Automatic Network Fingerprinting through Single-Node Motifs

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks.Comment: 16 pages (4 figures) plus supporting information 8 pages (5 figures

Natural variation in immune responses to neonatal mycobacterium bovis bacillus calmette-guerin (BCG) vaccination in a cohort of Gambian infants

Background There is a need for new vaccines for tuberculosis (TB) that protect against adult pulmonary disease in regions where BCG is not effective. However, BCG could remain integral to TB control programmes because neonatal BCG protects against disseminated forms of childhood TB and many new vaccines rely on BCG to prime immunity or are recombinant strains of BCG. Interferon-gamma (IFN-) is required for immunity to mycobacteria and used as a marker of immunity when new vaccines are tested. Although BCG is widely given to neonates IFN- responses to BCG in this age group are poorly described. Characterisation of IFN- responses to BCG is required for interpretation of vaccine immunogenicity study data where BCG is part of the vaccination strategy. Methodology/Principal Findings 236 healthy Gambian babies were vaccinated with M. bovis BCG at birth. IFN-, interleukin (IL)-5 and IL-13 responses to purified protein derivative (PPD), killed Mycobacterium tuberculosis (KMTB), M. tuberculosis short term culture filtrate (STCF) and M. bovis BCG antigen 85 complex (Ag85) were measured in a whole blood assay two months after vaccination. Cytokine responses varied up to 10 log-fold within this population. The majority of infants (89-98% depending on the antigen) made IFN- responses and there was significant correlation between IFN- responses to the different mycobacterial antigens (Spearman’s coefficient ranged from 0.340 to 0.675, p=10-6-10-22). IL-13 and IL-5 responses were generally low and there were more non-responders (33-75%) for these cytokines. Nonetheless, significant correlations were observed for IL-13 and IL-5 responses to different mycobacterial antigens Conclusions/Significance Cytokine responses to mycobacterial antigens in BCG-vaccinated infants are heterogeneous and there is significant inter-individual variation. Further studies in large populations of infants are required to identify the factors that determine variation in IFN- responses

Novel strategies to fight Candida species infection

In recent years, there has been a significant increase in the incidence of human fungal infections. The increase in cases of infection caused by Candida species, and the consequent excessive use of antimicrobials, has favored the emergence of resistance to conventional antifungal agents over the past decades. Consequently, Candida infections morbidity and mortality are also increasing. Therefore, new approaches are needed to improve the outcome of patients suffering from Candida infections, because it seems unlikely that the established standard treatments will drastically lower the morbidity of mucocutaneous Candida infections and the high mortality associated with invasive candidiasis. This review aims to present the last advances in the traditional antifungal therapy, and present an overview of novel strategies that are being explored for the treatment of Candida infections, with a special focus on combined antifungal agents, antifungal therapies with alternative compounds (plant extracts and essential oils), adjuvant immunotherapy, photodynamic therapy and laser therapy.Consolidating Research Expertise and Resources on Cellular and Molecular Biotechnology at CEB/IBB’’, Ref. FCOMP-01-0124-FEDER-027462BioHealth – Biotechnology and Bioengineering approaches to improve health quality’’, Ref. NORTE-07-0124-FEDER-000027 co-funded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER

Study of scattered radiation during fluoroscopy in hip surgery

Objetivo: Medir a intensidade da dose de radiação espalhada em diferentes posições simulando uma intervenção cirúrgica no quadril. Materiais e Métodos: Simulou-se uma intervenção cirúrgica no quadril com apoio da fluoroscopia para estudar a distribuição da radiação espalhada no bloco operatório. Para simular o paciente foi utilizado um simulador antropomórfico de corpo inteiro e para medir a radiação utilizou-se um detector específico para medir raios X. Realizaram-se incidências com um equipamento de raios X tipo arco em C móvel, em modo de escopia contínua, com a ampola a 0° (configuração 1) e a 90° (configuração 2). Os parâmetros operacionais utilizados (voltagem, corrente, tempo de exposição) foram determinados por meio de um estudo estatístico resultante da observação de cirurgias ortopédicas de quadril. Resultados: Em todas as medições observaram-se exposições mais elevadas na configuração 2. Nas medições em função da altura, observaram-se os valores máximos da taxa de dose de 1,167 (± 0,023) µSv/s e 2,278 (± 0,023) µSv/s nas configurações 1 e 2, respectivamente, correspondendo à altura do tórax dos profissionais. No estudo em torno do paciente os valores máximos registraramse na posição ocupada pelo médico cirurgião. Conclusão: Concluiu-se que a exposição à radiação dos profissionais é baixa, podendo ainda ser reduzida mediante o uso de equipamentos de proteção individualObjective: To measure the scattered radiation dose at different positions simulating hip surgery. Materials and Methods: We simulated fluoroscopy-assisted hip surgery in order to study the distribution of scattered radiation in the operating room. To simulate the patient, we used a anthropomorphic whole-body phantom, and we used an X-ray-specific detector to quantify the radiation. Radiographs were obtained with a mobile C-arm X-ray system in continuous scan mode, with the tube at 0° (configuration 1) or 90° (configuration 2). The operating parameters employed (voltage, current, and exposure time) were determined by a statistical analysis based on the observation of orthopedic surgical procedures involving the hip. Results: For all measurements, higher exposures were observed in configuration 2. In the measurements obtained as a function of height, the maximum dose rates observed were 1.167 (± 0.023) µSv/s and 2.278 (± 0.023) µSv/s in configurations 1 and 2, respectively, corresponding to the chest level of health care professionals within the operating room. Proximal to the patient, the maximum values were recorded in the position occupied by the surgeon. Conclusion: We can conclude that, in the scenario under study, health care professionals workers are exposed to low levels of radiation, and that those levels can be reduced through the use of personal protective equipmen

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector

The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV

Analysis of the influence of hydration of the epidermis on the bio-mechanical behaviour of in vivo skin

El comportamiento biomecánico de la piel humana in vivo es un indicador importante de una buena condicióncutánea en lo que es su organización funcional. Los tejidos subyacentes también contribuyen a estas propiedades,lo que imposibilita una evaluación estrictamente biomecánica de este comportamiento. Ocurre además, que lossistemas tecnológicos corrientemente utilizados para este tipo de evaluación in vivo, no permiten obtener la medidadirecta de las características biofísicas del órgano, ya que no es posible cuantificar la contribución relativa de cadatejido para este comportamiento. Las variables y los parámetros obtenidos deben ser, sobre todo, considerados como“descriptores” mecánicos, lo que enfatiza el cuidado especial que hay que tener al interpretar su variación. Tambiénpor este motivo una de las preguntas fundamentales en relación a la contribución relativa de la epidermis a estecomportamiento, sigue aun mal esclarecida.El presente protocolo fue elaborado en este complejo marco para responder, en especial, a esta última cuestión através de dos diferentes tratamientos tópicos susceptibles de modificar el equilibrio hídrico de la epidermis devoluntarios sanos (agua corriente y una solución al 10% de glicerina), registrándose la respectiva respuesta biológica.Los resultados obtenidos sugieren que el comportamiento biomecánico de la piel in vivo puede ser modificadoy eventualmente modulado a través de intervenciones tópicas, proponiendo que la epidermis influencia de hecho elcomportamiento biomecánico global de toda la piel.The Bio-mechanical properties of in vivo human skin are important indicators of a healthy skin condition, with regardto functional organisation. It seems that these properties do not only arise from the cutaneous structures themselves, butalso from the contribution of underlying tissues. Consequently, in the study of its behaviour a purely biomechanicalapproach cannot be taken. Furthermore, the technological systems used the in vivo assessment of these properties,cannot provide a direct measurement of the biophysical characteristics of the organ, due to the fact that it is not possibleto quantitatively identify the relative contribution of each tissue. The variables and parameters obtained as such, shouldtherefore, be considered as mechanical “descriptors”, meaning that greater care should be taken in the interpretationof the results. For this reason, one of the most relevant questions concerning these properties concerns the relativecontribution of the epidermis to the biomechanical behaviour of the entire organ .Facing such multiple complexities, the present protocol was designed to approach this last question. Two differenttreatments (water only and glycerine solution at 10%), inducing epidermal water equilibrium changes, were applied tohealthy volunteers and the respective biological response was recorded. The Results seem to indicate that the mechanicalbehaviour of human skin can be modified and eventually modulated by topical interventions, suggesting that theepidermis may influence the global bio-mechanical behaviour of the entire human skin

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Plectin as a prognostic marker in non-metastatic oral squamous cell carcinoma

Background: Oral squamous cell carcinoma (OSCC) is associated with a poor 5-year survival rate. In general, patients diagnosed with small tumors have a fairly good prognosis, but some small tumors have an aggressive behavior leading to early death. There are at present no reliable prognostic biomarkers for oral cancers. Thus, to optimize treatment for the individual patient, there is a need for biomarkers that can predict tumor behavior. Method: In the present study the potential prognostic value of plectin was evaluated by a tissue microarray (TMA) based immunohistochemical analysis of primary tumor tissue obtained from a North Norwegian cohort of 115 patients diagnosed with OSCC. The expression of plectin was compared with clinicopathological variables and 5 year survival. Results: The statistical analysis revealed that low expression of plectin in the tumor cells predicted a favorable outcome for patients with non-metastatic disease (p = 0.008). Furthermore, the expression of plectin was found to correlate (p = 0.01) with the expression of uPAR, which we have previously found to be a potential prognostic marker for T1N0 tumors. Conclusions: Our results indicate that low expression of plectin predicts a favorable outcome for patients with non-metastatic OSCC and the expression level of plectin may therefore be used in the treatment stratification for patients with early stage disease

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro