Miracle-dz/UniFAR-FTUs huggingface dataset:
Classifiers for decoding patterns in the response of an artificial retina

We present a neural classifier able to reliably determine the correlation between elementary image patterns and the characteristics of the chaotic regime of an artificial retina based on nonlinear dynamics. While the classifier is a typical neural one, it has the role of completing the neural retina with the equivalent of the upper layers of neurons in the nervous system of mammals. Without this classification stage, the proper use of the retina is imperfect, hence the significance of reporting on it. The performance of the classifier is discussed in relation to the application requirements. This paper represents a preliminary, abstracted version of a paper to be published in a journal.
Fatty Acid and Transcriptome Profiling of Longissimus Dorsi Muscles between Pig Breeds Differing in Meat Quality

Fat and lean pig breeds show obvious differences in meat quality characteristics including the fatty acid composition of muscle. However, the molecular mechanism underlying these phenotypes differences remains unknown. This study compared meat quality traits between Lantang (a Chinese indigenous breed) and Landrace (a typical lean breed). The Lantang pigs showed higher L* values and intramuscular fat content, lower pH45min, pH24h and shear force in longissimus dorsi (LD) muscle than Landrace (P < 0.05). Fatty acid analysis demonstrated the lower monounsaturated fatty acids (MUFA) and higher polyunsaturated fatty acids (PUFA) percentage in Lantang LD than that in Landrace LD (P < 0.05). To further identify candidate genes for fatty acid composition, the transcriptome of LD muscle from the two breeds were measured by microarrays. There were 586 transcripts differentially expressed, of which 267 transcripts were highly expressed in Lantang pigs. After the validation by real-time quantitative PCR, 13 genes were determined as candidate genes for fatty acid composition of muscle, including Stearoyl-CoA desaturase (SCD). Then, a SCD over-expression plasmid was transfected into C2C12 cells to reveal the effect of SCD on the fatty acid composition in vitro. The results showed that SCD over-expression significantly increased PUFA proportion, while reduced that of saturated fatty acids (SFA) in C2C12 cells (P < 0.05). In summary, this study compared the differences of fatty acid composition and transcriptome in two breeds differing in meat quality, and further identified the novel role of SCD in the regulation of PUFA deposition.
Differences in health-related quality of life among subjects with frequent bilateral or unilateral knee pain: data from the Osteoarthritis Initiative study.

STUDY DESIGN Cross-sectional study. OBJECTIVE To examine associations between frequent bilateral knee pain (BKP) and unilateral knee pain (UKP) and health-related quality of life (QoL). We hypothesized that frequent BKP would be associated with poorer health-related QoL than would frequent UKP and no knee pain. BACKGROUND Knee pain is one of the most frequently reported types of joint pain among adults in the United States. It is the most frequent cause of limited physical function, disability, and reduced QoL. METHODS Data were collected from the Osteoarthritis Initiative public-use data sets. Health-related QoL was assessed in 2481 participants (aged 45-79 years at baseline). The Knee injury and Osteoarthritis Outcome Score QoL subscale (knee-specific measure) and the physical component summary and mental component summary (MCS) scores of the Medical Outcomes Study 12-Item Short-Form Health Survey (SF-12) (generic measure) were used to assess health-related QoL. Multiple regression analyses were used to examine the relationships between frequent knee pain and health-related QoL, adjusted for sociodemographic and health covariates. RESULTS Compared with subjects with no knee pain, subjects with frequent BKP and UKP had significantly lower scores on the Knee injury and Osteoarthritis Outcome Score QoL subscale (mean difference, -35.2; standard error [SE], 0.86; P<.001 and mean difference, -29.2; SE, 0.93; P<.001; respectively) and the SF-12 physical component summary score (mean difference, -6.25; SE, 0.41; P<.001 and mean difference, -4.10; SE, 0.43; P<.001; respectively), after controlling for sociodemographic and health covariates. The SF-12 MCS score was lower among those with BKP (-1.29; SE, 0.42; P<.001). Frequent UKP was not associated with the SF-12 MCS. CONCLUSION Subjects with frequent BKP had lower health-related QoL than those with frequent unilateral or no knee pain, as reflected in lower Knee injury and Osteoarthritis Outcome Score QoL subscale and SF-12 physical component summary and MCS scores.
Optimal Reallocation under Additive and Ordinal Preferences

Reallocating resources to get mutually beneficial outcomes is a fundamental problem in various multi-agent settings. In the first part of the paper we focus on the setting in which agents express additive cardinal utilities over objects. We present computational hardness results as well as polynomial-time algorithms for testing Pareto optimality under different restrictions such as two utility values or lexicographic utilities. In the second part of the paper we assume that agents express only their (ordinal) preferences over single objects, and that their preferences are additively separable. In this setting, we present characterizations and polynomial-time algorithms for possible and necessary Pareto optimality.
Naturally Occurring Lactic Acid Bacteria Isolated from Tomato Pomace Silage

Silage making has become a significant method of forage conservation worldwide. To determine how tomato pomace (TP) may be used effectively as animal feed, it was ensilaged for 90 days and microbiology counts, fermentation characteristics and chemical composition of tomato pomace silage (TPS) were evaluated at the 30th, 60th, and 90th days, respectively. In addition, 103 lactic acid bacteria were isolated from TPS. Based on the phenotypic and chemotaxonomic characteristics, 16S rDNA sequence and carbohydrate fermentation tests, the isolates were identified as 17 species namely: Lactobacillus coryniformis subsp. torquens (0.97%), Lactobacillus pontis (0.97%), Lactobacillus hilgardii (0.97%), Lactobacillus pantheris (0.97%), Lactobacillus amylovorus (1.9%), Lactobacillus panis (1.9%), Lactobacillus vaginalis (1.9%), Lactobacillus rapi (1.9%), Lactobacillus buchneri (2.9%), Lactobacillus parafarraginis (2.9%), Lactobacillus helveticus (3.9%), Lactobacillus camelliae (3.9%), Lactobacillus fermentum (5.8%), Lactobacillus manihotivorans (6.8%), Lactobacillus plantarum (10.7%), Lactobacillus harbinensis (16.5%) and Lactobacillus paracasei subsp. paracasei (35.0%). This study has shown that TP can be well preserved for 90 days by ensilaging and that TPS is not only rich in essential nutrients, but that physiological and biochemical properties of the isolates could provide a platform for future design of lactic acid bacteria (LAB) inoculants aimed at improving the fermentation quality of silage.
Economically Enhanced MOSIX for Market-based Scheduling in Grid OS ∗

Applying economic principles to grids is deemed promising to improve the overall value provided by such systems. By introducing market mechanisms, end users can influence the allocation of resources by reporting valuations for these resources. Current market-based schedulers, however, are static, assume the availability of complete information about jobs (in particular with respect to processing times), and do not make use of the flexibility offered by computing systems. In this paper, we present our progress in implementing a novel market mechanism for MOSIX, a stateof-the-art management system for computing clusters and organizational grids. The market mechanism is designed so as to be able to work in large-scale settings with selfish agents. Facing incomplete information about jobs’ characteristics, it dynamically allocates jobs to computing nodes by leveraging preemption and process migration, two distinct features offered by the MOSIX system.
Forecasting hardwood stumpage price trends in Pennsylvania

Commonly used timber species with the longest time series in the Pennsylvania Timber Market Report (TMR) fell into three distinct groups of price growth over the 1984 to 2003 lifespan of the TMR. Black cherry and hard maple had the highest growth rates, followed by northern red oak, soft maple, and yellow-poplar that grew at lesser but still high rates, and lastly white oak and white ash showed the lowest growth rates. The 1984 to 2003 trends show 0.1 to 3.0 and -0.2 to 2.4 point lower nominal and real annual growth rates, respectively, compared to the 1984 to 2000 period due to the economic downturn of 2001. Using a generalized least squares regression model to compensate for strong autocorrelation, forecasts with the full autoregression model (including autoregressive parameters) were not significantly better than the structural linear model alone. Due to the volatility and cyclical nature of the price series, forecasts of more than one quarter have increasingly high errors.
Robust target estimation in compressive sensing based colocated MIMO radar

A colocated multiple-input multiple-output (MIMO) radar system is considered, in which the transmitters and receivers are nodes of a small scale wireless network. The sparsity of targets in the illuminated space allows target detection based on compressive sensing (CS) techniques. A receive node compresses the received signal via a linear transformation, Φ, referred to in CS theory a measurement matrix. The compressed samples are subsequently forwarded to a fusion center, where an ℓ1-optimization problem is formulated and solved for target information. CS-based MIMO radar achieves the same localization performance as do traditional methods but with many fewer measurements. Unlike previous work, we consider the case in which the targets might be located across several range bins, and the delay of the first reflected signal is unknown and, due to the small number of compressed samples, cannot be estimated accurately. A new measurement matrix is proposed that is constructed based on the transmit signal waveforms and also accounts for all possible discretized delays of target returns within a given time window. It is shown that reduced bandwidth transmit waveforms can lead to a measurement matrix that improves signal-to-interference ratio (SIR), but on the other hand, using waveforms that are too narrowband increases the coherence of the sensing matrix, thus invalidating the conditions for the application of the CS approach. Therefore, the transmit waveforms must be chosen carefully to guarantee the desired performance.
Point-of-care monitoring of vitamin K-antagonists: validation of CoaguChek XS test strips with International Standard thromboplastin

Aims Many patients treated with vitamin K-antagonists (VKA) use point-of-care (POC) whole blood coagulometers for self-testing. The majority of patients in the Netherlands use one type of POC coagulometer, that is, the CoaguChek XS. Each new lot of test strips for the CoaguChek XS is validated by a group of collaborating thrombosis centres. We assessed the International Normalised Ratio (INR) differences between each of 51 new lots of test strips and the International Standard for thromboplastin rTF/95 or its successor rTF/09. Methods Each year, a particular lot of CoaguChek XS test strips was used as reference lot. The reference lot was validated by comparison to the International Standard, yielding a relationship between the reference lot INR and International Standard INR. Successive lots of test strips were compared to the reference lot by three centres using 19–29 capillary blood samples obtained from VKA-treated patients. Each patient provided two blood drops from the same finger prick, one for the reference lot strip and one for the new lot. Results The mean INR differences between each lot and the International Standard varied between −8% and +4%. The mean absolute values of the relative differences varied between 2.4% and 8.1%. There were small but clinically unimportant differences in INR between the first and second drop of blood. Conclusions Accuracy of CoaguChek XS INR determinations can be assessed by a group of collaborating centres using a limited number of capillary blood samples. As the mean INR differences with the International Standard were smaller than 10%, the lots were approved for use by the Netherlands Thrombosis Services.
Evaluating the dynamic behaviour of Python applications

The Python programming language is typical among dynamic languages in that programs written in it are not susceptible to static analysis. This makes efficient static program compilation difficult, as well as limiting the amount of early error detection that can be performed. Prior research in this area tends to make assumptions about the nature of programs written in Python, restricting the expressiveness of the language. One may question why programmers are drawn to these languages at all, if only to use them in a static-friendly style. In this paper we present our results after measuring the dynamic behaviour of 24 production-stage open source Python programs. The programs tested included arcade games, GUI applications and non-interactive batch programs. We found that while most dynamic activity occurs during program startup, dynamic activity after startup cannot be discounted entirely.
Post hoc power estimation in large-scale multiple testing problems

BACKGROUND The statistical power or multiple Type II error rate in large-scale multiple testing problems as, for example, in gene expression microarray experiments, depends on typically unknown parameters and is therefore difficult to assess a priori. However, it has been suggested to estimate the multiple Type II error rate post hoc, based on the observed data. METHODS We consider a class of post hoc estimators that are functions of the estimated proportion of true null hypotheses among all hypotheses. Numerous estimators for this proportion have been proposed and we investigate the statistical properties of the derived multiple Type II error rate estimators in an extensive simulation study. RESULTS The performance of the estimators in terms of the mean squared error depends sensitively on the distributional scenario. Estimators based on empirical distributions of the null hypotheses are superior in the presence of strongly correlated test statistics. AVAILABILITY R-code to compute all considered estimators based on P-values and supplementary material is available on the authors web page http://statistics.msi. meduniwien.ac. at/index.php? page=pageszfnr.
Towards Automatic Software Lineage Inference

Software lineage refers to the evolutionary relationship among a collection of software. The goal of software lineage inference is to recover the lineage given a set of program binaries. Software lineage can provide extremely useful information in many security scenarios such as malware triage and software vulnerability tracking. In this paper, we systematically study software lineage inference by exploring four fundamental questions not addressed by prior work. First, how do we automatically infer software lineage from program binaries? Second, how do we measure the quality of lineage inference algorithms? Third, how useful are existing approaches to binary similarity analysis for inferring lineage in reality, and how about in an idealized setting? Fourth, what are the limitations that any software lineage inference algorithm must cope with? Towards these goals we build ILINE, a system for automatic software lineage inference of program binaries, and also IEVAL, a system for scientific assessment of lineage quality. We evaluated ILINE on two types of lineage-- straight line and directed acyclic graph--with large-scale real-world programs: 1,777 goodware spanning over a combined 110 years of development history and 114 malware with known lineage collected by the DARPA Cyber Genome program. We used IEVAL to study seven metrics to assess the diverse properties of lineage. Our results reveal that partial order mismatches and graph arc edit distance often yield the most meaningful comparisons in our experiments. Even without assuming any prior information about the data sets, ILINE proved to be effective in lineage inference--it achieves a mean accuracy of over 84% for goodware and over 72% for malware in our data sets.
The Clinical Dental Trial

T HE evaluation of the effects of tranquilizing drugs is subject to tremendous variation both in the effect on the patient and in the observation of the clinician. As a result, some observers feel that the effectiveness of ataractic drugs is either extremely limited or nonexistent, while others believe they are the answer to the problems of the management of the apprehensive patient. It is the purpose of this paper to describe a study of the clinical effectiveness of a new drug in making patients more relaxed for operative dentistry. Particular emphasis will be placed upon the design of the experiment.
Automatic organisation, segmentation, and filtering of user-generated audio content

Using solely the information retrieved by audio finger-printing techniques, we propose methods to treat a possibly large dataset of user-generated audio content, that (1) enable the grouping of several audio files that contain a common audio excerpt (i.e. are relative to the same event), and (2) give information about how those files are correlated in terms of time and quality inside each event. Furthermore, we use supervised learning to detect incorrect matches that may arise from the audio fingerprinting algorithm itself, whilst ensuring our model learns with previous predictions. All the presented methods were further validated by user-generated recordings of several different concerts manually crawled from YouTube.
Geometric Evaluation of Forced Convective Flows across an Arrangement of Four Circular Cylinders

The present study consists in a numerical evaluation of an arrangement formed by four cylinders submitted to an unsteady, two-dimensional, incompressible, laminar and forced convective flow. The geometric evaluation is performed through the Constructal Design method. The problem has two restrictions given by the sum of the area of the cylinders and one occupation area and has three degrees of freedom: ST1/D (the ratio between the transverse pitch of the frontal cylinders and the diameter of the cylinders), ST2/D (the ratio between the transverse pitch of the posterior cylinders and the diameter of the cylinders) and SL/D (ratio between the longitudinal pitch of the frontal and posterior cylinders and the diameter of the cylinders). For all simulations the Reynolds number is kept constant, ReD = 100, and two different Prandtl numbers of Pr = 0.71 and 5.83 are considered, which simulates respectively the use of air and water as a fluid. The conservation equations of mass, momentum and energy are solved with the Finite Volume Method (FVM). The main objective is to evaluate the effect of the degrees of freedom on the drag coefficient (CD) and the Nusselt number (NuD) between the cylinders and the surrounding flow, as well as the optimal ST2/D values for three ratios of ST1/D = 1.5, 3.0 and 4.0, these results being obtained for ratios of SL/D = 1.5 and 4.0. Results showed that the ratio changes of ST1/D and ST2/D have a great influence on the drag coefficients and on the Nusselt number of the arrangement formed by the four cylinders, as well as on the geometries leading to the best fluid dynamics and thermal performance.
A Data Structure to Significantly Speed up A Simulated Annealing Heuristic for Solving the Dynamic Facility Layout Problem

In this paper a data structure is designed to significantly speed up a simulated annealing heuristic for solving the dynamic facility layout problem (DFLP) existed in literature. The DFLP augments the static facility layout problem (SFLP) to take the flexibility of layout planning into account by considering that the material handling flows between each pair of departments may vary over time periods. Unlike that in the SFLP, the DFLP might require rearranging facility layout over periods to trade off costs between material handling flows and rearranging departments. By companioned the existing simulated annealing heuristic for the DFLP with our designed data structure, the revised version of the algorithm can significantly speeded up the computing time for solving problems, and the data structure can be applied as a useful tool to develop some more efficient solution methods for solving the DFLP related optimization problems in future.
Characterization of the Tumor-Microenvironment in Patient-Derived Cervix Xenografts (OCICx)

Rationale: The tumor microenvironment (TME) is heterogeneous including both malignant and host cell components as well as regions of hypoxia, elevated interstitial fluid pressure (IFP) and poor nutrient supply. The quantitative extent to which the microenvironmental properties of primary tumors are recapitulated in xenograft models is not well characterized. Methods: Xenografts were generated by implanting tumor biopsies directly into the cervix of mice to create a panel of orthotopically-passaged xenografts (OCICx). Tumors were grown to ~1 cm (diameter) and IFP measurements recorded prior to sacrifice. Enlarged para-aortic lymph nodes (>1–2 mm) were excised for histologic confirmation of metastatic disease. Quantitative histological analysis was used to evaluate hypoxia, proliferation, lymphatic and blood vessels in the epithelial and stromal regions of the xenografts and original patient tumour. Results: IFP and nodal disease were not correlated with tumor engraftment. IFP measurements in the xenografts were generally lower than those in the patient’s tumor. Lymphatic metastasis increased with passage number as did levels of hypoxia in the epithelial component of the xenografts. The blood vessel density in the stromal component of the xenografts increased in parallel. When all the markers were compared between the biopsy and the respective 3rd generation xenograft 10 of 11 tumors showed a good correlation. Conclusions: This ongoing study provides characterization about tumoral and stromal heterogeneity in a unique orthotopic xenograft model.
Healthy eating index for pregnancy: adaptation for use in pregnant women in Brazil.

OBJECTIVE To evaluate dietary quality in a sample of pregnant women based on one simple and objective parameter. METHODS Pregnant women (n = 712), between 16 and 36 weeks, attending primary care clinics in Porto Alegre and Bento Gonçalves, Southern Brazil, in 2010 were recruited to take part. The Healthy Eating Index for Brazilian Pregnancy (HEIP-B) was created, derived from the American instrument called Alternate Healthy Eating Index for Pregnancy (AHEI-P). Questionnaires on frequency of consumption and on socio-demographic factors were completed. Focused principal component analysis (ACPF) was used to assess the relationship between the index and nutrients relevant to pregnancy. RESULTS The median (interquartile range) of AHEI-P and HEIP-B were 66.6 (57.8-72.4) and 67.4 (60.0-73.4), respectively. The HEIP-B showed a good positive correlation with nutrients which are specifically recommended for pregnancy: folate (r = 0.8; p < 0.001), calcium (r = 0.6; p < 0.001) and iron (r = 0.7; p < 0.001). CONCLUSIONS The quality of the diet of the pregnant women in this study was classified as within the "improvements needed" cut off point, which demonstrates the need for more specific education on nutrition for this stage of life. The index showed good correlations and, thus, may be considered an effective tool for assessing the quality of nutrition during pregnancy.