Predicted genetic burden and frequency of phenotype-associated variants in the horse.

Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.

Dosimetric and biologic intercomparison between electron and proton FLASH beams.

BACKGROUND AND PURPOSE: The FLASH effect has been validated in different preclinical experiments with electrons (eFLASH) and protons (pFLASH) operating at an average dose rate above 40 Gy/s. However, no systematic intercomparison of the FLASH effect produced by eFLASHvs. pFLASH has yet been performed and constitutes the aim of the present study. MATERIALS AND METHODS: The electron eRT6/Oriatron/CHUV/5.5 MeV and proton Gantry1/PSI/170 MeV were used to deliver conventional (0.1 Gy/s eCONV and pCONV) and FLASH (≥110 Gy/s eFLASH and pFLASH) dose rates. Protons were delivered in transmission. Dosimetric and biologic intercomparisons were performed using previously validated dosimetric approaches and experimental murine models. RESULTS: The difference between the average absorbed dose measured at Gantry 1 with PSI reference dosimeters and with CHUV/IRA dosimeters was -1.9 % (0.1 Gy/s) and + 2.5 % (110 Gy/s). The neurocognitive capacity of eFLASH and pFLASH irradiated mice was indistinguishable from the control, while both eCONV and pCONV irradiated cohorts showed cognitive decrements. Complete tumor response was obtained after an ablative dose of 20 Gy delivered with the two beams at CONV and FLASH dose rates. Tumor rejection upon rechallenge indicates that anti-tumor immunity was activated independently of the beam-type and the dose-rate. CONCLUSION: Despite major differences in the temporal microstructure of proton and electron beams, this study shows that dosimetric standards can be established. Normal brain protection and tumor control were produced by the two beams. More specifically, normal brain protection was achieved when a single dose of 10 Gy was delivered in 90 ms or less, suggesting that the most important physical parameter driving the FLASH sparing effect might be the mean dose rate. In addition, a systemic anti-tumor immunological memory response was observed in mice exposed to high ablative dose of electron and proton delivered at CONV and FLASH dose rate.

Dosimetric and biologic intercomparison between electron and proton FLASH beams.

Background and purpose: The FLASH effect has been validated in different preclinical experiments with electrons (eFLASH) and protons (pFLASH) operating at a mean dose rate above 40 Gy/s. However, no systematic intercomparison of the FLASH effect produced by e vs. pFLASH has yet been performed and constitutes the aim of the present study. Materials and methods: The electron eRT6/Oriatron/CHUV/5.5 MeV and proton Gantry1/PSI/170 MeV were used to deliver conventional (0.1 Gy/s eCONV and pCONV) and FLASH (≥100 Gy/s eFLASH and pFLASH) irradiation. Protons were delivered in transmission. Dosimetric and biologic intercomparisons were performed with previously validated models. Results: Doses measured at Gantry1 were in agreement (± 2.5%) with reference dosimeters calibrated at CHUV/IRA. The neurocognitive capacity of e and pFLASH irradiated mice was indistinguishable from the control while both e and pCONV irradiated cohorts showed cognitive decrements. Complete tumor response was obtained with the two beams and was similar between e and pFLASH vs. e and pCONV. Tumor rejection was similar indicating that T-cell memory response is beam-type and dose-rate independent. Conclusion: Despite major differences in the temporal microstructure, this study shows that dosimetric standards can be established. The sparing of brain function and tumor control produced by the two beams were similar, suggesting that the most important physical parameter driving the FLASH effect is the overall time of exposure which should be in the range of hundreds of milliseconds for WBI in mice. In addition, we observed that immunological memory response is similar between electron and proton beams and is independent off the dose rate.

In situcorrection of recombination effects in ultra-high dose rate irradiations with protons.

Background.At the Center for Proton Therapy at the Paul Scherrer Institute (PSI) the delivery of proton radiation is controlled via gas-based ionization chambers: the beam is turned off when a certain amount of preset charge has been collected. At low dose rates the charge collection efficiency in these detectors is unity, at ultra-high dose rates it is less due to induced charge recombination effects. If not corrected, the latter would lead to an overdosage.Purpose.In the scope of this work, we developed a novel approach to anin situcharge recombination correction for our dose defining detectors, when irradiated with a proton beam at ultra-high dose rates. This approach is based on the Two-Voltage-Method.Methods.We have translated this method to two separate devices operated simultaneously at different conditions. By doing so, the charge collection losses can be corrected directly and without the need for empirical correction values. This approach has been tested at ultra-high dose rates; proton beam was delivered by the COMET cyclotron to Gantry 1 at PSI.Results.We were able to correct the charge losses caused by recombination effects at local beam currents of approximately 700 nA (i.e. instantaneous dose rate of 3600 Gy s-1at isocenter). The corrected collected charges in our gaseous detectors were compared against recombination-free measurements with a Faraday cup. The ratio of both quantities shows no significant dose rate dependence within their respective combined uncertainties.Conclusions. Correcting recombination effects in our gas-based detectors with the novel method greatly eases the handling of Gantry 1 as 'FLASH test bench'. Not only is the application of a preset dose more accurate compared to using an empirical correction curve, also the re-determination of empirical correction curves in the case of a beam phase space change can be omitted.

Genetic Variation and the Distribution of Variant Types in the Horse.

Genetic variation is a key contributor to health and disease. Understanding the link between an individual's genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.

Night-Time Ionospheric Localized Enhancements (NILE) Observed in North America Following Geomagnetic Disturbances.

The Ionospheric Data Assimilation Four-Dimensional (IDA4D) technique has been coupled to Sami3, which is another model of the ionosphere (SAMI3). In this application, ground-based and space-based GPS total electron content (TEC) data have been assimilated into SAMI3, while in-situ electron densities, autoscaled ionosonde NmF2, and reference GPS stations have been used for validation. IDA4D/SAMI3 shows that night-time ionospheric localized enhancements (NILE) are formed following geomagnetic storms in November 2003 and August 2018. The NILE phenomenon appears as a moderate, longitudinally extended enhancement of NmF2 at 30°-40°N MLAT, occurring in the late evening (20-24 LT) following much larger enhancements of the equatorial anomaly crests in the main phase of the storms. The NILE appears to be caused by upward and northward plasma transport around the dusk terminator, which is consistent with eastward polarization electric fields. Independent validation confirms the presence of the NILE, and indicates that IDA4D is effective in correcting random errors and systematic biases in SAMI3. In all cases, biases and root-mean-square errors are reduced by the data assimilation, typically by a factor of 2 or more. During the most severe part of the November 2003 storm, the uncorrected ionospheric error on a GPS 3D position at 1LSU (Louisiana) is estimated to exceed 34 m. The IDA4D/SAMI3 specification is effective in correcting this down to 10 m.

Vox Sanguinis International Forum on the use of prehospital blood products and pharmaceuticals in the treatment of patients with traumatic haemorrhage.

While specific practices and transported blood products vary around the world, most of the respondents in this International Forum transported at least one blood product for the transfusion to bleeding patients en route to the hospital. The most commonly carried product was RBCs, while the use of whole blood will likely increase given the recent reports of its successful use in the civilian setting, and because of the change in the AABB's Standards regulating its use. It will be interesting to see if plasma use in the prehospital setting becomes more widely used given today's enhanced appreciated of the coagulopathy of trauma and plasma's beneficial effect in reversing it, and if blood products are transported to the scene of injury by more vehicles, that is, not just predominantly in helicopters. It was not surprising that TXA is being widely administered as close to the time of injury as possible given its potential benefit in these patients. This International Forum highlights the importance of focusing attention on prehospital transfusion management with a need to further high­quality research in this area to guide optimal resuscitation strategies.

[Refeeding syndrome : Pathophysiology, risk factors, prevention, and treatment]. / Refeeding-Syndrom : Pathophysiologie, Risikofaktoren, Prophylaxe und Therapie.

Refeeding syndrome is a life-threatening complication that may occur after initiation of nutritional therapy in malnourished patients, as well as after periods of fasting and hunger. Refeeding syndrome can be effectively prevented and treated if its risk factors and pathophysiology are known. The initial measurement of thiamine level and serum electrolytes, including phosphate and magnesium, their supplementation if necessary, and a slow increase in nutritional intake along with close monitoring of serum electrolytes play an important role. Since refeeding syndrome is not well known and the symptoms can be extremely heterogeneous, this complication is poorly recognized, especially against the background of severe disease and multimorbidity. This overview aims to summarize the current knowledge and increase awareness about refeeding syndrome.

Porcine respiratory disease complex after the introduction of H1N1/2009 influenza virus in Brazil.

From 2009 to 2015, 74 lungs from suckling (6.8%), nursing (70.3%), fattening (20.3%) pigs and pregnant sows (2.7%) with respiratory signs from pig farms in Southern Brazil were submitted to a diagnostic laboratory for necropsy and/or histologic examination and screening for respiratory agents by RT-qPCR, immunohistochemistry (IHC), virus isolation (VI) and subtyping for influenza A virus (IAV), IHC and nested PCR for Mycoplasma hyopneumoniae (Mhyo), PCR for porcine circovirus 2 (PCV2), RT-qPCR for porcine reproductive and respiratory syndrome virus (PRRSV) and bacterial culture. All lung samples were positive for IAV using RT-qPCR. Seventy-two lungs had histologic lesions associated with acute to subacute IAV infection characterized by necrotizing bronchiolitis/bronchitis or bronchointerstitial pneumonia with lymphocytic peribronchiolitis and bronchiolar/bronchial hyperplasia, respectively. Forty-nine lungs (66.2%) were positive by IHC for IAV nucleoprotein. The H1N1/2009 was the most common subtype and the only IAV detected in 58.1% of lungs, followed by H1N2 (9.5%) and H3N2 (6.8%). Coinfection of IAV and Mhyo was seen in 23 (31%) cases. Although 14.9% of the lungs were positive for PCV2 using PCR, no suggestive lesions of PCV2 disease were observed. Porcine reproductive and respiratory syndrome virus (PRRSV) was not detected, consistent with the PRRS-free status of Brazil. Secondary bacterial infections (8/38) were associated with suppurative bronchopneumonia and/or pleuritis. Primary IAV infection with Mhyo coinfection was the most common agents found in porcine respiratory disease complex (PRDC) in pigs in Southern Brazil.

[Anemia and iron deficiency in the elderly. Prevalence, diagnostics and new therapeutic options]. / Anämie und Eisenmangel in der Geriatrie. Prävalenz, Diagnostik und neue Therapieoptionen.

The prevalence of anemia in geriatric patients is high. With some variation in different patient cohorts, prevalence of anemia can reach 40%. Anemia is not an age-related disease on its own, but is a symptom with multifactorial genesis and high risk potential. It directly influences mortality, morbidity, and the rate of hospitalization, particularly in older patients suffering from chronic heart failure or chronic kidney disease. The high prevalence of anemia in chronic kidney disease is explained by a combination of erythropoietin and iron deficiency. This review summarizes the recommendations of the iron symposium at the 2010 German Geriatric Society Meeting in Potsdam, Germany. It intends to provide current information on prevalence, diagnostic work-up, and therapeutic options for anemia in the rapidly growing group of elderly patients.

Associations between the concurrent use of clinical decision support and computerized provider order entry and the rates of appropriate prescribing at discharge.

INTRODUCTION: Electronic health record systems used in conjunction with clinical decision support (CDS) or computerized provider order entry (CPOE) have shown potential in improving quality of care, yet less is known about the effects of combination use of CDS and CPOE on prescribing rates at discharge. OBJECTIVES: This study investigates the effectiveness of combination use of CDS and CPOE on appropriate drug prescribing rates at discharge for AMI or HF patients. METHODS: Combination use of CDS and CPOE is defined as hospitals self-reporting full implementation across all hospital units of CDS reminders, CDS guidelines, and CPOE. Appropriate prescribing rates of aspirin, ACEI/ARBs, or beta blockers are defined using quality measures from Hospital Compare. Multivariate linear regressions are used to test for differences in mean appropriate prescribing rates between hospitals reporting combination use of CDS and CPOE, compared to those reporting the singular use of one or the other, or the absence of both. Covariates include hospital size, region, and ownership status. RESULTS: Approximately 10% of the sample reported full implementation of both CDS and CPOE, while 7% and 17% reported full use of only CPOE or only CDS, respectively. Hospitals reporting full use of CDS only reported between 0.2% (95% CI 0.04 - 1.0) and 1.6% (95% CI 0.6 - 2.6) higher appropriate prescribing rates compared to hospitals reporting use of neither system. Rates of prescribing by hospitals reporting full use of both CPOE and CDS did not significantly differ from the control group. CONCLUSIONS: Although associations found between full implementation of CDS and appropriate prescribing rates suggest that clinical decision tools are sufficient compared to basic EHR systems in improving prescribing at discharge, the modest differences raise doubt about the clinical relevance of the findings. Future studies need to continue investigating the causal nature and clinical relevance of these associations.

Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptations but not host specificity.

Establishing the risk of human infection is one of the goals of public health. For bacterial pathogens, the virulence and zoonotic potential can often be related to their host source. Escherichia coli bacteria are common contaminants of water associated with human recreation and consumption, and many strains are pathogenic. In this study, we analyzed three promoter-containing intergenic regions from 284 diverse E. coli isolates in an attempt to identify molecular signatures associated with specific host types. Promoter sequences controlling production of curli fimbriae, flagella, and nutrient import yielded a phylogenetic tree with isolates clustered by established phylogenetic grouping (A, B1, B2, and D) but not by host source. Virulence genes were more prevalent in groups B2 and D isolates and in human isolates. Group B1 isolates, primarily from nonhuman sources, were the most genetically similar, indicating that they lacked molecular adaptations to specific host environments and were likely host generalists. Conversely, B2 isolates, primarily from human sources, displayed greater genetic distances and were more likely to be host adapted. In agreement with these hypotheses, prevalence of σ(S) activity and the rdar morphotype, phenotypes associated with environmental survival, were significantly higher in B1 isolates than in B2 isolates. Based on our findings, we speculate that E. coli host specificity is not defined by genome-wide sequence changes but, rather, by the presence or absence of specific genes and associated promoter elements. Furthermore, the requirements for colonization of the human gastrointestinal tract may lead to E. coli lifestyle changes along with selection for increased virulence.

Glatiramer acetate-specific antibody titres in patients with relapsing / remitting multiple sclerosis and in experimental autoimmune encephalomyelitis.

Glatiramer acetate (GA) is an immunomodulatory drug approved for the treatment of clinically isolated syndrome (CIS) and relapsing/remitting multiple sclerosis (RRMS). As an antigen-based therapy, GA induces GA-specific antibodies in treated patients and animals. GA-specific antibodies do not neutralize therapeutic effects on relapses and disability. Rather, it has been suggested that GA-specific antibodies may be associated with improved clinical outcomes. We evaluated antibody responses in eight patients with RRMS treated with GA for 15 months and antibody responses in GA-treated C57BL/6 mice before and after induction of experimental autoimmune encephalomyelitis (EAE). There were no significant differences from pretreatment levels of total IgE or GA-specific IgE in patients with RRMS. Total IgG1, IgG3 and GA-specific IgG4 were significantly increased at 15 months of GA treatment. Antibody type and titre were not associated with clinical outcomes, i.e. expanded disability status scale (EDSS) score, disease burden on magnetic resonance images (MRI) or clinical relapses. In contrast, mice with EAE showed a marked increase in GA-specific IgE and GA-specific IgG1 antibody responses. GA-treated mice demonstrated improved clinical symptoms and lower mortality than untreated controls. Our results suggest that antibody responses to GA are heterogeneous among patients with RRMS, with no apparent association between antibody response and clinical outcomes. Clinical improvements in EAE-induced GA-treated mice suggest that GA-specific IgE and IgG1 may contribute to GA treatment effects in EAE.

Sequenced subjective accents for brain-computer interfaces.

Subjective accenting is a cognitive process in which identical auditory pulses at an isochronous rate turn into the percept of an accenting pattern. This process can be voluntarily controlled, making it a candidate for communication from human user to machine in a brain-computer interface (BCI) system. In this study we investigated whether subjective accenting is a feasible paradigm for BCI and how its time-structured nature can be exploited for optimal decoding from non-invasive EEG data. Ten subjects perceived and imagined different metric patterns (two-, three- and four-beat) superimposed on a steady metronome. With an offline classification paradigm, we classified imagined accented from non-accented beats on a single trial (0.5 s) level with an average accuracy of 60.4% over all subjects. We show that decoding of imagined accents is also possible with a classifier trained on perception data. Cyclic patterns of accents and non-accents were successfully decoded with a sequence classification algorithm. Classification performances were compared by means of bit rate. Performance in the best scenario translates into an average bit rate of 4.4 bits min(-1) over subjects, which makes subjective accenting a promising paradigm for an online auditory BCI.

Shared mechanisms in perception and imagery of auditory accents.

OBJECTIVE: An auditory rhythm can be perceived as a sequence of accented (loud) and non-accented (soft) beats or it can be imagined. Subjective rhythmization refers to the induction of accenting patterns during the presentation of identical auditory pulses at an isochronous rate. It can be an automatic process, but it can also be voluntarily controlled. We investigated whether imagined accents can be decoded from brain signals on a single-trial basis, and if there is information shared between perception and imagery in the contrast of accents and non-accents. METHODS: Ten subjects perceived and imagined three different metric patterns (two-, three-, and four-beat) superimposed on a steady metronome while electroencephalography (EEG) measurements were made. Shared information between perception and imagery EEG is investigated by means of principal component analysis and by means of single-trial classification. RESULTS: Classification of accented from non-accented beats was possible with an average accuracy of 70% for perception and 61% for imagery data. Cross-condition classification yielded significant performance above chance level for a classifier trained on perception and tested on imagery data (up to 66%), and vice versa (up to 60%). CONCLUSIONS: Results show that detection of imagined accents is possible and reveal similarity in brain signatures relevant to distinction of accents from non-accents in perception and imagery. SIGNIFICANCE: Our results support the idea of shared mechanisms in perception and imagery for auditory processing. This is relevant for a number of clinical settings, most notably by elucidating the basic mechanisms of rhythmic auditory cuing paradigms, e.g. as used in motor rehabilitation or therapy for Parkinson's disease. As a novel Brain-Computer Interface (BCI) paradigm, our results imply a reduction of the necessary BCI training in healthy subjects and in patients.

Polymorphism at the avpr1a locus in male prairie voles correlated with genetic but not social monogamy in field populations.

Integrative studies of genetics, neurobiology and behaviour indicate that polymorphism in specific genes contributes to variation observed in some complex social behaviours. The neuropeptide arginine vasopressin plays an important role in the regulation of a variety of social behaviours, including social attachment of males to females, through its action on the vasopressin 1a receptor (V1aR). In socially monogamous prairie voles (Microtus ochrogaster), polymorphism in the length of microsatellite DNA within the regulatory region of the gene (avpr1a) encoding the V1aR predicts differences among males in neural expression of V1aRs and partner preference under laboratory conditions. However, understanding the extent to which V1aR mediates variation in prairie vole social and reproductive behaviour observed in nature requires investigating the consequences of avpr1a polymorphism and environmental influences under ecologically relevant conditions. We examined the relationship between avpr1a length polymorphism and monogamy among male prairie voles living in 0.1 ha enclosures during a time similar to their natural lifespan. We found no evidence that avpr1a genotype of males predicts variation in social monogamy measured in the field but some indices of social monogamy were affected by population density. Parentage data indicated that a male's avpr1a genotype significantly influenced the number of females with which he sired offspring and the total number of offspring sired. Total brain concentrations of V1aR mRNA were not associated with either male behaviour or avpr1a genotype. These data show that melding ecological field studies with neurogenetics can substantially augment our understanding of the effects of genes and environment on social behaviours.

Decorin deficiency in diabetic mice: aggravation of nephropathy due to overexpression of profibrotic factors, enhanced apoptosis and mononuclear cell infiltration.

Although deficiency of the small leucine-rich proteoglycan decorin aggravates diabetic nephropathy in mice, the precise mechanisms of action are not fully understood. In the present study we used decorin-deficient mice (Dcn(-/-)) to further elucidate the molecular mechanisms involved in the protective action of decorin in diabetes. We discovered that streptozotocin-induced diabetes in Dcn(-/-) mice led to increased proteinuria associated with enhanced cyclin-dependent kinase inhibitor p27Kip1 in podocytes and tubular epithelial cells. Furthermore, lack of decorin increased the rate of apoptosis and caused overexpression of the IGF-IR in tubular epithelial cells of diabetic kidneys. In vitro experiments using human proximal renal epithelial cells showed that recombinant decorin was bound to the IGF-IR and protected against high glucose-mediated apoptosis. Furthermore, overexpression of TGFbeta1 and CTGF triggered by decorin deficiency resulted in enhanced accumulation of extracellular matrix in diabetic kidneys. Notably, diabetic Dcn(-/-) kidneys revealed marked upregulation of the proinflammatory proteoglycan biglycan and enhanced infiltration of mononuclear cells. Collectively, our results indicate that decorin is a protective agent during the development of diabetic nephropathy. Future therapeutic approaches that would either enhance the endogenous production of decorin or deliver recombinant decorin to the diseased kidney might improve the outcome of patients with diabetic nephropathy.

Digitally synthesized high purity, high-voltage radio frequency drive electronics for mass spectrometry.

Reported herein is development of a quadrupole mass spectrometer controller (MSC) with integrated radio frequency (rf) power supply and mass spectrometer drive electronics. Advances have been made in terms of the physical size and power consumption of the MSC, while simultaneously making improvements in frequency stability, total harmonic distortion, and spectral purity. The rf power supply portion of the MSC is based on a series-resonant LC tank, where the capacitive load is the mass spectrometer itself, and the inductor is a solenoid or toroid, with various core materials. The MSC drive electronics is based on a field programmable gate array (FPGA), with serial peripheral interface for analog-to-digital and digital-to-analog converter support, and RS232/RS422 communications interfaces. The MSC offers spectral quality comparable to, or exceeding, that of conventional rf power supplies used in commercially available mass spectrometers; and as well an inherent flexibility, via the FPGA implementation, for a variety of tasks that includes proportional-integral derivative closed-loop feedback and control of rf, rf amplitude, and mass spectrometer sensitivity. Also provided are dc offsets and resonant dipole excitation for mass selective accumulation in applications involving quadrupole ion traps; rf phase locking and phase shifting for external loading of a quadrupole ion trap; and multichannel scaling of acquired mass spectra. The functionality of the MSC is task specific, and is easily modified by simply loading FPGA registers or reprogramming FPGA firmware.