Olfactory bulb hypoplasia in Prokr2 null mice stems from defective neuronal progenitor migration and differentiation.

New neurons are added on a daily basis to the olfactory bulb (OB) of a mammal, and this phenomenon exists throughout its lifetime. These new cells are born in the subventricular zone and migrate to the OB via the rostral migratory stream (RMS). To examine the role of the prokineticin receptor 2 (Prokr2) in neurogenesis, we created a Prokr2 null mouse, and report a decrease in the volume of its OB and also a decrease in the number of bromodeoxyuridine (BrdU)-positive cells. There is disrupted architecture of the OB, with the glomerular layer containing terminal dUTP nick-end labeling (TUNEL) -positive nuclei and also a decrease in tyrosine hydroxylase-positive neurons in this layer. In addition, there are increased numbers of doublecortin-positive neuroblasts in the RMS and increased PSA-NCAM (polysialylated form of the neural cell adhesion molecule) -positive neuronal progenitors around the olfactory ventricle, indicating their detachment from homotypic chains is compromised. Finally, in support of this, Prokr2-deficient cells expanded in vitro as neurospheres are incapable of migrating towards a source of recombinant human prokineticin 2 (PROK2). Together, these findings suggest an important role for Prokr2 in OB neurogenesis

The length of homology required for gene targeting in embryonic stem cells

Homologous recombination has been used to introduce site-specific mutations into murine embryonic stem (ES) cells with both insertion and replacement vectors. In this study, we compared the frequency of gene targeting with various lengths of homology and found a dramatic increase in targeting with an increase in homology from 1.3 to 6.8 kb. We examined in detail the relationship between the length of homology and the gene-targeting frequency for replacement vectors and found that a critical length of homology is needed for targeting. Adding greater lengths of homology to this critical length has less of an effect on the targeting frequency. We also analyzed the lengths of homology necessary on both arms of the vector for gene replacement events and found that 472 bp of homology is used as efficiently as 1.2 kb in the formation and resolution of crossover junctions

High-density P300 enhancers control cell state transitions.

BACKGROUND: Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise extended clusters dubbed stretch- or super-enhancers (SEs). These SEs are located near key cell identity genes, and enriched for non-coding genetic variations associated with disease. Previously, SEs have been defined as having the highest density of Med1, Brd4 or H3K27ac by ChIP-seq. The histone acetyltransferase P300 has been used as a marker of enhancers, but little is known about its binding to SEs. RESULTS: We establish that P300 marks a similar SE repertoire in embryonic stem cells as previously reported using Med1 and H3K27ac. We also exemplify a role for SEs in mouse T helper cell fate decision. Similarly, upon activation of macrophages by bacterial endotoxin, we found that many SE-associated genes encode inflammatory proteins that are strongly up-regulated. These SEs arise from small, low-density enhancers in unstimulated macrophages. We also identified expression quantitative trait loci (eQTL) in human monocytes that lie within such SEs. In macrophages and Th17 cells, inflammatory SEs can be perturbed either genetically or pharmacologically thus revealing new avenues to target inflammation. CONCLUSIONS: Our findings support the notion that P300-marked SEs can help identify key nodes of transcriptional control during cell fate decisions. The SE landscape changes drastically during cell differentiation and cell activation. As these processes are crucial in immune responses, SEs may be useful in revealing novel targets for treating inflammatory diseases

On Discrimination Discovery and Removal in Ranked Data using Causal Graph

Predictive models learned from historical data are widely used to help companies and organizations make decisions. However, they may digitally unfairly treat unwanted groups, raising concerns about fairness and discrimination. In this paper, we study the fairness-aware ranking problem which aims to discover discrimination in ranked datasets and reconstruct the fair ranking. Existing methods in fairness-aware ranking are mainly based on statistical parity that cannot measure the true discriminatory effect since discrimination is causal. On the other hand, existing methods in causal-based anti-discrimination learning focus on classification problems and cannot be directly applied to handle the ranked data. To address these limitations, we propose to map the rank position to a continuous score variable that represents the qualification of the candidates. Then, we build a causal graph that consists of both the discrete profile attributes and the continuous score. The path-specific effect technique is extended to the mixed-variable causal graph to identify both direct and indirect discrimination. The relationship between the path-specific effects for the ranked data and those for the binary decision is theoretically analyzed. Finally, algorithms for discovering and removing discrimination from a ranked dataset are developed. Experiments using the real dataset show the effectiveness of our approaches.Comment: 9 page

Compact Infrasonic Windscreen

A compact windscreen has been conceived for a microphone of a type used outdoors to detect atmospheric infrasound from a variety of natural and manmade sources. Wind at the microphone site contaminates received infrasonic signals (defined here as sounds having frequencies <20 Hz), because a microphone cannot distinguish between infrasonic pressures (which propagate at the speed of sound) and convective pressure fluctuations generated by wind turbulence. Hence, success in measurement of outdoor infrasound depends on effective screening of the microphone from the wind. The present compact windscreen is based on a principle: that infrasound at sufficiently large wavelength can penetrate any barrier of practical thickness. Thus, a windscreen having solid, non-porous walls can block convected pressure fluctuations from the wind while transmitting infrasonic acoustic waves. The transmission coefficient depends strongly upon the ratio between the acoustic impedance of the windscreen and that of air. Several materials have been found to have impedance ratios that render them suitable for use in constructing walls that have practical thicknesses and are capable of high transmission of infrasound. These materials (with their impedance ratios in parentheses) are polyurethane foam (222), space shuttle tile material (332), balsa (323), cedar (3,151), and pine (4,713)

Novel components of the Toxoplasma inner membrane complex revealed by BioID.

UNLABELLED:The inner membrane complex (IMC) of Toxoplasma gondii is a peripheral membrane system that is composed of flattened alveolar sacs that underlie the plasma membrane, coupled to a supporting cytoskeletal network. The IMC plays important roles in parasite replication, motility, and host cell invasion. Despite these central roles in the biology of the parasite, the proteins that constitute the IMC are largely unknown. In this study, we have adapted a technique named proximity-dependent biotin identification (BioID) for use in T.&nbsp;gondii to identify novel components of the IMC. Using IMC proteins in both the alveoli and the cytoskeletal network as bait, we have uncovered a total of 19 new IMC proteins in both of these suborganellar compartments, two of which we functionally evaluate by gene knockout. Importantly, labeling of IMC proteins using this approach has revealed a group of proteins that localize to the sutures of the alveolar sacs that have been seen in their entirety in Toxoplasma species only by freeze fracture electron microscopy. Collectively, our study greatly expands the repertoire of known proteins in the IMC and experimentally validates BioID as a strategy for discovering novel constituents of specific cellular compartments of T.&nbsp;gondii. IMPORTANCE:The identification of binding partners is critical for determining protein function within cellular compartments. However, discovery of protein-protein interactions within membrane or cytoskeletal compartments is challenging, particularly for transient or unstable interactions that are often disrupted by experimental manipulation of these compartments. To circumvent these problems, we adapted an in vivo biotinylation technique called BioID for Toxoplasma species to identify binding partners and proximal proteins within native cellular environments. We used BioID to identify 19 novel proteins in the parasite IMC, an organelle consisting of fused membrane sacs and an underlying cytoskeleton, whose protein composition is largely unknown. We also demonstrate the power of BioID for targeted discovery of proteins within specific compartments, such as the IMC cytoskeleton. In addition, we uncovered a new group of proteins localizing to the alveolar sutures of the IMC. BioID promises to reveal new insights on protein constituents and interactions within cellular compartments of Toxoplasma

A Randomized Controlled Trial to Compare Computer-assisted Motivational Intervention with Didactic Educational Counseling to Reduce Unprotected Sex in Female Adolescents

Study Objective: To examine a computer-assisted, counselor-guided motivational intervention (CAMI) aimed at reducing the risk of unprotected sexual intercourse. Design, Setting, Participants, Interventions, and Main Outcome Measures: We conducted a 9-month, longitudinal randomized controlled trial with a multisite recruitment strategy including clinic, university, and social referrals, and compared the CAMI with didactic educational counseling in 572 female adolescents with a mean age of 17 years (SD = 2.2 years; range = 13-21 years; 59% African American) who were at risk for pregnancy and sexually transmitted diseases. The primary outcome was the acceptability of the CAMI according to self-reported rating scales. The secondary outcome was the reduction of pregnancy and sexually transmitted disease risk using a 9-month, self-report timeline follow-back calendar of unprotected sex. Results: We conducted a 9-month, longitudinal randomized controlled trial with a multisite recruitment strategy including clinic, university, and social referrals, and compared the CAMI with didactic educational counseling in 572 female adolescents with a mean age of 17 years (SD = 2.2 years; range = 13-21 years; 59% African American) who were at risk for pregnancy and sexually transmitted diseases. The primary outcome was the acceptability of the CAMI according to self-reported rating scales. The secondary outcome was the reduction of pregnancy and sexually transmitted disease risk using a 9-month, self-report timeline follow-back calendar of unprotected sex. Conclusion: Among those who completed the intervention, the CAMI reduced unprotected sex among an at-risk, predominantly minority sample of female adolescents. Modification of the CAMI to address methodological issues that contributed to a high drop-out rate are needed to make the intervention more acceptable and feasible for use among sexually active predominantly minority, at-risk, female adolescents

Arrays of Miniature Microphones for Aeroacoustic Testing

A phased-array system comprised of custom-made and commercially available microelectromechanical system (MEMS) silicon microphones and custom ancillary hardware has been developed for use in aeroacoustic testing in hard-walled and acoustically treated wind tunnels. Recent advances in the areas of multi-channel signal processing and beam forming have driven the construction of phased arrays containing ever-greater numbers of microphones. Traditional obstacles to this trend have been posed by (1) the high costs of conventional condenser microphones, associated cabling, and support electronics and (2) the difficulty of mounting conventional microphones in the precise locations required for high-density arrays. The present development overcomes these obstacles. One of the hallmarks of the new system is a series of fabricated platforms on which multiple microphones can be mounted. These mounting platforms, consisting of flexible polyimide circuit-board material (see left side of figure), include all the necessary microphone power and signal interconnects. A single bus line connects all microphones to a common power supply, while the signal lines terminate in one or more data buses on the sides of the circuit board. To minimize cross talk between array channels, ground lines are interposed as shields between all the data bus signal lines. The MEMS microphones are electrically connected to the boards via solder pads that are built into the printed wiring. These flexible circuit boards share many characteristics with their traditional rigid counterparts, but can be manufactured much thinner, as small as 0.1 millimeter, and much lighter with boards weighing as much as 75 percent less than traditional rigid ones. For a typical hard-walled wind-tunnel installation, the flexible printed-circuit board is bonded to the tunnel wall and covered with a face sheet that contains precise cutouts for the microphones. Once the face sheet is mounted, a smooth surface is established over the entire array due to the flush mounting of all microphones (see right side of figure). The face sheet is made from a continuous glass-woven-fabric base impregnated with an epoxy resin binder. This material offers a combination of high mechanical strength and low dielectric loss, making it suitable for withstanding the harsh test section environment present in many wind tunnels, while at the same time protecting the underlying polyimide board. Customized signal-conditioning hardware consisting of line drivers and antialiasing filters are coupled with the array. The line drivers are constructed using low-supply-current, high-gain-bandwidth operational amplifiers designed to transmit the microphone signals several dozen feet from the array to external acquisition hardware. The anti-alias filters consist of individual Chebyshev low-pass filters (one for each microphone channel) housed on small printed-circuit boards mounted on one or more motherboards. The mother/daughter board design results in a modular system, which is easy to debug and service and which enables the filter characteristics to be changed by swapping daughter boards with ones containing different filter parameters. The filter outputs are passed to commercially- available acquisition hardware to digitize and store the conditioned microphone signals. Wind-tunnel testing of the new MEMS microphone polyimide mounting system shows that the array performance is comparable to that of traditional arrays, but with significantly less cost of construction

Morphology of axisymmetric vesicles with encapsulated filaments and impurities

The shape deformation of a three-dimensional axisymmetric vesicle with encapsulated filaments or impurities is analyzed by integrating a dissipation dynamics. This method can incorporate systematically the constraint of a fixed surface area and/or a fixed volume. The filament encapsulated in a vesicle is assumed to take a form of a rod or a ring so as to imitate cytoskeletons. In both cases, results of the shape transition of the vesicle are summarized in phase diagrams in the phase space of the vesicular volume and a rod length or a ring radius. We also study the dynamics of a vesicle with impurities coupled to the membrane curvature. The phase separation and the associated shape deformation in the early stage of the dynamical evolution can well be explained by the linear stability analysis. Long runs of simulation demonstrate the nonlinear coarsening of the wavy deformation of the vesicle in the late stage.Comment: 9 pages, 9 figure