Underrepresentation of activating KIR gene expression in single-cell RNA-seq data is due to KIR gene misassignment

Standard single-cell RNA-sequencing alignment pipelines exhibit a propensity for misassigning killer immunoglobulin-like receptor (KIR) transcripts, thereby giving rise to inaccuracies in quantifying KIR expression. Alves et al. elucidated that these default workflows frequently misclassify activating KIR transcripts as inhibitory KIR expression, resulting in a skewed representation of the KIR repertoire.

Unpacking the Complexity of Epithelial Plasticity: From Master Regulator Transcription Factors to Non-Coding RNAs

Cellular plasticity in cancer enables adaptation to selective pressures and stress imposed by the tumor microenvironment. This plasticity facilitates the remodeling of cancer cell phenotype and function (such as tumor stemness, metastasis, chemo/radio resistance), and the reprogramming of the surrounding tumor microenvironment to enable immune evasion. Epithelial plasticity is one form of cellular plasticity, which is intrinsically linked with epithelial-mesenchymal transition (EMT). Traditionally, EMT has been regarded as a binary state. Yet, increasing evidence suggests that EMT involves a spectrum of quasi-epithelial and quasi-mesenchymal phenotypes governed by complex interactions between cellular metabolism, transcriptome regulation, and epigenetic mechanisms. Herein, we review the complex cross-talk between the different layers of epithelial plasticity in cancer, encompassing the core layer of transcription factors, their interacting epigenetic modifiers and non-coding RNAs, and the manipulation of cancer immunogenicity in transitioning between epithelial and mesenchymal states. In examining these factors, we provide insights into promising therapeutic avenues and potential anti-cancer targets.

Tracking of activated cTfh cells following sequential influenza vaccinations reveals transcriptional profile of clonotypes driving a vaccine-induced immune response

Introduction

A vaccine against influenza is available seasonally but is not 100% effective. A predictor of successful seroconversion in adults is an increase in activated circulating T follicular helper (cTfh) cells after vaccination. However, the impact of repeated annual vaccinations on long-term protection and seasonal vaccine efficacy remains unclear.

Methods

In this study, we examined the T cell receptor (TCR) repertoire and transcriptional profile of vaccine-induced expanded cTfh cells in individuals who received sequential seasonal influenza vaccines. We measured the magnitude of cTfh and plasmablast cell activation from day 0 (d0) to d7 post-vaccination as an indicator of a vaccine response. To assess TCR diversity and T cell expansion we sorted activated and resting cTfh cells at d0 and d7 post-vaccination and performed TCR sequencing. We also single cell sorted activated and resting cTfh cells for TCR analysis and transcriptome sequencing.

Results and discussion

The percent of activated cTfh cells significantly increased from d0 to d7 in each of the 2016-17 (p < 0.0001) and 2017-18 (p = 0.015) vaccine seasons with the magnitude of cTfh activation increase positively correlated with the frequency of circulating plasmablast cells in the 2016-17 (p = 0.0001) and 2017-18 (p = 0.003) seasons. At d7 post-vaccination, higher magnitudes of cTfh activation were associated with increased clonality of cTfh TCR repertoire. The TCRs from vaccine-expanded clonotypes were identified and tracked longitudinally with several TCRs found to be present in both years. The transcriptomic profile of these expanded cTfh cells at the single cell level demonstrated overrepresentation of transcripts of genes involved in the type-I interferon pathway, pathways involved in gene expression, and antigen presentation and recognition. These results identify the expansion and transcriptomic profile of vaccine-induced cTfh cells important for B cell help.

Probing the Cr3+ luminescence sensitization in β-Ga2O3 with ion-beam-induced luminescence and thermoluminescence

Ion-beam-induced luminescence (IBIL) measurements were performed in Cr-doped β-Ga₂O₃ using both protons and helium ions, showing a strong enhancement of the Cr³⁺ luminescence upon ion irradiation. Theoretical modelling of the IBIL intensity curves as a function of the fluence allowed estimating the effective cross-sections associated with the defect-induced IBIL enhancement and quenching processes. The results suggest that sensitizing the Cr³⁺ luminescence is more efficient for H⁺ than for He⁺ irradiation. Thermoluminescence (TL) studies were performed in the pristine sample, with no TL signal being observed in the spectral region corresponding to the Cr³⁺ emission. In agreement with the IBIL study, upon ion irradiation (with either protons or helium ions), this TL emission is activated. Moreover, it can be quenched by annealing at 923 K for 10 s, thus revealing the role played by the defects induced by the irradiation. These results show that the irradiation-induced defects play a major role in the activation of the Cr³⁺ luminescence, a fact that can be exploited for radiation sensing and dosimetry.

Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains

Adaptation to human leukocyte antigen (HLA)-associated immune pressure represents a major driver of human immunodeficiency virus (HIV) evolution at both the individual and population level. To date, there has been limited exploration of the impact of the initial cellular immune response in driving viral adaptation, the dynamics of these changes during infection and their effect on circulating transmitting viruses at the population level. Capturing detailed virological and immunological data from acute and early HIV infection is challenging as this commonly precedes the diagnosis of HIV infection, potentially by many years. In addition, rapid initiation of antiretroviral treatment following a diagnosis is the standard of care, and central to global efforts towards HIV elimination. Yet, acute untreated infection is the critical period in which the diversity of proviral reservoirs is first established within individuals, and associated with greater risk of onward transmissions in a population. Characterizing the viral adaptations evident in the earliest phases of infection, coinciding with the initial cellular immune responses is therefore relevant to understanding which changes are of greatest impact to HIV evolution at the population level. In this study, we utilized three separate cohorts to examine the initial CD8+ T cell immune response to HIV (cross-sectional acute infection cohort), track HIV evolution in response to CD8+ T cell-mediated immunity over time (longitudinal chronic infection cohort) and translate the impact of HLA-driven HIV evolution to the population level (cross-sectional HIV sequence data spanning 30 years). Using next generation viral sequencing and enzyme-linked immunospot interferon-gamma recall responses to peptides representing HLA class I-specific HIV T cell targets, we observed that CD8+ T cell responses can select viral adaptations prior to full antibody seroconversion. Using the longitudinal cohort, we uncover that viral adaptations have the propensity to be retained over time in a non-selective immune environment, which reflects the increasing proportion of pre-adapted HIV strains within the Western Australian population over an approximate 30-year period.

CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery

Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.

Cross-Reactivity to Mutated Viral Immune Targets Can Influence CD8+ T Cell Functionality: An Alternative Viral Adaptation Strategy

Loss of T cell immunogenicity due to mutations in virally encoded epitopes is a well-described adaptation strategy to limit host anti-viral immunity. Another described, but less understood, adaptation strategy involves the selection of mutations within epitopes that retain immune recognition, suggesting a benefit for the virus despite continued immune pressure (termed non-classical adaptation). To understand this adaptation strategy, we utilized a single cell transcriptomic approach to identify features of the HIV-specific CD8+ T cell responses targeting non-adapted (NAE) and adapted (AE) forms of epitopes containing a non-classical adaptation. T cell receptor (TCR) repertoire and transcriptome were obtained from antigen-specific CD8+ T cells of chronic (n=7) and acute (n=4) HIV-infected subjects identified by either HLA class I tetramers or upregulation of activation markers following peptide stimulation. CD8+ T cells were predominantly dual tetramer+, confirming a large proportion of cross-reactive TCR clonotypes capable of recognizing the NAE and AE form. However, single-reactive CD8+ T cells were identified in acute HIV-infected subjects only, providing the potential for the selection of T cell clones over time. The transcriptomic profile of CD8+ T cells was dependent on the autologous virus: subjects whose virus encoded the NAE form of the epitope (and who transitioned to the AE form at a later timepoint) exhibited an 'effective' immune response, as indicated by expression of transcripts associated with polyfunctionality, cytotoxicity and apoptosis (largely driven by the genes GZMB, IFNɣ, CCL3, CCL4 and CCL5). These data suggest that viral adaptation at a single amino acid residue can provide an alternative strategy for viral survival by modulating the transcriptome of CD8+ T cells and potentially selecting for less effective T cell clones from the acute to chronic phase.

Childbearing intentions after a very preterm delivery: a study among Portuguese mothers and fathers

Background

Adjustments to intended family size are strongly affected by life-course events, but data on childbearing plans after a very preterm delivery are lacking. This study intends to assess the childbearing intentions of mothers and fathers of very preterm infants, regarding the desired and intended number of children, the factors associated with the intention to have more children and the main reasons for not wanting to have more children.

Methods

Between May and July 2017, mothers and fathers of very preterm infants were invited to participate in a structured online questionnaire through the Portuguese association of parents for support to the premature baby, and 231 mothers and 21 fathers were included. The discrepancy between the ideal and intended number of children was assessed by the McNemar-Bowker test. To assess the main factors associated with the plan to have more children in the future, unconditional logistic regression models were fitted to compute odds ratios (OR) and 95% confidence intervals (95%CI), adjusted for age, number of children and time after the very preterm delivery.

Results

Participants intend to have fewer children than they ideally desired (p &lt; 0.001). Although 69.8% of parents would like to have more children, only 25% actually plan to conceive. After adjustment, participants aged above 34 years (OR = 0.27; 95%CI:0.08-0.86), with more than one offspring (OR = 0.34; 95%CI:0.14-0.69) and who experienced a very preterm delivery 5 or more years ago (OR = 0.28; 95%CI:0.09-0.90) were less likely to report the intention to have more children. The main reasons reported for not wanting to have more children were “having the desired number of children” (38.5%), “financial unavailability” (24.2%) and “being too old to have more children” (20.5%).

Conclusions

This study provides a comprehensive assessment of childbearing intentions after a very preterm delivery, advocating for reproductive counselling policies supportive of family planning.

Key messages

Discrepancy between the ideal and actual childbearing intentions support the enhancement of reproductive healthcare services for family planning. Socioeconomic and age-related constraints were the main motives presented by mothers and fathers of very preterm infants for not wanting to have more children.

Portuguese validation of the Adult Carer Quality of Life Questionnaire (AC-QoL)

Background

Assuring informal carers' quality of life (QoL) must be a priority for public health policies and practices. The Adult Carer Quality of Life Questionnaire (AC-QoL) is a recent and valid instrument, overpassing limitations of previous tools, and being already used among informal stroke carers. This study aimed to assess the feasibility, reliability and validity of the AC-QoL among Portuguese informal carers of stroke survivors.

Methods

The linguistic adaptation of the AC-QoL was performed. Informal carers (n = 212) of stroke survivors hospitalized between September 2018 and August 2019 in all Stroke Units of the North of Portugal (n = 12) were invited to participate, 18 to 24 months post-stroke. Data on sociodemographic characteristics, psychological profile, burden and QoL were collected using a structured questionnaire. The psychometric properties of the AC-QoL were investigated through exploratory and confirmatory factor analyses. Cronbach's alpha was used to measure internal consistency. Construct validity was assessed through the association of the overall score of AC-QoL with anxiety and depressive symptoms, burden and sociodemographic characteristics.

Results

Exploratory factor analysis supported the original eight-factor structure of the AC-QoL, revealing an adequate goodness of fit to the study sample (X2(674)=1145.926; CFI=0.916; TLI=0.908; RMSEA=0.058). The AC-QoL showed a high degree of reliability, with Cronbach's scores for the subscales ranging from 0.64 to 0.97 and a Cronbach's alpha of 0.91 for the overall score. Anxiety symptoms (p &lt; 0.001), depression symptoms (p &lt; 0.001) and burden (p &lt; 0.001) were inversely associated with the overall score of AC-QoL. Younger (p = 0.032) and employed (p = 0.021) informal carers presented more frequently higher scores of overall QoL, than those older and unemployed.

Conclusions

The Portuguese version of the AC-QoL is a comprehensive, simple, reliable and valid instrument to assess informal stroke carers' QoL.

Key messages

The Portuguese version of the AC-QoL is a comprehensive and valid instrument with a high degree of reliability, that can be briefly and easily applied to informal carers of stroke survivors. A comprehensive and brief assessment of informal carers’ QoL will contribute to devise strategies to promote well-being and social integration of stroke survivors and their informal carers.

Adaptation and learning processes of stroke survivors and family carers: a scoping review

Background

Knowledge on the processes of adaptation and learning after stroke are scarce, hindering the development of evidence-based public health strategies to promote survivors and family carers' health and wellbeing, across the post stroke trajectory. This study aims to assess the available evidence on the processes of adaptation and learning after stroke, by mapping the main barriers and enablers according to the perspectives of stroke survivors and family carers.

Methods

A scoping review was performed, following PRISMA-ScR guidelines. The electronic databases PubMed, ISI Web of Science, PsycINFO and SciELO were searched for empirical, peer-reviewed, original, and full-length studies on the processes of adaptation and learning of stroke survivors and family carers, in March 2021. Eligibility and data extraction were conducted by two independent researchers. The main qualitative data were explored by thematic content analysis and quantitative findings were synthesized.

Results

The included studies, 29 qualitative and 1 quantitative, were published between 1994 and 2019. Most of the studies were carried out with small samples and without a specific focus on the adaptation and learning processes after stroke. Barriers and enablers to stroke adaptation and learning processes were influenced by physical, psychological and social characteristics. The poor physical and functional status of survivors, the inability to maintaining the Activities of Daily Living, emotional disturbances, lack of support and information, and changes in roles, were identify as main barriers to stroke adaptation. Using coping strategies and having psychological, educational, and financial support were described as enablers.

Conclusions

Public health policies and practices should consider the physical, psychological and social barriers and enablers to the stroke adaptation and learning processes to ensure a high-quality long-term care centred on survivors and family carers.

Key messages

Robust theoretical and methodological studies, specifically designed to deeply explore and describe the post stroke adaptation and learning processes, are needed. Understand the main barriers and enablers to adaptation and learning after stroke may be useful for developing health education interventions centred on survivors and carers preferences and needs.

Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level

BACKGROUND

Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host's anti-viral immune response, in turn affecting the frequency of variants over time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally.

METHODS

Deep-sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. Results: Sequence analysis suggests that the 3 adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep-sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames.

CONCLUSIONS

The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans, resulting in both coding changes and novel sub-genomic RNA transcripts, suggests this as a mechanism for diversification and adaptation within its new host.

Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity

The activating immune receptor natural killer group member D (NKG2D) and its cognate ligands represent a fundamental surveillance system of cellular distress, damage or transformation. Signaling through the NKG2D receptor-ligand axis is critical for early detection of viral infection or oncogenic transformation and the presence of functional NKG2D ligands (NKG2D-L) is associated with tumor rejection and viral clearance. Many viruses and tumors have developed mechanisms to evade NKG2D recognition via transcriptional, post-transcriptional or post-translational interference with NKG2D-L, supporting the concept that circumventing immune evasion of the NKG2D receptor-ligand axis may be an attractive therapeutic avenue for antiviral therapy or cancer immunotherapy. To date, the complexity of the NKG2D receptor-ligand axis and the lack of specificity of current NKG2D-targeting therapies has not allowed for the precise manipulation required to optimally harness NKG2D-mediated immunity. However, with the discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins, novel opportunities have arisen in the realm of locus-specific gene editing and regulation. Here, we give a brief overview of the NKG2D receptor-ligand axis in humans and discuss the levels at which NKG2D-L are regulated and dysregulated during viral infection and oncogenesis. Moreover, we explore the potential for CRISPR-based technologies to provide novel therapeutic avenues to improve and maximize NKG2D-mediated immunity.

Reprogramming the anti-tumor immune response via CRISPR genetic and epigenetic editing

Precise clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genetic and epigenetic manipulation of the immune response has become a promising immunotherapeutic approach toward combating tumorigenesis and tumor progression. CRISPR-based immunologic reprograming in cancer therapy comprises the locus-specific enhancement of host immunity, the improvement of tumor immunogenicity, and the suppression of tumor immunoevasion. To date, the ex vivo re-engineering of immune cells directed to inhibit the expression of immune checkpoints or to express synthetic immune receptors (chimeric antigen receptor therapy) has shown success in some settings, such as in the treatment of melanoma, lymphoma, liver, and lung cancer. However, advancements in nuclease-deactivated CRISPR-associated nuclease-9 (dCas9)-mediated transcriptional activation or repression and Cas13-directed gene suppression present novel avenues for the development of tumor immunotherapies. In this review, the basis for development, mechanism of action, and outcomes from recently published Cas9-based clinical trial (genetic editing) and dCas9/Cas13-based pre-clinical (epigenetic editing) data are discussed. Lastly, we review cancer immunotherapy-specific considerations and barriers surrounding use of these approaches in the clinic.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Crystal mosaicity determined by a novel layer deconvolution Williamson–Hall method

An improvement to the classical Williamson–Hall method is developed to study several samples of AlGaN and α-MoO₃.

Multiple reflection optimization package for X-ray diffraction

New software for the simulation and fitting of 2θ–ω scans of symmetric and asymmetric reflections based on the dynamical theory of X-ray diffraction is presented.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products

Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.

Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV

Human immunodeficiency virus (HIV) can adapt to an individual’s T cell immune response via genomic mutations that affect antigen recognition and impact disease outcome. These viral adaptations are specific to the host’s human leucocyte antigen (HLA) alleles, as these molecules determine which peptides are presented to T cells. As HLA molecules are highly polymorphic at the population level, horizontal transmission events are most commonly between HLA-mismatched donor/recipient pairs, representing new immune selection environments for the transmitted virus. In this study, we utilised a deep sequencing approach to determine the HIV quasispecies in 26 mother-to-child transmission pairs where the potential for founder viruses to be pre-adapted is high due to the pairs being haplo-identical at HLA loci. This scenario allowed the assessment of specific HIV adaptations following transmission in either a non-selective immune environment, due to recipient HLA mismatched to original selecting HLA, or a selective immune environment, mediated by matched donor/recipient HLA. We show that the pattern of reversion or fixation of HIV adaptations following transmission provides insight into the replicative cost, and likely compensatory networks, associated with specific adaptations in vivo. Furthermore, although transmitted viruses were commonly heavily pre-adapted to the child’s HLA genotype, we found evidence of de novo post-transmission adaptation, representing new epitopes targeted by the child’s T cell response. High-resolution analysis of HIV adaptation is relevant when considering vaccine and cure strategies for individuals exposed to adapted viruses via transmission or reactivated from reservoirs.

Highly mutable pathogens utilise genetic variations within T cell epitopes as a mechanism of immune escape (viral adaptation). The diversity of the human leucocyte antigen (HLA) molecules that present viral targets to T cells in human populations partially protects against rapid population-level accumulation of human immunodeficiency virus (HIV) adaptations through horizontal transmissions. In contrast, vertical transmissions occur between haplo-identical mother/child pairs, and potentially include adaptive changes through father-mother-child transmission, representing a pathway to complete pre-adaptation to HLA alleles in child hosts over only two transmission events. We utilised next-generation sequencing to examine HIV evolution in the unique setting of vertical HIV transmission. We predict the in vivo replicative cost and immune benefit of specific HIV adaptations that could be used to inform vaccine design and cure strategies to combat viral immune adaptation.

The effect of profession on burnout in hospital staff

Background

A high level of burnout has been described in health professionals. However, literature regarding other hospital employees is scarce.

Aims

To assess the prevalence of burnout in different professional groups of hospital staff and how the professional category is associated with levels of burnout.

Methods

Employees of a University Hospital in Portugal completed a self-administered online questionnaire in 2014-2015. We used the Portuguese version of the Maslach Burnout Inventory-Human Services Survey and scored three dimensions of burnout (emotional exhaustion, depersonalization, personal accomplishment) as low, average or high. We estimated odds ratios (OR) and 95% confidence intervals (95% CI) by logistic regression, adjusting for age, sex, use of anxiolytic/antidepressant drugs and job satisfaction.

Results

There was a 10% response rate; 368 questionnaires were available for analysis. High levels of burnout due to emotional exhaustion were observed in all professional categories. Nurses, administrative staff and technicians more frequently scored higher levels of emotional exhaustion (59%, 50% and 50%, respectively) and lack of personal accomplishment (41%, 52% and 38%, respectively) than physicians and healthcare assistants. Not all professionals scored highly for depersonalization. Emotional exhaustion scores were significantly lower in healthcare assistants than nurses (adjusted OR 0.26, 95% CI 0.10-0.64).

Conclusions

Burnout affects all professional categories of hospital staff. Future studies should use larger, more representative samples of hospital staff, perform longitudinal analyses and analyse data on specifics of each professional category and other potential confounders.

Histodifferentiation of oil palm somatic embryo development at low auxin concentration

Large-scale propagation of oil palm (Elaeis guineensis, Jacq.) is difficult due to its single apical meristem. Thus, obtaining plants is mainly through seed germination, and a long growing period is required before oil production is possible. An alternative to large-scale seedling production is indirect somatic embryogenesis. The aim of this study was to analyze the somatic embryogenesis process in oil palm (E. guineensis Jacq.) with amino acids and low concentrations of auxins. The Tenera hybrid was analyzed by cytochemical and ultrastructural methods and was used to regenerate oil palm plants. First, calli were induced in MS culture media supplemented with 2,4-D and picloram. Two types of calli were obtained, characterized by beige or translucent color. Beige calli had embryogenic characteristics, such as large nuclei with prominent nucleoli, and they were multiplied for 8 months in MM culture (half strength MS, 1 mg L^-1 2,4-D, 2 mg L^-1 2iP, 1 mg L^-1 IBA, 250 mg L^-1 citric acid, 10 mg L^-1 cysteine, 100 mg L^-1 inositol, 1 mg L^-1 thiamine, 1 mg L^-1 pyridoxine, 1 mg L^-1 nicotinic acid, 1 mg L^-1 glycine, 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate). After multiplication, the MCB culture medium (half strength MS, supplemented with 0.25 mg L^-1 NAA, 2 mg L^-1 BAP, MM vitamins and 200 mg L^-1 malt extract, and 100 mg L^-1 casein hydrolysate) was the most efficient for embryo formation, showing meristematic centers with totipotent cells in histochemical analyses. The somatic embryos were developed and germinated in MG medium (half strength MS, 0.45 mg L^-1 IAA, 0.25 mg L^-1 BAP, and MM vitamins), transplanted into polyethylene tubes containing pine bark substrates, and acclimatized in a greenhouse, achieving a 97% survival rate. The use of picloram for callus induction and somatic embryogenesis is advantageous and multiplication in MM medium is an important step for increasing cell mass. The calli with light beige color and nodular structures have meristematic cells with dense cytoplasm and totipotential features that later give rise to protoderm, procambium, and ground meristem during the globular, cordiform, and torpedo embryogenesis phases. In MCB medium, the concentration of vitamins and amino acids are crucial for somatic embryogenesis.

Effects of genotype, wilting, and additives on the nutritive value and fermentation of bermudagrass silage

Bermudagrass is the main warm-season grass species used for livestock production in the southeastern United States; however, when it is ensiled, the silage fermentation parameters are often less than desirable. The objective of this study was to investigate the effects of management practices on the nutritive value and fermentation characteristics of bermudagrass silage. In Exp. 1, treatments were the factorial combinations of 2 bermudagrass genotypes, 'Jiggs' () and 'Tifton 85' ( sp.), 4 additives, and 2 DM concentrations at ensiling. The additives were 1) untreated control (deionized water), 2) Ecosyl, 3) B500, or 4) sugarcane molasses. The 2 DM concentrations at ensiling were low DM (22% DM) or high DM (53% DM). Treatments were replicated 3 times in a completely randomized design. Silage treated with molasses had a lesser ( < 0.05) pH and greater ( < 0.01) lactate concentrations than the control, Ecosyl, and B500 in silage with low DM concentrations and greater ( < 0.01) in vitro true digestibility (IVTD) and lesser ( < 0.01) ADF concentrations than the other treatments at either DM concentration. Silage treated with B500 had the greatest ( < 0.01) aerobic stability, whereas that treated with molasses had the least aerobic stability. However, all treatments presented long aerobic stability (≥150 h). Jiggs had lesser ( < 0.01) ADF and NDF and NDF digestibility (NDFD) concentrations than Tifton 85 and Tifton 85 had greater ( < 0.01) IVTD than Jiggs in the silage with a high DM concentration. In Exp. 2, Jiggs silage treated with either molasses (20 g molasses [DM]/kg forage [as-fed basis]) or nothing (control, untreated silage) was fed to 16 beef heifers ( sp.) in individual drylot pens in a completely randomized design with 8 replicates for voluntary DMI, in vivo apparent DM digestibility, and NDFD evaluations. There were no differences ( = 0.36) among treatments in NDFD; however, there was a trend ( < 0.08) for greater in vivo apparent DM digestibility and DMI in heifers fed the molasses-treated silage. Microbial inoculants had decreased effects on Jiggs and Tifton 85 bermudagrass silage ensiled at a low DM concentration; however, adding molasses was an effective management practice to improve its nutritive value and fermentation characteristics.

Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing

RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.

Nanoscale triboactivity of functionalized c-Si surfaces by Fe⁺ ion implantation

In the present work, we present a study of the effect of Fe(+) ion implantation on the tribological response at nanoscale contact lengths of crystalline silicon (c-Si) surfaces. (1 0 0) silicon wafers were implanted with Fe(+) at a fluence of 2  ×  10(17) cm(-2), followed by annealing treatments at temperatures of 800 °C and 1000 °C. After microstructural characterization, nanoabrasive wear tests were performed with an atomic force microscope (AFM) using an AFM diamond tip with a stiff steel cantilever that enables the application of loads between 1 μN and 8 μN. After the nanowear tests, the same AFM was used to visualize and measure the worn craters. It was observed that the as-implanted samples present the poorest nanowear response, i.e. the highest wear rate, even higher than that of the unimplanted Si wafers used as a reference. Nevertheless, annealing treatments result in a measurable increase in the nanowear resistance. In this way we show that Fe(+) ion implantation of c-Si, followed by the proper post-heat treatment, results in the formation of FeSi2 nanoprecipitates finely dispersed in a recrystallized matrix. This can be a valuable way of optimizing the nanotribological behavior of silicon.

Utilization of native oxygen in Eu(RE)-doped GaN for enabling device compatibility in optoelectronic applications

The detrimental influence of oxygen on the performance and reliability of V/III nitride based devices is well known. However, the influence of oxygen on the nature of the incorporation of other co-dopants, such as rare earth ions, has been largely overlooked in GaN. Here, we report the first comprehensive study of the critical role that oxygen has on Eu in GaN, as well as atomic scale observation of diffusion and local concentration of both atoms in the crystal lattice. We find that oxygen plays an integral role in the location, stability, and local defect structure around the Eu ions that were doped into the GaN host. Although the availability of oxygen is essential for these properties, it renders the material incompatible with GaN-based devices. However, the utilization of the normally occurring oxygen in GaN is promoted through structural manipulation, reducing its concentration by 2 orders of magnitude, while maintaining both the material quality and the favorable optical properties of the Eu ions. These findings open the way for full integration of RE dopants for optoelectronic functionalities in the existing GaN platform.

Peculiar Magnetoelectric Coupling in BaTiO₃:Fe₁₁₃ ppm Nanoscopic Segregations

We report polycrystalline BaTiO3 with cooperative magnetization behavior associated with the scarce presence of about 113 atomic ppm of Fe ions, clearly displaying magnetoelectric coupling with significant changes in magnetization (up to ΔM/M ≈ 32%) at the ferroelectric transitions. We find that Fe ions are segregated mostly at the interfaces between grain boundaries and an Fe-rich phase, forming a self-composite with high magnetoelectric coupling above room temperature. We compare our results with ab initio calculations and other experimental results found in the literature, proposing mechanisms that could be behind the magnetoelectric coupling within the ferroelectric matrix. These findings open the way for further strategies to optimize interfacial magnetoelectric couplings.

Analysis of the stability of InGaN/GaN multiquantum wells against ion beam intermixing

Ion-induced damage and intermixing was evaluated in InGaN/GaN multi-quantum wells (MQWs) using 35 keV N(+) implantation at room temperature. In situ ion channeling measurements show that damage builds up with a similar trend for In and Ga atoms, with a high threshold for amorphization. The extended defects induced during the implantation, basal and prismatic stacking faults, are uniformly distributed across the quantum well structure. Despite the extremely high fluences used (up to 4 × 10(16) cm(-2)), the InGaN MQWs exhibit a high stability against ion beam mixing.

Photoluminescence studies of a perceived white light emission from a monolithic InGaN/GaN quantum well structure

In this work we demonstrate by photoluminescence studies white light emission from a monolithic InGaN/GaN single quantum well structure grown by metal organic chemical vapour deposition. As-grown and thermally annealed samples at high temperature (1000 °C, 1100 °C and 1200 °C) and high pressure (1.1 GPa) were analysed by spectroscopic techniques, and the annealing effect on the photoluminescence is deeply explored. Under laser excitation of 3.8 eV at room temperature, the as-grown structure exhibits two main emission bands: a yellow band peaked at 2.14 eV and a blue band peaked at 2.8 eV resulting in white light perception. Interestingly, the stability of the white light is preserved after annealing at the lowest temperature (1000 °C), but suppressed for higher temperatures due to a deterioration of the blue quantum well emission. Moreover, the control of the yellow/blue bands intensity ratio, responsible for the white colour coordinate temperatures, could be achieved after annealing at 1000 °C. The room temperature white emission is studied as a function of incident power density, and the correlated colour temperature values are found to be in the warm white range: 3260–4000 K.