SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis.

BACKGROUND: SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution. OBJECTIVE: To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health. METHODS: Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed. RESULTS: The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination. CONCLUSION: There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%.There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-genehad the most mutations and the E-gene was the least mutated.

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations.

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

The role of neuropeptide W in energy homeostasis.

Neuropeptide W is the endogenous ligand for G-protein-coupled receptors GPR7 and GPR8. In this review, we summarize findings on the distribution of neuropeptide W and its receptors in the central nervous system and the periphery, and discuss the role of NPW in food intake and energy homeostasis.

Upper Gastrointestinal Function in Morbidly Obese Adolescents Before and 6 Months After Gastric Banding.

BACKGROUND: The effects of laparoscopic adjustable gastric band (LAGB) placement on upper gastrointestinal tract function in obese adolescents are unknown. Therefore, our aim was to determine the short-term effects of LAGB on esophageal motility, gastroesophageal reflux, gastric emptying, appetite-regulatory hormones, and perceptions of post-prandial hunger and fullness. METHODS: This study was part of a prospective cohort study (March 2009-December 2015) in one tertiary referral hospital. The study included obese adolescents (14-18 years) with a body mass index (BMI) > 40 (or ≥ 35 with comorbidities). Gastric emptying was assessed by 13C-octanoic acid breath test, pharyngeal, and esophageal motor function by high-resolution manometry with impedance (HRIM), and appetite and other perceptions using 100-mm visual analogue scales. Dysphagia symptoms were scored using a Dakkak questionnaire. Data were compared pre- and post-LAGB placement and at a 6-month follow-up. RESULTS: Based upon analysis of 15 adolescents, at the 6-month follow-up, LAGB placement: (i) led to a significant reduction in weight and BMI; (ii) increased fullness and decreased hunger post-meal; (iii) increased symptoms of dysphagia after solid food; and, despite these effects, (iv) caused little or no changes to appetite hormones, while (v) effects on gastric emptying, esophageal motility, esophageal bolus transport, and esophageal emptying were not significant. CONCLUSION: In adolescents, LAGB improved BMI and altered the sensitivity to nutrients without significant effects on upper gastrointestinal tract physiology at the 6-month follow-up.

Plasticity of gastrointestinal vagal afferent satiety signals.

The vagal link between the gastrointestinal tract and the central nervous system (CNS) has numerous vital functions for maintaining homeostasis. The regulation of energy balance is one which is attracting more and more attention due to the potential for exploiting peripheral hormonal targets as treatments for conditions such as obesity. While physiologically, this system is well tuned and demonstrated to be effective in the regulation of both local function and promoting/terminating food intake the neural connection represents a susceptible pathway for disruption in various disease states. Numerous studies have revealed that obesity in particularly is associated with an array of modifications in vagal afferent function from changes in expression of signaling molecules to altered activation mechanics. In general, these changes in vagal afferent function in obesity further promote food intake instead of the more desirable reduction in food intake. It is essential to gain a comprehensive understanding of the mechanisms responsible for these detrimental effects before we can establish more effective pharmacotherapies or lifestyle strategies for the treatment of obesity and the maintenance of weight loss.

Sex-specific alterations in glucose homeostasis and metabolic parameters during ageing of caspase-2-deficient mice.

Gender-specific differences are commonly found in metabolic pathways and in response to nutritional manipulation. Previously, we identified a role for caspase-2 in age-related glucose homeostasis and lipid metabolism using male caspase-2-deficient (Casp2 (-/-) ) mice. Here we show that the resistance to age-induced glucose tolerance does not occur in female Casp2 (-/-) mice and it appears to be independent of insulin sensitivity in males. Using fasting (18 h) as a means to further investigate the role of caspase-2 in energy and lipid metabolism, we identified sex-specific differences in the fasting response and lipid mobilization. In aged (18-22 months) male Casp2 (-/-) mice, a significant decrease in fasting liver mass, but not total body weight, was observed while in females, total body weight, but not liver mass, was reduced when compared with wild-type (WT) animals. Fasting-induced lipolysis of adipose tissue was enhanced in male Casp2 (-/-) mice as indicated by a significant reduction in white adipocyte cell size, and increased serum-free fatty acids. In females, white adipocyte cell size was significantly smaller in both fed and fasted Casp2 (-/-) mice. No difference in fasting-induced hepatosteatosis was observed in the absence of caspase-2. Further analysis of white adipose tissue (WAT) indicated that female Casp2 (-/-) mice may have enhanced fatty acid recycling and metabolism with expression of genes involved in glyceroneogenesis and fatty acid oxidation increased. Loss of Casp2 also increased fasting-induced autophagy in both male and female liver and in female skeletal muscle. Our observations suggest that caspase-2 can regulate glucose homeostasis and lipid metabolism in a tissue and sex-specific manner.

Patient outcomes and provider perceptions following implementation of a standardized perioperative care pathway for open liver resection.

BACKGROUND: Enhanced recovery after surgery (ERAS) pathways have been associated with improved perioperative outcomes following several surgical procedures. Less is known, however, regarding their use following hepatic surgery. METHODS: An evidence-based, standardized perioperative care pathway was developed and implemented prospectively among patients undergoing open liver surgery between 1 January 2014 and 31 July 2015. Perioperative outcomes, including length of hospital stay, postoperative complications and healthcare costs, were compared between groups of patients who had surgery before and after introduction of the ERAS pathway. Provider perceptions regarding the perioperative pathway were assessed using an online questionnaire. RESULTS: There were no differences in patient or disease characteristics between pre-ERAS (42 patients) and post-ERAS (75) groups. Although mean pain scores were comparable between the two groups, patients treated within the ERAS pathway had a marked reduction in opioid use on the first 3 days after surgery compared with those treated before introduction of the pathway (all P < 0·001). Duration of hospital stay was shorter in the post-ERAS group (median 5 (i.q.r. 4-7) days versus 6 (5-7) days in the pre-ERAS group; P = 0·037) and there was a lower incidence of postoperative complications (1 versus 10 per cent; P = 0·036). Implementation of the ERAS pathway was associated with a 40·7 per cent decrease in laboratory costs (-US $333; -€306, exchange rate 4 January 2016) and a 21·5 per cent reduction in medical supply costs (-US $394; -€362) per patient. Although 91·0 per cent of providers endorsed the ERAS pathway, 33·8 per cent identified provider aversion to a standardized protocol as the greatest hurdle to implementation. CONCLUSION: The introduction of a multimodal ERAS programme following open liver surgery was associated with a reduction in opioid use, shorter hospital stay and decreased hospital costs. ERAS was endorsed by an overwhelming majority of providers.

Combined friction force microscopy and quantum chemical investigation of the tribotronic response at the propylammonium nitrate-graphite interface.

The energetic origins of the variation in friction with potential at the propylammonium nitrate-graphite interface are revealed using friction force microscopy (FFM) in combination with quantum chemical simulations. For boundary layer lubrication, as the FFM tip slides energy is dissipated via (1) boundary layer ions and (2) expulsion of near-surface ion layers from the space between the surface and advancing tip. Simulations reveal how changing the surface potential changes the ion composition of the boundary and near surface layer, which controls energy dissipation through both pathways, and thus the friction.

Insights into carbon nanotube and graphene formation mechanisms from molecular simulations: a review.

The discovery of carbon nanotubes (CNTs) and graphene over the last two decades has heralded a new era in physics, chemistry and nanotechnology. During this time, intense efforts have been made towards understanding the atomic-scale mechanisms by which these remarkable nanostructures grow. Molecular simulations have made significant contributions in this regard; indeed, they are responsible for many of the key discoveries and advancements towards this goal. Here we review molecular simulations of CNT and graphene growth, and in doing so we highlight the many invaluable insights gained from molecular simulations into these complex nanoscale self-assembly processes. This review highlights an often-overlooked aspect of CNT and graphene formation-that the two processes, although seldom discussed in the same terms, are in fact remarkably similar. Both can be viewed as a 0D â†’ 1D â†’ 2D transformation, which converts carbon atoms (0D) to polyyne chains (1D) to a complete sp(2)-carbon network (2D). The difference in the final structure (CNT or graphene) is determined only by the curvature of the catalyst and the strength of the carbon-metal interaction. We conclude our review by summarizing the present shortcomings of CNT/graphene growth simulations, and future challenges to this important area.

Altered gastric vagal mechanosensitivity in diet-induced obesity persists on return to normal chow and is accompanied by increased food intake.

BACKGROUND AND AIMS: Gastric vagal afferents convey satiety signals in response to mechanical stimuli. The sensitivity of these afferents is decreased in diet-induced obesity. Leptin, secreted from gastric epithelial cells, potentiates the response of vagal afferents to mechanical stimuli in lean mice, but has an inhibitory effect in high-fat diet (HFD)-induced obese mice. We sought to determine whether changes in vagal afferent function and response to leptin in obesity were reversible by returning obese mice consuming a HFD to standard laboratory chow diet (SLD). METHODS: Eight-week-old female C57BL/6 mice were either fed a SLD (N=20) or HFD (N=20) for 24 weeks. A third group was fed a HFD for 12 weeks and then a SLD for a further 12 weeks (RFD, N=18). An in vitro gastro-oesophageal vagal afferent preparation was used to determine the mechanosensitivity of gastric vagal afferents and the modulatory effect of leptin (0.1-10 nM) was examined. Retrograde tracing and quantitative RT-PCR were used to determine the expression of leptin receptor (LepR) messenger RNA (mRNA) in whole nodose and specific cell bodies traced from the stomach. RESULTS: After 24 weeks, both the HFD and RFD mice had increased body weight, gonadal fat mass, plasma leptin, plasma insulin and daily energy consumption compared with the SLD mice. The HFD and RFD mice had reduced tension receptor mechanosensitivity and leptin further inhibited responses to tension in HFD, RFD but not SLD mice. Mucosal receptors from both the SLD and RFD mice were potentiated by leptin, an effect not seen in HFD mice. LepR expression was unchanged in the whole nodose, but was reduced in the mucosal afferents of the HFD and RFD mice. CONCLUSION: Disruption of gastric vagal afferent function by HFD-induced obesity is only partially reversible by dietary change, which provides a potential mechanism preventing maintenance of weight loss.

Modulation of murine gastric vagal afferent mechanosensitivity by neuropeptide W.

AIM: Neuropeptide W (NPW) is an endogenous ligand for the receptors GPR7 and GPR8 and is involved in central regulation of energy homeostasis. NPW in the periphery is found in gastric gastrin (G) cells. In the stomach, energy intake is influenced by vagal afferent signals, so we aimed to determine the effect of NPW on mechanosensitive gastric vagal afferents under different feeding conditions. METHODS: Female C57BL/6 mice (N > 10 per group) were fed a standard laboratory diet (SLD), high-fat diet (HFD) or were food restricted. The relationship between NPW immunopositive cells and gastric vagal afferent endings was determined by anterograde tracing and NPW immunohistochemistry. An in vitro gastro-oesophageal preparation was used to determine the functional effects of NPW on gastric vagal afferents. Expression of NPW in the gastric mucosa and GPR7 in whole nodose ganglia was determined by quantitative RT-PCR (QRT-PCR). The expression of GPR7 in gastric vagal afferent neurones was determined by retrograde tracing and QRT-PCR. RESULTS: Neuropeptide W immunoreactive cells were found in close proximity to traced vagal afferents. NPW selectively inhibited responses of gastric vagal tension receptors to stretch in SLD but not HFD or fasted mice. In the nodose ganglia, GPR7 mRNA was specifically expressed in gastric vagal afferent neurones. In fasted mice gastric mucosal NPW and nodose GPR7, mRNA was reduced compared with SLD. A HFD had no effect on gastric NPW mRNA, but down-regulated nodose GPR7 expression. CONCLUSION: Neuropeptide W modulates gastric vagal afferent activity, but the effect is dynamic and related to feeding status.

Enhanced de novo alloantibody and antibody-mediated injury in rhesus macaques.

Chronic allograft rejection is a major impediment to long-term transplant success. Humoral immune responses to alloantigens are a growing clinical problem in transplantation, with mounting evidence associating alloantibodies with the development of chronic rejection. Nearly a third of transplant recipients develop de novo antibodies, for which no established therapies are effective at preventing or eliminating, highlighting the need for a nonhuman primate model of antibody-mediated rejection. In this report, we demonstrate that depletion using anti-CD3 immunotoxin (IT) combined with maintenance immunosuppression that included tacrolimus with or without alefacept reliably prolonged renal allograft survival in rhesus monkeys. In these animals, a preferential skewing toward CD4 repopulation and proliferation was observed, particularly with the addition of alefacept. Furthermore, alefacept-treated animals demonstrated increased alloantibody production (100%) and morphologic features of antibody-mediated injury. In vitro, alefacept was found to enhance CD4 effector memory T cell proliferation. In conclusion, alefacept administration after depletion and with tacrolimus promotes a CD4+memory T cell and alloantibody response, with morphologic changes reflecting antibody-mediated allograft injury. Early and consistent de novo alloantibody production with associated histological changes makes this nonhuman primate model an attractive candidate for evaluating targeted therapeutics.

Increasing Age Is Associated with Worse Prognostic Factors and Increased Distant Recurrences despite Fewer Sentinel Lymph Node Positives in Melanoma.

Background. Advanced age is associated with a poorer prognosis in patients with melanoma. Despite this established finding, a decreased incidence of positive sentinel lymph nodes (SLNs) with advancing age has paradoxically been described. Methods. Using a single-institution database of melanoma patients between 1994 and 2009, the relationship between standard clinicopathologic variables and recurrence based on age was evaluated. Results. 1244 patients who underwent successful SLN biopsies were analyzed (mean followup 80.3 months). Increasing age was independently associated with worse survival on multivariable analysis (P = 0.02). SLN status was more likely to be negative if the patient was older (P = 0.01). Conclusions. Our data supports the paradox that increasing age is associated with a lower frequency of positive-SLN biopsies despite age itself being a poor prognostic factor. We propose that age-dependent variations in the primary tumor and the patient may predispose to a hematogenous route of spread for the older population, leading to worse survival.

Experience with a novel efalizumab-based immunosuppressive regimen to facilitate single donor islet cell transplantation.

Islet transplantation is an experimental therapy for selected patients with type 1 diabetes (T1DM). It remains limited by immunosuppressive drug toxicity, progressive loss of insulin independence, allosensitization and the need for multiple islet donors. We describe our experience with an efalizumab-based immunosuppressive regimen as compared to the prevailing standard regimen, the Edmonton protocol. Twelve patients with T1DM received islet transplants: eight were treated with the Edmonton protocol; four were treated with daclizumab induction, a 6-month course of tacrolimus, and maintenance with efalizumab and mycophenolate mofetil. The primary endpoint was insulin independence after one islet infusion. Only two Edmonton protocol treated patients achieved the primary endpoint; six required islets from multiple donors, and all experienced leukopenia, mouth ulcers, anemia, diarrhea and hypertransaminasemia. Four became allosensitized. All patients treated with the efalizumab-based regimen achieved insulin independence with normal hemoglobin A1c after a single islet cell infusion and remained insulin independent while on efalizumab. These patients experienced significantly fewer side effects and none became allosensitized. Trial continuation was terminated by withdrawal of efalizumab from the market. These data suggest that this efalizumab-based regimen prevents islet rejection, is well tolerated, and allows for single donor islet transplantation.

Freezing in the bulk controlled by prefreezing at a surface.

We use Monte Carlo simulations of the Lennard-Jones model to study the nucleation of a crystal phase at a flat surface. Our motivation is the observation that crystal phases almost always nucleate at a surface. We find that a surface phase transition (prefreezing) can control nucleation of the bulk crystal. This finding should be general and so surface phase behavior should be considered whenever nucleation of bulk phases at surfaces is considered. Also, nucleation of the bulk crystal transforms smoothly into the nucleation of a surface crystal layer as the bulk transition is crossed.

Two-step vapor-crystal nucleation close below triple point.

We present the results of Monte Carlo simulations of crystal nucleation from the vapor phase. We studied the Lennard-Jones system at conditions close to, but below, the triple point. This system is expected to show surface melting. The nucleation pathway that we observe consists of two distinct steps. In the first step, a liquid droplet nucleates from the vapor. Its nucleation rate depends strongly on the vapor supersaturation. In the second step, the final crystal phase nucleates in the liquid droplet, provided that this liquid droplet exceeds a minimum size. Our simulations show that within a liquid droplet the crystal nucleation rate does not depend on the vapor supersaturation. In a recent independent study Chen et al. [J. Phys. Chem. B 112, 4069 (2008)] investigated the same phenomenon using umbrella sampling to compute free energy barriers and hence nucleation rates. We use a different numerical approach where we focus on computing the nucleation rates directly using forward-flux sampling. Our results agree with the findings of Chen et al. and both methods observe two-step nucleation. This finding indicates that this nucleation process can be described with a quasiequilibrium theory. Due to different cutoffs for the interaction potential the results cannot be compared quantitatively.

Exercise-associated hyponatremia, renal function, and nonsteroidal antiinflammatory drug use in an ultraendurance mountain run.

OBJECTIVE: To study biochemical parameters and renal function in runners completing a 60 km mountain run and to investigate the incidence of exercise-associated hyponatremia (EAH). To assess the effects of nonselective nonsteroidal antiinflammatory medication (NSAIDs) and cyclooxygenase-2 (COX-2) selective nonsteroidal antiinflammatory medication (COXIBs) on these parameters. DESIGN: Observational cohort study. SETTING: Kepler Challenge 60 km mountain run, Te Anau, New Zealand, December 2003. PARTICIPANTS: One hundred thirty-one of the 360 runners entered in the race were prospectively enrolled as volunteers on the day before the race. MAIN OUTCOME MEASURES: Subjects were weighed at race registration the day before the race and at the finish line. Blood was taken within 5 minutes of finishing and was analyzed for serum sodium, creatinine, urea, and potassium concentrations, and hematocrit. Participants were questioned about medication use in the 24 hours before and during the race (NSAIDs, COXIBs, other medications). RESULTS: Complete data sets were obtained on 123 runners. Five athletes were biochemically hyponatremic [(Na) 130-134 mM] and four were hypernatremic [(Na) 146-148 mM]. Hyponatremia was associated with a mean weight gain of 1.32 kg (range, -1.5 to 1.6 kg). Serum [Na] varied inversely with weight change. Estimated creatinine clearance did not vary with percent weight loss. Estimated creatinine clearance declined with increasing runner age. Sixty-five percent of runners did not use any medication, whereas 20% had used NSAIDs and 15% had taken COXIBs. There were no statistically significant differences between NSAID and COXIB users in any measured parameters or between all NSAID and COXIB users when compared with nonusers. CONCLUSIONS: Mild asymptomatic EAH was found to occur in 4% of the volunteer ultraendurance mountain runner study group and was associated with a mean weight gain of 1.32 kg (range, -1.5 to 1.6 kg) during the race. Seven percent gained weight but remained normonatremic, suggesting other compensatory mechanisms. Hypernatremia was found in 3% and was associated with a mean weight loss. Postrace serum sodium concentration varied inversely with percent weight change. Runners using any NSAID were more likely to become hyponatremic. Estimated creatinine clearance increased with increasing age. Elevated serum creatinine concentration at the end of the race returned to normal when remeasured the week after the race. Thirty-five percent of runners were found to use NSAIDs or COXIBs. The measures of weight change and of serum sodium, potassium, urea, and creatine concentration did not differ between NSAID and COXIB users or between all nonsteroidal antiinflammatory users and nonusers.

Inhibition of mechanosensitivity in visceral primary afferents by GABAB receptors involves calcium and potassium channels.

GABA(B) receptors inhibit mechanosensitivity of visceral afferents. This is associated with reduced triggering of events that lead to gastro-esophageal reflux, with important therapeutic consequences. In other neuronal systems, GABA(B) receptor activation may be linked via G-proteins to reduced N-type Ca(2+) channel opening, increased inward rectifier K(+) channel opening, plus effects on a number of intracellular messengers. Here we aimed to determine the role of Ca(2+) and K(+) channels in the inhibition of vagal afferent mechanoreceptor function by the GABA(B) receptor agonist baclofen. The responses of three types of ferret gastro-esophageal vagal afferents (mucosal, tension and tension mucosal receptors) to graded mechanical stimuli were investigated in vitro. The effects of baclofen (200 microM) alone on these responses were quantified, and the effects of baclofen in the presence of the G-protein-coupled inward rectifier potassium channel blocker Rb(+) (4.7 mM) and/or the N-type calcium channel blocker omega-conotoxin GVIA (0.1 microM). Baclofen inhibition of mucosal receptor mechanosensitivity was abolished by both blockers. Its inhibitory effect on tension mucosal receptors was partly reduced by both. The inhibitory effect of baclofen on tension receptors was unaffected. The data indicate that the inhibitory action of GABA(B) receptors is mediated via different pathways in mucosal, tension and tension mucosal receptors via mechanisms involving both N-type Ca(2+) channels and inwardly rectifying K(+) channels and others.