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BackgroundCystine stone is a Mendelian genetic disease caused bySLC3A1orSLC7A9. In this study, we aimed to estimate the genetic prevalence of cystine stones and compare it with the clinical prevalence to better understand the disease etiology.MethodsWe analyzed genetic variants in the general population using the 1000 Genomes project and the Human Gene Mutation Database to extract allSLC3A1andSLC7A9pathogenic variants. All variants procured from both databases were intersected. Pathogenic allele frequency, carrier rate, and affected rate were calculated and estimated based on Hardy-Weinberg equilibrium.ResultsWe found that 9 uniqueSLC3A1pathogenic variants were carried by 26 people and 5 uniqueSLC7A9pathogenic variants were carried by 12 people, all of whom were heterozygote carriers. No homozygote, compound heterozygote, or double heterozygote was identified in the 1000 Genome database. Based on the Hardy-Weinberg equilibrium, the calculated genetic prevalence of cystine stone disease is 1 in 30,585.ConclusionThe clinical prevalence of cystine stone has been previously reported as 1 in 7,000, a notably higher figure than the genetic prevalence of 1 in 30,585 calculated in this study. This suggests that the etiology of cystine stone is more complex than what our current genetic knowledge can explain. Possible factors that may contribute to this difference include novel causal genes, undiscovered pathogenic variants, alternative inheritance models, founder effects, epigenetic modifications, environmental factors, or other modifying factors. Further investigation is needed to fully understand the etiology of cystine stone.

Exercise intolerance is a cardinal symptom in heart failure with preserved ejection fraction (HFpEF). The underlying pathophysiological mechanisms of HFpEF and their influence on exercise intolerance remains poorly understood. This study investigated the role of re-distribution of blood flow in modulating the increase in hindlimb muscle blood flow during HFpEF.We proposed that exercise intolerance is partially contributed by an impaired ability to divert blood flow from peripheral organs such as the kidney during exercise. We utilised an ovine model of HFpEF in which hypertension was established in aged female sheep. We then examined the mean arterial pressure, heart rate, cardiac output, renal blood flow and hindlimb blood flow response to treadmill exercise in both groups of conscious animals.Animals with HFpEF had elevated left ventricular end diastolic pressures (13 ± 6 vs. 0 ± 1 mmHg, p RR gratefully acknowledges granting support from the Health Research Council of New Zealand, the University of Auckland Faculty Research Development Fund and the National Heart Foundation of New Zealand. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Patients with chronic obstructive pulmonary disease (COPD) benefit from the immunomodulatory effect of azithromycin, but long-term administration may alter colonizing bacteria. Our goal was to identify changes in and during azithromycin treatment. Fifteen patients were followed while receiving prolonged azithromycin treatment (Hospital Universitari de Bellvitge, Spain). Four patients (P02, P08, P11, and P13) were persistently colonized by for at least 3 months and two (P04 and P11) by H. parainfluenzae. Isolates from these patients (53 and 18 H. parainfluenzae) were included to identify, by whole-genome sequencing, antimicrobial resistance changes and genetic variation accumulated during persistent colonization. All persistent lineages isolated before treatment were azithromycin-susceptible but developed resistance within the first months, apart from those belonging to P02, who discontinued the treatment. isolates from P08-ST107 acquired mutations in 23S rRNA, and those from P11-ST2480 and P13-ST165 had changes in L4 and L22. In H. parainfluenzae, P04 persistent isolates acquired changes in rlmC, and P11 carried genes encoding MefE/MsrD efflux pumps in an integrative conjugative element, which was also identified in P11-ST147. Other genetic variation occurred in genes associated with cell wall and inorganic ion metabolism. Persistent strains all showed changes in licA and hgpB genes. Other genes (lex1, lic3A, hgpC, and fadL) had variation in multiple lineages. Furthermore, persistent strains showed loss, acquisition, or genetic changes in prophage-associated regions. Long-term azithromycin therapy results in macrolide resistance, as well as genetic changes that likely favor bacterial adaptation during persistent respiratory colonization. IMPORTANCE The immunomodulatory properties of azithromycin reduce the frequency of exacerbations and improve the quality of life of COPD patients. However, long-term administration may alter the respiratory microbiota, such as , an opportunistic respiratory colonizing bacteria that play an important role in exacerbations. This study contributes to a better understanding of COPD progression by characterizing the clinical evolution of in a cohort of patients with prolonged azithromycin treatment. The emergence of macrolide resistance during the first months, combined with the role of as a reservoir and source of resistance dissemination, is a cause for concern that may lead to therapeutic failure. Furthermore, genetic variations in cell wall and inorganic ion metabolism coding genes likely favor bacterial adaptation to host selective pressures. Therefore, the bacterial pathoadaptive evolution in these severe COPD patients raise our awareness of the possible spread of macrolide resistance and selection of host-adapted clones.

Focal dermal hypoplasia (FDH), or Goltz syndrome, is a rare genodermatosis affecting tissues of mesodermal and ectodermal origin. The characteristic skin changes have been reported to symptomatically flare in response to certain triggers as well as to progress over time in some cases. We present the case of a 5-year-old girl with cutaneous flaring and progression of FDH in the setting of septic shock. This case adds to the growing body of literature on both flaring and progression of the cutaneous manifestations of FDH.

Developing digital healthcare solutions that facilitate rapid identification and effective management of patients with Alzheimer disease and related disorders (ADRD) is an area of intense study. A critical juncture for these efforts involves the early detection of cognitive decline. Because primary care providers (PCPs) are the first line of medical care, they are often the first to hear concerns about cognitive decline. However, under-diagnosis of ADRD in primary care settings is widely recognized, as are the many barriers to routine cognitive screening. While information about brief cognitive screening tools for detecting ADRD is plentiful, PCPs remain uncertain about which patients to assess, which tools to use and how to use them, and how to communicate results. The goal of this project was to design a risk assessment and cognitive screening (RACS) application that specifically addressed the needs and concerns of PCPs to facilitate identification of cognitive decline in primary care settings.We employed a multi-modal assessment approach in designing the RACS app, which first assesses risk for cognitive impairment and then assesses cognitive functioning using a working memory/processing speed task in combination with four speech/language tasks. We assembled a multidisciplinary team with the following expertise to develop and test the app: biostatistics, computational linguistics, computer science, computerized cognitive assessment, gaming/app development, engineering, neurology, neuropsychology, neuroscience, primary care, psychometrics, and speech-language pathology.Programming of app features and pilot testing with people with ADRD was completed in 3 months. Initial development of the connected speech analysis pipeline was completed in 4 months with ongoing testing. Data collection of 50 cognitively normal, 50 mild cognitive impairment, and 50 mild dementia participants is approximately 50% completed within 6 months. Preliminary results based on cognitive performance alone show good ability to discriminate groups. Reduction of speech-language variables for inclusion in a final cognitive performance score is underway using a variety of machine learning techniques, including the elastic net and random forests.The RACS app shows promise as a digital health solution to facilitate early detection of cognitive decline in primary care and may prove useful in other busy clinical settings.

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.

Objective To undertake the first comprehensive evaluation of the urinary microbiota associated with Hunner lesion (HL) interstitial cystitis/bladder pain syndrome (IC/BPS). Despite no previous identification of a distinct IC/BPS microbial urotype, HL IC/BPS, an inflammatory subtype of IC/BPS, was hypothesized most likely to be associated with a specific bacterial species or microbial pattern. Participants and methods The bacterial microbiota of midstream urine specimens from HL IC/BPS and age- and gender-matched IC/BPS patients without HL (non-HL IC/BPS) were examined using the pan-bacterial domain clinical-level molecular diagnostic Pacific Biosciences full-length 16S gene sequencing protocol, informatics pipeline and database. We characterized the differential presence, abundances, and diversity of species, as well as gender-specific differences between and among HL and non-HL IC/BPS patients. Results A total of 59 patients with IC/BPS were enrolled (29 HL, 30 non-HL; 43 women, 16 men) from a single centre and the microbiota in midstream urine specimens was available for comparison. The species abundance differentiation between the HL and non-HL groups (12 species) was not significantly different after Bonferroni adjustments for multiple comparisons. Similarly, the nine differentiating species noted between female HL and non-HL patients were not significantly different after similar statistical correction. However, four species abundances (out of the 10 species differences identified prior to correction) remained significantly different between male HL and non-HL subjects: Negativicoccus succinivorans, Porphyromonas somerae, Mobiluncus curtisii and Corynebacterium renale. Shannon diversity metrics showed significantly higher diversity among HL male patients than HL female patients (P = 0.045), but no significant diversity differences between HL and non-HL patients overall. Conclusions We were not able to identify a unique pathogenic urinary microbiota that differentiates all HL from all non-HL IC/BPS. It is likely that the male-specific differences resulted from colonization/contamination remote from the bladder. We were not able to show that bacteria play an important role in patients with HL IC/BPS.

Millions of motor vehicle crashes and tens of thousands of resulting deaths occur each year in the United States. While it is well known that wintry conditions make driving more difficult and dangerous, it is difficult to quantify and communicate the threat to motorists, especially in real time. This proof-of-concept research uses machine learning (ML) to approach this problem in a new way by creating a ML model that can identify snow on the road froma traf c camera image. This information is coupled with the number of coincident vehicular crashes to provide detailedconsideration of the impact of snow on the road to motorists and transportation agency decision-makers. It was foundthat, during meteorological winter, when the ML model determined there to be snow on the road in a traf c camera image, the chance of a vehicular crash pairing with that traf c camera increased by 61%. The systems developed as part of this research have potential to assist roadway of cials in assessing risk in real time and making informed decisionsabout snow removal and road closures. Moreover, the implementation of in-vehicle weather hazard information could promote driver safety and allow motorists to adjust their driving behavior and travel decision making as well.

A key to longevity assurance is the nutrient-sensing mTOR pathway. Inhibition of mTOR extends lifespan in a variety of organisms. However, the downstream effectors of the mTOR pathway for lifespan regulation are elusive. In a recent report, we described the role of Maf1 as a critical lifespan regulator downstream of the mTOR pathway in fission yeast. Maf1 is the master negative regulator of RNA polymerase III-directed transcription (e.g. tRNAs and 5S rRNAs) and is regulated by mTOR-mediated phosphorylation. We demonstrated that Maf1 is required for lifespan extension under calorie restriction or when mTOR is inhibited. We also showed that Maf1 prevents DNA damage at tRNA genes, which appears to contribute to lifespan maintenance by Maf1. Here we highlight these observations and present additional results to discuss the role of the mTOR-Maf1-Pol III axis in promoting genomic integrity in the face of DNA replication-transcription conflicts in order to maintain normal lifespan.

The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host–bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.

Theory predicts that local adaptation should favor the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine versus freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harboring multiple quantitative trait loci for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these “genomic islands” is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and lineage-specific genes (LSGs) were enriched around genomic islands, and that all three chromosomes harboring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9× and 2.9× more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.

Background/Objective: The Outpatient Arthroplasty Risk Assessment (OARA) score has been used successfully to identify patients who can safely undergo outpatient primary total joint arthroplasty (TJA) based on medical risk stratification. The targeted score (0 to 79) was conservatively established to ensure patient safety. However, the number of points associated with each of the 52 comorbidities in the OARA score were assigned based on physician experience with early discharge. This study applied machine learning (ML) to empirically identify the relative contribution/importance of each medical comorbidity to safe same-day discharge (SDD). Methods: 3,047 patients who underwent primary unilateral TJA by a single surgeon at a single institution were included in the analysis; 573 were SDDs. Before ML analysis, associations among binary (yes/no) comorbidities were examined using Cramér's V. A CART decision tree model using Gini method was used to develop a model for SDD (yes/no) based on the presence or absence of the comorbidities. Results: To produce interpretable results with acceptable face validity the 52 comorbidities were grouped in 19 common medical categories (heart disease, liver disease, etc.). Although the resulting model was less than perfectly predictive (AROC = 0.652, 95% CI 0.629–0.675), it resulted in an interpretable classification tree identifying heart disease, kidney disease, immunosuppression, chronic sedative use, pulmonary disease, thrombophilia, anemia, and history of stroke, in order, as the most important predictors of SDD. Conclusion: Model limitations expressed as AROC were not unexpected because the relative contribution (expressed as points) of comorbidities to the OARA score are based on physician decision-making, not empirical identification of the importance of each medical condition to safe SDD. Study results moved the goal of empirical classification forward but the low prevalence of many of the comorbidities limited variability and hence model performance and accuracy. Future work with a larger sample is being planned.

BACKGROUND Although there is interest in developing pharmacotherapies for the treatment of immune checkpoint inhibitor-associated enterocolitis (ICIC), there is currently no consensus on how to optimally measure disease activity in this condition. AIMS To identify all scoring indices used for the measurement of disease activity in ICIC, assess their operating properties, and explore their potential utility as outcome measures. METHODS We searched MEDLINE, EMBASE and the Cochrane Library from inception to November 2020 to identify studies that evaluated disease activity and severity in patients with ICI-associated enterocolitis. These scoring tools could be designed specifically for ICIC or adapted from other diseases, and assessed clinical, endoscopic, or histologic disease activity. RESULTS Sixty-four studies were included. The Common Terminology Criteria for Adverse Events is commonly used to describe symptoms, although has only been partially validated and was not designed as a disease activity index. Endoscopic and histologic indices used in inflammatory bowel disease have been adopted for ICIC including the Mayo Endoscopic Subscore, Ulcerative Colitis Endoscopic Index of Severity, Simple Endoscopic Score for Crohn's Disease, Nancy Histological Index, Robarts Histopathological Index, and Geboes Score, among others. None of these indices has been validated for use in ICIC, and all lacked content validity and responsiveness. CONCLUSIONS There are no validated clinical, endoscopic, or histologic outcomes to assess disease activity in ICIC. Development and validation of reliable and responsive outcome measures that can be used to measure disease activity will be paramount for both clinical practice and for the development of treatments.

We study a scheduling environment that finds many real-world manufacturing applications, in which there is a close connection between a hybrid multiprocessor open shop and multiple parallel identical flow shops. In this environment, there is an extended two-stage open shop, where in one stage we have a set of parallel identical machines, while in the other we have a two-machine flow shop. Our objective is to minimize the makespan, that is, the latest completion time of all jobs. We pursue approximation algorithms with provable performance, and we achieve a 2-approximation when the number of parallel identical machines is constant or is part of the input; we also design a 5/3-approximation for the special case where there is only one machine in the multiprocessor stage, which remains weakly NP-hard. Our empirical experiments show that both approximation algorithms perform much better in simulated instances; their average ratios over the proposed lower bound are around 1.5 and 1.2, respectively.

Background and Aims We aimed to quantify the magnitude of the association between endoscopic recurrence and clinical recurrence [symptom relapse] in patients with postoperative Crohn’s disease. Methods Databases were searched to October 2, 2020, for randomised controlled trials [RCTs] and cohort studies of adult patients with Crohn’s disease with ileocolonic resection and anastomosis. Summary effect estimates for the association between clinical recurrence and endoscopic recurrence were quantified by risk ratios [RR] and 95% confidence intervals [95% CI]. Mixed-effects meta-regression evaluated the role of confounders. Spearman correlation coefficients were calculated to assess the relationship between these outcomes as endpoints in RCTs. An exploratory mixed-effects meta-regression model with the logit of the rate of clinical recurrence as the outcome and the rate of endoscopic recurrence as a predictor was also evaluated. Results In all, 37 studies [N = 4053] were included. For eight RCTs with available data, the RR for clinical recurrence for patients who experienced endoscopic recurrence was 10.77 [95% CI 4.08 to 28.40; GRADE moderate certainty evidence]; the corresponding estimate from 11 cohort studies was 21.33 [95% CI 9.55 to 47.66; GRADE low certainty evidence]. A single cohort study showed a linear relationship between Rutgeerts score and clinical recurrence risk. There was a strong correlation between endoscopic recurrence and clinical recurrence treatment effect estimates as trial outcomes [weighted Spearman correlation coefficient 0.51]. Conclusions The associations between endoscopic recurrence and subsequent clinical recurrence lend support to the choice of endoscopic recurrence to monitor postoperative disease activity and as a primary endpoint in clinical trials of postoperative Crohn’s disease.

It has been estimated that more than 390 million people are infected with Dengue virus every year; around 96 millions of these infections result in clinical pathologies. To date, there is only one licensed viral vector-based Dengue virus vaccine CYD-TDV approved for use in dengue endemic areas. While initially approved for administration independent of serostatus, the current guidance only recommends the use of this vaccine for seropositive individuals. Therefore, there is a critical need for investigating the influence of Dengue virus serostatus and immunological mechanisms that influence vaccine outcome. Here, we provide comprehensive evaluation of sero-status and host immune factors that correlate with robust immune responses to a Dengue virus vector based tetravalent vaccine (TV003) in a Phase II clinical cohort of human participants. We observed that sero-positive individuals demonstrate a much stronger immune response to the TV003 vaccine. Our multi-layered immune profiling revealed that sero-positive subjects have increased baseline/pre-vaccination frequencies of circulating T follicular helper (cTfh) cells and the Tfh related chemokine CXCL13/BLC. Importantly, this baseline/pre-vaccination cTfh profile correlated with the vaccinees’ ability to launch neutralizing antibody response against all four sero-types of Dengue virus, an important endpoint for Dengue vaccine clinical trials. Overall, we provide novel insights into the favorable cTfh related immune status that persists in Dengue virus sero-positive individuals that correlate with their ability to mount robust vaccine specific immune responses. Such detailed interrogation of cTfh cell biology in the context of clinical vaccinology will help uncover mechanisms and targets for favorable immuno-modulatory agents.Author summaryDengue virus (DENV) is a worldwide threat that causes significant health and economic burden. Currently, there are several challenges in the development of a DENV vaccine including the existence of four different serotypes all; capable of causing disease and antibody dependent enhancement (ADE). For complete protection, a vaccine must be able to generate neutralizing antibodies against all 4 serotypes to avoid ADE. Currently, there is one licensed DENV vaccine, CYD-TDV (DENGVAXIATM). However, this vaccine is only efficacious in protecting against severe disease in DENV seropositive individuals therefore serostatus effect must be further studied for optimal vaccine design. A subset of CD4+ T cells called T-follicular helper (Tfh) cells have been well known to play a major role in aiding high affinity antibody production. Therefore, we chose to look at subsets of Tfh and the cytokines they produce in human blood that can serve as biomarkers for effective vaccine design. We found that DENV sero-positive participants had increased pre-vaccination frequencies of Tfh cells and higher levels of the Tfh related chemokine CXCL13/BLC that plays a role in directing antigen-specific responses. This pre-vaccination Tfh profile and CXCL13/BLC are then correlated positively with the vaccinees’ ability to produce neutralizing antibody against all four sero-types (breadth of the Response) of DENV, an important goal for all DENV vaccine trials.

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.

Background and Aims Quantifying placebo rates and the factors influencing them are essential to inform trial design. We provide a contemporary summary of clinical, endoscopic, histological and safety placebo rates in induction and maintenance clinical trials of ulcerative colitis, and identify factors influencing them. Methods MEDLINE, EMBASE and the Cochrane library were searched from April 2014 to April 2020, updating a prior meta-analysis that searched from inception to April 2014. We included placebo-controlled trials of aminosalicylates, corticosteroids, immunosuppressives, small-molecules and biologics in adults with ulcerative colitis. Placebo rates were pooled using random-effects and mixed-effects meta-regression models to assess the associated study-level. Results In 119 trials [92 induction, 27 maintenance] clinical, endoscopic and histological remission placebo rates for induction trials were 11% (95% confidence interval [CI] 9–13%), 19% [95% CI 15–23%] and 15% [95% CI 11–19%], respectively; for maintenance trials, clinical and endoscopic placebo remission rates were 18% [95% CI 12–25%] and 20% [95% CI 15–25%], respectively. Higher endoscopic subscore and a higher rate of exposure to prior biologic therapy at enrolment were associated with lower clinical and endoscopic placebo remission rates. Absence of central reading was associated with an increase in placebo endoscopic response and remission rates. More follow-up visits and increasing trial duration were associated with higher clinical placebo rates. Conclusions Placebo rates in ulcerative colitis trials vary according to the endpoint assessed, whether it is for assessment of response or remission, and whether the trial is designed for induction or maintenance. These contemporary rates across different endpoints and drug classes will help to inform trial design.

Description Neurocysticercosis, a parasitic infection of the central nervous system (CNS) caused by the Taenia solium cestode, presents clinically with a large and diverse spectrum of symptomatology, dependent upon lesion number, locale and ensuing inflammatory response. To this date, there are only two documented cases of psychosis presenting in patients with neurocysticercosis, both of which were published in India. This case presentation depicts the first documented case of Psychotic Disorder Due to Another Medical Condition: Neurocysticercosis in the United States. The authors postulate that the atypical presentation of the neuropsychiatric instability with the aberrant recurrence of neurocysticercosis is predominantly attributable to the parasitic infection itself, along with its resultant cyst formation and inflammatory response. Further research is necessary to expand upon our knowledge and understanding of the neuropsychiatric effects and optimal management of neurocysticercosis, as well as its possible recurrent nature.

A healthy, active woman in her 70s reported intermittent exertional dyspnoea for 2 months, notable during frequent open-water swimming. Symptoms were similar to an episode of travel-provoked pulmonary embolism 3 years prior. She denied chest pain, cough, fever, extremity complaints and symptoms at rest. Due to the COVID-19 pandemic, her healthcare system was using secure telemedicine to evaluate non-critical complaints. During the initial video visit, she appeared well, conversing normally without laboured breathing. An elevated serum D-dimer prompted CT pulmonary angiography, which identified acute lobar pulmonary embolism. After haematology consultation and telephone conversation with the patient, her physician prescribed rivaroxaban. Her symptoms rapidly improved. She had an uneventful course and is continuing anticoagulation indefinitely. The pandemic has increased the application of telemedicine for acute care complaints. This case illustrates its safe and effective use for comprehensive management of acute pulmonary embolism in the primary care setting.

Objective To derive and characterize the performance of various metrics of emergency transport time in assessing for sociodemographic disparities in the setting of residential segregation. Secondarily to characterize racial disparities in emergency transport time of suspected stroke patients in Austin, Texas. Data sources We used a novel dataset of 2518 unique entries with detailed spatial and temporal information on all suspected stroke transports conducted by a public emergency medical service in Central Texas between 2010 and 2018. Study design We conducted one-way ANOVA tests with post-hoc pairwise t-tests to assess how mean hospital transport times varied by patient race. We also developed a spatially-independent metric of emergency transport urgency, the ratio of expected duration of self-transport to a hospital and the measured transport time by an ambulance. Data collection/extraction We calculated ambulance arrival and destination times using sequential temporospatial coordinates. We excluded any entries in which patient race was not recorded. We also excluded entries in which ambulances' routes did not pass within 100 m of either the patient's location or the documented hospital destination. Principal findings We found that mean transport time to a hospital was 2.5 min shorter for black patients compared to white patients. However, white patients' transport times to a hospital were found to be, on average, 4.1 min shorter than expected compared to 3.4 min shorter than expected for black patients. One-way ANOVA testing for the spatially-independent index of emergency transport urgency was not statistically significant, indicating that average transport time did not vary significantly across racial groups when accounting for variations in transport distance. Conclusions Using a novel transport urgency index, we demonstrate that these findings represent race-based variation in spatial distributions rather than racial bias in emergency medical transport. These results highlight the importance of closely examining spatial distributions when utilizing temporospatial data to investigate geographically-dependent research questions.

Introduction: Numerous studies have found evidence of disparities in the treatment and health outcomes of patients with acute ischemic stroke. As minimizing time to treatment is essential in acute ischemic stroke management, we aimed to assess for racial disparities in emergency stroke transport. Emergency transport times are dependent on the geographic distribution of patients and hospitals, but previous studies have not controlled for racial variation in spatial distributions when assessing for disparity. Methods: Using a novel dataset of 2,518 unique entries with detailed spatial and temporal information on all suspected stroke transports conducted by a public emergency medical service in Central Texas over eight years, we conducted one-way ANOVA tests with post-hoc pairwise t-tests to assess how mean hospital transport time varied by patient race and developed a spatially-independent metric of emergency transport urgency. Results: Results are reported as means with standard errors and p-values from post-hoc pairwise testing. We found that mean transport time to a hospital was 2.5 minutes shorter for black patients (10.9 +/- 0.274 minutes) compared to white patients (13.4 +/- 0.174 minutes) with p < 0.0001. However, white patients’ transport times to a hospital were found to be, on average, 4.1 +/- 0.085 minutes shorter than expected compared to 3.4 +/- 0.124 minutes shorter than expected for black patients (p = 0.00015). Using a novel transport urgency index, we demonstrate that these findings represent race-based variation in spatial distributions rather than racial bias in emergency medical transport. Conclusion: In summary, these results highlight the importance of closely examining spatial distributions when utilizing spatial data to investigate geographically-dependent research questions.

20 pags., 7 figs., 2 tabs., Genetic variants arising from within-patient evolution shed light on bacterial adaptation during chronic infection. Contingency loci generate high levels of genetic variation in bacterial genomes, enabling adaptation to the stringent selective pressures exerted by the host. A significant gap in our understanding of phase-variable contingency loci is the extent of their contribution to natural infections. The human-adapted pathogen nontypeable Haemophilus influenzae (NTHi) causes persistent infections, which contribute to underlying disease progression. The phase-variable high-molecular-weight (HMW) adhesins located on the NTHi surface mediate adherence to respiratory epithelial cells and, depending on the allelic variant, can also confer high epithelial invasiveness or hyperinvasion. In this study, we characterize the dynamics of HMW-mediated hyperinvasion in living cells and identify a specific HMW binding domain shared by hyperinvasive NTHi isolates of distinct pathological origins. Moreover, we observed that HMW expression decreased over time by using a longitudinal set of persistent NTHi strains collected from chronic obstructive pulmonary disease (COPD) patients, resulting from increased numbers of simple-sequence repeats (SSRs) downstream of the functional P2hmw1A promoter, which is the one primarily driving HMW expression. Notably, the increased SSR numbers at the hmw1 promoter region also control a phenotypic switch toward lower bacterial intracellular invasion and higher biofilm formation, likely conferring adaptive advantages during chronic airway infection by NTHi. Overall, we reveal novel molecular mechanisms of NTHi pathoadaptation based on within-patient lifestyle switching controlled by phase variation. IMPORTANCE Human-adapted bacterial pathogens have evolved specific mechanisms to colonize their host niche. Phase variation is a contingency strategy to allow adaptation to changing conditions, as phase-variable bacterial loci rapidly and reversibly switch their expression. Several NTHi adhesins are phase variable. These adhesins are required for colonization but also immunogenic, in such a way that bacteria with lower adhesin levels are better equipped to survive an immune response, making their contribution to natural infections unclear. We show here that the major NTHi adhesin HMW1A displays allelic variation, which can drive a phase-variable epithelial hyperinvasion phenotype. Over time, hmw1A phase variation lowers adhesin expression, which controls an NTHi lifestyle switch from high epithelial invasiveness to lower invasion and higher biofilm formation. This reversible loss of function aligns with the previously stated notion that epithelial infection is essential for NTHi infection establishment, but once established, persistence favors gene inactivation, in this case facilitating biofilm growth., This work has been funded by grants SAF2015-66520-R and RTI2018-096369-B-I00 from MINECO, 875/2019 from SEPAR, and PC150-151-152 from the Gobierno de Navarra to J.G. and RTI2018-099985-B-I00 to M.M. CIBER is an initiative from the Instituto de Salud Carlos III (ISCIII), Madrid, Spain. A.T.-A. is funded by a Ministry of Science and Innovation grant (PID2019-105216GB-I00)

Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR–Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR–Cas9 DNA labeling. We first design a CRISPR–Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR–Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR–Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.

Both methionine restriction and rapamycin treatment are robust longevity-enhancing regimens for which the mechanisms remain unclear. Cellular senescence is a major contributor to the aging process, and we find that both the methionine and rapamycin regimens delay or prevent activation of the senescence program in human cells. Using a transcriptome-wide analysis, we examined the impact of methionine restriction and rapamycin treatment on senescence-associated gene expression in human cardiac fibroblasts. Our findings have been integrated into gene expression data sets from human lung and skin fibroblasts during senescence. The data demonstrate both common and tissue-specific aspects to the senescent phenotype in these cell types. For example, cardiac fibroblasts express brain naturetic peptide, a clinically relevant marker for cardiac failure, whereas senescent cells from all three tissues express at least one of the insulin-like growth factor (IGF)-binding proteins. The IGF-binding proteins are tissue-specific mediators of IGF-1, a growth factor required for proliferation of all tissues. These data suggest that senescent cells serve tissue-specific roles. Moreover, the prolongevity regimens produce distinct patterns of gene expression.

This study investigates how Australian employees perceive managerial support and the influence of union membership on their perception of managerial support using data from 4124 employed persons in Australia across a range of industry sectors. The results indicate that employee perceptions of the work environment (control over working hours, job security, pay equity and safety) influence their perceptions of managerial support, regardless of union membership. The findings imply that managers have a critical role to play in supporting the needs of employees, particularly as organizations confront the challenges posed by aging workforces, growing skill shortages and an increasingly diverse and mobile workforce. This article addresses the call for organizations to provide more support to their employees from governments and management scholars. It also addresses the issue of managers taking on greater prerogative as employee advocates in the light of declining union influence.

PurposeThe purpose of this paper is to study job attitudes between unionized and non-unionized employees in Australia as recent research on attitudes among unionized employees has centred on topics such as attitudes towards unionization and involvement, but not on work-related attitudes.Design/methodology/approachThis study uses a data set of over 5,000 responses from the Australia at Work survey. Ten attitudinal survey questions adapted from the Australian Workplace Industrial Relations Survey and the Australian Survey of Social Attitudes were used to compare work-related attitudinal differences between unionized and non-unionized employees.FindingsFindings show that unionized employees perceive less manager–employee consultation, health and safety, dispensability, time flexibility, workload flexibility, managerial trust, fair treatment and pay equity.Originality/valueNot much is known about the attitudinal differences between unionized and non-unionized employees, given the paucity of research on unionist job attitudes. Recent research in this area has centred on employee attitudes towards unionization and involvement as opposed to studying work-related attitudes. The findings can help the management predict behavioural responses between unionized and non-unionized employees for improved decision making.

Purpose This paper aims to investigate whether values enactment could be increased through frame-of-reference (FOR) training configured around values prototyping and behavioural domain training for managers within an Australian public sector organisation. Design/methodology/approach Employees from an Australian public sector organisation were studied to ascertain the effect of values training and development via a three-way longitudinal design with a control group. Findings The findings indicate that FOR training can increase employee values enactment clarity and, thereby, have a positive impact upon organisational values enactment. Practical implications The application of FOR training constitutes a new approach to supporting the development of employee values clarity, which, in turn, can support the achievement of organisational values enactment. Through FOR training, employees can learn to apply organisational values in their decision-making and other behaviours irrespective of whether they are highly congruent with their personal values. Originality/value Empirical research into values management is limited and there is a lack of consensus to what is needed to create a values-driven organisation. The article shows that FOR training can be a beneficial component of a broader human resource strategy aimed at increasing organisational values enactment. With reference to the resource-based view of the firm, it is argued that values enactment constitutes a distinctive capability that may confer sustained organisational advantage.

This paper explores the personalization of smartwatch-based fall detection models trained using a combination of deep neural networks with ensemble techniques. Deep neural networks face practical challenges when used for fall detection, which in general tend to have limited training samples and imbalanced datasets. Moreover, many motions generated by a wrist-worn watch can be mistaken for a fall. Obtaining a large amount of real-world labeled fall data is impossible as fall is a rare event. However, it is easy to collect a large number of non-fall data samples from users. In this paper, we aim to mitigate the scarcity of training data in fall detection by first training a generic deep learning ensemble model, optimized for high recall, and then enhancing the precision of the model, by collecting personalized false positive samples from individual users, via feedback from the SmartFall App. We performed real-world experiments with five volunteers and concluded that a personalized fall detection model significantly outperforms generic fall detection models, especially in terms of precision. We further validated the performance of personalization by using a new metric for evaluating the accuracy of the model via normalizing false positive rates with regard to the number of spikes of acceleration over time.

Objective: To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. Data sources: PubMed articles published since the last meeting in June 2015 up to June 2019. Review methods: A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. Conclusion: Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. Implications for practice: In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics. © 2020 Elsevier B.V.

Introduction: Drip and Ship (DNS) and Mothership (MS) are well-known emergency transport strategies in acute stroke care, but the criteria for choosing between the two is widely debated. Existing models define time-dependent outcomes but cannot resolve this debate with statistical significance because the independent variables are deterministic. We propose a novel stochastic framework that quantifies statistical significance between DNS and MS in a network of primary and comprehensive stroke centers. Methods: We represented the physiology of ischemic core growth as a stochastic first-order differential equation, enabling infarct volume at time of reperfusion to be calculated and mapped to 90-day mRS. Using Texas as a case study, we configured the state’s stroke network within 15,811 geographic blocks as defined by census data. For each block, we ran Monte Carlo simulations to generate Beta distributions of large- and small-vessel infarct volumes, which were then translated into cumulative distribution functions of mRS. A two-sample Kolmogorov-Smirnov test for significance, and Cohen’s d effect size statistic for practical significance were computed between each DNS and MS pair. Stable effect sizes were assured by sampling > 5,000 total infarct volumes for each block. All model parameters were established from large cohort studies or trials. Results: Of the 13,113 blocks where the primary stroke center is the closest hospital from origin, DNS produces significantly better stroke outcomes than MS in 79.0% (0.3% SEM; P < 0.05; 0.2 < d < 0.5). For the subset of patients with large-vessel strokes, MS produces significantly better outcomes in 44.6% of blocks (1.3% SEM; P < 0.05; 0.4 < d < 0.85). Conclusion: Stochastic methods enable the use of clinically relevant metrics for comparative significance of DNS and MS in a geographic region. This formalism, which has not been incorporated in previous models, can be further generalized beyond stochastic infarct volumes if sufficiently large datasets become available. For example, the kinetic growth model can integrate the statistical distributions of times (pre-hospital and hospital) leading up to intervention, and patient attributes that affect outcomes, such as the degree of collateral flow and comorbidities.

Summary The genomes of naturally competent Pasteurellaceae and Neisseriaceae have many short uptake sequences (USS), which allow them to distinguish self-DNA from foreign DNA. To fully characterize this preference we developed genome-wide maps of DNA uptake using both a sequence-based computational model and genomic DNA that had been sequenced after uptake by and recovery from competent Haemophilus influenzae cells. When DNA fragments were shorter than the average USS spacing of ∼1,000 bp, sharp peaks of uptake were centered at USS and separated by valleys with 1000-fold lower uptake. Long DNA fragments (1.5–17 kb) gave much less variation, with 90% of positions having uptake within 2-fold of the mean. All detectable uptake biases arose from sequences that fit the USS uptake motif. Simulated competition predicted that, in its respiratory tract environment, H. influenzae will efficiently take up its own DNA even when human DNA is present in 100-fold excess., Graphical Abstract, Highlights • For short DNA fragments, an uptake sequence (USS) improves DNA uptake 1000-fold • Most longer H. influenzae fragments have USS, giving even uptake across the genome • Preferred USS are stiff, so strand melting may facilitate kinking for uptake • H. influenzae will take up its own DNA 100-fold better than human DNA, Molecular Biology; Microbiology

Maf1 is the master repressor of RNA polymerase III responsible for transcription of tRNAs and 5S rRNAs. Maf1 is negatively regulated via phosphorylation by the mTOR pathway, which governs protein synthesis, growth control, and lifespan regulation in response to nutrient availability. Inhibiting the mTOR pathway extends lifespan in various organisms. However, the downstream effectors for the regulation of cell homeostasis that are critical to lifespan extension remain elusive. Here we show that fission yeast Maf1 is required for lifespan extension. Maf1’s function in tRNA repression is inhibited by mTOR‐dependent phosphorylation, whereas Maf1 is activated via dephosphorylation by protein phosphatase complexes, PP4 and PP2A. Mutational analysis reveals that Maf1 phosphorylation status influences lifespan, which is correlated with elevated tRNA and protein synthesis levels in maf1∆ cells. However, mTOR downregulation, which negates protein synthesis, fails to rescue the short lifespan of maf1∆ cells, suggesting that elevated protein synthesis is not a cause of lifespan shortening in maf1∆ cells. Interestingly, maf1∆ cells accumulate DNA damage represented by formation of Rad52 DNA damage foci and Rad52 recruitment at tRNA genes. Loss of the Rad52 DNA repair protein further exacerbates the shortened lifespan of maf1∆ cells. Strikingly, PP4 deletion alleviates DNA damage and rescues the short lifespan of maf1∆ cells even though tRNA synthesis is increased in this condition, suggesting that elevated DNA damage is the major cause of lifespan shortening in maf1∆ cells. We propose that Maf1‐dependent inhibition of tRNA synthesis controls fission yeast lifespan by preventing genomic instability that arises at tRNA genes., In response to nutrient availability, mTOR inactivates Maf1 via phosphorylation. This results in hyperactivation of Pol III‐mediated transcription, leading to DNA damage due to collisions between the replication and transcription machineries. Such DNA damage may shorten lifespan. mTOR‐mediated activation of cellular processes and increased energy expenditure also negatively affect lifespan.

The CRISPR/Cas9 system has been proposed as a cure strategy for HIV. However, few published guide RNAs (gRNAs) are predicted to cleave the majority of HIV-1 viral quasispecies (vQS) observed within and among patients. We report the design of a novel pipeline to identify gRNAs that target HIV across a large number of infected individuals. Next generation sequencing (NGS) of LTRs from 269 HIV-1-infected samples in the Drexel CARES Cohort was used to select gRNAs with predicted broad-spectrum activity. In silico, D-LTR-P4-227913 (package of the top 4 gRNAs) accounted for all detectable genetic variation within the vQS of the 269 samples and the Los Alamos National Laboratory HIV database. In silico secondary structure analyses from NGS indicated extensive TAR stem-loop malformations predicted to inactivate proviral transcription, which was confirmed by reduced viral gene expression in TZM-bl or P4R5 cells. Similarly, a high sensitivity in vitro CRISPR/Cas9 cleavage assay showed that the top-ranked gRNA was the most effective at cleaving patient-derived HIV-1 LTRs from five patients. Furthermore, the D-LTR-P4-227913 was predicted to cleave a median of 96.1% of patient-derived sequences from other HIV subtypes. These results demonstrate that the gRNAs possess broad-spectrum cutting activity and could contribute to an HIV cure.

Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest (e.g., disease state). Elucidating such relations is often difficult as microbiome data are compositional, sparse, and have high dimensionality. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to sample characteristics such as host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. Additionally, analyses that use taxonomic relative abundances to predict the abundances of different gene functions aggregate predicted functional profiles across taxa. This precludes straightforward identification of predicted functional components associated with subsets of co-occurring taxa. We provide an approach to explore co-occurring taxa using “topics” generated via a topic model and link these topics to specific sample features (e.g., disease state). Rather than inferring predicted functional content based on overall taxonomic relative abundances, we instead focus on inference of functional content within topics, which we parse by estimating interactions between topics and pathways through a multilevel, fully Bayesian regression model. We apply our methods to three publicly available 16S amplicon sequencing datasets: an inflammatory bowel disease dataset from Gevers et al., an oral cancer dataset from Schmidt et al., and a time-series dataset from David et al. Using our topic model approach to uncover latent structure in 16S rRNA amplicon surveys, investigators can (1) capture groups of co-occurring taxa termed topics; (2) uncover within-topic functional potential; (3) link taxa co-occurrence, gene function, and environmental/host features; and (4) explore the way in which sets of co-occurring taxa behave and evolve over time. These methods have been implemented in a freely available R package: https://github.com/EESI/themetagenomics.

Natural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacteriumHaemophilus influenzae, the genes needed for DNA uptake are induced by the CRP andSxytranscription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes,HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from aStreptococcusspecies. Deletion of the putative toxin(HI0660)restores uptake to the antitoxin mutant. The fulltoxTAoperon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy-and CRP-dependent-competence promoter,HI0659/660transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts withintoxTand will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency oftoxTandtoxTAdeletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects oftoxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.ABBREVIATED SUMMARYThe competence regulon ofHaemophilus influenzaeincludes an unprecedented toxin/antitoxin gene pair. When not opposed by antitoxin, the toxin completely prevents DNA uptake but causes only very minor decreases in cell growth and competence gene expression. The TA gene pair was acquired by horizontal gene transfer, and the toxin gene has undergone repeated deletions in other strains.

Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures—including immune responses and therapeutic interventions—shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2–20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.

Purpose The purpose of this study is to explain demographic influences on employee trust towards managers. Design/methodology/approach Drawing upon a data set of over 5,000 responses from the Australian workforce, this paper examines demographic influences on employee trust in their managers. Findings The findings show that demographic influences have an effect on employee trust towards managers. Employees who are male, older, public sector, permanent, longer tenured and unionised were found to be less likely to trust managers. Practical implications Relevant to human resource practice, the findings offer potential for the development of trust by identifying employees who are less likely to trust managers. The expected outcome is that such employees can be selected for programmes and practices aimed at improving trust, such as increased managerial contact, consultation and support. Originality/value There has been a general decline of employee trust in managers over the past two decades. Research on the antecedents of trust has been reported to lag behind theory, with a paucity of research relating to demographic influences on employee trust towards managers. This study fills this research gap and offers potential for the targeted development of trust towards managers among employees.