Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Shell Colour Pigments in Marine Snails Clanculus pharaonius and C. margaritarius (Trochoidea; Gastropoda)

Colour and pattern are key traits with important roles in camouflage, warning and attraction. Ideally, in order to begin to understand the evolution and ecology of colour in nature, it is important to identify and, where possible, fully characterise pigments using biochemical methods. The phylum Mollusca includes some of the most beautiful exemplars of biological pigmentation, with the vivid colours of sea shells particularly prized by collectors and scientists alike. Biochemical studies of molluscan shell colour were fairly common in the last century, but few of these studies have been confirmed using modern methods and very few shell pigments have been fully characterised. Here, we use modern chemical and multi-modal spectroscopic techniques to identify two porphyrin pigments and eumelanin in the shell of marine snails Clanculus pharaonius and C margaritarius. The same porphyrins were also identified in coloured foot tissue of both species. We use high performance liquid chromatography (HPLC) to show definitively that these porphyrins are uroporphyrin I and uroporphyrin III. Evidence from confocal microscopy analyses shows that the distribution of porphyrin pigments corresponds to the striking pink-red of C. pharaonius shells, as well as pink-red dots and lines on the early whorls of C. margaritarius and yellow-brown colour of later whorls. Additional HPLC results suggest that eumelanin is likely responsible for black spots. We refer to the two differently coloured porphyrin pigments as trochopuniceus (pink-red) and trochoxouthos (yellow-brown) in order to distinguish between them. Trochopuniceus and trochoxouthos were not found in the shell of a third species of the same superfamily, Calliostoma zizyphinum, despite its superficially similar colouration, suggesting that this species has different shell pigments. These findings have important implications for the study of colour and pattern in molluscs specifically, but in other taxa more generally, since this study shows that homology of visible colour cannot be assumed without identification of pigments.
Quantitative micro‐X‐ray fluorescence scanning spectroscopy of wet sediment based on the X‐ray absorption and emission theories: Its application to freshwater lake sedimentary sequences

Micro‐X‐ray fluorescence scanning spectroscopy of marine and lake sedimentary sequences can provide detailed palaeoenvironmental records through element intensity proxy data. However, problems with the effects of interstitial pore water on the micro‐X‐ray fluorescence intensities have been pointed out. This is because the X‐ray fluorescence intensities are measured directly at the surfaces of split wet sediment core samples. This study developed a new method for correcting X‐ray fluorescence data to compensate for the effects of pore water using a scanning X‐ray analytical microscope. This involved simultaneous use of micro‐X‐ray fluorescence scanning spectroscopy and an X‐ray transmission detector. To evaluate the interstitial pore water content from the X‐ray transmission intensities, a fine‐grained sediment core retrieved from Lake Baikal (VER99‐G12) was used to prepare resin‐embedded samples with smooth surfaces and uniform thickness. Simple linear regression between the linear absorption coefficients of the samples and their porosity, based on the Lambert–Beer law, enabled calculation of the interstitial pore spaces and their resin content with high reproducibility. The X‐ray fluorescence intensities of resin‐embedded samples were reduced compared with those of dry sediment samples because of: (i) the X‐ray fluorescence absorption of resin within sediment; and (ii) the sediment dilution effects by resin. An improved micro‐X‐ray fluorescence correction equation based on X‐ray fluorescence emission theory considers the instrument's sensitivity to each element, which provides a reasonable explanation of these two effects. The resin‐corrected X‐ray fluorescence intensity was then successfully converted to elemental concentrations using simple linear regression between the data from micro‐X‐ray fluorescence scanning spectroscopy and from the conventional analyzer. In particular, the calculated concentration of SiO2 over the depth of the core, reflecting diatom/biogenic silica concentration, was significantly changed by the calibrations, from a progressively decreasing trend to an increasing trend towards the top of the core.
Supporting oracle construction via static analysis

In software testing, the program under test is usually executed with test inputs and checked against a test oracle, which is a mechanism to verify whether the program behaves as expected. Selecting the right oracle data to observe is crucial in test oracle construction. In the literature, researchers have proposed two dynamic approaches to oracle data selection by analyzing test execution information (e.g., variables' values or interaction information). However, collecting such information during program execution may incur extra cost. In this paper, we present the first static approach to oracle data selection, SODS (Static Oracle Data Selection). In particular, SODS first identifies the substitution relationships between candidate oracle data by constructing a probabilistic substitution graph based on the definition-use chains of the program under test, then estimates the fault-observing capability of each candidate oracle data, and finally selects a subset of oracle data with strong fault-observing capability. For programs with analyzable test code, we further extend SODS via pruning the probabilistic substitution graph based on 0-1-CFA call graph analysis. The experimental study on 11 subject systems written in C or Java demonstrates that our static approach is more effective and much more efficient than state-of-the-art dynamic approaches in most cases.
Biodegradation of PAHs by Burkholderia sp. VITRSB1 Isolated from Marine Sediments

The polycyclic aromatic hydrocarbons (PAHs) pollution to the environment is a major threat to the living organisms, and hence the degradation of these PAHs is necessary. Studies on PAHs degrading bacteria have focussed on terrestrial microbes and the potential of marine derived microbes is undermined. Herein we report the isolation and characterization of PAHs degrading Burkholderia sp. from lagoon sediments collected at the Southern coast of India. The strain was Gram negative, rod-shaped, motile, and ∼2–5 μm in length. Based on the phylogenetic data the strain was identified as Burkholderia and designated as VITRSB1. Initial PAHs degradation ability of the strain was assessed using basal salt medium supplemented with diesel, kerosene, toluene, aniline, naphthalene, and phenol. The strain was found to be effectively degrading kerosene, diesel, toluene, and aniline even at higher concentration (1%). However, naphthalene and aniline were degraded only at lower concentration (0.1%) and phenol, camphor, and DAP inhibited the growth of the strain. Furthermore, the degraded end products of the PAHs were determined using FTIR. Notably, none of the end products were found to be toxic to the biosphere. Our results indicate that the isolated Burkholderia sp. could be a prospective candidate for the effective degradation of selective PAHs.
Glycogen Synthase Kinase 3 Beta Predicts Survival in Resected Adenocarcinoma of the Pancreas

Purpose: GSK3β is a protein kinase that can suppress a number of key oncoproteins. We have previously shown in preclinical models of pancreatic ductal adenocarcinoma (PDAC) that inhibition of GSK3β causes stabilization and nuclear translocation of β-catenin, poor differentiation, proliferation, and resistance to radiation. The objective of this study was to determine its utility as a biomarker of clinical outcomes. Experimental Design: Automated Quantitative Immunofluorescence Analysis (AQUA) of GSK3β was performed on a tissue microarray with samples from 163 patients treated on RTOG 9704. On the basis of findings in an exploratory cohort, GSK3β was analyzed as a categorical variable using its upper quartile (>Q3) as a cut point. Overall survival (OS) and disease-free survival (DFS) were estimated with the Kaplan–Meier method, and GSK3β groupings were compared using the log-rank test. Univariable and multivariable Cox proportional hazards models were used to determine associations between GSK3β and OS/DFS. Results: The 3-year OS rates for GSK3β≤Q3 versus GSK3β >Q3 were 16% (95% confidence intervals; CI, 10%–23%) and 30% (95% CI, 17%–44%), respectively, P = 0.0082. The 3-year DFS rates were 9% (95% CI, 5%–15%) and 20% (95% CI, 9%–33%) respectively, P value = 0.0081. On multivariable analysis, GSK3β was a significant predictor of OS. Patients with GSK3β >Q3 had a 46% reduced risk of dying of pancreatic cancer (HR, 0.54; 95% CI, 0.31–0.96, P value = 0.034). The HR for DFS was 0.65 (95% CI, 0.39–1.07; P value = 0.092). Conclusions: GSK3β expression is a strong prognosticator in PDAC, independent of other known factors such as tumor (T) stage, nodal status, surgical margins and CA19-9. Clin Cancer Res; 21(24); 5612–8. ©2015 AACR.
Attribute-Based Encryption With Verifiable Outsourced Decryption

Attribute-based encryption (ABE) is a public-key-based one-to-many encryption that allows users to encrypt and decrypt data based on user attributes. A promising application of ABE is flexible access control of encrypted data stored in the cloud, using access polices and ascribed attributes associated with private keys and ciphertexts. One of the main efficiency drawbacks of the existing ABE schemes is that decryption involves expensive pairing operations and the number of such operations grows with the complexity of the access policy. Recently, Green et al. proposed an ABE system with outsourced decryption that largely eliminates the decryption overhead for users. In such a system, a user provides an untrusted server, say a cloud service provider, with a transformation key that allows the cloud to translate any ABE ciphertext satisfied by that user's attributes or access policy into a simple ciphertext, and it only incurs a small computational overhead for the user to recover the plaintext from the transformed ciphertext. Security of an ABE system with outsourced decryption ensures that an adversary (including a malicious cloud) will not be able to learn anything about the encrypted message; however, it does not guarantee the correctness of the transformation done by the cloud. In this paper, we consider a new requirement of ABE with outsourced decryption: verifiability. Informally, verifiability guarantees that a user can efficiently check if the transformation is done correctly. We give the formal model of ABE with verifiable outsourced decryption and propose a concrete scheme. We prove that our new scheme is both secure and verifiable, without relying on random oracles. Finally, we show an implementation of our scheme and result of performance measurements, which indicates a significant reduction on computing resources imposed on users.
Simple Decentralized Cell Association Method for Heterogeneous Networks in Fading Channel

This paper proposes an extension to our previously reported simple decentralized cell association method for heterogeneous networks, where low transmission-power pico or femto base stations (BSs) overlay onto a high transmission-power macro BS, to accommodate the effects from a fading channel and proportional fair (PF)-based scheduling. The focus of this investigation is on the downlink and the purpose of the cell association is to increase the minimum user throughput (worst user throughput). In the proposed method, appropriate cell association for all users within a cell is achieved in an iterative manner based on the feedback information of each individual user regarding the throughput gain by connecting a new BS assisted by a small amount of broadcast information from the respective BSs regarding the allowable resource allocation and multiuser diversity gain. The proposed method does not require cooperation between BSs. The proposed method can be applied to the case with inter-cell interference coordination (ICIC) through the use of protected radio resources exclusively used by the pico/femto BSs. Based on numerical results, we show that the proposed method adaptively achieves better cell association for all users according to the user location distributions compared to the conventional cell range expansion (CRE) method. The advantage of the proposed method over CRE is further enhanced in an ICIC scenario.
GENERALIZED SCHUR COMPLEMENTS OF MATRICES AND COMPOUND MATRICES

In this paper, we obtain some formulas for compound matrices of generalized Schur complements of matrices. Further, we give some Lowner partial orders for compound matrices of Schur complements of positive semidefinite Hermitian matrices, and obtain some estimates for eigenvalues of Schur complements of sums of positive semidefinite Hermitian matrices.
Different Mechanisms for Histone Acetylation by Ethanol and Its Metabolite Acetate in Rat Primary Hepatocytes

Ethanol and its major metabolite acetate both induced histone H3 acetylation in primary culture of rat hepatocytes. The acetylation by ethanol was dependent on the reactive oxygen species and mitogen-activated protein kinase pathway, whereas that by acetate was independent of both pathways. Ethanol increased CYP2E1 protein expression but acetate had negligible effect. The level of phospho-H2AX, an indicator of DNA breaks, was elevated by ethanol but not by acetate. Ethanol and acetate differentially activated mRNA expression for different genes, e.g., IL-6, PPARγ, c-Fos, Egr-1, and PNPLA3 in hepatocytes. The most striking increase (3-fold) was in PNPLA3 mRNA by ethanol with little change by acetate. It was further shown that acetate inhibited histone deacetylase activity. Taken together, these data establish for the first time that ethanol and acetate exhibit differences in their effects on hepatocytes in gene expression, P-H2AX levels, and the mechanism of histone H3 acetylation. The implications of these differences in the actions of ethanol in liver are discussed.
The use of GIS for studying cultural heritage and historical urban landscape: the case of Perm and Usolie (Russia)

espanolPerm y Usolie son ciudades en el territorio de la region de Perm (Rusia), que posee un rico patrimonio cultural. Debido a factores antropogenicos y naturales, la planificacion urbana historica de estas ciudades y su patrimonio cultural se ven amenazados con una perdida. Los sistemas de Informacion Geografica (SIG) son una excelente herramienta para el tratamiento de las fuentes documentales geoespaciales, del siglo XVIII a principios del siglo XX. Se realizaron modelos geoinformaticos con la colaboracion del departamento de Historia Antigua y Medieval Rusa de la Universidad Perm State Humanitarian Pedagogical University y el departamento de Cartografia y Geoinformatica de la Perm State University. Estos modelos contienen informacion de monumentos historicos, arquitectura y planes urbanisticos de acuerdo con el Registro de Patrimonio Cultural de Rusia. El procesado de fuentes cartograficas a traves de SIG ayuda a visualizar los edificios historicos perdidos y a combinar informacion sobre todos los objetos del patrimonio cultural. Proporciona el uso efectivo de datos historicos en la preservacion del patrimonio cultural y la elaboracion de planes urbanisticos. EnglishPerm and Usolie are cities in the territory of Perm region (Russia) which hold a rich cultural heritage. The historic urban planning of these cities is threatened due to anthropogenic and natural factors. Geographic Information Systems (GIS) are an excellent tool for operating archival geospatial sources, dating back to the 18th – beginning 20th centuries. With the cooperation of the Department of Ancient and Medieval History of Russia at Perm State Humanitarian Pedagogical University and the Department of Cartography and Geoinformatics at Perm State University, geospatial models that contain information of monuments of history, architecture and urban planning in according to the national cultural heritage register of Russia were developed. Processing of cartographic sources through GIS allowed visualizing the lost historical buildings and to combine information about all objects of cultural heritage. It provides the management of historical data in the preservation of cultural heritage and development of urban-planning regulations.
Structure of the Archaeal Pab87 Peptidase Reveals a Novel Self-Compartmentalizing Protease Family

Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D 4 symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 Å resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 Å wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 Å wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.
Incorporating Non-Coding Annotations into Rare Variant Analysis

Background The success of collapsing methods which investigate the combined effect of rare variants on complex traits has so far been limited. The manner in which variants within a gene are selected prior to analysis has a crucial impact on this success, which has resulted in analyses conventionally filtering variants according to their consequence. This study investigates whether an alternative approach to filtering, using annotations from recently developed bioinformatics tools, can aid these types of analyses in comparison to conventional approaches. Methods & Results We conducted a candidate gene analysis using the UK10K sequence and lipids data, filtering according to functional annotations using the resource CADD (Combined Annotation-Dependent Depletion) and contrasting results with ‘nonsynonymous’ and ‘loss of function’ consequence analyses. Using CADD allowed the inclusion of potentially deleterious intronic variants, which was not possible when filtering by consequence. Overall, different filtering approaches provided similar evidence of association, although filtering according to CADD identified evidence of association between ANGPTL4 and High Density Lipoproteins (P = 0.02, N = 3,210) which was not observed in the other analyses. We also undertook genome-wide analyses to determine how filtering in this manner compared to conventional approaches for gene regions. Results suggested that filtering by annotations according to CADD, as well as other tools known as FATHMM-MKL and DANN, identified association signals not detected when filtering by variant consequence and vice versa. Conclusion Incorporating variant annotations from non-coding bioinformatics tools should prove to be a valuable asset for rare variant analyses in the future. Filtering by variant consequence is only possible in coding regions of the genome, whereas utilising non-coding bioinformatics annotations provides an opportunity to discover unknown causal variants in non-coding regions as well. This should allow studies to uncover a greater number of causal variants for complex traits and help elucidate their functional role in disease.
Advanced Human-Computer Interaction with the Berlin Brain-Computer Interface

Brain-Computer Interfaces (BCIs) are systems capable of decoding neural activity in real time, thereby allowing a computer application to be directly controlled by the brain. Since the characteristics of such direct brain-to-computer interaction are limited in several aspects, one major challenge in BCI research is intelligent front-end design. Here we present the mental text entry application ‘Hex-o-Spell’ which incorporates principles of Human-Computer Interaction research into BCI feedback design. The system utilises the high visual display bandwidth to help compensate for the extremely limited control bandwidth which operates with only two mental states, where the timing of the state changes encodes most of the information. The display is visually appealing, and control is robust. The effectiveness and robustness of the interface was demonstrated at the CeBIT 2006 (world’s largest IT fair) where two subjects operated the mental text entry system at a speed of up to 7.6 char/min.
W A Device Pair Classification based Channel Slot ReUtilization Optimization for Scalability Enhancement in Wireless Mesh Network

Wireless mesh networks (WMNs) are multihop systems which can develop the scope of remote systems, with the benefits of fast and easy deployment, high transfer speed, simple establishment and upkeep, low front expense. They are potential methods to assemble the cutting edge remote correspondence frameworks. IEEE 802.11 standard is currently the most commonly used radio technique for WMNs. Due to tremendous growth of the wireless based application services are increasing the demand for wireless communication techniques that use bandwidth more effectively. Channel slot re-utilization in multiradio wireless mesh networks is a very challenging problem. WMNs have been adopted as back haul to connect various networks such as Wi-Fi (802.11), WI-MAX (802.16e) etc. to the internet. The slot re-utilization technique proposed so far suffer due to high collision due to improper channel slot usage approximation error. To overcome this here the author propose the cross layer optimization technique by designing a device classification based channel slot re-utilization routing strategy which considers the channel slot and node information from various layers and use some of these parameters to approximate the risk involve in channel slot re-utilization in order to improve the QoS of the network. The simulation and analytical results show the effectiveness of our proposed approach in term of channel slot re-utilization efficiency and thus helps in reducing latency for data transmission and reduce channel slot collision.
Scaling-up Knowledge for a Cognizant Robot

This paper takes a new approach to the old adage that knowledge is the key for artificial intelligence. A cognizant robot is a robot with a deep and immediately accessible understanding of its interaction with the environment—an understanding the robot can use to flexibly adapt to novel situations. Such a robot will need a vast amount of situated, revisable, and expressive knowledge to display flexible intelligent behaviors. Instead of relying on human-provided knowledge, we propose that an arbitrary robot can autonomously acquire pertinent knowledge directly from everyday interaction with the environment. We show how existing ideas in reinforcement learning can enable a robot to maintain and improve its knowledge. The robot performs a continual learning process that scales-up knowledge acquisition to cover a large number of facts, skills and predictions. This knowledge has semantics that are grounded in sensorimotor experience. We see the approach of developing more cognizant robots as a necessary key step towards broadly competent robots.