Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomic insight into designed carbamate-based derivatives as acetylcholine esterase (AChE) inhibitors: a computational study by multiple molecular docking and molecular dynamics simulation

Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker, and Hex-Cuda, to study the effect of alteration in the structure of carbamate-based acetylcholyne esterase (AChE) inhibitors. Sixteen selected systems were then subjected to 14 ns molecular dynamics (MD) simulations. Results from all the docking methods are in agreement. Variants that involved biphenyl substituents possess the most negative binding energies in the −37.64 to −39.31 kJ mol−1 range due to their π–π interactions with AChE aromatic residues. The root mean square deviation values showed that all of these components achieved equilibration after 6 ns. Gyration radius (Rg) and solvent accessibility surface area were calculated to further investigate the AChE conformational changes in the presence of these components. MD simulation results suggested that these components might interact with AChE, possibly with no major changes in AChE secondary and tertiary structures.
Insect recognition based on integrated region matching and dual tree complex wavelet transform

To provide pest technicians with a convenient way to recognize insects, a novel method is proposed to classify insect images by integrated region matching (IRM) and dual tree complex wavelet transform (DTCWT). The wing image of the lepidopteran insect is preprocessed to obtain the region of interest (ROI) whose position is then calibrated. The ROI is first segmented with the k-means algorithm into regions according to the color features, properties of all the segmented regions being used as a coarse level feature. The color image is then converted to a grayscale image, where DTCWT features are extracted as a fine level feature. The IRM scheme is undertaken to find K nearest neighbors (KNNs), out of which the nearest neighbor is searched by computing the Canberra distance of DTCWT features. The method was tested with a database including 100 lepidopteran insect species from 18 families and the recognition accuracy was 84.47%. For the forewing subset, a recognition accuracy of 92.38% was achieved. The results showed that the proposed method can effectively solve the problem of automatic species identification of lepidopteran specimens.
An overview of current ontology meta-matching solutions

Abstract Nowadays, there are a lot of techniques and tools for addressing the ontology matching problem; however, the complex nature of this problem means that the existing solutions are unsatisfactory. This work intends to shed some light on a more flexible way of matching ontologies using ontology meta-matching. This emerging technique selects appropriate algorithms and their associated weights and thresholds in scenarios where accurate ontology matching is necessary. We think that an overview of the problem and an analysis of the existing state-of-the-art solutions will help researchers and practitioners to identify the most appropriate specific features and global strategies in order to build more accurate and dynamic systems following this paradigm.
The WNT/MYB pathway suppresses KIT expression to control the timing of salivary proacinar differentiation and duct formation

Growth factor signaling is involved in the development of various organs, but how signaling regulates organ morphogenesis and differentiation in a coordinated manner remains to be clarified. Here, we show how WNT signaling controls epithelial morphogenetic changes and differentiation using the salivary gland as a model. Experiments using genetically manipulated mice and organ cultures revealed that WNT signaling at an early stage (E12-E15) of submandibular salivary gland (SMG) development inhibits end bud morphogenesis and differentiation into proacini by suppressing Kit expression through the upregulation of the transcription factor MYB, and concomitantly increasing the expression of distal progenitor markers. In addition, WNT signaling at the early stage of SMG development promoted end bud cell proliferation, leading to duct formation. WNT signaling reduction at a late stage (E16-E18) of SMG development promoted end bud maturation and suppressed duct formation. Thus, WNT signaling controls the timing of SMG organogenesis by keeping end bud cells in an undifferentiated bipotent state. Highlighted article: During branching morphogenesis of the salivary gland, mesenchymal WNT signals promote duct formation and inhibit KIT-mediated proacinar differentiation.
Ultra-long-haul 40-Gbit/s-based DWDM transmission using optically prefiltered CS-RZ signals

Ultra-long-haul 42.7-Gbit/s-based dense wavelength-division multiplexing (DWDM) transmission using optically prefiltered carrier-suppressed return-to-zero (CS-RZ) signal has been experimentally investigated. First, we have numerically and experimentally evaluated the impact of 3-dB bandwidth and filter detuning of bandlimiting filters on the 42.7-Gbit/s CS-RZ signal in back-to-back condition. We found that the asymmetrically filtered CS-RZ signal had a great potential for ultra-DWDM applications. Next, we have numerically and experimentally investigated the basic transmission characteristics of a 45-GHz-wide prefiltered CS-RZ signal, such as the robustness against residual dispersion, nonlinear effects, and PMD, and have confirmed that the prefiltered CS-RZ signal had less tolerance against fiber nonlinearity than an unfiltered CS-RZ signal. Finally, we have experimentally investigated the optimum filtering condition for 65- or 45-GHz-wide prefiltered CS-RZ signals in the ultra-long-haul DWDM transmission and have conducted the 70- and 50-GHz spaced 32 /spl times/ 42.7Gbit/s transmission using prefiltered CS-RZ signals. Through these experiments, we have confirmed the effectiveness of prefiltered CS-RZ signal ultra-long-haul DWDM transmission.
Structural basis of rifampin inactivation by rifampin phosphotransferase

Significance Rifampin phosphotransferases (RPH) belong to a recently identified antibiotic-resistance protein family that inactivates rifampin, the first-line drug against tuberculosis, by phosphorylation. By determining the structures of RPH from Listeria monocytogenes (LmRPH) in different conformations, we reveal a toggle-switch mechanism of the LmRPH catalytic process in which the C-terminal His domain swings between the ATP-binding domain and the rifampin-binding domain to transfer phosphate from ATP to rifampin. These structures explain the low substrate selectivity of RPH for the rifamycins. The residues involved in rifampin phosphorylation are identified also. The structural mechanism revealed in this study will guide the development of a new generation of rifamycins. Rifampin (RIF) is a first-line drug used for the treatment of tuberculosis and other bacterial infections. Various RIF resistance mechanisms have been reported, and recently an RIF-inactivation enzyme, RIF phosphotransferase (RPH), was reported to phosphorylate RIF at its C21 hydroxyl at the cost of ATP. However, the underlying molecular mechanism remained unknown. Here, we solve the structures of RPH from Listeria monocytogenes (LmRPH) in different conformations. LmRPH comprises three domains: an ATP-binding domain (AD), an RIF-binding domain (RD), and a catalytic His-containing domain (HD). Structural analyses reveal that the C-terminal HD can swing between the AD and RD, like a toggle switch, to transfer phosphate. In addition to its catalytic role, the HD can bind to the AD and induce conformational changes that stabilize ATP binding, and the binding of the HD to the RD is required for the formation of the RIF-binding pocket. A line of hydrophobic residues forms the RIF-binding pocket and interacts with the 1-amino, 2-naphthol, 4-sulfonic acid and naphthol moieties of RIF. The R group of RIF points toward the outside of the pocket, explaining the low substrate selectivity of RPH. Four residues near the C21 hydroxyl of RIF, His825, Arg666, Lys670, and Gln337, were found to play essential roles in the phosphorylation of RIF; among these the His825 residue may function as the phosphate acceptor and donor. Our study reveals the molecular mechanism of RIF phosphorylation catalyzed by RPH and will guide the development of a new generation of rifamycins.
Using a collection of humans as an execution testbed for swarm algorithms

To gain insight into swarm algorithms, researchers can study insect societies and other natural collectives, program multi-agent software simulations or build groups of cooperating robots. In our research, we consider another resource: swarms of humans. Human swarms provide three primary benefits: quick feedback and evaluation of swarm algorithms, experience with high-level swarm directives instead of low-level agent programs, and a source of swarm algorithms that can potentially be reverse-engineered for use in other applications. Planning is a human's preferred problem solving methodology because we are intelligent creatures with high-level communication skills. Due to the intelligence of the agents, human swarms can be quickly programmed, for subsequent observation and analysis. This paper describes human swarm experiments designed for gathering information on swarm algorithms. At these events 100 volunteers, wearing data-encoded T-shirts, work together to perform tasks of differing degrees of complexity. Researchers provide simple instructions for each task (programming the swarm), record the swarm's behavior (videotaped observation) and analyze the results (problem identification and algorithm-mining). We demonstrate the viability of this research by presenting the quick identification of a swarm algorithm "bug" and by producing a software implementation of a swarm algorithm gleaned from our observations.
Characterization of a novel laccase produced by the wood-rotting fungus Phellinus ribis.

The white-rot fungus Phellinus ribis produced a single form of laccase, which was purified to apparent electrophoretic homogeneity from cultures induced with 2,5-xylidine. This protein was a dimer, consisting of two subunits of 76 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Carbohydrate analysis revealed that the enzyme contained about 28% carbohydrate content. The laccase appeared to be different from other known laccases by the UV-visible absorption spectrum analysis. One enzyme molecule contained one copper, one manganese, and two zinc atoms. The laccase showed optimal activity at pH 4.0-6.0, 5.0, and 6.0 with 2,6-dimethoxyphenol, ABTS [2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid)], and syringaldazine, respectively. The enzyme preferably oxidized dimethoxyphenol and aromatic amine compounds. The stability of the laccase was low at acidic pH, whereas it showed high stability at neutral pH and mild temperature. The N-terminal amino acid sequence revealed a very low homology with other microbial laccases. With some substrates, the addition of manganese and H2O2 resulted in a remarkable increase in the oxidation rate. Without an appropriate phenolic substrate, the enzyme could not oxidize Mn(II) in the presence of H2O2 or pyrophosphate.
Nucleotide sequence of the Schizosaccharomyces pombe lys1 + Gene and Similarities of the lys1+ protein to peptide antibiotic synthetases

The 4·2 kbp lys1+ gene of Schizosaccharomyces pombe encoding the large subunit of α‐aminoadipate reductase (EC1.2.1.31), an enzyme specific to lysine synthesis in higher fungi, was completely sequenced at the nucleotide level from pLYS1H. The S. pombe lys1+ gene product consists of 1415 amino acid residues and has a putative molecular weight of 155·8 kDa. The encoded protein converts α‐aminoadipic acid to α‐aminoadipate‐δ‐semialdehyde by an ATP‐mediated adenylation. Analysis of the sequence showed that the putative protein encoded by lys1+ shares strong homology with the peptide antibiotic synthetases which also use an adenylation step. The sequence data reported in this paper have been submitted to GenBank database (Washington DC, USA) under the Accession Number U15923. © 1998 John Wiley & Sons, Ltd.
T1ρ and T2 Mapping of the Intervertebral Disk: Comparison of Different Methods of Segmentation

BACKGROUND AND PURPOSE: Intervertebral disk biochemical composition could be accessed in vivo by T1ρ and T2 relaxometry. We found no studies in the literature comparing different segmentation methods for data extraction using these techniques. Our aim was to compare different manual segmentation methods used to extract T1ρ and T2 relaxation times of intervertebral disks from MR imaging. Seven different methods of partial-disk segmentation techniques were compared with whole-disk segmentation as the reference standard. MATERIALS AND METHODS: Sagittal T1ρ and T2 maps were generated by using a 1.5T MR imaging scanner in 57 asymptomatic volunteers 20–40 years of age. Two hundred eighty-five lumbar disks were separated into 2 groups: nondegenerated disk (Pfirrmann I and II) and degenerated disk (Pfirrmann III and IV). In whole-disk segmentation, the disk was segmented in its entirety on all sections. Partial-disk segmentation methods included segmentation of the disk into 6, 5, 4, 3, and 1 sagittal sections. Circular ROIs positioned in the nucleus pulposus and annulus fibrosus were also used to extract T1ρ and T2, and data were compared with whole-disk segmentation RESULTS: In the nondegenerated group, segmentation of ≥5 sagittal sections showed no statistical difference with whole-disk segmentation. All the remaining partial-disk segmentation methods and circular ROIs showed different results from whole-disk segmentation (P < .001). In the degenerated disk group, all methods were statistically similar to whole-disk segmentation. All partial-segmentation methods, including circular ROIs, showed strong linear correlation with whole-disk segmentation in both the degenerated and nondegenerated disk groups. CONCLUSIONS: Manual segmentation showed strong reproducibility for T1ρ and T2 and strong linear correlation between partial- and whole-disk segmentation. Absolute T1ρ and T2 values extracted from different segmentation techniques were statistically different in disks with Pfirrmann grades I and II.
Teleoperation system with haptic feedback for physical interaction with remote environment

The paper focuses on the teleoperation system TeleTA with haptic feedback designed to realize haptic communication with remote human, to achieve high level of maneuverability of robot arm in unstructured environment, and to increase effectiveness of physical Human-Robot interaction. The human operator directs the robot arm to the target position, while manipulator sensory system provides safe physical interaction with environment. In order to achieve awareness of collision, to support operator with valuable information (stiffness and shape of contacting object), and to realize robot-mediated haptic communication, we developed the innovative tactile and haptic displays, namely, BraTact (for presenting the cutaneous information) and FlexTorque (for presenting the kinaethetic feedback).
The Partial Information Decomposition of Generative Neural Network Models

In this work we study the distributed representations learnt by generative neural network models. In particular, we investigate the properties of redundant and synergistic information that groups of hidden neurons contain about the target variable. To this end, we use an emerging branch of information theory called partial information decomposition (PID) and track the informational properties of the neurons through training. We find two differentiated phases during the training process: a first short phase in which the neurons learn redundant information about the target, and a second phase in which neurons start specialising and each of them learns unique information about the target. We also find that in smaller networks individual neurons learn more specific information about certain features of the input, suggesting that learning pressure can encourage disentangled representations.
CD73, a novel cell surface antigen that characterizes retinal photoreceptor precursor cells.

PURPOSE The authors sought to identify cell surface markers of photoreceptor and its precursor cells. METHODS The expression of surface CD antigens that label both temporally and spatially distinct populations of mouse retinal cells were examined. Of the antibodies that showed positive signals in retinal cells, CD73 was focused on for more detailed analyses. RESULTS Mouse retinal subpopulations that expressed CD73 first appeared around birth and subsequently increased dramatically in number, eventually representing more than 90% of the retinal cells in the adult. CD73(+) cells were postmitotic and mostly rhodopsin-negative at postnatal day 1. However, in the adult retina, most of these cells expressed rhodopsin but not s-opsin. In reaggregation cultures, CD73(+) cells differentiated into rhodopsin-positive cells more rapidly than CD73(-) cells, which supports the idea that CD73 is an early photoreceptor lineage marker. The effects of ectopic expression in retinal cells of Nrl and Crx, both of which are transcription factors known to be expressed in photoreceptor lineage, suggest that CD73 is genetically downstream of Crx in the rod cell differentiation lineage. Adult retina of the common marmoset monkey also showed correlation of the expression pattern of rhodopsin and CD73. CONCLUSIONS CD73 is a cell surface marker of cone/rod common precursors and mature rod cells in mice and is genetically localized between Nrl and Crx. The expression of CD73 was conserved in primate rod cells, and CD73 provides an useful tool to purify photoreceptor cells for transplantation aimed at the regeneration of photoreceptors.
A Taxonomy of Privacy Salience Research

Privacy is an intuitive concept in the physical world, with all of us needing some escape from the public gaze. However, while individuals might recognise a locked door as protecting one’s privacy, they have difficulty practising equivalent actions online. Privacy salience considers the tangibility of this important principle, one which is often obscured in digital environments. By categorising existing work, we can both develop a deeper understanding of privacy and identify areas rich in research. Therefore, through surveying a range of prior studies, we iteratively construct a taxonomy of privacy salience. By coding research and identifying commonalities, we converge on several methodological categories, including surveys, tools and observations. These groups are further subdivided, presenting the range of techniques employed in privacy salience research. Exploring gaps in this taxonomy, we consider opportunities for further work, such as psychological analyses of privacy perceptions. We finish by discussing potential extensions to the taxonomy, based on growing trends in the field. It is through refining our understanding of this important topic that we can highlight the subject of privacy.
IpaB of Shigella flexneri causes entry into epithelial cells and escape from the phagocytic vacuole.

By creating mutations within the Shigella flexneri ipaB gene, we have demonstrated that the invasion of epithelial cells is a three‐step process encompassing adhesion on the cell surface, entry and lysis of the phagocytic vacuole allowing subsequent access to the cytoplasm. SC403, an insertion mutant which lacks expression of IpaB but still expresses downstream genes, has been particularly studied. It is non‐invasive, does not elicit actin polymerization, but binds to HeLa cells indicating that an adhesion step occurs immediately prior to the entry process. The consequence of the inactivation of ipaB on the intracellular behaviour of S.flexneri was investigated using the macrophage cell line J774. SC403 was unable to lyse the phagocytic vacuole; moreover, this strain did not display the contact mediated haemolytic activity characteristics of Shigella. In addition to being a major component of the invasion complex, IpaB acts as a membrane‐lysing toxin enabling escape to the cytoplasmic compartment.
Enhancing phosphorus uptake and yield of wheat with phosphoric acid application in calcareous soil.

BACKGROUND Low phosphorus (P) availability to wheat from commercial fertilizers is one of the reasons for lower grain yield and hence justifies search for more efficient P source under alkaline calcareous soils. RESULTS Phosphoric acid (PA) and diammonium phosphate (DAP), applied through conventional and modified methods, were assessed for P supply and wheat yield in a calcareous soil. Under laboratory conditions, pre-incubated soil with 70 mg P kg-1 soil as PA and DAP was assessed for solution P (Cp ) for 4 weeks. Phosphorus sorption data were fitted using the Freundlich model for describing analyzed sorption in soil incubated with or without DAP and PA. The fitted model equations exhibited comparatively higher effluxes of P from the solution system in control treatment. Compared to DAP, lower quantities (19.6%) of P for PA-treated soil were required for producing optimum P concentration in soil solution, i.e. 0.2 mg P L-1 . The greenhouse study involved 32 P tracer technique to quantify the proportion of applied P derived by wheat from fertilizer or soil. The results showed that P derived from fertilizer was highest (47.5%) in PA placement, while the lowest (31.5%) was in DAP broadcast treatment. The field study also showed similar trends to that of the greenhouse study. The PA placement treatment resulted in highest (23.4%) phosphorus use efficiency, whereas the lowest one (17.1%) was recorded for DAP broadcast treatment. CONCLUSION PA proved to be a better P source than DAP for improving P content and achieving higher yield and recovery of applied P by wheat grown in alkaline calcareous soils. © 2016 Society of Chemical Industry.
Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences

A method for quantifying eubacterial cell densities in dilute communities of small bacterioplankton is presented. Cells in water samples were stained with 4',6-diamidino-2-phenylindole (DAPI), transferred to gelatin-coated slides, and hybridized with rhodamine-labeled oligonucleotide probes specific for kingdom-level 16S rRNA sequences. Between 48 and 69% of the cells captured on membrane filters were transferred to gelatin-coated slides. The number of DAPI-stained cells that were visualized with eubacterial probes varied from 35 to 67%. Only 2 to 4% of these cells also fluoresced following hybridization with a probe designed to target a eukaryotic 16S rRNA sequence. Between 0.1 and 6% of the bacterioplankton in these samples were autofluorescent and may have been mistaken as cells that hybridized with fluorescent oligonucleotide probes. Dual staining allows precise estimates of the efficiency of transfers of cells to gelatin films and can be used to measure the percentage of the total bacterioplankton that also hybridize with fluorescent oligonucleotide probes, indicating specific phylogenetic groups.
Compact band notch ultra wide band microstrip antenna for short distance wireless applications

In this paper a simple design, compact size, and low cost ultra wide band (UWB) rectangular patch antenna with defective ground plane with WLAN (5.5GHz) band notched characteristics is proposed. The band notch is created by inverted V slot on rectangular patch. The proposed antenna is designed on FR4 substrate of size 18 × 24 × 0.8mm. The antenna achieves an operational bandwidth from 3.3 GHz to more than 10.6GHz up to 12.3 GHz which can be used to increase the wireless data transfer rate for short distance wireless devices.