Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of carbon on whole-biofilm metabolic response to high doses of streptomycin

Biofilms typically exist as complex communities comprising multiple species with the ability to adapt to a variety of harsh conditions. In clinical settings, antibiotic treatments based on planktonic susceptibility tests are often ineffective against biofilm infections. Using a CO2 evolution measurement system we delineated the real-time metabolic response in continuous flow biofilms to streptomycin doses much greater than their planktonic susceptibilities. Stable biofilms from a multispecies culture (containing mainly Pseudomonas aeruginosa and Stenotrophomonas maltophilia), Gram-negative environmental isolates, and biofilms formed by pure culture P. aeruginosa strains PAO1 and PAO1 ΔMexXY (minimum planktonic inhibitory concentrations between 1.5 and 3.5 mg/l), were exposed in separate experiments to 4000 mg/l streptomycin for 4 h after which growth medium resumed. In complex medium, early steady state multispecies biofilms were susceptible to streptomycin exposure, inferred by a cessation of CO2 production. However, multispecies biofilms survived high dose exposures when there was extra carbon in the antibiotic medium, or when they were grown in defined citrate medium. The environmental isolates and PAO1 biofilms showed similar metabolic profiles in response to streptomycin; ceasing CO2 production after initial exposure, with CO2 levels dropping toward baseline levels prior to recovery back to steady state levels, while subsequent antibiotic exposure elicited increased CO2 output. Monitoring biofilm metabolic response in real-time allowed exploration of conditions resulting in vulnerability after antibiotic exposure compared to the resistance displayed following subsequent exposures.
The Pharmacological Chaperone AT2220 Increases the Specific Activity and Lysosomal Delivery of Mutant Acid Alpha-Glucosidase, and Promotes Glycogen Reduction in a Transgenic Mouse Model of Pompe Disease

Pompe disease is an inherited lysosomal storage disorder that results from a deficiency in acid α-glucosidase (GAA) activity due to mutations in the GAA gene. Pompe disease is characterized by accumulation of lysosomal glycogen primarily in heart and skeletal muscles, which leads to progressive muscle weakness. We have shown previously that the small molecule pharmacological chaperone AT2220 (1-deoxynojirimycin hydrochloride, duvoglustat hydrochloride) binds and stabilizes wild-type as well as multiple mutant forms of GAA, and can lead to higher cellular levels of GAA. In this study, we examined the effect of AT2220 on mutant GAA, in vitro and in vivo, with a primary focus on the endoplasmic reticulum (ER)-retained P545L mutant form of human GAA (P545L GAA). AT2220 increased the specific activity of P545L GAA toward both natural (glycogen) and artificial substrates in vitro. Incubation with AT2220 also increased the ER export, lysosomal delivery, proteolytic processing, and stability of P545L GAA. In a new transgenic mouse model of Pompe disease that expresses human P545L on a Gaa knockout background (Tg/KO) and is characterized by reduced GAA activity and elevated glycogen levels in disease-relevant tissues, daily oral administration of AT2220 for 4 weeks resulted in significant and dose-dependent increases in mature lysosomal GAA isoforms and GAA activity in heart and skeletal muscles. Importantly, oral administration of AT2220 also resulted in significant glycogen reduction in disease-relevant tissues. Compared to daily administration, less-frequent AT2220 administration, including repeated cycles of 4 or 5 days with AT2220 followed by 3 or 2 days without drug, respectively, resulted in even greater glycogen reductions. Collectively, these data indicate that AT2220 increases the specific activity, trafficking, and lysosomal stability of P545L GAA, leads to increased levels of mature GAA in lysosomes, and promotes glycogen reduction in situ. As such, AT2220 may warrant further evaluation as a treatment for Pompe disease.
Embodied valuation: Directional action is associated with item values

We have a lifetime of experience interacting with objects we value. Although many economic theories represent valuation as a purely cognitive process independent of the sensorimotor system, embodied cognitive theory suggests that our memories for items’ value should be linked to actions we use to obtain them. Here, we investigated whether the value of real items was associated with specific directional movements toward or away from the body. Participants priced a set of food items to determine their values; they then used directional actions to classify each item as high- or low-value. To determine if value is linked to specific action mappings, movements were referenced either with respect to the object (push toward high-value items; pull away from low-value items) or the self (pull high-value items toward self; push low-value items away). Participants who were assigned (Experiment 1) or chose (Experiment 2) to use an object-referenced action mapping were faster than those using a self-referenced mapping. A control experiment (Experiment 3) using left/right movements found no such difference when action mappings were not toward/away from the body. These results indicate that directional actions toward items are associated with the representation of their value, suggesting an embodied component to economic choice.
Practical Data Hiding in TCP/IP

This work relates the areas of steganography, network protocols and security for practical data hiding in communication networks employing TCP/IP. Two approaches are proposed based on packet header manipulation and packet ordering within the IPSec framework. For the former the Internet protocol IPv4 header is analyzed to identify covert channels by exploiting redundancy and multiple interpretations of protocol strategies; by passing supplementary information through IPv4 headers we demonstrate how security mechanisms can be enhanced in routers, firewalls, and for services such as authentication, audit and logging without considerable additions to software or hardware. For the latter approach, we show the use of packet sorting for steganographic embedding with IPSec can allow for enhanced network security.
Comparison of Geant4 electromagnetic physics models against the NIST reference data

The Geant4 Simulation Toolkit provides an ample set of physics models describing electromagnetic interactions of particles with matter. This paper presents the results of a series of comparisons for the evaluation of Geant4 electromagnetic processes with respect to United States National Institute of Standards and Technologies (NIST) reference data. A statistical analysis was performed to estimate quantitatively the compatibility of Geant4 electromagnetic models with NIST data; the statistical analysis also highlighted the respective strengths of the different Geant4 models.
Peptide-Lipid Interactions: Experiments and Applications

The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining new potent pharmaceutical agents whose biological action is dependent on the binding of peptides to lipid-bilayers. Several issues need to be addressed such as secondary structure, orientation, oligomerization and localization inside the membrane. At the same time, the structural effects which the peptides cause on the lipid bilayer are important for the interactions and need to be elucidated. The structural characterization of membrane active peptides in membranes is a harsh experimental challenge. It is in fact accepted that no single experimental technique can give a complete structural picture of the interaction, but rather a combination of different techniques is necessary.
Harnessing Fluorine–Sulfur Contacts and Multipolar Interactions for the Design of p53 Mutant Y220C Rescue Drugs

Many oncogenic mutants of the tumor suppressor p53 are conformationally unstable, including the frequently occurring Y220C mutant. We have previously developed several small-molecule stabilizers of this mutant. One of these molecules, PhiKan083, 1-(9-ethyl-9H-carbazole-3-yl)-N-methylmethanamine, binds to a mutation-induced surface crevice with a KD = 150 μM, thereby increasing the melting temperature of the protein and slowing its rate of aggregation. Incorporation of fluorine atoms into small molecule ligands can substantially improve binding affinity to their protein targets. We have, therefore, harnessed fluorine–protein interactions to improve the affinity of this ligand. Step-wise introduction of fluorines at the carbazole ethyl anchor, which is deeply buried within the binding site in the Y220C–PhiKan083 complex, led to a 5-fold increase in affinity for a 2,2,2-trifluoroethyl anchor (ligand efficiency of 0.3 kcal mol–1 atom–1). High-resolution crystal structures of the Y220C–ligand complexes combined with quantum chemical calculations revealed favorable interactions of the fluorines with protein backbone carbonyl groups (Leu145 and Trp146) and the sulfur of Cys220 at the mutation site. Affinity gains were, however, only achieved upon trifluorination, despite favorable interactions of the mono- and difluorinated anchors with the binding pocket, indicating a trade-off between energetically favorable protein–fluorine interactions and increased desolvation penalties. Taken together, the optimized carbazole scaffold provides a promising starting point for the development of high-affinity ligands to reactivate the tumor suppressor function of the p53 mutant Y220C in cancer cells.
Off-the-shelf assessment of information ergonomics

Maintaining performance in ubiquitous work environments is increasingly dependent on the quality of physical, cognitive and organizational ergonomics of work. Since most knowledge workers operate in digital work environments, there is a need to elaborate the study of work ergonomics particularly with respect to information ergonomics in the field of human-computer interaction (HCI). The paper introduces the concept of information ergonomics (IE) and operationalizes it by specifying measures to use in studying knowledge work in the field. The empirical data were gathered from 35 participants, including application log data of PC use and heart rate variability data. Based on the empirical findings, the paper also reflects theoretical propositions for the development of IE research. The study contributes to the methodological development of IE research by operationalizing and validating measurement of IE and presents a practical assessment method.
Interaction between BiP and Sec63p is required for the completion of protein translocation into the ER of Saccharomyces cerevisiae

To clarify the roles of Kar2p (BiP) and Sec63p in translocation across the ER membrane in Saccharomyces cerevisiae, we have utilized mutant alleles of the essential genes that encode these proteins: kar2-203 and sec63-1. Sanders et al. (Sanders, S. L., K. M. Whitfield, J. P. Vogel, M. D. Rose, and R. W. Schekman. 1992. Cell. 69:353-365) showed that the translocation defect of the kar2-203 mutant lies in the inability of the precursor protein to complete its transit across the membrane, suggesting that the lumenal hsp70 homologue Kar2p (BiP) binds the transiting polypeptide in order to facilitate its passage through the pore. We now show that mutation of a conserved residue (A181-->T) (Nelson, M. K., T. Kurihara, and P. Silver. 1993. Genetics. 134:159- 173) in the lumenal DnaJ box of Sec63p (sec63-1) results in an in vitro phenotype that mimics the precursor stalling defect of kar2-203. We demonstrate by several criteria that this phenotype results specifically from a defect in the lumenal interaction between Sec63p and BiP: Neither a sec62-1 mutant nor a mutation in the cytosolically exposed domain of Sec63p causes precursor stalling, and interaction of the sec63-1 mutant with the membranebound components of the translocation apparatus is unimpaired. Additionally, dominant KAR2 suppressors of sec63-1 partially relieve the stalling defect. Thus, proper interaction between BiP and Sec63p is necessary to allow the precursor polypeptide to complete its transit across the membrane.
On the usefulness of Meyer wavelets for deconvolution and density estimation

The aim of this paper is to show the usefulness of Meyer wavelets for the classical problem of density estimation and for density deconvolution from noisy observations. By using such wavelets, the computation of the empirical wavelet coefficients relies on the fast Fourier transform of the data and on the fact that Meyer wavelets are band-limited functions. This makes such estimators very simple to compute and this avoids the problem of evaluating wavelets at non-dyadic points which is the main drawback of classical wavelet-based density estimators. Our approach is based on term-by-term thresholding of the empirical wavelet coefficients with random thresholds depending on an estimation of the variance of each coefficient. Such estimators are shown to achieve the same performances of an oracle estimator up to a logarithmic term. These estimators also achieve near-minimax rates of convergence over a large class of Besov spaces. A simulation study is proposed to show the good finite sample performances of the estimator for both problems of direct density estimation and density deconvolution.
Experimental evaluation of the lateral load distribution in the elastic-plastic phase of timber-steel hybrid structures with a novel light timber-steel diaphragm

A cyclic loading experiment involving a timber-steel hybrid structure consisting of a steel frame and a novel light timber-steel diaphragm is presented to quantify the flexibility of the diaphragm and its ability to distribute lateral loads in the elastic-plastic phase of the structure. A lateral load-distribution factor was proposed, and its relationship to the ratio of the stiffness of the diaphragm to that of the lateral load-resisting elements was investigated. The diaphragm was classified based on these variables. The results indicated that the failure modes of the structure were associated with the forms of damage experienced by the lateral load-resisting elements, whereas little damage was observed for the diaphragm. The diaphragm exhibited the ability to continuously adjust the distribution of lateral loads to each lateral load-resisting element; accordingly, each lateral load-resisting element had approximately the same shear force, the same lateral stiffness, and the same lateral displacement during the loading process. As the lateral displacement increased, the stiffness ratio and load-distribution factor both gradually increased, and the diaphragm correspondingly changed from semi-rigid to rigid. At times, as the lateral displacement increased, the diaphragm rapidly became rigid, and it was unnecessarily rigid during the initial loading phase when the in-plane stiffness reached a certain threshold.
Optical 3D Surface Reconstruction by a Multi-Period Phase Shift Method

One problem of classical phase shifting for optical 3D surface reconstruction is the occurrence of ambiguities due to the use of fringe projection. We generally derive a number-theoretical approach to calculate absolute phase measurements which can be used as a base for a reliable surface reconstruction without any ambiguity. The essence of our method is the application of pattern sequences with different periods whereby we homogeneously use all pictures which were taken for the measurement. This leads to a higher average accuracy in the surface reconstruction. Furthermore we propose a technique to avoid typical calculation errors that are produced in classical phase shifting caused by discontinuities, occlusions and reflections on the surface.
Mining and Migrating Interlinear Glossed Text

The World Wide Web is rapidly becoming the primary source for disseminating data on the world’s languages. Language researchers, linguists and language communities are regularly posting a variety of language data to the Web, including lexicons, teaching materials, language recordings and transcriptions, language descriptions, and grammars. Also posted in large quantities are scholarly papers on language, posted regularly by innovative online-only publications (e.g., Snippets), by traditional linguistic publications offering online editions, and by linguists themselves. Of significant potential utility to
MEX vocabulary: a lightweight interchange format for machine learning experiments

Over the last decades many machine learning experiments have been published, giving benefit to the scientific progress. In order to compare machine-learning experiment results with each other and collaborate positively, they need to be performed thoroughly on the same computing environment, using the same sample datasets and algorithm configurations. Besides this, practical experience shows that scientists and engineers tend to have large output data in their experiments, which is both difficult to analyze and archive properly without provenance metadata. However, the Linked Data community still misses a lightweight specification for interchanging machine-learning metadata over different architectures to achieve a higher level of interoperability. In this paper, we address this gap by presenting a novel vocabulary dubbed MEX. We show that MEX provides a prompt method to describe experiments with a special focus on data provenance and fulfills the requirements for a long-term maintenance.
Effect of geometry and green density on the anisotropic sintering shrinkage of axisymmetric iron parts

Sintering shrinkage of prior cold compacted iron rings with different geometry (height to wall thickness ratio) and green density in the 6.5–7.3 g/cm3 range was investigated. It displays a minimum at an intermediate green density. Axial, tangential and radial shrinkages are different, due to the gradients of green density along the axial and the radial directions. Therefore, the effect of height on shrinkage and its anisotropy is the result of their effect on the stress distribution in the green parts during cold compaction, and the resulting green density and deformation experienced by the powder. Anisotropy decreases on increasing shrinkage.
Morphology- and ion size-induced actuation of carbon nanotube architectures

ABSTRACT Future adaptive applications require lightweight and stiff materials with high active strain but low energy consumption. A suitable combination of these properties is offered by carbon nanotube-based actuators. Papers made of carbon nanotubes (CNTs) are charged within an electrolyte, which results in an electrical field forming a double-layer of ions at their surfaces and a deflection of the papers can be detected. Until now, there is no generally accepted theory for the actuation mechanism. This study focuses on the actuation mechanism of CNT papers, which represent architectures of randomly oriented CNTs. The samples are tested electrochemically in an in-plane set-up to detect the free strain. The elastic modulus of the CNT papers is analyzed in a tensile test facility. The influence of various ion sizes of water-based electrolytes is investigated. During the tests, four parameters that have a significant influence on the mechanical performance of CNT papers were identified: the test conditions, the electrical charging, the microstructure and the ion size. All of these influencing factors point to the mechanically weak inter-tube linking at which the actuation seems to take place. Quadratic voltage-strain correlation suggests a combination of electrostatic and volumetric effects as the possible reason for CNT paper actuation. Abbreviations: CNT: carbon nanotubes; CV: cyclic voltammetry; CVD: chemical vapor deposition; HiPCO: high pressure carbon monoxide; IL: ionic liquid; MWCNT: multi-walled carbon nanotube; MW: multi-walled; NHE: normal hydrogen electrode; PDMS: polydimethylsiloxane; PMMA: polymethylmethacrylate; PPy: polypyrrole; PVDF: polyvinylidenefluoride; SCE: saturated calomel electrode; SWCNT: single-walled carbon nanotube; SW: single-walled; 1M: one molar concentration
Practical Parsing of Parallel Multiple Context-Free Grammars

We discuss four previously published parsing algorithms for parallell multiple context-free grammar (PMCFG), and argue that they are similar to each other, and implement an Earley-style top-down algorithm. Starting from one of these algorithms, we derive three modifications ‐ one bottom-up and two variants using a left corner filter. An evaluation shows that substantial improvements can be made by using the algorithm that performs best on a given grammar. The algorithms are implemented in Python and released under an open-source licence.
Validating the Behavioral Equivalence of TTCN-3 Test Cases

Refactoring has been proven as useful means to improve the quality of source code. However, when improperly applied, it may introduce undesired changes to the observable behavior of the software. In this paper, an equivalence checking approach is presented to validate the behavior preservation after the application of refactoring in the domain of test cases specified using the Testing and Test Control Notation Version 3 (TTCN-3). The approach is based on bisimulation and incrementally checks the observable behavior of two test cases at runtime for equivalence. The approach is implemented prototypically and sample experiments are conducted to evaluate the effectiveness of the approach.
Three-component antibacterial membrane of poly(butylene carbonate), poly(lactic acid) and chitosan prepared by electrospinning

ABSTRACT The poly(butylene carbonate) (PBC)/poly(lactic acid) (PLA)/chitosan (CS) blend nanofibre membranes have been prepared by electrospinning. Trifluoroacetic acid was found to be the best co-solvent for PBC/PLA/CS blend. The nanofibre microstructure was studied by scanning electron microscopy and showed good fibre diameter distribution when CS content was 0.08%. As the content of CS increases, the diameter of the fibres became finer. Fourier transform infrared spectrometer shows that there was no chemical reaction between the PBC and PLA, and CS was successfully added to the PBC/PLA. Thermogravimetry analysis indicates that the addition of CS can improve the thermal stability of the PBC/PLA membrane. The PBC/PLA/CS membranes exhibit good improvements in mechanical property. The tensile strength of nanofibres increases with the addition of 0.04% CS but reduces with further addition of 0.12% g CS. The PBC/PLA/CS membranes also have an excellent hydrophilic property. As the amount of CS increases, the contact angle gradually decreases. The PBC/PLA/CS membranes showed high antimicrobial activity against Escherichia coli and Staphylococcus aureus in vitro test.
Image Segmentation Based on Spatially Coherent Gaussian Mixture Model

It has been demonstrated that a finite mixture model (FMM) with Gaussian distribution is a powerful tool in modeling probability density function of image data, with wide applications in computer vision and image analysis. We propose a simple-yet-effective way to enhance robustness of finite mixture models (FMM) by incorporating local spatial constraints. It is natural to make an assumption that the label of an image pixel is influenced by that of its neighboring pixels. We use mean template to represent local spatial constraints. Our algorithm is better than other mixture models based on Markov random fields (MRF) as our method avoids inferring the posterior field distribution and choosing the temperature parameter. We use the expectation maximization (EM) algorithm to optimize all the model parameters. Besides, the proposed algorithm is fully free of empirically adjusted hyperparameters. The idea used in our method can also be adopted to other mixture models. Several experiments on synthetic and real-world images have been conducted to demonstrate effectiveness, efficiency and robustness of the proposed method.