Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural, Functional, and Bioinformatic Studies Demonstrate the Crucial Role of an Extended Peptide Binding Site for the SH3 Domain of Yeast Abp1p*

SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite Kd values for these peptides ranging from 0.3 to 6 μm. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell.
[Emergence of plasmid-mediated resistance to quinolones in Enterobacteriaceae].

Although quinolone resistance results mostly from chromosomal mutations in Enterobacteriaceae, it may also be mediated by plasmid-encoded Qnr determinants. Qnr proteins protect DNA from quinolone binding and compromise the efficacy of quinolones such as nalidixic acid. Qnr proteins (QnrA-like, QnrB and QnrS) have been identified worldwide with a quite high prevalence among Asian isolates with a frequent association with clavulanic acid inhibited expanded-spectrum beta-lactamases and plasmid-mediated cephalosporinases. The qnrA genes are embedded in complex sul1-type integrons. A very recent identification of the origin of QnrA determinants in the water-borne species Shewanella algae underlines the role of the environment as a reservoir for this emerging threat. It may help to determine the location of in vivo transfer of qnrA genes. Further analysis of the role (if any) of quinolones for enhancing this gene transfer may be conducted. This could prevent the spread, if still possible, of this novel antibiotic resistance mechanism.
Autonomous mobile robots: From conceptualisation to prototyping and real life

This paper describes several concept and development steps of mobile robots towards application in the health care and medical field. First, a basic concept of the Mobile Robot Application Platform (MORAP) will be defined. Based on this basic concept, a “ real” platform has been realised, consisting of various technologies addressing different aspects of application based requirements. The relevant results are composed into an experimental environment. All the components will be described as well as the integration of the selected systems. The potential use of MORAP in health care and medical tasks is presented as well as the current work undertaken with the platform so far.
Mechanisms of neural crest cell migration

Neural crest cells are remarkable in their extensive and stereotypic patterns of migration. The pathways of neural crest migration have been documented by cell marking techniques, including interspecific neural tube grafts, immunocytochemistry and Dil‐labelling. In the trunk, neural crest cells migrate dorsally under the skin or ventrally through the somites, where they move in a segmental fashion through the rostral half of each sclerotome. The segmental migration of neural crest cells appears to be prescribed by the somites, perhaps by an inhibitory cue from the caudal half. Within the rostral sclerotome, neural crest cells fill the available space except for a region around the notochord, suggesting the notochord may inhibit neural crest cells in its vicinity. In the cranial region, antibody perturbation experiments suggest that multiple cell‐matrix interactions are required for proper in vivo migration of neural crest cells. Neural crest cells utilize integrin receptors to bind to a number of extracellular matrix molecules. Substrate selective inhibition of neural crest cell attachment in vitro by integrin antibodies and antisense oligonucleotides has demonstrated that they possess at least three integrins, one being an α1β1 integrin which functions in the absence of divalent cations. Thus, neural crest cells utilize complex sets of interactions which may differ at different axial levels.
B7-H3 and Its Role in Antitumor Immunity

B7-H3 is one of the most recently identified members of the B7/CD28 superfamily of costimulatory molecules serving as an accessory modulator of T-cell response. Recently, B7-H3 expression has been reported in several human cancers indicating an additional function of B7-H3 as a regulator of antitumor immunity. However, its precise physiologic role is still elusive, because both stimulatory and inhibitory capacities have been demonstrated. This paper summarizes the available data on B7-H3 in the regulation of T-cell response focusing on its potential role in antitumor immunity.
Pathogenesis and Diagnosis of Shiga Toxin-Producing Escherichia coli Infections

SUMMARY Since their initial recognition 20 years ago, Shiga toxin-producing Escherichia coli (STEC) strains have emerged as an important cause of serious human gastrointestinal disease, which may result in life-threatening complications such as hemolytic-uremic syndrome. Food-borne outbreaks of STEC disease appear to be increasing and, when mass-produced and mass-distributed foods are concerned, can involve large numbers of people. Development of therapeutic and preventative strategies to combat STEC disease requires a thorough understanding of the mechanisms by which STEC organisms colonize the human intestinal tract and cause local and systemic pathological changes. While our knowledge remains incomplete, recent studies have improved our understanding of these processes, particularly the complex interaction between Shiga toxins and host cells, which is central to the pathogenesis of STEC disease. In addition, several putative accessory virulence factors have been identified and partly characterized. The capacity to limit the scale and severity of STEC disease is also dependent upon rapid and sensitive diagnostic procedures for analysis of human samples and suspect vehicles. The increased application of advanced molecular technologies in clinical laboratories has significantly improved our capacity to diagnose STEC infection early in the course of disease and to detect low levels of environmental contamination. This, in turn, has created a potential window of opportunity for future therapeutic intervention.
Terahertz Technology and Applications: 3D Printing and Art Conservation

Terahertz methods have developed strongly in recent years resulting in an emergence of applications spanning many research fields. This is owing to desirable properties of the terahertz wave; large penetration depths in dielectric materials with nonionisation, coupled with the origin of many physical phenomena, like vibrational modes, occurring at terahertz frequencies. This thesis explores these advantages in two contemporary research areas; 3D printing and art conservation science. 3D printing is shown to be a desirable modality to couple with terahertz techniques with printable dielectric materials allowing for rapid, customisable terahertz components, even with the cheapest and simplest form, fused filament fabrication. Specifically, commercial filament materials are characterised and evaluated in the terahertz regime in conjunction to producing functional components, namely diffractive optics and a hyperuniform waveguide. Terahertz applications in art conservation science are investigated through critical analysis of a series of synthetic and natural pigments. Quinacridone and phthalocyanine, the most important synthetic pigments in red-violet and blue-green shades respectively are shown to have ‘fingerprint’ spectra, with associated temperature dependence. Terahertz photons distinguish polymorphs of these pigments, not achievable with competing modalities using x-rays. Earth-based iron oxide pigments found in many indigenous and culturally significant artefacts also show characteristic, sometimes temperature dependent, absorptions for terahertz frequencies. Strong distinction is shown for natural and synthetic counterparts of the same pigment class with subtle variations in similar pigments from varying geographical origins. Terahertz spectroscopy confirms utility in this research field in identifying optically similar materials, fraud detection in reproductions, dating of artworks and sourcing the geographical origin of culturally significant items.
Reduced Aeration Affects the Expression of the NorB Efflux Pump of Staphylococcus aureus by Posttranslational Modification of MgrA

ABSTRACT We previously showed that at acid pH, the transcription of norB, encoding the NorB efflux pump, increases due to a reduction in the phosphorylation level of MgrA, which in turn leads to a reduction in bacterial killing by moxifloxacin, a substrate of the NorB efflux pump. In this study, we demonstrated that reduced oxygen levels did not affect the transcript levels of mgrA but modified the dimerization of the MgrA protein, which remained mostly in its monomeric form. Under reduced aeration, we also observed a 21.7-fold increase in the norB transcript levels after 60 min of growth that contributed to a 4-fold increase in the MICs of moxifloxacin and sparfloxacin for Staphylococcus aureus RN6390. The relative proportions of MgrA in monomeric and dimeric forms were altered by treatment with H2O2, but incubation of purified MgrA with extracts of cells grown under reduced but not normal aeration prevented MgrA from being converted to its dimeric DNA-binding form. This modification was associated with cleavage of a fragment of the dimerization domain of MgrA without change in MgrA phosphorylation and an increase in transcript levels of genes encoding serine proteases in cells incubated at reduced aeration. Taken together, these data suggest that modification of MgrA by proteases underlies the reversal of its repression of norB and increased resistance to NorB substrates in response to reduced-aeration conditions, illustrating a third mechanism of posttranslational modification, in addition to oxidation and phosphorylation, that modulates the regulatory activities of MgrA.
Otitis-prone Children Have Immunologic Deficiencies in Naturally Acquired Nasopharyngeal Mucosal Antibody Response after Streptococcus pneumoniae Colonization

Objectives: Acute otitis media (AOM) is the most common pediatric bacterial infection, and stringently defined otitis-prone (sOP) children have immunologic deficiencies. We recently found that nasopharyngeal (NP) colonization by Streptococcus pneumoniae (Spn) elicits a NP mucosal antibody response to vaccine candidate pneumococcal proteins that correlate with protection from AOM in non-sOP (NOP) children. Here, we sought to determine if sOP children experience significantly higher colonization rates with Spn than NOP children, develop lower naturally acquired NP mucosal antibody responses to those same pneumococcal proteins after colonization by Spn, and suffer greater frequency of AOM as a consequence. Methods: NP samples were collected from 130 NOP and 45 sOP children during 270 healthy visits and 201 AOM visits between 6 and 24 months of age. Spn were identified by standard culture. NP mucosal IgG and IgA levels to vaccine candidate proteins pneumococcal histidine triad protein D, pneumococcal choline binding protein A (PcpA) and pneumolysin D1 were measured by quantitative enzyme-linked immunosorbent assay. Results: sOP children had significantly higher colonization frequency by Spn (P < 0.0001) and significantly lower IgG and IgA levels to all 3 vaccine candidate proteins studied compared with NOP children (all P values <0.05) except IgG to Ply D1 (P = 0.31). Spn colonization in NOP children led to 2-fold to 5-fold increase in mucosal IgG and IgA levels to all 3 proteins (all P values <0.01), whereas Spn colonization in sOP children generally failed to elicit antibody responses (all P values >0.05). PcpA was unique in inducing significant increases in mucosal IgA (P = 0.02). When high mucosal IgG levels to all 3 proteins and IgA to PcpA were measured, they correlated with reduced AOM in sOP children. Conclusion: sOP children experience significantly higher colonization rates with Spn, develop lower naturally acquired NP mucosal antibody responses to pneumococcal vaccine candidate proteins pneumococcal histidine triad protein D, PcpA and pneumolysin D1 after colonization by Spn, and suffer greater frequency of AOM if they do not generate high mucosal antibody to the studied proteins.
Semantic Networks Generated from Early Linguistic Input

Semantic networks generated from different word corpora show common structural characteristics, including high degrees of clustering, short average path lengths, and scale free degree distributions. Previous research has disagreed about whether these features emerge from internally or externally driven properties (i.e. words already in the lexicon vs. regularities in the external world), mapping onto preferential attachment and preferential acquisition accounts, respectively (Steyvers & Tenenbaum, 2005; Hills, Maouene, Maouene, Sheya, & Smith, 2009). Such accounts suggest that inherent semantic structure shapes new lexical growth. Here we extend previous work by creating semantic networks using the SEEDLingS corpus, a newly collected corpus of linguistic input to infants. Using a recently developed LSA-like approach (GLoVe vectors), we confirm the presence of previously reported structural characteristics, but only in certain ranges of semantic similarity space. Our results confirm the robustness of certain aspects of network organization, and provide novel evidence in support of preferential acquisition accounts.
Learning personalized video highlights from detailed MPEG-7 metadata

We present a new framework for generating personalized video digests from detailed event metadata. In the new approach high level semantic features (e.g., number of offensive events) are extracted from an existing metadata signal using time windows (e.g., features within 16 sec. intervals). Personalized video digests are generated using a supervised learning algorithm which takes as input examples of important/unimportant events. Window-based features are extracted from the metadata and used to train the system and build a classifier that, given metadata for a new video, classifies segments into important and unimportant, according to a specific user, to generate personalized video digests. Our experimental results using soccer video suggest that extracting high level semantic information from existing metadata can be used effectively (80% precision and 85% recall using cross validation) in generating personalized video digests.
Calmodulin in a Heartbeat

Calmodulin is the primary sensor of intracellular calcium (Ca2+) levels in eukaryotic cells playing a key role in the proper deciphering of Ca2+ signalling. Given the versatility of Ca2+ as a secondary messenger, it is not surprising that calmodulin interacts with a vast number of proteins. Calmodulin is an extraordinarily conserved protein, which has not evolved since the genesis of the vertebrate lineage, and further is encoded by three different non‐allelic genes in the human genome. The protein displays a high degree of conformational plasticity, allowing for target proteins to evolve specific modes of calmodulin interaction and regulation during Ca2+ sensing. The recent identification of two calmodulin mutations giving rise to a heart arrhythmia with catecholaminergic polymorphic ventricular tachycardia‐like symptoms and sudden cardiac death in young individuals, and the following identification of another three calmodulin mutations linked to recurrent cardiac arrest in infants, is in many ways intriguing. How can mutations result in cardiac‐specific phenotypes when calmodulin is fundamental for correct Ca2+ signal interpretation in virtually all cells in vertebrate organisms? Are there specific cardiac target protein interactions that are affected by these mutations? Another challenge is to elucidate how one mutated allele out of six encoding an identical calmodulin protein results in a dominant phenotype. Here we aim to give an overview of components in the cardiac contraction cycle whose function is modulated by calmodulin. In principle, these may all be implicated in the pathogenic molecular mechanism linking calmodulin mutations to cardiac arrhythmia and sudden cardiac death.
RoXOR: Re-thinking retransmissions in WiFi

It is widely believed that future small-cell unmanaged wireless networks will be dominated by interference caused by packet collisions and not by signal-to-noise issues. In such a network, a large fraction of the collisions are caused by hidden terminals. Here we present the design and evaluation of RoXOR, a system that can effectively combat random collisions caused by bursty traffic from hidden terminals. RoXOR relies on jointly using both the amount of redundancy and the structure of the redundancy, as expressed by a code. Using these degrees of freedom, we design and experimentally evaluate an iterative rateless code that with high probability achieves better performance as compared to methods such as ZigZag. The mean improvement, as measured by the per packet delay, is 12-18% for values typically used for a 802.11× protocol.
A Computational Paradigm for Three Dimensional Scene Analysis.

Abstract : This paper presents a computational paradigm for a system which will dynamically model the contents of a three dimensional scene. The dynamic scene model may be made available to processes which analyze and interpret the scene as a composition of objects, and processes which plan and execute actions based on the composition of the surfaces or objects in the scene. This computational paradigm is presented as a collection of processes and data structures, many of which are currently areas of active research. The system receives information in the form of a time sequence of stereo images. These images are immediately converted into an initial representation which facilitates the processing of later stages. The initial representation is then passed to a number of independent processes called shape experts. Each shape expert extracts information about three dimensional surfaces from a different source. Surface information is integrated with the information obtained over time to maintain a Composite Surface Model. The Composite Surface Model is then made available to process for planning, analysis, or object recognition. The framework is introduced, and then each of the components are examined. The problems associated with each component are discussed, and a brief description is given of current research in that area.
The neural substrates of mindfulness: An fMRI investigation

“Mindfulness” is a capacity for heightened present-moment awareness that we all possess to a greater or lesser extent. Enhancing this capacity through training has been shown to alleviate stress and promote physical and mental well-being. As a consequence, interest in mindfulness is growing and so is the need to better understand it. This study employed functional magnetic resonance imaging (fMRI) to identify the brain regions involved in state mindfulness and to shed light on its mechanisms of action. Significant signal decreases were observed during mindfulness meditation in midline cortical structures associated with interoception, including bilateral anterior insula, left ventral anterior cingulate cortex, right medial prefrontal cortex, and bilateral precuneus. Significant signal increase was noted in the right posterior cingulate cortex. These findings lend support to the theory that mindfulness achieves its positive outcomes through a process of disidentification.
A implementation of fully integrated frequency synthesizer For ISM band transceiver

A fully integrated frequency synthesizer for ISM band transceiver has to exhibit low phase noise characteristic and small chip size. For the designed frequency synthesizer, the center frequency is 1.2 GHz and linear tuning range of over 450 MHz. To improve the performance of the frequency synthesizer, the phase noise of voltage controlled oscillator is minimized by enhancing Q-factor of the inductor through an inductor design modeling. In addition, an improved charge pump is proposed to minimize non-ideal effect of its performance. The simulation showed the proposed charge pump improved the jitter to 1.5 ns compared with 2.37 ns of the conventional charge pump. The designed circuits have been implemented with 0.18 mum RF CMOS technology.
Parallel Scheduling of Task Trees with Limited Memory

This article investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents some large data. A task can only be executed if all input and output data fit into memory, and a data can only be removed from memory after the completion of the task that uses it as an input data. Such trees arise in the multifrontal method of sparse matrix factorization. The peak memory needed for the processing of the entire tree depends on the execution order of the tasks. With one processor, the objective of the tree traversal is to minimize the required memory. This problem was well studied, and optimal polynomial algorithms were proposed. Here, we extend the problem by considering multiple processors, which is of obvious interest in the application area of matrix factorization. With multiple processors comes the additional objective to minimize the time needed to traverse the tree—that is, to minimize the makespan. Not surprisingly, this problem proves to be much harder than the sequential one. We study the computational complexity of this problem and provide inapproximability results even for unit weight trees. We design a series of practical heuristics achieving different trade-offs between the minimization of peak memory usage and makespan. Some of these heuristics are able to process a tree while keeping the memory usage under a given memory limit. The different heuristics are evaluated in an extensive experimental evaluation using realistic trees.
Classification-Based Predictive Channel Selection for Cognitive Radios

The proposed method classifies traffic patterns of primary channels in cognitive radio systems and applies different prediction rules to different types of traffic. This allows a more accurate prediction of the idle times of primary channels. An intelligent channel selection scheme then uses the prediction results to find the channels with the longest idle times for secondary use. We tested the method with Pareto and exponentially distributed stochastic traffic and with deterministic traffic. The predictive method using past information improves the throughput of the system compared to a system based on instantaneous idle time information. The classification-based predictive method improves the performance compared to pure prediction when the channels of interest include both stochastic and deterministic traffic. The amount of collisions with a primary user can drop 60 % within a given interval compared to a predictive system operating without classification.