gebhart/patrepeval huggingface dataset:
Wild Patterns Reloaded: A Survey of Machine Learning Security against Training Data Poisoning (2022)

The success of machine learning is fueled by the increasing availability of computing power and large training datasets. The training data is used to learn new models or update existing ones, assuming that it is sufficiently representative of the data that will be encountered at test time. This assumption is challenged by the threat of poisoning, an attack that manipulates the training data to compromise the model's performance at test time. Although poisoning has been acknowledged as a relevant threat in industry applications, and a variety of different attacks and defenses have been proposed so far, a complete systematization and critical review of the field is still missing. In this survey, we provide a comprehensive systematization of poisoning attacks and defenses in machine learning, reviewing more than 100 papers published in the field in the last 15 years. We start by categorizing the current threat models and attacks, and then organize existing defenses accordingly. While we focus mostly on computer-vision applications, we argue that our systematization also encompasses state-of-the-art attacks and defenses for other data modalities. Finally, we discuss existing resources for research in poisoning, and shed light on the current limitations and open research questions in this research field.
Ranking Under Uncertainty (2012)

Ranking objects is a simple and natural procedure for organizing data. It is often performed by assigning a quality score to each object according to its relevance to the problem at hand. Ranking is widely used for object selection, when resources are limited and it is necessary to select a subset of most relevant objects for further processing. In real world situations, the object's scores are often calculated from noisy measurements, casting doubt on the ranking reliability. We introduce an analytical method for assessing the influence of noise levels on the ranking reliability. We use two similarity measures for reliability evaluation, Top-K-List overlap and Kendall's tau measure, and show that the former is much more sensitive to noise than the latter. We apply our method to gene selection in a series of microarray experiments of several cancer types. The results indicate that the reliability of the lists obtained from these experiments is very poor, and that experiment sizes which are necessary for attaining reasonably stable Top-K-Lists are much larger than those currently available. Simulations support our analytical results.
Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction (2016)

The engineering of robust protein/nanomaterial interfaces is critical in the development of bioelectrocatalytic systems. We have used computational protein design to identify two amino acid mutations in the small laccase protein (SLAC) from Streptomyces coelicolor to introduce new inter-protein disulfide bonds. The new dimeric interface introduced by these disulfide bonds in combination with the natural trimeric structure drive the self-assembly of SLAC into functional aggregates. The mutations had a minimal effect on kinetic parameters, and the enzymatic assemblies exhibited an increased resistance to irreversible thermal denaturation. The SLAC assemblies were combined with single-walled carbon nanotubes (SWNTs), and explored for use in oxygen reduction electrodes. The incorporation of SWNTs into the SLAC aggregates enabled operation at an elevated temperature and reduced the reaction overpotential. A current density of 1.1 mA/cm(2) at 0 V versus Ag/AgCl was achieved in an air-breathing cathode system. Biotechnol. Bioeng. 2016;113: 2321-2327. © 2016 Wiley Periodicals, Inc.
The nonlinear OPC technique for laser beam control in turbulent atmosphere (2012)

This paper discusses a novel type of beam director for effective laser beacon formation in deep turbulence conditions. The concept of the proposed beam director is based on an innovative approach employing a Brillouin enhanced four-wave mixing (BEFWM) mechanism for generating a tight (small spot size) laser beacon on a remote image-resolved target. The BEFWM technique enables both amplification and total (phase and amplitude) conjugation of the beacon-forming beam without the need for wavefront sensors, deformable mirrors or predictive feedback algorithms. Total conjugation is critical for beam control in the presence of strong turbulence, whereas conventional adaptive optics methods do not have this capability. The phase information retrieved from the beacon beam can be used in conjunction with an AO system to propagate laser beams in deep turbulence.
Paenibacillus koleovorans sp. nov., able to grow on the sheath of Sphaerotilus natans. (2002)

Two bacterial strains that are able to grow specifically on the sheath of a sheathed filamentous bacterium, Sphaerotilus natans, were isolated from soil samples. The sheath-degrading organisms, designated strains TB(T) and TK, are facultatively anaerobic and form endospores. The Gram reaction was negative at all stages of cultivation. The optimum growth temperature and pH were 30 degrees C and pH 7. The DNA G+C content was 54.0-55.8 mol%. MK-7 was the predominant menaquinone and anteiso-C15:0 was the major fatty acid. Phylogenetic analysis based on the 16S rDNA sequences revealed that the isolates were closely related to Paenibacillus chondroitinus, Paenibacillus alginolyticus, Paenibacillus koreensis, Paenibacillus validus, Paenibacillus larvae subsp. larvae and P. larvae subsp. pulvifaciens. The sequences were found to contain consensus sequences characteristic of all Paenibacillus species. The isolates were able to lyse and utilize the purified sheath of S. natans as the sole carbon and energy source. Acid was not produced from common carbon sources, allowing easy distinction from other members of Paenibacillus. It is concluded that the two strains represent a novel Paenibacillus species, for which the name Paenibacillus koleovorans sp. nov. is proposed. The type strain is strain TB(T) (= JCM 11186T = IAM 14926T = KCTC 13912T).
Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism (2020)

The present study attempted a computer simulation of the metabolism of a model cyanobacteria, <i>Synechocystis</i> sp. PCC 6803 (PCC 6803) to predict allosteric inhibitions that are likely to occur in photoautotrophic and mixotrophic conditions as well as in a metabolically engineered strain. PCC 6803 is a promising host for direct biochemical production from CO<sub>2</sub>; however, further investigation of allosteric regulation is required for rational metabolic engineering to produce target compounds. Herein, ensemble modeling of microbial metabolism was applied to build accurate predictive models by synthesizing the results of multiple models with different parameter sets into a single score to identify plausible allosteric inhibitions. The data driven-computer simulation using metabolic flux, enzyme abundance, and metabolite concentration data successfully identified candidates for allosteric inhibition. The enzyme assay experiment using the recombinant protein confirmed isocitrate was a non-competitive inhibitor of phosphoribulokinase as a novel allosteric regulation of cyanobacteria metabolism.
Encapsulation of parallelism and architecture-independence in extensible database query execution (1993)

Emerging database application domains demand not only high functionality, but also high performance. To satisfy these two requirements, the Volcano query execution engine combines the efficient use of parallelism on a wide variety of computer architectures with an extensible set of query processing operators that can be nested into arbitrarily complex query evaluation plans. Volcano's novel exchange operator permits designing, developing, debugging, and tuning data manipulation operators in single-process environments but executing them in various forms of parallelism. The exchange operator shields the data manipulation operators from all parallelism issues. The design and implementation of the generalized exchange operator are examined. The authors justify their decision to support hierarchical architectures and argue that the exchange operator offers a significant advantage for development and maintenance of database query processing software. They discuss the integration of bit vector filtering into the exchange operator paradigm with only minor modifications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fitting behaviors of Fourier transform and Zernike polynomials (2007)

Fourier transform reconstructed ocular wavefront and corneal topographic maps more accurately than Zernike polynomials up to the 10th order. Clinical implications require further study.
Quantitative evaluation of plasma-damaged SiN/Si structures using bias-dependent admittance analysis (2022)

Plasma process-induced damage (PID) to SiN dielectric films was investigated by using an impedance (admittance)-based technique. Multi-layered equivalent circuits were introduced to assign the spatial and energy distribution of defects created in the SiN/Si system. We propose to use admittance as the principal parameter for damaged SiN/Si systems after Ar and He plasma exposures. The change in the border trap density was determined from the admittance in accumulation, whereas the interface state density and energy profile that was created was determined from the admittance in depletion. Plasma source-dependent damage-creation mechanisms are discussed. It was found that the extracted border trap density in the He plasma-damaged sample was larger than that in the Ar plasma-damaged sample under the same ion dosage. The proposed characterization scheme is useful for assessing PID to dielectric/Si systems.
Purification, Characterization, and cDNA Cloning of a Lectin from the MushroomPleurocybella porrigens (2009)

A lectin, PPL, was purified from the mushroom Pleurocybella porrigens. The results of SDS-PAGE, gel filtration, and MALDI-TOF-mass of PPL indicated that its molecular mass was 56 kDa, and it was composed of four 14 kDa subunits with no disulfide bonds. In hemagglutination inhibition assay, PPL exhibited the strongest binding specificity toward GalNAc among the mono- and oligo-saccharides tested. Among the glycoproteins, asialo-bovine submaxillary mucin (asialo-BSM) showed the strongest inhibitory effect. In surface plasmon resonance analysis, asialo-BSM, porcine stomach mucin (PSM), and BSM exhibited potent binding affinity. The complete amino acid sequence was determined by amino acid sequencing of intact and of enzyme-digested PPL. The cDNA of PPL was cloned from RNA extracted from the mushroom. The open reading frame of the cDNA of the protein consisted of 411 bp, encoding 137 amino acids. This is the first report of isolation of a lectin of the genus Pleurocybella.
Barakacin: A Thiazolyl-indole Alkaloid Isolated from a Ruminal Pseudomonas sp. (2012)

A new thiazolyl-indole alkaloid, barakacin (1), has been isolated from the ruminal bacterium Pseudomonas aeruginosa strain ZIO. On the basis of detailed spectroscopic analyses and comparison with the data of related compounds, its structure has been determined as 2-{4-[bis-(1H-indol-3- yl)-methyl]-thiazol-2-yl}-phenol. In addition, the known compounds phenazine-1-carboxylic acid, 3-(hydroxyacetyl)-indole, indole-3-carbaldehyde, and glycolipid A were isolated. The discovery of compounds with a new skeleton emphasizes the importance for exploring new ecological niches like the rumen of bovines for the detection of new natural products. This paper describes the fermentation, isolation, structure elucidation and biological activities of compound 1.
Characterization of two molluscan crystal‐modulating biomineralization proteins and identification of putative mineral binding domains (2003)

Ethylenediamine-tetraacetic acid extracted water-soluble matrix proteins in molluscan shells secreted from the mantle epithelia are believed to control crystal nucleation, morphology, orientation, and phase of the deposited mineral. Previously, atomic force microscopy demonstrated that abalone nacre proteins bind to growing step edges and to specific crystallographic faces of calcite, suggesting that inhibition of calcite growth may be one of the molecular processes required for growth of the less thermodynamically stable aragonite phase. Previous experiments were done with protein mixtures. To elucidate the role of single proteins, we have characterized two proteins isolated from the aragonitic component of nacre of the red abalone, Haliotis rufescens. These proteins, purified by hydrophobic interaction chromatography, are designated AP7 and AP24 (aragonitic protein of molecular weight 7 kDa and 24 kDa, respectively). Degenerate oligonucleotide primers corresponding to N-terminal and internal peptide sequences were used to amplify cDNA clones by a polymerase chain reaction from a mantle cDNA library; the deduced primary amino acid sequences are presented. Preliminary crystal growth experiments demonstrate that protein fractions enriched in AP7 and AP24 produced CaCO(3) crystals with morphology distinct from crystals grown in the presence of the total mixture of soluble aragonite-specific proteins. Peptides corresponding to the first 30 residues of the N-terminal sequences of both AP7 and AP24 were generated. The synthetic peptides frustrate the progression of step edges of a growing calcite surface, indicating that sequence features within the N-termini of AP7 and AP24 include domains that interact with CaCO(3). CD analyses demonstrate that the N-terminal peptide sequences do not possess significant percentages of alpha-helix or beta-strand secondary structure in solution. Instead, in both the presence and absence of Ca(II), the peptides retain unfolded conformations that may facilitate protein-mineral interaction.
Pseudo Identities Based on Fingerprint Characteristics (2008)

This paper presents the integrated project TURBINE which is funded under the EU 7th research framework programme. This research is a multi-disciplinary effort on privacy enhancing technology, combining innovative developments in cryptography and fingerprint recognition. The objective of this project is to provide a breakthrough in electronic authentication for various applications in the physical world and on the Internet. On the one hand it will provide secure identity verification thanks to fingerprint recognition. On the other hand it will reliably protect the biometric data through advanced cryptography technology. In concrete terms, it will provide the assurance that i) the data used for the authentication, generated from the fingerprint, cannot be used to restore the original fingerprint sample, ii) the individual will be able to create different "pseudo-identities" for different applications with the same fingerprint, whilst ensuring that these different identities (and hence the related personal data) cannot be linked to each other, and iii) the individual is enabled to revoke an biometric identifier (pseudo-identity) for a given application in case it should not be used anymore.
Future Wireless Communication Infrastructure with Application to Emergency Scenarios (2007)

Establishing and accessing a reliable communication infrastructure at crisis site is a challenging research problem. Failure in communication infrastructure and information exchange impedes the early response efforts resulting in huge loss of lives and economical impacts. Reliability, robustness, interoperability and minimum interdependencies are specific requirements of communication technology within the context of emergency applications. We present the real measurements obtained over the deployment of a quickly configurable and easily reconfigurable wireless mesh test bed at disaster site. This is followed by an analytical discussion of the important observations concerning the factors that impact performance or cause bottlenecks.
Monocarboxylate transporter expression at the onset of skeletal muscle regeneration (2013)

The onset of skeletal muscle regeneration is characterized by proliferating myoblasts. Proliferating myoblasts have an increased energy demand and lactate exchange across the sarcolemma can be used to address this increased demand. Monocarboxylate transporters (MCTs) are involved in lactate transport across the sarcolemma and are known to be affected by various physiological stimuli. However, MCT expression at the onset of skeletal muscle regeneration has not been determined. The purpose of this study was to determine if skeletal muscle regeneration altered MCT expression in regenerating tibialis anterior (TA) muscle. Male C57/BL6 mice were randomly assigned to either a control (uninjured) or bupivacaine (injured) group. Three days post injection, the TA was extracted for determination of protein and gene expression. A 21% decrease in muscle mass to tibia length (2.4 ± 0.1 mg/mm vs. 1.9 ± 0.2 mg/mm, P < 0.02) was observed. IGF-1 and MyoD gene expression increased 5.0-fold (P < 0.05) and 3.5-fold (P < 0.05), respectively, 3 days post bupivacaine injection. MCT-1 protein was decreased 32% (P < 0.03); however, MCT-1 gene expression was not altered. There was no difference in MCT4 protein or gene expression. Lactate dehydrogenase (LDH)-A protein expression increased 71% (P < 0.0004). Protein levels of LDH-B and mitochondrial enzyme cytochrome C oxidase subunit decreased 3 days post bupivacaine injection. CD147 and PKC-θ protein increased 64% (P < 0.03) and 79% (P < 0.02), respectively. MCT1 but not MCT4 expression is altered at the onset of skeletal muscle regeneration possibly in an attempt to regulate lactate uptake and use by skeletal muscle cells.
Acoustic direction of arrival estimation, a comparison between root-music and SRP-PHAT (2004)

Conference and video telephony, home automation and Surveillance appliances use microphone arrays for localization of sound sources. It is therefore of interest to study different algorithms with respect to implementation and performance in real environments. Three algorithms have been employed in this study: Coherent Wideband Root-MUSIC and near-field and far-field versions of an algorithm based on Steered Response Power - Phase Transform. Results show that Root- MUSIC is the most computationally efficient. However due to simplistic model assumptions it fails in highly reverberant environments. The two algorithms employing Steered Response Power - Phase Transform maintain good performance measures even under reverberant conditions and low signal to noise ratios.
Catheter Ablation of Mitral Isthmus Ventricular Tachycardia Using Electroanatomically Guided Linear Lesions (2000)

Mitral isthmus ventricular tachycardia uses a reentrant circuit with a critical isthmus of conduction bounded by the mitral valve proximally and a remote inferior infarction scar distally. Successful catheter ablation requires placement of a lesion to transect the isthmus so as to prevent wavefront propagation. We report a case with previously unsuccessful ablation in which focal isthmus ablation failed to eliminate arrhythmia. Electroanatomic mapping demonstrated a wide tachycardia isthmus, and a linear lesion placed from the edge of the inferior infarct (as demonstrated on the three-dimensional voltage electroanatomic map) to the base of the mitral valve successfully eliminated tachycardia. In some patients with mitral isthmus VT, a wide isthmus requires linear lesion placement to fully transect the isthmus and eliminate tachycardia. Electroanatomic mapping can be used to define isthmus boundaries and thus guide successful ablation.
Embelin inhibits TNF-α converting enzyme and cancer cell metastasis: molecular dynamics and experimental evidence (2014)

Based on the molecular dynamics and experimental data, embelin is proposed as a natural anti-inflammatory and anticancer drug.
Safety, anxiety and natalizumab continuation in JC virus-seropositive MS patients (2013)

The use of natalizumab in multiple sclerosis has been restricted by the risk of progressive multifocal leukoencephalopathy (PML). JC virus carriership, duration of natalizumab treatment and past immunosuppression are known risk factors. This has allowed for calculated risk assessment for individual patients to be implemented. Not much data are available about the effect of JCV carriership on patient willingness to continue natalizumab. Here, we evaluated the impact of JCV seropositivity on safety feelings, anxiety and treatment continuation for patients treated with natalizumab, using a visual analog scale, the Hospital Anxiety and Depression Scale and a decisional conflict scale. Seropositivity led to an elevated anxiety level for PML (p = 0.004). However, so far only 3% of patients have discontinued natalizumab because of JCV positivity in our cohort.
Expression of Epstein-Barr virus genes in different cell types after microinjection of viral DNA. (1980)

Gene expression of Epstein-Barr virus (EBV) was studied after microinjection of viral DNA into different types of cells. Raji TK- cells, known to express viral gene functions after superinfection with the EBV-P3HR-1 virus strain, were attached to plastic dishes by using anti-lymphocyte IgG, phytohemagglutinin, or concanavalin A as a ligand. It was difficult to inject DNA into the small and fragile Raji cells. After formation of polykaryons by cell fusion, microinjection became more efficient. At 24 hr after injection of P3HR-1 virus DNA, 90-100% of the injected cells expressed the early antigen complex as observed by immunofluorescence staining; 70-80% of the cells simultaneously incorported [3H]thymidine, indicating that thymidine kinase is expressed after injection of viral DNA. Additionally, synthesis of the virus capsid antigen was demonstrated in 20-30% of the recipient Raji cells. Human diploid fibroblasts, African green monkey kidney cells, and rat fibroblasts, which do not represent natural target cells for EBV, could also be induced to synthesis of early antigen complex by injection of P3HR-1 virus DNA.
Organo-Lewis acids of enhanced utility, uses thereof, and products based thereon (2023)

The organo-Lewis acids are novel triarylboranes which are highly fluorinated. Triarylboranes of one such type contain at least one ring substituent other than fluorine. These organoboranes have a Lewis acid strength essentially equal to or greater than that of the corresponding organoborane in which the substituent is replaced by fluorine, or have greater solubility in organic solvents. Another type of new organoboranes have 1-3 perfluorinated fused ring groups and 2-0 perfluorophenyl groups. When used as a cocatalyst in the formation of novel catalytic complexes with d- or f-block metal compounds having at least one leaving group such as a methyl group, these triorganoboranes, because of their ligand abstracting properties, produce corresponding anions which are capable of only weakly, if at all, coordinating to the metal center, and thus do not interfere in various polymerization processes such as are described.