The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Association of Low B Cell Count and IgG Levels With Infection, and Poor Vaccine Response With All-Cause Mortality in an Immunosuppressed Vasculitis Population.

OBJECTIVE: Patients with systemic vasculitis (SV) have an increased risk of all-cause mortality, often due to infection, compared to the healthy population. We investigated whether humoral response to vaccination and biomarkers of immune dysfunction were associated with infection and death. METHODS: Patients with SV in remission were vaccinated with pneumococcal 7-valent conjugate, Haemophilus influenzae type b, and meningococcal group C conjugate vaccine and meningococcal polysaccharide groups A, C, Y, and W135 vaccines. Total IgG and antibody titers against specific antigens and lymphocyte subset analysis were performed before vaccination. Postvaccination antibody titers were measured at 4 weeks and 2 years, from which an antibody response score was calculated. Infections and death following vaccination were collected prospectively following vaccination. RESULTS: A total of 92 patients were safely vaccinated with no increase in disease relapse, median followup 4.6 years (interquartile range [IQR] 3.6-4.8 years). Eighteen patients died at a median of 2 years and the overall infection rate was 0.4 (IQR 0.2-1.3) infections/patient/year. Reduced serum IgG, B cell count, and CD4+ cell counts predicted poor vaccine response and infection but not death. The response rates to individual vaccine antigens was highly variable, with a median response rate of 46% (IQR 39-58%) of patients responding to each individual antigen. Vaccine response, age, and reduced renal function were independent predictors of all-cause mortality in multivariate analysis. CONCLUSION: Total IgG and B cell counts predict infection and response to vaccination. Vaccination in patients with SV in remission is safe and the response predicts all-cause mortality. Vaccine response is a surrogate marker of immune system health.

Dynamics of among-individual behavioral variation over adult lifespan in a wild insect.

Investigating patterns of among and within-individual trait variation in populations is essential to understanding how selection shapes phenotypes. Behavior is often the most flexible aspect of the phenotype, and to understand how it is affected by selection, we need to examine how consistent individuals are. However, it is not well understood whether among-individual differences tend to remain consistent over lifetimes, or whether the behavior of individuals relative to one another varies over time. We examined the dynamics of 4 behavioral traits (tendency to leave a refuge, shyness, activity, and exploration) in a wild population of field crickets (Gryllus campestris). We tagged individuals and then temporarily removed them from their natural environment and tested them under laboratory conditions. All 4 traits showed among-individual variance in mean levels of expression across the adult lifespan, but no significant differences in how rapidly expression changed with age. For all traits, among-individual variance increased as individuals got older. Our findings reveal seldom examined changes in variance components over the adult lifetime of wild individuals. Such changes will have important implications for the relationship between behavioral traits, life-histories, and fitness and the consequences of selection on wild individuals.

Pairing context determines condition-dependence of song rate in a monogamous passerine bird.

Condition-dependence of male ornaments is thought to provide honest signals on which females can base their sexual choice for genetic quality. Recent studies show that condition-dependence patterns can vary within populations. Although long-term association is thought to promote honest signalling, no study has explored the influence of pairing context on the condition-dependence of male ornaments. In this study, we assessed the influence of natural variation in body condition on song rate in zebra finches (Taeniopygia guttata) in three different situations: during short and long encounters with an unfamiliar female, and within heterosexual mated pairs. We found consistent individual differences in male directed and undirected song rate. Moreover, body condition had a positive effect on song rate in paired males. However, male song rate was not influenced by body condition during short or long encounters with unfamiliar females. Song rate appears to be an unreliable signal of condition to prospective females as even poor-condition birds can cheat and sing at a high rate. By contrast, paired females can reliably use song rate to assess their mate's body condition, and possibly the genetic quality. We propose that species' characteristics, such as mating system, should be systematically taken into account to generate relevant hypotheses about the evolution of condition-dependent male ornaments.

Handling stress does not reflect personality in female zebra finches (Taeniopygia guttata).

Although increasing attention is given to both the causes and consequences of variation in animal personality, the measurement of personality in captive or free-ranging individuals remains an issue. In particular, one important question concerns whether personality should be established from the existence of complex behavioral syndromes (a suite of correlated behavioral traits) or could be more easily deduced from a single variable. In that context, it has recently been suggested that handling stress, measured through breathing rate during handling, could be a good descriptor of personality, at least in passerine birds. The authors experimentally investigated to what extent handling stress was correlated with personality in female zebra finches (Taeniopygia guttata), as assessed from a suite of repeatable behavioral traits, including activity, exploratory behavior, neophobia, and reaction to startle. Although breathing rate was repeatable across individuals, it was not related to any behavioral trait, suggesting that it cannot be used to quickly predict personality, at least in zebra finches. Breathing rate during handling, in addition, was related to morphology, questioning the fact that breathing rate during handling reflects personality irrespective of individual state. The authors suggest that inference on global personality from a reduced number of traits should be performed with caution.

Personality may confound common measures of mate-choice.

The measurement of female mating preferences is central to the study of the evolution of male ornaments. Although several different methods have been developed to assess sexual preference in some standardized way, the most commonly used procedure consists of recording female spatial association with different males presented simultaneously. Sexual preference is then inferred from time spent in front of each male. However, the extent to which the measurement of female mate-choice is related to exploration tendencies has not been addressed so far. In the present study we assessed the influence of variation in exploration tendencies, a trait closely associated to global personality, on the measurement of female mating preference in the zebra finch (Taeniopygia guttata) using the widely used four-chamber choice-apparatus. The number of movements performed within both exploration and mate-choice apparatus was consistent within and across the two contexts. In addition, personality explained variation in selectivity, preference strength and consistency. High-exploratory females showed lower selectivity, lower preference scores and displayed more consistent preference scores. Our results suggest that variation in personality may affect the measurement of female mating preference and may contribute to explain existing inconsistencies across studies.

Towards image guided robotic surgery: multi-arm tracking through hybrid localization.

OBJECTIVE: Use of the robotic assisted surgery has been increasing in recent years, due both the continuous increase in the number of applications and the clinical benefits that surgical robots can provide. Currently robotic assisted surgery relies on endoscopic video for navigation, providing only surface visualization, thus limiting subsurface vision. To be able to visualize and identify subsurface information, techniques in image-guidance can be used. As part of designing an image guidance system, all arms of the robot need to be co-localized in a common coordinate system. METHODS: In order to track multiple arms in a common coordinate space, intrinsic and extrinsic tracking methods can be used. First, the intrinsic tracking of the daVinci, specifically of the setup joints is analyzed. Because of the inadequacy of the setup joints for co-localization a hybrid tracking method is designed and implemented to mitigate the inaccuracy of the setup joints. Different both optical and magnetic tracking methods are examined for setup joint localization. RESULTS: The hybrid localization method improved the localization accuracy of the setup joints. The inter-arm accuracy in hybrid localization was improved to 3.02 mm. This inter-arm error value was shown to be further reduced when the arms are co-registered, thus reducing common error.

Toward image guided robotic surgery: system validation.

PURPOSE: Navigation for current robotic assisted surgical techniques is primarily accomplished through a stereo pair of laparoscopic camera images. These images provide standard optical visualization of the surface but provide no subsurface information. Image guidance methods allow the visualization of subsurface information to determine the current position in relationship to that of tracked tools. MATERIALS AND METHODS: A robotic image guided surgical system was designed and implemented based on our previous laboratory studies. A series of experiments using tissue mimicking phantoms with injected target lesions was performed. The surgeon was asked to resect "tumor" tissue with and without the augmentation of image guidance using the da Vinci robotic surgical system. Resections were performed and compared to an ideal resection based on the radius of the tumor measured from preoperative computerized tomography. A quantity called the resection ratio, that is the ratio of resected tissue compared to the ideal resection, was calculated for each of 13 trials and compared. RESULTS: The mean +/- SD resection ratio of procedures augmented with image guidance was smaller than that of procedures without image guidance (3.26 +/- 1.38 vs 9.01 +/- 1.81, p <0.01). Additionally, procedures using image guidance were shorter (average 8 vs 13 minutes). CONCLUSIONS: It was demonstrated that there is a benefit from the augmentation of laparoscopic video with updated preoperative images. Incorporating our image guided system into the da Vinci robotic system improved overall tissue resection, as measured by our metric. Adding image guidance to the da Vinci robotic surgery system may result in the potential for improvements such as the decreased removal of benign tissue while maintaining an appropriate surgical margin.

Ant repellent effect of the sternal gland secretion ofPolistes dominulus (Christ) andP. sulcifer (Zimmermann). (Hymenoptera: Vespidae).

The long-chain carboxylic acids identified in the sternal gland secretion ofPolistes dominulus andP. sulcifer females were tested individually on three species of ants,Crematogaster scutellaris, Formica cunicularia, andLasius sp., in order to verify if they have a repellent effect. The unsaturated acids (palmitoleic, linoleic, and oleic) act as repellents of all three ant species, while the saturated acids (lauric, myristic, palmitic, and stearic) have no effect. The mixture reproducing the secretion of the sternal glands ofP. dominulus maintained its repellency for at least four days.

Chemical analysis of sternal gland secretion of paper waspPolistes dominulus (Christ) and its social parasitePolistes sulcifer (Zimmermann) (Hymenoptera: Vespidae).

The secretion of the tegumental glands of the fifth and sixth gastral sternites ofP. dominulus and of its social parasiteP. sulcifer was analyzed by gas chromatography-mass spectrometry. Seven long-chain carboxylic acids have been identified: hexadecanoic, octadecadienoic and octadecenoic acids are the major components of the gland secretion ofP. dominulus and octadecenoic acid the main compounds ofP. sulcifer sternal gland secretion. The same carboxylic acids have been found on the nest pedicel.

Volatile secretions of old world army antAenictus rotundatus and chemotaxonomic implications of army ant dufour gland chemistry.

The Dufour glands ofAenictus rotundatus contain a complex mixture of terpenoids with geranylgeraniol comprising over 50% of the secretion. Some novel compounds have been tentatively identified as higher homologs of 1,3,3-trimethyl-2,7-dioxabicyclo[2,2,1]heptane based on GC-MS data. The Dufour gland secretion ofA. rotundatus is more similar in composition to the secretions of members of the subfamily Ecitoninae than to its closer relatives from the tribe Dorylini, a result that further complicates studies on the phylogeny of army ants. The mandibular glands ofA. rotundatus contain a mixture of 4-methyl-3-heptanone and limonene in trace amounts, and the well-developed postpygidial glands contain methyl anthranilate only.