Miracle-dz/UniFAR-FTUs huggingface dataset:
Cadmium-Induced Autophagy and Autophagic Contribution to Cell Death in Cadmium-Treated Mesangial Cells

Cadmium (Cd) is a nephrotoxic metal that has a number of consequences for renal function. Cells exposed to Cd may have methods to counteract toxic effects with processes like autophagy. Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome. This study investigated the mechanism of Cd-induced autophagy, and the relationship between autophagy and cell survival. At 10 μM exposure for 24 hours, Cd-induced autophagy was found to be reactive oxygen species-independent, and suppressed with thapsigargin treatment, suggesting the necessity of intracellular Ca. Inhibition of the Jun-N-Terminal Kinase resulted in the greatest suppression of Cd-induced autophagy. Autophagy was found to be protective against cell death elicited by the toxic metal, and the absence of autophagy resulted in increased apoptosis in mouse embryonic fibroblast cells. This study adds insight to the mechanism and protective effects of Cd-induced autophagy, and provides the groundwork for
Quantitative translational modeling to facilitate preclinical to clinical efficacy & toxicity translation in oncology

Significant scientific advances in biomedical research have expanded our knowledge of the molecular basis of carcinogenesis, mechanisms of cancer growth, and the importance of the cancer immunity cycle. However, despite scientific advances in the understanding of cancer biology, the success rate of oncology drug development remains the lowest among all therapeutic areas. In this review, some of the key translational drug development objectives in oncology will be outlined. The literature evidence of how mathematical modeling could be used to build a unifying framework to answer these questions will be summarized with recommendations on the strategies for building such a mathematical framework to facilitate the prediction of clinical efficacy and toxicity of investigational antineoplastic agents. Together, the literature evidence suggests that a rigorous and unifying preclinical to clinical translational framework based on mathematical models is extremely valuable for making go/no-go decisions in preclinical development, and for planning early clinical studies.
Building a Sentiment Lexicon for Swedish

In this paper we will present our ongoing project to build and evaluate a sentiment lexicon for Swedish. Our main resource is SALDO, a lexical resource of modern Swedish developed at Sprakbanken, University of Gothenburg. Using a semi-supervised approach, we expand a manually chosen set of six core words using parent-child relations based on the semantic network structure of SALDO. At its current stage the lexicon consists of 175 seeds, 633 children, and 1319 grandchildren.
A high potential organophosphorus pesticide- degrading enzyme from a newly characterized, Pseudomonas aeruginosa NL01

in the presence of CoCl2 and CaCl2, each at 2 mM, while addition of ZnCl2, MgCl2, FeCl3, SDS and EDTA, each at 2 mM inhibited the enzyme by 0.93, 0.92, 0.51, 0.06 and 0.00 fold, respectively. The OPH NL07 seems to be suitable as biocatalyst for practical use in bioremediation of organophosphorus pesticides (OPs)-contaminated soils.
Tapering-induced enhancement of light extraction efficiency of nanowire deep ultraviolet LED by theoretical simulations

A nanowire (NW) structure provides an alternative scheme for deep ultraviolet light emitting diodes (DUV-LEDs) that promises high material quality and better light extraction efficiency (LEE). In this report, we investigate the influence of the tapering angle of closely packed AlGaN NWs, which is found to exist naturally in molecular beam epitaxy (MBE) grown NW structures, on the LEE of NW DUV-LEDs. It is observed that, by having a small tapering angle, the vertical extraction is greatly enhanced for both transverse magnetic (TM) and transverse electric (TE) polarizations. Most notably, the vertical extraction of TM emission increased from 4.8% to 24.3%, which makes the LEE reasonably large to achieve high-performance DUV-LEDs. This is because the breaking of symmetry in the vertical direction changes the propagation of the light significantly to allow more coupling into radiation modes. Finally, we introduce errors to the NW positions to show the advantages of the tapered NW structures can be projected to random closely packed NW arrays. The results obtained in this paper can provide guidelines for designing efficient NW DUV-LEDs.
Formulas for Friction Factor in Transitional Regimes

This note concerns variations of the friction factor in the two transitional regimes, one between laminar and turbulent flows and the other between fully smooth and fully rough turbulent flows. An interpolation approach is developed to derive a single explicit formula for computing the friction factor in all flow regimes. The results obtained for pipe flows give a better representation of Nikuradse’s experimental data, in comparison with other implicit formulas available in the literature. Certain modifications are also made for applying the obtained friction formula to open-channel flows.
Workload-Aware Runtime Energy Management for HPC Systems

Energy efficiency has become a crucial factor in high-performance computing, mainly due to its effect on operating costs and failure rates of computing platforms. To improve the energy efficiency of such systems, processors are equipped with low-power techniques such as dynamic voltage and frequency scaling (DVFS) and power capping. These techniques have to be controlled carefully as per the workload; otherwise, it may result in significant performance loss and/or power consumption due to system overheads (e.g. DVFS transition latency). Existing approaches are not effective in adapting to workload variations as they do not consider the combined effect of application compute-/memory-intensity, thread synchronization contention, and non¬uniform memory accesses (NUMAs) owing to the underlying processor architecture. In this work, we propose a workload- aware runtime energy management technique that takes the aforementioned factors into account for efficient V-f control. The proposed technique measures the processor workload using Memory Accesses Per Micro-operation (MAPM), and also considers the thread synchronization contention and latency due to NUMAs to select an appropriate V-f setting. This approach also uses workload prediction for pro-active V-f control to improve the energy consumption and performance loss. The proposed technique has been implemented on the 12-core (24 threads) Intel Xeon E5-2630 and 61-core (244 threads) Xeon Phi many- core platforms, supporting per-core and system-wide DVFS, respectively. When evaluated with different application scenarios, results show an improvement in energy efficiency of up to 81.2% compared to existing approaches.
Capability, Sustainability, and Collective Action: An Examination of a River Water Dispute

In this paper, a framework is developed to consider collective action, sustainability and the capability approach with regard to resolution of water disputes, followed by a brief discussion of how identity can hinder cooperation or the development of universalism. This framework is then examined with a case study of the Cauvery river dispute in India. At the heart of river water disputes are issues related to justice and fairness, which depend to a significant extent on: how citizens perceive their claims over river water (shaped by cultural and historical factors); the extent to which citizens are able to collectivize their claims through location, economic activity and identity, and use their voice to influence the state; the extent to which the state policy and actions reflect the ‘voice’ and collective interests of different groups; and how the various riparian states recognize and deal with each others' claims. The framework discussed here suggests that the capability approach provides us with a much broader framework than collective action or Robert Solow's sustainability as inter‐generational fairness. These are conjectures for further exploration.
Application of nonrigid registration in ablation of liver cancer

Ablation is a kind of successful treatment for cancer. The technique inserts a special needle into a tumor and produces heat from Radiofrequency at the needle tip to ablate the tumor. Open configure MR system can take MR images almost real time and now is applied in liver cancer treatments. During a surgery, surgeons select images in which liver tumors are seen clearly, and use them to guide the surgery. However, in some cases with severe chirrhosis, the tumors can't be visualized in the MR images. In such cases, the combination of preoperative CT images will be greatly helpful, if CT images can be registered to the position of MR images accurately. It is a difficult work since the shape of the liver in the MR image is different from that of CT images due to the influent of the surgery. In this paper, we use Bspline based FFD nonrigid image registration to attack the problem. The method includes four steps. Firstly the MRI inhomogeneity is corrected. Secondly, parametric active contour with the gradient vector flow is used to extract the liver as region of interest (ROI) because the method is robust and can obtain satisfied results. Thirdly, affine registration is use to match CT and MR images roughly. Finally, Bspline based FFD nonrigid registration is applied to obtain accuracy registration. Experiments show the proposed method is robust and accuracy.
A Survey on Quality Perspective and Software Quality Models

This paper presents acomprehensive overview ofQuality, definition of quality by different person and alsothis paper present overview on Software Quality Models, McCall's Quality Model, Boehm's Quality Model, Dromey's Quality Model, FURPS Quality Model, ISO 9126 Quality Modeland a comparison among these models are presented.
One-Dimensional and Two-Dimensional ZnO Nanostructured Materials on a Plastic Substrate and Their Field Emission Properties

One-dimensional ZnO nanopillars of diameter 80−120 nm and two-dimensional nanowalls of thickness 100−300 nm are electrochemically grown at 70 °C on a flexible polyester substrate. The low turn-on electric fields measured at a current density of 1 μA/cm2 for nanopillars (1.2 V/μm) and nanowalls (2.2 V/μm) illustrate their superior field emission properties to most of the reported ZnO nanostructures. The present method of direct electrodeposition of ZnO on plastic without the need of template or catalyst offers a low-cost technique for fabricating field emission devices on flexible substrates for large-area display and other technologies.
birds: evidence from whole-island telemetry Body fat influences departure from stopover sites in migratory

Migration remains one of the great mysteries ofanimal life. Small migratory birds rely on refuel-ling stopovers after crossing ecological barrierssuch as deserts or seas. Previous studies havesuggested that fuel reserves may determine stop-over duration but this hypothesis could not betested because of methodological limitations.Here, we provide evidence that subcutaneous fatstores determine stopover duration by measuringthe permanence of migratory garden warblers(Sylvia borin) on a small Mediterranean islandduring spring migration with telemetry methods.Garden warblers with large amounts of fat storesdeparted the island signiﬁcantly sooner than leanbirds. All except one fat bird left the island on thesame evening after capture, with a mean totalstopover estimate of 8.8 hours. In contrast, themean estimated total stopover duration oflean birds was 41.3 hours. To our knowledge,this is the ﬁrst study that measures the true mini-mum stopover duration of a songbird duringmigration.Keywords: migration; garden warbler; stopover;subcutaneous body fat; telemetry;physiology of migration1. INTRODUCTIONMany species of birds migrate each year and crossdeserts or seas where food is not available. Migrationacross such ecological barriers relies on refuelling atstopover sites. The duration of a stopover is inﬂuencedby environmental factors including availability of foodand weather conditions, and by endogenous pro-grammes (reviewed in Gwinner & Helm 2003;Jenni & Schaub 2003). At the individual level, it hasbeen suggested that subcutaneous fat deposits are themain physiological determinant of stopover duration(e.g. Bairlein 1985; Biebach 1985; Biebach et al.1986; Cherry 1982; Gannes 2002; Moore & Kerlinger1987, but see Kuenzi et al. 1991; Lyons & Haig 1995). This idea has never been tested properly, becauseactual departure from stopover sites in relation to fatstores has never been measured. Previous estimatesfrom capture–recapture studies did not take intoaccount the fact that lean birds are more activeduring the day when they search for food and henceare more likely to be recaptured than fat birds whichfeed less (Lindstro¨m & Alerstam 1992; Salewski S Yong & Moore 1993; Titov1999; Fusani et al. 2009). If this differential mobilityis incorporated into capture–recapture studies andthe entire stopover duration is estimated instead ofminimum stopover, subcutaneous body fat does notappear to inﬂuence the stopover duration (Salewski &Schaub 2007). To overcome the shortcomings of indirect estimatesof stopover duration, we studied the inﬂuence of sub-cutaneous fat stores on stopover duration, at thesame time minimizing variation in environmental par-ameters. In a quasi-experimental approach, wemonitored radio-tagged lean and fat garden warblers(Sylvia borin) on a stopover site during consecutivedays with constant optimal weather conditions.Because fat and lean birds were tagged at the sametime, we were able to control for environmental vari-ables, as any change in the latter would have equallyaffected the two groups.2. MATERIAL AND METHODS
A family of quantum graph vertex couplings interpolating between different symmetries

The paper discusses quantum graphs with a vertex coupling which interpolates between the common one of the δ type and a coupling introduced recently by two of the authors which exhibits a preferred orientation. Describing the interpolation family in terms of circulant matrices, we analyze the spectral and scattering property of such vertices, and investigate the band spectrum of the corresponding square lattice graph.
Use of Discourse Knowledge to Improve Lexicon-based Sentiment Analysis

Sentiment Analysis deals with the computational tre atment of sentiment in texts. Discourse is a linguistic level of analysis where the author represents ideas and links concepts in a rational chain of tho ug ts. One important representation of discourse is the Rhetorical Struc tu e Theory (RST). The objective of this work consists in to use discourse knowledge to improve a lexicon-based sentiment classifier. To achieve this goal it presents a lexiconbased algorithm adapted to weight portions of text under particular RST relations distinctly. Two experiments are reported. The first experiment verifies if the RST improves sentiment classificati on. It also shows the discourse relations which are most important in the process. The second experiment incorporates discourse markers in the al gorithm in order to eliminate the necessity of a RST annotated corpus. It uses the weights learned in the first experiment to perform the sent iment classification.
Dynamic programming algorithm for contrast correction in medical images

Dynamic programming (DP) algorithms are frequently used in speech processing for dynamic time warping of speech signals. In this approach, DP is applied to image processing for contrast correction. Defining one image as reference, the object image is contrast-corrected by DP based on the (cumulative) grayscale value histograms of the images. DP ensures a nonlinear histogram warping, and therefore an optimal nonlinear mapping between grayscale values of the images. If no path restrictions are used, assignments can be ambiguous; i.e., the grayscale value of the object image can be assigned to more than one grayscale value of the reference image. In this case, histogram-based analysis selects the most probable grayscale value. The algorithm works on the condition that image contents of the images to be compared are equal and differences only based on contrast. Unfortunately, medical images of follow-up studies or slices of 3D data volumes differ not only in contrast, but also in image content. The condition can then be met only approximately. For example, neighboring slices of gradient-spoiled T1-weighted 3D- FLASH image data are contrast-corrected with this method. In experiments with simulated 3D MRI images, the DP approach performs best compared to another nonlinear method or to linear mapping.
Probabilistic Tensor Factorization and Model Selection

The well-known formal equivalence between non-negative matrix factorization and multinomial mixture models extends in a fairly straightforward manner to tensors. Among interesting practical implications of this equivalence, this suggests some principled ways to choose the number of factors in the decomposition. We discuss and illustrate two methods to do this in Positive Tensor Factorization.
African Swine Fever in Uganda : Epidemiology and Socio-economic Impact in the Smallholder Setting

In the last decade millions of people have been able to leave poverty, increasing the regional demand for meat and livestock products. In combination with reforms in market and agricultural policy, this has led to an increase in pig production in sub-Saharan Africa, most notably in Uganda. The growing pig sector could be an important contributor to poverty reduction among smallholder pig keepers. However, the growing pig population has been followed by an increase in African swine fever (ASF) incidence. ASF is a contagious, typically very lethal, haemorrhagic, viral disease of domestic pigs. The overall goal of this doctoral project was to develop the understanding of ASF epidemiology in the smallholder setting in Uganda. Four studies were conducted in two districts in northern Uganda among smallholder farmers, other pig production valuechain actors, and a medium-sized farm. The studies included groupand individual interviews as well as biological and environmental sampling and testing for the virus. Data were analysed using semi-qualitative and quantitative methods. The thesis concluded that ASF was endemic in the study area, and that outbreaks could be detected using retrospective and real-time farmer reports. ASF outbreaks were associated with activities of humans, such as trade in pigs and pig products and free-range management systems. ASF outbreaks had long-term negative social and economic impact for pig production value-chain actors on all investigated levels in the value chain. For smallholder farmers, the impact was aggravated with increasing herd size. Trade and consumption of sick and dead pigs were commonly used as coping strategies. Farm-level biosecurity was insufficient for ASF protection and awareness of control methods did not guarantee their implementation. The continuous ASF transmission in the study area was not driven by lack of knowledge, but rather by cultural circumstances, taboos and poverty. Therefore, in order for control methods to be successfully and sustainably implemented, they need to be developed in participation with the communities, adapted to the local context, socially acceptable, flexible, and cost-effective.
Cadmium, Nickel and Vanadium Accumulation by Three Strains of Marine Bacteria

Three marine bacteria, Pseudomonas putida PTCC 1664, Bacillus cereus PTTC 1665 and Pseudomonas pseudoalkaligenes PTCC 1666 isolated from the East Anzali wetland sediments of the Caspian Sea, were resistant to heavy metals of Cadmium (Cd), Nickel (Ni) and Vanadium (V). Pseudomonas pseudoalkaligenes PTCC 1666 was found to be resistant to all 3 metals Ni, Cd, V. Heavy metal uptake was determined in both the biomass and supernatant by the Atomic Absorption Spectrophotometer (AAS). These bacteria showed enhanced absorption and growth in the presence of Cd and Ni at 80-100 mg/l and V at 40 mg/l concentrations. The high uptake of Cd, Ni and V was directly proportional to their respective concentrations, 5-100 mg/l for Cd and Ni and 5 - 40 mg/l for V. The maximum amount of heavy metal uptake occurred during stationary phase when cells were incubated at 30°C for 72h. The results revealed that these bacteria accumulated approximately 40-50% Cd, 5-6% Ni and 10-12% V. Bacterial cells Immobilized in alginate gel showed more efficiency in biosorbing heavy metals than free cells (80%). Scanning Electron Microscopy (SEM) results indicated that the marine bacteria were capable of accumulating several metals, showing that the isolated bacterial strains can be used as potential candidates for bioremediation, with respect to Cd, Ni and V removal from aqueous effluents.
3-2009 Economic Analysis of Simulation Selection Problems

Ranking and selection procedures are standard methods for selecting the best of a finite number of simulated design alternatives based on a desired level of statistical evidence for correct selection. But the link between statistical significance and financial significance is indirect, and there has been little or no research into it. This paper presents a new approach to the simulation selection problem, one that maximizes the expected net present value of decisions made when using stochastic simulation. We provide a framework for answering these managerial questions: When does a proposed system design, whose performance is unknown, merit the time and money needed to develop a simulation to infer its performance? For how long should the simulation analysis continue before a design is approved or rejected? We frame the simulation selection problem as a “stoppable” version of a Bayesian bandit problem that treats the ability to simulate as a real option prior to project implementation. For a single proposed system, we solve a free boundary problem for a heat equation that approximates the solution to a dynamic program that finds optimal simulation project stopping times and that answers the managerial questions. For multiple proposed systems, we extend previous Bayesian selection procedures to account for discounting and simulation-tool development costs.
Intra-cardiac 2D US to 3D CT image registration

Intra-cardiac echocardiography (ICE) is commonly used to guide intra-cardiac procedures, such as the treatment of atrial fibrillation (AF). However, effective surgical navigation based on ICE images is not trivial, due to the low signal-to-noise ratio (SNR) and limited field of view of ultrasound (US) images. The interpretation of ICE can be significantly improved if correctly placed in the context of three-dimensional magnetic resonance (MR) or computed tomography (CT) images by simultaneously presenting the complementary anatomical information from the two modalities. The purpose of this research is to demonstrate the feasibility of multimodality image registration of 2D intra-cardiac US images with 3D computed tomography (CT) images. In our previous work, a two-step registration procedure has been proposed to register US images with MR images and was validated on a patient dataset. In this work, we extend the two-step method to intra-cardiac procedures and provide a detailed assessment of registration accuracy by determining the target registration errors (TRE) on a heart phantom, which had fiducial markers affixed to the surface to facilitate evaluation of registration accuracy. The resultant TRE on the heart phantom was 3.7 mm. This result is considered to be acceptable for guiding a probe in the heart during ablative therapy for atrial fibrillation. To our knowledge, there is no previous report describing multimodality registration of 2D intra-cardiac US to high-resolution 3D CT.