An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.

Half tetrad analysis in alfalfa using multiple restriction fragment length polymorphism markers.

A maximum likelihood approach of half tetrad analysis (HTA) based on multiple restriction fragment length polymorphism (RFLP) markers was developed. This procedure estimates the relative frequencies of 2n gametes produced by mechanisms genetically equivalent to first division restitution (FDR) or second division restitution and simultaneously locates the centromere within a linkage group of RFLP marker loci. The method was applied to the diploid alfalfa clone PG-F9 (2n = 2x = 16) previously selected because of its high frequency of 2n egg production. HTA was based on four RFLP loci for which PG-F9 was heterozygous with codominant alleles that were absent in the tetraploid tester. Models including three linked and one unlinked RFLP loci were developed and tested. Results of the HTA showed that PG-F9 produced 6% FDR and 94% second division restitution 2n eggs. Information from a marker locus belonging to one linkage group was used to more precisely locate the centromere on a different linkage group. HTA, together with previous cytological analysis, indicated that in PG-F9, FDR 2n eggs are likely produced by diplospory, a mechanism common among apomictic species. The occurrence of FDR 2n eggs in plant species and their importance for crop evolution and breeding is discussed together with the potential applicability of multilocus HTA in the study of reproductive mutants.

Simultaneous assessment of loss of heterozygosity at multiple microsatellite loci using semi-automated fluorescence-based detection: subregional mapping of chromosome 4 in cervical carcinoma.

Detection of loss of heterozygosity (LOH) by comparison of normal and tumor genotypes using PCR-based microsatellite loci provides considerable advantages over traditional Southern blotting-based approaches. However, current methodologies are limited by several factors, including the numbers of loci that can be evaluated for LOH in a single experiment, the discrimination of true alleles versus "stutter bands," and the use of radionucleotides in detecting PCR products. Here we describe methods for high throughput simultaneous assessment of LOH at multiple loci in human tumors; these methods rely on the detection of amplified microsatellite loci by fluorescence-based DNA sequencing technology. Data generated by this approach are processed by several computer software programs that enable the automated linear quantitation and calculation of allelic ratios, allowing rapid ascertainment of LOH. As a test of this approach, genotypes at a series of loci on chromosome 4 were determined for 58 carcinomas of the uterine cervix. The results underscore the efficacy, sensitivity, and remarkable reproducibility of this approach to LOH detection and provide subchromosomal localization of two regions of chromosome 4 commonly altered in cervical tumors.

Human immunodeficiency virus (HIV) type 2-mediated inhibition of HIV type 1: a new approach to gene therapy of HIV-infection.

Human immunodeficiency virus (HIV) type 2, the second AIDS-associated human retrovirus, differs from HIV-1 in its natural history, infectivity, and pathogenicity, as well as in details of its genomic structure and molecular behavior. We report here that HIV-2 inhibits the replication of HIV-1 at the molecular level. This inhibition was selective, dose-dependent, and nonreciprocal. The closely related simian immunodeficiency provirus also inhibited HIV-1. The selectivity of inhibition was shown by the observation that HIV-2 did not significantly downmodulate the expression of the unrelated murine leukemia virus; neither did the murine leukemia virus markedly affect HIV-1 or HIV-2 expression. Moreover, while HIV-2 potently inhibited HIV-1, the reverse did not happen, thus identifying yet another and remarkable difference between HIV-1 and HIV-2. Mutational analysis of the HIV-2 genome suggested that the inhibition follows a complex pathway, possibly involving multiple genes and redundant mechanisms. Introduction of inactivating mutations into the structural and regulatory/accessory genes did not render the HIV-2 provirus ineffective. Some of the HIV-2 gene defects, such as that of tat and rev genes, were phenotypically transcomplemented by HIV-1. The HIV-2 proviruses with deletions in the putative packaging signal and defective for virus replication were effective in inducing the suppressive phenotype. Though the exact mechanism remains to be defined, the inhibition appeared to be mainly due to an intracellular molecular event because it could not be explained solely on the basis of cell surface receptor mediated interference. The results support the notion that the inhibition likely occurred at the level of viral RNA, possibly involving competition between viral RNAs for some transcriptional factor essential for virus replication. Induction of a cytokine is another possibility. These findings might be relevant to the clinical-epidemiological data suggesting that infection with HIV-2 may offer some protection against HIV-1 infection.

Human Trafficking for sexual exploitation in Europe. Towards a true “EU approach”?

La presente tesi analizza il reato di traffico di esseri umani in Europa, con particolare attenzione al fenomeno dello sfruttamento sessuale. La ricerca è stata condotta in parte nell’ambito del progetto “FIDUCIA. New European crimes and trust-based policy” (www.fiduciaproject.eu). La tesi è composta da 5 capitoli. Il primo capitolo introduce il reato di tratta di esseri umani, a livello globale e, successivamente, nello specifico, in Europa. Vengono presentati i fattori determinanti e le origini del fenomeno. Inoltre, ne vengono fornite le definizioni e le principali caratteristiche, in linea con i più importanti documenti internazionali sul tema. Il capitolo si chiude con una panoramica statistica, che affronta anche le criticità della raccolta di dati relativi ai reati. Il secondo capitolo analizza l’approccio correntemente adottato a livello domestico ed europeo contro la tratta. Le misure vengono presentate prima dal punto di vista teorico; successivamente ne vengono forniti esempi concreti, ad esempio convenzioni internazionali, direttive, ma anche progetti di ricerca, collaborazioni internazionali tra autorità ed ONG. Il terzo capitolo si concentra sulla tratta a fini di sfruttamento sessuale. Vengono analizzati il potenziale legame con la prostituzione, e l’approccio europeo. Segue un approfondimento dei modelli legali implementati a livello europeo ed uno studio comparato di cinque paesi membri, rappresentativi dei vari modelli di regolamentazione della prostituzione (Italia, Belgio, Polonia, Germania e Svezia). Il quarto capitolo raccoglie le interviste condotte con diversi esperti che si occupano di contrasto alla tratta: ONG italiane e straniere, referenti nazionali anti-tratta di Italia, Belgio e Germania, FRONTEX, membri del Parlamento Europeo. Nelle conclusioni, vengono proposte prima una valutazione complessiva del quadro attuale, e poi alcune raccomandazioni ai governi nazionali e agli organismi sopranazionali. In particolare, visto l’obiettivo di un contrasto omogeneo e coordinato della tratta (per sfruttamento sessuale specificamente) a livello europeo, si ritiene che un modello regolamentare uniforme della prostituzione negli stati membri possa contribuire a migliorare uniformità ad efficacia dell’approccio europeo alla tratta.

COMPENDIUM: a text summarisation tool for generating summaries of multiple purposes, domains, and genres

In this paper, we present a Text Summarisation tool, compendium, capable of generating the most common types of summaries. Regarding the input, single- and multi-document summaries can be produced; as the output, the summaries can be extractive or abstractive-oriented; and finally, concerning their purpose, the summaries can be generic, query-focused, or sentiment-based. The proposed architecture for compendium is divided in various stages, making a distinction between core and additional stages. The former constitute the backbone of the tool and are common for the generation of any type of summary, whereas the latter are used for enhancing the capabilities of the tool. The main contributions of compendium with respect to the state-of-the-art summarisation systems are that (i) it specifically deals with the problem of redundancy, by means of textual entailment; (ii) it combines statistical and cognitive-based techniques for determining relevant content; and (iii) it proposes an abstractive-oriented approach for facing the challenge of abstractive summarisation. The evaluation performed in different domains and textual genres, comprising traditional texts, as well as texts extracted from the Web 2.0, shows that compendium is very competitive and appropriate to be used as a tool for generating summaries.

Optimization of test and maintenance of ageing components consisting of multiple items and addressing effectiveness

There are many models in the literature that have been proposed in the last decades aimed at assessing the reliability, availability and maintainability (RAM) of safety equipment, many of them with a focus on their use to assess the risk level of a technological system or to search for appropriate design and/or surveillance and maintenance policies in order to assure that an optimum level of RAM of safety systems is kept during all the plant operational life. This paper proposes a new approach for RAM modelling that accounts for equipment ageing and maintenance and testing effectiveness of equipment consisting of multiple items in an integrated manner. This model is then used to perform the simultaneous optimization of testing and maintenance for ageing equipment consisting of multiple items. An example of application is provided, which considers a simplified High Pressure Injection System (HPIS) of a typical Power Water Reactor (PWR). Basically, this system consists of motor driven pumps (MDP) and motor operated valves (MOV), where both types of components consists of two items each. These components present different failure and cause modes and behaviours, and they also undertake complex test and maintenance activities depending on the item involved. The results of the example of application demonstrate that the optimization algorithm provide the best solutions when the optimization problem is formulated and solved considering full flexibility in the implementation of testing and maintenance activities taking part of such an integrated RAM model.

A flexible, scaleable approach to the international patent 'name game'. Bruegel Working Paper 2014/10i, September 2014

The inventors in PATSTAT are often duplicates: the same person or company may be split into multiple entries in PATSTAT, each associated to different patents. In this paper, we address this problem with an algorithm that efficiently de-duplicates the data. It needs minimal manual input and works well even on consumer-grade computers. Comparisons between entries are not limited to their names, and thus this algorithm is an improvement over earlier ones that required extensive manual work or overly cautious clean-up of the names.

The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa

Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.

A Unified Approach to Automatic Testing of Architectural Constraints

Architectural decisions are often encoded in the form of constraints and guidelines. Non-functional requirements can be ensured by checking the conformance of the implementation against this kind of invariant. Conformance checking is often a costly and error-prone process that involves the use of multiple tools, differing in effectiveness, complexity and scope of applicability. To reduce the overall effort entailed by this activity, we propose a novel approach that supports verification of human- readable declarative rules through the use of adapted off-the-shelf tools. Our approach consists of a rule specification DSL, called Dicto, and a tool coordination framework, called Probo. The approach has been implemented in a soon to be evaluated prototype.

Constructing, Creating and Contesting Cityscapes. A Socio-Anthropological Approach to Urban Transformation in Southern Xinjiang, People’s Republic of China

This manuscript is based on a PhD thesis submitted at the Institute of Social Anthropology at the University of Bern in 2014. The dissertation was part of the research project „Xinjiang Uyghur Autonomous Region and Chinese Territoriality. The Development of Infrastructure and Han Migration into the Region“ under the supervision of Prof. Dr. Heinzpeter Znoj and financed by the Swiss National Science Foundation SNSF. Madlen Kobi analyzes the architectural and socio-political transformation of public places and spaces in rapidly urbanizing southern Xinjiang, P.R. China, and in doing so pays particular attention to the cities of Aksu and Kaxgar. As the Xinjiang Uyghur Autonomous Region lies in between China and Central Asia, it is especially characterized by differing political, cultural, and religious influences, and, furthermore, due to its being a multiethnic region, by multiple identities. One might expect cultural and social identities in this area to be negotiated by referring to history, religion, or food. However, they also become visible by the construction and reconstruction, if not demolition, of public places, architectural landmarks, and private residences. Based on ethnographic fieldwork performed in 2011 and 2012, the study explores everyday life in a continuously transforming urban environment shaped by the interaction of the interests of government institutions, investment companies, the middle class, and migrant workers, among many other actors. Here, urban planning, modernization, and renewal form a highly sensitive lens through which the author inspects the tense dynamics of ethnic, religious, and class-based affiliations. She respects varieties and complexities while thoroughly grounding unfolding transformation processes in everyday lived experiences. The study provides vivid insights into how urban places and spaces in this western border region of China are constructed, created, and eventually contested.

Downscaled land surface temperatures obtained by a particle smoothing approach, with links to NetCDF files

This dataset contains continuous time series of land surface temperature (LST) at spatial resolution of 300m around the 12 experimental sites of the PAGE21 project (grant agreement number 282700, funded by the EC seventh Framework Program theme FP7-ENV-2011). This dataset was produced from hourly LST time series at 25km scale, retrieved from SSM/I data (André et al., 2015, doi:10.1016/j.rse.2015.01.028) and downscaled to 300m using a dynamic model and a particle smoothing approach. This methodology is based on two main assumptions. First, LST spatial variability is mostly explained by land cover and soil hydric state. Second, LST is unique for a land cover class within the low resolution pixel. Given these hypotheses, this variable can be estimated using a land cover map and a physically based land surface model constrained with observations using a data assimilation process. This methodology described in Mechri et al. (2014, doi:10.1002/2013JD020354) was applied to the ORCHIDEE land surface model (Krinner et al., 2005, doi:10.1029/2003GB002199) to estimate prior values of each land cover class provided by the ESA CCI-Land Cover product (Bontemps et al., 2013) at 300m resolution . The assimilation process (particle smoother) consists in simulating ensemble of LST time series for each land cover class and for a large number of parameter sets. For each parameter set, the resulting temperatures are aggregated considering the grid fraction of each land cover and compared to the coarse observations. Miniminizing the distance between the aggregated model solutions and the observations allow us to select the simulated LST and the corresponding parameter sets which fit the observations most closely. The retained parameter sets are then duplicated and randomly perturbed before simulating the next time window. At the end, the most likely LST of each land cover class are estimated and used to reconstruct LST maps at 300m resolution using ESA CCI-Land Cover. The resulting temperature maps on which ice pixels were masked, are provided at daily time step during the nine-year analysis period (2000-2009).

Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation.

We conducted a genome-wide association study (GWAS) on multiple sclerosis (MS) susceptibility in German cohorts with 4888 cases and 10,395 controls. In addition to associations within the major histocompatibility complex (MHC) region, 15 non-MHC loci reached genome-wide significance. Four of these loci are novel MS susceptibility loci. They map to the genes L3MBTL3, MAZ, ERG, and SHMT1. The lead variant at SHMT1 was replicated in an independent Sardinian cohort. Products of the genes L3MBTL3, MAZ, and ERG play important roles in immune cell regulation. SHMT1 encodes a serine hydroxymethyltransferase catalyzing the transfer of a carbon unit to the folate cycle. This reaction is required for regulation of methylation homeostasis, which is important for establishment and maintenance of epigenetic signatures. Our GWAS approach in a defined population with limited genetic substructure detected associations not found in larger, more heterogeneous cohorts, thus providing new clues regarding MS pathogenesis.

Integrating multiple taxa in a biological stream rating system.

"This report is based largely on work done by Leslie Bol and Leon Hinz of the Illinois Natural History Survey, and Ann Marie Holtrop of the IDNR. Their work was funded by IDNR through the Illinois State Wildlife Grant Program (T-20-P-001)." -- acknowledgments.

A transdisciplinary approach to adolescent forensic mental health

Objective: To examine new strategies which may be implemented to address the significant mental health and substance abuse problems of young people within the juvenile justice system. Method: Wide-ranging literature review of mental health problems within the juvenile justice population is given, illustrating the high prevalence of mental health problems within this cohort of young people. Reference is made to the differing demographics and agendas of the American justice system compared to that found in Australia. Results: It is suggested that new initiatives stemming from quality Australian studies are required in order to facilitate reform within adolescent forensic mental health. Psychiatrists need to be at the forefront of innovative policy delivery within the juvenile justice system. Conclusions: A transdisciplinary approach is required to meet the changing needs of young people within the juvenile justice system. Such a system of care recognizes that these young people and their families have multiple needs that cross traditional boundaries and a collaborative approach across agencies is essential at both the policy and practical level. Psychiatrists have an important role to play in the development of these services. A systemic process to address such needs is offered.