Discussions and decisions of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group,January 2012–June 2013

The International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group prepares proposals on the classification and nomenclature of filoviruses to reflect current knowledge or to correct disagreements with the International Code of Virus Classification and Nomenclature (ICVCN). In recent years, filovirus taxonomy has been corrected and updated, but parts of it remain controversial, and several topics remain to be debated. This article summarizes the decisions and discussion of the currently acting ICTV Filoviridae Study Group since its inauguration in January 2012.     

A user-study measuring the effects of lexical simplification and coherence enhancement on perceived and actual text difficulty

PurposeLow patient health literacy has been associated with cost increases in medicine because it contributes to inadequate care. Providing explanatory text is a convenient approach to distribute medical information and increase health literacy. Unfortunately, writing text that is easily understood is challenging. This work tests two text features for their impact on understanding: lexical simplification and coherence enhancement.MethodsA user study was conducted to test the features’ effect on perceived and actual text difficulty. Individual sentences were used to test perceived difficulty. Using a 5-point Likert scale, participants compared eight pairs of original and simplified sentences. Abstracts were used to test actual difficulty. For each abstract, four versions were created: original, lexically simplified, coherence enhanced, and lexically simplified and coherence enhanced. Using a mixed design, one group of participants worked with the original and lexically simplified documents (no coherence enhancement) while a second group worked with the coherence enhanced versions. Actual difficulty was measured using a Cloze measure and multiple-choice questions.ResultsUsing Amazon's Mechanical Turk, 200 people participated of which 187 qualified based on our data qualification tests. A paired-samples t-test for the sentence ratings showed a significant reduction in difficulty after lexical simplification (p < .001). Results for actual difficulty are based on the abstracts and associated tasks. A two-way ANOVA for the Cloze test showed no effect of coherence enhancement but a main effect for lexical simplification, with the simplification leading to worse scores (p = .004). A follow-up ANOVA showed this effect exists only for function words when coherence was not enhanced (p = .008). In contrast, a two-way ANOVA for answering multiple-choice questions showed a significant beneficial effect of coherence enhancement (p = .003) but no effect of lexical simplification.ConclusionsLexical simplification reduced the perceived difficulty of texts. Coherence enhancement reduced the actual difficulty of text when measured using multiple-choice questions. However, the Cloze measure results showed that lexical simplification can negatively impact the flow of the text.     

Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations

It has previously been shown that, in the heterozygous state, mutations in the SOX9 gene cause campomelic dysplasia (CD) and the often associated autosomal XY sex reversal. In 12 CD patients, 10 novel mutations and one recurrent mutation were characterized in one SOX9 allele each, and in one case, no mutation was found. Four missense mutations are all located within the high mobility group (HMG) domain. They either reduce or abolish the DNA-binding ability of the mutant SOX9 proteins. Among the five nonsense and three frameshift mutations identified, two leave the C-terminal transactivation (TA) domain encompassing residues 402-509 of SOX9 partly or almost completely intact. When tested in cell transfection experiments, the recurrent nonsense mutation Y440X, found in two patients who survived for four and more than 9 years, respectively, exhibits some residual transactivation ability. In contrast, a frameshift mutation extending the protein by 70 residues at codon 507, found in a patient who died shortly after birth, showed no transactivation. This is apparently due to instability of the mutant SOX9 protein as demonstrated by Western blotting. Amino acid substitutions and nonsense mutations are found in patients with and without XY sex reversal, indicating that sex reversal in CD is subject to variable penetrance. Finally, none of 18 female patients with XY gonadal dysgenesis (Swyer syndrome) showed an altered SOX9 banding pattern in SSCP assays, providing evidence that SOX9 mutations do not usually result in XY sex reversal without skeletal malformations.      

Methods and Findings from the National Violent Death Reporting System for Identifying Gang-Like Homicides, 2005–2008

Background

The National Violent Death Reporting System (NVDRS) captures homicides that law enforcement or coroner/medical examiners deem as gang-related but the criteria used may vary across locations. Also, the existing gang-related variable likely underestimates the number of homicides that are associated with gang activity. This study utilizes NVDRS data to identify “gang-like” homicides which are not currently captured as “gang-related.”

Systems biology: integrating technology,biology, and computation

The Human Genome Project has changed the worlds of biology and medicine-helping to catalyze two major paradigm changes: systems biology and predictive, preventive and personalized medicine. These two themes will dominate 21st century biology and medicine. I will discuss these changes and indicate how they may interface with with the process of aging.     

Diagnostic considerations regarding pediatric delirium: a review and a proposal for an algorithm for pediatric intensive care units

Context  

If delirium is not diagnosed, it is unlikely that any effort will be made to reverse it. Given evidence for under-diagnosis, tools that aid recognition are required.     

Schlieren photography study of energy absorption by uric acid nuclei

Previous studies using microfocus x-ray radiography on concentric laminated uric acid calculi following in vitro extracorporeal shock-wave lithotripsy (ESWL) has demonstrated the enlargement of the matrix layers. The Schlieren technique was used to verify the hypothesis that the incident energy would be concentrated in the matrix layers by total internal reflection. Because of the rough surface of the stone, the ultrasonic beam (4 MHz) was incident at various angles. At the critical Rayleigh angle (45.9 degrees +/- 0.5 degrees ), the reflected beam consisted of a spectacularly reflected lobe and a reradiated leaky Rayleigh wave. Different critical Lamb angles, theta(L), of 30.8 degrees, 38.1 degrees and 50.8 degrees (experimental uncertainty 0.5 degrees ) were also determined. Depending on the angle of incidence on the stone surface, a Rayleigh wave can be produced and/or one or more layers, as a whole, are set into vibration (Lamb excitation), with the result that shell-like fragments consisting of one or more layers, break off the stones at sites of weaker bonding, as has been noted in previous in vitro lithotripsy experiments by our group.     

Problems stemming from pregnancy in a woman with phenylketonuria

A normal infant was born to a 25 year-old mother with phenylketonuria who had never been treated. The mother had been fed a phenylalanine restricted diet for 3 months before the beginning of the pregnancy. Dietary control was maintained throughout the whole gestation. The problems of dietary control in a mentally retarded woman are analysed.