Association analyses of porcine SERPINE1 reveal sex-specific effects on muscling, growth, fat accretion and meat quality

The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM_213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F(2) population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation.

Automation of an extracorporeal support system with adaptive fuzzy controllers

For patients suffering from cardiogenic shock cardiopulmonary resuscitation may not be sufficient to restore normal heart function. However, their chances of survival may be increased with the use of an extracorporeal support system. With this system the patient's organs are perfused while being transported to the nearest hospital for proper treatment. In the automation of an extracorporeal support system the patient's vital signals are constantly monitored and proper adjustments are performed to improve organ perfusion. In this paper, an adaptive fuzzy controller is proposed that uses the knowledge and expertise of a perfusionist as a starting point and reference for regulation. Furthermore it is able to adapt to the patient's specific reactions by manipulating the rule base of the fuzzy controller. The performance of the adaptive fuzzy controller is tested with a simulation model of the cardiovascular system.

Probe based surface modification of polymers below 30 nm pitch

Heated probes are used to modify the surface of polymeric thin films by thermomechanical indentation and local evaporation of material. The resolution of the processes is discussed for probe-storage and surface patterning-applications. As storage densities exceed 1 Tbit/in2, the depth of the indents becomes comparable to the natural surface roughness of the polymer. By templating an atomically flat surface this limitation can be overcome, enabling storage densities of up to 4 Tbit/in2, corresponding to an indentation half-pitch of 7.5 nm.

Wear-less floating contact imaging of polymer surfaces

An atomic force microscopy (AFM) technique is described combining two operating modes that previously were mutually exclusive: gentle imaging of delicate surfaces requiring slow dynamic AFM techniques, and passive feedback contact mode AFM enabling ultra-fast imaging. A high-frequency force modulation is used to excite resonant modes in the MHz range of a highly compliant cantilever force sensor with a spring constant of 0.1 N m( - 1). The high-order mode acts as a stiff system for modulating the tip-sample distance and a vibration amplitude of 1 nm is sufficient to overcome the adhesion interaction. The soft cantilever provides a force-controlled support for the vibrating tip, enabling high-speed intermittent contact force microscopy without feedback control of the cantilever bending. Using this technique, we were able to image delicate polymer surfaces and to completely suppress the formation of the ripple wear patterns that are commonly observed in contact AFM.

Efficacy of the non-adenosine analogue A1 adenosine receptor agonist (BR-4935) on cardiovascular function after cardiopulmonary bypass

BACKGROUND

We tested the hypothesis that pharmacological preconditioning with a newly developed, potent non-adenosine analogue A1AdoR agonist (BR-4935) improves biventricular cardiac and endothelial function after cardiopulmonary bypass.

METHODS

Twelve anesthetized dogs underwent cardiopulmonary bypass. Dogs were divided into two groups: group 1 (n = 6) received saline vehicle, group 2 (n = 6) received BR-4935 before cardiopulmonary bypass. Biventricular hemodynamic variables were measured using a combined pressure-volume conductance catheter. Coronary blood flow, ATP content, malondialdehyde and myeloperoxidase levels and vasodilatative responses to acetylcholine and sodium nitroprusside were also determined.

RESULTS

Administration of the A1AdoR agonist led to a significantly better recovery of left and right ventricular systolic function after 60 minutes of reperfusion. Although the vasodilatative response to sodium nitroprusside was similar in both groups, acetylcholine resulted in a significantly greater increase in coronary blood flow in the BR-4935 group. In addition, the ATP content was significantly higher in the same group. Furthermore, malondialdehyde and myeloperoxidase levels significantly decreased in the A1AdoR group.

CONCLUSION

Pharmacological preconditioning with a new, potent non-adenosine analogue A1AdoR agonist improves biventricular function recovery and endothelial function after hypothermic cardiac arrest.

Design of a fuzzy controller for the automation of an extracorporeal support system with the use of a simulation environment

The automation of a portable extracorporeal support system may greatly help people who suffer from cardiogenic shock by providing them with an optimal oxygen perfusion and avoid mult-organ failure while being transported to a hospital. This however requires the creation of tools that help in the design of the ideal controller. In this paper a simulation environment is described were a cardiovascular model from the ISR Physiome database was used together with a model of a portable extracorporeal support system. Additionally a model of an oxygenator/blender model is introduced to allow the simulation of oxygen perfusion. Fuzzy controlling was used for automation since it allows a straightforward implementation of expert knowledge. Through the simulation environment different scenarios may be created where intensive testing is possible and constant repetition for control optimization. Initial simulation results are given of the fuzzy controller adjusting the extracorporeal flow rate and oxygen administration for a case of low cardiac output.

Volume ray casting with peak finding and differential sampling

Direct volume rendering and isosurfacing are ubiquitous rendering techniques in scientific visualization, commonly employed in imaging 3D data from simulation and scan sources. Conventionally, these methods have been treated as separate modalities, necessitating different sampling strategies and rendering algorithms. In reality, an isosurface is a special case of a transfer function, namely a Dirac impulse at a given isovalue. However, artifact-free rendering of discrete isosurfaces in a volume rendering framework is an elusive goal, requiring either infinite sampling or smoothing of the transfer function. While preintegration approaches solve the most obvious deficiencies in handling sharp transfer functions, artifacts can still result, limiting classification. In this paper, we introduce a method for rendering such features by explicitly solving for isovalues within the volume rendering integral. In addition, we present a sampling strategy inspired by ray differentials that automatically matches the frequency of the image plane, resulting in fewer artifacts near the eye and better overall performance. These techniques exhibit clear advantages over standard uniform ray casting with and without preintegration, and allow for high-quality interactive volume rendering with sharp C0 transfer functions.

Multi Tbit/in(2) storage densities with thermomechanical probes

Exploiting the spatial resolution of scanning probes presents an attractive approach for novel data storage technologies in particular for large-scale data repositories because of their inherent potential for high storage density. We show that multi-Tbit/in(2) density can be achieved by means of thermomechanically embossing the information as indentation marks into a polymer film. The data density is determined by the nonlinear interaction between closely spaced indents and the fundamental scaling relations governing the shape and size of the indents. We find that cooperative effects in polymers give rise to a minimum indentation radius on the order of the correlation length of the cooperatively rearranged region even if formed by an infinitely sharp indenter. Thus, cooperativity coupled to alpha-transitions in polymers is evinced in a real space geometrical experiment. Furthermore, we predict that indentation marks cannot be made smaller than 5 nm in diameter, which limits the feature resolution for embossing technologies in general.

Phase II efficacy results using an oncolytic herpes simplex virus (NV1020) in patients with colorectal cancer metastatic to liver (mCRC)

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Background: NV1020 is a genetically engineered oncolytic Herpes virus. Published Phase 1 dose-ranging results reported no significant related toxicity except for a mild (<24 hr) viral syndrome. Initial Phase 2 tumor response data using the optimal biological dose (OBD) are now presented. Methods: Patients with heavily pretreated, progressing liver mCRC received 4 doses of NV1020 (1 X108 pfu) by weekly hepatic artery infusion followed by two cycles of conventional chemotherapy. Follow-up (≥1 year) evaluation included 4 X 3-monthly scans, then telephone contact to determine survival. Blinded, independent radiologists interpreted CT (modified RECIST) and FDG PET (EORTC) scans. Results: All 22 patients had prior 5FU-based treatment: 77% and 58% also had oxaliplatin or irinotecan, respectively (50% both agents); 86% had one targeted therapy (24% ≥2 such agents); 29% had radiofrequency ablation. Mean time from primary resection was 95 weeks, mean CEA was 182 ng/mL, and 55% had pulmonary lesions. Two patients received only 2 NV1020 infusions due to rapidly progressing disease. Virus tolerability was unchanged from Phase 1 and no related, serious or Grade 4 toxicity was found. NV1020 neutralizing antibodies rose in all patients but no NV1020 was shed (saliva, skin). After NV1020 alone, 10/22 (45%) and 8/20 (40%) on CT and PET, respectively, showed stable disease. 21 patients subsequently received chemotherapy, 45% with drugs to which they were previously refractory and 36% with only one new drug. 14% refused both planned cycles. Best response observed with CT was 55% (1 CR, 1 PR, 10 SD) and 59% (5 PR, 8 SD) with PET. Despite intrahepatic delivery, some remote responses were observed. Response did not correlate with initial tumor size, SUV, or CEA, with time since primary resection, pre- or post NV1020 chemotherapy type. Nine (41%) remain alive > 1 year. Kaplan-Meier median time to progression is 28 weeks (95% CI [9–37]); median survival probability is 52 weeks (95% CI [36–90]). Conclusions: NV1020 stabilizes liver metastases in highly advanced mCRC and may sensitize tumors to salvage chemotherapy resulting in extended overall survival. A controlled Phase 2/3 trial is justified.

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Relaxation kinetics of nanoscale indents in a polymer glass

Nanometer scale indents have been written in a cross-linked polystyrene sample, and their relaxation has been studied at annealing temperatures well below the glass transition of the polymer. The indents represent a highly nonequilibrium state of the polymer which is subjected to mechanical stress of up to 0.4 GPa and thermal quench rates on the order of 10{8} K/s during writing. It is shown that the relaxation towards equilibrium evolves logarithmically over more than 10 orders of magnitude in time. The relaxation kinetics are accurately described in terms of a thermally activated process with an energy barrier whose magnitude decreases linearly with the distance from equilibrium.

Nanoscale shape-memory function in highly cross-linked polymers

Topographic engraving of structures in polymer surfaces attracts widespread interest for application in imprint lithography and data storage. We study the nonlinear interaction of nanoindents written in close proximity, 20-100 nm, to one another in a highly cross-linked polystyrene matrix. The indents are created thermomechanically by applying heat and force stimuli of 10 micros duration to a tip, thereby raising the polymer temperature to 250 degrees C and exerting contact pressures of up to 1 GPa. We show that on the nanoscale plastic deformation is highly reversible providing outstanding shape-memory functionality of the material.

Self-similarity and finite-size effects in nano-indentation of highly cross-linked polymers

The scalability of thermomechanical polymer deformations in the sub-10 nm regime is of particular importance for nano-imprint techniques, hardness measurements of thin films by nano-indentations, and scanning-probe-based thermomechanical data storage. We investigate nano-indentation in the sub-10 nm regime performed on highly cross-linked polymer films of different thicknesses. It is shown that the lateral and vertical geometric characteristics of the indents independently scale down to an indent depth of 1 nm and that the scaling parameters are functions of the film thickness and the temperature of the indenter. However, in the limit of shallow indents the scaling of the cross-coupling between lateral and vertical dimensions is lost. It is argued that the breakdown of self-similarity is due to a minimum strain requirement originating from the co-operative nature of the polymer response induced by α transitions which lock the indent in the deformed state. The results shed new light on the fundamental processes and size effects involved in nanoscale plastic replication, in general.

Informatics and medicine--from molecules to populations

OBJECTIVES

To clarify challenges and research topics for informatics in health and to describe new approaches for interdisciplinary collaboration and education.

METHODS

Research challenges and possible solutions were elaborated by scientists of two universities using an interdisciplinary approach, in a series of meetings over several months.

RESULTS AND CONCLUSION

In order to translate scientific results from bench to bedside and further into an evidence-based and efficient health system, intensive collaboration is needed between experts from medicine, biology, informatics, engineering, public health, as well as social and economic sciences. Research challenges can be attributed to four areas: bioinformatics and systems biology, biomedical engineering and informatics, health informatics and individual healthcare, and public health informatics. In order to bridge existing gaps between different disciplines and cultures, we suggest focusing on interdisciplinary education, taking an integrative approach and starting interdisciplinary practice at early stages of education.

Interactive isosurface ray tracing of time-varying tetrahedral volumes

We describe a system for interactively rendering isosurfaces of tetrahedral finite-element scalar fields using coherent ray tracing techniques on the CPU. By employing state-of-the art methods in polygonal ray tracing, namely aggressive packet/frustum traversal of a bounding volume hierarchy, we can accomodate large and time-varying unstructured data. In conjunction with this efficiency structure, we introduce a novel technique for intersecting ray packets with tetrahedral primitives. Ray tracing is flexible, allowing for dynamic changes in isovalue and time step, visualization of multiple isosurfaces, shadows, and depth-peeling transparency effects. The resulting system offers the intuitive simplicity of isosurfacing, guaranteed-correct visual results, and ultimately a scalable, dynamic and consistently interactive solution for visualizing unstructured volumes.

New SNPs in the IGF2 gene and association between this gene and backfat thickness and lean meat content in Large White pigs

IGF2-in3-G3072A is a causative mutation for paternally expressed quantitative trait loci on the p arm of porcine chromosome 2 with substantial effect on muscle growth and backfat thickness. The linkage disequilibrium between IGF2-in3-G3072A and IGF2-in7-G162C (IGF2-NciI) in four breeds and associations between these polymorphisms and growth and meat performance in pigs of the Large White breed were analysed. A significant effect of these polymorphisms on backfat thickness and lean meat content was found. In addition, we identified two new single nucleotide polymorphisms (SNPs) in intron 7 of the gene. The existence of complete linkage disequilibrium between IGF2-in3-G3072A locus in the population under study where the locus segregated and SNPs in intron 7 of the IGF2 gene detectable with simple and reliable polymerase chain reaction-restriction fragment length polymorphism techniques (G162C, C179G and G186T) offer possibilities to use these SNPs for genotyping of quantitative trait nucleotide in Large White and Landrace breeds.

SNaPshot Minisequencing and a Panel of Candidate Genes for Complex Routine Testing of Meat Performance Traits in Pigs

The aim of the study was to introduce a convenient method for identification of differences among individual animals in genes supposed to influence meat performance in pigs. The set of seven candidate genes (IGF2, FOS, MC4R, DGAT1, MYF4, MYF, and MC3R) was used. To determine the genotypes, multiplex polymerase chain reaction (PCR) and minisequencing using SNaPshot system (Applied Biosystems; Forster City, CA, USA) were applied. The efficiency of this gene panel for routine testing in pigs was verified in the Black Pied Prestice pig breed by the statistical general linear model. The results showed that both the method and the gene panel are convenient for meat quality testing and offer reproducible results.

Impact of MYOD family genes on pork traits in Large White and Landrace pigs

Porcine myogenic differentiation genes (MYOD) family play a key role in growth and muscle development and are therefore considered as candidate genes for meat production traits. The objective of the study was to investigate the polymorphisms at four loci belonging to the MYOD genes family and analyse their associations with variation in meat production traits in Czech pig breeds. To verify the associations between the polymorphisms and the selected meat traits, altogether 254 pigs, including full- and half-sibs, of Large White and Landrace breeds were tested. The studied meat characteristics were weight of neck, loin, shoulder and ham, lean meat content (LMC), backfat thickness, intramuscular fat (IMF), remission, dry matter content and test daily gain. Statistically significant associations were observed between MYOG gene and fat and neck weight, and between MYF5 gene and IMF and LMC. High significant differences were observed between genotypes AA and AB of MYOD1 in IMF and between genotypes AB and BB of MYF5 in loin weight.

Porcine OGN and ASPN: mapping, polymorphisms and use for quantitative trait loci identification for growth and carcass traits in a Meishan × Pietrain intercross

The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.