Miracle-dz/UniFAR-FTUs huggingface dataset:
Can You Give Me a Lift?

Static Analysis (SA) is the practice of examining computer program source code for errors or vulnerabilities outside the compiler’s capabilities. To carry out Static Analysis on computer programs, various tools exist that parse and examine each line for known issues. These tools do not compile the program, nor do they run the program. Instead, they analyse the source code directly and infer properties about the program without executing it - thus “static” analysis. Static analysis is not new. Early UNIX contained a program called “lint” for static analysis; a tool that has now existed since the late 1970s (Johnson 1978). Increasingly, however, modern static analysis practices indicate a more focused intent; find cybersecurity weaknesses. At the 22nd European Conference on Cyber Warfare and Security, the authors presented the background of Intermediate Representations (IRs) and described how this “middleware” representation can be utilized for static analysis of source code for cybersecurity weaknesses. By examining an IR, potential flaws in the source code can be located. When utilizing the IR as opposed to the original high-level language, the static analysis process becomes independent of the original source language; if several languages such as C, Rust, and others all compile into the same IR, static analysis of the IR allows the analysis process to no longer be tied to the high-level language grammar or syntax. The previous paper implemented a literature survey of available IR analysis tools to discover prior work; the authors have subsequently advanced the research and are actively using an IR framework, LLVM, for vulnerability analysis. In this research, source code in a high-level language is first compiled to LLVM and the resulting IR is used for analysis. This approach uses a “code-to-IR” SA analysis preparation paradigm. At the same time, there is the potential for binary “lifters” to be used. These tools “lift” an executable program – binary machine instructions – back to LLVM. In this way, the paradigm can also be reversed such that static analysis of LLVM can be performed on source code compiled into LLVM, or on executable programs in the field that are “lifted”. This begs: how effective are these “lifters”? In this work, the authors present experiences in installation and operation of several binary “lifters” available as open-source projects. Some are supported better than others, some operate better than others, and some don’t operate at all. Those that do lead to the follow-up: Is the “lifted” code suitable for static analysis, or is it too obfuscated relative to the original program? This paper describes just that – our efforts and results in locating a binary “lifter” suitable for bringing executable program test cases back to LLVM for analysis by the cybersecurity vulnerability tool concurrently under development.
Hybrid model predictive control using time-instant optimization for the Rhine-Meuse Delta

In order to provide safety against high sea water levels, in many low-lying countries on the one hand dunes are maintained at a certain safety level and dikes are built, while on the other hand large control structures that can be controlled dynamically are constructed. Currently, these structures are often operated purely locally, without coordination on actions between different structures. Automatically coordinating the actions is particularly difficult, since open water systems are complex, hybrid systems, in the sense that continuous dynamics (e.g., the evolution of the water levels) are mixed with discrete events (e.g., the opening or closing of barriers). In low-lands, this complexity is increased further due to bi-directional water flows resulting from backwater effects and interconnectivity of flows in different parts of river deltas. In this paper, we propose a model predictive control (MPC) approach that is aimed at automatically coordinating the different actions. Hereby, the hybrid nature is explicitly addressed. In order to reduce the computational effort required to solve the hybrid MPC problem we propose to use TIO-MPC, where TIO stands for time-instant optimization. A simulation study illustrates the potential of the proposed controller in comparison with the current setup in the Rhine-Meuse delta in The Netherlands.
Timescales of Growth Response of Microbial Mats to Environmental Change in an Ice-Covered Antarctic Lake

Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm−2 y−1. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure.
Epsilon-Lexicase Selection for Regression

Lexicase selection is a parent selection method that considers test cases separately, rather than in aggregate, when performing parent selection. It performs well in discrete error spaces but not on the continuous-valued problems that compose most system identification tasks. In this paper, we develop a new form of lexicase selection for symbolic regression, named ε-lexicase selection, that redefines the pass condition for individuals on each test case in a more effective way. We run a series of experiments on real-world and synthetic problems with several treatments of ε and quantify how ε affects parent selection and model performance. ε-lexicase selection is shown to be effective for regression, producing better fit models compared to other techniques such as tournament selection and age-fitness Pareto optimization. We demonstrate that ε can be adapted automatically for individual test cases based on the population performance distribution. Our experiments show that ε-lexicase selection with automatic ε produces the most accurate models across tested problems with negligible computational overhead. We show that behavioral diversity is exceptionally high in lexicase selection treatments, and that ε-lexicase selection makes use of more fitness cases when selecting parents than lexicase selection, which helps explain the performance improvement.
Video Retrieval Using Search and Browsing

We describe our experiments for the shot boundary detection, high-level feature extraction, search and story boundary detection tasks. In the shot boundary detection task, we employ our proven method based on the calculation of distances between colour histograms of frames over a range of timescales. In the feature detection task we con(cid:12)ned our e(cid:11)ort to the basketball feature. For the search task, we test a complete redesign of last year’s interface. Like last year, content-based search is complemented with NN k browsing functionality. We compare performance of two interactive runs, one including search and browsing, the other including search only. Overall search performance falls behind that of last year, a result which we would like to attribute to the stronger emphasis on motion in this year’s search task.
Expression of fibroblast growth factor receptors in peri‐implantation mouse embryos

FGF receptor (FGFR) function is essential during peri‐implantation mouse development. To understand which receptors are functioning, we tested for the expression of all four FGF receptors in peri‐implantation blastocysts. By RT‐PCR, FGFR‐3 and FGFR‐4 were detected at high levels, FGFR‐2 at lower levels, and FGFR‐1 was detected at background levels compared to control tissues. Because FGFR‐3 and FGFR‐4 were detected at the highest levels, we studied these in detail. Between 3.5 days after fertilization (E3.5) and E6.0, FGFR‐4 mRNA was detected ubiquitously in the peri‐implantation embryo, restricted to the inner cell mass (ICM) and its derivatives and primitive endoderm by E6.0, and was not detected at E6.5. FGFR‐3 mRNA was detected ubiquitously in the peri‐implantation embryo with a tendency towards extraembryonic cells. We tested blastocyst outgrowths, a model for implantation, for FGFR‐3 and FGFR‐4 protein. FGFR‐3 protein was detected in all cells early during the outgrowth. Later, FGFR‐3 was detected in the extraembryonic endoderm and trophoblast giant cells (TGC), but not in the ICM. FGFR‐4 protein was detected in all cells of the implanting embryo, but was restricted to the ICM/primitive endoderm in later stage outgrowths. The distribution of the receptor proteins in the blastocyst outgrowths is similar to the distribution of the mRNA detected by in situ hybridization of sections of embryos. The data suggest roles for FGFR‐3 and FGFR‐4 in peri‐implantation development. Mol. Reprod. Dev. 51:254–264, 1998. © 1998 Wiley‐Liss, Inc.
Correlating Genetic Results with Biometric Analysis on Metapodial Bones

the ancient Dna research from three geographically close caves in the ach valley, namely geißenklösterle, hohle Fels and Sirgenstein, revealed two different cave bear haplogroups, haplogroup 1 (Ursus spelaeus) and haplogroup 4 (Ursus ingressus). the latter replaced the former around 28,000 years Bp (hofreiter et al., 2002). the goal of this analysis is to find species or taxa defining characteristics using biometrical analysis. Beside teeth (rabeder, 1999, Baryshnikov et al., 2003; grandal d’anglade and lopez-gonzalez, 2005), metapodials are one of the most promising elements of the postcranium in respect of evolutionary trends, species distinction and sexual dimorphism. after a preliminary statistical investigation (distribution, variance, correlation) each metapodial was classified and allocated to either species or taxon by discriminant analysis. these results were cross-checked due to stratigraphical provenience of the items correlated with the date of replacement.
The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles

We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
A Four PDZ Domain-containing Splice Variant Form of GRIP1 Is Localized in GABAergic and Glutamatergic Synapses in the Brain*

We have isolated, from a rat brain cDNA library, a clone corresponding to a 2779-bp cDNA encoding a novel splice form of the glutamate receptor interacting protein-1 (GRIP1). We call this 696-amino acid splice form GRIP1c 4-7 to differentiate it from longer splice forms of GRIP1a/b containing seven PDZ domains. The four PDZ domains of GRIP1c 4-7 are identical to PDZ domains 4-7 of GRIP1a/b. GRIP1c 4-7 also contains 35 amino acids at the N terminus and 12 amino acids at the C terminus that are different from GRIP1a/b. In transfected HEK293 cells, a majority of GRIP1c 4-7 was associated with the plasma membrane. GRIP1c 4-7 interacted with GluR2/3 subunits of the α-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid receptor. In low density hippocampal cultures, GRIP1c 4-7 clusters colocalized with GABAergic (where GABA is γ-aminobutyric acid) and glutamatergic synapses, although a higher percentage of GRIP1c 4-7 clusters colocalized with γ-aminobutyric acid, type A, receptor (GABAAR) clusters than with α-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid receptor clusters. Transfection of hippocampal neurons with hemagglutinin-tagged GRIP1c 4-7 showed that it could target to the postsynaptic complex of GABAergic synapses colocalizing with GABAAR clusters. GRIP1c 4-7-specific antibodies, which did not recognize previously described splice forms of GRIP1, recognized a 75-kDa protein that is enriched in a postsynaptic density fraction isolated from rat brain. EM immunocytochemistry experiments showed that in intact brain GRIP1c 4-7 concentrates at postsynaptic complexes of both type I glutamatergic and type II GABAergic synapses although it is also presynaptically localized. These results indicate that GRIP1c 4-7 plays a role not only in glutamatergic synapses but also in GABAergic synapses.
Combinatorial estimates by the switching method

The method of switchings is a standard tool for enumerative and probabilistic applications in combinatorics. In its simplest form, it analyses a relation between two sets to estimate the ratio of their sizes. In a more complicated setting, there is a family of sets connected by some relations. By bounding properties of the relations, bounds can be inferred on the relative sizes of the sets. In this paper we extend the treatment of Fack and McKay (2007) to allow the graph of sets and relations to be an arbitrary directed graph. A special case that frequently occurs in bounding tails of distributions is analysed in detail.
Uncorrelated multilinear principal component analysis through successive variance maximization

Tensorial data are frequently encountered in various machine learning tasks today and dimensionality reduction is one of their most important applications. This paper extends the classical principal component analysis (PCA) to its multilinear version by proposing a novel unsupervised dimensionality reduction algorithm for tensorial data, named as uncorrelated multilinear PCA (UMPCA). UMPCA seeks a tensor-to-vector projection that captures most of the variation in the original tensorial input while producing uncorrelated features through successive variance maximization. We evaluate the UMPCA on a second-order tensorial problem, face recognition, and the experimental results show its superiority, especially in low-dimensional spaces, through the comparison with three other PCA-based algorithms.
Evaluation of water use efficiency in irrigated agriculture supported by satellite images

Palacios-Velez, E. , Palacios-Sanchez, L. A. , & Espinosa- Espinosa, J. L. January-February, 2018). Evaluation of water use efficiency in irrigated agriculture supported by satellite images. Water Technology and Sciences (in Spanish), 9 (1), 31- 38, DOI: 10.24850/j-tyca-2018-01-02. To evaluate the water use efficiency is a necessary condition to improve water productivity. The overall water use efficiency is the product of conveyance efficiency in the largest and minor irrigation canal systems, multiplied by the application efficiency at the users´ plots. Conveyance efficiency is achieved by measuring the water delivered at the irrigated plots between the amounts of water taken from the sources of supply. These measurements are generally carried out by the personnel operating the irrigation systems. In most of the districts, these measurements are usually carried mandatory to report to the National Water Commission, with a variable precision. However, the water application efficiency in the users´ plots is much more difficult to be done, because the measurement of water consumption by plants is not easy to assess. Indeed, the efficiency in plot irrigation, is the ratio of crop water evapotranspiration between the amounts of water applied, both measurements are difficult to perform. However, in recent years it has been possible to estimate water consumption by crops using satellite imagery. Thus, in this paper, a methodology used in the Mayo River Irrigation District in Sonora, Mexico is shown for the last agricultural cycle 2015-2016 using Landsat 7 and 8 satellite images, with acceptable results. This methodology is based on the PLEIADES project 2007 – 2010.
A cellular automata based model for traffic in congested city

This work targets modeling traffic flow in roads of a congested city. The Cellular Automata (CA) have been configured for such modeling. The urban traffic models [2], in general, concentrate on low traffic density. The inabilities of traditional models to address the issues arise out of heavy traffic in crowded cities of third world countries are properly addressed in the proposed elementary CA based model. The effectiveness of the model is verified considering the traffic in Kolkata. It is established that the model can fairly reproduce various traffic conditions as found empirically. Further, the proposed model succeeds the limitations of traffic flow models in congestion and also reproduces the empirical results.
Systems-Level Comparison of Host-Responses Elicited by Avian H5N1 and Seasonal H1N1 Influenza Viruses in Primary Human Macrophages

Human disease caused by highly pathogenic avian influenza (HPAI) H5N1 can lead to a rapidly progressive viral pneumonia leading to acute respiratory distress syndrome. There is increasing evidence from clinical, animal models and in vitro data, which suggests a role for virus-induced cytokine dysregulation in contributing to the pathogenesis of human H5N1 disease. The key target cells for the virus in the lung are the alveolar epithelium and alveolar macrophages, and we have shown that, compared to seasonal human influenza viruses, equivalent infecting doses of H5N1 viruses markedly up-regulate pro-inflammatory cytokines in both primary cell types in vitro. Whether this H5N1-induced dysregulation of host responses is driven by qualitative (i.e activation of unique host pathways in response to H5N1) or quantitative differences between seasonal influenza viruses is unclear. Here we used microarrays to analyze and compare the gene expression profiles in primary human macrophages at 1, 3, and 6 h after infection with H5N1 virus or low-pathogenic seasonal influenza A (H1N1) virus. We found that host responses to both viruses are qualitatively similar with the activation of nearly identical biological processes and pathways. However, in comparison to seasonal H1N1 virus, H5N1 infection elicits a quantitatively stronger host inflammatory response including type I interferon (IFN) and tumor necrosis factor (TNF)-α genes. A network-based analysis suggests that the synergy between IFN-β and TNF-α results in an enhanced and sustained IFN and pro-inflammatory cytokine response at the early stage of viral infection that may contribute to the viral pathogenesis and this is of relevance to the design of novel therapeutic strategies for H5N1 induced respiratory disease.
Reactive oxygen species, antioxidant mechanisms and serum cytokine levels in cancer patients: impact of an antioxidant treatment.

OBJECTIVE So far, it is not well established whether oxidative stress found in cancer patients results from an increased production of oxidants in the body or from a failure of physiological antioxidant systems. To further investigate this question we have assessed the blood levels of reactive oxygen species as a marker of free radicals producing oxidative stress and the most relevant of the physiological body enzymes counteracting reactive oxygen species, namely glutathione peroxidase and superoxide dismutase. Serum levels of proinflammatory cytokines and IL-2 were also investigated. All these parameters were studied in relation to the clinically most important index of disease progression, namely Performance Status (ECOG PS). We also tested the reducing ability of different antioxidant agents on reactive oxygen species levels by measuring the increase in glutathione peroxidase activity, and the reduction of serum levels of IL-6 and TNF. DESIGN, SETTING AND SUBJECTS We carried out an open non randomized study on 28 advanced stage cancer patients (stage III, 10.7%, and stage IV, 89.3%) with tumours at different (8) sites: all were hospitalized in the Medical Oncology Dept, University of Cagliari Interventions. The patients were divided into 5 groups and a different antioxidant treatment was administered to each group. The selected antioxidants were: alpha lipoic acid 200 mg/day orally, N-acetylcysteine 1800 mg/day i.v. or carboxycysteine-lysine salt 2.7 g/day orally, amifostine 375 mg/day i.v. , reduced glutathione 600 mg/day i.v. , vitamin A 30000 IU/day orally plus vitamin E 70 mg/day orally plus Vitamin C 500 mg/day orally. The antioxidant treatment was administered for 10 consecutive days. RESULTS Our results show that all but one of the antioxidants tested were effective in reducing reactive oxygen species levels and 2 of them (cysteine-containing compounds and amifostine) had the additional effect of increasing glutathione peroxidase activity. Comprehensively, the "antioxidant treatment" was found to have an effect both on reactive oxygen species levels and glutathione peroxidase activity. The antioxidant treatment also reduced serum levels of IL-6 and TNF. Patients in both ECOG PS 0-1 and ECOG PS 2-3 responded to antioxidant treatment.