Miracle-dz/UniFAR-FTUs huggingface dataset:
Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen

Popcoen is a method for configurational entropy estimation of proteins based on machine-learning. Entropy is predicted with an artificial neural network which was trained on simulation trajectories of a large set of representative proteins. Popcoen is extremely fast compared to other approaches based on the sampling of a multitude of microstates. Consequently, Popcoen can be incorporated into a large class of protein software which currently neglects configurational entropy for performance reasons. Here, we apply Popcoen to various conformations of the Cas4 protein SSO0001 of Sulfolobus solfataricus, a protein that assembles to a decamer of known toroidal shape. We provide numerical evidence that the native state (NAT) of a SSO0001 monomer has a similar structure to the protomers of the oligomer, where NAT of the monomer is stabilized mainly entropically. Due to its large amount of configurational entropy, NAT has lower free energy than alternative conformations of very low enthalpy and solvation free-energy. Hence, SSO0001 serves as an example case where neglecting configurational entropy leads to incorrect conclusion. Our results imply that no refolding of the subunits is required during oligomerization which suggests that configurational entropy is employed by nature to largely enhance the rate of assembly.
Exploring the Nanotechnology-Based Drug Delivery Systems for AIDS Treatment

The Acquired Immunodeficiency Syndrome (AIDS) and Human Immunodeficiency Virus (HIV) infection are a worldwide public health challenge. The emergence of antiretroviral therapy agents has significantly increased the life expectancy and the patient s quality of life. In the 1990’s, there was a great improvement in the knowledge of the disease, enlargement of therapeutic resources, a rise in life expectancy and the epidemiologic profile. Since the mid-1990’s, the advancement of pharmacology studies and the arrival of protease inhibitor antiretroviral have given rise to a new era of anti-HIV agents, known as Highly Active Antiretroviral Therapy (HAART) (Geocze et al., 2010, Richman et al., 2009). The HAART’s adhesion improved the clinical results, the control of the advancement of the disease and decreased the mortality rate, which resulted in an improvement of the patient’s life quality. Despite the successful administration of HAART, latently infected cells can escape the viral immune response and persist for long periods of time (Alexaki et al., 2008). In addition, the HAART presents several collateral effects, such as fatigue, nausea, sickness, diarrhea and lipodystrophy. These symptoms contribute to a lack of treatment adhesion in the patient, resulting in a rise in the blood viral load and a decline in CD4+ T cells count, as well as an increased tolerance of anti-HIV drugs, treatment failure, increased opportunistic infections and in wasted investments (Geocze et al., 2010). Moreover, many antiretroviral drugs undergo extensive pre-systemic metabolism and instability in the gastrointestinal environment, resulting in inadequate and erratic oral absorption as well as low bioavailability. The half-life for most anti-HIV drugs is short, and thus, it requires frequent dosage administrations, leading to a decrease in patient compliance. Also, some antiretroviral classes present poor solubility, low absorption and limited bioavailability. Another limitation of the current HAART is the inefficiency of the regimens to eradicate HIV from various anatomical reservoirs (e.g., central nervous system (CNS) and gastrointestinal tract) and intracellular sites (e.g., macrophages, hepatocytes, dendritic cells and Langerhans cells) (Ojewole et al., 2008, Saksena & Haddad, 2003). Large concentrations are essential for eliminating HIV from these reservoirs to achieve the desired therapeutic effect, but these large doses contribute to severe side effects associated with anti-HIV therapy (Ojewole et al., 2008). Because drug development in the HIV field has slowed
Seismic Illumination Analysis with One-Way Wave Propagators Coupled with Reflection/Transmission Coefficients in 3D Complex Media

Seismic illumination analysis can help us to better understand how various seismic acquisition parameters and configuration affect seismic image qualities. It allows us to design effective seismic survey systems to provide reliable high-resolution seismic images for complex structures in both theoretical and exploration seismology. It is also a useful tool for estimation of the potential detecting power of a specific acquisition system for a given velocity structure of the medium. Most existing techniques for calculating illumination intensity distributions can be divided into two categories: one is based on ray tracing methods (Berkhout, 1997; Schneider, 1999; Bear et al., 2000; Muerdter et al., 2001a, 2001b, 20001c); and the other based on wave equation methods (Wu & Chen, 2002; Xie et al., 2006; Wu & Chen, 2006; Sun et al., 2007). The ray tracing is quite efficient and inexpensive. However, it bears large errors in complex areas because of the multi-path problem, the high frequency approximation and the singularity problem of the ray theory (Hoffmann, 2001). These factors limit its accuracy severely in complex areas. The wave-equation-based methods can provide reliable and accurate illumination intensity distributions in complex media. Full-wave finite-difference (FD) method is commonly employed for seismic forward modelling, i.e., wave propagation simulation for a known interval velocity model. But it is too expensive for illumination analysis in industrial application, especially for 3D case. Recently, One-way wave propagators have been widely used to seismic modelling and migration for its huge memory-saving and high computational efficiency. Localized illumination methods based on the Gabor-Daubechies frame decomposition or the local slant stack have been presented, which can give local information both in space and direction (e.g., Xie and Wu, 2002; Wu et al., 2000; Xie et al., 2003; Wu & Chen, 2006; Mao & Wu, 2007; Cao & Wu, 2008). However, its computational burden is still unacceptable due to the wavefield decomposition in every spatial point.
Bond Pricing under Knightian Uncertainty. A Short Rate Model with Drift and Volatility Uncertainty

It is shown how to construct an arbitrage-free short rate model under uncertainty about the drift and the volatility. The uncertainty is represented by a set of priors, which naturally leads to a G-Brownian motion. Within this framework, it is shown how to characterize the whole term structure without admitting arbitrage. The pricing of zero-coupon bonds in such a setting differs substantially from the traditional models, since the prices need to be chosen in a different way in order to exclude arbitrage.
UvA-DARE ( Digital Academic Repository ) Renegotiation or Bankruptcy ? The Effects of Out-of-Court Costs on Distress Resolution

A recent change to the U.S. tax code (IRS Regulation TD9599) lowered the costs certain creditors incur when restructuring debt out of court. We use this setting to show how CDS spreads gauge the cost wedge between inversus out-of-court distress resolution. CDS spreads declined by record figures on the regulation’s announcement, with declines concentrated among distressed firms with higher ratios of syndicated loans — the credit category treated by TD9599. Critically, distressed firm’s loan renegotiation rates more than doubled, reducing their exposure to financial distress costs, which we estimate are up to 36% of firm value. Those firms’ access to syndicated loans increased while associated interest markups declined.
Liquid Biopsy in Colorectal Cancer-Current Status and Potential Clinical Applications

Colorectal cancer is one of the most frequent solid malignancies worldwide. The treatment is either surgical or multimodal and depends on the stage of the disease at diagnosis. Accurate disease assessment is thus of great importance for choosing the most optimal treatment strategy. However, the standard means of disease assessment by radiological imaging or histopathological analysis of the removed tumor tissue lack the sensitivity in detecting the early systemic spread of the disease. To overcome this deficiency, the concept of liquid biopsy from the peripheral blood of patients has emerged as a new, very promising diagnostic tool. In this article, we provide an overview of the current status of clinical research on liquid biopsy in colorectal cancer. We also highlight the clinical situations in which the concept might be of the greatest benefit for the management of colorectal cancer patients in the future.
HDTcrypt: Compression and encryption of RDF datasets

The publication and interchange of RDF datasets online has experienced significant growth in recent years, promoted by different but complementary efforts, such as Linked Open Data, the Web of Things and RDF stream processing systems. However, the current Linked Data infrastructure does not cater for the storage and exchange of sensitive or private data. On the one hand, data publishers need means to limit access to confidential data (e.g. health, financial, personal, or other sensitive data). On the other hand, the infrastructure needs to compress RDF graphs in a manner that minimises the amount of data that is both stored and transferred over the wire. In this paper, we demonstrate how HDT - a compressed serialization format for RDF - can be extended to cater for supporting encryption. We propose a number of different graph partitioning strategies and discuss the benefits and tradeoffs of each approach.
Stock assessment of the Australian east coast sea mullet (Mugil cephalus) fishery 2018

The sea mullet (Mugil cephalus) is found in tropical and subtropical waters around the world. On the east coast of Australia, sea mullet are harvested from a single continous stock which occurs from Baffle Creek in Queensland to Eden in New South Wales. Sea mullet undertake annual migrations along ocean beaches to spawn that make them susceptible to overfishing. This stock assessment covers the Australian east coast and incorporates Queensland and NSW catch data up to 2016. The vast majority of the harvest is taken in the commercial fishery, with the catch in NSW exceeding the Queensland catch (approximately 65% and 35% of the catch respectively). The current assessment combined data in an annual age-structured population model tailored for the biology, management and fishing history of sea mullet and estimates the sea mullet biomass in 2016 is around 50 per cent of unfished exploitable biomass (all sectors and jurisdictions). Biological information for sea mullet has revealed a cyclic pattern of new fish recruitment over years. This has produced a cyclic fluctuation in the exploitable biomass results with a midpoint at around 50% of virgin levels which is trending downward. The final year of the model occurs during a downward phase in a long term cycle of biomass peaks and troughs and fishing could exacerbate this downward biomass trend. The assessment noted that the Bundaberg to Noosa stock range was experiencing below average harvests. Further assessment of the extent of regional decline will increase our understanding of the relationshop between historical levels of fishing and environmental change. The assessment provides estimates of the maximum sustainable yield (MSY) and recommends a total allowable catch to rebuild the stock to the Sustainable Fisheries Strategy (SFS) longer term target of 60% unfished biomass (as a proxy for MEY) by 2027.
Resveratrol ameliorated gestational diabetes through regulation of AMPKmediated NF-kB signaling pathway

Gestational diabetes mellitus is one kind of complications of pregnancy, which influence the health of maternal-child in clinical. Evidences have showed that Resveratrol presents benefits for the treatment of gestational diabetes. However, potential mechanisms of Resveratrol-mediated improvements of glucose and lipid metabolism have not been well understood so far. In this study, we investigated the therapeutic effects and potential mechanism of Resveratrol-mediated treatments for gestational diabetes. We investigated the inflammation, oxidative stress, apoptosis and adenosine monophosphateactivated protein kinase (AMPK) in embryos in embryonic day 16 in a mice model of gestational diabetes induced by streptozotocin. Glucose, insulin resistance and glucose and lipid metabolism were also analyzed in mice model of gestational diabetes after treatment with Resveratrol. Our results showed that Resveratrol treatment significantly decreased inflammatory factors expression, such as IL-1β, IL-6, CRP and TNF-α. Resveratrol (8.0 mg/kg) administration decreased expression levels of SOD, ROS, CAT and GSH in oxidative stress. Apoptosis of pancreatic cells in rats was inhibited by Resveratrol treatment through decreasing pro-apoptosis protein expression and increasing anti-apoptosis protein expression. Results also demonstrated that Resveratrol administration down-regulated AMPK expression and activity, which further inhibited expression levels of p65, Ikkβ and IkBα in embryonic cells. Mechanism analyses demonstrated that Resveratrol inhibited inflammatory pathway of embryonic cells through AMPK-mediated NF-κB signaling pathway. In vivo assays showed that metabolism of glucose and lipid were improved and tolerance of glucose and insulin were meliorated in mice model of gestational diabetes mellitus. In conclusion, these results indicate that resveratrol treatment decreased inflammation, prevented apoptosis, decreased embryonic oxidative stress, improved metabolism of glucose and lipid, and meliorated glucose and insulin levels of gestational diabetes mellitus mice, which suggest Resveratrol may be promising agent for the treatment of diabetic pregnancy.
Unique lasing mechanism of localized dispersive nanostructures in InAs / InGaAlAs quantum dash broad interband laser

The authors report on the nanowires-like and nanodots-like lasing behaviors in addition to multiple-wavelength interband transitions from InAs/InAlGaAs quantum dash (Qdash) lasers in the range of ~1550 nm. The presence of lasing actions simultaneously from two different dash ensembles, after postgrowth intermixing for crystalline quality improvement, indicate the absence of optical phonon emission due to the small variation in quantized interband transition energies. This effect is reproducible and shows different lasing characteristics from its quantum dot and quantum wire laser counterparts. Furthermore, the small energy spacing of only 25 nm (at center lasing wavelength of ~1550 nm) and the subsequent quenching of higher energy transition states at higher bias level in Qdash lasers suggest the absence of excited-state transition in highly inhomogeneous self-assembled Qdash structures. However, the appearance of a second lasing line in a certain range of high injection level, which is due to the presence of different sizes of dash assembles, corresponds to the transition from smaller size of Qdash ensembles in different planar active medium. This unique transition mechanism will affect the carrier dynamics, relaxation process in particular and further indicates localized finite carrier lifetime in all sizes of Qdash ensembles. These phenomena will lead to important consequences for the ground-state lasing efficiency and frequency modulation response of Qdash devices. In addition, these imply that proper manipulation of the Qdash ensembles will potentially result in localized nanolasers from individual ensemble and thus contributing towards enormously large envelope lasing coverage from semiconductor devices.
Analysis of El Niño Southern Oscillation using Koopman Operator Framework using Reproducing Kernel Hilbert Space

The climate system consists of coupled interactions among different components of the Earth’s atmospheres and other layers. The asymmetry and quasiperiodicity of the El Niño Southern Oscillation (ENSO), in particularly, hinder the ability to forecast future climate trends. There is a need to understand the predictable signal of this ocean-atmosphere exchange. This study aims to investigate the dominant frequencies and reduce the unpredictable noise using a newly introduced data-driven method called the Koopman Operator. This approach can extract favorable predictability properties from the time-ordered data without any prior knowledge of the underlying dynamical evolution equations. The results are then compared with other classical methods. We hope to obtain critical information that permits longer lead ENSO forecasts.
A localized real-time MAC-Routing protocol for wireless sensor networks

Last years, research on Wireless Sensor Networks (WSNs) mainly focused on self-organization and energy issues. This is due to the intrinsic characteristics of sensors: they run on batteries and they are often inaccessible once deployed. Nevertheless some applications require more than those features. Reliability and the respect of time constraints are characteristics that are required by critical applications on which depend costly equipments or even human life. In this paper we present the problem of real-time communications in WSNs. We show that existing solutions either are not capable to respect time bounds or are not suited to WSNs particularities. We propose a localized MAC and routing real-time protocol that addresses both issues.
Regulierung und Beschäftigung: Eine empirische Wirkungsanalyse für 22 OECD-Länder

Gesetze, Vorschriften und burokratische Hindernisse bremsen die wirtschaftliche Entwicklung in vielen OECD-Staaten. Auf Basis eines vom Institut der deutschen Wirtschaft Koln entwickelten internationalen Regulierungsindexes konnen die Auswirkungen von Regulierungen empirisch nachgewiesen werden. Aufgrund der nach einzelnen Markten und Politikfeldern differenzierten Datenerfassung beim IWRegulierungsindex konnen auch die Folgen der Arbeitsmarktregulierung gesondert ermittelt werden. Eine Wirkungsanalyse zeigt den negativen Einfluss der gesamtwirtschaftlichen Regulierungsintensitat auf die Erwerbstatigenquote und den der Arbeitsmarktregulierung auf die Langzeitarbeitslosigkeit. Wurde man die Regulierungsdichte in Deutschland auf das Niveau der skandinavischen oder angelsachsischen Lander zuruckfuhren, dann konnte das Beschaftigungsniveau mittelfristig um 2,4 bis 4,9 Millionen Personen hoher liegen. Die Anzahl der Langzeitarbeitslosen konnte um bis zu einer Million Personen gesenkt und damit fast halbiert werden.
VIG: Data scaling for OBDA benchmarks

In this paper we describe VIG, a data scaler for Ontology-Based Data Access (OBDA) benchmarks. Data scaling is a relatively recent approach, proposed in the database community, that allows for quickly scaling an input data instance to s times its size, while preserving certain application-specific characteristics. The advantages of the scaling approach are that the same generator is general, in the sense that it can be re-used on different database schemas, and that users are not required to manually input the data characteristics. In the VIG system, we lift the scaling approach from the pure database level to the OBDA level, where the domain information of ontologies and mappings has to be taken into account as well. VIG is efficient and notably each tuple is generated in constant time. To evaluate VIG, we have carried out an extensive set of experiments with three datasets (BSBM, DBLP, and NPD), using two OBDA systems (Ontop and D2RQ), backed by two relational database engines (MySQL and PostgreSQL), and compared with real-world data, ad-hoc data generators, and random data generators. The encouraging results show that the data scaling performed by VIG is efficient and that the scaled data are suitable for benchmarking OBDA systems.
Curve Path Detection in Autonomous Vehicle using Deep Learning

: In the field of autonomous vehicles, lane detection and control play an important role. In autonomous driving the vehicle has to follow the path to avoid the collision. A deep learning technique is used to detect the curved path in autonomous vehicles. In this paper a customized lane detection algorithm was implemented to detect the curvature of the lane. A ground truth labelling tool box for deep learning is used to detect the curved path in autonomous vehicle. By mapping point to point in each frame 80-90% computing efficiency and accuracy is achieved in detecting path.
Inspection of a LOCA Test Rod at the Halden Reactor Project using Gamma Emission Tomography

The LOCA test series IFA-650 conducted at the OECD Halden Reactor Project (HRP) has provided unique data on the performance of fuel rods during LOCA transients. One focus of the current investigations is the performance of the fuel in the ballooning stage of the LOCA transient. In this stage, relocation of fuel material is a possibility, in which case pellet fragments fall down to fill the void introduced by the increased volume of the ballooned cladding. This increases the heat load in that region, further promoting corrosion of the cladding. A special concern in the case of high-burnup fuels is the increasing number of small fuel fragments, which may be expected to cause a higher packing fraction in the ballooned region. In this work, a novel technique is presented for assessing the average density of the fuel material in the ballooned region of LOCA test rods. The investigation is based on non-destructive gamma emission tomography measurements, using the dedicated instrument recently developed at the HRP in collaboration with Westinghouse (Sweden) and Uppsala University. In this approach, the gamma radiation field surrounding the test rod has been measured with a narrowly collimated HPGe detector. Tomographic reconstruction of the data was performed, providing the radial gamma-ray source distribution within the measured volume, which reveals the fuel fragment distribution. From this, the density of the fuel in the measured volume (i.e., the packing fraction) may be calculated. The technique has been used to investigate a LOCA test rod of the Halden Reactor Project LOCA series. The LOCA experiment was carried out about one month prior to the gamma tomography examination. The results show that the distribution of the relocated fuel can be imaged using gamma rays from fission products. The reconstructions of the 662 keV rays from 137Cs and 1596 keV from 140Ba/La are demonstrated. In addition, the peaks of activation products offer valuable information on the location of the test rig structures, which may be utilized in a quantitative tomographic reconstruction to assess the spatially resolved packing fraction.