Miracle-dz/UniFAR-FTUs huggingface dataset:
Key Visual Features for Rapid Categorization of Animals in Natural Scenes

In speeded categorization tasks, decisions could be based on diagnostic target features or they may need the activation of complete representations of the object. Depending on task requirements, the priming of feature detectors through top–down expectation might lower the threshold of selective units or speed up the rate of information accumulation. In the present paper, 40 subjects performed a rapid go/no-go animal/non-animal categorization task with 400 briefly flashed natural scenes to study how performance depends on physical scene characteristics, target configuration, and the presence or absence of diagnostic animal features. Performance was evaluated both in terms of accuracy and speed and d′ curves were plotted as a function of reaction time (RT). Such d′ curves give an estimation of the processing dynamics for studied features and characteristics over the entire subject population. Global image characteristics such as color and brightness do not critically influence categorization speed, although they slightly influence accuracy. Global critical factors include the presence of a canonical animal posture and animal/background size ratio suggesting the role of coarse global form. Performance was best for both accuracy and speed, when the animal was in a typical posture and when it occupied about 20–30% of the image. The presence of diagnostic animal features was another critical factor. Performance was significantly impaired both in accuracy (drop 3.3–7.5%) and speed (median RT increase 7–16 ms) when diagnostic animal parts (eyes, mouth, and limbs) were missing. Such animal features were shown to influence performance very early when only 15–25% of the response had been produced. In agreement with other experimental and modeling studies, our results support fast diagnostic recognition of animals based on key intermediate features and priming based on the subject's expertise.
Multidrug Therapy and Evolution of Antibiotic Resistance: When Order Matters

ABSTRACT The evolution of drug resistance among pathogenic bacteria has led public health workers to rely increasingly on multidrug therapy to treat infections. Here, we compare the efficacy of combination therapy (i.e., using two antibiotics simultaneously) and sequential therapy (i.e., switching two antibiotics) in minimizing the evolution of multidrug resistance. Using in vitro experiments, we show that the sequential use of two antibiotics against Pseudomonas aeruginosa can slow down the evolution of multiple-drug resistance when the two antibiotics are used in a specific order. A simple population dynamics model reveals that using an antibiotic associated with high costs of resistance first minimizes the chance of multidrug resistance evolution during sequential therapy under limited mutation supply rate. As well as presenting a novel approach to multidrug therapy, this work shows that costs of resistance not only influences the persistence of antibiotic-resistant bacteria but also plays an important role in the emergence of resistance.
Phase Separation of Integral Membrane Proteins in Triton X-114 Solution

A solution of the nonionic detergent Triton X-114 is homogeneous at 0°C but separates in an aqueous phase and a detergent phase above 20°C. The extent of this detergent phase separation increases with the temperature and is sensitive to the presence of other surfactants. The partition of proteins during phase separation in solutions of Triton X-114 is investigated. Hydrophilic proteins are found exclusively in the aqueous phase, and integral membrane proteins with an amphiphilic nature are recovered in the detergent phase. Triton X-114 is used to solubilize membranes and whole cells, and the soluble material is submitted to phase separation. Integral membrane proteins can thus be separated from hydrophilic proteins and identified as such in crude membrane or cellular detergent extracts.
Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa

Purpose To identify nucleotide sequence variations in the rhodopsin (RHO) gene of Japanese patients with retinitis pigmentosa (RP) in order to search for mutations or haplotypes responsible for RP. Methods The entire region of RHO locus including a promoter region and introns was sequenced using blood-derived genomic DNA samples donated by 68 patients with RP and 68 control subjects. Results We found 39 single nucleotide substitutions including 17 rare substitutions of less than 1% in frequency, one insertion/deletion polymorphism, and one CA-repeat polymorphism in a 7.8 kbp region spanning the promoter, five exons, and four introns of the RHO gene locus. There were no affected subjects with amino acid substitutions in RHO, and there was 1 control subject with a novel substitution (Ala42Thr) who had no symptoms of RP. Fine analysis of single nucleotide polymorphism (SNPs) revealed eight haplotype structures of the Japanese RHO locus. There was no significant difference between RP patients and controls in terms of haplotype frequency. Conclusions No mutation causing an amino acid substitution of RHO was observed in 68 Japanese patients with RP, but 1 control subject did have a novel amino acid substitution. The Japanese RHO locus is comprised of eight major haplotypes. The RP-associated haplotype was not identified. The haplotype-tagging SNPs identified in this study will be useful as markers for the linkage-based screening of RP patients.
A New Method for the Characterization of Strain-Specific Conformational Stability of Protease-Sensitive and Protease-Resistant PrPSc

Although proteinacious in nature, prions exist as strains with specific self-perpetuating biological properties. Prion strains are thought to be associated with different conformers of PrPSc, a disease-associated isoform of the host-encoded cellular protein (PrPC). Molecular strain typing approaches have been developed which rely on the characterization of protease-resistant PrPSc. However, PrPSc is composed not only of protease-resistant but also of protease-sensitive isoforms. The aim of this work was to develop a protocol for the molecular characterization of both, protease-resistant and protease-sensitive PrPSc aggregates. We first set up experimental conditions which allowed the most advantageous separation of PrPC and PrPSc by means of differential centrifugation. The conformational solubility and stability assay (CSSA) was then developed by measuring PrPSc solubility as a function of increased exposure to GdnHCl. Brain homogenates from voles infected with human and sheep prion isolates were analysed by CSSA and showed strain-specific conformational stabilities, with mean [GdnHCl]1/2 values ranging from 1.6 M for MM2 sCJD to 2.1 for scrapie and to 2.8 M for MM1/MV1 sCJD and E200K gCJD. Interestingly, the rank order of [GdnHCl]1/2 values observed in the human and sheep isolates used as inocula closely matched those found following transmission in voles, being MM1 sCJD the most resistant (3.3 M), followed by sheep scrapie (2.2 M) and by MM2 sCJD (1.6 M). In order to test the ability of CSSA to characterise protease-sensitive PrPSc, we analysed sheep isolates of Nor98 and compared them to classical scrapie isolates. In Nor98, insoluble PrPSc aggregates were mainly protease-sensitive and showed a conformational stability much lower than in classical scrapie. Our results show that CSSA is able to reveal strain-specified PrPSc conformational stabilities of protease-resistant and protease-sensitive PrPSc and that it is a valuable tool for strain typing in natural hosts, such as humans and sheep.
5-Hydroxytryptamine 1 A Receptor-Mediated Increases in Receptor Expression and Activation of Nuclear Factor-k B in Transfected Chinese Hamster Ovary Cells

The regulation in expression of human 5-hydroxytryptamine1A (5-HT1A) receptors by agonists and antagonists was studied in a stable transfected Chinese hamster ovary cell line expressing the human 5-HT1A receptor. Receptor density and affinity were measured with [I]4-(29-methoxyphenyl)-1-[29-[N-(29-pyridinyl)-p-iodobenzamido]ethyl]piperazine ([I]p-MPPI), a selective antagonist of 5-HT1A receptors. Treatment of Chinese hamster ovary cells with serotonin or the selective agonist (6)-8hydroxy-N,N-dipropyl-2-aminotetralin stimulated a 2.5-fold increase in receptor density. The antagonists 4-(29-methoxyphenyl)-1-[29-[N-(29-pyridinyl)-p-iodobenzamidoethyl]piperazine, (2)-(S)-pindolol, and spiperone also stimulated upregulation of receptor expression. Agonistand antagoniststimulated up-regulations of receptor expression were mechanistically different. The effect of agonists was inhibited by pertussis toxin, actinomycin D, and cycloheximide. Antagonist-stimulated up-regulation was inhibited by cycloheximide, only partially inhibited by actinomycin D, and not inhibited by pertussis toxin. In the course of identifying potential pathways for coupling of the receptor to activation of transcription, we demonstrated that agonists activate the transcription regulatory factor nuclear factor-kB (NF-kB). Agonists were found to stimulate degradation of the inhibitory subunit, IkBa, and to increase the activity of a NF-kB-dependent CAT reporter gene. In contrast, the antagonist 4-(29-methoxyphenyl)-1-[29-[N-(29pyridinyl)-p-iodobenzamidoethyl]piperazine neither elicited degradation of Ik-Ba nor increased reporter activity. Our data suggest that expression of 5-HT1A receptors can be regulated by both agonists and antagonists and that the agonist but not antagonist stimulation occurs concomitantly with activation of NF-kB.
Identifying emotion by keystroke dynamics and text pattern analysis

Emotion is a cognitive process and is one of the important characteristics of human beings that makes them different from machines. Traditionally, interactions between humans and machines like computers do not exhibit any emotional exchanges. If we could build any system that is intelligent enough to interact with humans that involves emotions, that is, it can detect user emotions and change its behaviour accordingly, then using machines could be more effective and friendly. Many approaches have been taken to detect user emotions. Affective computing is the field that detects user emotion in a particular moment. Our approach in this paper is to detect user emotions by analysing the keyboard typing patterns of the user and the type of texts (words, sentences) typed by them. This combined analysis gives us a promising result showing a substantial number of emotional states detected from user input. Several machine learning algorithms were used to analyse keystroke timing attributes and text pattern. We have chosen keystroke because it is the cheapest and most available medium to interact with computers. We have considered seven emotional classes for classifying the emotional states. For text pattern analysis, we have used vector space model with Jaccard similarity method to classify free-text input. Our combined approach showed above 80% accuracies in identifying emotions.
Backtesting for Risk-Based Regulatory Capital

In this paper we present a framework for backtesting all currently popular risk measurement methods (including value-at-risk and expected shortfall) using the functional delta method.Estimation risk can be taken explicitly into account.Based on a simulation study we provide evidence that tests for expected shortfall with acceptable low levels have a better performance than tests for value-at-risk in realistic financial sample sizes.We propose a way to determine multiplication factors, and find that the resulting regulatory capital scheme using expected shortfall compares favorably to the current Basle Accord backtesting scheme.
Some Variations on the PC Algorithm

This paper proposes some possible modi(cid:12)cations on the PC basic learning algorithm and makes some experiments to study their behaviour. The variations are: to determine minimum size cut sets between two nodes to study the deletion of a link, to make statistical decisions taking into account a Bayesian score instead of a classical Chi-square test, to study the re(cid:12)nement of the learned network by a greedy optimization of a Bayesian score, and to solve link ambiguities taking into account a measure of their strength. It will be shown that some of these modi(cid:12)cations can improve PC performance, depending of the objective of the learning task: discovering the causal structure or approximating the joint probability distribution for the problem variables.
Using Semantic Clustering for Detecting Bengali Multiword Expressions

Multiword Expressions (MWEs), a known nuisance for both linguistics and NLP, blur the lines between syntax and semantics. The semantic of a MWE cannot be expressed after combining the semantic of its constituents. In this study, we propose a novel approach called "semantic clustering" as an instrument for extracting the MWEs especially for resource constraint languages like Bengali. At the beginning, it tries to locate clusters of the synonymous noun tokens present in the document. These clusters in turn help measure the similarity between the constituent words of a potential candidate using a vector space model. Finally the judgment for the suitability of this phrase to be a MWE is carried out based on a predefined threshold. In this experiment, we apply the semantic clustering approach only for noun-noun bigram MWEs; however we believe that it can be extended to any types of MWEs. We compare our approach with the state-ofthe- art statistical approach. The evaluation results show that the semantic clustering outperforms all other competing methods. As a byproduct of this experiment, we have started developing a standard lexicon in Bengali that serves as a productive Bengali linguistic thesaurus.
Cephalosporin-Glycopeptide Combinations for Use against Clinical Methicillin-Resistant Staphylococcus aureus Isolates: Enhanced In vitro Antibacterial Activity

The empirical combination of both a beta-lactam and glycopeptide to counter potential staphylococcal pathogens may improve the clinical outcomes for cases of Staphylococcus aureus bacteremia. We reported comparative in vitro studies of combination effects of different cephalosporins (i.e., cefazolin, cefmetazole, cefotaxime, and cefepime) combined with glycopeptides for 34 randomly selected methicillin-resistant S. aureus (MRSA) isolates by three methods, including the checkerboard, time-killing, and combination MIC measurement methods. Thirteen SCCmec type III isolates with a cefazolin MIC of ≥ 128 μg/mL were classified as the high-cefazolin MIC (HCM) group, whereas 13 SCCmec type IV and 8 SCCmec type V isolates were classified as the low-cefazolin MIC (LCM) group. With the checkerboard method, synergism was present for vancomycin-based combinations at 30.8–69.2 and 13.6–66.7%, as well as teicoplanin-based combinations of 38.5–84.6 and 0–47.6%, of the HCM and LCM isolates, respectively. No antagonism was noted. The in vitro inhibitory activity was evident even at a low concentration of 1/512x MIC of cephalosporin combined with sub-inhibitory concentrations (1/2x MIC) of a glycopeptide. With time-killing assays, synergism was noted at 1/2x or 1x susceptible breakpoint concentrations (SBCs) of a cephalosporin combined with 1/4 or 1/2 MIC of a glycopeptide. In the presence of 1/2 SBC of a cephalosporin, vancomycin or teicoplanin MICs decreased an average of 2.0- to 6.6- or 1.6- to 5.5-fold, respectively. With 8 μg/mL cephalosporin, the decline of glycopeptide MICs was most obvious in the presence of cefmetazole. In conclusion, cephalosporin-glycopeptide combinations at clinically achievable concentrations can exhibit in vitro synergistic antibacterial activity against clinical MRSA isolates. Such combinations require more clinical data to support their application for use in human MRSA infections.
DIstributed Kalman Filtering Using The Internal Model Average Consensus Estimator

We apply the internal model average consensus estimator in [1] to distributed Kalman filtering. The resulting distributed Kalman filter and the embedded average consensus estimator update at the same frequency. We show that if the internal model average consensus estimator is stable, the estimation error of the distributed Kalman filter is zero mean in steady state and has bounded covariance even when the dynamical system to be estimated is neutrally stable or unstable.
Towards a better understanding of adaptive multitasking by individuals

This paper reports work in progress on understanding how multitasking performance is influenced by two factors: task difficulty and task priority. In a task that involved switching between typing and controlling a cursor, these two factors were experimentally manipulated and shown to affect the chosen strategy, where a strategy was defined as the number of digits typed per visit. A cognitive model was used to explore the range of strategies and associated individual differences. The implications for using cognitive models to predict multitasking performance are explored.
A common contrast pooling rule for suppression within and between the eyes

Abstract Recent work has revealed multiple pathways for cross-orientation suppression in cat and human vision. In particular, ipsiocular and interocular pathways appear to assert their influence before binocular summation in human but have different (1) spatial tuning, (2) temporal dependencies, and (3) adaptation after-effects. Here we use mask components that fall outside the excitatory passband of the detecting mechanism to investigate the rules for pooling multiple mask components within these pathways. We measured psychophysical contrast masking functions for vertical 1 cycle/deg sine-wave gratings in the presence of left or right oblique (±45 deg) 3 cycles/deg mask gratings with contrast C%, or a plaid made from their sum, where each component (i) had contrast 0.5Ci%. Masks and targets were presented to two eyes (binocular), one eye (monoptic), or different eyes (dichoptic). Binocular-masking functions superimposed when plotted against C, but in the monoptic and dichoptic conditions, the grating produced slightly more suppression than the plaid when Ci ≥ 16%. We tested contrast gain control models involving two types of contrast combination on the denominator: (1) spatial pooling of the mask after a local nonlinearity (to calculate either root mean square contrast or energy) and (2) “linear suppression” (Holmes & Meese, 2004, Journal of Vision4, 1080–1089), involving the linear sum of the mask component contrasts. Monoptic and dichoptic masking were typically better fit by the spatial pooling models, but binocular masking was not: it demanded strict linear summation of the Michelson contrast across mask orientation. Another scheme, in which suppressive pooling followed compressive contrast responses to the mask components (e.g., oriented cortical cells), was ruled out by all of our data. We conclude that the different processes that underlie monoptic and dichoptic masking use the same type of contrast pooling within their respective suppressive fields, but the effects do not sum to predict the binocular case.
COMPRESSION LIBRARY FOR PALM OS PLATFORM By NEBOJA ĆIRIĆ A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA

of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science COMPRESSION LIBRARY FOR PALM OS PLATFORM By Neboja Ćirić May 2003 Chair: Dr. Douglas Dankel II Major Department: Computer and Information Science and Engineering This thesis presents the design and implementation of a compression library (CLP) for the Palm Operating System (OS) platform. Data compression is a well-researched field in information theory and there are numerous programs and libraries available for almost every platform and OS in the market. Porting an existing library from the UNIX or MS Windows OS to the Palm OS is a nontrivial task because of constraints imposed by the handheld platforms memory size and organization. That is why CLP implemented simple, yet effective algorithms with small memory requirements. CLP contains two algorithms: the static Huffman compression and the static arithmetic compression. It would be easy to expand the library with new algorithms, if needed, because it was designed and implemented using an object oriented approach. CLP uses a simple interface, exposing only a few methods to the user, thus decreasing deployment time and increasing productivity.
Analyzing impact of multiple ABB and AVS domains on throughput of power and thermal-constrained multi-core processors

Recently, semiconductor industries have integrated more cores in a single die, which substantially improves the throughput of the processors running highly-parallel applications. However, many existing applications do not have high enough parallelism to exploit multiple cores in a die, slowing the transition to many-core processors with smaller and more cores that benefit future applications with high parallelism. In this paper, we analyze the impact of multiple adaptive voltage scaling (AVS) and adaptive body biasing (ABB) domains on the throughput of power and thermal-constrained multi-core processors when they are combined with per-core power-gating (PCPG). Both AVS and ABB can be effectively used to either increase frequency (thus throughput) or decrease power consumption of the processors. Meanwhile, PCPG can provide extra power and thermal headroom when application's parallelism is limited. First, we analyze the throughput impact of applying AVS, ABB, and PCPG for power and thermal constrained multi-core processors. Second, we investigate the impact of multiple AVS and ABB domains on the throughput, and recommend the most cost-effective number of domains for AVS and ABB in 16 and 8-core processors. Our analysis using the 32nm predictive technology model considering within-die variations suggests that the most cost-effective number of domains for AVS and/or ABB should be one for each when they are combined with PCPG in both 16 and 8-core processors. Since within-die core-to-core variations provide many choices in terms of core frequency and power consumption for limited-parallelism applications, one AVS or ABB domain can leads to the throughput improvement by 1.77∼2.49x; more than one AVS and/or ABB domains only improve the throughput marginally.
Fixed and random effects.

In performing a multilevel analysis, what is a level? And when should a variable have a random slope? This depends on whether the units in the design should be regarded as being representative of a population and on whether the researcher wishes to draw conclusions primarily about the observed units or primarily about the population. Keywords: fixed effects; random effects; linear model; multilevel analysis; mixed model; population; dummy variables