Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses.

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with Nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40 × improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher automation platform.

Hydrogel particles improve detection of SARS-CoV-2 RNA from multiple sample types.

Here we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from contrived transport medium and saliva samples using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus from 1 mL samples prior to RNA extraction, substantially improving detection of virus using real-time RT-PCR across a range of viral titers (100-1,000,000 viral copies/mL) and enabling detection of virus using the 2019 nCoV CDC EUA Kit down to 100 viral copies/mL. This method is compatible with commercially available nucleic acid extraction kits (i.e., from Qiagen) and a simple heat and detergent method that extracts viral RNA directly off the particle, allowing a sample processing time of 10 min. We furthermore tested our method in transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2, showing that our method not only correctly identified all positive samples but also substantially improved detection of the virus in low viral load samples. The average improvement in cycle threshold value across all viral titers tested was 3.1. Finally, we illustrate that our method could potentially be used to enable pooled testing, as we observed considerable improvement in the detection of SARS-CoV-2 RNA from sample volumes of up to 10 mL.

Exceptional continental record of biotic recovery after the Cretaceous-Paleogene mass extinction.

We report a time-calibrated stratigraphic section in Colorado that contains unusually complete fossils of mammals, reptiles, and plants and elucidates the drivers and tempo of biotic recovery during the poorly known first million years after the Cretaceous-Paleogene mass extinction (KPgE). Within ~100 thousand years (ka) post-KPgE, mammalian taxonomic richness doubled, and maximum mammalian body mass increased to near pre-KPgE levels. A threefold increase in maximum mammalian body mass and dietary niche specialization occurred at ~300 ka post-KPgE, concomitant with increased megafloral standing species richness. The appearance of additional large mammals occurred by ~700 ka post-KPgE, coincident with the first appearance of Leguminosae (the bean family). These concurrent plant and mammal originations and body-mass shifts coincide with warming intervals, suggesting that climate influenced post-KPgE biotic recovery.

Tracing of particulate organic C sources across the terrestrial-aquatic continuum, a case study at the catchment scale (Carminowe Creek, southwest England).

Soils deliver crucial ecosystem services, such as climate regulation through carbon (C) storage and food security, both of which are threatened by climate and land use change. While soils are important stores of terrestrial C, anthropogenic impact on the lateral fluxes of C from land to water remains poorly quantified and not well represented in Earth system models. In this study, we tested a novel framework for tracing and quantifying lateral C fluxes from the terrestrial to the aquatic environment at a catchment scale. The combined use of conservative plant-derived geochemical biomarkers n-alkanes and bulk stable δ13C and δ15N isotopes of soils and sediments allowed us to distinguish between particulate organic C sources from different land uses (i.e. arable and temporary grassland vs. permanent grassland vs. riparian woodland vs. river bed sediments) (p<0.001), showing an enhanced ability to distinguish between land use sources as compared to using just n-alkanes alone. The terrestrial-aquatic proxy (TAR) ratio derived from n-alkane signatures indicated an increased input of terrestrial-derived organic matter (OM) to lake sediments over the past 60years, with an increasing contribution of woody vegetation shown by the C27/C31 ratio. This may be related to agricultural intensification, leading to enhanced soil erosion, but also an increase in riparian woodland that may disconnect OM inputs from arable land uses in the upper parts of the study catchment. Spatial variability of geochemical proxies showed a close coupling between OM provenance and riparian land use, supporting the new conceptualization of river corridors (active river channel and riparian zone) as critical zones linking the terrestrial and aquatic C fluxes. Further testing of this novel tracing technique shows promise in terms of quantification of lateral C fluxes as well as targeting of effective land management measures to reduce soil erosion and promote OM conservation in river catchments.

Are migratory behaviours of bats socially transmitted?

To migrate, animals rely on endogenous, genetically inherited programmes, or socially transmitted information about routes and behaviours, or a combination of the two. In long-lived animals with extended parental care, as in bats, migration tends to be socially transmitted rather than endogenous. For a young bat to learn migration via social transmission, they would need to follow an experienced individual, most likely one roosting nearby. Therefore, we predicted that bats travelling together originate from the same place. It is also likely that young bats would follow their mothers or other kin, so we predicted that bats travelling together are more closely related to each other than bats not travelling together. To test our predictions, we used microsatellite genotypes and stable isotope values of δ (13)C, δ (15)N and δ (2)H to analyse the relatedness and geographical origins of migrating hoary bats (Lasiurus cinereus/Aeorestes cinereus (Baird et al. 2015 J. Mammal. 96, 1255-1274 (doi:10.1093/jmammal/gyv135)); n = 133) and silver-haired bats (Lasionycteris noctivagans; n = 87) killed at wind turbines over two consecutive autumn migrations. Contrary to our predictions, there was no evidence that related dyads of hoary bats or silver-haired bats were killed on the same night more frequently than expected by chance, or that the number of days between the fatalities of dyad members was influenced by relatedness or latitude of origin. Our data suggest that these bats do not socially transmit migration routes and behaviours among close kin.

Each one teach one: training students for diabetes and nutrition peer education in schools

OBJECTIVE: To provide a Diabetes (DM) in-school support system; to enable peer education in a general setting without discrimination. DESIGN AND METHODS: 200 student leaders aged 10-14 were chosen from 18 schools. We used the Novo Nordisk “Changing Diabetes in Children” presentations to teach about DM and Nutrition. 162 questionnaires were given to assess the students’ knowledge of type 1 DM. RESULTS: 22 (13.5%) students said in type 1 DM the body makes insulin but more insulin is needed, while 67 (41.4%) said the body does not make insulin and the treatment is pills and plenty water only. 33 (20.4%) said Diabetes affects only old people, 126 (77.8%) said all children can get DM. 157 (96.9%) said eating a variety of vegetables, legumes and some fruits are important in Diabetes management. 11 (6.8%) and 9 (5.6%) respectively, said if their friend had Diabetes they should not play or talk with them anymore and 142 (87.7%) said they should show love and support. 147 (90.7%) said if they learnt about Diabetes, everyone should learn too, 15 (9.3%) said they should keep it to themselves, share with family or “their secret keepers” only. 96 (59.3%) said children with Diabetes can take part in all activities and 23 (14.2%) said if they have DM they cannot go to school. CONCLUSION: Diabetes and nutrition education is necessary for understanding the illness and to facilitate students with DM. Good teaching aids are needed and the “Changing Diabetes in Children” tools were beneficial.

Resolution of pancreatico-pleural fistula with endoscopic ultrasound-guided therapy.

Pancreatico-pleural fistula is an uncommon cause of recurrent pleural effusion. Delayed diagnosis may occur if fluid amylase level is not obtained early in the clinical course. As most cases of pancreatico-pleural effusion are due to chronic pancreatitis, endoscopic therapy may be effective if pancreatic fluid secretion can be diverted to a more physiologic pathway. However, when severe pancreatitis leads to disconnection of the pancreatic duct, it precludes conventional endoscopic treatment via transpapillary stenting of the pancreatic duct. We describe a patient with a chronic, refractory pancreatico-pleural fistula arising from chronic pancreatitis with a disconnected pancreatic duct syndrome, which resolved following endoscopic ultrasound-guided therapy.

Association between prospective owner viewing of the parents of a puppy and later referral for behavioural problems.

A case-control study was designed to test whether there is an association between the owners seeing the mother of a puppy, and later development of behavioural problems. The sample consisted of dogs that were seen by animal behaviourists (members of the Association of Pet Behaviour Counsellors) and equivalent dogs (without a behavioural problem, but the owners would consider referral to an animal behaviourist were the dog to develop a behavioural problem) seen at a veterinary practice that referred to each animal behaviourist. After adjustment for confounding factors using multivariable logistic regression, case dogs were more likely to be younger than controls (P < 0.001); less likely to be obtained at six (OR = 0.27, 95 per cent CI = 0.09 to 0.85, P = 0.03), nine (OR = 0.22, 95 per cent CI = 0.06 to 0.80, P = 0.02) or 10 weeks (OR = 0.35, 95 per cent CI = 0.12 to 1.01, P = 0.05), than eight weeks; more likely for the owner to have seen only one parent (OR = 2.49, 95 per cent CI = 1.15 to 5.37, P = 0.02) than both parents, and more likely to have not seen either parent (OR = 3.82, 95 per cent CI = 1.12 to 12.97, P = 0.03) than both. Advice to 'see the mother' has been shown to be partly scientifically accurate in relation to future unwanted behavioural problems among dogs; in fact, it may be better for prospective owners to be recommended to view both parents.

Analysis of Wnt pathway genes during ex vivo expansion and neutrophil differentiation of umbilical-cord-blood-derived CD34 cells.

Previous work has shown that optimal ex vivo expansion and differentiation of CD34(+) progenitor cells into neutrophils is by addition of Flt3-L, SCF and G-CSF. Here we report that a variety of genes involved in the WNT pathway are transcriptionally active in both undifferentiated and differentiated umbilical cord blood CD34(+) cells, however statistically significant changes in gene expression are not always consistent across UCB samples.

Management of liver trauma.

BACKGROUND: Blunt and penetrating liver trauma is common and often presents major diagnostic and management problems. METHODS: A literature review was undertaken to determine the current consensus on investigation and management strategies. RESULTS: The liver is the most frequently injured organ following abdominal trauma. Immediate assessment with ultrasound has replaced diagnostic peritoneal lavage in the resuscitation room, but computerised tomography remains the gold standard investigation. Nonoperative management is preferred in stable patients but laparotomy is indicated in unstable patients. Damage control techniques such as perihepatic packing, hepatotomy plus direct suture, and resectional debridement are recommended. Major complex surgical procedures such as anatomical resection or atriocaval shunting are now thought to be redundant in the emergency setting. Packing is also recommended for the inexperienced surgeon to allow control and stabilisation prior to transfer to a tertiary centre. Interventional radiological techniques are becoming more widely used, particularly in patients who are being managed nonoperatively or have been stabilised by perihepatic packing. CONCLUSIONS: Management of liver injuries has evolved significantly throughout the last two decades. In the absence of other abdominal injuries, operative management can usually be avoided. Patients with more complex injuries or subsequent complications should be transferred to a specialist centre to optimise final outcome.

Splanchnic microcirculation protection by hydroxyethyl starches during abdominal aortic aneurysm surgery.

OBJECTIVE: To specifically compare the effect of two hydroxyethyl starches (HES) on the splanchnic microcirculation and systemic inflammation during abdominal aortic aneurysm (AAA) surgery. MATERIALS AND METHODS: A prospective randomised study was carried out on 62 patients who received HES of molecular-weight 200 kDa (HES200/0.62), 130 kDa (HES130/0.4) or gelatine for 24h peri-operatively. Gastric-mucosal pHi (GpHi) and anti-endotoxin antibody were used as markers of splanchnic perfusion and endotoxaemia respectively. C-reactive protein (CRP) and lung-injury score (LIS) were used as markers of systemic inflammation and end-organ dysfunction respectively. Data was collected prospectively. RESULTS: The drop in GpHi was least with HES200/0.62 compared to HES130/0.4 and gelatine at reperfusion (7.32 vs 7.28 and 7.28, p=0.017 and 0.009 respectively) and compared to gelatine at 2h as well (7.43 vs 7.28, p=0.001). GpHi dropped less with HES130/0.4 compared to gelatine at 2h (7.39 vs 7.28, p=0.002). Endotoxaemia increased only with gelatine. CRP was lower with HES200/0.62 (178 mg/mL) than gelatine (221 mg/mL) and HES130/0.4 (223 mg/mL) at 48 h (p=0.049 and p=0.009 respectively). There was no difference in LIS but ventilation duration was less with HES200/0.62 compared with gelatine (4 vs 11h, p=0.012). CONCLUSION: During AAA surgery, HES200/0.62 provides the best splanchnic microcirculation protection, also reducing inflammation and duration of ventilation.

Anal carcinoma: prognostic value of endorectal ultrasound (ERUS). Results of a prospective multicenter study.

BACKGROUND AND STUDY AIMS: The classification of anal carcinoma is based on the clinical examination and the estimation of the tumor height (Union Internationale Contre le Cancer (UICC) 1987 Classification). This classification has a direct therapeutic application since tumors which are designated T1 and T2 are generally treated by radiotherapy whereas T3, T4 or N+ lesions are treated by concomitant radiation and chemotherapy. The aim of this prospective multicenter study was to evaluate endorectal ultrasound (ERUS) and to define an ERUS-based classification. PATIENTS AND METHODS: Between January 1994 and May 1997, 146 patients (42 men and 104 women; mean age, 63) from eight different centers were studied prospectively. The ERUS classification incorporates disease of the anal canal and the perirectal lymph nodes, thus: usT1 describes involvement of the mucosa and submucosa with sparing of the internal sphincter; usT2, involvement of the internal sphincter with sparing of the external sphincter; usT3, involvement of the external sphincter; usT4, involvement of a pelvic organ; N0 describes no suspicious perirectal lymph nodes, and N+, perirectal lymph nodes fulfilling endosonographic criteria for malignancy (e.g. round, hypoechoic). Tumors classified as UICC T1-T2 (<4cm) N0 were treated by radiotherapy alone, whereas lesions with a UICC classification of T2 (> 4 cm), T3-T4, N0-N1-2-3 received combined radiochemotherapy. RESULTS: Data concerning the treatment and follow-up were available for 115/146 patients (78.7%). We compared the prognostic importance of the two classification schemes for treatment response and the rate of local relapse (chi-squared test). A significantly greater proportion of T1-T2N0 lesions classified by ERUS had a complete response to treatment than those classified by conventional UICC staging (94.5% vs. 80%, respectively; P = 0.008). The ERUS T and N stage were significant predictors of relapse (P=0.001 and P=0.03, respectively) whereas the corresponding clinical (UICC) stages were not (P = 0.4 and P = 0.5, respectively). Using a Cox model, usT stage was the only significant predictive factor for patient survival. CONCLUSION: This muticenter prospective study demonstrated the superiority of ERUS-based staging over traditional clinical staging in the prediction of important outcomes such as local tumor recurrence and patient survival.

Ulcerative colitis of the appendix ('ulcerative appendicitis') mimicking acute appendicitis.

Appendiceal involvement in ulcerative colitis may occur in the setting of either diffuse or distal disease, and is usually diagnosed incidentally at the time of proctocolectomy. The present patient had a rare case of 'ulcerative appendicitis' occurring on a background of clinically quiescent ulcerative colitis, and presented with the signs and symptoms of acute appendicitis.

Application of a time-resolved fluoroimmunoassay for the analysis of normal prion protein in human blood and its components.

BACKGROUND AND OBJECTIVES: To quantify the cellular isoform of prion protein (PrP(c)) in human blood using a new time-resolved dissociation-enhanced fluoroimmunoassay (DELFIA). MATERIALS AND METHODS: The DELFIA was optimised for human blood samples and applied to isolated cell and plasma fractions from blood donations. The physicochemical properties of PrP(c) were analysed. RESULTS: 26. 5% of blood PrP(c) was associated with the platelet fraction, 0.8% with polymorphonuclear leucocytes, 2.4% with mononuclear leucocytes, 1.8% with red cells and 68.5% with plasma (mean values from 4 processed donations). CONCLUSION: The majority of blood PrP(c) is found in the platelet and plasma compartments.