Automating the application of smart materials for protein crystallization

The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as 'smart materials') for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials. © 2015, IUCR. All rights reserved

Adverse obstetric and perinatal outcomes following treatment of adolescent and young adult cancer: A population-based cohort study

Objective - To investigate obstetric and perinatal outcomes among female survivors of adolescent and young adult (AYA) cancers and their offspring. Methods - Using multivariate analysis of statewide linked data, outcomes of all first completed pregnancies (n = 1894) in female survivors of AYA cancer diagnosed in Western Australia during the period 1982–2007 were compared with those among females with no cancer history. Comparison pregnancies were matched by maternal age-group, parity and year of delivery. Results - Compared with the non-cancer group, female survivors of AYA cancer had an increased risk of threatened abortion (adjusted relative risk 2.09, 95% confidence interval 1.51–2.74), gestational diabetes (2.65, 2.08–3.57), pre-eclampsia (1.32, 1.04–1.87), post-partum hemorrhage (2.83, 1.92–4.67), cesarean delivery (2.62, 2.22–3.04), and maternal postpartum hospitalization>5 days (3.01, 1.72–5.58), but no excess risk of threatened preterm delivery, antepartum hemorrhage, premature rupture of membranes, failure of labor to progress or retained placenta. Their offspring had an increased risk of premature birth (<37 weeks: 1.68, 1.21–2.08), low birth weight (<2500 g: 1.51, 1.23–2.12), fetal growth restriction (3.27, 2.45–4.56), and neonatal distress indicated by low Apgar score (<7) at 1 minute (2.83, 2.28–3.56), need for resuscitation (1.66, 1.27–2.19) or special care nursery admission (1.44, 1.13–1.78). Congenital abnormalities and perinatal deaths (intrauterine or ≤7 days of birth) were not increased among offspring of survivors. Conclusion - Female survivors of AYA cancer have moderate excess risks of adverse obstetric and perinatal outcomes arising from subsequent pregnancies that may require additional surveillance or intervention

Identifying drivers of spatio-temporal dynamics in Barley Yellow Dwarf Virus epidemiology as a critical factor in disease control

Barley yellow dwarf virus (BYDV) is one of the most important viral diseases of small grains worldwide. An understanding of its epidemiology is crucial to control this disease in a sustainable way. The virus moves through the agricultural landscape via cereal aphids as vectors. Understanding movement of these aphids in space and time is of key importance and in doing so, the spatial and temporal variables that influence BYDV epidemiology can be identified. The presence of summer hosts, crop rotation, crop diversity, agricultural practices and climate variables are crucial. Through digitalization, spatial (e.g. land-use) and temporal (e.g. weather) information is becoming more readily available. Including this information into a prediction model could improve decision support systems that will rationalize the decision-making process towards a more integrated control of the disease

X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection

The X-CHIP (X-ray Crystallography High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process

National Survey of Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongatus Nordmann) on Fish Farms in Ireland – 2019

Farmed stocks of Atlantic salmon in Ireland are inspected on 14 occasions throughout the year to monitor sea lice levels as part of a national programme. Sea lice are a naturally occurring parasite found on marine fish, including salmonids. They are small ecto-parasitic copepod crustaceans and there are approximately 559 species. The objectives of the National Sea Lice Monitoring Programme are: To provide an objective measurement of infestation levels on farms. To investigate the nature of infestations. To provide management information to drive the implementation of control and management strategies. To facilitate further development and refinement of this strategy. The sea lice control and management strategy has five principal components: Separation of generations. Annual fallowing of sites. Early harvest of two-sea-winter fish. Targeted treatment regimes, including synchronous treatments. Agreed husbandry practices

The Pupillary Light Reflex as a Biomarker of Concussion.

The size of our pupils changes continuously in response to variations in ambient light levels, a process known as the pupillary light reflex (PLR). The PLR is not a simple reflex as its function is modulated by cognitive brain function and any long-term changes in brain function secondary to injury should cause a change in the parameters of the PLR. We performed a retrospective clinical review of the PLR of our patients using the BrightLamp Reflex iPhone app. The PLR variables of latency, maximum pupil diameter (MaxPD), minimum pupil diameter (MinPD), maximum constriction velocity (MCV), and the 75% recovery time (75% PRT) were associated with significant differences between subjects who had suffered a concussion and those that had not. There were also significant differences in PLR metrics over the life span and between genders and those subjects with and without symptoms. The differences in PLR metrics are modulated not only by concussion history but also by gender and whether or not the person has symptoms associated with a head injury. A concussive injury to the brain is associated with changes in the PLR that persist over the life span, representing biomarkers that might be used in clinical diagnosis, treatment, and decision making

Paleo-denudation rates suggest variations in runoff drove aggradation during last glacial cycle, Crete, Greece

Fluvial aggradation and incision are often linked to Quaternary climate cycles, but it usually remains unclear whether variations in runoff or sediment supply or both drive channel response to climate variability. Here we quantify sediment supply with paleo-denudation rates and provide geochronological constraints on aggradation and incision from the Sfakia and Elafonisi alluvial-fan sequences in Crete, Greece. We report seven optically stimulated luminescence and ten radiocarbon ages, eight 10Be and eight 36Cl denudation rates from modern channel and terrace sediments. For five samples, 10Be and 36Cl were measured on the same sample by measuring 10Be on chert and 36Cl on calcite. Results indicate relatively steady denudation rates throughout the past 80 kyr, but the aggradation and incision history indicates a link with climate shifts. At the Elafonisi fan, we identify four periods of aggradation coinciding with Marine Isotope Stages (MIS) 2, 4, 5a/b, and likely 6, and three periods of incision coinciding with MIS 1, 3, and likely 5e. At the Sfakia fan, rapid aggradation occurred during MIS 2 and 4, followed by incision during MIS 1. Nearby climate and vegetation records show that MIS 2, 4, and 6 stadials were characterized by cold and dry climates with sparse vegetation, whereas forest cover and more humid conditions prevailed during MIS 1, 3, and 5. Our data thus suggest that past changes in climate had little effect on landscape-wide denudation rates but exerted a strong control on the aggradation–incision behaviour of alluvial channels on Crete. During glacial stages, we attribute aggradation to hillslope sediment release promoted by reduced vegetation cover and decreased runoff; conversely, incision occurred during relatively warm and wet stages due to increased runoff. In this landscape, past hydroclimate variations outcompeted changes in sediment supply as the primary driver of alluvial deposition and incision

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

<p>Abstract</p> <p>Background</p> <p>Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist.</p> <p>Results</p> <p>We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV.</p> <p>Conclusions</p> <p>To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects.</p> <p>Availability and Implementation</p> <p>Available on the web at: <url>http://sourceforge.net/projects/cnv</url></p

The Viscous Nonlinear Dynamics of Twist and Writhe

Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature and twist density embodies the dynamic interplay of twist and writhe. These are used to illustrate a novel nonlinear phenomenon: ``geometric untwisting" of open filaments, whereby twisting strains relax through a transient writhing instability without performing axial rotation. This may explain certain experimentally observed motions of fibers of the bacterium B. subtilis [N.H. Mendelson, et al., J. Bacteriol. 177, 7060 (1995)].Comment: 9 pages, 4 figure

Can the Relationship between Doctors and Drug Companies Ever Be a Healthy One?

Emma D'Arcy and Ray Moynihan debate whether doctors and drug companies can form healthy alliances or whether these will always be prone to the corrupting influence of drug company money