Miracle-dz/UniFAR-FTUs huggingface dataset:
Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)

Background Determination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches. Methodology/Principal Findings Prey-specific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (crèche) stage. These trends followed those observed in the penguins' stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented. Conclusions/Significance The present study is one of the first to examine the full breadth of a predator's diet using DNA-based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds.
Case Studies of SCADA Firewall Configurations and the Implications for Best Practices

Firewall configuration is an important activity for any modern day business. It is particularly a critical task for the supervisory control and data acquisition (SCADA) networks that control power stations, water distribution, factory automation, etc. Lack of automation tools to assist with this critical task has resulted in unoptimised, error prone configurations that expose these networks to cyber attacks. Automation can make designing firewall configurations more reliable and their deployment increasingly cost-effective. Best practices have been proposed by the industry for developing high-level security policy (e.g., ANSI/ISA 62443-1-1). But these best practices lack specification in several key aspects needed to allow a firewall to be automatically configured. For instance, the standards are vague on how firewall management policies should be captured at a high-level using its specifications. In this paper, we uncover these missing pieces and propose extensions. We apply our extended best-practice specification to real-world firewall case studies to achieve multiple objectives: 1) to evaluate the usefulness of the refined best-practice in the automated specification of firewalls and 2) to illustrate that even in simple cases, SCADA networks are often insecure due to their misconfigured firewalls.
Applying a Fuzzy and Neural Approach for Forecasting the Foreign Exchange Rate

Accurately forecasting the foreign exchange rate is important for export-oriented enterprises. For this purpose, a fuzzy and neural approach is applied in this study. In the fuzzy and neural approach, multiple experts construct fuzzy linear regression FLR equations from various viewpoints to forecast the foreign exchange rate. Each FLR equation can be converted into two equivalent nonlinear programming problems to be solved. To aggregate these fuzzy foreign exchange rate forecasts, a two-step aggregation mechanism is applied. At the first step, fuzzy intersection is applied to aggregate the fuzzy forecasts into a polygon-shaped fuzzy number to improve the precision. A back propagation network is then constructed to defuzzify the polygon-shaped fuzzy number and generate a representative/crisp value to enhance accuracy. To evaluate the effectiveness of the fuzzy and neural approach, a practical case of forecasting the foreign exchange rate in Taiwan is used. According to the experimental results, the fuzzy and neural approach improved both the precision and accuracy of the foreign exchange rate forecasting by 79% and 81%, respectively.
Web mining for Web image retrieval

The popularity of digital images is rapidly increasing due to improving digital imaging technologies and convenient availability facilitated by the Internet. However, how to find user-intended images from the Internet is nontrivial. The main reason is that the Web images are usually not annotated using semantic descriptors. In this article, we present an effective approach to and a prototype system for image retrieval from the Internet using Web mining. The system can also serve as a Web image search engine. One of the key ideas in the approach is to extract the text information on the Web pages to semantically describe the images. The text description is then combined with other low-level image features in the image similarity assessment. Another main contribution of this work is that we apply data mining on the log of users' feedback to improve image retrieval performance in three aspects. First, the accuracy of the document space model of image representation obtained from the Web pages is improved by removing clutter and irrelevant text information. Second, to construct the user space model of users' representation of images, which is then combined with the document space model to eliminate mismatch between the page author's expression and the user's understanding and expectation. Third, to discover the relationship between low-level and high-level features, which is extremely useful for assigning the low-level features' weights in similarity assessment.
Constrained Simulations of the Real Universe: The Local Supercluster

We present cosmological simulations that closely mimic the real uiverse within ~100 Mpc of the Local Group. The simulations, called constrained simulations, reproduce the large-scale density field with major nearby structures, including the Local Group, the Coma and Virgo Clusters, the Great Attractor, the Perseus-Pisces Supercluster, and the Local Supercluster, in approximately correct locations. The MARK III survey of peculiar velocities of the observed structures inside an 80 h-1 Mpc sphere is used to constrain the initial conditions. Fourier modes on scales larger than a (Gaussian) resolution of ≈Rg = 5 h-1 Mpc are dominated by the constraints, while small-scale waves are essentially random. The main aim of this paper is the structure of the Local Supercluster region (LSC; ~30 h-1 Mpc around the Virgo Cluster) and the Local Group environment. We find that at the current epoch most of the mass (≈7.5 × 1014 h-1 M☉) of the LSC is located in a filament roughly centered on the Virgo Cluster and extending over ~40 h-1 Mpc. The simulated Local Group (LG) is located in an adjacent smaller filament, which is not a part of the main body of the LSC and has a peculiar velocity of ≈250 km s-1 toward the Virgo Cluster. The peculiar velocity field in the LSC region is complicated and is drastically different from the field assumed in the Virgocentric infall models. We find that the peculiar velocity flow in the vicinity of the LG in the simulation is relatively "cold": the peculiar line-of-sight velocity dispersion within 7 h-1 Mpc of the LG is ≲60 km s-1, comparable to the observed velocity dispersion of nearby galaxies.
Using motion planning to study protein folding pathways

We present a framework for studying protein folding pathways and potential landscapes which is based on techniques recently developed in the robotics motion planning community. In particular, our work uses Probabilistic Roadmap (PRM) motion planning techniques which have proven to be very successful for problems involving high-dimensional configuration spaces. Our results applying PRM techniques to several small proteins (60 residues) are very encouraging. The framework enables one to easily and efficiently compute folding pathways from any denatured starting state to the native fold. This aspect makes our approach ideal for studying global properties of the protein's potential landscape. For example, our results show that folding pathways from different starting denatured states sometimes share some common `gullies', mainly when they are close to the native fold. Such global issues are difficult to simulate and study with other methods. Our focus in this work is to study the protein folding mechanism assuming we know the native fold. Therefore, instead of performing fold prediction, we aim to study issues related to the folding process, such as the formation of secondary and tertiary structure, and the dependence on the initial conformation. Our results indicate that for some proteins, secondary structure clearly forms first while for others the tertiary structure is obtained more directly, and moreover, these situations seem to be differentiated in the distributions of the conformations sampled by our technique. We also find that the formation order is independent of the starting denatured conformation. We validate our results by comparing the secondary structure formation order on our paths to known pulse-labeling experimental results. This indicates the promise of our approach for studying proteins for which experimental results are not available.
Intra-Industry Credit Contagion: Evidence from the Credit Default Swap Market and the Stock Market

Motivated by the observation of clustering and cascading of credit events, new generation credit risk models have increasingly recognized the importance of credit contagion. However, the empirical significance of credit contagion has not been assessed to date. To provide a solid empirical foundation for such models, I study the effects of a firm's credit event on the default risk of its industry counterparts, captured in the Credit Default Swaps (CDS) Market. I find that these effects are heterogeneous conditional on the nature of credit events. Industry credit contagion is strongest when a firm is struck by a credit spread shock. It is partially offset by competition effect in the event of Chapter 11 bankruptcies, and is dominated by competition effect around Chapter 7 filings. This finding is consistent with theories of counterparty risk and updating of beliefs. I further investigate drivers of contagion and competition effects within a unified framework incorporating macroeconomic, industry and firm-specific factors. Particularly I identify new factors that help explain the high default correlation during economic downturns. Furthermore, this paper uncovers evidence of pure contagion beyond macroeconomic and industry common factors. Finally, I find that credit contagion is captured in the CDS market in an earlier, cleaner and stronger way than in the stock market. The results can be used to improve credit risk models, and have rich implications for credit-sensitive portfolio management.
Insight into bubble nucleation at high-pressure drop rate

This paper presents insight in bubble nucleation in polymer foaming with physical blowing agent using a batch foaming technique. In our experiments the bubble nucleation is triggered by a sudden pressure drop that causes the supersaturation in the polymer gas solution. In fact, the pressure drop rate is an important process variable since it plays a role in both bubble nucleation and growth. Herein, we investigated very high pressure drop rates, and confirmed the great importance of the pressure drop rate as foaming process variable. The results show that the number of nucleated bubbles increases of one order of magnitude and the foam density is reduced if the pressure drop rate is increased from 50 to 500 MPa/s. Interestingly, the number of nucleated bubble increases linearly in a bi-logarithmic scale as function of pressure drop rate at all the investigated temperatures. Moreover, in the current paper, it is discussed how talc used as nucleating agent plays a role in cooperation with pressure drop rate on bubble nucleation at different foaming temperatures.
Cesarean section delivery and development of food allergy and atopic dermatitis in early childhood

Delivery by Cesarean section (CS) may predispose to allergic disorders, presumably due to alterations in the establishment of normal gut microbiota in early infancy. In this study, we sought to investigate the association between CS and physician‐diagnosed food allergy and atopic dermatitis during the first 3 years of life, using data from a homogeneous, population‐based, birth cohort.
Improving Security Levels of IEEE802.16e Authentication by Involving Diffie-Hellman PKDS

In this paper, we propose an authentication key management approach, called Diffie-Hellman-PKDS-based authentication method (DiHam for short) to improve current security level of facility authentication between IEEE802.16e’s BS and SS by using a secret door asymmetric one-way function, PKDS. With the Initialization Vector transmitted between SS and BS, messages including those conveying user data and authentication parameters, such as the AKs and TEKs, can then be more safely delivered.
Effects of Nicotinic and Muscarinic Agents on an Identified Motoneurone and its Direct Afferent Inputs in Larval Manduca Sexta

The principal locomotory appendages of larval Manduca sexta , the prolegs, bear at their tips an array of mechanosensory hairs (the planta hairs). Each of the single sensory neurones associated with a planta hair sends an axon into the ganglion of the same segment where the afferent terminals make synaptic contact with interneurones and motoneurones. Electrical stimulation of a single afferent elicits a monosynaptic excitatory postsynaptic potential (EPSP) in PPR, one of the motoneurones controlling the prolegs. We have used this synapse to study the pharmacology of sensory transmission in M. sexta . The following observations were made. 1. The EPSP was reversibly inhibited in a dose-dependent fashion by the cholinergic antagonists d -tubocurarine, atropine and mecamylamine, indicating that the planta hair afferent neurones use acetylcholine (ACh) as a neurotransmitter. α-Bungarotoxin (αBGTX) also suppressed the EPSP but required concentrations above 1×10 −6 mol l −1 . 2. PPR depolarized in response to ionophoretic or bath application of cholinergic agonists, but compared to motoneurones of a non-nicotine-resistant insect such as the cockroach, PPR was relatively insensitive to nicotine. 3. Application of N -methyl nicotinamide (NMN) to the nerve cord to inhibit putative alkaloid pumps in the central nervous system (CNS) only weakly potentiated PPR9s response to nicotine. This suggests that such pumps do not markedly contribute to PPR9s nicotine resistance. 4. PPR9s responses to nicotinic agents showed several pharmacological differences from those reported for other insects, indicating that the nicotinic ACh receptors of M. sexta may be specifically adapted to accommodate a nicotine-rich diet. 5. During the application of muscarinic agonists to isolated abdominal ganglia, the firing rate of motoneurones, as monitored in the ventral nerve, increased dramatically. PPR responded to muscarinic agents even during synaptic blockade, suggesting that muscarinic receptors may be present on PPR itself. The main effect of muscarine on PPR was to lower its spike threshold. 6. Bath-applied muscarinic agents also affected the afferent-evoked EPSP in a manner consistent with the presence of another group of receptors that, when stimulated, act presynaptically to inhibit the release of ACh from the sensory terminals. These apparent pre- and postsynaptic actions of muscarinic agents are the first reported findings of muscarinic physiology in an identified insect neurone and its synaptic inputs.
A Multi-Objective, Linked-Simulation-Optimization of Henry's Saltwater Intrusion Problem using HST3D and Box's Method

A multi-objective linked simulation and optimization (LSO) model for a three dimensional saltwater intrusion problem has been developed. The LSO employs HST3D and Box’s algorithm. The weighting method of multi-objective optimization solves the multi-objective planning problem. The model is capable of determining the optimal pumping rates that minimize the saline concentration at the well sites, as well as, the cost associated with pumping, while satisfying an exogenous water demand. The model is valid for a wide range of applications as explicitly defined by the simulation model. The application of the model was limited to a modified version of Henry’s saltwater intrusion problem. Henry’s problem was modified to include a third spatial dimension and well sites. The multi-objective optimization yielded explicit tradeoff information between the two objectives.
A Theory of Bank Liquidity Requirements

We develop a theory of bank liquidity (cash reserve) requirements. Because cash is both observable and riskless, greater cash holdings improve bank incentives to manage risk in the remaining, non-cash portfolio of risky assets. In a model with a single bank, cash is held voluntarily to stem depositors' incentives to withdraw funds early in response to adverse news. In a model with multiple banks and information externalities, deposit insurance may be optimal, and cash reserve requirements are needed to incentivize prudent behavior by banks. In a model with multiple banks subject to liquidity shocks, an interbank market can emerge as long as the group of banks imposes a cash requirement to prevent free riding on interbank liquidity assistance. Our theory has several implications for the design of liquidity regulation that are absent from existing regulatory initiatives.
Novel mutations in emb B gene of ethambutol resistant isolates of Mycobacterium tuberculosis: a preliminary report.

BACKGROUND & OBJECTIVE Ethambutol (EMB) resistance, thought to be occurring due to mutations in embB gene of Mycobacterium tuberculosis on the rise is a cause of grave concern. The present study was planned to investigate the presence of EMB resistance in M. tuberculosis isolates and to look for prevalent mutations in embB gene. METHODS A total of 591(283 from new and 308 from previously treated cases) sputum samples from the same number of pulmonary tuberculosis cases were cultured. Isolates were tested by 1 per cent proportion method for resistance to isoniazid, rifampicin streptomycin and ethambutol. Minimum inhibitory concentration (MIC) of EMB was measured by absolute concentration method. Ten randomly selected isolates were subjected to single strand conformational polymorphism (SSCP) and direct DNA sequencing to look for mutation in 364 bp segments of embB gene. RESULTS Of 353 isolates of M. tuberculosis from 591 sputum samples, 62 (17.58%) were resistant to EMB, of which, 16 (25.8%) showed initial resistance and 46 (74.2%) acquired. Mono resistance to EMB was rare. Only two isolates showed resistance to EMB alone. From 62 EMB resistant isolates, 88.7 per cent (55) were resistant to INH, 82.2 per cent (51) to rifampicin and 61.2 per cent (38) were resistant to streptomycin. Co-resistance to isoniazid and rifampicin (multidrug resistant, MDR-TB) with EMB resistance was seen in 41(66.1%) isolates. High level of EMB resistance was seen in 16.5 per cent isolates. SSCP showed altered mobility in 8 of 10 isolates tested. Among the 8 mutants, 4 had known mutations at codon Met 306 being replaced by Val/ Leu. The second most frequent mutation encountered was at codon Phe 287 being replaced by Val, Cys or Leu (novel mutations). Sequence analysis revealed 10 novel mutations in codon 221, 225, 227, 271, 272, 281, 282, 287, 293 and 294 within embB gene. INTERPRETATION & CONCLUSION Presence of high frequency of EMB resistance, occurrence of high level EMB resistance, co-existence of MDR-TB with EMB resistance and novel mutations in emb B gene of M. tuberculosis clinical isolates reported highlight the need to work on larger samples to identify the diagnostic marker of EMB resistance in mycobacteria.
Regulation of macrophage activation and human immunodeficiency virus production by invasive Salmonella strains

Salmonellae possess the ability to adhere to and invade macrophages and in so doing trigger a number of intracellular events that are associated with cellular activation. As an initial approach to defining the mechanisms by which invasive salmonellae alter macrophage function, we have explored the impact of Salmonella infection on the production of human immunodeficiency virus (HIV) in U1 cells, a promonocytic cell line latently infected with the virus. Infection of U1 cells with a pathogenic strain of Salmonella enteritidis resulted in a marked induction of macrophage activation and HIV production. The stimulatory effect of salmonellae was mediated by signals other than lipopolysaccharide. Salmonella mutants with specific defects in invasion or intracellular survival were markedly less effective in the induction of HIV production. In contrast to S. enteritidis, strains of Yersinia enterocolitica, Legionella pneumophila, and Escherichia coli did not induce HIV production. However, all of these bacteria induced comparable levels of gene expression mediated by the HIV long terminal repeat. The results of this study are consistent with the notion that invasive salmonellae possess the ability to activate the macrophage by at least one mechanism that is not shared with several other species of gram-negative bacteria. Furthermore, the expression of this unique property is maximal with Salmonella strains that are not only invasive but also capable of prolonged survival within the macrophage. Our results indicate that the U1 cell line may be a very useful model system with which to examine the biochemical pathways by which internalized salmonellae modulate the activation state of the macrophage.
a , but Not by TNF- b IL-1Up-Regulated in Human Epithelial Cells by Neutrophil Gelatinase-Associated Lipocalin Is

Synthesis of the antimicrobial protein neutrophil gelatinase-associated lipocalin (NGAL) increases dramatically in bronchial epithelial cells and alveolear type II pneumocytes during lung inﬂammation. IL-1 (cid:1) induces a > 10-fold up-regulation of NGAL expression in the type II pneumocyte-derived cell line A549 cells, whereas TNF- (cid:2) , IL-6, and LPS had no effect. Similar IL-1 (cid:1) selectivity was demonstrated in primary bronchial epithelial cells and epidermal keratinocytes and for an NGAL promoter fragment transfected into A549 cells. By deletion and substitution analysis of the NGAL promoter, a 40-bp region containing an NF- (cid:3) B consensus site was found to control the IL-1 (cid:1) -speciﬁc up-regulation. Involvement of the NF- (cid:3) B site was demonstrated by site-directed mutagenesis, by transfection with a dominant-negative inhibitor of the NF- (cid:3) B pathway, and by EMSA. TNF- (cid:2) activation of NF- (cid:3) B, in contrast, did not increase NGAL synthesis, even though induced binding of NF- (cid:3) B to the NGAL promoter was observed in vitro. IL-1 (cid:1) speciﬁcity was not contained within the NF- (cid:3) B site of the NGAL promoter, as determined by exchanging the NGAL promoter (cid:1) s NF- (cid:3) B-binding sequence with that of the IL-8 promoter or with the NF- (cid:3) B consensus sequence and by testing the NF- (cid:3) B-binding sequence of the NGAL promoter against the heterologous SV40 promoter. Selectivity for the IL-1 pathway was substantiated by demonstrating that NGAL promoter activity could be induced by LPS stimulation of A549 cells transiently expressing Toll-like receptor 4, which use the same intracellular signaling pathway as the IL-1R. Together, this demonstrates a selective up-regulation of NGAL by the IL-1 pathway. The Journal of Immunology, 2003, 171: 6630–6639.