Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-induced Conformational Change*

Surfactant protein A (SP-A), a C-type lectin, plays an important role in innate lung host defense against inhaled pathogens. Crystallographic SP-A·ligand complexes have not been reported to date, limiting available molecular information about SP-A interactions with microbial surface components. This study describes crystal structures of calcium-dependent complexes of the C-terminal neck and carbohydrate recognition domain of SP-A with d-mannose, d-α-methylmannose, and glycerol, which represent subdomains of glycans on pathogen surfaces. Comparison of these complexes with the unliganded SP-A neck and carbohydrate recognition domain revealed an unexpected ligand-associated conformational change in the loop region surrounding the lectin site, one not previously reported for the lectin homologs SP-D and mannan-binding lectin. The net result of the conformational change is that the SP-A lectin site and the surrounding loop region become more compact. The Glu-202 side chain of unliganded SP-A extends out into the solvent and away from the calcium ion; however, in the complexes, the Glu-202 side chain translocates 12.8 Å to bind the calcium. The availability of Glu-202, together with positional changes involving water molecules, creates a more favorable hydrogen bonding environment for carbohydrate ligands. The Lys-203 side chain reorients as well, extending outward into the solvent in the complexes, thereby opening up a small cation-friendly cavity occupied by a sodium ion. Binding of this cation brings the large loop, which forms one wall of the lectin site, and the adjacent small loop closer together. The ability to undergo conformational changes may help SP-A adapt to different ligand classes, including microbial glycolipids and surfactant lipids.
Food Reformulation, Responsive Regulation, and “Regulatory Scaffolding”: Strengthening Performance of Salt Reduction Programs in Australia and the United Kingdom

Strategies to reduce excess salt consumption play an important role in preventing cardiovascular disease, which is the largest contributor to global mortality from non-communicable diseases. In many countries, voluntary food reformulation programs seek to reduce salt levels across selected product categories, guided by aspirational targets to be achieved progressively over time. This paper evaluates the industry-led salt reduction programs that operate in the United Kingdom and Australia. Drawing on theoretical concepts from the field of regulatory studies, we propose a step-wise or “responsive” approach that introduces regulatory “scaffolds” to progressively increase levels of government oversight and control in response to industry inaction or under-performance. Our model makes full use of the food industry’s willingness to reduce salt levels in products to meet reformulation targets, but recognizes that governments remain accountable for addressing major diet-related health risks. Creative regulatory strategies can assist governments to fulfill their public health obligations, including in circumstances where there are political barriers to direct, statutory regulation of the food industry.
Prevalence and Characterization of Virulence Genes Toxin-producing Escherichia coli Enterohemorragic 0157:H7 Strain Isolated from Frozen Imported Bovine Meat in Algeria

The presence of E. coli enterohemorragic O157:H7 was inspected in 756 samples of frozen bovine meat imported from different countries, Argentina, Australia, Brazil, Ireland and Uruguay, using the microbiological standard method of culture and serotyping technique. The pathogen strain of E. coli was detected in five samples (0.66 %). All the isolates were tested using the method of KIRBY and BAUER according to the nccls standards to view resistance to antibiotics and was considered sensitive to the sixteen antimicrobial agents tested. All isolates were further characterized by serotyping and molecular methodology. The PCR technique showed that all the strains carried the stx2 and the ehxA genes 1 isolate carried stx1 genes, 1 both stx1 and stx 2. Intimin ( eae c) virulence genes were detected in 4 isolates. The interaction with lactic acid bacteria revealed that all E. coli O157:H7 isolates were inhibited.
Confocal Microscopy, Computer Modeling, and Quantification of Glomerular Vascular Corrosion Casts

Corrosion-casted capillary systems of the kidney glomerulus were imaged with confocal microscopy because of the fluorescence properties of the casting plastic. Acquisition of a z-series through the glomerular capillaries provided three-dimensional data sets from which surface-rendered models were generated. These models could be rotated and viewed from any angle and also contained quantitative information allowing cast surface area and volume measurements to be calculated. The computer-generated models were also skeletonized to form a one-voxel-thick skeleton of the original model. The skeleton exhibited the three-dimensional topology and network of the capillary bed, and interior capillary relations could also be viewed. Quantitative information such as the total capillary length and number of capillary intersects was calculated from the skeletonized model. Extending this method to noncorroded kidney specimens revealed not only the casted vessels but also cellular features of the adjacent tissues surrounding the capillaries.
Improved Knowledge Base Completion by Path-Augmented TransR Model

Knowledge base completion aims to infer new relations from existing information. In this paper, we propose path-augmented TransR (PTransR) model to improve the accuracy of link prediction. In our approach, we base PTransR model on TransR, which is the best one-hop model at present. Then we regularize TransR with information of relation paths. In our experiment, we evaluate PTransR on the task of entity prediction. Experimental results show that PTransR outperforms previous models.
Evidence for treating rheumatoid arthritis to target: results of a systematic literature search update

Objective A systematic literature review (SLR; 2009–2014) to compare a target-oriented approach with routine management in the treatment of rheumatoid arthritis (RA) to allow an update of the treat-to-target recommendations. Methods Two SLRs focused on clinical trials employing a treatment approach targeting a specific clinical outcome were performed. In addition to testing clinical, functional and/or structural changes as endpoints, comorbidities, cardiovascular risk, work productivity and education as well as patient self-assessment were investigated. The searches covered MEDLINE, EMBASE, Cochrane databases and Clinicaltrial.gov for the period between 2009 and 2012 and separately for the period of 2012 to May of 2014. Results Of 8442 citations retrieved in the two SLRs, 176 articles underwent full-text review. According to predefined inclusion/exclusion criteria, six articles were included of which five showed superiority of a targeted treatment approach aiming at least at low-disease activity versus routine care; in addition, publications providing supportive evidence were also incorporated that aside from expanding the evidence provided by the above six publications allowed concluding that a target-oriented approach leads to less comorbidities and cardiovascular risk and better work productivity than conventional care. Conclusions The current study expands the evidence that targeting low-disease activity or remission in the management of RA conveys better outcomes than routine care.
Analysis and Evaluation of Random Placement Strategies in Wireless Sensor Networks

Wireless sensor networks (WSNs) are an attractive choice for many applications where sensors are densely and efficiently deployed in an area of interest. For example, in surveillance applications, where deterministic placement is not applicable, the sensors have to be randomly deployed entirely or partially in an area. Whether random or deterministic, the strategy of deploying the sensors has a large impact on the performance of WSNs. In this paper, we propose a systematic methodology for sensors placement based on several random distributions. The quality of deployment is evaluated using a set of proposed measures, the significance of which highly depends on the WSN application. The impact of these deployment strategies on the network performance is thoroughly studied. Moreover, we propose a new hybrid deployment strategy that aims to achieve the best performance based on the suggested deployment quality measures. Both the placement strategies with the deployment quality measures are evaluated using exte.
Urogenital disorders associated with oestrogen deficiency: the role of promestriene as topical oestrogen therapy

Urogenital disorders associated with oestrogen deficiency affect many women throughout menopausal transition. Symptoms such as vaginal dryness, burning, pruritus, dyspareunia, urinary tract urgency/frequency and incontinence have a significant impact on the individual's quality of life. For younger and healthy menopausal women, systemic oestrogen replacement may improve both vasomotor and urogenital symptoms and will be the treatment of choice. However, a proportion of women on systemic therapy still experience symptoms associated with urogenital atrophy, and patients with oestrogen-dependent cancers may be at risk from systemic oestrogen replacement. For women with mainly urogenital symptoms, local oestrogen is a logical choice and it is often more effective than systemic hormone replacement therapy. Generally speaking, there are no contraindications to local therapy. In terms of which topical preparation to use, a wide range of products are available. Promestriene is an analogue of oestradiol which is minimally absorbed and it has been shown to be effective in reversing atrophic changes caused by oestrogen deficiency in women undergoing natural or surgically induced menopause. Given the absence of systemic activity, promestriene may be a good choice in women requiring purely locally oestrogen, and those who have survived, or who are at risk of breast cancer and who have severe vulvo-vaginal symptoms.
Induction of hepatocyte growth factor expression by maleic acid in human fibroblasts through MAPK activation

Carboxylic acids have various biological activities and play critical roles in cellular metabolic pathways such as the tricarboxylic acid (TCA) cycle. It has been shown that some carboxylic acids induce cell proliferation and production of cytokines or growth factors. However, there have been no reports on effects of carboxylic acids on hepatocyte growth factor (HGF) expression. In this study, we found that only maleic acid among various carboxylic acids examined markedly induced HGF production from human dermal fibroblasts. Maleic acid also induced HGF production from human lung fibroblasts and neuroblastoma cells. The stimulatory effect was accompanied by upregulation of HGF gene expression. Increase in phosphorylation of extracellular signal‐regulated protein kinase (ERK) and c‐Jun N‐terminal kinase (JNK) but not in phosphorylation of p38 was observed from 6 h and up to 24 h after maleic acid addition. The ERK kinase inhibitor PD98059 and the JNK inhibitor SP600125 potently inhibited maleic acid‐induced HGF production, while the p38 inhibitor SB203580 did not significantly inhibit the production. The protein synthesis inhibitor cycloheximide completely inhibited upregulation of HGF mRNA induced by maleic acid but superinduced HGF mRNA expression upregulated by 12‐O‐tetradecanoylphorbol 13‐acetate (TPA). These results suggest that maleic acid indirectly induced HGF expression from human dermal fibroblasts through activation of ERK and JNK and that de novo protein synthesis is required for maleic acid‐induced upregulation of HGF mRNA. J. Cell. Biochem. 104: 1465–1476, 2008. © 2008 Wiley‐Liss, Inc.
Edinburgh Research Explorer Revealing Novel-Strain-Specific and Shared Epitopes of Infectious Bronchitis Virus Spike Glycoprotein Using Chemical Linkage of Peptides onto Scaffolds Precision Epitope Mapping

: The avian coronavirus, infectious bronchitis virus (IBV), is an economically important infectious disease affecting chickens, with a diverse range of serotypes found globally. The major surface protein, spike (S), has high diversity between serotypes, and amino acid differences in the S1 sub-unit are thought to be responsible for poor cross-protection afforded by vaccination. Here, we attempt to address this, by using epitope mapping technology to identify shared and serotype-speciﬁc immunogenic epitopes of the S glycoprotein of three major circulating strains of IBV, M41, QX, and 4/91, via CLIPS peptide arrays based on peptides from the S1 sub-units. The arrays were screened with sera from chickens immunised with recombinant IBV, based on Beau-R backbone expressing heterologous S, generated in two independent vaccination/challenge trials. The screening of sera from rIBV vaccination experiments led to the identiﬁcation of 52 immunogenic epitopes on the S1 of M41, QX, and 4/91. The epitopes were assigned into six overlapping epitope binding regions. Based on accessibility and location in the hypervariable regions of S, three sequences, 25 YVYYYQSAFRPPNGWHLQGGAYAVVNSTN 54 , 67 TVGVIKDVYNQSVASI 82 , and 83 AMTVPPAGMSWSVS 96 , were selected for further investigation, and synthetic peptide mimics were recognised by polyclonal sera. These epitopes may have the potential to contribute towards a broader cross-protective IBV vaccine.
The Role of Body Image in the Relationship Between Internet Use and Bulimic Symptoms: Three Theoretical Frameworks

Exposure to traditional media has been associated with bulimic symptoms. However, to date, little is known regarding the effects of Internet exposure. The aim of this study was to explore the relationships between Internet use and bulimic symptoms within the competing frameworks of sociocultural, impression management, and self-objectification theory. A sample of 289 French women aged 18-25 years completed an online questionnaire assessing bulimic symptoms, body dissatisfaction, body image avoidance, self-surveillance, body shame, and weekly Internet use. Bootstrapping analyses revealed that body shame and body image avoidance mediated the effect of weekly Internet use on bulimic symptoms. Furthermore, when entered into a multiple mediation analysis, these two variables provided independent mediation pathways of equal magnitude. The findings support the usefulness of both the self-objectification and impression management frameworks for investigating the relationship between Internet use and bulimic symptoms. Longitudinal research would help to clarify these pathways further.
A simple and flexible activity-based simulation for Belgium

The VirtualBelgium project aims at developing understanding of the evolution of the Belgian population using agent-based simulations and considering various aspects of this evolution such as demographics, residential choices, activity patterns, mobility, etc. This simulation is based on a validated synthetic population consisting of approximately 10,000,000 individuals and 4,350,000 households localized in the 589 municipalities of Belgium. The work presented in this paper focuses only on the mobility behaviour, simulated using an activitybased approach in which the travel demand is derived from the activities performed by the individuals. The proposed model is distribution based and requires only minimal information, but is designed for easily taking advantage of any additional network-related data available. The proposed activity-based has been applied on the Belgian synthetic population. The quality of the agent behaviour is discussed using statistical criteria extracted from the literature and it is shown that VirtualBelgium produces satisfactory results.
Initial Results From European Road Safety Inspection (eursi) Mobile Mapping Project

Mobile mapping systems are becoming a popular method for collecting high quality near 3D information of terrestrial scenes. Modern mobile mapping systems can produce millions of georeferenced points per minute. These can be used to gather quantitative information about surfaces and objects. With this geospatial data it is becoming possible to segment and extract the road surface. In this paper, we will detail a novel LIDAR based road edge extraction algorithm which is applicable to both urban and rural road sections.
Designing care: towards a permanent resilience of the city

In contemporary cities, natural and industrial risks are accompanied by an environmental risk (climatic, pollution.) that affects the most vulnerable populations. Designing care allows promoting permanent resilience which can mitigate the effects of these environmental risks. Designing care, the resilience is not only a process of recognition and regeneration built a posteriori, but a permanent awareness of the complexity of contemporary urbanity. This topic is based on research carried out between 2013 and 2017 in a sector of the 5th arrondissement of Paris. This urban laboratory has made it possible to construct a system of projects, by scaling and rescaling their effects in the urban life. These projects help to build a constant and multi-partnership resilience.
Trajectory anonymity in publishing personal mobility data

Recent years have witnessed pervasive use of location-aware devices such as GSM mobile phones, GPS-enabled PDAs, location sensors, and active RFID tags. The use of these devices generates a huge collection of spatio-temporal data, variously called moving object data, trajectory data, or moblity data. These data can be used for various data analysis purposes such as city traffic control, mobility management, urban planning, and location-based service advertisements. Clearly, the spatio-temporal data so collected may help an attacker to discover personal and sensitive information like user habits, social customs, religious and sexual preferences of individuals. Consequently, it raises serious concerns about privacy. Simply replacing users' real identifiers (name, SSN, etc.) with pseudonyms is insufficient to guarantee anonymity. The problem is that due to the existence of quasi-identifiers, i.e., spatio-temporal data points that can be linked to external information to re-identify individuals, the attacker may be able to trace the anonymous spatio-temporal data back to individuals. In this survey, we discuss recent advancement on anonymity preserving data publishing of moving object databases in an off-line fashion. We first introduce several anonymity models, then we describe in detail some of the proposed techniques to enforce trajectory anonymity, discussing their merits and limitations. We conclude by identifying challenging open problems that need attention.
DETECTION AND RECOGN I TION OF TRAFFIC SIGNS FROM DATA COLLECTED BY THE MOBILE MAPPING SYSTEM

: Autonomous vehicles and high-resolution maps are key elements of future transport systems. Detection and recognition of traffic signs is an important element for the safe driving of autonomous vehicles and the development of high-resolution maps. In this study, it is aimed to accurately detect and identify traffic signs based on the data collected by the mobile mapping system in order to ensure the safe movement of autonomous vehicles in traffic. A low-cost method is proposed with the ResNet-50 model for an autonomous vehicle to automatically detect and recognise traffic signs while moving on the road. As a result of the model training, 0.99 accuracy and 0.016 loss were obtained. The success of the method was first observed on images randomly selected from the dataset. Then, a real-time test was performed on a low-cost webcam. The tests showed that the handled method detects and identifies the traffic sign quickly and accurately
Honey for Wound Healing, Ulcers, and Burns; Data Supporting Its Use in Clinical Practice

The widespread existence of unhealed wounds, ulcers, and burns has a great impact on public health and economy. Many interventions, including new medications and technologies, are being used to help achieve significant wound healing and to eliminate infections. Therefore, to find an intervention that has both therapeutic effect on the healing process and the ability to kill microbes is of great value. Honey is a natural product that has been recently introduced in modern medical practice. Honey's antibacterial properties and its effects on wound healing have been thoroughly investigated. Laboratory studies and clinical trials have shown that honey is an effective broad-spectrum antibacterial agent. This paper reviews data that support the effectiveness of natural honey in wound healing and its ability to sterilize infected wounds. Studies on the therapeutic effects of honey collected in different geographical areas on skin wounds, skin and gastric ulcers, and burns are reviewed and mechanisms of action are discussed. (Ulcers and burns are included as an example of challenging wounds.) The data show that the wound healing properties of honey include stimulation of tissue growth, enhanced epithelialization, and minimized scar formation. These effects are ascribed to honey's acidity, hydrogen peroxide content, osmotic effect, nutritional and antioxidant contents, stimulation of immunity, and to unidentified compounds. Prostaglandins and nitric oxide play a major role in inflammation, microbial killing, and the healing process. Honey was found to lower prostaglandin levels and elevate nitric oxide end products. These properties might help to explain some biological and therapeutic properties of honey, particularly as an antibacterial agent or wound healer. The data presented here demonstrate that honeys from different geographical areas have considerable therapeutic effects on chronic wounds, ulcers, and burns. The results encourage the use of honey in clinical practice as a natural and safe wound healer.
Anti‐inflammatory properties of dairy lactobacilli

Background: The intestinal microbiota plays an important role in human health through the modulation of innate immune responses. While selected commensal bacteria are marketed in specific probiotic products to control these responses, relatively little is known about the immune modulation potential of dairy bacteria that have principally been selected for their fermentation properties. The modulation of innate immune responses may reduce chronic inflammation in inflammatory bowel diseases like ulcerative colitis. Methods: A collection of dairy Lactobacillus delbrueckii strains was screened for immune modulation effects in vitro through the quantification of nuclear factor kappa B (NF‐&kgr;B) activation in a human intestinal epithelial cell line. Selected bacterial strains were then tested in vivo in a mouse dextran sodium sulfate (DSS) colitis model. Results: All L. delbrueckii strains tested showed anti‐inflammatory effects in vitro, to an extent that varied between strains. These effects rely on bacterial surface exposed proteins and affect the central part of the NF‐&kgr;B activation pathway. One of the selected strains significantly reduced the macroscopic and microscopic symptoms of DSS‐induced colitis in the mouse intestinal tract, diminished body weight loss, and improved survival. Conclusions: The results of this study show that dairy lactobacilli that often are part of a regular diet can modulate innate immune responses, and may thus affect health more than generally thought. One of the strains tested alleviated the symptoms of DSS‐induced colitis in mice, a model of human ulcerative colitis. (Inflamm Bowel Dis 2011;)