Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated multi-objective calibration of biological agent-based simulations

Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termed objectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both established a priori and previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate simulations that generate more informative biological predictions.
Realized Jumps on Financial Markets and Predicting Credit Spreads

This paper extends the jump detection method based on bipower variation to identify realized jumps on financial markets and to estimate parametrically the jump intensity, mean, and variance. Finite sample evidence suggests that the jump parameters can be accurately estimated and that the statistical inferences are reliable under the assumption that jumps are rare and large. Applications to equity market, treasury bond, and exchange rate data reveal important differences in jump frequencies and volatilities across asset classes over time. For investment grade bond spread indices, the estimated jump volatility has more forecasting power than interest rate factors and volatility factors including option-implied volatility, with control for systematic risk factors. The jump volatility risk factor seems to capture the low frequency movements in credit spreads and comoves countercyclically with the price-dividend ratio and corporate default rate.
The Development Activities of Innovative and Non-Innovative New Retail Financial Products: Implications for Success

This article reports the results of a research project into the development process of 100 new retail financial products, 42 innovative and 58 noninnovative, which is part of a broader study conducted on the development and launching practices of new financial products in Greece. The study revealed that innovative and non-innovative products follow similar development patterns, but with quite different emphasis placed on the distinctive parts of the NSD process. The analysis has shown that three development stages are significant determinants of non-innovative products' performance, namely (i) market analysis and commercialization, (ii) technical development, with a positive effect and (iii) operational testing with a negative impact on performance. In the case of innovative products, four development stages were found to impact their performance significantly and positively, namely (i) idea generation and screening, (ii) internal marketing and training, (iii) market analysis and commercialization and (iv) technical development.
AUDENS: a tool for automated peptide de novo sequencing.

We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides from MS/MS data. We implemented a dynamic programming algorithm and combined it with a flexible preprocessing module which is designed to distinguish between signal and other peaks. By applying a user-defined set of heuristics, AUDENS screens through the spectrum and assigns high relevance values to putative signal peaks. The algorithm constructs a sequence path through the MS/MS spectrum using the peak relevances to score each suggested sequence path, i.e., the corresponding amino acid sequence. At present, we consider AUDENS a prototype that unfolds its biggest potential if used in parallel with other de novo sequencing tools. AUDENS is available open source and can be downloaded with further documentation at http://www.ti. inf.ethz. ch/pw/software/audens/ .
A Comparison Study on Types of PV for Grid Connected Photovoltaic Power

Grid connected photovoltaic (PV) power systems is today’s breakthrough for renewable energy source in electricity generation Grid-connected photovoltaic (PV) power systems have the advantage of more effective utilization for highest renewable source of electricity generation and tendency to continual growth in the next years. The output performance grid connected photovoltaic (PV) power systems is influenced by the impact of cell temperature or ambient temperature and solar irradiance of the solar module. This paper highlights the effect of output energy of solar module by implementing different types of solar module technology and selecting the highest energy output of the module technology for modelling and simulating the design of grid connected photovoltaic (PV) power system using Matlab/Simulink.
Analyzing the Effect of Channel Mismatch on the SRI Language Recognition Evaluation 2015 System

We present the work done by our group for the 2015 language recognition evaluation (LRE) organized by the National Insti-tute of Standards and Technology (NIST), along with an ex-tended post-evaluation analysis. The focus of this evaluation was the development of language recognition systems for clusters of closely related languages using training data released by NIST. This training data contained a highly imbalanced sample from the languages of interest. The SRI team submitted several systems to LRE’15. Major components included (1) bottleneck features extracted from Deep Neural Networks (DNNs) trained to predict English senones, with multiple DNNs trained using a variety of acoustic features; (2) data-driven Discrete Cosine Transform (DCT) contextualization of features for traditional Universal Background Model (UBM) i-vector extraction and for input to a DNN for bottleneck feature extraction; (3) adaptive Gaussian backend scoring; (4) a newly developed multi-resolution neural network backend; and (5) cluster-speciﬁc N-way fusion of scores. We compare results on our development dataset with those on the evaluation data and ﬁnd signiﬁcantly different conclusions about which techniques were useful for each dataset. This difference was due mostly to a large unex-pected mismatch in acoustic and channel conditions between the two datasets. We provide a post-evaluation analysis reveal-ing that the successful approaches for this evaluation included the use of bottleneck features, and a well-deﬁned development dataset appropriate for mismatched conditions.
Exercise Metabolism in Nonobese Patients with Type 2 Diabetes Following the Acute Restoration of Normoglycaemia

This study investigated how acute restoration of normoglycaemia affected energy metabolism during exercise in nonobese patients with type 2 diabetes. Six subjects (mean ± SEM) aged 56.2 ± 2.7 years, with a BMI of 24.5 ± 1.5 kg/m2 and a VO2 peak of 28.7 ml/kg/min, attended the lab on two randomised occasions for a four-hour resting infusion of insulin or saline, followed by 30 minutes cycling at 50% VO2 peak. During the 4 h resting infusion, there was a greater (P < 0.0001) reduction in blood glucose in insulin treatment (INS) (from 11.2 ± 0.6 to 5.6 ± 0.1 mmol/l) than in saline treatment/control (CON) (from 11.5 ± 0.7 to 8.5 ± 0.6 mmol/l). This was associated with a lower (P < 0.05) resting metabolic rate in INS (3.87 ± 0.17) than in CON (4.39 ± 0.30 kJ/min). During subsequent exercise, blood glucose increased significantly in INS from 5.6 ± 0.1 at 0 min to 6.3 ± 0.3 mmol/l at 30 min (P < 0.01), which was accompanied by a lower blood lactate response (P < 0.05). Oxygen uptake, rates of substrate utilization, heart rate, and ratings of perceived exertion were not different between trials. Insulin-induced normoglycaemia increased blood glucose during subsequent exercise without altering overall substrate utilization.
Impact of Russian Non-Tariff Measures on European Union Agricultural Exports

Nowadays non-tariff measures become more and more widely used. Russia is one of world largest importers of agri-products. In order to protect domestic production different non-tariff measures (NTMs) are used, which create difficulties for the exporters because NTMs are strict, changeable and difficult to deal with. This article analyses Russian non-tariff measures and their influence on the European Union exports of agri-products by using gravity model. The results show that Russian trade resistance is weaker for EU agricultural products exporters than for the USA exporters but stronger than for Chinese agricultural products exporters. The results do not prove that Russiai¯s NTMs have bigger impact on the EU exports than on the other countriesi¯ exports such as India, Kyrgyz Republic, and the Ukraine. The NTM of such countries as China and Mexico also have much greater influence on the EU exports of agri-products than Russian NTMs.
High D‐dimer level is associated with increased 15‐d and 3 months mortality through a more central localization of pulmonary emboli and serious comorbidity

High D‐dimer levels are predictors of death in patients with pulmonary embolism (PE), as are more proximally located, larger emboli. The direct link between these three has not yet been described. A cohort of 674 consecutive patients with confirmed PE was studied. Patients were followed up for 3 months. D‐dimer levels were measured only in patients with an unlikely clinical probability (n = 262). The odds ratio (OR) for death of all variables was calculated. Multivariate analysis was performed to identify independent risk factors for mortality. The best predictive D‐dimer cut‐off point for mortality was a concentration >3000 ng/ml FEU (OR 7·29). High D‐dimer levels were correlated with active malignancy and age over 65 years, both being indicators of 3‐month mortality. High D‐dimer levels were also correlated with centrally located pulmonary emboli and 15‐d mortality. The combination of high D‐dimer levels and central emboli increased early mortality risk by 2·2. High D‐dimer levels in patients with an unlikely clinical probability were associated with fatal outcome after PE. Centrally located pulmonary emboli were associated with higher D‐dimer levels and worse 15‐d mortality. Active malignancy, being an inpatient at time of diagnosis and age over 65 years were associated with higher D‐dimer levels and worse 3‐month survival.
Pathogenicity and Antigenicity of Clones from Strains of Marek's Disease Virus and the Herpesvirus of Turkeys

Virus was extracted by filtration from chicken embryo fibroblast cultures infected with the JM, high passage JM(JMHP), GA, and RPL39 strains of Marek's disease virus (MDV) and from the herpesvirus of turkeys (HVT) and purified by cloning. The plaques produced by clones of HVT, JMHP, and other MDV strains differed in morphology from one another. Clones of MDV varied greatly in pathogenicity for chickens, but JMHP and HVT were nonpathogenic. Two pathogenic clones of JM virus and a clone of JMHP virus lacked the A precipitin antigen present in all other clones tested. All clones had at least one B antigen in common. HVT and MDV clones with and without the A precipitin antigen could be distinguished from each other by the indirect fluorescent antibody test. Changes in virus-host cell relationships, loss of pathogenicity, and loss of the A antigens were independent events.
Dietary restriction and 2‐deoxyglucose administration improve behavioral outcome and reduce degeneration of dopaminergic neurons in models of Parkinson's disease

Parkinson's disease (PD) is an age‐related disorder characterized by progressive degeneration of dopaminergic neurons in the substantia nigra (SN) and corresponding motor deficits. Oxidative stress and mitochondrial dysfunction are implicated in the neurodegenerative process in PD. Although dietary restriction (DR) extends lifespan and reduces levels of cellular oxidative stress in several different organ systems, the impact of DR on age‐related neurodegenerative disorders is unknown. We report that DR in adult mice results in resistance of dopaminergic neurons in the SN to the toxicity of 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP). MPTP‐induced loss of dopaminergic neurons and deficits in motor function were ameliorated in DR rats. To mimic the beneficial effect of DR on dopaminergic neurons, we administered 2‐deoxy‐D‐glucose (2‐DG; a nonmetabolizable analogue of glucose) to mice fed ad libitum. Mice receiving 2‐DG exhibited reduced damage to dopaminergic neurons in the SN and improved behavioral outcome following MPTP treatment. The 2‐DG treatment suppressed oxidative stress, preserved mitochondrial function, and attenuated cell death in cultured dopaminergic cells exposed to the complex I inhibitor rotenone or Fe2+. 2‐DG and DR induced expression of the stress proteins heat‐shock protein 70 and glucose‐regulated protein 78 in dopaminergic cells, suggesting involvement of these cytoprotective proteins in the neuroprotective actions of 2‐DG and DR. The striking beneficial effects of DR and 2‐DG in models of PD, when considered in light of recent epidemiological data, suggest that DR may prove beneficial in reducing the incidence of PD in humans. J. Neurosci. Res. 57:195–206, 1999. © 1999 Wiley‐Liss, Inc.
Contribution of photovoltaic power generation systems to AC short circuits — A survey of current modeling practices and challenges

As an important part of evaluating the transmission and distribution system impacts of interconnecting new generation sources, network operators must assess the impact of these sources on fault interrupting capabilities of automatic switching devices and protective relay coordination for balanced and unbalanced faults on the network. A growing component of these new generation sources is solar photovoltaic-based systems. Modeling of these sources for short circuit studies is complicated by the non-linear control characteristics of their associated inverters. These characteristics preclude the use of linear circuit analysis techniques based on Thévenin equivalents that are the prevalent methodologies relied upon in most commercial short circuit analysis tools. This paper contrasts the physical characteristics of well-understood synchronous generator technology with that of modern-day PV inverter technology. Limitations of commercial short circuit analysis tools for addressing solar PV generation systems, and recommendations for development of industry consensus standard analysis methods, are presented.
Performance of very low dark current SWIR PIN arrays

Boeing Spectrolab has grown, fabricated and tested InGaAs PIN arrays with less than 1 nA/cm2 dark current density at 280 °K. The PIN diodes display greater than 1 A/W responsivity at -100 mV reverse bias with about 50 fF of diode capacitance.
Contract complexity and contract administration costs in small supplier alliances in the Norwegian offshore market

This research focuses on the problem of perceived contract administration costs among small service suppliers in the Norwegian offshore market. Based on transaction cost economics (TCE), resource-dependence theory (RDT) and supply chain management literature, the authors analyse the association between several contract administration issues and perceived contract administration costs, and in particular in service supplier alliances. A mail survey among 109 Norwegian service suppliers makes the research design of this study, and the empirical findings demonstrate that when the contract complexity becomes substantial, the small contractors face substantial contract administration costs. This problem enlarges significantly for small service contractors with preference for participation in supplier alliances with other service suppliers, and sub suppliers. The reason is that such cooperative arrangements have to deal with a broader set of contracting partners, contract issues in the regulation and enforcement of contractual terms related to division of work, payment clauses, service performance and project fulfilment.
Partial Excision of blaKPC from Tn4401 in Carbapenem-Resistant Klebsiella pneumoniae

ABSTRACT We describe a novel Tn4401 variant (Tn4401d) in epidemic Klebsiella pneumoniae clone ST258, from which a partial blaKPC fragment has been excised along with ISKpn7 and a partial tnpA fragment. Nested-PCR experiments confirmed that this region can be removed from distinct Tn4401 isoforms in both K. pneumoniae and Escherichia coli. This study highlights that the region surrounding blaKPC is undergoing recombination and that Tn4401 itself is heterogeneous and highly plastic.
Is Slacktivism Underrated? Measuring the Value of Slacktivists for Online Social Movements

We measure the value of “slacktivists” involved in more than 80 protest movement hashtags on Twitter, focusing on their value for content generation, communication, encouragement, and content diversity. Further, we move beyond the existing literature which primarily focuses on direct content contributions by investigating whether slacktivists induce further contributions from other activists by providing them simple cues of encouragement that enhance non-slacktivists’ commitment to a movement. Our findings suggest that slacktivist actions, unlike those by dedicated activists, do not encourage others, and if anything, discourage them.
Measuring Performance Through Capital Structure: Evidence from Banking Sector of Pakistan

Capital structure of the financial institutions and banks determine agency cost of financial sector of the economy. In this study we explore the agency cost hypothesis of banking sector of Pakistan using panel data of 22 banks for the period 2002 to 2009. We employed the idea of using profit as a measure of efficiency of banks following Berger (2002) and the idea of using Tobin’s Q as a measure of firm’s performance following Morck, Shleifer, and Vishny (1988); Treece et al. (1994). Our study differs from the others in terms of methodology of panel data models which provide a better substitute for SUR and simultaneous equations employed by the other studies. Pooled data results prove agency cost hypothesis and the findings are in accordance with those of Pratomo and Ismail (2007) Berger and Di Patti (2002). Size of banks and consumer banking seem to have played significant role in their profit efficiency during the period from 2002 to 2009. Random effects and fixed effects models nevertheless, proved Miller-Modigliani (1958) proposition that capital structure does not affect value of the banks.
Web Technology in Recreational sports

Without question, the Internet continues to influence the way business is provided in our society. The development of the Internet and the World Wide Web will also play a pivotal and exciting role in how one delivers collegiate recreational sports programs. A review of the related literature reveals that there have been no studies in this decade investigating the status of the Web in collegiate recreational sports. The purpose of this study was to examine the current status of the use of the Web in collegiate recreational sports. A survey was administered to 200 recreational sport administrators soliciting their opinions on the current and future use of the Web. Of the 200 administrators, 138 (69%) responded. The findings of the study indicated that Web technology is definitely emerging as one of the most powerful tools at the recreational sports practitioners' command. Implications of the results are discussed along with recommendations for future study.
Simplified colorimetric determination of thiocyanate in biological fluids, and its application to investigation of the toxic amblyopias.

A colorimetric procedure for determination of small amounts of cyanide and thiocyanate, involving the synthesis of a pyridine dyestuff by the reaction of pyridine and an aromatic amine, has been simplified for the estimation of thiocyanate alone in biological fluids. Replacement of benzidine with p -phenylenediamine in the colorimetric reaction has both improved the precision of the analytical procedure and avoided a carcinogenic hazard. This method has been used to follow the decrease in plasma thiocyanate associated with abstinence from cigarette smoking, and its subsequent increase upon resumption. It has also been used to measure the plasma and urinary thiocyanate concentrations of patients suffering from the particular toxic amblyopias—tobacco amblyopia and Leber’s hereditary optic atrophy— believed to be associated with cyanide toxicity, and to follow the increased thiocyanate concentrations that accompany significant improvements in the patients’ vision brought about by various treatments.
Investment Strategies, Performance, And Trading Information Impact

This paper examines a set of investment strategies based on past market information to evaluate performance and trading impact on the Canadian Market 1 . In doing so, we assess whether trading information adds value to the effectiveness of these strategies. Utilizing variant models of four different methodologies, we find strong evidence that supported the Momentum Investment Strategy, which buys past winner stocks and sells past loser stocks. Our evidence did not support Contrarian Investment Strategy, which posits that investors overreact to good and bad news. Our winners’ portfolios outperform our losers’ portfolios. The Negative Volume Effect Strategy did not work, which is contrary to the Foerster, Prihar and Schmitz (1995) study. We found that winners’ stocks did not reverse in cases of heavy volume; nor did loser stocks reverse in a high volume context. However, we did find that trading information has an impact on stock returns and thus adds value to investment strategies for the 1990 to 2000 investment period. Investors who combine past price and trading volume information in constructing their investment strategies would achieve higher returns than investors who base their portfolio construction decisions solely on stock prices.
Sensor fusion for vehicle tracking with camera and radar sensor

In recent years, as demands for the vehicle safety and autonomous driving of the automobile industry have increased, it becomes important to more accurately recognize the position and velocity of surrounding vehicles. In this paper, heuristic fusion with adaptive gating and track to track fusion are applied to track fusion of camera and radar sensor for forward vehicle tracking system and the two algorithms are compared. To compare the two algorithms, simulation was carried out in 10 scenarios and the accuracy of sensor fusion results was measured with optimal subpattern assignment (OSPA) metric. The results of this metric are compared to show that the track to track fusion is superior to the adaptive gating for the target estimation.