Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases.

As part of the ongoing bacterial-phage arms race, CRISPR-Cas systems in bacteria clear invading phages whereas anti-CRISPR proteins (Acrs) in phages inhibit CRISPR defenses. Known Acrs have proven extremely diverse, complicating their identification. Here, we report a deep learning algorithm for Acr identification that revealed an Acr against type VI-B CRISPR-Cas systems. The algorithm predicted numerous putative Acrs spanning almost all CRISPR-Cas types and subtypes, including over 7,000 putative type IV and VI Acrs not predicted by other algorithms. By performing a cell-free screen for Acr hits against type VI-B systems, we identified a potent inhibitor of Cas13b nucleases we named AcrVIB1. AcrVIB1 blocks Cas13b-mediated defense against a targeted plasmid and lytic phage, and its inhibitory function principally occurs upstream of ribonucleoprotein complex formation. Overall, our work helps expand the known Acr universe, aiding our understanding of the bacteria-phage arms race and the use of Acrs to control CRISPR technologies.

What the public think about participation in medical research during an influenza pandemic: an international cross-sectional survey.

OBJECTIVES: The public and patients are primary contributors and beneficiaries of pandemic-relevant clinical research. However, their views on research participation during a pandemic have not been systematically studied. We aimed to understand public views regarding participation in clinical research during a hypothetical influenza pandemic. STUDY DESIGN: This is an international cross-sectional survey. METHODS: We surveyed the views of nationally representative samples of people in Belgium, Poland, Spain, Ireland, the United Kingdom, Canada, Australia and New Zealand, using a scenario-based instrument during the 2017 regional influenza season. Descriptive and regression analyses were conducted. RESULTS: Of the 6804 respondents, 5572 (81.8%) thought pandemic-relevant research was important, and 5089 (74.8%) thought 'special rules' should be applied to make this research feasible. The respondents indicated willingness to take part in lower risk (4715, 69.3%) and higher risk (3585, 52.7%) primary care and lower risk (4780, 70.3%) and higher risk (4113, 60.4%) intensive care unit (ICU) study scenarios. For primary care studies, most (3972, 58.4%) participants preferred standard enrolment procedures such as prospective written informed consent, but 2327 (34.2%) thought simplified procedures would be acceptable. For ICU studies, 2800 (41.2%) preferred deferred consent, and 2623 (38.6%) preferred prospective third-party consent. Greater knowledge about pandemics, trust in a health professional, trust in the government, therapeutic misconception and having had ICU experience as a patient or carer predicted increased willingness to participate in pandemic-relevant research. CONCLUSIONS: Our study indicates current public support for pandemic-relevant clinical research. Tailored information and initiatives to advance research literacy and maintain trust are required to support pandemic-relevant research participation and engagement.

Anxiety and anxious-depression in Parkinson's disease over a 4-year period: a latent transition analysis.

BACKGROUND: Depression and anxiety in Parkinson's disease are common and frequently co-morbid, with significant impact on health outcome. Nevertheless, management is complex and often suboptimal. The existence of clinical subtypes would support stratified approaches in both research and treatment. METHOD: Five hundred and thirteen patients with Parkinson's disease were assessed annually for up to 4 years. Latent transition analysis (LTA) was used to identify classes that may conform to clinically meaningful subgroups, transitions between those classes over time, and baseline clinical and demographic features that predict common trajectories. RESULTS: In total, 64.1% of the sample remained in the study at year 4. LTA identified four classes, a 'Psychologically healthy' class (approximately 50%), and three classes associated with psychological distress: one with moderate anxiety alone (approximately 20%), and two with moderate levels of depression plus moderate or severe anxiety. Class membership tended to be stable across years, with only about 15% of individuals transitioning between the healthy class and one of the distress classes. Stable distress was predicted by higher baseline depression and psychiatric history and younger age of onset of Parkinson's disease. Those with younger age of onset were also more likely to become distressed over the course of the study. CONCLUSIONS: Psychopathology was characterized by relatively stable anxiety or anxious-depression over the 4-year period. Anxiety, with or without depression, appears to be the prominent psychopathological phenotype in Parkinson's disease suggesting a pressing need to understanding its mechanisms and improve management.

Parasaccharibacter apium, gen. nov., sp. nov., Improves Honey Bee (Hymenoptera: Apidae) Resistance to Nosema.

The honey bee, Apis mellifera L., is host to a variety of microorganisms. The bacterial community that occupies the adult worker gut contains a core group of approximately seven taxa, while the hive environment contains its own distribution of bacteria that is in many ways distinct from the gut. Parasaccharibacter apium, gen. nov., sp. nov., is a hive bacterium found in food stores and in larvae, worker jelly, worker hypopharyngeal glands, and queens. Parasaccharibacter apium increases larval survival under laboratory conditions. To determine if this benefit is extended to colonies in the field, we tested if P. apium 1) survives and reproduces in supplemental pollen patty, 2) is distributed throughout the hive when added to pollen patty, 3) benefits colony health, and 4) increases the ability of bees to resist Nosema. Parasaccharibacter apium survived in supplemental diet and was readily consumed by bees. It was distributed throughout the hive under field conditions, moving from the pollen patty to hive larvae. While P. apium did not significantly increase colony brood production, food stores, or foraging rates, it did increase resistance to Nosema infection. Our data suggest that P. apium may positively impact honey bee health.

Rituximab-based therapy and long-term control of autoimmune autonomic ganglionopathy.

We present a patient with autoimmune autonomic ganglionopathy (AAG) who had persistently positive ganglionic nicotinic acetylcholine receptor antibody levels despite immunosuppressive therapy. Rituximab-based therapy for an incidental lymphoma was associated with prolonged symptomatic and serological control of AAG.

The impact of physician posture during oncology patient encounters.

Non-verbal communication is an important component of the physician-patient interaction. Oncology patients face specific emotional and psychological issues requiring additional physician emotional support. Multiple studies in oncology patients have revealed that patients perceive physicians seated during the medical interview to be more compassionate, caring, and likely to spend more time with the patients. These are all associated with improved patient outcomes. Barriers to sitting may be due to those imposed by time, space, and reduced perceived benefit of sitting by the physician. Although a sitting posture alone is unlikely to compensate for poor communication skills, assessing patient preference to physician posture, and following their preference, can be a simple way of improving communication, and thus patient outcomes, especially in oncology patients. The widespread introduction of the electronic medical record (EMR) system over the last decade has added a "third wheel" to the original dyadic physician-patient relationship. Physician posture and eye gaze towards to the EMR and its components has a deleterious effect on communication. Appropriate training and sensitization in this regard should be provided for physicians.

Parents of children with neurogenic bowel dysfunction: their experiences of using transanal irrigation with their child.

BACKGROUND: Neurogenic bowel dysfunction in children is a lifelong condition often resulting in the need for active bowel management programmes, such as transanal irrigation. Parents are central in the decision-making process to initiate and carry out treatments until such a time their child becomes independent. Minimal research has focussed on examining parents' experiences of undertaking transanal irrigation with their child. This study aimed to explore parents' experiences of learning about and using irrigation with their child and how parents motivated their children to become independent. METHODS: Semi-structured telephone interviews were conducted with parents with experience of using transanal irrigation with their child. Interviews were undertaken by a parent researcher. Data were analysed using qualitative content analysis. RESULTS: Eighteen telephone interviews (16 mothers, 1 father and 1 carer) were conducted. Parents shared how they had negotiated getting started and using transanal irrigation with their child. They discussed a sense of success derived from their confidence in using and mastering irrigation, the process of making decisions to continue or stop using irrigation and how they motivated themselves and their child to continue with the irrigation regime. Challenges included minimizing their child's distress during the irrigation procedure and how they negotiated and moved towards their child becoming independent. CONCLUSION: Despite the emotional difficulty parents experienced as a result of the invasive nature of transanal irrigation most parents reported an improvement in their child's faecal continence which positively impacted on the child and family's lives. The child's physical ability and emotional readiness to develop independent irrigation skills in the future concerned some parents. The experiences shared by parents in this study has the capacity to inform transanal irrigation nursing and medical care.

Hip bone geometry in HIV/HCV-co-infected men and healthy controls.

UNLABELLED: People with both HIV and hepatitis C are more likely than those with HIV alone to have wrist, hip, and spine fractures. We compared hip strength between HIV/HCV-co-infected men and healthy men and found that HIV/HCV-co-infected men had decreased hip strength due to lower lean body mass. INTRODUCTION: Hepatitis C co-infection is a risk factor for fragility fracture among HIV-infected populations. Whether bone strength is compromised in HIV/HCV-co-infected patients is unknown. METHODS: We compared dual-energy x-ray absorptiometry (DXA)-derived hip geometry, a measure of bone strength, in 88 HIV/HCV-co-infected men from the Johns Hopkins HIV Clinic to 289 men of similar age and race and without HIV or HCV from the Boston Area Community Health Survey/Bone Survey. Hip geometry was assessed at the narrow neck, intertrochanter, and shaft using hip structural analysis. Lean body mass (LBM), total fat mass (FM), and fat mass ratio (FMR) were measured by whole-body DXA. Linear regression was used to identify body composition parameters that accounted for differences in bone strength between cohorts. RESULTS: HIV/HCV-co-infected men had lower BMI, LBM, and FM and higher FMR compared to controls (all p < 0.05). At the narrow neck, significant differences were observed between HIV/HCV-co-infected men and controls in bone mineral density, cross-sectional area, section modulus, buckling ratio, and centroid position. After adjustment for race, age, smoking status, height, and weight, only buckling ratio and centroid position remained significantly different between cohorts (all p < 0.05). Substituting LBM, FM, and FMR for weight in the multivariate model revealed that differences in LBM, but not FM or FMR, accounted for differences in all narrow neck parameters between cohorts, except buckling ratio and centroid position. CONCLUSION: HIV/HCV-co-infected men have compromised hip strength at the narrow neck compared to uninfected controls, which is attributable in large part to lower lean body mass.

Long-term follow-up of patients with monoclonal gammopathy of undetermined significance after kidney transplantation.

INTRODUCTION: Long-term data regarding kidney transplantation (KTx) patients with monoclonal gammopathy of undetermined significance (MGUS) are scarce. We evaluated the long-term outcomes of these patients in a single-center retrospective study from the Mayo Clinic, Rochester, Minn., USA. METHODS: Patients who had an MGUS before transplant or developed one after KTx were selected. Monoclonal protein was screened as part of the KTx evaluation by serum protein electrophoresis. Screening for posttransplant lymphoproliferative disorder (PTLD) or MGUS after transplant was not required by protocol. Patients with multiple myeloma, dysproteinemia-related kidney disease or no pretransplant serum protein electrophoresis were excluded. RESULTS: Between 1963 and 2006, 3,518 patients underwent KTx. MGUS was identified in 42 patients, with 23 before transplant and 19 after transplant. Median follow-up for these patients was 8.5 years (range 0.3-37). Four (17.4%) pretransplant MGUS patients developed a hematologic malignancy: 2 smoldering multiple myeloma and 2 PTLD - an Epstein-Barr virus-positive diffuse large cell lymphoma and a Hodgkin lymphoma. None of the 19 patients who developed an MGUS after transplant progressed to multiple myeloma, but 2 (10.5%) developed Epstein-Barr virus-negative T cell lymphoproliferative disorders at 16 and 26 years after transplant. Median survival was 26.1 and 28.0 years for the pretransplant and posttransplant MGUS groups, respectively. CONCLUSION: Progression from true MGUS to multiple myeloma is rare after KTx. KTx appears safe in true MGUS patients if the monoclonal gammopathy was not the cause of the kidney disease. None of the patients progressed to multiple myeloma, but 2 developed smoldering multiple myeloma and several developed PTLD. Further studies are needed to explain the relationship between MGUS and PTLD.

Contributions of GeneXpert® to TB diagnosis in Myanmar.

BACKGROUND: Xpert® MTB/RIF, a rapid, molecular TB diagnostic assay, can detect Mycobacterium tuberculosis and rifampin resistance directly from clinical sputum samples in <2 h with high sensitivity and specificity. The added diagnostic value of Xpert over smear microscopy at a national level in Myanmar has not been previously reported.METHODS: We evaluated 339,358 Xpert and demographic records captured from January 2015 to December 2018 as part of the Myanmar National TB Program Data Utilization and Connectivity Project to examine the additional diagnostic yield of Xpert relative to smear for the detection of M. tuberculosis for TB diagnosis in Myanmar, with a focus on people living with HIV (PLHIV) and sample type.RESULTS: Use of Xpert increased TB case detection by 40% compared to smear microscopy results. Among PLHIV, use of Xpert increased TB case detection by almost 100% compared to smear microscopy results.CONCLUSION: Xpert testing identified more patients with TB than smear microscopy alone, particularly in cohorts with significant proportions of PLHIV. The use of Xpert as a screening tool in countries with a high burden of TB could lead to significantly increased diagnosis of TB at a regional and national level.

Mapping Local Failure Following Bladder Radiotherapy According to Dose.

AIMS: To determine the relationship between local relapse following radical radiotherapy for muscle-invasive bladder cancer (MIBC) and radiation dose. MATERIALS AND METHODS: Patients with T2-4N0-3M0 MIBC were recruited to a phase II study assessing the feasibility of intensity-modulated radiotherapy to the bladder and pelvic lymph nodes. Patients were planned to receive 64 Gy/32 fractions to the bladder tumour, 60 Gy/32 fractions to the involved pelvic nodes and 52 Gy/32 fractions to the uninvolved bladder and pelvic nodes. Pre-treatment set-up was informed by cone-beam CT. For patients who experienced local relapse, cystoscopy and imaging (CT/MRI) was used to reconstruct the relapse gross tumour volume (GTVrelapse) on the original planning CT . GTVrelapse D98% and D95% was determined by co-registering the relapse image to the planning CT utilising deformable image registration (DIR) and rigid image registration (RIR). Failure was classified into five types based on spatial and dosimetric criteria as follows: A (central high-dose failure), B (peripheral high-dose failure), C (central elective dose failure), D (peripheral elective dose failure) and E (extraneous dose failure). RESULTS: Between June 2009 and November 2012, 38 patients were recruited. Following treatment, 18/38 (47%) patients experienced local relapse within the bladder. The median time to local relapse was 9.0 months (95% confidence interval 6.3-11.7). Seventeen of 18 patients were evaluable based on the availability of cross-sectional relapse imaging. A significant difference between DIR and RIR methods was seen. With the DIR approach, the median GTVrelapse D98% and D95% was 97% and 98% of prescribed dose, respectively. Eleven of 17 (65%) patients experienced type A failure and 6/17 (35%) patients type B failure. No patients had type C, D or E failure. MIBC failure occurred in 10/17 (59%) relapsed patients; of those, 7/11 (64%) had type A failure and 3/6 (50%) had type B failure. Non-MIBC failure occurred in 7/17 (41%) patients; 4/11 (36%) with type A failure and 3/6 (50%) with type B failure. CONCLUSION: Relapse following radiotherapy occurred within close proximity to the original bladder tumour volume and within the planned high-dose region, suggesting possible biological causes for failure. We advise caution when considering margin reduction for future reduced high-dose radiation volume or partial bladder radiotherapy protocols.

Structure, morphology and magnetic properties of Mg((x))Zn((1 - x))Fe2O4 ferrites prepared by polyol and aqueous co-precipitation methods: a low-toxicity alternative to Ni((x))Zn((1 - x))Fe2O4 ferrites.

The synthesis and properties of Mg((x))Zn((1 - x))Fe(2)O(4) spinel ferrites as a low-toxicity alternative to the technologically significant Ni((x))Zn((1 - x))Fe(2)O(4) ferrites are reported. Ferrite nanoparticles have been formed through both the polyol and aqueous co-precipitation methods that can be readily adapted to industrial scale synthesis to satisfy the demand of a variety of commercial applications. The structure, morphology and magnetic properties of Mg((x))Zn((1 - x))Fe(2)O(4) were studied as a function of composition and particle size. Scanning electron microscopy images show particles synthesised by the aqueous co-precipitation method possess a broad size distribution (i.e. ∼ 80-120 nm) with an average diameter of the order of 100 nm ± 20 nm and could be produced in high process yields of up to 25 g l(-1). In contrast, particles synthesised by the polyol-based co-precipitation method possess a narrower size distribution with an average diameter in the 30 nm ± 5 nm range but are limited to smaller yields of ∼ 6 g l(-1). Furthermore, the polyol synthesis method was shown to control average particle size by varying the length of the glycol surfactant chain. Particles prepared by both methods are compared with respect to their phase purity, crystal structure, morphology, magnetic properties and microwave properties.

Platelet and red blood cell indices in Harris platelet syndrome.

Inherited thrombocytopenias, including inherited giant platelet disorders (IGPD) or macro thrombocytopenias are relatively rare, but their prevalence is likely underestimated from complexities of diagnosis and a spectrum of subclinical phenotypes. Harris platelet syndrome (HPS) is the most common IGPD reported from the Indian subcontinent. Of note there are an increased number of hemoglobinopathies reported from the geographic location. We analysed red blood cell and platelet indices of blood donors with HPS from the north eastern part of India and compared them with blood indices of blood donors of south India. We found a statistically significant lower platelet count in blood donors with HPS (median, range) 132 (71-267) vs. 252 (160-478) as compared to donors from south India (P < 0.001). Mean platelet volume (MPV) was higher in donors with HPS 13.1, (range 12-21.9 fl) as compared to donors from south India 7.35 (range 6-9.2 fl) (P < 0.001). This study showed that blood donors with HPS had a low median platelet bio-mass 0.17 (0.10-0.38%) vs. 0.19 (0.13-0.28%) in donors from south India. The platelet distribution width (PDW) was 17.4 (14.9-19.6) in donors with HPS vs. 16.38 (15.2-18.5) in south Indian blood donors (P < 0.001). Thirty-three donors with HPS had a normal platelet count with MPV more than 12 fL. Only donors with HPS had giant platelets and thrombocytopenia on peripheral blood smear examination. None of these donors had Dohle body inclusion in their leukocytes. Compared to donors from south India, donors with HPS had a significantly lower hemoglobin 13.8 (12-16.3 gm/dL) vs. 14.8 (12-18) respectively (P < 0.001) while red distribution width (RDW) was higher in HPS 13.6 (11.5-16.7) vs. 12.8 (11.4-15.1). However we did not find any statistically significant difference in MCV, MCH, MCHC between the two groups. Peripheral blood smear did not show any obvious abnormal red blood cell morphology. In the blood donors with HPS we found a statistically higher MPV, RDW and a lower platelet count and platelet biomass. A population-based study will be helpful in determining the existence of any hemoglobinopathies among subjects with HPS.