Miracle-dz/UniFAR-FTUs huggingface dataset:
The biochemistry of ras p 21

If ever there was a structure in search of a function it is ras p21. Since their discovery as the cellular homologues of the 21 kDa (thus p21) transforming proteins of the Harvey and Kirsten murine sarcoma viruses (H-ras and K-ras), ras proteins have been the subject of exhaustive study to such an extent that we now know their primary structures, three-dimensional structure (to 1.35 A), post-translational modifications, features in common with a number of related polypeptides, subcellular localization, and the mechanism of guanine nucleotide binding and hydrolase (GTPase) activity. The sum of our knowledge, in biochemical and biophysical terms, of p21 is immense and yet its function within the cell remains virtually unknown. It seems an appropriate time, therefore, to take stock of all this accumulated structural data, together with the results of a large number of more biological studies, and see whether they provide any significant clues to the role of p21 in the normal cell as well as to examine how a single amino acid substitution (at one of a very limited number of sites) produces an 'activated' protein which, even though its ability to bind GDP is normally unchanged, is capable of transforming cells in vitro and possibly plays a major part in tumourigenesis in vivo. By analogy with classical Gproteins, Ras polypeptides are considered to be in an active (possibly signal transducing) 'on conformation' in the presence of GTP and 'off' in the presence of GDP. In this Review we have tried to examine these themes, amongst others, and to give an overview of the biochemistry ofmammalian ras p21. We have, however, paid relatively little attention to other related, well-characterized members of the GTPase family (such as elongation factor Tu or the a subunits of heterotrimeric G proteins) or to the RAS proteins in yeast. Readers requiring a more detailed consideration of these aspects are referred to excellent recent reviews by Bourne et al. (1990, 1991) and Broach & Deschenes (1990).
Foodborne listeriosis * WHO WORKING GROUP Listeria monocytogenes

Listeria monocytogenes is widely distributed in the environment and may be transmitted to man through contamination offoodstuffs at anypointfrom source to kitchen. Milk and dairy products, meat, poultry, vegetables, salads and seafoods have all beenfound to be contaminated. Unlike most otherfoodborne pathogens, L. monocytogenes can multiply in refrigerators (4-6 OC). Pasteurization reduces their numbers in raw milk to levels that do not pose an appreciable risk to human health. The infection has relatively low morbidity but a high case fatality. At greatest risk are pregnant women and the unborn child, alcoholics, drug abusers, diabetics, patients receiving treatment which alters their natural immunity, AIDS patients, and the elderly. Surveillance systems in countries should monitor sporadic cases and outbreaks ofhuman listeriosis, with the support of a network of reference laboratories for sero-, phageand otherforms of typing at local, national and international levels. The Working Group made recommendations for action by public health authorities and by the food industry in order to control and prevent these infections.
De l'origine du chien et de sa diffusion à l'aune de sa mythologie

RÉSUMÉ Il est possible, en utilisant des outils phylogénétiques, de reconstruire la façon dont les mythes ayant trait aux chiens se sont diffusés sur la planète, ainsi que leur point d'origine probable. L'arbre construit à partir des motifs mythologiques liés au chien s'enracine entre l'Asie centrale et l'Asie de l'Est. Il montre deux diffusions des motifs en Amérique, la seconde ne touchant que la partie septentrionale du continent. Les motifs semblent avoir suivi les mêmes routes de diffusion que leur objet, ce qui permet de corroborer les acquis de la génétique et de l'archéologie. Par ailleurs, l'approche phylogénétique rend possible l'identification des premiers récits mythologiques liés aux chiens: « Un homme épouse une femme-chien»; « 1/Le chien est le maître, le garde ou le guide vers les terres de la mort ou 2/Les chiens vivent sur la route qui mène aux terres de la mort»; « Des créatures présentent à la fois des caractères humains et canins, le plus souvent un corps d'homme avec une tête de chien»; « Les chiens ou les hommes à tête de chien sont mariés à des femmes humaines» et « Sirius est associé à un chien ou à un loup». Ces reconstructions, également associées aux loups sur l'aire d'origine considérée, permettent d'expliquer, avec un haut degré de probabilité, divers vestiges archéologiques.
The ethics and politics of data sets in the age of machine learning: deleting traces and encountering remains

Individuals and communities increasingly depend on, and fill their lives with, machine cultures, in the form of both interfaces and infrastructures. This global push for machine cultures has given rise to an increasing demand for data and engendered a proliferation of public, private and public-private dataset repositories. While datasets form a foundational element of machine cultures, they rarely come into focus as objects of critical study. But in recent years a critical discursive formation on datasets has begun to emerge, which disturbs the idea of datasets as operational instruments of digital knowledge production and seek to instead ‘bring people back in’. The present article identifies these preliminary explorations as ‘critical dataset studies’ and draws on critical archival studies to articulate the ethico-political surfaced by these studies. Specifically it argues that critical dataset studies shows the need for an expanded ethical and conceptual approach to datasets that not only relies on linear notions of deletion and accountability but also on iterative frameworks of remains and response-ability.
A Bifunctional Enzyme of Legionella that Distinctly Regulates Phosphoribosyl Ubiquitination of the SidE Family Effectors

Legionella pneumophila is a Gram-negative intracellular pathogen that can replicate within freshwater amoeba and mammalian alveolar macrophages. In order to establish an intracellular niche permissive for its replication, Legionella translocates over 300 different effector proteins into the host cytosol via its Dot/Icm secretion system. [1] Among these, members of the SidE effector family (SidE, SdeA, SdeB, and SdeC) regulate multiple cellular processes by a unique phosphoribosyl (PR) ubiquitination mechanism that bypasses the canonical ubiquitination machinery, [1] and two phosphoglycosyl ubiquitin (PR-Ub)-specific deubiquitinases of Legionella (DupA and DupB) could cleave the PR-Ub induced by SidEs from PR-ubiquitinated substrates. The activity of the SidE family is regulated by a calmodulin (CaM)-dependent glutamylase effector of Legionella , named SidJ. Activated SidJ inhibits the adenosine diphosphate (ADP)-ribotransferase activity of SidEs by covalently
Emergence of non-gravitational fields in dimensional reduction of 4d spin foam models

A Kaluza-Klein like approach for a 4d spin foam model is considered. By applying this approach to a model based on group field theory in 4d (TOCY model), and using the Peter-Weyl expansion of the gravitational field, reconstruction of new non gravitational fields and interactions in the action are found. The perturbative expansion of the partition function produces graphs colored with su(2) algebraic data, from which one can reconstruct a 3d simplicial complex representing space-time and its geometry; (like in the Ponzano-Regge formulation of pure 3d quantum gravity) , as well as the Feynman graph for typical matter fields. Thus a mechanism for generation of matter and construction of new dimensions are found from pure gravity.
Fluoridated milk enhances the mineral density of artificial proximal carious lesions in situ

Abstract Objective To compare the mineral density (MD) of non-fluoridated-milk (non-F-milk), fluoridated-milk (F-milk), adjunctive to 1000-ppm-fluoride dentifrice (FD), and 1000-ppm-FD alone of proximal artificial enamel carious lesions (AECL) in high caries-risk patients. Materials and methods This double-blind, cross-over in situ study comprised seven high caries-risk volunteers. Orthodontic brackets with one slab of AECL were fixed randomly to each volunteer per phase. The study comprised three experimental periods with a 7-d wash-out period using FD between sessions; (1) A four-week tooth brushing with FD 2×/day by all subjects as a control. The participants were then randomly allocated to (2) drinking 2.5-ppm-F-milk 1×/day or (3) non-F-milk 1×/day, adjunctive to tooth-brushing with FD for 4-weeks. The subjects crossed over from each type of milk and continued the same protocol for another four weeks. After each phase, the MD of each specimen was analyzed using micro-computed tomography (Micro-CT). Results The baseline MD was not significantly differences (p = .653). When brushing with FD and drinking F-milk, the MD gain was significantly higher (11.68 ± 2.89%) compared with brushing with FD and drinking non-F-milk (4.59 ± 1.78%) (p = .003) or brushing with FD alone (5.30 ± 2.10%) (p = .003). Conclusions F-milk adjunctive to FD significantly increased MD gain compared with non-F-milk + FD or FD alone.
E-cadherin mediated Apical Membrane Initiation Site localisation

Individual cells within de novo polarising tubes and cavities must integrate their forming apical domains into a centralised apical membrane initiation site (AMIS). This is necessary to enable organised lumen formation within multi-cellular tissue. Despite the well documented importance of cell division in localising the AMIS, we have found a division-independent mechanism of AMIS localisation that relies instead on Cadherin-mediated cell-cell adhesion. Our study of de novo polarising mouse embryonic stem cells (mESCs) cultured in 3D suggest that cell-cell adhesion localises apical proteins such as PAR-6 to a centralised AMIS. Unexpectedly, we also found that mESC cell clusters lacking functional E-cadherin still formed a lumen-like cavity in the absence of AMIS localisation but did so at a later stage of development via a ‘closure’ mechanism, instead of via hollowing. This work suggests that there are two, interrelated mechanisms of apical polarity localisation: cell adhesion and cell division. Alignment of these mechanisms in space allows for redundancy in the system and ensures the development of a coherent epithelial structure within a growing organ.
High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance

Background Antibiotic treatments are often associated with a late slowdown in bacterial killing. This separates the killing of bacteria into at least two distinct phases: a quick phase followed by a slower phase, the latter of which is linked to treatment success. Current mechanistic explanations for the in vitro slowdown are either antibiotic persistence or heteroresistance. Persistence is defined as the switching back and forth between susceptible and non-susceptible states, while heteroresistance is defined as the coexistence of bacteria with heterogeneous susceptibilities. Both are also thought to cause a slowdown in the decline of bacterial populations in patients and therefore complicate and prolong antibiotic treatments. Reduced bacterial death rates over time are also observed within tuberculosis patients, yet the mechanistic reasons for this are unknown and therefore the strategies to mitigate them are also unknown. Methods and Findings We analyse a dose ranging trial for rifampicin in tuberculosis patients and show that there is a slowdown in the decline of bacteria. We show that the late phase of bacterial killing depends more on the peak drug concentrations than the total drug exposure. We compare these to pharmacokinetic-pharmacodynamic models of rifampicin heteroresistance and persistence. We find that the observation on the slow phase’s dependence on pharmacokinetic measures, specifically peak concentrations are only compatible with models of heteroresistance and incompatible with models of persistence. The quantitative agreement between heteroresistance models and observations is very good . To corroborate the importance of the slowdown, we validate our results by estimating the time to sputum culture conversion and compare the results to a different dose ranging trial. Conclusions Our findings indicate that higher doses, specifically higher peak concentrations may be used to optimize rifampicin treatments by accelerating bacterial killing in the slow phase. It adds to the growing body of literature supporting higher rifampicin doses for shortening tuberculosis treatments.
SO(DA)2: End-to-end Generation of Specialized Reconfigurable Architectures (Invited Talk)

Modern data analysis applications are complex workflows composed of algorithms with diverse behaviors. They may include digital signal processing, data filtering, reduction, compression, graph algorithms, and machine learning. Their performance is highly dependent on the volume, the velocity, and the structure of the data. They are used in many different domains (from small, embedded devices, to large-scale, high-performance computing systems) but in all cases they need to provide answers with very low latency to enable real-time decision making and autonomy. Coarse-grained reconfigurable arrays (CGRAs), i.e., architectures composed of functional units able to perform complex operations interconnected through a network-on-chip and configure the datapath to map complex kernels, are a promising platform to accelerate these applications thanks to their adaptability. They provide higher flexibility than application-specific integrated circuits (ASICs) while offering increased energy efficiency and faster reconfiguration speed with respect to field-programmable gate arrays (FPGAs). However, designing and specializing CGRAs requires significant efforts. The inherent flexibility of these devices makes the application mapping process equally important to the hardware design generation. To obtain efficient systems, approaches that simultaneously considers software and hardware optimizations are necessary. In this paper, we discuss the Software Defined Architectures for Data Analytics (SO(DA) 2 ) toolchain, an end-to-end hardware/software codesign framework to generate custom reconfigurable architectures for data analytics applications. (SO(DA) 2 ) is composed of a high-level compiler (SODA-OPT) and a hardware generator (OpenCGRA) and can automatically explore and generate optimal CGRA designs starting from high-level programming frameworks. SO(DA) 2 considers partial dynamic reconfiguration as key element of the system design. We discuss the various elements of the framework and demonstrate the flow on the case study of a partial dynamic reconfigurable CGRA design for data streaming applications.
Dual Deep Modeling of Business Processes A Contribution to the Multi-Level Process Challenge

Multi-level modeling (MLM) facilitates conceptual modeling at multiple levels, with clabjects as basic modeling constructs that combine characteristics of metaclasses, classes and objects. Different MLM approaches differ, among others, in the meaning and structure of levels and clabjects, in the strictness or flexibility regarding cross-level relationships, and in the mechanisms for deep characterization by which clabjects at higher levels describe and constrain clabjects at multiple lower levels. The Multi-level Process Challenge provides a testbed for MLM approaches to highlight design decisions regarding these aspects. In this paper we solve the challenge using Dual Deep Modeling (DDM), a MLM approach that features dual potencies which facilitate high flexibility for cross-level relationships. With relationships with dual potencies, a single clabject can play multiple roles at different levels of instantiation, thereby DDM facilitates very compact multi-level models.
Integrability and MHV diagrams

We apply MHV diagrams to the derivation of the one-loop dilatation operator of N = 4 super Yang-Mills in the SO(6) sector. We find that in this approach the calculation reduces to the evaluation of a single MHV diagram in dimensional regularisation. This provides the first application of MHV diagrams to an off-shell quantity. We also discuss other applications of the method and future directions. § {a.brandhuber, b.penante, g.travaglini, d.young}@qmul.ac. uk ar X iv :1 41 2. 10 19 v1 [ he pth ] 2 D ec 2 01 4
Advances in FDTD Computational Electrodynamics: Photonics and Nanotechnology

Subpixel Smoothing of Curved Material Surfaces. Wave Source Conditions and Local Density of States. Perfectly Matched Layers and Adiabatic Absorbers. Plasmonics. Resonant Device Modeling and Design. Metamaterials and Negative Refraction. Transformation Optics. Meep (MIT FDTD Free Software). Biophotonics. Lithography. Computational Microscopy. Spatial Solutions. Quantum Phenomena. Hardware Acceleration.
9.2.3 A Rationale and Framework for Integrating Systems Engineering and Software Engineering

As illustrated in the harmonization of ISO 15288 and ISO 12207, the disciplines of systems engineering and software engineering share many processes, methods, and concerns. In most systems of interest, software now provides a significant majority of functionality and increasingly is a significant component in determining non‐functional attributes. Failures in system acquisition and implementation are often attributed to systems and/or software engineering shortfalls. The need to apply systems engineering to software design and development, as well as the need to incorporate software engineering concepts into systems engineering decisions, implies that a closer relationship between the two disciplines is appropriate. This paper states a clear rationale for integrating the two disciplines, defines a framework that establishes a vocabulary for discussing integration, and presents initial findings in using that framework to describe systems and software integration in ongoing defence programs.
Extraction of Gelatin From Poultry Byproduct: Influence of Drying Method on Structural, Thermal, Functional, and Rheological Characteristics of the Dried Gelatin Powder

The poultry processing industrial wastes are rich sources of gelatin protein, which can be utilized for various industrial sectors. The present investigation was conducted to evaluate the effect of freeze-drying (FD) and hot air drying (HAD) on the physicochemical, structural, thermal, and functional characteristics of chicken feet gelatin. The yield (%) of extracted FD and HAD gelatin was 14.7 and 14.5%, respectively. The gelatin samples showed lower percent transmittance in the UV region. The FTIR bands were at 3,410–3,448 cm−1, 1,635 cm−1, 1,527–334 cm−1, and 1,242–871 cm−1 representing amide-A, amide-I, amide-II, and amide-III bands, respectively. The water activity of HAD was higher (0.43) than in FD (0.21) samples and pH were 5.23 and 5.14 for HAD and FD samples, respectively. The flow index (n) of 6.67% gelatin solutions was 0.104 and 0.418 with consistency coefficient (k) of 37.94 and 31.68 for HAD and FD samples, respectively. The HAD sample shows higher gel strength (276 g) than the FD samples (251 g). The foaming capacity (FC) and foaming stability (FS) of FD samples were 81 and 79.44% compared to 62 and 71.28% for HAD, respectively. The emulsion capacity and emulsion stability of HAD gelatin were higher at 53.47 and 52.66% than FD gelatin. The water holding capacity (WHC) and oil binding capacity (OBC) of FD were lower, that is, 14.3 and 5.34 mL/g compared to HAD gelatin having 14.54 and 6.2 mL/g WHC and OBC, respectively. Hence, the present study indicated that gelatin samples can be utilized in various food products for enhancing functionality and can be used for developing edible packaging materials.
Art and Perception: Using Empirical Aesthetics in Research on Consciousness

Understanding consciousness is a major frontier in the natural sciences. However, given the nuanced and ambiguous sets of conditions regarding how and when consciousness appears to manifest, it is also one of the most elusive topics for investigation. In this context, we argue that research in empirical aesthetics—specifically on the experience of art—holds strong potential for this research area. We suggest that empirical aesthetics of art provides a more exhaustive description of conscious perception than standard laboratory studies or investigations of the less artificial, more ecological perceptual conditions that dominate this research, leading to novel and better suited designs for natural science research on consciousness. Specifically, we discuss whether empirical aesthetics of art could be used for a more adequate picture of an observer’s attributions in the context of conscious perception. We point out that attributions in the course of conscious perception to (distal) objects versus to media (proximal objects) as origins of the contents of consciousness are typically swift and automatic. However, unconventional or novel object-media relations used in art can bring these attributions to the foreground of the observer’s conscious reflection. This is the reason that art may be ideally suited to study human attributions in conscious perception compared to protocols dedicated only to the most common and conventional perceptual abilities observed under standard laboratory or “natural”/ecological conditions alone. We also conclude that art provides an enormous stock of such unconventional and novel object-media relations, allowing more systematic falsification of tentative conclusions about conscious perception versus research protocols covering more conventional (ecological) perception only. We end with an outline of how this research could be carried out in general.
Functional Dissection of Protein Kinases in Sexual Development and Female Receptivity of Drosophila

Protein phosphorylation is crucial for a variety of biological functions, but how it is involved in sexual development and behavior is rarely known. In this study, we performed a screen of RNA interference targeting 177 protein kinases in Drosophila and identified 13 kinases involved in sexual development in one or both sexes. We further identified that PKA and CASK promote female sexual behavior while not affecting female differentiation. Knocking down PKA or CASK in about five pairs of pC1 neurons in the central brain affects the fine projection but not cell number of these pC1 neurons and reduces virgin female receptivity. We also found that PKA and CASK signaling is required acutely during adulthood to promote female sexual behavior. These results reveal candidate kinases required for sexual development and behaviors and provide insights into how kinases would regulate neuronal development and physiology to fine tune the robustness of sexual behaviors.