De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification.

Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. These tools have been particularly useful for detecting introgression of cattle genome within bison herds but are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. An assembly (Bison_UMD1.0) based on 75X genome coverage by Illumina and 454 reads was generated using the MaSuRCA assembler, generating a 2.81 Gigbases de novo reference genome from American bison. Comparison of bison and domestic cattle references identified 28 443 364 single nucleotide variants and 2 627 645 insertions/deletions distinguishing the species. Sequence alignment of an additional 12 modern bison samples and two historic bison samples to domestic cattle and bison references provides a dataset of genomic variants defining the different species and within-species variation. This first annotated draft assembly represents a resource for the management and conservation of bison, as well as a means to study the effects on the genome of interspecies hybridization. The comparisons of historical bison sequences with the new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support the application of genomics to enhance future research on disease, the establishment of satellite conservation herds and insight into bison and cattle speciation. The first genome assembly for bison and dataset provides a foundation that can be built upon as genetic technologies improve over the years.

Blastocyst conversion rate and ploidy in patients with structural rearrangements.

OBJECTIVE: The primary objective of this study was to test the hypotheses that compared to IVF cycles undergoing preimplantation genetic testing for aneuploidy (PGT-A) with or without testing for monogenic disorders (PGT-M), IVF cycles undergoing PGT for structural rearrangements (PGT-SR) will have (1) a poorer blastocyst conversion rate and (2) fewer usable blastocysts available for transfer. Secondarily, the study aimed to compare pregnancy outcomes among PGT groups. PATIENTS: Retrospective cohort study including cycles started from January 1, 2012, to March 30, 2020, with the intent of pursuing PGT-A, PGT-A with PGT-M, and PGT-SR, with trophectoderm biopsy on days 5 or 6. RESULTS: A total of 658 women underwent 902 cycles, including 607 PGT-A, 216 PGT-A&M, and 79 PGT-SR cycles. When compared with the blastocyst conversion rate for the PGT-A group (59.4%), and after adjustment for patient age, total number of mature oocytes, BMI, and ICSI, there were no significant differences for either the PGT-A&M (69.7%, aRR 1.03, 95% CI 0.96-1.10) or PGT-SR (63.2%, aRR1.04, 95% CI 0.96-1.13) groups. Compared to the PGT-A group, the proportion of usable blastocysts was statistically significantly lower in the PGT-SR group: 35.1% versus 24.4% (aRR 0.57, 95% CI 0.46-0.71) and the PGT-A&M group: 35.1% versus 31.5% (aRR 0.68, 95% CI 0.58-0.81). Implantation, pregnancy, and miscarriage rates were equivalent for all groups. CONCLUSION: Patients with structural rearrangements have similar blastocyst development but significantly fewer usable blastocysts available for transfer compared to PGT-A testers. Nevertheless, with the transfer of a usable embryo, PGT-SR testers perform as well as those testing for PGT-A.

Effects of hyperaemia on left ventricular longitudinal strain in patients with suspected coronary artery disease : A first-pass stress perfusion cardiovascular magnetic resonance imaging study.

AIMS: Myocardial perfusion imaging during hyperaemic stress is commonly used to detect coronary artery disease. The aim of this study was to investigate the relationship between left ventricular global longitudinal strain (GLS), strain rate (GLSR), myocardial early (E') and late diastolic velocities (A') with adenosine stress first-pass perfusion cardiovascular magnetic resonance (CMR) imaging. METHODS AND RESULTS: 44 patients met the inclusion criteria and underwent CMR imaging. The CMR imaging protocol included: rest/stress horizontal long-axis (HLA) cine, rest/stress first-pass adenosine perfusion and late gadolinium enhancement imaging. Rest and stress HLA cine CMR images were analysed using feature-tracking software for the assessment of myocardial deformation. The presence of perfusion defects was scored on a binomial scale. In patients with hyperaemia-induced perfusion defects, rest global longitudinal strain GLS (-16.9 ± 3.7 vs. -19.6 ± 3.4; p-value = 0.02), E' (-86 ± 22 vs. -109 ± 38; p-value = 0.02), GLSR (69 ± 31 vs. 93 ± 38; p-value = 0.01) and stress GLS (-16.5 ± 4 vs. -21 ± 3.1; p < 0.001) were significantly reduced when compared with patients with no perfusion defects. Stress GLS was the strongest independent predictor of perfusion defects (odds ratio 1.43 95% confidence interval 1.14-1.78, p-value <0.001). A threshold of -19.8% for stress GLS demonstrated 78% sensitivity and 73% specificity for the presence of hyperaemia-induced perfusion defects. CONCLUSIONS: At peak myocardial hyperaemic stress, GLS is reduced in the presence of a perfusion defect in patients with suspected coronary artery disease. This reduction is most likely caused by reduced endocardial blood flow at maximal hyperaemia because of transmural redistribution of blood flow in the presence of significant coronary stenosis.

Heart valve service provision in the United Kingdom and the effect of the COVID 19 pandemic; improved but must do better. A British Heart Valve Society national survey.

BACKGROUND: Outpatient care for patients with heart valve disease (HVD) is best provided by valve clinics delivered by specialists. Modern day practice in the United Kingdom (UK) is currently poorly understood and has not been evaluated for nearly a decade. Furthermore, the COVID 19 pandemic changed the management of many chronic diseases, and how this has impacted patients with heart valve disease is unclear. METHODS: A British Heart Valve Society survey was sent to 161 hospitals throughout the UK. RESULTS: There was a general valve clinic in 46 of the 68 hospitals (68%), in 19 of 23 Heart Centres (83%) and 29 of 45 DGHs (64%). Across all settings, 3824 new patients and 17,980 follow up patients were seen in valve clinics per annum. The mean number of patients per hospital were 197 (median 150, range 48-550) for new patients and 532 (median 400, range 150-2000) for follow up. On the day echocardiography was available in 55% of valve clinics. In patients with severe HVD, serum brain natriuretic peptide (BNP) was measured routinely in 39% of clinics and exercise testing routinely performed in 49% of clinics. A patient helpline was available in 27% of clinics. 78% of centres with a valve clinic had a valve multidisciplinary team meeting (MDT). 45% centres had an MDT co-ordinator and MDT outcomes were recorded on a database in 64%. COVID-19 had a major impact on valve services in 54 (95%) hospitals. CONCLUSIONS: There has been an increase in the number of valve clinics since 2015 from 21 to 68% but the penetration is still well short of the expected 100%, meaning that valve clinics only serve a small proportion of patients requiring surveillance for HVD. COVID-19 had a major impact on the care of patients with HVD in the majority of UK centres surveyed.

Angle-stable interlocking nailing in a canine critical-sized femoral defect model for bone regeneration studies: In pursuit of the principle of the 3R's.

Introduction: Critical-sized long bone defects represent a major therapeutic challenge and current treatment strategies are not without complication. Tissue engineering holds much promise for these debilitating injuries; however, these strategies often fail to successfully translate from rodent studies to the clinical setting. The dog represents a strong model for translational orthopedic studies, however such studies should be optimized in pursuit of the Principle of the 3R's of animal research (replace, reduce, refine). The objective of this study was to refine a canine critical-sized femoral defect model using an angle-stable interlocking nail (AS-ILN) and reduce total animal numbers by performing imaging, biomechanics, and histology on the same cohort of dogs. Methods: Six skeletally mature hounds underwent a 4 cm mid-diaphyseal femoral ostectomy followed by stabilization with an AS-ILN. Dogs were assigned to autograft (n = 3) or negative control (n = 3) treatment groups. At 6, 12, and 18 weeks, healing was quantified by ordinal radiographic scoring and quantified CT. After euthanasia, femurs from the autograft group were mechanically evaluated using an established torsional loading protocol. Femurs were subsequently assessed histologically. Results: Surgery was performed without complication and the AS-ILN provided appropriate fixation for the duration of the study. Dogs assigned to the autograft group achieved radiographic union by 12 weeks, whereas the negative control group experienced non-union. At 18 weeks, median bone and soft tissue callus volume were 9,001 mm3 (range: 4,939-10,061) for the autograft group and 3,469 mm3 (range: 3,085-3,854) for the negative control group. Median torsional stiffness for the operated, autograft treatment group was 0.19 Nm/° (range: 0.19-1.67) and torque at failure was 12.0 Nm (range: 1.7-14.0). Histologically, callus formation and associated endochondral ossification were identified in the autograft treatment group, whereas fibrovascular tissue occupied the critical-sized defect in negative controls. Conclusion: In a canine critical-sized defect model, the AS-ILN and described outcome measures allowed refinement and reduction consistent with the Principle of the 3R's of ethical animal research. This model is well-suited for future canine translational bone tissue engineering studies.

Community care of North Carolina: improving care through community health networks.

The United States leads the world in health care costs but ranks far below many developed countries in health outcomes. Finding ways to narrow this gap remains elusive. This article describes the response of one state to establish community health networks to achieve quality, utilization, and cost objectives for the care of its Medicaid recipients. The program, known as Community Care of North Carolina, is an innovative effort organized and operated by practicing community physicians. In partnership with hospitals, health departments, and departments of social services, these community networks have improved quality and reduced cost since their inception a decade ago. The program is now saving the State of North Carolina at least $160 million annually. A description of this experience and the lessons learned from it can inform others seeking to implement effective systems of care for patients with chronic illness.

Microalbuminuria as a screening tool in cystic fibrosis-related diabetes.

The improving longevity of cystic fibrosis (CF) subjects has resulted in an increased prevalence and duration of cystic fibrosis-related diabetes (CFRD). Microvascular complications were reported in CFRD. Microalbuminuria is well-established as a sensitive indicator of progression to diabetic nephropathy in non-CF diabetes, but confounding factors may make it less sensitive for CF subjects. We performed a cross-sectional study to look for the presence of microalbuminuria in samples from 40 CF subjects (34 without diabetes; CFND) attending the Exeter CF Clinic, compared with 43 nondiabetic, non-CF controls. The albumin-creatinine ratio (ACR) was raised in CF subjects both with (P < 0.001) and without (P < 0.0001) diabetes compared to controls. This reflected an increase in urinary albumin and a reduction in urinary creatinine in CF subjects. In single samples, microalbuminuria was present in 66.7%, 32.4%, and 15.4% of subjects in CFRD, CFND, and control groups. Repeat samples showed that 12% of CFND subjects and 17% of CFRD subjects met the criteria for a diagnosis of persistent microalbuminuria. In conclusion, CF subjects, even when not diabetic, have increased urinary albumin excretion due to chronic infection, and reduced urinary creatinine excretion due to low muscle mass. This results in subjects, who are not developing diabetic nephropathy, meeting the conventional criteria for microalbuminuria. We feel that further studies are required to clarify whether this measure is a useful tool to predict progression to diabetic nephropathy in subjects with CFRD.

Stroke prevention in atrial fibrillation: are we following the guidelines?

BACKGROUND: Warfarin therapy substantially reduces stroke in atrial fibrillation (AF), yet medical literature reports it is only prescribed in 15-60% of eligible patients. No current national benchmarks for warfarin use in AF patients exist, and it is unclear whether the reported poor compliance represents current rates within primary care practices. The primary study objective was to measure the rate of warfarin use in eligible, high-risk AF patients in a large southeastern group family practice. Secondary objectives were to report the demographics, stroke-risk profiles, contraindications, and reasons for discontinuation of warfarin therapy METHODS: A retrospective chart review was performed on all active patients with documented AF in a large southeastern group family practice/residency between July 1, 2000 and June 30, 2002. Data was abstracted on warfarin use, contraindications, stroke risk, and reasons for discontinuation. RESULTS: Four hundred ninety-one (491) patients were identified from the electronic billing system as potential study subjects. Two hundred eighty-three (283) patients met study criteria, with 210 patients considered to be at high-risk of stroke without contraindications to warfarin therapy. Ninety-four percent (198/210) of these patients were prescribed warfarin during the study period, and 87% (172/198) continued warfarin throughout the study period. CONCLUSION: Family physicians in this practice prescribe warfarin in AF more frequently than published rates demonstrating that high rates of physician adherence to standards are achievable in primary care. Most patients in this setting were considered high-risk for stroke.

Localised non-Hodgkin's lymphoma: the Sheffield Lymphoma Group experience (1970-1995).

We report a retrospective study of all patients with localised non-Hodgkin's lymphoma referred to the Sheffield Lymphoma Group (1970-1995). A total of 1,979 patients with non-Hodgkin's lymphoma were seen: 553 (28%) presented with stage I or II disease, 411 (21%) extranodal, 142 (7%) nodal. The commonest extranodal sites were head and neck, gastrointestinal tract, skin and central nervous system, accounting for 87% of patients. Most patients received primary localised radiotherapy. Overall observed survival was 52.5% at 5 years in the extranodal group and 65% in the nodal group. For both groups the 10-year observed survival was 42.5%. An age of 45 years and over was a poor prognostic factor in both groups (p<0.001). Patients with skin and non-Waldeyer's head and neck lymphomas survived best (5-year observed survivals 67 and 70% respectively) and CNS worst (5-year survival 38%). There is no cause for complacency in the management of localised non-Hodgkin's lymphoma, particularly for the less common extranodal sites where multicentre clinical studies are still essential.

The 3' untranslated region of tumor necrosis factor-alpha is highly conserved in idiopathic pulmonary fibrosis (IPF).

Tumour necrosis factor alpha (TNF-alpha), a pro-inflammatory cytokine essential for the function of the immune system, has been implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF). Production of TNF-alpha is regulated at both the transcriptional and post-transcriptional levels by a number of factors including interleukin-10 (IL-10). We have shown that there is significant TNF-alpha activity in patients with IPF, despite the presence of significant amounts of IL-10 and Il-10R. IL-10 is thought to influence the tight translational repression of TNF-alpha mRNA in pulmonary macrophages. The essential element in this regulation is the AU-rich element (ARE) present in the 3' untranslated region of TNF-alpha. We hypothesised that polymorphism in the 3' UTR region of TNF-alpha explains the apparent failure of IL-10 to down regulate TNF-alpha in patients with IPF. Using single strand conformation polymorphism (SSCP) analysis, we have screened this region in 96 patients with IPF, using nine sets of overlapping PCR primers. All samples were successfully amplified for each primer set, but SSCP analysis was unable to detect point mutations or polymorphisms in the patients in any of the nine fragments. Results from this study suggest that the 3' UTR region of TNF-alpha is highly conserved in IPF and mutation of this region is unlikely to be involved in the pathogenesis of IPF.

Some protozoan parasites of wild birds from the vicinity of Onderstepoort.

The protozoan parasites of wild birds from the vicinity of Onderstepoort are recorded. New host records for the Republic of South Africa are: Haemoproteus in Threskiornis aethiopicus, Francolinus swainsonii, Columba guinea and Streptopelia senegalensis; Leucocytozoon in Anas erythrorhyncha, Netta Erythrophthalma, C. guinea and Passer domesticus and Plasmodium in Numida meleagris.

NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings.

Two siblings with a severe multiorgan polycystic disease presenting in the neonatal period were identified. Their genetic testing identified compound heterozygous NPHP3 gene mutations, parents being heterozygous carriers. The mutations included a splice-site (c.958-2A>G) and a missense mutation (c.2342G>A; p.G781D), both being extremely rare. NPHP3 encodes for nephrocystin 3 present on the cilia-centrosome complex. We hypothesize that these mutations lead to defective cilia-based signaling, required for normal development of the renal, pancreatic, biliary and portal system. This report outlines a rare neonatal ciliopathy presentation of NPHP3 mutations leading to severe multiorgan failure in two siblings.

During ablation for atrial fibrillation, is simultaneous renal artery ablation appropriate?

Over the past few decades, the mainstay of hypertension management has been pharmacological therapy; however, there is now a growing body of evidence that drug-resistant hypertension can be managed effectively by renal artery ablation. Several studies have documented the feasibility and safety of this treatment, although data regarding long-term outcomes are still emerging. Atrial fibrillation (AF) and hypertension commonly coexist, and recent work has demonstrated improved outcomes from catheter ablation of AF with concomitant renal artery denervation at little extra cost in terms of time and resource. The aim of this review is to explore the link between hypertension and AF, the synergistic effect of renal artery ablation on AF ablation, explain how this may work and address unanswered questions.