‎101011 manuscripts: Perl and the Chronicle of Matthew of Edessa‎

The Chronicle of Matthew of Edessa is a twelfth-century Armenian history that survives in 43 manuscripts, held in ten libraries in eight countries. My task is to create a definitive text that is based on all of them. I will talk about the problems of medieval text editing, the ways in which Perl and phylogenetics have come to my rescue, and show a few pretty pictures of manuscripts

10001 manuscripts in practice: Perl, XML, medieval chronicles, and why Unicode rocks‎

I work in the field of Armenian historiography. This means I get to play with medieval manuscripts. The things I'm doing with the manuscripts are theoretically interesting, but pretty boring in practice, so I'm using Perl to program away the most boring bits. I will talk about the problems of text criticism in general, what sorts of things can and can't be done by the computer, my initial aversion to XML, how I was shown (some of) the error of my ways, and how I'm combining a bunch of isolated pieces of technology that were mostly already in use to achieve fame and fortune in the world of Armenian studies.

The Mycoplasma conjunctivae genome sequencing, annotation and analysis

BACKGROUND: The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., Capra ibex, Rupicapra rupicapra). METHODS: The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database. RESULTS: The annotated sequence is deposited in the EMBL database (FM864216) and uploaded into the mollicutes database MolliGen http://cbi.labri.fr/outils/molligen/ allowing for comparative genomics. CONCLUSION: We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).

Expression of Foxi3 is regulated by ectodysplasin in skin appendage placodes

BACKGROUND Foxi3 is a member of the large forkhead box family of transcriptional regulators, which have a wide range of biological activities including manifold developmental processes. Heterozygous mutation in Foxi3 was identified in several hairless dog breeds characterized by sparse fur coat and missing teeth. A related phenotype called hypohidrotic ectodermal dysplasia (HED) is caused by mutations in the ectodysplasin (Eda) pathway genes. RESULTS Expression of Foxi3 was strictly confined to the epithelium in developing ectodermal appendages in mouse embryos, but no expression was detected in the epidermis. Foxi3 was expressed in teeth and hair follicles throughout embryogenesis, but in mammary glands only during the earliest stages of development. Foxi3 expression was decreased and increased in Eda loss- and gain-of-function embryos, respectively, and was highly induced by Eda protein in embryonic skin explants. Also activin A treatment up-regulated Foxi3 mRNA levels in vitro. CONCLUSIONS Eda and activin A were identified as upstream regulators of Foxi3. Foxi3 is a likely transcriptional target of Eda in ectodermal appendage placodes suggesting that HED phenotype may in part be produced by compromised Foxi3 activity. In addition to hair and teeth, Foxi3 may have a role in nail, eye, and mammary, sweat, and salivary gland development.

A compendium of strategies to prevent healthcare-associated infections in acute care hospitals: 2014 updates

Since the publication of "A Compendium of Strategies to Prevent Healthcare-Associated Infections in Acute Care Hospitals" in 2008, prevention of healthcare-associated infections (HAIs) has become a national priority. Despite improvements, preventable HAIs continue to occur. The 2014 updates to the Compendium were created to provide acute care hospitals with up-to-date, practical, expert guidance to assist in prioritizing and implementing their HAI prevention efforts. They are the product of a highly collaborative effort led by the Society for Healthcare Epidemiology of America (SHEA), the Infectious Diseases Society of America (IDSA), the American Hospital Association (AHA), the Association for Professionals in Infection Control and Epidemiology (APIC), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise, including the Centers for Disease Control and Prevention (CDC), the Institute for Healthcare Improvement (IHI), the Pediatric Infectious Diseases Society (PIDS), the Society for Critical Care Medicine (SCCM), the Society for Hospital Medicine (SHM), and the Surgical Infection Society (SIS).

A compendium of strategies to prevent healthcare-associated infections in acute care hospitals: 2014 updates.

Since the publication of "A Compendium of Strategies to Prevent Healthcare-Associated Infections in Acute Care Hospitals" in 2008, prevention of healthcare-associated infections (HAIs) has become a national priority. Despite improvements, preventable HAIs continue to occur. The 2014 updates to the Compendium were created to provide acute care hospitals with up-to-date, practical, expert guidance to assist in prioritizing and implementing their HAI prevention efforts. They are the product of a highly collaborative effort led by the Society for Healthcare Epidemiology of America (SHEA), the Infectious Diseases Society of America (IDSA), the American Hospital Association (AHA), the Association for Professionals in Infection Control and Epidemiology (APIC), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise, including the Centers for Disease Control and Prevention (CDC), the Institute for Healthcare Improvement (IHI), the Pediatric Infectious Diseases Society (PIDS), the Society for Critical Care Medicine (SCCM), the Society for Hospital Medicine (SHM), and the Surgical Infection Society (SIS).

Uncertain Belongings. Absent mourning, burial, and post-mortem repatriations at the external border of the EU in Spain

Since the mid-1980s, migrants from North African and sub-Saharan countries have irregularly crossed the Strait of Gibraltar, in the hope of a better future for themselves and their families. Travelling in small, poorly equipped boats without experienced captains has cost the lives of myriad border crossers. Many of these bodies will never be recovered and the bereaved will never know whether their relatives and friends are alive or not. The bereaved are thus condemned to a state of not knowing and uncertainty. Exploring the junction of death and belonging, I firstly open a discussion about the enigmatic relation between a dead body and a dead person and argue for the importance of the physical presence of the body for mourning. Secondly, I show how the anonymity of dead border crossers and their uncertain belongings are generated, concealed, or rewritten. Following the story of an undertaker, I thirdly examine post-mortem border crossings. Depicting the power relations within identification processes, I outline the ambiguity of the term belonging by emphasising the constitutive significance of personal belongings such as clothes to restore a person’s identity. Reflecting on the ethical relationships which different actors (including the researcher) undertake with the deceased, I aim at gaining a better understanding of the multiple belonging of dead border crossers found on Spanish shores.