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Background We present a novel simulation method for generating connected differential expression signatures. Traditional methods have struggled with the lack of reliable benchmarking data and biases in drug–disease pair labeling, limiting the rigorous benchmarking of connectivity-based approaches. Objective Our aim is to develop a simulation method based on a statistical framework that allows for adjustable levels of parametrization, especially the connectivity, to generate a pair of interconnected differential signatures. This could help to address the issue of benchmarking data availability for connectivity-based drug repurposing approaches. Methods We first detailed the simulation process and how it reflected real biological variability and the interconnectedness of gene expression signatures. Then, we generated several datasets to enable the evaluation of different existing algorithms that compare differential expression signatures, providing insights into their performance and limitations. Results Our findings demonstrate the ability of our simulation to produce realistic data, as evidenced by correlation analyses and the log2 fold-change distribution of deregulated genes. Benchmarking reveals that methods like extreme cosine similarity and Pearson correlation outperform others in identifying connected signatures. Conclusion Overall, our method provides a reliable tool for simulating differential expression signatures. The data simulated by our tool encompass a wide spectrum of possibilities to challenge and evaluate existing methods to estimate connectivity scores. This may represent a critical gap in connectivity-based drug repurposing research because reliable benchmarking data are essential for assessing and advancing in the development of new algorithms. The simulation tool is available as a R package (General Public License (GPL) license) at https://github.com/cgonzalez-gomez/cosimu. [ABSTRACT FROM AUTHOR]

Nipah virus (NiV) is a zoonotic paramyxovirus that was first identified as the cause of an outbreak of encephalitis in humans in Malaysia and Singapore during 1998-1999 (1). Although NiV [...]

The article describes the activities at 'The Precedent in International Arbitration', the International Arbitration Institute (IAI) seminar held December 14, 2007.

Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus , for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius , (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats' ability to control viral infections. [ABSTRACT FROM AUTHOR]

Several eminent arbitration practitioners spoke on the new trends in the field at the first CEMAJ arbitration conference on 'New Developments in International Commercial Arbitration', held at the University of Neuchatel on October 26, 2007.

The article offers information on the International Centre for Settlement of Investment Disputes (ICSID) decisions and awards from 2015-2016. Among the cases mentioned are Postova Banka and Istrokapital v. Greece on qualification of Greek Government Bonds (GGBs), Ping An Life Insurance Co. Ltd. and Ping An Insurance (Group) Co. Ltd. v. The Government of Belgium on interpretation of bilateral investment treaties (BITs) between Belgium and China, and decision on liability and jurisdiction.

The article looks at the decision of the Russian Permanent Court of Arbitration (PCA) in the "Yukos v. Russian Federation" case involving provisional application of the Energy Charter Treaty (ECT). It mentions that the court charged the claimants' damages in investment arbitration. It also looks at the related to rights and duties in international arbitration.

The purpose of the ICSID case law review is to present and discuss all awards, decisions and orders published by ICSID arbitral tribunals during a given period of time. This ICSID case law review covers a selection of awards, decisions and orders published during the second, third and fourth trimester of 2012 with the analysis of a total of six awards, eleven decisions and one order. [ABSTRACT FROM AUTHOR]

Under the ICSID Convention, an ad hoc Committee may stay enforcement of an award pending its decision on annulment and, if the applicant requests a stay of enforcement of the award in its application, enforcement will be stayed provisionally until the ad hoc Committee rules on that request. This article examines the legal framework for stay of enforcement of awards, as well as the interpretation of this framework by ad hoc Committees. This author suggests that ad hoc Committees continue the stay of enforcement almost automatically, which deviates from the intent of the drafters and the text of the Convention. Moreover, there is an absence of homogeneity in conditioning the continuation of a stay of enforcement. [ABSTRACT FROM PUBLISHER]

Abstract The ICSID case law review aims at discussing all the decisions published during a given period of time. This review covers the first semester 2011 with the analysis of three orders, eight decisions and six awards. [ABSTRACT FROM AUTHOR]

Information about the Arbitration Conference dedicated to New Developments in International Commercial Arbitration held at the University of Neuchâtel on October 26, 2007 is presented. Topics include appeals in international arbitration under the new Swiss Federal Tribunal Statute, Article 186(1bis) and the hard choice between an award and an order. The conference featured arbitration practitioners including Markus Wirth, Bernhard Berger and Sébastien Besson.

This article attempts to clarify the different issues regarding the links and the possible conflicts of interest between the World Bank, the parent institution, and the International Centre for the Settlement of Investment Disputes (ICSID), the child. Structural issues, philosophical problems concerning the possible bias when judging World Bank's policies, and the involvement of former Bank officials in ICSID tribunals will be considered in turn. The amendment of the Arbitration Rules in April 2006 raised many hopes but fell short of solving some of the practical problems that result from the close ties between these two Washingtonian institutions. Some necessary structural changes should thus be envisaged for ICSID. [ABSTRACT FROM AUTHOR]

An increasing amount of evidence indicates a relatively high prevalence of superinfections associated with coronavirus disease 2019 (COVID-19), including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection, we determine and compare the host transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) versus Aspergillus superinfection, using a model of reconstituted human airway epithelium. Our analyses reveal that both simple infection and superinfection induce strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte and neutrophil associated chemokines, that could be useful for the understanding of Aspergillus-associated COVID-19 and also the management of severe forms of aspergillosis in this specific context. [ABSTRACT FROM AUTHOR]

Background: We present a novel simulation method for generating connected differential expression signatures. Traditional methods have struggled with the lack of reliable benchmarking data and biases in drug-disease pair labeling, limiting the rigorous benchmarking of connectivity-based approaches., Objective: Our aim is to develop a simulation method based on a statistical framework that allows for adjustable levels of parametrization, especially the connectivity, to generate a pair of interconnected differential signatures. This could help to address the issue of benchmarking data availability for connectivity-based drug repurposing approaches., Methods: We first detailed the simulation process and how it reflected real biological variability and the interconnectedness of gene expression signatures. Then, we generated several datasets to enable the evaluation of different existing algorithms that compare differential expression signatures, providing insights into their performance and limitations., Results: Our findings demonstrate the ability of our simulation to produce realistic data, as evidenced by correlation analyses and the log2 fold-change distribution of deregulated genes. Benchmarking reveals that methods like extreme cosine similarity and Pearson correlation outperform others in identifying connected signatures., Conclusion: Overall, our method provides a reliable tool for simulating differential expression signatures. The data simulated by our tool encompass a wide spectrum of possibilities to challenge and evaluate existing methods to estimate connectivity scores. This may represent a critical gap in connectivity-based drug repurposing research because reliable benchmarking data are essential for assessing and advancing in the development of new algorithms. The simulation tool is available as a R package (General Public License (GPL) license) at https://github.com/cgonzalez-gomez/cosimu., (© The Author(s) 2024. Published by Oxford University Press.)