Impact of Different Active-Speech-Ratios on PESQ’s Predictions in Case of Independent and Dependent Losses (in Presence of Receiver-Side Comfort-Noise)

This paper deals with the investigation of PESQ’s behavior under independent and dependent loss conditions from an Active-Speech-Ratio perspective in presence of receiver-side comfort-noise. This reference signal characteristic is defined very broadly by ITU-T Recommendation P.862.3. That is the reason to investigate an impact of this characteristic on speech quality prediction more in-depth. We assess the variability of PESQ’s predictions with respect to Active-Speech-Ratios and loss conditions, as well as their accuracy, by comparing the predictions with subjective assessments. Our results show that an increase in amount of speech in the reference signal (expressed by the Active-Speech-Ratio characteristic) may result in an increase of the reference signal sensitivity to packet loss change. Interestingly, we have found two additional effects in this investigated case. The use of higher Active-Speech-Ratios may lead to negative shifting effect in MOS domain and also PESQ’s predictions accuracy declining. Predictions accuracy could be improved by higher packet losses

Multiplexed single-cell analysis of organoid signaling networks

Organoids are biomimetic tissue models comprising multiple cell types and cell states. Post-translational modification (PTM) signaling networks control cellular phenotypes and are frequently dysregulated in diseases such as cancer. Although signaling networks vary across cell types, there are limited techniques to study cell type–specific PTMs in heterocellular organoids. Here, we present a multiplexed mass cytometry (MC) protocol for single-cell analysis of PTM signaling and cell states in organoids and organoids co-cultured with fibroblasts and leukocytes. We describe how thiol-reactive organoid barcoding in situ (TOBis) enables 35-plex and 126-plex single-cell comparison of organoid cultures and provide a cytometry by time of flight (CyTOF) signaling analysis pipeline (CyGNAL) for computing cell type–specific PTM signaling networks. The TOBis MC protocol takes ~3 d from organoid fixation to data acquisition and can generate single-cell data for >40 antibodies from millions of cells across 126 organoid cultures in a single MC run

Cell-type-specific signaling networks in heterocellular organoids

Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simultaneous analysis by mass cytometry of 28 PTMs in >1 million single cells derived from small intestinal organoids reveals cell-type- and cell-state-specific signaling networks in stem, Paneth, enteroendocrine, tuft and goblet cells, as well as enterocytes. Integrating single-cell PTM analysis with thiol-reactive organoid barcoding in situ (TOBis) enables high-throughput comparison of signaling networks between organoid cultures. Cell-type-specific PTM analysis of colorectal cancer organoid cocultures reveals that shApc, KrasG12D and Trp53R172H cell-autonomously mimic signaling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform high-throughput multivariate cell-type-specific signaling analysis of healthy and cancerous organoids

Biochemical responses and oxidative stress in Francisella tularensis infection: a European brown hare model

<p>Abstract</p> <p>Background</p> <p>The aim of the present study was to investigate biochemical and oxidative stress responses to experimental <it>F. tularensis </it>infection in European brown hares, an important source of human tularemia infections.</p> <p>Methods</p> <p>For these purposes we compared the development of an array of biochemical parameters measured in blood plasma using standard procedures of dry chemistry as well as electrochemical devices following a subcutaneous infection with a wild <it>Francisella tularensis </it>subsp. <it>holarctica </it>strain (a single dose of 2.6 × 10⁹CFU <it>pro toto</it>).</p> <p>Results</p> <p>Subcutaneous inoculation of a single dose with 2.6 × 10⁹colony forming units of a wild <it>F. tularensis </it>strain <it>pro toto </it>resulted in the death of two out of five hares. Plasma chemistry profiles were examined on days 2 to 35 post-infection. When compared to controls, the total protein, urea, lactate dehydrogenase, aspartate aminotransferase and alanine aminotransferase were increased, while albumin, glucose and amylase were decreased. Both uric and ascorbic acids and glutathione dropped on day 2 and then increased significantly on days 6 to 12 and 6 to 14 post-inoculation, respectively. There was a two-fold increase in lipid peroxidation on days 4 to 8 post-inoculation.</p> <p>Conclusions</p> <p>Contrary to all expectations, the present study demonstrates that the European brown hare shows relatively low susceptibility to tularemia. Therefore, the circumstances of tularemia in hares under natural conditions should be further studied.</p

Effect of mobile phase additives on solute retention at low aqueous pH in hydrophilic interaction liquid chromatography

© 2016 Elsevier B.V. Trifluoracetic acid (TFA) added to the aqueous acetonitrile mobile phase induces some unexpected changes in the ionic component of retention in hydrophilic interaction separations when using Type B silica and amide-bonded silica columns. TFA use results in anion exchange properties which contrast with the cation exchange typically found with ammonium salt buffers. The significant cation exchange properties of silica hydride columns are also moderated by TFA. Similar behaviour was shown in a metal- free amide column operated on a system washed with a metal complexing agent, suggesting that adsorbed metal cations were not responsible for this anion exchange behaviour. Both suppression of silanol ionisation at low pH and ion pairing of bases with TFA could contribute to this effect. It is also possible that the column surface acquires some positive charges at the low pH of TFA. A surprising reversal of the properties of the columns back to predominately cation exchange behaviour was shown using methanesulfonic acid (MSA), which appears to be a stronger acid than TFA in high concentrations of acetonitrile. MSA maintains sufficient ionic strength in the mobile phase even at low concentrations, giving good peak shape, which could be useful for mass spectrometry detection. Besides giving different selectivity to TFA, MSA also gives different selectivity to that of ammonium salt buffers, suggesting it may be useful in manipulating the selectivity of a separation. Similar changes to the selectivity with TFA could be achieved by adding neutral methylsulfonate salts to the TFA mobile phase. While it is possible that methylsulfonate ions are retained on the stationary phase surface, experiments using ion pair reagents of opposite charge yielded the same results as MSA salts. It therefore seems more likely that the higher ionic strength of these solutions negates the influence of charges that may be formed in TFA solutions. Ion pairing effects with MSA are expected to be limited

Abnormal LDIflare but Normal Quantitative Sensory Testing and Dermal Nerve Fiber Density in Patients with Painful Diabetic Neuropathy

OBJECTIVE—Abnormal small nerve fiber function may be an early feature of diabetic neuropathy and may also underlie painful symptoms. Methods for assessing small-fiber damage include quantitative sensory testing (QST) and determining intraepidermal nerve fiber density. We recently described a reproducible physiological technique, the LDIflare, which assesses small-fiber function and thus may reflect early dysfunction before structural damage. The value of this technique in painful neuropathy was assessed by comparing it with QST and dermal nerve fiber density (NFD)

BCL11A deletions result in fetal hemoglobin persistence and neurodevelopmental alterations

A transition from fetal hemoglobin (HbF) to adult hemoglobin (HbA) normally occurs within a few months after birth. Increased production of HbF after this period of infancy ameliorates clinical symptoms of the major disorders of adult ß-hemoglobin: ß-thalassemia and sickle cell disease. The transcription factor BCL11A silences HbF and has been an attractive therapeutic target for increasing HbF levels; however, it is not clear to what extent BCL11A inhibits HbF production or mediates other developmental functions in humans. Here, we identified and characterized 3 patients with rare microdeletions of 2p15-p16.1 who presented with an autism spectrum disorder and developmental delay. Moreover, these patients all exhibited substantial persistence of HbF but otherwise retained apparently normal hematologic and immunologic function. Of the genes within 2p15-p16.1, only BCL11A was commonly deleted in all of the patients. Evaluation of gene expression data sets from developing and adult human brains revealed that BCL11A expression patterns are similar to other genes associated with neurodevelopmental disorders. Additionally, common SNPs within the second intron of BCL11A are strongly associated with schizophrenia. Together, the study of these rare patients and orthogonal genetic data demonstrates that BCL11A plays a central role in silencing HbF in humans and implicates BCL11A as an important factor for neurodevelopment

Decision Support Intervention for people with advanced dementia residing in a nursing home: A study protocol for an International advance care planning intervention (mySupport study)

Background Where it has been determined that a resident in a nursing home living with dementia loses decisional capacity, nursing home staff must deliver care that is in the person's best interests. Ideally, decisions should be made involving those close to the person, typically a family carer and health and social care providers. The aim of the Family Carer Decisional Support intervention is to inform family carers on end-of-life care options for a person living with advanced dementia and enable them to contribute to advance care planning. This implementation study proposes to; 1) adopt and apply the intervention internationally; and, 2) train nursing home staff to deliver the family carer decision support intervention. Methods This study will employ a multiple case study design to allow an understanding of the implementation process and to identify the factors which determine how well the intervention will work as intended. We will enrol nursing homes from each country (Canada n = 2 Republic of Ireland = 2, three regions in the UK n = 2 each, The Netherlands n = 2, Italy n = 2 and the Czech Republic n = 2) to reflect the range of characteristics in each national and local context. The RE-AIM (reach, effectiveness, adoption, implementation, maintenance) framework will guide the evaluation of implementation of the training and information resources. Our mixed methods study design has three phases to (1) establish knowledge about the context of implementation, (2) participant baseline information and measures and (3) follow up evaluation. Discussion The use of a multiple case study design will enable evaluation of the intervention in different national, regional, cultural, clinical, social and organisational contexts, and we anticipate collecting rich and in-depth data. While it is hoped that the intervention resources will impact on policy and practice in the nursing homes that are recruited to the study, the development of implementation guidelines will ensure impact on wider national policy and practice. It is our aim that the resources will be sustainable beyond the duration of the study and this will enable the resources to have a longstanding relevance for future advance care planning practice for staff, family carers and residents with advanced dementia