly conserved motifs characteristic of cytochrome P450 proteins. Using docking studies, we identified Ser-79, Leu-81, Val-231, Val-279, Val-383, Ala-232, Thr-236 and Thr-283 as important active site residues capable of stabilizing interactions with several potential substrates, including vitamin D3, 25-hydroxyvitamin D3 and 1a-hydroxyvitamin D3, in which all substrates docked proximally to the enzyme’s heme center. Biochemical analysis indicated that CYP107CB2 is a biologically active protein to produce 1a,25-dihydroxyvitamin D3 from 1a-hydroxyvitamin D3. Based on these results, we conclude that the novel CYP107CB2 identified from B. lehensis G1 is a putative vitamin D hydroxylase which is possibly capable of catalyzing the bioconversion of parental vitamin D3 to calcitriol, or related metabolic products. ã 2015 Elsevier Ltd. All rights reserved.
2.1 Introduction

This chapter describes recent advances in genetic programming of machine code. Evolutionary program induction using binary machine code is the fastest known Genetic Programming method. It is, in addition, the most well studied Genetic Programming system that uses a linear genome. Evolutionary program induction using binary machine code was originally referred to as Compiling Genetic Programming System(CGPS). For clarity, the name was changed in early 1998 to Au matic Induction of Machine Code—Genetic Programming (AIM-GP). AIM-GP stores evolved programs as linear strings of native binary machine code, which are directly executed by the processor. The absence of an interpreter and complex memory handling increases the speed of AIM-GP by about two orders of magnitude. AIM-GP has so far been applied to processors with a fixed instruction length (RISC) using integer and floating-point arithmetic. We also describe several recent advances in the AIM-GP technology. Such advances include enabling the induction of code for CISC processors such as the INTEL x86 as well as JAVA and many embedded processors. The new techniques also make AIM-GP more portable in general and simplify the adaptation to any processor architecture. Other additions include the use of floating point instructions, control flow instructions, ADFs and new genetic operators e.g. aligned homologous crossover. This chapter also discusses the benefits and drawbacks of register machine GP versus tree-based GP. This chapter is directed towards the practitioner, who wants to extend AIM-GP to new architectures and application domains.
Predicting Argumentative Influence Probabilities in Large-Scale Online Civic Engagement

Large-scale online civic engagements (OCEs) with more than 100 participants have become possible due to recent developments in online social media technology. OCEs have the potential to achieve consensus building and collective decision-making with a large number of citizens, which is difficult to achieve in face-to-face contexts. However, most users in a large-scale OCE are rarely constantly active. Therefore, an important problem for the activation of a large-scale OCE is to facilitate the discussion by predicting which citizens will have significant influence in the discussion. This paper examines the activation prediction problem in a large-scale OCE. We propose a novel influence model based on the impulse response of activity histories and argumentative pressures, as well as an effective testing algorithm. The experimental results demonstrate that the proposed models with impulse response and the lexical pressures show better accuracy compared with baselines. In addition, the testing time required by the proposed method can be reduced significantly by employing a node-cutting algorithm.
SDTM, Plus or Minus

The CDISC Study Data Tabulation Model (SDTM) has become the industry standard for the regulatory submission of clinical trials data. The CDISC Analysis Data Model (ADaM) is not far behind in emerging as the industry standard for the analysis SAS datasets based upon the collected data. Pharmaceutical companies have begun to implement SDTM and, to some extent, ADaM. As part of this process, companies are evaluating whether to use the SDTM standard only for the regulatory submission, for which it is designed, or incorporate it into their operational standard as well. Some companies that are adopting SDTM as their operational standard are finding that a near-SDTM standard works better than strict conformance to the SDTM standard. When a near-SDTM standard is used at various stages in the full business process, the data contains either less than exact-SDTM (“SDTM-minus” as it is sometimes called) or more than exact-SDTM (“SDTM-plus” as it is sometimes called) or a mixture of both. This paper will discuss the use of SDTM as an operational data standard, the use of a near-SDTM standard with its SDTM-plus and SDTM-minus aspects, and how this relates to the development of analysis (ADaM) datasets.
How to model and analyze gossiping protocols?

During coffee breaks, birthday parties, and even sometimes at business meetings, gossiping is a common acitivity in which most people kindly engage. Gossiping forms one of the oldest and most common means of spreading and sharing facts and views. It has, however, a somewhat negative connotation as most people understand gossip as a means to spread dust and misinformation, as, e.g., a discussion of scandals of (mostly female) Hollywood celibrities (see, e.g., topgossips.com). In this special issue of ACM PER, however, gossiping is interpreted in a more positive sense, namely, to spread information such as measured data, routing information or the like, in distributed systems. The main focus is on modeling and quantitative analysis of such gossiping protocols.
Low Mach number flow induced noise prediction of a wall-mounted airfoil using a hybrid RANS-BEM technique

A hybrid RANS-BEM technique for the prediction of low Mach number flow induced noise produced by a body immersed in the flow is presented. Hydrodynamic data including turbulent kinetic energy and turbulent dissipation rate are obtained from a steady-state Reynolds Averaged Navier-Stokes (RANS) simulation. Using a model of the turbulence cross spectrum, statistical noise sources are obtained and then combined with a boundary element method (BEM) model of the body to predict the far-field sound. The results from the hybrid RANS-BEM technique are presented for turbulent flow past a wall mounted NACA0012 airfoil, with Reynolds number based on chord of Rec=1.1×10 and a Mach number of M=0.12 at zero angle of attack. The computed aerodynamic and acoustic results are in good agreement with experimental results.
Ground-level ozone in four Chinese cities: Precursors, regional transport and heterogeneous processes

Abstract. We analyzed the measurements of ozone (O3) and its precursors made at rural/suburban sites downwind of four large Chinese cities – Beijing, Shanghai, Guangzhou and Lanzhou, to elucidate their pollution characteristics, regional transport, in situ production, and impacts of heterogeneous processes. The same measurement techniques and observation-based model were used to minimize uncertainties in comparison of the results due to difference in methodologies. All four cities suffered from serious O3 pollution but showed different precursor distributions. The model-calculated in situ O3 production rates were compared with the observed change rates to infer the relative contributions of on-site photochemistry and transport. At the rural site downwind of Beijing, export of the well-processed urban plumes contributed to the extremely high O3 levels (up to an hourly value of 286 ppbv), while the O3 pollution observed at suburban sites of Shanghai, Guangzhou and Lanzhou was dominated by intense in situ production. The O3 production was in a volatile organic compound (VOC)-limited regime in both Shanghai and Guangzhou, and a NOx-limited regime in Lanzhou. The key VOC precursors are aromatics and alkenes in Shanghai, and aromatics in Guangzhou. The potential impacts on O3 production of several heterogeneous processes, namely, hydrolysis of dinitrogen pentoxide (N2O5), uptake of hydro peroxy radical (HO2) on particles and surface reactions of NO2 forming nitrous acid (HONO), were assessed. The analyses indicate the varying and considerable impacts of these processes in different areas of China depending on the atmospheric abundances of aerosol and NOx, and suggest the urgent need to better understand these processes and represent them in photochemical models.
Application-Level Jitter Reduction Scheme for Multimedia Communication over ATM-ABR Service

SUMMARY The ATM-ABR service category provides minimum cell rate (MCR) guarantees and robust connections even with insufficient network resources. Recently proposed rate-management algorithms for supporting multimedia applications over ABR mainly aim at minimizing the cell loss and delay. However, jitter is also an important element of QoS for multimedia applications. In this paper, we focus our attention on the arrival point of the critical cell corresponding to the end of data packet and propose a simple cell scheduling scheme for source node to reduce the jitter on application level over the ATM-ABR service class. In our proposed method, critical cells are delayed intentionally and the packet stream at application level becomes smooth. We verify the effectiveness of our proposed algorithm by an analytical model and simulation. From those results, we find that our proposed scheduling algorithm is effective in reducing the application level jitter even when the tagged cell stream is transmitted along the
Factors controlling the depth habitat of planktonic foraminifera in the subtropical eastern North Atlantic

Abstract. Planktonic foraminifera preserved in marine sediments archive the physical and chemical conditions under which they built their shells. To interpret the paleoceanographic information contained in fossil foraminifera, the recorded proxy signals have to be attributed to the habitat and life cycle characteristics of individual species. Much of our knowledge on habitat depth is based on indirect methods, which reconstruct the depth at which the largest portion of the shell has been calcified. However, habitat depth can be best studied by direct observations in stratified plankton nets. Here we present a synthesis of living planktonic foraminifera abundance data in vertically resolved plankton net hauls taken in the eastern North Atlantic during 12 oceanographic campaigns between 1995 and 2012. Live (cytoplasm-bearing) specimens were counted for each depth interval and the vertical habitat at each station was expressed as average living depth (ALD). This allows us to differentiate species showing an ALD consistently in the upper 100 m (e.g., Globigerinoides ruber white and pink), indicating a shallow habitat; species occurring from the surface to the subsurface (e.g., Globigerina bulloides, Globorotalia inflata, Globorotalia truncatulinoides); and species inhabiting the subsurface (e.g., Globorotalia scitula and Globorotalia hirsuta). For 17 species with variable ALD, we assessed whether their depth habitat at a given station could be predicted by mixed layer (ML) depth, temperature in the ML and chlorophyll a concentration in the ML. The influence of seasonal and lunar cycle on the depth habitat was also tested using periodic regression. In 11 out of the 17 tested species, ALD variation appears to have a predictable component. All of the tested parameters were significant in at least one case, with both seasonal and lunar cyclicity as well as the environmental parameters explaining up to > 50 % of the variance. Thus, G. truncatulinoides, G. hirsuta and G. scitula appear to descend in the water column towards the summer, whereas populations of Trilobatus sacculifer appear to descend in the water column towards the new moon. In all other species, properties of the mixed layer explained more of the observed variance than the periodic models. Chlorophyll a concentration seems least important for ALD, whilst shoaling of the habitat with deepening of the ML is observed most frequently. We observe both shoaling and deepening of species habitat with increasing temperature. Further, we observe that temperature and seawater density at the depth of the ALD were not equally variable among the studied species, and their variability showed no consistent relationship with depth habitat. According to our results, depth habitat of individual species changes in response to different environmental and ontogenetic factors and consequently planktonic foraminifera exhibit not only species-specific mean habitat depths but also species-specific changes in habitat depth.
Report for CSE 5339 2018 — ( OTMLSA ) Optimal Transport in Machine Learning and Shape Analysis From OT to generative modeling : the VEGAN cookbook

where cpx, yq : X ˆ X Ñ R` is any measurable cost function and PpX „ P, Y „ Qq is a set of all joint distribution of X,Y with marginals P and Q respectively. An element in the set PpX „ P, Y „ Qq is also called a coupling. When we choose pX , dq as a metric space and cpx, yq “ dppx, yq for p ě 1, the distance Wp is called the p-Wasserstein distance. The Kantorovich-Rubinstein theorem gives a duality for the 1-Wasserstein distance, which holds under mild assumptions on P and Q:
A prospective 5-year follow-up after population-based systematic screening for atrial fibrillation.

Aims Thrombo-embolic stroke risk in atrial fibrillation (AF) is significantly reduced with oral anticoagulant (OAC) treatment. Atrial fibrillation is often asymptomatic (silent) and therefore undiagnosed. The long-term course of silent AF as well as OAC treatment adherence after AF screening is not known. We aim at studying long-term adherence to OAC treatment, AF symptoms, and stroke incidence on population level after systematic AF screening. Methods and results All inhabitants in a Swedish municipality who were born in 1934 and 1935 (n = 1335) were invited to participate in an AF screening trial between 2010 and 2012. Participants with a previously known or screening-detected AF were invited to a 5-year follow-up. Time trends of ischaemic stroke incidence were compared for population groups residing in the intervention municipality and in a surrounding control area where no AF screening trial was carried out. After the screening procedure, 103 of 121 participants (85%) with AF were treated with OAC. At the follow-up examination, 94 of 106 living patients (88%) were still on OAC treatment. Among the 23 long-term surviving patients who were diagnosed with paroxysmal AF during screening, 6 had developed permanent silent AF. The incidence of ischaemic stroke between ages 76-80 years declined significantly after the AF screening trial in the intervention area (P = 0.003) but not in the control area. Conclusion Adherence to OAC treatment 5 years after AF screening was high. Silent AF has a natural course similar to symptomatic AF. The observed incidences of ischaemic stroke suggest a beneficial population-level effect of systematic AF screening.
A Novel Method For Image Retrieval Based On Visually Significant Feature Point Maps

AbstractIn this paper, we present a new algorithm for visually significant feature points detection for efficient image indexing and retrieval. We propose a hybrid feature point detector based on edge maps obtained via spatial and wavelet methods. Proposed method is compared with other existing interest point detectors. Robustness of feature points to geometric transformations like rotation and scaling is analyzed. Hausdorff distance measure is used for indexing and ranking of results.
ocal development during postnatal growth and ear morphology in a hrew that generates seismic vibrations , Diplomesodon pulchellum lexandra

The ability of adult and subadult piebald shrews (Diplomesodon pulchellum) to produce 160 Hz seismic waves is potentially reflected in their vocal ontogeny and ear morphology. In this study, the ontogeny of call variables and body traits was examined in 11 litters of piebald shrews, in two-day intervals from birth to 22 days (subadult), and ear structure was investigated in two specimens using micro-computed tomography (micro-CT). Across ages, the call fundamental frequency (f0) was stable in squeaks and clicks and increased steadily in screeches, representing an unusual, non-descending ontogenetic pathway of f0. The rate of the deep sinusoidal modulation (pulse rate) of screeches increased from 75 Hz at 3–4 days to 138 Hz at 21–22 days, probably relating to ontogenetic changes in contraction rates of the same
Endoscopic Monitoring of Postoperative Sinonasal Mucosa Wounds Healing

Nasal epithelium lies on the basement membrane, situated on the lamina propria. Pseudostratified columnar (respiratory) epithelium is composed of four major types of cells: ciliated cells, nonciliate cells, goblet cells and basal cells, ensuring mucus production and transport, resorption of surface materials, and formation of new epithelial cells. Lamina propria consists of two layers of seromucous glands, i.e. superficial and deep layers. Just beneath the basement membrane, lymphocytes and plasma cells form a lymphoid layer. Maintenance of normal ventilation/aeration of sinus spaces is necessary for normal functioning of paranasal sinuses. The sinus labyrinth spaces and ostia of various sinus areas can be visualized by use of endoscopic techniques, e.g., in functional endoscopic sinus surgery (FESS). Ventilation and normal sinus function can be maintained by this minimally invasive method. Endoscopic sinus surgery (ESS) is the superior surgical method of treatment for recurrent acute sinusitis, chronic sinusitis, obstructive nasal polyposis, extramucous fungal sinusitis, periorbital abscess, rhinoliquorrhea, antrochoanal polyp, foreign body extraction, mucocele, dacryocystorhinostomy, excision of various tumors of the sinuses, nose, anterior, middle and posterior cranial fossa, epistaxis control, optic nerve decompression, choanal atresia, and orbit decompression. Functional endoscopic sinus surgery (FESS), a minimally invasive technique, remains the most widely accepted therapy for chronic rhinosinusitis (CRS) and nasal polyposis (NP) after failure of medical treatment. FESS aims to remove inflammatory mucosa and to restore both ventilation and drainage of the sinus cavities. However, healing quality significantly influences the functional outcome. The exact mechanism of mucosal healing after sinus operation remains unclear. Postoperative wound healing is a highly coordinated process that includes coagulation, i.e. clot formation, inflammatory stage, and tissue formation and remodeling. During the process of healing, the extracellular matrix of nasal mucosa may be directly influenced by the growth factor (GF), while the expression of GF receptors may influence the cell phenotype and its adhesion. Endoscopic observation of the nasal and sinus mucosa healing after FESS revealed four clinical stages: stage 1 characterized by the formation of abundant crusts, lasting for 1-10 days; stage 2 characterized by obstructive lymphedema, with pronounced swelling of residual mucosa, lasting for up to 30 days; stage 3 characterized by mesenchymal growth, when pale, edematous mucosa is transformed to red mucosa, lasting for up to 3 months; and stage 4 characterized by cicatrix formation, lasting for 3-6 months.
Stylometry-based Approach for Detecting Writing Style Changes in Literary Texts

In this paper, we present an approach to identify changes in the writing style of 7 writers of novels written in English. We defined 3 stages of writing for each author, each stage contains 3 novels with a maximum of 3 years between each publication. We propose several stylometric features to represent the novels in a vector space model We use supervised learning algorithms to determine if by means of his stylometric-based representation is possible to identify to which stage of writing each novel belongs.
The Extracellular Environment of the CNS: Influence on Plasticity, Sprouting, and Axonal Regeneration after Spinal Cord Injury

The extracellular environment of the central nervous system (CNS) becomes highly structured and organized as the nervous system matures. The extracellular space of the CNS along with its subdomains plays a crucial role in the function and stability of the CNS. In this review, we have focused on two components of the neuronal extracellular environment, which are important in regulating CNS plasticity including the extracellular matrix (ECM) and myelin. The ECM consists of chondroitin sulfate proteoglycans (CSPGs) and tenascins, which are organized into unique structures called perineuronal nets (PNNs). PNNs associate with the neuronal cell body and proximal dendrites of predominantly parvalbumin-positive interneurons, forming a robust lattice-like structure. These developmentally regulated structures are maintained in the adult CNS and enhance synaptic stability. After injury, however, CSPGs and tenascins contribute to the structure of the inhibitory glial scar, which actively prevents axonal regeneration. Myelin sheaths and mature adult oligodendrocytes, despite their important role in signal conduction in mature CNS axons, contribute to the inhibitory environment existing after injury. As such, unlike the peripheral nervous system, the CNS is unable to revert to a “developmental state” to aid neuronal repair. Modulation of these external factors, however, has been shown to promote growth, regeneration, and functional plasticity after injury. This review will highlight some of the factors that contribute to or prevent plasticity, sprouting, and axonal regeneration after spinal cord injury.