The LaTeX project: A case study of open-source software

This is a case study of TeX, a typesetting software that was developed by Donald E. Knuth in the late 70's. Released with an open source license, it has become a reference in scientific publishing. TeX is now used to typeset and publish much of the world's scientific literature in physics and mathematics. This case study is part of a wider effort by academics to understand the open-source phenomenon. That development model is similar to the organization of the production of knowledge in academia; there is no set organization with a hierarchy, but free collaboration that is coordinated spontaneously and winds up generating complex products that are the property of all who can understand its functioning. The case study was led by gathering qualitative data via interviews with TeX developers and quantitative data on the TeX community -- the program's code, the software that is part of the TeX distribution, the newsgroups dedicated to the software, and many other indicators of the evolution and activity in that open-source project. The case study is aimed at economists who want to develop models to understand and analyze the open-source phenomenon. It is also geared towards policy-makers who would like to encourage or regulate open- source, and towards open-source developers who wonder what are the efficient strategies to make an open-source project successful.TeX, LaTeX, case study, open source, software, innovation, organisational structure, economic history, knowledge production, knowledge diffusion.

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

No. 04: Silenced by Nation-Building: African Immigrants and Language Policy in the New South Africa

All people in South Africa have constitutionallyguaranteed language rights. To what extent do these rights apply to non-citizens and are they actually observed by various state departments and officials? This report presents the results of a preliminary investigation into this question by focusing on the rights and treatment of foreigners in South Africa, particularly foreigners from other African countries. The report was commissioned by the Southern African Migration Project (SAMP) as part of a broader programme to understand the reception and treatment of non-South Africans in the new South Africa. Our aim, as authors, is to encourage government departments and nongovernmental organisations (NGO’s) to continue to work towards policies which enhance the guarantee of multilingualism enshrined in the Constitution, and which enable marginalised constituencies to be recognised and heard. The report focuses on the national departments of Home Affairs, Safety and Security, and Justice. These are the main points of immigrant and migrant contact with the state, and therefore the most likely to require policy guidelines. Other departments dealing with immigrants – such as Correctional Services, Defence, Health, Education and Welfare, as well as their provincial counterparts – will also require investigation in order to get a comprehensive picture account of current language policies and practices. To this end, the report includes recommendations for further research. Two assumptions inform this report. Firstly, we assume that the interests of structures like the Pan South African Labour Board (PanSALB) as well as NGOs are distinct from the interests vying for power within government and state structures. We therefore conclude that various civil society groups and possibly the PanSALB will actively defend the Constitution and advance a progressive and inclusive approach to language policy that benefits everyone. In a country where language has been used to divide and undermine certain political, social, economic and cultural interests, it would seem necessary for language policy to become central in the elaboration of democracy and human rights. Secondly, we assume that it is in the long term interests of the new political order in South Africa to use sensible language planning to maintain peace (by promoting tolerance of diversity), and prosperity (by using linguistic resources effectively). It should be possible for nongovernmental interests to forge a consensus with government on the use of language policy to promote and sustain democracy (through promotion of diverse voices, in an inclusive and participatory political system). However, the research for this report provided a striking reminder that few state officials have considered the impact of language policy (and its absence) on broader issues of transformation. Although faced daily with language capacity problems, and the visible manifestation of contested uses of language, state officials interviewed tend not to see a link between their immediate concerns and the role of language policy in providing solutions in both the short and long term. Furthermore, senior civil servants are not necessarily aware of the link between language policy at departmental level, and national priorities of reconstruction and development. Administrative justice and state bureaucratic procedures concerning migrants and immigrants are currently not informed by an explicit, coherent language policy. In some cases there may be violations of constitutionally guaranteed language rights, particularly in situations involving detained persons where their rights, including the written provision of reasons for negative administrative action, are not adequately communicated; and in courts where inadequate language facilitation discriminates against individuals on the basis of language and place of origin. Reasons for the lack of a coherent policy include: Absence of co-ordination between legislative and bureaucratic decision-making on language issues; Inadequate understanding in most government departments of the role and function of language policy; Poor co-ordination within and between departments on language issues; Lack of consultation, negotiation and transparency in decision-making within departments; Inadequate human resource management, including the management of linguistic resources which exist within departments; Avoidance of multilingual policy due to the current power struggle between newly appointed, English speakers in the civil service, and existing Afrikaans speakers; The weak capacity of African migrants and immigrants to advocate on their own behalf; and Increasing xenophobia against, and exclusion of, African immigrants, which is partially an expression of the ambiguity of nation-building. The nature of internal departmental policies and practice, including that of language, directly impacts on public service delivery. The absence of language policy in general contributes to the lack of policy regarding language facilitation for immigrants. This contributes to an overall governmental silence about the legitimate linguistic and cultural presence of other Africans in South Africa. This silence has the potential to obscure real and potential human rights abuses by government, civil society and South African citizens. It is in the interests of democracy and the integrity of the new Constitution to reach into the silence and make apparent the presence and rights of speakers of officially unacknowledged languages of African provenance. The actions taken to make this policy area explicit and to ensure the upholding of the Constitution for marginalised constituencies, can contribute to making language policy and practice part of inclusive democratic state building rather than exclusive nation- building. Redress and correction of the current situation would provide an opportunity to replace the idea of “language as a problem” with “language as a resource”. Hence, immigrants’ linguistic and cultural resources could be recognised as contributing to South African reconstruction and development, and the multilingual abilities of civil servants would be acknowledged, promoted and rewarded. Owing to the complex power dynamics within the state bureaucracy, it is necessary to assign particular responsibility within government and state departments for redress and corrective action, and for organisations of civil society to be made aware and become vigilant on the issue of language access

[Review of] Marcyliena Morgan , ed. Language and the Social Construction of Identity in Creole Situations

The result of a 1990 conference on The Social Significance of Creole Language Studies sponsored by Pomona and Pitzer of the Claremont Colleges and the University of California, Los Angeles, this stimulating collection of six papers enriches the field of pidgin and creole studies by exploring the manner in which language and language choice reflect and mediate the social landscape.

The LaTeX project: A case study of open source software

The TeX typesetting software was developed by Donald E. Knuth in the late 1970s. It was released with an open source license and has become a reference in scientific publishing. TeX is now used to typeset and publish much of the world’s scientific literature in physics and mathematics. This case study serves as a critical examination of the stylized facts uncovered in previous studies of other open source software projects, such as GNU/Linux, an operating system, and Apache, a web server. It is sponsored by CNRS, a French research agency, and is supported by the University of Toulouse in France and the School of Information Management and Systems in Berkeley. The comparison centers on the historical development of the project, the organization, both formal and informal, that supports it, the motivations of the developers, and the various dynamics that are at work and influence the project. The case study explores the economic impact of the TeX software which is sold through TeX-based commercial applications and used in the typesetting industry and various institutions. It is an exploration of how the open source nature of the program made a di erence relative to what would have happened had it been commercial software.TeX, open source, Tug, software, case study, innovation, knowledge production, licenses, intellectual property, open systems

Cultural Diffusion and Trends in Facebook Photographs

Online social media is a social vehicle in which people share various moments of their lives with their friends, such as playing sports, cooking dinner or just taking a selfie for fun, via visual means, that is, photographs. Our study takes a closer look at the popular visual concepts illustrating various cultural lifestyles from aggregated, de-identified photographs. We perform analysis both at macroscopic and microscopic levels, to gain novel insights about global and local visual trends as well as the dynamics of interpersonal cultural exchange and diffusion among Facebook friends. We processed images by automatically classifying the visual content by a convolutional neural network (CNN). Through various statistical tests, we find that socially tied individuals more likely post images showing similar cultural lifestyles. To further identify the main cause of the observed social correlation, we use the Shuffle test and the Preference-based Matched Estimation (PME) test to distinguish the effects of influence and homophily. The results indicate that the visual content of each user's photographs are temporally, although not necessarily causally, correlated with the photographs of their friends, which may suggest the effect of influence. Our paper demonstrates that Facebook photographs exhibit diverse cultural lifestyles and preferences and that the social interaction mediated through the visual channel in social media can be an effective mechanism for cultural diffusion.Comment: 10 pages, To appear in ICWSM 2017 (Full Paper

Continuous Positive Airway Pressure Treatment in Patients with Alzheimer's Disease: A Systematic Review

Background: Epidemiological studies have suggested a pathophysiological relationship between obstructive sleep apnea syndrome (OSAS) and Alzheimer's disease (AD). The aim of this study is to evaluate the treatment of obstructive sleep apnea with continuous positive airway pressure (CPAP) in AD and its relationship with neurocognitive function improvement. Methods: Systematic review conducted following PRISMA's statements. Relevant studies were searched in MEDLINE, PEDro, SCOPUS, PsycINFO, Web of Science, CINAHL and SportDicus. Original studies in which CPAP treatment was developel in AD patients have been included. Results: 5 studies, 3 RCTs (Randomized controlled trials) and 2 pilot studies. In all RCTs the CPAP intervention was six weeks; 3 weeks of therapeutic CPAP vs. 3 weeks placebo CPAP (pCPAP) followed by 3 weeks tCPAP in patients with AD and OSA. The two pilot studies conducted a follow-up in which the impact on cognitive impairment was measured. Conclusions: CPAP treatment in AD patients decreases excessive daytime sleepiness and improves sleep quality. There are indications that cognitive deterioration function measured with the Mini Mental Scale decreases or evolves to a lesser extent in Alzheimer's patients treated with CPAP. Caregivers observe stabilization in disease progression with integration of CPAP. More research is needed on the topic presented