What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and their weights have on the overall system performance. In order to overcome this explanatory gap, we first determined optimal feature configurations using the Sequential Model-based Algorithm Configuration (SMAC) program and applied its output to a BM25-based search engine. We then ran an ablation study to systematically assess the individual contributions of relevant system features: BM25 parameters, query type and weighting schema, query expansion, stop word filtering, and keyword boosting. For evaluation, we employed the gold standard data from the three TREC-PM installments to evaluate the effectiveness of different features using the commonly shared infNDCG metric.Comment: Accepted for SIGIR2020, 10 page

Profit enhancing competitive pressure in vertically related industries

Coevolution of viruses and their hosts represents a dynamic molecular battle between the immune system and viral factors that mediate immune evasion. After the abandonment of smallpox vaccination, cowpox virus infections are an emerging zoonotic health threat, especially for immunocompromised patients. Here we delineate the mechanistic basis of how cowpox viral CPXV012 interferes with MHC class I antigen processing. This type II membrane protein inhibits the coreTAP complex at the step after peptide binding and peptide-induced conformational change, in blocking ATP binding and hydrolysis. Distinct from other immune evasion mechanisms, TAP inhibition is mediated by a short ER-lumenal fragment of CPXV012, which results from a frameshift in the cowpox virus genome. Tethered to the ER membrane, this fragment mimics a high ER-lumenal peptide concentration, thus provoking a trans-inhibition of antigen translocation as supply for MHC I loading. These findings illuminate the evolution of viral immune modulators and the basis of a fine-balanced regulation of antigen processing

TMJ response to mandibular advancement surgery: an overview of risk factors

Objective: In order to understand the conflicting information on temporomandibular joint (TMJ) pathophysiologic responses after mandibular advancement surgery, an overview of the literature was proposed with a focus on certain risk factors. Methods: A literature search was carried out in the Cochrane, PubMed, Scopus and Web of Science databases in the period from January 1980 through March 2013. Various combinations of keywords related to TMJ changes [disc displacement, arthralgia, condylar resorption (CR)] and aspects of surgical intervention (fixation technique, amount of advancement) were used. A hand search of these papers was also carried out to identify additional articles. Results: A total of 148 articles were considered for this overview and, although methodological troubles were common, this review identified relevant findings which the practitioner can take into consideration during treatment planning: 1- Surgery was unable to influence TMJ with preexisting displaced disc and crepitus; 2- Clicking and arthralgia were not predictable after surgery, although there was greater likelihood of improvement rather than deterioration; 3- The amount of mandibular advancement and counterclockwise rotation, and the rigidity of the fixation technique seemed to influence TMJ position and health; 4- The risk of CR increased, especially in identified high-risk cases. Conclusions: Young adult females with mandibular retrognathism and increased mandibular plane angle are susceptible to painful TMJ, and are subject to less improvement after surgery and prone to CR. Furthermore, thorough evidenced-based studies are required to understand the response of the TMJ after mandibular advancement surgery

Thermal decomposition of allantoin as probed by matrix isolation FTIR spectroscopy

The optimized geometries, energies of the possible conformers of allantoin (2,5-dioxo-4-imidazolidinyl urea, the diureide of glyoxylic acid) as well as the barriers for conformational interconversion have been calculated using the density functional theory [DFT(B3LYP)/6-311++G(d,p)] method. The calculations predicted the existence of four conformers (gC, tT, g′C, and g′T; where the first and second symbols in the name of the conformers designate the conformation around the exocyclic NHC–NHCO and CNH–CO axes, respectively), with the gC form contributing to more than 98% of the population in gas phase at room temperature. This conformer is different from that corresponding to the monomeric unit found in crystalline RS-allantoin (g′C; Mootz, D. Acta Crystallogr.1965, 19, 726), stressing the importance of intermolecular H-bonding in determining the structure of the crystal. Upon sublimation under vacuum (10−6 mbar), the compound was found to undergo extensive decomposition to urea, isocyanic acid, NH3, and carbon. The identification of the decomposition products was made by using matrix isolation infrared spectroscopy. In consonance with the theoretical predictions, the allantoin molecules surviving thermal decomposition were found to undergo conformational isomerization and be present in the cryogenic argon matrix in both the gC and g′C conformations. The solid state room temperature infrared spectrum of allantoin was also investigated and assigned

A negative feedback modulator of antigen processing evolved from a frameshift in the cowpox virus genome

Coevolution of viruses and their hosts represents a dynamic molecular battle between the immune system and viral factors that mediate immune evasion. After the abandonment of smallpox vaccination, cowpox virus infections are an emerging zoonotic health threat, especially for immunocompromised patients. Here we delineate the mechanistic basis of how cowpox viral CPXV012 interferes with MHC class I antigen processing. This type II membrane protein inhibits the coreTAP complex at the step after peptide binding and peptide-induced conformational change, in blocking ATP binding and hydrolysis. Distinct from other immune evasion mechanisms, TAP inhibition is mediated by a short ER-lumenal fragment of CPXV012, which results from a frameshift in the cowpox virus genome. Tethered to the ER membrane, this fragment mimics a high ER-lumenal peptide concentration, thus provoking a trans-inhibition of antigen translocation as supply for MHC I loading. These findings illuminate the evolution of viral immune modulators and the basis of a fine-balanced regulation of antigen processing

Sports related maxillofacial injuries: the first maxillofacial trauma database in Switzerland

Background: With the increase in the amount of medical data handled by emergency units, advances in computerisation have become necessary. New computer technology should have a major influence on accident analysis and prevention and the quality of research in the future. Objectives: To investigate the occurrence of sports related maxillofacial injuries using a newly installed relational database. To establish the first sports trauma database in Switzerland. Methods: The Qualicare databank was used to prospectively review 57 248 case histories of patients treated in the Department of Emergency Medicine between January 2000 and December 2002. Pre-defined key words were used to collect data on sports related maxillofacial injuries. Results: A total of 750 patients with maxillofacial injuries were identified. Ninety (12%) were sports related maxillofacial fractures. Most (27%) were sustained during skiing and snowboarding, 22% during team sports such as soccer or ice hockey, and 21% were from cycling accidents. Sixty eight per cent of the cyclists, 50% of the ice hockey players and soccer players, and 48% of the skiers and snowboarders had isolated fractures of the midface. Fractures of the mandible were noted predominantly in contact sports. Conclusions: Computerisation of trauma and emergency units and the introduction of customised software can significantly reduce the workload of researchers and doctors. The effective use of new computer technology should have a considerable influence on research and the quality of future prospective and retrospective studies