Immune responses of a liposome/ISCOM vaccine adjuvant against streptococcal fibronectin binding protein 1 (Sfb1) in mice.
The fibronectin binding protein Sfb1 of Streptococcus pyogenes is a well characterised antigen which induces protection against lethal challenge with group A streptococcus (GAS) when adjuvanted with cholera toxin B-subunit (CTB). As an alternative to CTB adjuvanted intranasal immunisations we investigated the immune responses generated in mice using Sfb1 incorporated in to the skin and mucosal adjuvant SAMA4. Mice (BALB/c) were vaccinated intradermally with 100 microl of either SAMA4 (adjuvant only group) or SAMA4/Sfb1 and were boosted 7 days later. Mice vaccinated with CTB based vaccines were immunised by intranasal inoculation with a mixture containing 30 microg Sfb1 and 10 microg CTB on days 1, 3, 5 and 15. At 14 days after the last booster immunisation the immune response was characterised and mice were challenged with 10(8) CFU of S. pyogenes. Mice vaccinated with SAMA4/Sfb1 elicited a Sfb1-specific IgG response in the sera that was significantly higher than that seen in control mice and mice immunised with the adjuvant only (P<0.05). No significant differences were seen for specific IgA antibodies in the sera in all groups examined. Compared with non-immunised and adjuvant only immunised controls, mice immunised with the Sfb1/SAMA4 vaccine exhibited a significant increase (P<0.05) in the number of Sfb1 reactive spleen cells in lymphoproliferation assays which were three fold higher than those seen for mice vaccinated with the Sfb1/CTB vaccine. Mice vaccinated with CTB/Sfb1 had the highest level of protection (80%) as where mice vaccinated with SAMA4 and SAMA4/Sfb1 displayed no protection (20% and 40%). These data suggest that the SAMA4 adjuvant used in this study fails to elicit protective immunity in BALB/c mice when used to adjuvant the known protective antigen Sfb1.


A health risk for consumers: the presence of adulterated food supplements in the Netherlands.
The use of food supplements is increasing. They are marketed as beneficial for health, well-being, physical or mental condition and performance, or to prevent diseases. Producers add synthetic compounds or illicit herbal material to food supplements to claim desired effects. Claims made to support marketing without scientific evidence are, however, illegal. Intake of adulterated food supplements may lead to serious adverse effects. The aim of this paper is to report the results of analyses of (adulterated) food supplements conducted by the Netherlands Food and Consumer Product Safety Authority between October 2013 and October 2018. In total, 416 supplements were analysed of which 264 (64%) contained one or more pharmacological active substances or plant toxins, such as caffeine, synephrine, sildenafil, icariin, sibutramine, higenamine, hordenine, phenethylamine, methylsynephrine, DMAA, phenolphthalein, octopamine and ephedrine. When compared to dose levels that are considered safe, daily doses of the substances in the food supplements were sometimes much higher, causing a risk for consumers who are unaware of the presence of these pharmacologically active substances. In many cases, neither food nor medicines legislation (easily) enables enforcement actions. This means that some products containing pharmacologically active substances (i.e. synthetic medicines and their illicit analogues), stay available on the market. An undesirable situation because for many of these substances no detailed toxicity data are available.


Partnering Support Interventions with Bariatric Surgery to Maximize Health Outcomes in Adolescents with Severe Obesity.
Rates of adolescents with severe obesity continue to rise worldwide, with concurrent increases in metabolic and bariatric surgery (MBS) uptake. The gap between support (lifestyle, pharmacotherapy) interventions and MBS as treatment options for adolescents has been understudied. This review, couched in a socio-ecological framework, investigates how support interventions for adolescents with severe obesity could be combined or sequenced with MBS to optimize health outcomes. A comprehensive search revealed 36 published articles between 1995 and 2019 that included the combination of support interventions and MBS among adolescents. There were no studies that specifically reported outcomes or effect sizes for the combination of lifestyle intervention with MBS. Previous studies have reported individual results for either lifestyle intervention or MBS but not for their compound effect. As rates of adolescents with severe obesity are on the rise globally, future research should focus on how partnering support interventions with MBS can amplify positive short- and long-term health outcomes and within a socio-ecological framework. Understanding the sequence of these approaches will be of particular importance. High-risk and vulnerable populations such as ethnic minorities who have suffered a disproportionate burden of the obesity epidemic must be included in rigorously tested future trials of combination interventions to maximize health outcomes worldwide.


The Shelterin TIN2 Subunit Mediates Recruitment of Telomerase to Telomeres.
Dyskeratosis Congenita (DC) is a heritable multi-system disorder caused by abnormally short telomeres. Clinically diagnosed by the mucocutaneous symptoms, DC patients are at high risk for bone marrow failure, pulmonary fibrosis, and multiple types of cancers. We have recapitulated the most common DC-causing mutation in the shelterin component TIN2 by introducing a TIN2-R282H mutation into cultured telomerase-positive human cells via a knock-in approach. The resulting heterozygous TIN2-R282H mutation does not perturb occupancy of other shelterin components on telomeres, result in activation of telomeric DNA damage signaling or exhibit other characteristics indicative of a telomere deprotection defect. Using a novel assay that monitors the frequency and extension rate of telomerase activity at individual telomeres, we show instead that telomerase elongates telomeres at a reduced frequency in TIN2-R282H heterozygous cells; this recruitment defect is further corroborated by examining the effect of this mutation on telomerase-telomere co-localization. These observations suggest a direct role for TIN2 in mediating telomere length through telomerase, separable from its role in telomere protection.


IoT-Based Home Monitoring: Supporting Practitioners' Assessment by Behavioral Analysis.
This paper introduces technical solutions devised to support the Deployment Site - Regione Emilia Romagna (DS-RER) of the ACTIVAGE project. The ACTIVAGE project aims at promoting IoT (Internet of Things)-based solutions for Active and Healthy ageing. DS-RER focuses on improving continuity of care for older adults (65+) suffering from aftereffects of a stroke event. A Wireless Sensor Kit based on Wi-Fi connectivity was suitably engineered and realized to monitor behavioral aspects, possibly relevant to health and wellbeing assessment. This includes bed/rests patterns, toilet usage, room presence and many others. Besides hardware design and validation, cloud-based analytics services are introduced, suitable for automatic extraction of relevant information (trends and anomalies) from raw sensor data streams. The approach is general and applicable to a wider range of use cases; however, for readability's sake, two simple cases are analyzed, related to bed and toilet usage patterns. In particular, a regression framework is introduced, suitable for detecting trends (long and short-term) and labeling anomalies. A methodology for assessing multi-modal daily behavioral profiles is introduced, based on unsupervised clustering techniques. The proposed framework has been successfully deployed at several real-users' homes, allowing for its functional validation. Clinical effectiveness will be assessed instead through a Randomized Control Trial study, currently being carried out.


Renal protection of losartan 50 mg in normotensive Chinese patients with nondiabetic chronic kidney disease.
Nondiabetic chronic kidney disease (CKD) is the leading major cause of end-stage renal disease in developing countries including China. Among the 5 stages of CKD, it is critical to retard the progression of stage 3 because renal disorder could accelerate aggravation behind that stage. Data suggest that high dosages of angiotensin receptor blockers (ARBs) could retard the progression of renal disease in hypertensive and/or diabetic patients. Nevertheless, in daily practice of nephrology, quite a number of nondiabetic patients with CKD who are normotensive do not tolerate even moderate dosages of ARBs because of adverse effects such as systemic hypotension, epically for Chinese patients. The aim of this study was to investigate the renoprotective effects of relatively low dosages of ARBs in normotensive Chinese patients with nondiabetic stage 3 CKD. A prospective, randomized, parallel-group, open-label study was performed over a period of 12 months. A total of 238 enrolled patients were randomly allocated to treatment with losartan 50 mg (n = 119) or placebo (n = 119). All patients were followed up at 2-month intervals. At each visit, blood pressure was measured, and urinalysis and serum biochemistry tests were performed. Finally, 112 patients given losartan and 114 patients given placebo completed the study. In the losartan group, there was a significant and biphasic time-dependent decline in proteinuria during therapy (1.72 ± 0.47 to 0.99 ± 0.48 g/d; P < 0.001). Conversely, placebo did not simultaneously change the amount of proteinuria (1.73 ± 0.49 to 1.64 ± 0.50 g/d; P = 0.337). Estimated glomerular filtration rate remained stable during the entire study period in the patients given losartan (44.8 ± 8.1 to 44.1 ± 7.7 mL/min per 1.73 m; P = 0.120) but were significantly reduced in the placebo group (44.5 ± 8.5 to 39.1 ± 7.4 mL/min per 1.73 m, P < 0.001). The changes in blood pressure were kept constant in the 2 groups. All adverse events were minimal and nonfatal. For normotensive patients with nondiabetic stage 3 CKD, therapy with a daily dose of losartan, 50 mg, may perform effective renoprotection without changing blood pressure and be generally safe and well tolerated.


The Fort Collins Commuter Study: Impact of route type and transport mode on personal exposure to multiple air pollutants.
Traffic-related air pollution is associated with increased mortality and morbidity, yet few studies have examined strategies to reduce individual exposure while commuting. The present study aimed to quantify how choice of mode and route type affects personal exposure to air pollutants during commuting. We analyzed within-person difference in exposures to multiple air pollutants (black carbon (BC), carbon monoxide (CO), ultrafine particle number concentration (PNC), and fine particulate matter (PM2.5)) during commutes between the home and workplace for 45 participants. Participants completed 8 days of commuting by car and bicycle on direct and alternative (reduced traffic) routes. Mean within-person exposures to BC, PM2.5, and PNC were higher when commuting by cycling than when driving, but mean CO exposure was lower when cycling. Exposures to CO and BC were reduced when commuting along alternative routes. When cumulative exposure was considered, the benefits from cycling were attenuated, in the case of CO, or exacerbated, in the case of particulate exposures, owing to the increased duration of the commute. Although choice of route can reduce mean exposure, the effect of route length and duration often offsets these reductions when cumulative exposure is considered. Furthermore, increased ventilation rate when cycling may result in a more harmful dose than inhalation at a lower ventilation rate.


Impact of coastal defence structures (tetrapods) on a demersal hard-bottom fish community in the southern North Sea.
In the coming decades, artificial defence structures will increase in importance worldwide for the protection of coasts against the impacts of global warming. However, the ecological effects of such structures on the natural surroundings remain unclear. We investigated the impact of experimentally introduced tetrapod fields on the demersal fish community in a hard-bottom area in the southern North Sea. The results indicated a significant decrease in fish abundance in the surrounding area caused by migration effects towards the artificial structures. Diversity (HB) and evenness (E) values exhibited greater variation after the introduction of the tetrapods. Additionally, a distinct increase in young-of-the-year (YOY) fish was observed near the structures within the second year after introduction. We suggest that the availability of adequate refuges in combination with additional food resources provided by the artificial structures has a highly species-specific attraction effect. However, these findings also demonstrate that our knowledge regarding the impact of artificial structures on temperate fish communities is still too limited to truly understand the ecological processes that are initiated by the introduction of artificial structures. Long-term investigations and additional experimental in situ work worldwide will be indispensable for a full understanding of the mechanisms by which coastal defence structures interact with the coastal environment.


Transoral laser microsurgery versus radiation therapy in the management of T1 and T2 laryngeal glottic carcinoma: which modality is cost-effective within the UK?
To identify the most cost-effective treatment strategy in patients with early stage (T1 and T2) cancers of the laryngeal glottis. A Markov decision model populated using data from updated systematic reviews and meta-analyses, with attributable costs from NHS sources. Data on local control and mortality were obtained from updates of existing systematic reviews conducted for the NICE guideline on cancer of the upper aerodigestive tract. Procedure costs were sourced from NHS reference costs 2013/14 by applying tariffs associated with the appropriate health resource group code SETTING: The UK National Health Service. Patients with early stage (T1 and T2) cancers of the laryngeal glottis. Transoral laser microsurgery (TLM) and radiation therapy (RT). Total costs, incremental costs and quality adjusted life years (QALYs) over a 10-year time horizon. Radiation therapy as the initial treatment strategy was found to be more expensive (£2654 versus £623) and less effective (QALY reduction of 0.141 and 0.04 in T1a and T1b-T2 laryngeal cancers, respectively) than TLM. The dominance of TLM for T1a cancers was unchanged in most scenarios modelled in sensitivity analysis. For T1b-T2 laryngeal cancers, the result changed in numerous scenarios. In probabilistic sensitivity analysis, TLM was found to have a 71% and 58% probability of being cost-effective in T1a and T1b-T2 laryngeal cancers, respectively. Transoral laser microsurgery is a cost-effective strategy to adopt in the management of T1a laryngeal cancers. Uncertainty remains over the optimal strategy to adopt in T1b-T2 laryngeal cancers.


Enhanced intracellular heat shock protein 70 expression of leukocytes and serum interleukins release: comparison of on-pump and off-pump coronary artery surgery.
Coronary artery bypass grafting (CABG) employing cardiopulmonary bypass (CPB; "on-pump" technique) is known to induce a systemic inflammatory response and heat-shock protein 70 kDa (HSP70) expression. The objective of the present study was to investigate the perioperative intracellular HSP70 expression of leukocytes and serum interleukin (IL) release in CABG conducted with both on-pump and off-pump techniques. Thirty-seven patients referred for elective CABG were enrolled in this study. These patients were categorized into the following three groups: on-pump cardioplegic arrest (n = 12); on-pump beating heart (n = 13); and off-pump (n = 12). Blood samples were collected at four time points during the perioperative period. Enzyme-linked immunosorbent assay (ELISA) was used to determine the serum level of IL-8, IL-10, IL-12, and HSP70. Flow cytometric analysis of intracellular HSP70 was performed in populations of lymphocytes, monocytes, and granulocytes. The clinical outcomes were comparable among the three groups. Elevated serum IL-8, IL-10, IL-12 were found in all three groups during the perioperative period. Serum HSP70 was elevated in all three groups and was significantly lower in the off-pump group than in the on-pump cardioplegic arrest and on-pump beating-heart groups. Heat shock protein-70 expression was found in leukocytes and showed a faster response in monocytes and granulocytes than in lymphocytes. The inflammatory response in the off-pump group was less than in either of the on-pump groups. During the perioperative period, activation of inflammatory response was associated with enhanced expression of HSP70 within leukocytes in CABG patients.


Threshold-driven optimization for reference-based auto-planning.
We study threshold-driven optimization methodology for automatically generating a treatment plan that is motivated by a reference DVH for IMRT treatment planning. We present a framework for threshold-driven optimization for reference-based auto-planning (TORA). Commonly used voxel-based quadratic penalties have two components for penalizing under- and over-dosing of voxels: a reference dose threshold and associated penalty weight. Conventional manual- and auto-planning using such a function involves iteratively updating the preference weights while keeping the thresholds constant, an unintuitive and often inconsistent method for planning toward some reference DVH. However, driving a dose distribution by threshold values instead of preference weights can achieve similar plans with less computational effort. The proposed methodology spatially assigns reference DVH information to threshold values, and iteratively improves the quality of that assignment. The methodology effectively handles both sub-optimal and infeasible DVHs. TORA was applied to a prostate case and a liver case as a proof-of-concept. Reference DVHs were generated using a conventional voxel-based objective, then altered to be either infeasible or easy-to-achieve. TORA was able to closely recreate reference DVHs in 5-15 iterations of solving a simple convex sub-problem. TORA has the potential to be effective for auto-planning based on reference DVHs. As dose prediction and knowledge-based planning becomes more prevalent in the clinical setting, incorporating such data into the treatment planning model in a clear, efficient way will be crucial for automated planning. A threshold-focused objective tuning should be explored over conventional methods of updating preference weights for DVH-guided treatment planning.


Efficient corner-pumped Yb:YAG/YAG composite slab laser.
A high efficiency Yb:YAG/YAG composite slab laser is presented, in which the corner-pumped scheme is adopted. The slab is a composite crystal of Yb:YAG bonded thermally with undoped YAG at both edges. The pump light from diode arrays is coupled into the slab through four chamfers at the four corners independently. The pump absorption efficiency is studied, and an analysis method has been developed as a guide to optimize the geometric parameters of the composite slab, to obtain higher pump absorption efficiency and uniformity. The influence of the internal thermal lens on the laser resonator is analyzed. A 1016 W continuous-wave output has been obtained with the slope efficiency and optical-to-optical efficiency of 42.8% and 34.4%, respectively.


Instrumentation and metrology for single RNA counting in biological complexes or nanoparticles by a single-molecule dual-view system.
Limited by the spatial resolution of optical microscopy, direct detection or counting of single components in biological complexes or nanoparticles is challenging, especially for RNA, which is conformationally versatile and structurally flexible. We report here the assembly of a customized single-molecule dual-viewing total internal reflection fluorescence imaging system for direct counting of RNA building blocks. The RNA molecules were labeled with a single fluorophore by in vitro transcription in the presence of a fluorescent AMP. Precise calculation of identical or mixed pRNA building blocks of one, two, three, or six copies within the bacteriophage phi29 DNA packaging motor or other complexes was demonstrated by applying a photobleaching assay and evaluated by binomial distribution. The dual-viewing system for excitation and recording at different wavelengths simultaneously will enable the differentiation of different complexes with different labels or relative motion of each labeled component in motion machines.


Pulmonary exposure to carbon black by inhalation or instillation in pregnant mice: effects on liver DNA strand breaks in dams and offspring.
Effects of maternal pulmonary exposure to carbon black (Printex 90) on gestation, lactation and DNA strand breaks were evaluated. Time-mated C57BL/6BomTac mice were exposed by inhalation to 42 mg/m(3) Printex 90 for 1 h/day on gestation days (GD) 8-18, or by four intratracheal instillations on GD 7, 10, 15 and 18, with total doses of 11, 54 and 268 μg/animal. Dams were monitored until weaning and some offspring until adolescence. Inflammation was assessed in maternal bronchoalveolar lavage (BAL) 3-5 days after exposure, and at weaning. Levels of DNA strand breaks were assessed in maternal BAL cells and liver, and in offspring liver. Persistent lung inflammation was observed in exposed mothers. Inhalation exposure induced more DNA strand breaks in the liver of mothers and their offspring, whereas intratracheal instillation did not. Neither inhalation nor instillation affected gestation and lactation. Maternal inhalation exposure to Printex 90-induced liver DNA damage in the mothers and the in utero exposed offspring.


Polymer imprinting with iron-oxo-hydroxo clusters: [Fe6O2(OH)2(O2CC(Cl)=CH2)12(H2O)2], [Fe6O2(OH)2(O2C-Ph-(CH)=CH2)12(H2O)2] and [{Fe(O2CC(Cl)=CH2)(OMe)2}10].
We report the syntheses of imprinted polymers using iron-oxo-hydroxo clusters as templates. Three new iron clusters, [Fe(6)O(2)(OH)(2)(O(2)CC(Cl)=CH(2))(12)(H(2)O)(2)] (1), [{Fe(O(2)CC(Cl)=CH(2))(OMe)(2)}(10)] (2) and [Fe(6)O(2)(OH)(2)(O(2)C-Ph-(CH)=CH(2))(12)(H(2)O)(2)] (3) have been prepared from commercially-available carboxylic acids. Cluster-imprinted-polymers (CIPs) of 1, 2 and 3 were prepared with ethylene glycol dimethacrylate monomer, and of 1 with methyl methacrylate monomer. The imprinted sites within the CIPs were examined using EXAFS and diffuse reflectance UV/vis spectroscopy, demonstrating that the clusters 1, 2 and 3 were incorporated intact within the polymers. Extraction of the clusters from the CIPs imprinted with 1 and 3 gave new polymers that showed evidence of an imprinting effect.


Dual endothelin receptor antagonism prevents remodeling of resistance arteries in diabetes.
Vascular remodeling, characterized by extracellular matrix deposition and increased media-to-lumen (M/L) ratio, contributes to the development of microvascular complications in diabetes. We have previously shown in type 2 diabetic Goto-Kakizaki (GK) rats that selective ETA receptor blockade prevents medial thickening of mesenteric arteries via regulation of matrix metalloproteases (MMP), whereas selective ETB receptor blockade augments this thickening. The goal of this study was to determine the effect of combined ETA and ETB receptor blockade on resistance vessel remodeling. Vessel structure, MMP activity, and extracellular matrix proteins were assessed in control Wistar and diabetic GK rats treated with vehicle or bosentan (100 mg/kg per day) for 4 weeks (n = 7-9 per group). Bosentan completely prevented the increase in M/L ratio and MMP-2 activity in diabetes but paradoxically increased M/L ratio and MMP activation in control animals. Collagenase (MMP-13) activity and protein levels were significantly decreased in diabetes. Accordingly, collagen deposition was augmented in GK rats. Dual ET receptor antagonism improved enzyme activity and normalized MMP-13 levels in diabetic animals but blunted MMP-13 activity in control animals. In summary, current findings suggest that diabetes-mediated remodeling of resistance arteries is prevented by dual blockade of ETA and ETB receptors and that the relative role of ET receptors in the regulation of vascular structure differs in the control and disease states.


A vision for chronic disease prevention intervention research: report from a workshop.
The Population Studies Research Network of Cancer Care Ontario hosted a strategic planning workshop to establish an agenda for a prevention intervention research program in Ontario, including priority topics for investigation and design considerations. The two-day workshop included: presentations on background papers developed to facilitate participants' preparation for and discussions in the workshop; keynote presentations on intervention research concerning primary prevention of chronic diseases, design and study implementation considerations; a dedicated session on critical and creative thinking to stimulate participation and discussion topics; break out groups to identify, discuss and present study ideas, designs, implementation considerations; and a consensus process to discuss and identify recommendations for research priorities and next steps. The retreat yielded the following recommendations: 1) develop an intervention research agenda that includes working with existing large-scale cohorts; 2) develop an intervention research agenda that includes novel research designs that could target individuals or groups; and 3) develop an intervention research agenda in which studies collect data on costs, define stakeholders, and ensure clear strategies for stakeholder engagement and knowledge transfer. The Population Studies Research Network will develop options from these recommendations and release a call for proposals in 2014 for intervention research pilot projects that reflect these recommendations. Pilot projects will be evaluated based on their fit with the retreat's recommendations, and their potential to scale up to full studies and application in practice.


A high throughput screen identifies benzoquinoline compounds as inhibitors of Ebola virus replication.
Ebola virus (EBOV) is an enveloped negative-sense, single-stranded RNA virus of the filovirus family that causes severe disease in humans. Approved therapies for EBOV disease are lacking. EBOV RNA synthesis is carried out by a virus-encoded complex with RNA-dependent RNA polymerase activity that is required for viral propagation. This complex and its activities are therefore potential antiviral targets. To identify potential lead inhibitors of EBOV RNA synthesis, a library of small molecule compounds was screened against a previously established assay of EBOV RNA synthesis, the EBOV minigenome assay (MGA), in 384 well microplate format. The screen identified 56 hits that inhibited EBOV MGA activity by more than 70% while exhibiting less than 20% cell cytotoxicity. Inhibitory chemical scaffolds included angelicin derivatives, derivatives of the antiviral compound GSK983 and benzoquinolines. Structure-activity relationship (SAR) studies of the benzoquinoline scaffold produced ∼50 analogs and led to identification of an optimized compound, SW456, with a submicromolar IC50 in the EBOV MGA and antiviral activity against infectious EBOV in cell culture. The compound was also active against a MGA for another deadly filovirus, Marburg virus. It also exhibited antiviral activity towards a negative-sense RNA virus from the rhabdovirus family, vesicular stomatitis virus, and a positive-sense RNA virus, Zika virus. Overall, these data demonstrate the potential of the EBOV MGA to identify anti-EBOV compounds and identifies the benzoquinoline series as a broad-spectrum antiviral lead.


Gene duplication and fragmentation in the zebra finch major histocompatibility complex.
Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.


Targeting Nrf2 for the treatment of Duchenne Muscular Dystrophy.
Imbalances in redox homeostasis can result in oxidative stress, which is implicated in various pathological conditions including the fatal neuromuscular disease Duchenne Muscular Dystrophy (DMD). DMD is a complicated disease, with many druggable targets at the cellular and molecular level including calcium-mediated muscle degeneration; mitochondrial dysfunction; oxidative stress; inflammation; insufficient muscle regeneration and dysregulated protein and organelle maintenance. Previous investigative therapeutics tended to isolate and focus on just one of these targets and, consequently, therapeutic activity has been limited. Nuclear erythroid 2-related factor 2 (Nrf2) is a transcription factor that upregulates many cytoprotective gene products in response to oxidants and other toxic stressors. Unlike other strategies, targeted Nrf2 activation has the potential to simultaneously modulate separate pathological features of DMD to amplify therapeutic benefits. Here, we review the literature providing theoretical context for targeting Nrf2 as a disease modifying treatment against DMD.


Estimating fine particulate matter component concentrations and size distributions using satellite-retrieved fractional aerosol optical depth: part 1--method development.
We develop a method that uses both the total column aerosol optical depth (AOD) and the fractional AOD values for different aerosol types, derived from Multiangle Imaging SpectroRadiometer (MISR) aerosol data, to estimate ground-level concentrations of fine particulate matter (PM2.5) mass and its major constituents in eastern and western United States. Compared with previous research on linking column AOD with ground-level PM2.5, this method treats various MISR aerosol components as individual predictor variables. Therefore, the contributions of different particle types to PM2.5 concentrations can be estimated. When AOD is greater than 0.15, MISR is able to distinguish dust from non-dust particles with an uncertainty level of approximately 4%, and light-absorbing from non-light-absorbing particles with an uncertainty level of approximately 20%. Further analysis shows that MISR Version 17 aerosol microphysical properties have good sensitivity and internal consistency among different mixture classes. The retrieval uncertainty of individual fractional AODs ranges between 5 and 11% in the eastern United States, and between 11 and 31% in the west for non-dust aerosol components. These results provide confidence that the fractional AOD models with their inherent flexibility can make more accurate predictions of the concentrations of PM2.5 and its constituents.


Selective enhancement of the interaction of curare with the nicotinic acetylcholine receptor.
Alteration of the ligand-binding domain of the nicotinic acetylcholine receptor through site-directed mutagenesis offers a powerful approach to the elucidation of structure-function relations in the receptor. Several conserved tyrosine residues in the large extracellular amino terminus of the alpha subunit of the receptor have been implicated by both chemical labeling and mutagenesis studies as playing an important role in the interaction of acetylcholine with the receptor. We and others have previously shown that substitution of phenylalanine for tyrosine at position 198 of the alpha subunit (alpha Y198F) leads to a rightward shift in the dose-response curve for acetylcholine-elicited currents. We have further investigated this particular mutation by examining the interaction of the competitive antagonist d-tubocurarine (curare) with the receptor. In contrast to the effect on the interaction of agonists with the receptor, this mutation leads to a marked increase in the affinity of the receptor for curare. Furthermore, this enhancement in affinity is selective for curare and is not seen with other competitive antagonists (pancuronium, beta-erythroidine, and gallamine). Examination of the structures of these competitive antagonists leads to the proposal that this enhancement is due to the formation of an aromatic-aromatic interaction between the phenylalanine ring at position alpha 198 in the mutant and one of the aromatic rings of curare and that this can provide information about the spatial arrangement of this residue in the binding site.


Effect of high-fidelity simulation on Pediatric Advanced Life Support training in pediatric house staff: a randomized trial.
To assess the effect of high-fidelity simulation (SIM) on cognitive performance after a training session involving several mock resuscitations designed to teach and reinforce Pediatric Advanced Life Support (PALS) algorithms. Pediatric residents were randomized to high-fidelity simulation (SIM) or standard mannequin (MAN) groups. Each subject completed 3 study phases: (1) mock code exercises (asystole, tachydysrhythmia, respiratory arrest, and shock) to assess baseline performance (PRE phase), (2) a didactic session reviewing PALS algorithms, and (3) repeated mock code exercises requiring identical cognitive skills in a different clinical context to assess change in performance (POST phase). SIM subjects completed all 3 phases using a high-fidelity simulator (SimBaby, Laerdal Medical, Stavanger, Norway), and MAN subjects used SimBaby without simulated physical findings (ie, as a standard mannequin). Performance in PRE and POST was measured by a scoring instrument designed to measure cognitive performance; scores were scaled to a range of 0 to 100 points. Improvement in performance from PRE to POST phases was evaluated by mixed modeling using a random intercept to account for within subject variability. Fifty-one subjects (SIM, 25; MAN, 26) completed all phases. The PRE performance was similar between groups. Both groups demonstrated improvement in POST performance. The improvement in scores between PRE and POST phases was significantly better in the SIM group (mean [SD], 11.1 [4.8] vs. 4.8 [1.7], P = 0.007). The use of high-fidelity simulation in a PALS training session resulted in improved cognitive performance by pediatric house staff. Future studies should address skill and knowledge decays and team dynamics, and clearly defined and reproducible outcome measures should be sought.


Are men well served by family planning programs?
Although the range of contraceptives includes methods for men, namely condoms, vasectomy and withdrawal that men use directly, and the Standard Days Method (SDM) that requires their participation, family planning programming has primarily focused on women. What is known about reaching men as contraceptive users? This paper draws from a review of 47 interventions that reached men and proposes 10 key considerations for strengthening programming for men as contraceptive users. A review of programming shows that men and boys are not particularly well served by programs. Most programs operate from the perspective that women are contraceptive users and that men should support their partners, with insufficient attention to reaching men as contraceptive users in their own right. The notion that family planning is women's business only is outdated. There is sufficient evidence demonstrating men's desire for information and services, as well as men's positive response to existing programming to warrant further programming for men as FP users. The key considerations focus on getting information and services where men and boys need it; addressing gender norms that affect men's attitudes and use while respecting women's autonomy; reaching adolescent boys; including men as users in policies and guidelines; scaling up successful programming; filling gaps with implementation research and monitoring & evaluation; and creating more contraceptive options for men.


A qualitative evaluation of a new community living model: medical foster home placement.
The Department of Veterans Affairs (VA) Medical Foster Home (MFH) program is an alternative to nursing home (NH) placement for veterans who are NH-eligible but prefer to receive care in private homes. Program expansion is ongoing; however, inefficiencies exist in targeting Veterans for enrollment. Semi-structured interviews were conducted with 35 individuals, 9 national MFH coordinators, 14 Primary Care Team Members, 2 veterans living in MFHs, 4 of their family members, 3 caregivers, and 3 family members of veterans who declined to participate in the program. Transcripts were analyzed using a general inductive approach supported by Archive for Technology, Lifeworld and Everyday language, text interpretation (ATLAS ti) V6.2. Three themes were identified as key facilitators of successful MFH placement: 1) The Environment - veterans needed to have appropriate and comfortable physical space that ensured safety and was in a desirable geographic location; 2) The Match - a collaborative relationship between veterans, care providers, and the medical team providing care within the home was essential; and 3) Perceptions and Expectations about the ability for needs to be met in MFHs and challenges related to health concerns, relocation, and costs. These themes, when integrated into the Social Ecological Model, provide a theoretical framework from which to guide future research and understand policy implications. MFHs represent a novel alternative to NH placement. This evaluation provides an understanding of factors that lead to successful MFH placement and integrates these themes into a theoretical framework designed to assist both VA policymakers interested in expanding the program and those within the civilian community seeking to study alternatives to traditional NH care.


The effect of cellulose overproduction on binding and biofilm formation on roots by Agrobacterium tumefaciens.
Agrobacterium tumefaciens growing in liquid attaches to the surface of tomato and Arabidopsis thaliana roots, forming a biofilm. The bacteria also colonize roots grown in sterile quartz sand. Attachment, root colonization, and biofilm formation all were markedly reduced in celA and chvB mutants, deficient in production of cellulose and cyclic beta-(1,2)-D-glucans, respectively. We have identified two genes (celG and cell) in which mutations result in the overproduction of cellulose as judged by chemical fractionation and methylation analysis. Wild-type and chvB mutant strains carrying a cDNA clone of a cellulose synthase gene from the marine urochordate Ciona savignyi also overproduced cellulose. The overproduction in a wild-type strain resulted in increased biofilm formation on roots, as evaluated by light microscopy, and levels of root colonization intermediate between those of cellulose-minus mutants and the wild type. Overproduction of cellulose by a nonattaching chvB mutant restored biofilm formation and bacterial attachment in microscopic and viable cell count assays and partially restored root colonization. Although attachment to plant surfaces was restored, overproduction of cellulose did not restore virulence in the chvB mutant strain, suggesting that simple bacterial binding to plant surfaces is not sufficient for pathogenesis.


Occurrence of tick-borne pathogens in questing Ixodes ricinus ticks from Wester Ross, Northwest Scotland.
Lyme borreliosis and other tick-borne diseases emerge from increased interactions between humans, other animals, and infected ticks. The risk of acquiring a tick-borne infection varies across space and time, so knowledge of the occurrence and prevalence of pathogens in ticks can facilitate disease diagnosis in a specific area and the implementation of mitigation measures and awareness campaigns. Here we identify the occurrence and prevalence of several pathogens in Ixodes ricinus ticks in Wester Ross, Northwest Scotland, a region of high tourism and tick exposure, yet data-poor in terms of tick-borne pathogens. Questing I. ricinus nymphs (n = 2828) were collected from 26 sites in 2018 and 2019 and tested for the presence of tick-borne pathogens using PCR-based methods. Prevalence was compared with other regions of Scotland, England, Wales, and the Netherlands. Anaplasma phagocytophilum (4.7% prevalence), Borrelia burgdorferi sensu lato (s.l.) (2.2%), Babesia from clade X (0.2%), Rickettsia helvetica (0.04%), and Spiroplasma ixodetis (0.4%) were detected, but no Neoehrlichia mikurensis, Borrelia miyamotoi, or Babesia microti. Typing of A. phagocytophilum using a fragment of the GroEL gene identified the presence of both ecotype I and ecotype II. Genospecies identification of Borrelia burgdorferi s.l. revealed B. afzelii (53% of infected nymphs), B. garinii (9%), B. burgdorferi sensu stricto (7%), and B. valaisiana (31%). We found similar prevalence of A. phagocytophilum in Wester Ross as in the Netherlands, but higher than in other parts of Great Britain. We found lower B. burgdorferi s.l. prevalence than in England or the Netherlands, and similar to some other Scottish studies. We found higher prevalence of B. valaisiana and lower prevalence of B. garinii than in other Scottish studies. We found S. ixodetis at much lower prevalence than in the Netherlands, and R. helvetica at much lower prevalence than in England and the Netherlands. As far as we know, this is the first description of S. ixodetis in Great Britain. The results are relevant for disease surveillance and management for public and veterinary health. The findings can also aid in designing targeted public health campaigns and in raising awareness among outdoor recreationists and professionals.


Management of latent Mycobacterium tuberculosis infection: WHO guidelines for low tuberculosis burden countries.
Latent tuberculosis infection (LTBI) is characterised by the presence of immune responses to previously acquired Mycobacterium tuberculosis infection without clinical evidence of active tuberculosis (TB). Here we report evidence-based guidelines from the World Health Organization for a public health approach to the management of LTBI in high risk individuals in countries with high or middle upper income and TB incidence of <100 per 100 000 per year. The guidelines strongly recommend systematic testing and treatment of LTBI in people living with HIV, adult and child contacts of pulmonary TB cases, patients initiating anti-tumour necrosis factor treatment, patients receiving dialysis, patients preparing for organ or haematological transplantation, and patients with silicosis. In prisoners, healthcare workers, immigrants from high TB burden countries, homeless persons and illicit drug users, systematic testing and treatment of LTBI is conditionally recommended, according to TB epidemiology and resource availability. Either commercial interferon-gamma release assays or Mantoux tuberculin skin testing could be used to test for LTBI. Chest radiography should be performed before LTBI treatment to rule out active TB disease. Recommended treatment regimens for LTBI include: 6 or 9 month isoniazid; 12 week rifapentine plus isoniazid; 3-4 month isoniazid plus rifampicin; or 3-4 month rifampicin alone.


Gender, Contraceptive Attitudes, and Condom Use in Adolescent Romantic Relationships: A Dyadic Approach.
Although sexual risk behavior occurs in a dyadic context, most studies of adolescent sexual behavior focus on individuals. This study uses couple data (N = 488 couples) from the National Longitudinal Study of Adolescent Health to examine how partners' contraceptive attitudes correlate over time and whether male or female partners' attitudes are better predictors of condom use. Net of their own prior attitudes, partners' prior attitudes predicted both male and female adolescents' Wave 2 attitudes. This association was stronger for female than for male adolescents, suggesting that female attitudes were influenced more by males' prior attitudes than vice versa. When entered together, only male adolescents' attitudes predicted dyadic condom use. Findings suggest that male partners may have greater influence on adolescent contraceptive decisions, and that prevention programs should emphasize the relational context of sexual behavior.


Sperm chromatin quality and DNA integrity in partial versus total globozoospermia.
Globozoospermia is a severe form of teratozoospermia with low incidence in infertile patients, considered as one of the important causes of male infertility. The objective was to investigate the chromatin/DNA integrity as well as apoptosis in ejaculated spermatozoa of cases with partial or total globozoospermia. Fifty-seven semen samples were divided into three groups of partial globozoospermia (n = 17), total globozoospermia (n = 10) and normozoospermia (control; n = 30). Sperm chromatin condensation, DNA integrity and apoptosis were assessed using cytochemical assays. The results showed significant differences in sperm parameters of count and motility between two case groups versus controls. The percentages of spermatozoa with abnormal chromatin packaging and protamine deficiency were significantly higher in total and partial globozoospermic men compared to normozoospermic samples. Also, the rates of TUNEL-positive spermatozoa were significantly increased in both globozoospermic cases with respect to the control (18.3 ± 10.1 and 12.3 ± 9.2 versus 5.9 ± 3 respectively). However, no significant differences were noticed between two subgroups of patients with regard to sperm DNA denaturation, DNA fragmentation and apoptosis. Abnormal chromatin packaging, DNA damage and apoptosis were significantly higher in cases than controls. The sperm chromatin/DNA anomalies may be considered as one of the main aetiology of ART failure in globozoospermic patients.


New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering.
Red clover necrotic mosaic virus (RCNMV) is a 36-nm-diameter, T = 3 icosahedral plant virus with a genome that is split between two single-stranded RNA molecules of approximately 3.9 kb and 1.5 kb, as well as a 400-nucleotide degradation product. The structure of the virus capsid and its response to removing Ca(2+) and Mg(2+) was previously studied by cryo-electron microscopy (cryo-EM) (Sherman et al. J Virol 80:10395-10406, 2006) but the structure of the RNA was only partially resolved in that study. To better understand the organization of the RNA and conformational changes resulting from the removal of divalent cations, small-angle neutron scattering with contrast variation experiments were performed. The results expand upon the cryo-EM results by clearly showing that virtually all of the RNA is contained in a thin shell that is in contact with the interior domains of the viral capsid protein, and they provide new insight into changes in the RNA packing that result from removal of divalent cations.


Cow's milk and type 1 diabetes: the real debate is about mucosal immune function.
The hypothesis that early exposure of the infant to cow's milk (or lack of breast-feeding) predisposes the child to type 1 diabetes dates from the 1980s. It has important implications, but remains controversial because the evidence on which it is based has been indirect and is open to criticism. Two meta-analyses of multiple studies in which diabetes prevalence was associated retrospectively with infant feeding revealed only a marginal increase in relative risk. Two recent prospective studies found no apparent association between development of antibodies to islet antigens and feeding patterns in high-risk infants with a first-degree type 1 diabetic relative. Studies reporting increased humoral and cellular immunity to cow's milk proteins in children with type 1 diabetes often lack appropriate controls and standardization and do not, in themselves, establish a causal connection to disease pathogenesis. A review of published data leads to the conclusion that increased immunity to cow's milk proteins is not disease-specific, but reflects genetic predisposition to increased immunity to dietary proteins in general, associated with the HLA haplotype A1-B8-DR3-DQ2 (A1*0501, B1*0201), which also predisposes to celiac disease and selective IgA deficiency. We suggest that the cow's milk hypothesis could be productively reframed around mucosal immune function in type 1 diabetes. Breast milk contains growth factors, cytokines, and other immunomodulatory agents that promote functional maturation of intestinal mucosal tissues. In the NOD mouse model, environmental cleanliness may influence diabetes incidence through mucosal mechanisms, and exposure of the mucosa to insulin (present in breast milk) induces regulatory T-cells and decreases diabetes incidence. The mucosa is a major immunoregulatory barrier, and cow's milk happens to be the first dietary protein it encounters. The basic question is whether impaired mucosal immune function predisposes to type 1 diabetes.


Health-related quality of life among patients with comorbid diabetes and kidney disease attending a codesigned integrated model of care: a longitudinal study.
To evaluate the impact of an integrated diabetes and kidney disease model of care on health-related quality of life (HRQOL) of patients with comorbid diabetes and chronic kidney disease (CKD). A longitudinal study of adult patients (over 18 years) with comorbid diabetes and CKD (stage 3a or worse) who attended a new diabetes kidney disease service was conducted at a tertiary hospital. A questionnaire consisting of demographics, clinical data, and the Kidney Disease Quality of Life (KDQOL-36) was administered at baseline and after 12 months. Paired t-tests were used to compare baseline and 12-month scores. A subgroup analysis examined the effects by patient gender. Multiple regression analysis examined the factors associated with changes in scores. 179 patients, 36% of whom were female, with baseline mean±SD age of 65.9±11.3 years, were studied. Across all subscales, HRQOL did not significantly change over time (p value for all mean differences >0.05). However, on subgroup analysis, symptom problem list and physical composite summary scores increased among women (MD=9.0, 95% CI 1.25 to 16.67; p=0.02 and MD=4.5, 95% CI 0.57 to 8.42; p=0.03 respectively) and physical composite scores decreased among men (MD=-3.35, 95% CI -6.26 to -0.44; p=0.03). The HRQOL of patients with comorbid diabetes and CKD attending a new codesigned, integrated diabetes and kidney disease model of care was maintained over 12 months. Given that HRQOL is known to deteriorate over time in this high-risk population, the impact of these findings on clinical outcomes warrants further investigation.


A meta-analysis of prehospital airway control techniques part I: orotracheal and nasotracheal intubation success rates.
Airway management is a key component of prehospital care for seriously ill and injured patients. Although endotracheal intubation has been a commonly performed prehospital procedure for nearly three decades, the safety and efficacy profile of prehospital intubation has been challenged in the last decade. Reported intubation success rates vary widely, and established benchmarks are lacking. We sought to determine pooled estimates for oral endotracheal intubation (OETI) and nasotracheal intubation (NTI) placement success rates through a meta-analysis of the literature. We performed a systematic literature search for all English-language articles reporting placement success rates for prehospital intubation. Studies of field procedures performed by prehospital personnel from any nation were included. All titles were reviewed independently by two authors using prespecified inclusion criteria. Pooled estimates of success rates for each airway technique, including drug-facilitated intubation (DFI) and rapid-sequence intubation (RSI), were calculated using a random-effects model. Historical trends were evaluated using meta-regression. Of 2,005 identified titles reviewed, 117 studies addressed OETI and 23 addressed NTI, encompassing a total of 57,132 prehospital patients. There was substantial interrater reliability in the review process (kappa = 0.81). The pooled estimates (and 95% confidence intervals [CIs]) for intervention success for nonphysician clinicians were as follows: overall non-RSI/non-DFI OETI success rate: 86.3% (82.6%-89.4%); OETI for non-cardiac arrest patients: 69.8% (50.9%-83.8%); DFI 86.8% (80.2%-91.4%); and RSI 96.7% (94.7%-98.0%). For pediatric patients, the paramedic OETI success rate was 83.2% (55.2%-95.2%). The overall NTI success rate for nonphysician clinicians was 75.9% (65.9%-83.7%). The historical trend of OETI reflects a 0.49% decline in success rates per year. We provide pooled estimates of placement success rates for prehospital airway interventions. For some patient and clinician characteristics, OETI has relatively low success rates. For nonarrest patients, DFI and RSI appear to increase success rates. Across all clinicians, NTI has a low rate of success, raising questions about the safety and efficacy of this procedure.


Carrier-envelope phase locking of multi-pulse lasers with an intra-cavity Mach-Zehnder interferometer.
We propose the use of an intra-cavity Mach Zehnder interferometer (MZI), for increasing the repetition rate at which carrier-envelope phase-locked pulses are generated in passively mode-locked fiber lasers. The attractive feature of the proposed scheme is that light escaping through the open output ports of the MZI can be used as a monitor signal feeding a servo loop that allows multiple pulses to co-exist in the cavity, while rigidly controlling their separation. The proposed scheme enables in principle a significant increase in the pulse-rate with no deterioration in the properties of the generated pulses.


Thermodynamics and bioenergetics.
Bioenergetics is concerned with the energy conservation and conversion processes in a living cell, particularly in the inner membrane of the mitochondrion. This review summarizes the role of thermodynamics in understanding the coupling between the chemical reactions and the transport of substances in bioenergetics. Thermodynamics has the advantages of identifying possible pathways, providing a measure of the efficiency of energy conversion, and of the coupling between various processes without requiring a detailed knowledge of the underlying mechanisms. In the last five decades, various new approaches in thermodynamics, non-equilibrium thermodynamics and network thermodynamics have been developed to understand the transport and rate processes in physical and biological systems. For systems not far from equilibrium the theory of linear non-equilibrium thermodynamics is used, while extended non-equilibrium thermodynamics is used for systems far away from equilibrium. All these approaches are based on the irreversible character of flows and forces of an open system. Here, linear non-equilibrium thermodynamics is mostly discussed as it is the most advanced. We also review attempts to incorporate the mechanisms of a process into some formulations of non-equilibrium thermodynamics. The formulation of linear non-equilibrium thermodynamics for facilitated transport and active transport, which represent the key processes of coupled phenomena of transport and chemical reactions, is also presented. The purpose of this review is to present an overview of the application of non-equilibrium thermodynamics to bioenergetics, and introduce the basic methods and equations that are used. However, the reader will have to consult the literature reference to see the details of the specific applications.


Inhibitory action of benzo[α]pyrene on hepatic lipoprotein receptors in vitro and on liver lipid homeostasis in mice.
Dyslipidemia associated with obesity often manifests as increased plasma LDL and triglyceride-rich lipoprotein levels suggesting changes in hepatic lipoprotein receptor status. Persistent organic pollutants have been recently postulated to contribute to the obesity etiology by increasing adipogenesis, but little information is available on their potential effect on hepatic lipoprotein metabolism. The objective of this study was to investigate the effect of the common environmental pollutant, benzo[α]pyrene (B[α]P) on two lipoprotein receptors, the LDL-receptor and the lipolysis-stimulated lipoprotein receptor (LSR) as well as the ATP-binding cassette transporter A1 (ABCA1) using cell and animal models. LSR, LDL-receptor as well as ABCA1 protein levels were significantly decreased by 26-48% in Hepa1-6 cells incubated (<2 h) in the presence of B[α]P (≤1 µM). Real-time PCR analysis and lactacystin studies revealed that this effect was due primarily to increased proteasome, and not lysosomal-mediated degradation rather than decreased transcription. Furthermore, ligand blots revealed that lipoproteins exposed to 1 or 5 µM B[α]P displayed markedly decreased (42-86%) binding to LSR or LDL-receptor. B[α]P-treated (0.5 mg/kg/48 h, i.p. 15 days) C57BL/6J mice displayed higher weight gain, associated with significant increases in plasma cholesterol, triglycerides, and liver cholesterol content, and decreased hepatic LDL-receptor and ABCA1 levels. Furthermore, correlational analysis revealed that B[α]P abolished the positive association observed in control mice between the LSR and LDL-receptor. Interestingly, levels of other proteins involved in liver cholesterol metabolism, ATP-binding cassette transporter G1 and scavenger receptor-BI, were decreased, while those of acyl-CoA:cholesterol acyltransferase 1 and 2 were increased in B[α]P-treated mice. B[α]P demonstrates inhibitory action on LSR and LDL-R, as well as ABCA1, which we propose leads to modified lipid status in B[α]P-treated mice, thus providing new insight into mechanisms underlying the involvement of pollutants in the disruption of lipid homeostasis, potentially contributing to dyslipidemia associated with obesity.


Polyalanine reconstruction from Calpha positions using the program CALPHA can aid initial phasing of data by molecular replacement procedures.
The Calpha positions for a protein can provide a scaffold for the reconstruction of more complete models. Reconstructions can be by manual rebuilding, from geometric solutions to the constraints on main-chain torsion angles or from databases of known protein structures. The last method is usually the most convenient and reliable. This paper describes a database reconstruction program, CALPHA, and assesses its accuracy and reliability by test reconstructions of well refined structures. Typically, backbone atoms are repositioned to within 0.3 A of their original positions. This corresponds to regenerating main-chain torsion angles to within 15 degrees. Uses of CALPHA for automating refinement procedures are discussed. In particular, the uses of Calpha-only and rcconstructed polyalanine models of HIV-1 reverse transcriptase for cross-rotation and translation function searches are compared. The CALPHA polyalanine model is found to provide more selectivity for approximately correct orientations. The effect on the translation function is dependent on the resolution shell employed. It is expected that these observations will be applicable in other cases.


Human epidermal growth factor receptor 2 status modulates subcellular localization of and interaction with estrogen receptor alpha in breast cancer cells.
Approximately two-thirds of breast cancer patients respond to endocrine therapy, and this population of patients is estrogen receptor (ER) positive. However, a significant proportion of patients do not respond to hormone therapy. ER hormone responsiveness is widely believed to be influenced by enhanced cross-talk of ER with overexpressed human epidermal growth factor receptor 2 (HER2), and a subgroup of ER-positive tumors coexpress high HER2. Breast cancer cells with or without HER2 overexpression were analyzed for ER status, subcellular localization, and interactions with HER2 signaling components by biochemical and immunological methods. Experiments explored the regulatory interactions between the HER2 and ER pathways and the sensitivity of breast cancer cells to tamoxifen. Stable or transient or natural HER2 overexpression in ER-positive breast cancer cells promoted the nucleus-to-cytoplasm relocalization of ER, enhanced interactions of ER with HER2, inhibited ER transactivation function, and induced resistance to tamoxifen-mediated growth inhibition of breast cancer cells. In addition, HER2 up-regulation resulted in ER interaction with Sos, a component of Ras signaling, and hyperstimulation of the mitogen-activated protein kinase extracellular signal-regulated kinase 1/2 (ERK1/2). Conversely, down-regulation of HER2 by the anti-HER2 monoclonal antibody Herceptin led to suppression of ERK1/2 stimulation, restoration of ER to the nucleus, and potentiation of the growth-inhibitory action of tamoxifen. The results presented here show for the first time that ER redistribution to the cytoplasm and its interaction with HER2 are important downstream effects of HER2 overexpression, that ERK1/2 is important for ER cytoplasmic localization, and that subcellular localization of ER may play a mechanistic role in determining the responsiveness of breast cancer cells to tamoxifen.


Prolonged SARS-CoV-2 detection and reversed RT-PCR results in mild or asymptomatic patients.
The clinical course and viral detection period in mild or asymptomatic coronavirus disease 2019 (COVID-19) patients are not yet known. The presumed low diagnostic sensitivity of upper respiratory specimens for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) makes it difficult to confirm infection and recommend de-isolation. We retrospectively reviewed real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test results of mild or asymptomatic COVID-19 patients who were admitted at the Daegu-Gyeongbuk 7th community treatment centre in Korea between 9 March 2020 and 10 April 2020. Patients underwent an upper respiratory RT-PCR test every week until discharge. From the RT-PCR results, we evaluated the rate of prolonged (>3 weeks) SARS-CoV-2 RNA positivity. We analysed the proportion of reversed results, defined as a positive or indeterminate result one day after a negative RT-PCR result, according to time (<14, 15-21, 22-28, >28 days) from the initial positive RT-PCR result. In 23% (69/300) of patients, SARS-CoV-2 was detected more than 3 weeks after the initial positive RT-PCR. In 14% (42/300) of patients, the RT-PCR results were positive for more than 4 weeks. For 37.5% (152/405) of negative RT-PCR results, the results were reversed in the next day's test. And 43.5% (123/283) of negative RT-PCR results were reversed within 3 weeks of diagnosis. The detection of SARS-CoV-2 lasting more than 3 weeks was common in mild or asymptomatic patients. Upper respiratory RT-PCR results were frequently reversed from negative to positive.


Trends in Mortality Due to Cancer in the United States by Age and County-Level Income, 1999-2015.
Disparities in cancer mortality by county-level income have increased. It is unclear whether these widening disparities have affected older and younger adults equally. National death certificate data were utilized to ascertain cancer deaths during 1999-2015. Average annual percent changes in mortality rates and mortality rate ratios (RRs) were estimated by county-level income quintile and age (25-64 vs ≥65 years). Among 25- to 64-year-olds, cancer mortality rates were 30% higher (RR = 1.30, 95% confidence interval [CI] = 1.29 to 1.31) in the lowest-vs the highest-income counties in 1999-2001 and 56% higher (RR = 1.56, 95% CI = 1.55 to 1.57) in 2013-2015; the disparities among those 65 years and older were smaller but also widened over time (RR1999-2001 = 1.04, 95% CI = 1.03 to 1.05; RR2013-2015 = 1.14, 95% CI = 1.13 to 1.14). Widening disparities occurred across cancer sites. If all counties had the mortality rates of the highest-income counties, 21.5% of cancer deaths among 25- to 64-year-olds and 7.3% of cancer deaths in those 65 years and older would have been avoided in 2015. These results highlight an ongoing need for equity-focused interventions, particularly among younger adults.


DipA, a pore-forming protein in the outer membrane of Lyme disease spirochetes exhibits specificity for the permeation of dicarboxylates.
Lyme disease Borreliae are highly dependent on the uptake of nutrients provided by their hosts. Our study describes the identification of a 36 kDa protein that functions as putative dicarboxylate-specific porin in the outer membrane of Lyme disease Borrelia. The protein was purified by hydroxyapatite chromatography from Borrelia burgdorferi B31 and designated as DipA, for dicarboxylate-specific porin A. DipA was partially sequenced, and corresponding genes were identified in the genomes of B. burgdorferi B31, Borrelia garinii PBi and Borrelia afzelii PKo. DipA exhibits high homology to the Oms38 porins of relapsing fever Borreliae. B. burgdorferi DipA was characterized using the black lipid bilayer assay. The protein has a single-channel conductance of 50 pS in 1 M KCl, is slightly selective for anions with a permeability ratio for cations over anions of 0.57 in KCl and is not voltage-dependent. The channel could be partly blocked by different di- and tricarboxylic anions. Particular high stability constants up to about 28,000 l/mol (in 0.1 M KCl) were obtained among the 11 tested anions for oxaloacetate, 2-oxoglutarate and citrate. The results imply that DipA forms a porin specific for dicarboxylates which may play an important role for the uptake of specific nutrients in different Borrelia species.


Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions.
Chromosomal microarray analysis (CMA) is recognized as the first-tier test in the genetic evaluation of children with developmental delays, intellectual disabilities, congenital anomalies and autism spectrum disorders of unknown etiology. To optimize detection of clinically relevant copy number variants associated with these conditions, we designed a whole-genome microarray, FirstStepDx PLUS (FSDX). A set of 88,435 custom probes was added to the Affymetrix CytoScanHD platform targeting genomic regions strongly associated with these conditions. This combination of 2,784,985 total probes results in the highest probe coverage and clinical yield for these disorders. Clinical testing of this patient population is validated on DNA from either non-invasive buccal swabs or traditional blood samples. In this report we provide data demonstrating the analytic and clinical validity of FSDX and provide an overview of results from the first 7,570 consecutive patients tested clinically. We further demonstrate that buccal sampling is an effective method of obtaining DNA samples, which may provide improved results compared to traditional blood sampling for patients with neurodevelopmental disorders who exhibit somatic mosaicism.


Effect of auranofin on cytokine induced secretion of granule proteins from adherent human neutrophils in vitro.
The effect of auranofin on granule protein secretion from neutrophils was investigated by a haemolytic plaque assay which can detect release of lactoferrin and myeloperoxidase from single adherent neutrophils. Lactoferrin secretion in response to N-formyl-methionyl-leucyl-phenylalanine (fMLP) was enhanced at low (0.25-1.0 micrograms/ml) and inhibited at high concentrations of auranofin (50% inhibition (IC50) at 3.7 micrograms/ml). A similar biphasic effect was also seen on degranulation mediated by granulocyte-macrophage colony stimulating factor (GM-CSF) (IC50 1.8 micrograms/ml). In contrast, exocytosis mediated by tumour necrosis factor was inhibited even at low concentrations of auranofin (IC50 0.6 micrograms/ml). Secretion induced by phorbol 12-myristate 13-acetate and A23187 was only inhibited at very high auranofin concentrations (IC50 10 and 8 micrograms/ml respectively). The effect of auranofin on myeloperoxidase secretion was also assessed and the IC50 values for the respective agents were as follows: tumour necrosis factor 0.7 micrograms/ml, fMLP 1.6 micrograms/ml, and phorbol myristate acetate 7.6 micrograms/ml. When neutrophils were preincubated with auranofin (4 micrograms/ml) and then exposed to fMLP, tumour necrosis factor, or GM-CSF in the absence of auranofin, lactoferrin release was enhanced if the preincubation time was short (one to three minutes) and inhibited when the time of preincubation was longer. It was concluded that auranofin, at concentrations achieved in the serum of patients, is a potent inhibitor of cytokine induced release of granule proteins from adherent neutrophils. This finding may be of clinical importance and shed light on the mechanism by which auranofin acts in rheumatoid arthritis.


A 12-Lead ECG-Based System With Physiological Parameters and Machine Learning to Identify Right Ventricular Hypertrophy in Young Adults.
The presence of right ventricular hypertrophy (RVH) accounts for approximately 5-10% in young adults. The sensitivity estimated by commonly used 12-lead electrocardiographic (ECG) criteria for identifying the presence of RVH is under 20% in the general population. The aim of this study is to develop a 12-lead ECG system with the related information of age, body height and body weight via machine learning to increase the sensitivity and the precision for detecting RVH. In a sample of 1,701 males, aged 17-45 years, support vector machine is used for the training of 31 parameters including age, body height and body weight in addition to 28 ECG data such as axes, intervals and wave voltages as the inputs to link the output RVH. The RVH is defined on the echocardiographic finding for young males as right ventricular anterior wall thickness > 5.5 mm. On the system goal for increasing sensitivity, the specificity is controlled around 70-75% and all data tested in the proposed method show competent sensitivity up to 70.3%. The values of area under curve of receiver operating characteristic curve and precision-recall curve using the proposed method are 0.780 and 0.285, respectively, which are better than 0.518 and 0.112 using the Sokolow-Lyon voltage criterion, respectively, for detecting unspecific RVH. We present a method using simple physiological parameters with ECG data to effectively identify more than 70% of the RVH among young adults. Clinical Impact: This system provides a fast, precise and feasible diagnosis tool to screen RVH.


Immune responses and protection induced by mucosal and systemic immunisation with recombinant measles nucleoprotein in a mouse model of measles virus-induced encephalitis.
In this study the immunogenicity of recombinant nucleoprotein (Np) administered intranasally or intraperitoneally, and its ability to support a systemic protective anti-virus antibody response was examined, in a mouse model of measles virus (MV)-induced encephalitis. Although both intranasal and intraperitoneal routes of immunisation resulted in priming Np- and MV-specific T-cell responses, the intraperitoneal route was shown to prime for a predominantly IgG2a serum anti-MV antibody response of high avidity, which confered complete protection following intracranial challenge with a neuroadapted strain of MV. On the other hand, intranasal priming resulted in a mixed IgG1, IgG2a serum anti-MV antibody response of low avidity, and only 43% of immunised mice survived following intracranial challenge with the neuroadapted strain of MV. These findings suggest that the route of immunisation in combination with an appropriate adjuvant could influence the induction of a quality antibody response with protective capacity.


Prom1 function in development, intestinal inflammation, and intestinal tumorigenesis.
Prom1/CD133 has been identified in colorectal, hepatocellular, and pancreatic cancer as a cancer stem cell marker and has been used as such to predict colon cancer recurrence in humans. Its potential molecular function as well as its role as a marker of intestinal regeneration is still not fully known. We evaluated the role of Prom1 in intestinal regeneration in inflammatory bowel disease (IBD), determined the function of Prom1, and characterized the effect of a lack of Prom1 on intestinal tumor formation in animal models. Our results suggest that Apc mutations lead to an increase in Prom1 expressing cells in the intestinal crypt stem cell compartment and in early intestinal adenomas. Also, Prom1 knockout mice are more susceptible to intestinal tumor formation. We conclude that Prom1 likely plays a role in regulating intestinal homeostasis and that these results clearly illustrate the role of Prom1 in intestinal regeneration. We further conclude that Prom1 may provide a novel therapeutic target for patients with gastrointestinal conditions such as IBD, short bowel syndrome, and colorectal cancer.


Missing Food, Missing Data? A Critical Review of Global Food Losses and Food Waste Data.
Food losses and food waste (FLW) have become a global concern in recent years and emerge as a priority in the global and national political agenda (e.g., with Target 12.3 in the new United Nations Sustainable Development Goals). A good understanding of the availability and quality of global FLW data is a prerequisite for tracking progress on reduction targets, analyzing environmental impacts, and exploring mitigation strategies for FLW. There has been a growing body of literature on FLW quantification in the past years; however, significant challenges remain, such as data inconsistency and a narrow temporal, geographical, and food supply chain coverage. In this paper, we examined 202 publications which reported FLW data for 84 countries and 52 individual years from 1933 to 2014. We found that most existing publications are conducted for a few industrialized countries (e.g., the United Kingdom and the United States), and over half of them are based only on secondary data, which signals high uncertainties in the existing global FLW database. Despite these uncertainties, existing data indicate that per-capita food waste in the household increases with an increase of per-capita GDP. We believe that more consistent, in-depth, and primary-data-based studies, especially for emerging economies, are badly needed to better inform relevant policy on FLW reduction and environmental impacts mitigation.


Using HIV-attributable mortality to assess the impact of antiretroviral therapy on adult mortality in rural Tanzania.
The Tanzanian national HIV care and treatment programme has provided free antiretroviral therapy (ART) to HIV-positive persons since 2004. ART has been available to participants of the Kisesa open cohort study since 2005, but data to 2007 showed a slow uptake of ART and a modest impact on mortality. Additional data from the 2010 HIV serological survey provide an opportunity to update the estimated impact of ART in this setting. The Kisesa Health and Demographic Surveillance Site (HDSS) has collected HIV serological data and demographic data, including verbal autopsy (VA) interviews since 1994. Serological data to the end of 2010 were used to make two estimates of HIV-attributable mortality, the first among HIV positives using the difference in mortality between HIV positives and HIV negatives, and the second in the population using the difference between the observed mortality rate in the whole population and the mortality rate among the HIV negatives. Four time periods (1994-1999, 2000-2004, 2005-2007, and 2008-2010) were used and HIV-attributable mortality estimates were analysed in detail for trends over time. A computer algorithm, InterVA-4, was applied to VA data to estimate the HIV-attributable mortality for the population, and this was compared to the estimates from the serological survey data. Among HIV-positive adults aged 45-59 years, high mortality rates were observed across all time periods in both males and females. In HIV-positive men, the HIV-attributable mortality was 91.6% (95% confidence interval (CI): 84.6%-95.3%) in 2000-2004 and 86.3% (95% CI: 71.1%-93.3%) in 2008-2010, while among women, the HIV-attributable mortality was 87.8% (95% CI: 71.1%-94.3%) in 2000-2004 and 85.8% (95% CI: 59.6%-94.4%) in 2008-2010. In the whole population, using the serological data, the HIV-attributable mortality among men aged 30-44 years decreased from 57.2% (95% CI: 46.9%-65.3%) in 2000-2004 to 36.5% (95% CI: 18.8%-50.1%) in 2008-2010, while among women the corresponding decrease was from 57.3% (95% CI: 49.7%-63.6%) to 38.7% (95% CI: 27.4%-48.2%). The HIV-attributable mortality in the population using estimates from the InterVA model was lower than that from HIV sero-status data in the period prior to ART, but slightly higher once ART became available. In the Kisesa HDSS, ART availability corresponds with a decline in adult overall mortality, although not as large as expected. Using InterVA to estimate HIV-attributable mortality showed smaller changes in HIV-related mortality following ART availability than the serological results.


Cardiovascular disease in autoimmune rheumatic diseases.
Various autoimmune rheumatic diseases (ARDs), including rheumatoid arthritis, spondyloarthritis, vasculitis and systemic lupus erythematosus, are associated with premature atherosclerosis. However, premature atherosclerosis has not been uniformly observed in systemic sclerosis. Furthermore, although experimental models of atherosclerosis support the role of antiphospholipid antibodies in atherosclerosis, there is no clear evidence of premature atherosclerosis in antiphospholipid syndrome (APA). Ischemic events in APA are more likely to be caused by pro-thrombotic state than by enhanced atherosclerosis. Cardiovascular disease (CVD) in ARDs is caused by traditional and non-traditional risk factors. Besides other factors, inflammation and immunologic abnormalities, the quantity and quality of lipoproteins, hypertension, insulin resistance/hyperglycemia, obesity and underweight, presence of platelets bearing complement protein C4d, reduced number and function of endothelial progenitor cells, apoptosis of endothelial cells, epigenetic mechanisms, renal disease, periodontal disease, depression, hyperuricemia, hypothyroidism, sleep apnea and vitamin D deficiency may contribute to the premature CVD. Although most research has focused on systemic inflammation, vascular inflammation may play a crucial role in the premature CVD in ARDs. It may be involved in the development and destabilization of both atherosclerotic lesions and of aortic aneurysms (a known complication of ARDs). Inflammation in subintimal vascular and perivascular layers appears to frequently occur in CVD, with a higher frequency in ARD than in non-ARD patients. It is possible that this inflammation is caused by infections and/or autoimmunity, which might have consequences for treatment. Importantly, drugs targeting immunologic factors participating in the subintimal inflammation (e.g., T- and B-cells) might have a protective effect on CVD. Interestingly, vasa vasorum and cardiovascular adipose tissue may play an important role in atherogenesis. Inflammation and complement depositions in the vessel wall are likely to contribute to vascular stiffness. Based on biopsy findings, also inflammation in the myocardium and small vessels may contribute to premature CVD in ARDs (cardiac ischemia and heart failure). There is an enormous need for an improved CVD prevention in ARDs. Studies examining the effect of DMARDs/biologics on vascular inflammation and CV risk are warranted.


Effects of oregano essential oil on brain TLR4 and TLR2 gene expression and depressive-like behavior in a rat model.
The aim of the present study was to evaluate the effects of oregano essential oil (OEO) on the hippocampus and prefrontal cortex TLR 2/4 gene expression and depressive like behavior induced by chronic unpredictable stress (CUS). Sucrose preference and forced swim tests were adopted to examine the antidepressant effect. Control (CON), OEO, CUS, and CUS + OEO groups were used. The OEO and CUS + OEO groups received OEO (0.2 mL/kg, i.p.), CON and CUS received saline (0.2 mL/kg, i.p.), and the positive drug groups of CUS rats received fluoxetine (10 mg/kg) and diazepam (3 mg/kg) once daily for 14 days. The expression of TLR 2/4 was determined using real time quantitative polymerase chain reaction with the SYBR green reporter dye. The compositions of the OEO were determined by gas chromatography-mass spectroscopy. The main constituents were thymol (20.72%), gamma-terpinene (8.83%), borneol (8.72%), cymene (6.83%), carvacrol (6.274%), alfa-terpinene (5.26%), and sabinene (4.92%). Administration of OEO significantly alleviated the depressive symptoms of CUS. A higher level of TLR2/4 mRNA was seen in the brain of CUS group (P < 0.05). The CUS-induced increases in the TLR2/4 levels were not reversed by OEO. According to the present study OEO may have the antidepressant-like activity but have no effect on the stress-induced TLR-2/4 upregulation.


Association between type 2 diabetes mellitus and anthropometric measurements - a case control study in South India.
Obesity is a major risk factor for type 2 diabetes mellitus (T2DM). Clinical evidence indicates a stronger association of diabetes with central obesity than general obesity. The present study aimed to compare the association between type 2 diabetes mellitus and different anthropometric measurements and evaluate the usefulness of these measurements in clinical practice. A case-control study was done among 102 individuals; of whom 51 cases included diagnosed T2DM (≥ 20 years age) patients attending the Medicine out-patient consultation of a tertiary care hospital and 51 controls who were screen negative for T2DM and recruited from the local community. Various anthropometric measurements were used according to standard World Health Organization (WHO) protocols. Data was entered and analyzed using Statistical Package for Social Sciences (SPSS) version 15. The proportion of cases with Body Mass Index (BMI) ≥ 25 kg/m2 was 55% as compared to 22% of controls and this association was statistically significant (p < 0.05). The proportion of cases with high waist circumference cut-offs (WC) was 74.5% as compared to 45.1% healthy individuals and this association was also statistically significant (p < 0.05, OR = 3.56). A Receiver Operating Characteristic (ROC) curve for both gender revealed highest area under the curve for body mass index (area = 0.787). Body mass index had the best discriminatory power. Waist to hip ratio was not a sensitive marker especially for females. A strong association between obesity indices and diabetes was identified. BMI and WC could be used in clinical practice for suggesting life style modifications.


Voltage-dependent conductance changes in the store-operated Ca2+ current ICRAC in rat basophilic leukaemia cells.
Tight-seal whole-cell patch-clamp experiments were carried out in order to investigate the effects of different holding potentials on the rate of development and amplitude of the Ca2+ release-activated Ca2+ current ICRAC in rat basophilic leukaemia (RBL-1) cells. ICRAC was monitored at -80 mV from fast voltage ramps, spanning 200 mV in 50 ms. At hyperpolarised potentials, the macroscopic CRAC conductance was lower than that seen at depolarised potentials. The conductance increased almost 5-fold over the voltage range -60 to +40 mV and was seen when the stores were depleted either by the combination of IP3 and thapsigargin in high Ca2+ buffer, or passively with 10 mM EGTA or BAPTA. The voltage-dependent conductance of the CRAC channels could not be fully accounted for by Ca2+-dependent fast inactivation, nor by other slower inhibitory mechanisms. It also did not seem to involve intracellular Mg2+ or the polycations spermine and spermidine. Voltage step relaxation experiments revealed that the voltage-dependent conductance changes developed and reversed slowly, with a time constant of several seconds at -60 mV. In the presence of physiological levels of intracellular Ca2+ buffers, ICRAC was barely detectable when cells were clamped at -60 mV and dialysed with IP3 and thapsigargin, but at 0 mV the current in low Ca2+ buffer was as large as that seen in high Ca2+ buffer. Our results suggest that CRAC channels exhibit slow voltage-dependent conductance changes which can triple the current amplitude over the physiological range of voltages normally encountered by these cells. The role of this conductance change and possible underlying mechanisms are discussed.


Infant death in San Francisco 1989-1990.
This paper examines all of the unexplained and violent deaths of children less than one year of age in the City and County of San Francisco during the years 1989-1990. A total of 62 cases were collected and analyzed retrospectively. Among the cases we examined, 34 deaths were determined as SIDS, while seven were moded as accidents and two as homicides. The deaths were examined with respect to the following parameters: sex, race, age, height and weight, cause and manner of death, significant autopsy and microscopic findings; circumstances of death including place, the person discovering or reporting the death, the presence of siblings or previous child death in the family and previous illness in the same child. A particular stress is given to the definition and diagnosis of SIDS, according to the international literature, and to the criteria adopted to distinguish SIDS cases from accidents and homicides. A review of both the American and European literature shows that most articles do not include comparisons of data from both the autopsy and the scene. Additionally there is little standardization in the investigation and the extent of postmortem examinations performed. An international standardization of these methods appears necessary and the use of protocols to assure complete investigation and postmortem examination will allow more intensive evaluation of data. Here we give a brief presentation of the necropsy protocol for Sudden Unexpected Infant Death recently written and approved by the California Department of Health Services and used in the Chief Medical Examiner's Office in San Francisco.


The Genomedata format for storing large-scale functional genomics data.
We present a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format. We show that retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. Reference implementation in Python and C components available at http://noble.gs.washington.edu/proj/genomedata/ under the GNU General Public License.


A computational framework for cortical microtubule dynamics in realistically shaped plant cells.
Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to two dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, cell-edge induced catastrophes and cell-face induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells of Arabidopsis thaliana, Nicotiana benthamiana and Hedera helix. We show that our simulations can predict multiple features of the microtubule array structure in these cells, revealing, among others, strong constraints on the orientation of division planes.


Communication support through multimodal supplementation: a scoping review.
Speech supplementation strategies improve spoken communication for people with motor speech disorders who experience reduced speech intelligibility. The purpose of this review was to summarize the literature on traditional supplementation strategies (e.g., alphabet supplementation, topic supplementation, and gestural supplementation) and to expand the definition of speech supplementation to include additional modalities, such as augmenting speech with pictures via mobile technology, and conversation management strategies. Results showed that studies of traditional supplementation consistently reported positive outcomes, including increased intelligibility, decreased speech rate, and positive attitudes toward speakers. New modalities, such as supplementing speech through digital photos, may come to be integrated with traditional approaches, given the proliferation of digital photography and mobile tablet technologies. In addition, new research is exploring the role of communication partners in dyads where one speaker has dysarthria, as well as strategies that communication partners employ to understand dysarthric speech.


Enteral fish oil supplementation in the resolution of parenteral nutrition associated cholestasis.
To analyze safety, tolerance and efficacy of enteral omega-3 fatty acids (FAs) in the resolution of Parenteral Nutrition Associated Cholestasis (PNAC) and postnatal growth among preterm neonates. This is a single center retrospective case-control study of all neonates born less than 32 weeks of gestation and developed PNAC (Direct bilirubin >2 mg/dl). Infants who received enteral omega-3 FAs supplementation (1 g/Kg/d) served as cases and were compared with gestational age, gender and direct bilirubin level matched controls who did not receive enteral omega-3 FAs supplementation. A total of 48 infants were analyzed, 24 who received enteral omega-3 fatty acids were matched with 24 controls. The omega-3 FAs and control groups were similar in gestational age (weeks) and birth weight (gram). Overall there were no differences between the two groups in infants' demographics or clinical characteristics including risk factors for the development of PNAC. Infants who received enteral omega-3 FAs had significantly fewer days of cholestasis (p = 0.025) and a higher average daily weight gain (grams/day) (p = 0.011) than their controls. In a linear regression analysis with days of cholestasis as the dependent variable and Ursodeoxycholic acid (UDCA) and Omega-3 FAs as independent variables, enteral omega-3 FAs remained associated with a shorter duration of cholestasis, p < 0.001. Enteral fish oil is inexpensive, safe & well tolerated in preterm neonates with no contraindications to enteral feeding. Enteral omega-3 FAs are easy to administer and help in rapid resolution of PNAC while promoting postnatal weight gain in preterm infants.


Novel modification of tracheostomy tube to allow speech and manage tracheal stenosis.
Mid-tracheal, postintubation stenosis can be managed with an extended length tracheostomy tube to bypass the stenotic area. However these extra-long tracheostomy tubes are not fenestrated, and when the stenotic tracheal lumen sits against the tracheostomy tube, phonation is not possible as there is no translaryngeal airflow. A 59-year-old man developed distal tracheal stenosis following a prolonged intubation and tracheostomy after a motorcycle accident. He eventually required an extra-long tracheostomy tube to bypass the stenotic region. We modified a silicone tracheostomy tube by creating a fenestration on its posterior wall. This relieved the obstruction while still allowing phonation and speech.


Prediction of global left ventricular functional recovery in patients with heart failure undergoing surgical revascularisation, based on late gadolinium enhancement cardiovascular magnetic resonance.
The new gold standard for myocardial viability assessment is late gadolinium enhancement-cardiovascular magnetic resonance (LGE-CMR); this technique has demonstrated that the transmural extent of scar predicts segmental functional recovery. We now asked how the number of viable and number of viable+normal, segments predicted recovery of global left ventricular (LV) function in patients undergoing CABG. Finally, we examined which segmental transmural threshold of scarring best predicted global LV recovery. Fifty patients with reduced LV ejection fraction (EF) referred for CABG were recruited, and 33 included in this analysis. Patients underwent CMR to assess LV function and viability pre-operatively at 6 days and 6 months. Mean LVEF 38% ± 11, which improved to 43% ± 12 after surgery. 21/33 patients improved EF by ≥3% (EF before 38% ± 13, after 47% ± 13), 12/33 did not (EF before 39% ± 6, after 37% ± 8). The only independent predictor for global functional recovery after revascularisation was the number of viable+normal segments: Based on a segmental transmural viability cutoff of <50%, ROC analysis demonstrated ≥10 viable+normal segments predicted ≥3% improvement in LVEF with a sensitivity of 95% and specificity of 75% (AUC = 0.9, p < 0.001). Transmural viability cutoffs of <25 and <75% and a cutoff of ≥4 viable segments were less useful predictors of global LV recovery. Based on a 50% transmural viability cutoff, patients with ≥10 viable+normal segments improve global LV function post revascularisation, while patients with fewer such segments do not. LGE-CMR is a simple and powerful tool for identifying which patients with impaired LV function will benefit from CABG. Research Ethics Committee Unique Identifier: NRES:05/Q1603/42. The study is listed on the Current Controlled Trials Registry: ISRCTN41388968.URL: http://www.controlled-trials.com.


Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples.
High-throughput sequencing furnishes a large number of short sequence reads from uncloned DNA and has rapidly become a major tool for identifying viruses in biological samples, and in particular when the target sequence is undefined. In this study, we assessed the analytical sensitivity of a pipeline for detection of viruses in biological samples based on either the Roche-454 genome sequencer or Illumina genome analyzer platforms. We sequenced biological samples artificially spiked with a wide range of viruses with genomes composed of single or double-stranded DNA or RNA, including linear or circular single-stranded DNA. Viruses were added at a very low concentration most often corresponding to 3 or 0.8 times the validated level of detection of quantitative reverse transcriptase PCRs (RT-PCRs). For the viruses represented, or resembling those represented, in public nucleotide sequence databases, we show that the higher output of Illumina is associated with a much greater sensitivity, approaching that of optimized quantitative (RT-)PCRs. In this blind study, identification of viruses was achieved without incorrect identification. Nevertheless, at these low concentrations, the number of reads generated by the Illumina platform was too small to facilitate assembly of contigs without the use of a reference sequence, thus precluding detection of unknown viruses. When the virus load was sufficiently high, de novo assembly permitted the generation of long contigs corresponding to nearly full-length genomes and thus should facilitate the identification of novel viruses.