Profile Comparer: a program for scoring and aligning profile hidden Markov models

Summary: Profile Comparer (PRC) is a stand-alone program for scoring and aligning profile hidden Markov models (HMMs) of protein families. PRC can read models produced by SAM and HMMER, two popular profile HMM packages, as well as PSI-BLAST checkpoint files. This application note provides a brief description of the profile–profile algorithm used by PRC

Colombia's Armed Conflict and Dental Caries among Adults.

INTRODUCTION: This study aimed to determine the association between residing in municipalities with armed conflict and dental caries among adults in Colombia. METHODS: Data from 9194 18-79-year-olds, who participated in the Fourth National Oral Health Survey in 2014, were linked with information on the presence and intensity of the armed conflict experienced in their municipality of residence between 2000 and 2012 (extracted from the Resource Centre for Conflicts Analysis). Dental caries was determined through clinical examinations and summarised using the numbers of decayed teeth (DT), decayed and filled teeth (DFT) and decayed, missing and filled teeth (DMFT). Two-level negative binomial regression models were fitted, with adults nested within municipalities, to test the association between armed conflict indicators and caries outcomes after adjustment for covariates. RESULTS: The mean DT, DFT and DMFT scores were 1.75 (SD=2.36), 6.03 (SD=4.53), and 10.27 (SD=7.11), respectively. Of the 197 municipalities included in the analysis, 12.2% experienced conflict permanently and 18.3% experienced high intensity conflict. In crude analysis, adults living in municipalities with more presence and intensity of armed conflict had lower DT and DMFT, but not DFT scores. After adjustment for covariates, only the (high) intensity of conflict was associated with lower DT (Rate Ratio: 0.64; 95% Confidence Interval: 0.47-0.87), DFT (RR: 0.82; 95% CI: 0.71-0.95) and DMFT scores (RR: 0.81; 95% CI: 0.74-0.89). CONCLUSIONS: This study found that Colombian adults residing in municipalities with high intensity of conflict had lower levels of untreated disease and caries experience

To Look or Not to Look: Acknowledging Facial Stigmas in the Interview to Reduce Discrimination

As the use of technology-mediated interviews (e.g., Skype) is becoming a standard method to interview applicants, it is important to understand how discrimination can still manifest in these types of interviews. Because technology-mediated interviews focus on applicants’ faces, discrimination based on facial stigmas can be particularly inevitable. Thus, the purpose of the current study is to examine how a facial stigma affects visual attention during a technology-mediated interview and acknowledgment as a remediation strategy that individuals might use to reduce the amount of visual attention on a facial stigma. We used a 2 (acknowledge: yes or no) x 2 (target gender: male or female) experimental design. The participants heard a computer-mediated interview while viewing one of the manipulated images. For half of the conditions, the participants heard the applicant acknowledge their stigma. Using an eye tracker, visual attention to the stigma was measured every 30 seconds during the 8-minute interview, producing 16 different time points and a total of 1,792 data points. Multilevel growth curve model analysis examined variation in the trajectory of visual attention to the stigma. The results showed that facial stigmas draw visual attention during a computer-mediated interview, which decreased over time. However, the trajectory of the decrease in visual attention depended on whether an applicant acknowledged their stigma during the interview. The decrease in visual attention was faster in the acknowledgment condition than in the control condition. The current research provides a better understanding to how a facial stigma influences the interview process and provides a theoretical rationale for why acknowledging a facial stigma benefits the interview process

El análisis de redes en el estudio de la colaboración científica

El análisis de redes sociales es una herramienta que se usa cada vez más para determinar las relaciones entre los diferentes elementos bibliográficos que componen un trabajo científico. Desde tiempo atrás, las asociaciones entre coautores y entre sus instituciones y países de adscripción, se toman como una formar de medir las colaboraciones en ciencia. En nuestra presentación examinamos cómo el análisis de redes sociales se emplea para lograr una interpretación más acertada de estas relaciones tomando como ejemplo las colaboraciones bilaterales entre los países latinoamericanos.Social network analysis is a tool used increasingly by bibliometricians to determine the relationships between the different bibliographical elements present in a scientific paper. The associations between coauthors or between the institutions or countries they represent, have long been used as an manifestation of collaboration in science. In this presentation we look at how social network analysis is employed to assist in the interpretation of these relationships using examples taken from our work on bilateral collaborations between countries in Latin America

Sexual dimorphism in the badlands cricket (Orthoptera, Gryllinae, Gryllus personatus)

Sexual dimorphism (SD) is a common phenomenon in sexual species and can manifest in a variety of ways. Sexual size dimorphism (SSD) is commonly investigated, but it can be confounded with sexual shape dimorphism (SShD) if multivariate measures of size are not used. Univariate studies may also overestimate the prevalence or direction of SSD when the sexes are strikingly different in shape, which may be an issue in taxa such as Orthoptera and other terrestrial arthropods where maximum body size is strongly constrained. Here we tested for the occurrence of both SSD and SShD in the badlands cricket Gryllus personatus (Orthoptera, Gryllinae). We measured four body size dimensions—maxillae span, head width, pronotum length, and mean hind femur length—and used multivariate methods to test whether male and female adult badlands crickets were sexually dimorphic in size and/or shape. All the univariate dimensions were sexually dimorphic, with males having wider heads and maxillae than females and females having longer pronota and hind femora than males, which indicates SShD. However, multivariate methods failed to detect SSD, instead confirming that the sexes primarily differ in body shape. We show how a simple ratio of head width to pronotum length captures SShD in badlands crickets and apply it to iNaturalist, a citizen science platform, to broaden our findings. We propose that orthopterists studying SD minimally measure head width, pronotum length, and hind femur length as a standard that will allow a more repeatable and generalizable assessment of the prevalence and direction of both SSD and SShD

Effects of leas and mecury on the blood proteome of children

Heavy metal exposure in children has been associated with a variety of physiological and neurological problems. The goal of this study was to utilize proteomics to enhance the understanding of biochemical interactions responsible for the health problems related to lead and mercury exposure at concentrations well below CDC guidelines. Blood plasma and serum samples from 34 children were depleted of their most abundant proteins using antibody-based affinity columns and analyzed using two different methods, LC-MS/MS and 2-D electrophoresis coupled with MALDI-TOF/MS and tandem mass spectrometry. Apolipoprotein E demonstrated an inverse significant association with lead concentrations (average being one microgram/deciliter) as deduced from LC-MS/MS and 2-D electrophoresis and confirmed by Western blot analysis. This coincides with prior findings that Apolipoprotein E genotype moderates neurobehavioral effects in individuals exposed to lead. Fifteen other proteins were identified by LC-MS/MS as proteins of interest exhibiting expressional differences in the presence of environmental lead and mercury. Brooks Gump is currently at Syracuse University