Non-parametric estimation of the case fatality ratio with competing risks data: an application to Severe Acute Respiratory Syndrome (SARS).
For diseases with some level of associated mortality, the case fatality ratio measures the proportion of diseased individuals who die from the disease. In principle, it is straightforward to estimate this quantity from individual follow-up data that provides times from onset to death or recovery. In particular, in a competing risks context, the case fatality ratio is defined by the limiting value of the sub-distribution function, F(1)(t) = Pr(T <or=t and J = 1), associated with death, as t --> infinity, where T denotes the time from onset to death (J = 1) or recovery (J = 2). When censoring is present, however, estimation of F(1)(infinity) is complicated by the possibility of little information regarding the right tail of F(1), requiring use of estimators of F(1)(t(*)) or F(1)(t(*))/(F(1)(t(*))+F(2)(t(*))) where t(*) is large, with F(2)(t) = Pr(T <or=t and J = 2) being the analogous sub-distribution function associated with recovery. With right censored data, the variability of such estimators increases as t(*) increases, suggesting the possibility of using estimators at lower values of t(*) where bias may be increased but overall mean squared error be smaller. These issues are investigated here for non-parametric estimators of F(1) and F(2). The ideas are illustrated on case fatality data for individuals infected with Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003.


Diagnosing major depression in medical outpatients: acceptability of telephone interviews.
To assess the acceptability to patients of a diagnostic interview for depression (Structured Clinical Interview for DSM-IV; SCID) conducted over the telephone to their homes. Postal questionnaire survey of patients who had attended an oncology outpatient clinic where they had scored high on a screening questionnaire and had subsequently undergone an SCID interview over the telephone. Of the 224 patients telephoned, five refused the diagnostic interview. Of the 219 who were interviewed, 184 satisfactorily completed and returned the postal questionnaire (84% response rate). Only 17% reported the interview to be distressing. Ninety-four percent of all questionnaire respondents and 84% (n=31) of those who reported the interview to have been distressing endorsed the item "Had I known in advance what answering the questions would have been like for me, I would still have agreed to take part". Perceiving the interview as distressing was associated with having major depression (P<.001). Forty-seven percent said that, given the choice, they would have preferred a face-to-face interview. Telephone-administered diagnostic interviews are acceptable to most cancer patients and may even be preferred to face-to-face interviews at the hospital. This finding, together with the existing evidence of its validity, should encourage the use of telephone diagnostic interviews for depression, particularly when face-to-face interviews are impracticable, in both research studies and clinical practice. Indeed, a substantial proportion of patients may actually prefer them.


Biomarkers in acutely decompensated heart failure with preserved or reduced ejection fraction.
Acute decompensated heart failure (ADHF) occurs with preserved (heart failure with preserved ejection fraction [HFpEF] ≥50%) or reduced (heart failure with reduced ejection fraction [HFrEF] <50%) ejection fraction. Natriuretic peptide (NP) levels are lower in HFpEF than HFrEF. We hypothesized that lower NP levels in HFpEF may be associated with other differences in biomarkers, specifically, renin-angiotensin-aldosterone system (RAAS) activation, oxidative stress, and a biomarker that reflects collagen synthesis. In this prespecified ancillary analysis of patients with ADHF enrolled in the Diuretic Optimization Strategies Evaluation study, clinical features and N-terminal pro-B-type NP, cystatin C, plasma renin activity, aldosterone, oxidative stress (uric acid), and procollagen type III N-terminal peptide were compared in HFpEF and HFrEF at enrollment and 60-day follow-up. Compared with HFrEF (n = 219), HFpEF (n = 81) patients were older, heavier, more commonly female, less treated with RAAS antagonists, but with similar New York Heart Association class, jugular venous pressure, and edema severity. N-terminal pro-B-type NP was lower, and systolic blood pressure and cystatin C were higher in HFpEF. Despite higher systolic blood pressure and less RAAS antagonist use in HFpEF, plasma renin activity and aldosterone levels were similar in HFpEF and HFrEF as were uric acid and procollagen type III N-terminal peptide levels. Changes in biomarker levels from enrollment to 60 days were similar between HFrEF (n = 149) and HFpEF (n = 50). Lower NP levels in decompensated HFpEF occur in association with similar ADHF severity, more impaired vascular and renal function but similar elevation of biomarkers that reflect RAAS activation, oxidative stress, and collagen synthesis as in HFrEF.


Balance diagnostics for comparing the distribution of baseline covariates between treatment groups in propensity-score matched samples.
The propensity score is a subject's probability of treatment, conditional on observed baseline covariates. Conditional on the true propensity score, treated and untreated subjects have similar distributions of observed baseline covariates. Propensity-score matching is a popular method of using the propensity score in the medical literature. Using this approach, matched sets of treated and untreated subjects with similar values of the propensity score are formed. Inferences about treatment effect made using propensity-score matching are valid only if, in the matched sample, treated and untreated subjects have similar distributions of measured baseline covariates. In this paper we discuss the following methods for assessing whether the propensity score model has been correctly specified: comparing means and prevalences of baseline characteristics using standardized differences; ratios comparing the variance of continuous covariates between treated and untreated subjects; comparison of higher order moments and interactions; five-number summaries; and graphical methods such as quantile-quantile plots, side-by-side boxplots, and non-parametric density plots for comparing the distribution of baseline covariates between treatment groups. We describe methods to determine the sampling distribution of the standardized difference when the true standardized difference is equal to zero, thereby allowing one to determine the range of standardized differences that are plausible with the propensity score model having been correctly specified. We highlight the limitations of some previously used methods for assessing the adequacy of the specification of the propensity-score model. In particular, methods based on comparing the distribution of the estimated propensity score between treated and untreated subjects are uninformative.


Efficacy and Safety of Tamsulosin in the Medical Expulsion Therapy for Distal Ureteral Calculi: A Systematic Review and Meta-Analysis of Placebo-Controlled Trials.
Tamsulosin, a medical expulsive therapy (MET), was always recommended for patients with distal ure-teral calculi less than 10 mm. The aim of the systematic review was to assess the efficacy and safety of tamsulosin in MET compared with placebo. A comprehensive search was conducted in the databases PubMed, EMBASE and Web of Science for relevant articles, covering all the literatures published until April 2018. All placebo controlled trails were identified in which patients were randomized to receive either tamsulosin or placebo for distal ureteral calculi. A total of seven placebo controlled studies including 4135 patients met the inclusion criteria and were involved in the review. We found that tamsulosin was associated with a significantly higher expulsion rate (ESR) [odds ratio (OR) = 1.10, 95% confidence interval (CI) = 1.00-1.21] than placebo in patients with distal ureteral stones less than 7 mm. The ESR ranged from 67.0%-90.7%. But the significant difference was better seen in pa-tients with distal ureteral stones less than 10 mm (OR = 1.11, 95% CI = 1.01-1.21). Even though tamsulosin has a higher incidence of retrograde ejaculation than placebo, no significant difference was observed in the incidence of other adverse events. The results of the current meta-analysis indicated that tamsulosin was superior to placebo in its effi-cacy for distal ureteral stones though retrograde ejaculation was worse with tamsulosin use. It should be a safe and effective medical expulsive therapy choice for distal ureteral stones when stone sizes are less than 10 mm.


Evaluating the management of septic shock using patient simulation.
Develop a scoring system that can assess the management of septic shock by individuals and teams. Retrospective review of videotapes of critical care house staff managing a standardized simulation of septic shock. Academic medical center; videotapes were made in a recreated intensive care unit environment using a high-fidelity patient simulator. Residents in medicine, surgery, and anesthesiology who had participated in the intensive care unit rotation. The septic patient was managed by the intensive care unit team in a graded manner with interns present for the first 10 mins and more senior-level help arriving after 10 mins. The intern was graded separately for the first 10 mins, and the team was graded for the entire 35-min performance. Both technical and nontechnical scoring systems were developed to rate the management of septic shock. Technical scores are based on guidelines and principles of managing septic shock. Team leadership, communication, contingency planning, and resource utilization were addressed by the nontechnical rating. Technical scores were calculated for both interns and teams; nontechnical scores applied only to the team. Of 16 technical checklist items, interns completed a mean of 7 with a range of 1.5-11. Team technical ratings had a mean of 9.3 with a range of 3.3-13. Nontechnical scores showed similar intergroup variability with a mean of 26 and a range of 10-35. Technical and nontechnical scores showed a modest correlation (r = .40, p = .05). Interrater reliabilities for intern and team technical scores were both r = .96 and for nontechnical scores r = .88. Objective measures of both knowledge-based and behavioral skills pertinent to the management of septic shock were made. Scores identified both adequate and poor levels of performance. Such assessments can be used to benchmark clinical skills of individuals and groups over time and may allow the identification of interventions that improve clinical effectiveness in sepsis management.


Does treatment of hepatitis B virus (HBV) infection reduce hepatitis delta virus (HDV) replication in HIV-HBV-HDV-coinfected patients?
Hepatitis delta virus (HDV) has a unique replication process that requires coinfection with hepatitis B virus (HBV). Treatment is currently limited to interferon therapy. The role of potent nucleos(t)ide analogues active against HBV has not been well examined in chronic delta hepatitis (CDH). HIV-positive patients with CDH attending our hospital were identified and longitudinally studied. Serum HBV DNA, HDV RNA and HIV RNA, treatment regimens, and biochemical and serological markers were assessed at yearly intervals. Liver fibrosis was measured by transient elastography during the last 2 years. Sixteen patients were identified and treated with anti-HBV therapy (median time 6.1 years). The majority were male and previous intravenous drug users. Median baselines were: HDV RNA 7 log10 copies/ml, HIV RNA 1.7 log10 copies/ml, HBV DNA 1.1 log10 IU/ml and alanine aminotransferase (ALT) 98 IU/ml. A significant correlation was found between HDV RNA and HBV DNA (r=0.226, P=0.015), aspartate aminotransferase (r=0.430, P<0.0001), ALT (r=0.441, P<0.0001) and hepatitis B surface antigen (HBsAg) (r=0.557, P<0.0001). Overall, 13 patients showed a reduction in HDV viraemia and ALT levels, and three of them achieved undetectable HDV RNA and normal ALT levels. Patients undergoing successful anti-HBV therapy with potent nucleos(t)ide analogues seem to indirectly benefit from suppression of HDV replication, albeit not very efficiently. Hypothetically, a significant and sustained reduction in serum HDV RNA might only be seen when a reduction in HBV covalently closed circular DNA or HBV surface antigen is achieved, which may require long periods of successful anti-HBV therapy. To our knowledge, this is the first evidence of the benefit of potent anti-HBV nucleos(t)ide analogue therapy in CDH.


The human plasminogen activator inhibitor type I gene promoter targets to kidney.
The plasminogen activator inhibitor type 1 (PAI-1) gene encodes the physiological inhibitor of tissue-type and urokinase-type plasminogen activators and is induced by cytokines such as transforming growth factor-beta (TGF-beta). Studies have identified DNA sequence elements within the first 1.3 kb of the 5'-upstream DNA that mediate cytokine responsiveness in transfected cells in vitro. However, the DNA sequences that mediate PAI-1 expression in vivo have not yet been delineated. To define these regulatory sequences, we generated transgenic mice that expressed a hybrid gene comprising sequences between -1,272 and +75 of the human PAI-1 gene ligated to a LacZ reporter gene. Transgene expression detected in two independent lines was observed only in kidney from embryonic day 13 to adult and was seen primarily in proximal tubule cells of the outer medulla. Transgene expression and activity were unchanged in response to TGF-beta and remained restricted to kidney. Thus we have identified a promoter region within the PAI-1 gene that targets transgene expression to kidney but, unlike the native promoter, is unresponsive to TGF-beta in the experimental protocol used.


Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera.
Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo. We show that AmLAM is inhibited in vitro by swainsonine albeit at slightly higher concentrations than in other animals. Dietary exposure of growing larvae to swainsonine leads to pronounced metabolic changes affecting not only saccharides, but also amino acids, polyols and polyamines. Interestingly, the abundance of two fatty acids implicated in epigenetic regulation is significantly reduced in treated individuals. Additionally, swainsonie causes loco-like symptoms, increased mortality and a subtle decrease in the rate of larval growth resulting in a subsequent developmental delay in pupal metamorphosis. We consider our findings in the context of cellular LAM function, larval development, environmental toxicity and colony-level impacts. The observed developmental heterochrony in swainsonine-treated larvae with lower LAM activity offer a plausible explanation for the existence of epialleles with impaired LAM expression. Individuals carrying such epialleles provide an additional level of epigenetic diversity that could be beneficial for the functioning of a colony whereby more flexibility in timing of adult emergence might be useful for task allocation.


Analysis of transactivation capability and conformation of p53 temperature-dependent mutants and their reactivation by amifostine in yeast.
The p53 gene is often mutated during cancer development. Frequency and functional consequences of these mutations vary in different tumor types. We analysed conformation and temperature dependency of 23 partially inactivating temperature-dependent (td) p53 mutants derived from various human tumors in yeast. We found considerable differences in transactivation capabilities and discriminative character of various p53 mutants. No correlations in transactivation rates and conformations of the td p53 proteins were detected. Amifostine-induced p53 reactivation occurred only in 13 of 23 td mutants, and this effect was temperature dependent and responsive element specific. The most of the p53 mutations (10/13) reactivated by amifostine were located in the part of the p53 gene coding for hydrophobic beta-sandwich structure of the DNA-binding domain.


Optical coherence tomography under general anesthesia in a child with nystagmus.
To describe a method that permits optical coherence tomography scanning to be performed under general anesthesia. Observational case report. A 7-year-old child underwent optical coherence tomography scanning under general anesthesia. He was positioned prone, with the neck extended to enable vertical facial alignment on the scanner. An anti-Trendelenburg trend on the operating table minimized the degree of neck extension required. Intravenous fluids, modest ventilator airway pressures, and compression stockings were used to minimize perioperative hemodynamic disturbance and the potential for orthostatic hypotension associated with the anti-Trendelenburg trend. High-quality, diagnostically important optical coherence tomography scans were obtained. With appropriate patient positioning and anesthetic management, optical coherence tomography scanning can be performed on uncooperative adults and children under general anesthesia.


Dominance of 'Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge.
Heavy metal-contaminated, pH 6 mine water discharge created new streams and iron-rich terraces at a creek bank in a former uranium-mining area near Ronneburg, Germany. The transition from microoxic groundwater with ~5 mm Fe(II) to oxic surface water may provide a suitable habitat for microaerobic iron-oxidizing bacteria (FeOB). In this study, we investigated the potential contribution of these FeOB to iron oxidation and metal retention in this high-metal environment. We (i) identified and quantified FeOB in water and sediment at the outflow, terraces, and creek, (ii) studied the composition of biogenic iron oxides (Gallionella-like twisted stalks) with scanning and transmission electron microscopy (SEM, TEM) as well as confocal laser scanning microscopy (CLSM), and (iii) examined the metal distribution in sediments. Using quantitative PCR, a very high abundance of FeOB was demonstrated at all sites over a 6-month study period. Gallionella spp. clearly dominated the communities, accounting for up to 88% of Bacteria, with a minor contribution of other FeOB such as Sideroxydans spp. and 'Ferrovum myxofaciens'. Classical 16S rRNA gene cloning showed that 96% of the Gallionella-related sequences had ≥ 97% identity to the putatively metal-tolerant 'Gallionella capsiferriformans ES-2', in addition to known stalk formers such as Gallionella ferruginea and Gallionellaceae strain R-1. Twisted stalks from glass slides incubated in water and sediment were composed of the Fe(III) oxyhydroxide ferrihydrite, as well as polysaccharides. SEM and scanning TEM-energy-dispersive X-ray spectroscopy revealed that stalk material contained Cu and Sn, demonstrating the association of heavy metals with biogenic iron oxides and the potential for metal retention by these stalks. Sequential extraction of sediments suggested that Cu (52-61% of total sediment Cu) and other heavy metals were primarily bound to the iron oxide fractions. These results show the importance of 'G. capsiferriformans' and biogenic iron oxides in slightly acidic but highly metal-contaminated freshwater environments.


Neutrophil Extracellular Traps and By-Products Play a Key Role in COVID-19: Pathogenesis, Risk Factors, and Therapy.
Understanding of the pathogenesis of the coronavirus disease-2019 (COVID-19) remains incomplete, particularly in respect to the multi-organ dysfunction it may cause. We were the first to report the analogous biological and physiological features of COVID-19 pathogenesis and the harmful amplification loop between inflammation and tissue damage induced by the dysregulation of neutrophil extracellular traps (NETs) formation. Given the rapid evolution of this disease, the nature of its symptoms, and its potential lethality, we hypothesize that COVID-19 progresses under just such an amplifier loop, leading to a massive, uncontrolled inflammation process. Here, we describe in-depth the correlations of COVID-19 symptoms and biological features with those where uncontrolled NET formation is implicated in various sterile or infectious diseases. General clinical conditions, as well as numerous pathological and biological features, are analogous with NETs deleterious effects. Among NETs by-products implicated in COVID-19 pathogenesis, one of the most significant appears to be elastase, in accelerating virus entry and inducing hypertension, thrombosis and vasculitis. We postulate that severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) may evade innate immune response, causing uncontrolled NETs formation and multi-organ failure. In addition, we point to indicators that NETS-associated diseases are COVID-19 risk factors. Acknowledging that neutrophils are the principal origin of extracellular and circulating DNA release, we nonetheless, explain why targeting NETs rather than neutrophils themselves may in practice be a better strategy. This paper also offers an in-depth review of NET formation, function and pathogenic dysregulation, as well as of current and prospective future therapies to control NETopathies. As such, it enables us also to suggest new therapeutic strategies to fight COVID-19. In combination with or independent of the latest tested approaches, we propose the evaluation, in the short term, of treatments with DNase-1, with the anti-diabetic Metformin, or with drugs targeting elastase (i.e., Silvelestat). With a longer perspective, we also advocate a significant increase in research on the development of toll-like receptors (TLR) and C-type lectin-like receptors (CLEC) inhibitors, NET-inhibitory peptides, and on anti-IL-26 therapies.


Weight monitoring of breastfed babies in the United Kingdom--interpreting, explaining and intervening.
Weighing infants in their first 6 months is an important aspect of growth monitoring and a common activity of child health care services worldwide. During the same 6 months, support for establishing breastfeeding and the promotion of continued exclusive breastfeeding are important activities of health professionals. Parents and health professionals may perceive conflicts between achieving both robust growth and continuing breastfeeding. In this narrative review, the literature on weighing breastfed babies in the United Kingdom is examined. A companion paper examined issues of growth charts, scales and weighing frequency and accuracy. This paper considers issues of interpretation of the plotted weight values for individual breastfed babies, noting the complexities of growth patterns, which may lead to difficulties of accurate identification of those individuals whose growth merits further investigation. Little attention has been given to issues of explaining the interpreted growth curves to parents and this issue is explored and noted as of importance for further study. Research evidence on choosing appropriate interventions to improve the growth of breastfed babies is reviewed. The paucity of such evidence leads to suggestions for future study. This review gathers together a wide range of literature from many different perspectives, with the hope of informing weight monitoring practice so that this can both identify infants whose weight may be of concern, and who may need appropriate intervention, and support continued breastfeeding.


Heightened Exercise-Induced Oxidative Stress at Simulated Moderate Level Altitude vs. Sea Level in Trained Cyclists.
Altitude exposure can exaggerate the transient increase in markers of oxidative stress observed following acute exercise. However, these responses have not been monitored in endurance-trained cyclists at altitudes typically experienced while training. Endurance trained males (n = 12; mean (± SD) age: 28 ± 4 years, V̇O2max 63.7 ± 5.3 ml/kg/min) undertook two 75-min exercise trials at 70% relative V̇O2max; once in normoxia and once in hypobaric hypoxia, equivalent to 2000m above sea level (hypoxia). Blood samples were collected before, immediately after and 2 h postexercise to assess plasma parameters of oxidative stress (protein carbonylation (PC), thiobarbituric acid reactive substances (TBARS), total antioxidant capacity (TAC) and catalase activity (CAT)). Participants cycled at 10.5% lower power output in hypoxia vs. normoxia, with no differences in heart rate, blood lactate or rating of perceived exertion observed. PC increased and decreased immediately after exercise in hypoxia and normoxia respectively (nmol/mg/protein: Normoxia-0.3 ± 0.1, Hypoxia + 0.4 ± 0.1; both p < .05). CAT increased immediately postexercise in both trials, with the magnitude of change greater in hypoxia (nmol/min/ml: Normoxia + 12.0 ± 5.0, Hypoxia + 27.7 ± 4.8; both p < .05). CAT was elevated above baseline values at 2 h postexercise in Hypoxia only (Normoxia + 0.2 ± 2.4, Hypoxia + 18.4 ± 5.2; p < .05). No differences were observed in the changes in TBARS and TAC between hypoxia and normoxia. Trained male cyclists demonstrated a differential pattern/ timecourse of changes in markers of oxidative stress following submaximal exercise under hypoxic vs. normoxic conditions.


Different mechanisms are responsible for chlorophyll dephytylation during fruit ripening and leaf senescence in tomato.
Chlorophyll breakdown occurs in different green plant tissues (e.g. during leaf senescence and in ripening fruits). For different plant species, the PHEOPHORBIDE A OXYGENASE (PAO)/phyllobilin pathway has been described to be the major chlorophyll catabolic pathway. In this pathway, pheophorbide (i.e. magnesium- and phytol-free chlorophyll) occurs as a core intermediate. Most of the enzymes involved in the PAO/phyllobilin pathway are known; however, the mechanism of dephytylation remains uncertain. During Arabidopsis (Arabidopsis thaliana) leaf senescence, phytol hydrolysis is catalyzed by PHEOPHYTINASE (PPH), which is specific for pheophytin (i.e. magnesium-free chlorophyll). By contrast, in fruits of different Citrus spp., chlorophyllase, hydrolyzing phytol from chlorophyll, was shown to be active. Here, we enlighten the process of chlorophyll breakdown in tomato (Solanum lycopersicum), both in leaves and fruits. We demonstrate the activity of the PAO/phyllobilin pathway and identify tomato PPH (SlPPH), which, like its Arabidopsis ortholog, was specifically active on pheophytin. SlPPH localized to chloroplasts and was transcriptionally up-regulated during leaf senescence and fruit ripening. SlPPH-silencing tomato lines were impaired in chlorophyll breakdown and accumulated pheophytin during leaf senescence. However, although pheophytin transiently accumulated in ripening fruits of SlPPH-silencing lines, ultimately these fruits were able to degrade chlorophyll like the wild type. We conclude that PPH is the core phytol-hydrolytic enzyme during leaf senescence in different plant species; however, fruit ripening involves other hydrolases, which are active in parallel to PPH or are the core hydrolases in fruits. These hydrolases remain unidentified, and we discuss the question of whether chlorophyllases might be involved.


Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human.
We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock-captured single-nucleotide polymorphisms (SNPs) from the transcriptome. We characterized four cell lines established from two human subjects in the Personal Genome Project. Approximately 11-22% of the heterozygous mRNA-associated SNPs showed allele-specific expression in each cell line and 4.3-8.5% were tissue-specific, suggesting the presence of tissue-specific cis regulation. When we applied allelotyping to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines. We found that the variation of allelic ratios in gene expression among different cell lines was primarily explained by genetic variations, much more so than by specific tissue types or growth conditions. Comparison of expressed SNPs on the sense and antisense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts.


Long noncoding RNAs with enhancer-like function in human cells.
While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation.


Observational and modeling constraints on global anthropogenic enrichment of mercury.
Centuries of anthropogenic releases have resulted in a global legacy of mercury (Hg) contamination. Here we use a global model to quantify the impact of uncertainty in Hg atmospheric emissions and cycling on anthropogenic enrichment and discuss implications for future Hg levels. The plausibility of sensitivity simulations is evaluated against multiple independent lines of observation, including natural archives and direct measurements of present-day environmental Hg concentrations. It has been previously reported that pre-industrial enrichment recorded in sediment and peat disagree by more than a factor of 10. We find this difference is largely erroneous and caused by comparing peat and sediment against different reference time periods. After correcting this inconsistency, median enrichment in Hg accumulation since pre-industrial 1760 to 1880 is a factor of 4.3 for peat and 3.0 for sediment. Pre-industrial accumulation in peat and sediment is a factor of ∼ 5 greater than the precolonial era (3000 BC to 1550 AD). Model scenarios that omit atmospheric emissions of Hg from early mining are inconsistent with observational constraints on the present-day atmospheric, oceanic, and soil Hg reservoirs, as well as the magnitude of enrichment in archives. Future reductions in anthropogenic emissions will initiate a decline in atmospheric concentrations within 1 year, but stabilization of subsurface and deep ocean Hg levels requires aggressive controls. These findings are robust to the ranges of uncertainty in past emissions and Hg cycling.


Bladder cancer risk in painters: a meta-analysis.
The International Agency for Research on Cancer has classified occupational exposure as a painter as 'carcinogenic to humans', largely based on increased risks of bladder and lung cancer. A meta-analysis, including more than 2900 incident cases or deaths from bladder cancer among painters reported in 41 cohort (n=2), record linkage (n=9) and case-control (n=30) studies, was conducted to quantitatively compare the results of the different study designs and the potential confounding effect of smoking as well as other occupational exposures. The summary relative risk (meta-RR, random effects) for bladder cancer in painters was 1.25 (95% CI 1.16 to 1.34; 41 studies) overall and 1.28 (95% CI 1.15 to 1.43; 27 studies) when including only smoking adjusted risk estimates. The elevated risk persisted when restricted to studies that adjusted for other occupational exposures (meta-RR 1.27; 95% CI 0.99 to 1.63; 4 studies). The results remained robust when stratified by study design, gender and study location. Furthermore, exposure-response analyses suggested that the risk increased with duration of employment. There was no evidence of publication bias. Taken together, these results support the conclusion that occupational exposures in painters are causally associated with the risk of bladder cancer.


Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma.
Purpose: Angiotensin system inhibitors (ASI) can improve prognosis in multiple cancer types, including pancreatic ductal adenocarcinoma (PDAC). However, no study has examined the effect of ASIs alone or combined with adjuvant chemotherapy in resected PDAC patients.Experimental Design: We performed an analysis of the records of ASI users and nonuser patients with PDAC seen at Massachusetts General Hospital (Boston, MA) between January 2006 and December 2010. To identify mechanisms of ASIs in PDAC, we performed RNA sequencing (RNA-Seq) of resected primary lesions.Results: A total of 794 consecutive patients were included. In 299 resected patients, ASI users experienced longer overall survival (OS) in both univariate (median OS, 36.3 vs. 19.3 months, P = 0.011) and adjusted multivariate [HR, 0.505; 95% confidence interval (CI), 0.339-0.750; P = 0.001] analyses. Propensity score-adjusted analysis also showed a longer median OS for chronic ASI users. In unresected patients, the beneficial effect of ASIs was significant in patients with locally advanced disease, but not in metastatic patients. RNA-Seq analysis revealed in tumors of ASI users (lisinopril) a normalized extracellular matrix, a reduced expression of genes involved in PDAC progression (e.g., WNT and Notch signaling), and an increased expression of genes linked with the activity of T cells and antigen-presenting cells. Finally, chronic use of ASI was associated with a gene expression signature that is predictive of survival in independent validation cohorts.Conclusions: In patients with nonmetastatic PDAC, chronic ASI use is associated with longer OS independently of chemotherapy. Our RNA-Seq analysis suggests that ASIs reduce the malignant potential of cancer cells and stimulate the immune microenvironment in primary PDAC. Clin Cancer Res; 23(19); 5959-69. ©2017 AACR.


Evaluating a brief self-report measure of neighborhood environments for physical activity research and surveillance: Physical Activity Neighborhood Environment Scale (PANES).
Neighborhood environment attributes of walkability and access to recreation facilities have been related to physical activity and weight status, but most self-report environment measures are lengthy. The 17-item PANES (Physical Activity Neighborhood Environment Scale) was developed to be comprehensive but brief enough for use in multipurpose surveys. The current study evaluated test-retest and alternate-form reliability of PANES items compared with multi-item subscales from the longer NEWS-A (Neighborhood Environment Walkability Scale--Abbreviated). Participants were 291 adults recruited from neighborhoods that varied in walkability in 3 US cities. Surveys were completed twice with a 27-day interval. Test-retest ICCs for PANES items ranged from .52 to .88. Spearman correlations for the PANES single item vs NEWS-A subscale comparisons ranged from .27 to .81 (all P < .01). PANES items related to land use mix, residential density, pedestrian infrastructure, aesthetic qualities, and safety from traffic and crime were supported by correlations with NEWS-A subscales. Access to recreation facilities and street connectivity items were not supported. The brevity of PANES allows items to be included in studies or surveillance systems to expand knowledge about neighborhood environments.


Genome-wide association analyses based on a multiple-trait approach for modeling feed efficiency.
Genome-wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 cows from 16 stations in 4 counties. Of these cows, 4,916 had genotypes on 57,347 single nucleotide polymorphism (SNP) markers. We compared a GWA analysis based on the more classical residual feed intake (RFI) model with one based on a previously proposed multiple trait (MT) approach for modeling FE using an alternative measure (DMI|MILKE,MBW). Both models were based on a single-step genomic BLUP procedure that allowed the use of phenotypes from both genotyped and nongenotyped cows. Estimated effects for single SNP markers were small and not statistically important but virtually identical for either FE measure (RFI vs. DMI|MILKE,MBW). However, upon further refining this analysis to develop joint tests within nonoverlapping 1-Mb windows, significant associations were detected between either measure of FE with a window on each of Bos taurus autosomes BTA12 and BTA26. There was, as expected, no overlap between detected genomic regions for DMI|MILKE,MBW and genomic regions influencing the energy sink traits (i.e., MILKE and MBW) because of orthogonal relationships clearly defined between the various traits. Conversely, GWA inferences on DMI can be demonstrated to be partly driven by genetic associations between DMI with these same energy sink traits, thereby having clear implications when comparing GWA studies on DMI to GWA studies on FE-like measures such as RFI.


Doxepin therapy for postprandial symptomatic hypoglycaemic patients: neurochemical, hormonal and metabolic disturbances.
1. Three oral glucose tolerance tests were performed in each of 32 symptomatic postprandial hypoglycaemic patients (before placebo, before doxepin therapy and after doxepin therapy). Plasma neurotransmitters were determined in parallel with assays of plasma insulin and glucose levels. 2. Three different types of patients were distinguished. Type I showed a low noradrenaline/adrenaline ratio, high dopamine levels and low platelet 5-hydroxytryptamine (serotonin) levels during basal periods. After a glucose load, late peaks of dopamine and free 5-hydroxytryptamine, which coincided with the symptoms but not with the nadir of plasma glucose, were observed. Type II showed a low basal plasma noradrenaline/adrenaline ratio. After a glucose load, progressive increases in adrenaline and decreases in glucose were seen. Adrenergic symptoms coincided with the nadir of glucose. Although type III patients showed hyperinsulinaemia after a glucose load similar to the other types of patient, they did not show hyperglycaemia, but rather exhibited a sustained and progressive reduction in plasma glucose. These patients were characterized by a high basal plasma noradrenaline/adrenaline ratio, high basal plasma levels of 4-hydroxy-3-methoxyphenylethyleneglycol and high basal levels of platelet 5-hydroxytryptamine, all of which increased after a glucose load. Systolic and diastolic blood pressure decreases paralleled reductions in heart rate and glucose. The nadir of plasma glucose occurred simultaneously with the appearance of symptoms (weakness, heartburn, oppressive chest pain, tension headache, abdominal cramps, dizziness, etc.). Therapy with doxepin led to disappearance of the symptoms within 3-4 weeks. Normalization of all other disordered variables (cardiovascular, metabolic and neurochemical, and the clonidine test) paralleled the disappearance of the symptoms. 3. Symptoms varied in the three types of patients and we conclude that they are related to hypoglycaemia-induced disorders of plasma neurotransmitters, rather than to hypoglycaemia per se. We postulate that an uncoping stress situation (type I and II patients) and depression (type III patients) underlie the physiopathological mechanisms.


Adherence to dietary recommendations among Spanish and immigrant adolescents living in Spain; the AFINOS study.
This study compares the adherence of immigrant and Spanish adolescents residing in the Madrid region (Spain) to national dietary recommendations. The factors compared were the consumption of items from the eight basic food groups (vegetables, fruits, bread/cereals, meat, eggs, fish, legumes and milk/dairy products), including the excessive or deficient consumption of eggs, meat and fish. In addition, the evaluation of excessive sweet foods or soft drinks in the diet was also considered. Subsequently, the influence of length of residence on dietary habits was examined. Self-reported data were collected in a cross-sectional survey conducted over the period November 2007 to February 2008. The study participants were a representative sample of adolescents aged 13 to 17 years (n=2081, 1055 girls) living in the Madrid region. Participants were recruited from secondary schools (grades 7th to 10th) randomly selected according to the geographic distribution of adolescents in the region. Immigrant adolescents showed a greater likelihood of not fulfilling recommendations for the consumption of meat, fish, eggs, legumes, bread/cereals, and milk/dairy products. Their diets were also more likely to lack sufficient fish and they also consumed more eggs and more sweet foods and soft drinks than their native counterparts. Spanish adolescents were more likely not to meet recommendations for the intake of vegetables. Length of residence weakly affected dietary habits, with both negative and positive effects observed. The likelihood of not fulfilling dietary recommendations was higher among the immigrant adolescents with the exception of the intake of fruits and vegetables.


Temperature-dependence of Weibel-Palade body exocytosis and cell surface dispersal of von Willebrand factor and its propolypeptide.
Weibel-Palade bodies (WPB) are endothelial cell (EC) specific secretory organelles containing Von Willebrand factor (VWF). The temperature-dependence of Ca(2+)-driven WPB exocytosis is not known, although indirect evidence suggests that WPB exocytosis may occur at very low temperatures. Here we quantitatively analyse the temperature-dependence of Ca(2+)-driven WPB exocytosis and release of secreted VWF from the cell surface of ECs using fluorescence microscopy of cultured human ECs containing fluorescent WPBs. Ca(2+)-driven WPB exocytosis occurred at all temperatures studied (7-37°C). The kinetics and extent of WPB exocytosis were strongly temperature-dependent: Delays in exocytosis increased from 0.92 s at 37°C to 134.2 s at 7°C, the maximum rate of WPB fusion decreased from 10.0±2.2 s(-1) (37°C) to 0.80±0.14 s(-1) (7°C) and the fractional extent of degranulation of WPBs in each cell from 67±3% (37°C) to 3.6±1.3% (7°C). A discrepancy was found between the reduction in Ca(2+)-driven VWF secretion and WPB exocytosis at reduced temperature; at 17°C VWF secretion was reduced by 95% but WPB exocytosis by 75-80%. This discrepancy arises because VWF dispersal from sites of WPB exocytosis is largely prevented at low temperature. In contrast VWF-propolypeptide (proregion) dispersal from WPBs, although slowed, was complete within 60-120 s. Novel antibodies to the cleaved and processed proregion were characterised and used to show that secreted proregion more accurately reports the secretion of WPBs at sub-physiological temperatures than assay of VWF itself. We report the first quantitative analysis of the temperature-dependence of WPB exocytosis. We provide evidence; by comparison of biochemical data for VWF or proregion secretion with direct analysis of WPB exocytosis at reduced temperature, that proregion is a more reliable marker for WPB exocytosis at reduced temperature, where VWF-EC adhesion is increased.


Decentralized peri-urban wastewater treatment technologies assessment integrating sustainability indicators.
Selection of treatment technologies without considering the environmental, economic and social factors associated with each geographical context risks the occurrence of negative impacts that were not properly foreseen, working against the sustainable performance of the technology. The principal aim of this study was to evaluate 12 technologies for decentralized treatment of domestic wastewater applicable to peri-urban communities using sustainability approaches and, at the same time, continuing a discussion about how to address a more integrated assessment of overall sustainability. For this, a set of 13 indicators that embody the environmental, economic and social approach for the overall sustainability assessment were used by means of a target plot diagram as a tool for integrating indicators that represent a holistic analysis of the technologies. The obtained results put forward different degrees of sustainability, which led to the selection of: septic tank+land infiltration; up-flow anaerobic reactor+high rate trickling filter and septic tank+anaerobic filter as the most sustainable and attractive technologies to be applied in peri-urban communities, according to the employed indicators.


The desmosomal plaque and the cytoskeleton.
Two major plasma membrane domains are involved in the architectural organization of the cytoskeleton. Both are junctions of the adherens category characterized by the presence of dense plaques associated with the cytoplasmic surface of their membranes. The plaques serve as specific anchorage structures for two different types of cytoplasmic filaments. Intermediate-sized filaments (IF) of several types, i.e. cytokeratin IF in epithelial cells, desmin IF in cardiac myocytes and vimentin IF in arachnoidal cells of meninges, meningiomas and several other cells, attach to the desmosomal plaques, whereas actin-containing microfilaments associate with non-desmosomal adhering junctions such as the zonula adherens, fascia adherens and punctum adherens. The plaques of both kinds of adhering junctions contain a common acidic polypeptide of Mr 83,000 identical to 'band 5 protein' of bovine snout epidermal desmosomes. However, other plaque components are mutually exclusive to one of the two subclasses of adhering junctions. The desmosomal plaque structure, which does not contain vinculin and alpha-actinin, comprises representatives of cytoplasmic, non-membrane-integrated proteins such as desmoplakin(s) and the cytoplasmic portions of transmembrane glycoproteins such as 'band 3 glycoprotein'. The analysis of both categories of junction-associated plaques should provide a basis for understanding the establishment and the dynamics of junction-cytoskeleton interaction.


Medical ethnobotany of the Teribes of Bocas del Toro, Panama.
Ethnomedical uses of 108 medicinal plant species, belonging to 52 families, 89 genera, used by the Teribe Amerindians of Bocas del Toro Province in Panama, along with their socio-cultural practices are reported here. The methods of administration of the herbal remedies, the plant parts used, their families and local names are also documented. The recorded medicinal plants were used mainly for fever, various type of pain and inflammation. The potential value of 26 plants and their traditional uses was elucidated through literature search.


The role of the surfaces in the photon absorption in Ge nanoclusters embedded in silica.
The usage of semiconductor nanostructures is highly promising for boosting the energy conversion efficiency in photovoltaics technology, but still some of the underlying mechanisms are not well understood at the nanoscale length. Ge quantum dots (QDs) should have a larger absorption and a more efficient quantum confinement effect than Si ones, thus they are good candidate for third-generation solar cells. In this work, Ge QDs embedded in silica matrix have been synthesized through magnetron sputtering deposition and annealing up to 800°C. The thermal evolution of the QD size (2 to 10 nm) has been followed by transmission electron microscopy and X-ray diffraction techniques, evidencing an Ostwald ripening mechanism with a concomitant amorphous-crystalline transition. The optical absorption of Ge nanoclusters has been measured by spectrophotometry analyses, evidencing an optical bandgap of 1.6 eV, unexpectedly independent of the QDs size or of the solid phase (amorphous or crystalline). A simple modeling, based on the Tauc law, shows that the photon absorption has a much larger extent in smaller Ge QDs, being related to the surface extent rather than to the volume. These data are presented and discussed also considering the outcomes for application of Ge nanostructures in photovoltaics.PACS: 81.07.Ta; 78.67.Hc; 68.65.-k.


The Relationship between Age at First Birth and Mother's Lifetime Earnings: Evidence from Danish Data.
Having children creates career interruptions and reductions in labor income for women. This study documents the relation between the age at first birth (AFB) and women's labor income. We study these dynamics in the short run (i.e. ratio between labor income at AFB and two years prior to AFB) and long run (i.e., positive/negative differences in total lifetime labor income). Using unique Danish administrative register data for the entire Danish population, we estimate the age-income profiles separately for college and non-college women conditional on marital status, and mothers' age at first birth (AFB). We compute the lifetime labor income differentials by taking the differences between the labor income of women with and without children at each AFB. The short-run loss in labor income, defined as the difference in percentages between the income earned two years prior to AFB and income earned at AFB, ranges from 37% to 65% for college women and from 40% to 53% for non-college women. These losses decrease monotonically with respect to AFB for both education groups. Our results on the lifetime labor income differentials between mothers and women without children also show a net effect that is monotonic (from negative to positive) in AFB. With AFB<25, the lifetime labor income loss for college women is -204% of their average annual labor income and this figure is -252% for non-college women. There are lifetime labor income gains with AFB>31. The largest gains for college women are 13% of their average annual income and this figure is 50% for non-college women. Women have a large and unambiguous short-run reduction in labor income at their AFB. In terms of lifetime labor income, both college and non-college women, compared to childless women, are associated with lower income of more than twice their respective average annual income when bearing a child at AFB<25. In other words, women with AFB<25 are associated with a lower lifetime income of more than two years of annual labor income. The lifetime labor incomes for college and non-college women associated with AFB>31 are relatively higher.


Making psychiatric semiology great again: A semiologic, not nosologic challenge.
This article analyzes whether psychiatric disorders can be considered different from non-psychiatric disorders on a nosologic or semiologic point of view. The supposed difference between psychiatric and non-psychiatric disorders relates to the fact that the individuation of psychiatric disorders seems more complex than for non-psychiatric disorders. This individuation process can be related to nosologic and semiologic considerations. The first part of the article analyzes whether the ways of constructing classifications of psychiatric disorders are different than for non-psychiatric disorders. The ways of establishing the boundaries between the normal and the pathologic, and of classifying the signs and symptoms in different categories of disorder, are analyzed. Rather than highlighting the specificity of psychiatric disorders, nosologic investigation reveals conceptual notions that apply to the entire field of medicine when we seek to establish the boundaries between the normal and the pathologic and between different disorders. Psychiatry is thus very important in medicine because it exemplifies the inherent problem of the construction of cognitive schemes imposed on clinical and scientific medical information to delineate a classification of disorders and increase its comprehensibility and utility. The second part of this article assesses whether the clinical manifestations of psychiatric disorders (semiology) are specific to the point that they are entities that are different from non-psychiatric disorders. The attribution of clinical manifestations in the different classifications (Research Diagnostic Criteria, Diagnostic Statistic Manual, Research Domain Criteria) is analyzed. Then the two principal models on signs and symptoms, i.e. the latent variable model and the causal network model, are assessed. Unlike nosologic investigation, semiologic analysis is able to reveal specific psychiatric features in a patient. The challenge, therefore, is to better define and classify signs and symptoms in psychiatry based on a dual and mutually interactive biological and psychological perspective, and to incorporate semiologic psychiatry into an integrative, multilevel and multisystem brain and cognitive approach.


Utility of host markers detected in Quantiferon supernatants for the diagnosis of tuberculosis in children in a high-burden setting.
The diagnosis of childhood tuberculosis (TB) disease remains a challenge especially in young and HIV-infected children. Recent studies have identified potential host markers which, when measured in Quantiferon (QFT-IT) supernatants, show promise in discriminating between Mycobacterium tuberculosis (M.tb) infection states. In this study, the utility of such markers was investigated in children screened for TB in a setting with high TB incidence. 76 children (29% HIV-infected) with or without active TB provided blood specimens collected directly into QFT-IT tubes. After overnight incubation, culture supernatants were harvested, aliquoted and frozen for future immunological research purposes. Subsequently, the levels of 12 host markers previously identified as potential TB diagnostic markers were evaluated in these supernatants for their ability to discriminate between M.tb infection and disease states using the Luminex platform. Of the 76 children included, 19 (25%) had culture confirmed TB disease; 26 (46%) of the 57 without TB had positive markers of M.tb infection defined by a positive QFT-IT test. The potentially most useful analytes for diagnosing TB disease included IFN-α2, IL-1Ra, sCD40L and VEGF and the most useful markers for discriminating between QFT-IT positive children as TB or latent infection included IL-1Ra, IP-10 and VEGF. When markers were used in combinations of four, 84% of all children were accurately classified into their respective groups (TB disease or no TB), after leave-one-out cross validation. Measurement of the levels of IFN-α2, IL-1Ra, sCD40L, IP-10 and VEGF in QFT-IT supernatants may be a useful method for diagnosing TB disease and differentiating between active TB disease and M.tb infection in children. Our observations warrant further investigation in larger well-characterized clinical cohorts.


Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains.
Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single- or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.


Variability among isolates of Pseudomonas syringae pv. savastanoi from the phylloplane of the olive.
Leaves of three or four different ages were taken from olive plants quarterly in 1974-1980. One thousand and fifty isolates of Pseudomonas syringae pv. savastanoi from the phylloplane were tested for virulence to the olive and subjected to numerical phenetic analysis using 60 unit characters. The data were analysed using unweighted average linkage (UPGMA) and single linkage clustering on the simple matching (SSM) and pattern (SP) coefficients. The isolates obtained from leaves of a given age at a given time of the year shared higher percentage similarity (S) values between themselves than with the others. Cluster composition was only marginally affected by different coefficients and methods of clustering. UPGMA analysis on the SSM coefficient recovered 92% of the isolates in 10 major clusters at 75% S. Of the isolates from leaves of the same age collected at the same time of the year, 81-99% fell in the same cluster. Conversely, 91-97% of the isolates in five of the major clusters were from leaves of the same type. Of the isolates in the other major clusters, 95-98% were from two different sources but most of the isolates from leaves of one type segregated into discrete subclusters at 85-90% S. Hypothetical median organisms (HMOs) were constructed to represent all the isolates obtained from the leaves of each type each year. The resulting relationships between the HMOs confirmed those described above for the individual isolates.


Mismatch repair deficiency in colorectal cancer patients in a low-incidence area.
In a previous study we identified 206 patients with colorectal adenocarcinoma in the Northern Cape province of South Africa, diagnosed between January 2002 and February 2009. The age-standardised incidence was 4.2/100 000 per year world standard population. This is 10% of the rate reported in First-World countries. In high-incidence areas, the rate of abnormal mismatch repair gene expression in colorectal cancers is 2 - 7%. The aim of this study was to determine the prevalence of hMLH1- and hMSH2-deficient colorectal cancer in the Northern Cape. Formalin-fixed paraffin wax-embedded tissue blocks from 87 colorectal adenocarcinomas identified in the previous study were retrieved. Standard immunohistochemical staining methods were used to detect the expression of hMLH1 and hMSH2 (i.e. products of the hMLH1 and hMSH2 genes) in the tumours using heat-induced antigen retrieval and diaminobenzidene as a chromogen. Results. In 8 blocks there was insufficient tumour tissue and in 1 case the immunohistochemical staining failed, probably owing to poor fixation, leaving 78 cases for analysis. In 11 cases hMLH1 was deficient and in 6 cases hMSH2 was deficient. Overall, 21.8% of cancers were deficient for hMLH1 or hMSH2. Presuming that 80% of all hMLH1 deficiencies are due to hypermethylation of the gene, we found 10.5% of colorectal cancers in an area with a low incidence of colorectal cancer to be deficient in the product of the mismatch repair gene/s. This is approximately three times the reported rate in high-incidence areas.


Spherical Deconvolution of Multichannel Diffusion MRI Data with Non-Gaussian Noise Models and Spatial Regularization.
Spherical deconvolution (SD) methods are widely used to estimate the intra-voxel white-matter fiber orientations from diffusion MRI data. However, while some of these methods assume a zero-mean Gaussian distribution for the underlying noise, its real distribution is known to be non-Gaussian and to depend on many factors such as the number of coils and the methodology used to combine multichannel MRI signals. Indeed, the two prevailing methods for multichannel signal combination lead to noise patterns better described by Rician and noncentral Chi distributions. Here we develop a Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD) technique, intended to deal with realistic MRI noise, based on a Richardson-Lucy (RL) algorithm adapted to Rician and noncentral Chi likelihood models. To quantify the benefits of using proper noise models, RUMBA-SD was compared with dRL-SD, a well-established method based on the RL algorithm for Gaussian noise. Another aim of the study was to quantify the impact of including a total variation (TV) spatial regularization term in the estimation framework. To do this, we developed TV spatially-regularized versions of both RUMBA-SD and dRL-SD algorithms. The evaluation was performed by comparing various quality metrics on 132 three-dimensional synthetic phantoms involving different inter-fiber angles and volume fractions, which were contaminated with noise mimicking patterns generated by data processing in multichannel scanners. The results demonstrate that the inclusion of proper likelihood models leads to an increased ability to resolve fiber crossings with smaller inter-fiber angles and to better detect non-dominant fibers. The inclusion of TV regularization dramatically improved the resolution power of both techniques. The above findings were also verified in human brain data.


How Have Leukocyte In Vitro Chemotaxis Assays Shaped Our Ideas about Macrophage Migration?
Macrophage chemotaxis is crucial during both onset and resolution of inflammation and unique among all leukocytes. Macrophages are able to switch between amoeboid and mesenchymal migration to optimise their migration through 3D environments. This subtle migration phenotype has been underappreciated in the literature, with macrophages often being grouped and discussed together with other leukocytes, possibly due to the limitations of current chemotaxis assays. Transwell assays were originally designed in the 1960s but despite their long-known limitations, they are still one of the most popular methods of studying macrophage migration. This review aims to critically evaluate transwell assays, and other popular chemotaxis assays, comparing their advantages and limitations in macrophage migration studies.


Recombinant basic fibroblast growth factor stimulates wound healing in healing-impaired db/db mice.
The stimulatory effect of recombinant basic fibroblast growth factor (bFGF) on wound healing was assessed using healing-impaired (db/db) mice. Full-thickness wounds were made in female diabetic C57BL/KsJ db/db mice, and their normal (db/+) littermates with a punch biopsy instrument. Recombinant bFGF was applied locally to the open wound once a day. The mice were later killed and histological sections of the wounds were prepared. The degree of wound healing was evaluated using several histological parameters such as degree of reepithelialization, granulation tissue thickness, matrix density, number of infiltrated cells, and number of capillaries. Wounds from normal mice displayed good reepithelialization rates and granulation tissue formation, while wounds from db/db mice had poor responses, especially in the dermal parameters. Although the application of bFGF to wounds in the normal (db/+) mice had little effect, application of bFGF to wounds in db/db mice induced significant responses in all of the dermal parameters compared with nontreated db/db mice (p less than 0.001). In the presence of bFGF, these parameters approximated those observed in nontreated littermates. A minimum of 0.5 microgram bFGF in either single or multiple applications was required for a significant effect. bFGF that was either boiled or pretreated with neutralizing antibody had little stimulatory effect. Time-course experiments indicated that the granulation response in bFGF-treated mice peaked between 8 and 12 d, and decreased after 12 d, while matrix density continued to increase until the 18th day (p less than 0.05). The breaking strength of healed linear wounds in db/db mice was also decreased when compared with heterozygous littermates. This parameter was also improved by the administration of bFGF to the wounds (p less than 0.05).


Extensive developmental and metabolic alterations in cybrids Nicotiana tabacum (+ Hyoscyamus niger) are caused by complex nucleo-cytoplasmic incompatibility.
The genetic basis of multiple phenotypic alterations was studied in cell-engineered cybrids Nicotiana tabacum (+ Hyoscyamus niger) combining the nuclear genome of N. tabacum, plastome of H. niger and recombinant mitochondria. The plants possess a complex, maternally inheritable syndrome of nucleo-cytoplasmic incompatibility, severely affecting growth, metabolism and development. In vivo, the syndrome was manifested as: late germination of seeds; dramatic decrease of chlorophyll and carotenoids in cotyledons and leaves; altered morphology of cotyledons, leaves and flowers; and dwarfism. The leaf phenotype depended on light intensity. In 'green flowers' (an extreme phenotype), homeotic function B was downregulated. In vitro, the incompatibility syndrome was restricted to the pigment deficiency of cotyledons. Electron microscopy revealed perturbations in the differentiation of chloroplasts and palisade parenchyma cells in bleached leaves. The pigment deficiency accompanied by retarded growth is discussed as a result of plastome-genome incompatibility, whereas other features are likely to be due to nucleo-mitochondrial incompatibilities.


Pseudotachylytes generated during seismic faulting and eclogitization of the deep crust.
Pseudotachylytes are typically interpreted to have formed by frictional melting during coseismic faulting within the upper to middle crust. Pseudotachylytes in the Bergen arcs of western Norway contain microlites including omphacite, garnet, plagioclase, and quartz. This eclogite facies assemblage is stable at temperatures of about 800 degrees C and pressures of 18 to 19 kilobars, corresponding to depths of 60 kilometers or more. The pseudotachylytes are exposed in Grenvillian granulites that locally underwent fluid-induced eclogitization and corresponding volume reduction of approximately 10 percent during the Caledonian continental collision. The pseudotachylytes may have formed as a result of the rapid relaxation of stresses caused by the eclogitization process.


Synthesis of polyaspartic acid-capped 2-aminoethylamino acid as a green water treatment agent and study of its inhibition performance and mechanism for calcium scales.
Polyaspartic acid (PASP), a well-known green scale inhibitor for industrial water treatment, might be decomposed with prolonged duration, and its anti-scaling performance against CaCO3 and CaSO4 is diminished at a low concentration (<10 mg L-1) and a high temperature. With semi-ethylenediaminetetraacetic acid (EDTA) tetrasodium salt as the mimicking model, novel phosphorus-free PASP-capped 2-aminoethylamino acid (PASP-ED2A) containing side chains bearing multi-functional groups is rationally designed and successfully prepared via the ring-opening reaction of cheap poly(succinimide) under mild reaction conditions with the assistance of readily available 2-aminoethyl amino acid. The static scale inhibition method is used to evaluate the scale inhibition performance of the as-synthesized PASP derivative. Scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy are utilized to monitor the crystallization process of calcium carbonate and calcium sulfate scales, and density functional theory calculations are conducted to shed light on the relationship between the molecular structure and scale inhibition mechanism of PASP-ED2A. Results show that the as-prepared PASP-ED2A shows better scale inhibition performance for CaCO3 and CaSO4 than PASP with a low concentration, a high temperature, and an extended duration. Particularly, PASP-ED2A with a concentration of 10 mg L-1 exhibits the best scale inhibition performance for CaCO3; its scale inhibition capacity is about two times as much as that of PASP. The reason lies in that the coordination atoms in the molecular structure of PASP-ED2A can chelate with Ca2+ to inhibit the combination of Ca2+ with anions and prevent the generation of CaCO3 and CaSO4 scales. The PASP-ED2A derivative can more efficiently retard the formation and growth of CaCO3 and CaSO4 crystal nuclei and exerts better inhibition performance against CaCO3 and CaSO4 scales than PASP.


An improved in vivo method for atrioventricular node ablation via thoracotomy.
The atrioventricular (AV) node is permanently damaged in approximately 3% of congenital heart surgery operations, requiring implantation of a permanent pacemaker. Improvements in pacemaker design and in alternative treatment modalities require an effective in vivo model of complete heart block (CHB) before testing can be performed in humans. Such a model should enable accurate, reliable, and detectable induction of the surgical pathology. Through our laboratory's efforts in developing a tissue engineering therapy for CHB, we describe here an improved in vivo model for inducing chronic AV block. The method employs a right thoracotomy in the adult rabbit, from which the right atrial appendage may be retracted to expose an access channel for the AV node. A novel injection device was designed, which both physically restricts needle depth and provides electrical information via electrocardiogram interface. This combination of features provides real-time guidance to the researcher for confirming contact with the AV node, and documents its ablation upon formalin injection. While all animals tested could be induced to acute AV block, those with ECG guidance were more likely to maintain chronic heart block >12 h. Our model enables the researcher to reproduce both CHB and the associated peripheral fibrosis that would be present in an open congenital heart surgery, and which would inevitably impact the design and utility of a tissue engineered AV node replacement.


Axonal structure and function after axolemmal leakage in the squid giant axon.
Membrane leakage is a common consequence of traumatic nerve injury. In order to measure the early secondary effects of different levels of membrane leakage on axonal structure and function we studied the squid giant axon after electroporation at field strengths of 0.5, 1.0, 1.6, or 3.3 kV/cm. Immediately after mild electroporation at 0.5 kV/cm, 40% of the axons had no action potentials, but by 1 h all of the mildly electroporated axons had recovered their action potentials. Many large organelles (mitochondria) were swollen, however, and their transport was reduced by 62% 1 h after this mild electroporation. One hour after moderate electroporation at 1.0 kV/cm, most of the axons had no action potentials, most large organelles were swollen, and their transport was reduced by 98%, whereas small organelle transport was reduced by 75%. Finally at severe electroporation levels of 1.65-3.0 kV/cm all conduction and transport was lost and the gel-like axoplasmic structure was clumped or liquefied. The structural damage and transport block seen after severe and moderate poration were early secondary injuries that could be prevented by placing the porated axons in an intracellular-type medium (low in Ca2+, Na+, and Cl-) immediately after poration. In moderately, but not severely, porated axons this protection of organelle transport and structure persisted, and action potential conduction returned when the axons were returned to the previously injurious extracellular-type medium. This suggests that the primary damage, the axolemmal leak, was repaired while the moderately porated axons were in the protective intracellular-type medium.


Blockade of GABA(A) receptors in the paraventricular nucleus of the hypothalamus attenuates voluntary ethanol intake and activates the hypothalamic-pituitary-adrenocortical axis.
The paraventricular nucleus (PVN) in the hypothalamus is the main integration site that controls the hypothalamic-pituitary-adrenal (HPA) neuroendocrine stress system. Disruption of this system has been linked with alcoholism, but the specific role of the PVN has not been fully explored. Of particular interest is the ability of γ-aminobutyric acid type A receptors (GABA(A)Rs) in the PVN, to regulate ethanol self-administration behavior, as these receptors appear to play an essential role in mediating the effects of ethanol in the central nervous system and in the regulation of PVN activity. We observed that Long-Evans rats, in the intermittent access to 20% ethanol paradigm, consumed high amounts of ethanol and subsequently developed ethanol dependence. Microinjection of the GABA(A)R antagonist picrotoxin into the PVN, but not to the lateral ventricle of the brain, significantly reduced the intake of ethanol, but not the intake of sucrose. Picrotoxin-induced reduction was mimicked by another GABA(A)R antagonist bicuculline but was attenuated by the GABA(A)R agonist muscimol. Moreover, increased ethanol consumption was associated with lowered blood corticosterone levels, indicating a blunted HPA signaling, which was reversed by intra-PVN injection of picrotoxin, as indicated by the increased Fos immunostaining-positive cells in the PVN and the increased blood corticosterone levels. Taken together, our data provide evidence that in ethanol-dependent rats, the function of GABA(A)Rs in the PVN is upregulated, leading to a dampened HPA system. Moreover, it demonstrates that the GABA(A)R antagonists normalize HPA axis signaling and reduce excessive ethanol drinking. Therefore, drugs targeting GABA(A)Rs may be beneficial for alcoholics.


Addressing spirituality during critical illness: A review of current literature.
The purpose of this review is to provide an overview of research on spirituality and religiosity in the intensive care setting that has been published since the 2004-2005 American College of Critical Care Medicine (ACCM) Clinical Practice Guidelines for the Support of Family in the Patient-Centered Intensive Care Unit with an emphasis on its application beyond palliative and end-of-life care. ACCM 2004-2005 guidelines emphasized the importance of spiritual and religious support in the form of four specific recommendations: [1] assessment and incorporation of spiritual needs in ICU care plan; [2] spiritual care training for doctors and nurses; [3] physician review of interdisciplinary spiritual need assessments; and [4] honoring the requests of patients to pray with them. We reviewed 26 studies published from 2006 to 2016 and identified whether studies strengthened the grade of these recommendations. We further categorized findings of these studies to understand the roles of spirituality and religiosity in surrogate perceptions and decision-making and patient and family experience. Spiritual care has an essential role in the treatment of critically ill patients and families. Current literature offers few insights to support clinicians in navigating this often-challenging aspect of patient care and more research is needed.


An audit of INR control in the Australian indigenous setting.
Warfarin management can be difficult; many factors can impact on INR control with some factors being unique to the Australian indigenous setting. An audit at an urban Aboriginal community controlled health service calculated the time all patients on warfarin were in the target INR therapeutic range. Those patients with the best and the worst values for time in therapeutic range (TTR) were then compared. The 26 identified patients on warfarin were in the target INR therapeutic range 44.9% of the time. Patients with better INR control were older than those with the worst control. There appeared to be no difference between the two groups when comparing other factors. INR control was below the cited benchmark for TTR of 60%. However, this may be better than expected in this clinical setting. The small number of patients included in the audit means that any discussion of the causes of better and poorer control must be treated with caution.


Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium.
We previously reported the risks of ovarian carcinoma for common polymorphisms in one-carbon transfer genes. We sought to replicate associations for DPYD rs1801265, DNMT3A rs13420827, MTHFD1 rs1950902, MTHFS rs17284990, and TYMS rs495139 with risk of ovarian carcinoma overall and to use the large sample of assembled cases to investigate associations by histologic type. Associations were evaluated in the Ovarian Cancer Association Consortium, including 16 studies of 5,593 epithelial ovarian carcinoma cases and 9,962 controls of white non-Hispanic origin. Odds ratios (OR) and 95% confidence intervals (CI) were adjusted for age and study site. The five polymorphisms were not associated with ovarian carcinoma overall (P(trend) > 0.13); however, associations for the minor allele at TYMS rs495139 were observed for carcinomas of mucinous type (OR, 1.19; 95% CI, 1.03-1.39; P = 0.02), clear cell type (OR, 0.86; 95% CI, 0.75-0.99; P = 0.04), and endometrioid type (OR, 0.90; 95% CI, 0.81-0.99; P = 0.04; P(heterogeneity) = 0.001). Restriction to low-grade mucinous carcinomas further strengthened the association for the mucinous type (OR, 1.32; 95% CI, 1.07-1.62; P = 0.01). TYMS rs495139 was not associated with serous type (OR, 1.06; 95% CI, 1.00-1.13; P = 0.05). TYMS rs495139 may be associated with a differential risk of ovarian carcinoma types, indicating the importance of accurate histopathologic classification. Biomarkers that distinguish ovarian carcinoma types are few, and TYMS rs495139 may provide a novel clue to type etiology.


Asthma management by monitoring sputum neutrophil count.
We report the utility of quantitative cell counts in sputum in monitoring therapy of a patient with poorly controlled asthma. Recurrent neutrophilic bronchitis without an eosinophilic bronchitis led to the identification of Chlamydophila pneumoniae as the cause of bronchitis and asthma exacerbation. Serial examination of blood and sputum by polymerase chain reaction for C pneumoniae helped to prevent exacerbations by prophylactic antibiotic therapy, reduce the dose of prednisone and inhaled corticosteroids, and improve asthma control.


Comparison of the plasmonic performances between lithographically fabricated and chemically grown gold nanorods.
Noble metal nanostructures, especially gold nanocrystals, have attracted intensive interest due to their rich plasmonic properties and enormous potential technological applications. The preparation process of gold nanocrystals can strongly affect their plasmonic properties and therefore their performances in various applications. Chemically synthesized colloidal gold nanocrystals are usually employed in biomedical fields, while lithographically fabricated ones are highly preferred for constructing optical meta-structures. A detailed careful comparison of the plasmonic performances between lithographical and chemical metal nanostructures is strongly desired for using them for different applications. Herein, we experimentally measured and quantitatively compared the plasmonic properties, including longitudinal localized surface plasmon wavelengths (LLSPWs) and plasmon peak widths, scattering intensities, and local electric field enhancements, of lithographically fabricated and chemically grown gold nanorods. The lithographical nanorods exhibit much weaker scattering, largely broadened spectral widths, and considerably reduced electric field enhancements. Electrodynamic simulations suggest that the reduction in the plasmonic performance of the lithographical nanorods is caused mainly by the use of an adhesive metal layer and slightly by their polycrystalline nature. Our quantitative comparison results will be very helpful in guiding the selection of proper types of metal nanostructures for targeted technological applications.


Loss of Methyltransferase Function and Increased Efflux Activity Leads to Doxycycline Resistance in Burkholderia pseudomallei.
The soil-dwelling bacterium Burkholderia pseudomallei is the causative agent of the potentially fatal disease melioidosis. The lack of a vaccine toward B. pseudomallei means that melioidosis treatment relies on prolonged antibiotic therapy, which can last up to 6 months in duration or longer. Due to intrinsic resistance, few antibiotics are effective against B. pseudomallei The lengthy treatment regimen required increases the likelihood of resistance development, with subsequent potentially fatal relapse. Doxycycline (DOX) has historically played an important role in the eradication phase of melioidosis treatment. Both primary and acquired DOX resistances have been documented in B. pseudomallei; however, the molecular mechanisms underpinning DOX resistance have remained elusive. Here, we identify and functionally characterize the molecular mechanisms conferring acquired DOX resistance in an isogenic B. pseudomallei pair. Two synergistic mechanisms were identified. The first mutation occurred in a putative S-adenosyl-l-methionine-dependent methyltransferase (encoded by BPSL3085), which we propose leads to altered ribosomal methylation, thereby decreasing DOX binding efficiency. The second mutation altered the function of the efflux pump repressor gene, amrR, resulting in increased expression of the resistance-nodulation-division efflux pump, AmrAB-OprA. Our findings highlight the diverse mechanisms by which B. pseudomallei can become resistant to antibiotics used in melioidosis therapy and the need for resistance monitoring during treatment regimens, especially in patients with prolonged or recrudesced positive cultures for B. pseudomallei.


Cytomegalovirus hepatitis and ganciclovir treatment in immunocompetent children.
Ganciclovir treatment in children with cytomegalovirus (CMV) infection is still controversial and only indicated in selected cases. The aim of thi study was to evaluate clinical and demographic features of CMV hepatitis in immunocompetent children and to determine the effect of ganciclovir treatment in these patients retrospectively. The study was carried out in a group o 29 children with CMV hepatitis. All the patients were investigated for signs of infection, inborn errors of metabolism, genetic diseases, extrahepatic biliary atresia and other causes of hepatitis. Two patients with congenital CMV infection and two patients with biliary atresia were excluded from the study group. The patients included in the study were divided into two groups: non-cholestatic hepatitis (n=16) as Group I and cholestatic hepatitis (n=9) as Group II. Four (25%) patients in the non-cholestatic group and four (44.4 in the cholestatic group were treated with ganciclovir for a median of 21 days. The mean age was 9.6+/- 10.9 months (median age 6 months) in Group I, while cholestatic hepatitis patients in Group II were significantly younger, with a mean age of 2.7+/-0.9 months (p<0.01). The most prominent symptoms at admission were diarrhea and vomiting (25%) in Group I. In Group I, all cases (100%) and in Group II, three of four cases (75%) treated with ganciclovir had recovery from acute CMV hepatitis. In the non-cholestatic group, no relapses were observed while one patient in the cholestatic group relapsed and progressed into chronic liver disease. Patients who received supportive treatment showed a marked decrease in GGT, ALT, AST and bilirubin levels spontaneously and no relapses of hepatitis were observed in at least one year of follow-up. Although ganciclovir therapy is not indicated particularly in immunocompetent cases, since most were self-limited infections, in case of progressive and persistent hepatitis, such as in our cases, ganciclovir was a treatment option; no side effect due to ganciclovir therapy was observed in our cases. Although ganciclovir seems to be effective in progressive CMV hepatitis, multicenter randomized studies in a large study group are necessar to determine the efficacy and indications for ganciclovir treatment.


Use of Survival Analysis to Determine the Postincubation Time-to-Death of Papaya Due to Yellow Crinkle Disease in Australia.
The current management recommendation for papaya (Carica papaya) plants exhibiting symptoms of yellow crinkle disease in Australia is the practice of ratooning infected plants. Ratooning involves removing the main stem of diseased papaya plants and allowing a lateral stem (supposedly pathogen-free) to develop and replace the diseased stem. Using nonparametric and parametric methods of survival analysis, we tested different hypotheses regarding plant factors that may influence the postincubation period survival time of phytoplasma-infected papaya. The factors included plant age, the season (wet versus dry) when papaya plants first became symptomatic, and the two predominant phytoplasma strains causing papaya yellow crinkle: tomato big bud (TBB) or sweet potato little leaf strain V4 (SPLL-V4). Median survival time was estimated to be from 4 to 5 months. Therefore, we estimated that the infectious period (incubation period plus the period from postincubation to time-to-death period) of infected papaya ranges from 6 to 9 months. Using parametric accelerated failure modeling and nonparametric Cox proportional hazard modeling, no significant improvement from a null model (no covariates) was found when analyzing plant age, the season a plant was observed to be symptomatic, or phytoplasma strain. However, the season in which a papaya plant became symptomatic differed between the two phytoplasma strains, indicating that the TBB and SPLL-V4 strains may have different modes of insect acquisition and transmission. Because of the long infectious period and the rate of plantto-plant spread, we question the use of ratooning as the primary management tactic for managing papaya yellow crinkle.


Pathgroups, a dynamic data structure for genome reconstruction problems.
Ancestral gene order reconstruction problems, including the median problem, quartet construction, small phylogeny, guided genome halving and genome aliquoting, are NP hard. Available heuristics dedicated to each of these problems are computationally costly for even small instances. We present a data structure enabling rapid heuristic solution to all these ancestral genome reconstruction problems. A generic greedy algorithm with look-ahead based on an automatically generated priority system suffices for all the problems using this data structure. The efficiency of the algorithm is due to fast updating of the structure during run time and to the simplicity of the priority scheme. We illustrate with the first rapid algorithm for quartet construction and apply this to a set of yeast genomes to corroborate a recent gene sequence-based phylogeny. http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html firstname.lastname@example.com Supplementary data are available at Bioinformatics online.


Simultaneous monitoring of cerebral perfusion and cytochrome c oxidase by combining broadband near-infrared spectroscopy and diffuse correlation spectroscopy.
Preterm infants born with very low birth weights are at a high risk of brain injury, in part because the premature brain is believed to be prone to periods of low cerebral blood flow (CBF). Tissue damage is likely to occur if reduction in CBF is sufficient to impair cerebral energy metabolism for extended periods. Therefore, a neuromonitoring method that can detect reductions in CBF, large enough to affect metabolism, could alert the neonatal intensive care team before injury occurs. In this report, we present the development of an optical system that combines diffuse correlation spectroscopy (DCS) for monitoring CBF and broadband near-infrared spectroscopy (B-NIRS) for monitoring the oxidation state of cytochrome c oxidase (oxCCO) - a key biomarker of oxidative metabolism. The hybrid instrument includes a multiplexing system to enable concomitant DCS and B-NIRS measurements while avoiding crosstalk between the two subsystems. The ability of the instrument to monitor dynamic changes in CBF and oxCCO was demonstrated in a piglet model of neonatal hypoxia-ischemia (HI). Experiments conducted in eight animals, including two controls, showed that oxCCO exhibited a delayed response to ischemia while CBF and tissue oxygenation (StO2) responses were instantaneous. These findings suggest that simultaneous neuromonitoring of perfusion and metabolism could provide critical information regarding clinically significant hemodynamic events prior to the onset of brain injury.


A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.
Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).


Serotyping of Toxoplasma gondii Infection Using Peptide Membrane Arrays.
The intracellular parasite Toxoplasma gondii can cause chronic infections in most warm-blooded animals, including humans. In the USA, strains belonging to four different Toxoplasma clonal lineages (types 1, 2, 3, and 12) are commonly isolated, whereas strains not belonging to these lineages are predominant in other continents such as South America. Strain type plays a pivotal role in determining the severity of Toxoplasma infection. Therefore, it is epidemiologically relevant to develop a non-invasive and inexpensive method for determining the strain type in Toxoplasma infections and to correlate the genotype with disease outcome. Serological typing is based on the fact that many host antibodies are raised against immunodominant parasite proteins that are highly polymorphic between strains. However, current serological assays can only reliably distinguish type 2 from non-type 2 infections. To improve these assays, mouse, rabbit, and human infection serum were reacted against 950 peptides from 62 different polymorphic Toxoplasma proteins by using cellulose membrane peptide arrays. This allowed us to identify the most antigenic peptides and to pinpoint the most relevant polymorphisms that determine strain specificity. Our results confirm the utility of previously described peptides and identify novel peptides that improve and increase the specificity of the assay. In addition, a large number of novel proteins showed potential to be used for Toxoplasma diagnosis. Among these, peptides derived from several rhoptry, dense granule, and surface proteins represented promising candidates that may be used in future experiments to improve Toxoplasma serotyping. Moreover, a redesigned version of the published GRA7 typing peptide performed better and specifically distinguished type 3 from non-type 3 infections in sera from mice, rabbits, and humans.


The effect of digested sludge on the common carp, Cyprinus carpio L.
The effects of sewage sludge on the survival of the common carp, Cyprinus carpio, were investigated. It was noted that, when the concentrations of the sludge used for rearing carp exceeded 0.6%, the fish died within 42 days, whereas those reared in 0.2% sludge remained alive and healthy during the trial period. The body and the gills of the dead fish were covered by a veil-like film which looked like coagulated mucus and was formed by the heavy metal ions from the sludge reacting with some constituents of the mucus secreted by the gill. The histopathological symptoms of the various organs further demonstrated that internal injury in liver and kidney was also an important feature of the intoxicants as well as external damage, especially the particles observed around the gills. It was concluded that the optimum concentration of sludge to any species of fish should be determined by testing a series of concentrations before using it as a supplementary fish feed or fish pond fertilizer.


Collaboration between therapists in the simultaneous treatments of a father and son with disorders of masculine identity formation.
A chronically depressed, middle-aged man with numerous intermittent psychotherapies since adolescence, sought treatment for difficulties provoked by his corrupt, former boss. Because of inadequate fathering, he had been unable to consolidate his identity as a man and a father, which inhibited the development of masculine and paternal identity in his oldest son. This patient enacted and worked through massive resistance to experiencing the idealized, paternal transference so lacking in his relationship with his own father; thereby enhancing his son's development and aiding his own separation from his mother and his wife. But this upset the family equilibrium and angered the wife, as she could no longer protect and control her husband and son, thereby enacting her transference to her alcoholic father. The psychotherapists' close collaboration helped elucidate this family's complex, interwoven psychopathology. Simultaneous treatment with collaboration thus contributed to the separation and individuation of father, mother, and son and facilitated later resolution of their oedipal conflicts.


Conceptualising the technical relationship of animal disease surveillance to intervention and mitigation as a basis for economic analysis.
Surveillance and intervention are resource-using activities of strategies to mitigate the unwanted effects of disease. Resources are scarce, and allocating them to disease mitigation instead of other uses necessarily involves the loss of alternative sources of benefit to people. For society to obtain the maximum benefits from using resources, the gains from disease mitigation must be compared to the resource costs, guiding decisions made with the objective of achieving the optimal net outcome. Economics provides criteria to guide decisions aimed at optimising the net benefits from the use of scarce resources. Assessing the benefits of disease mitigation is no exception. However, the technical complexity of mitigation means that economic evaluation is not straightforward because of the technical relationship of surveillance to intervention. We argue that analysis of the magnitudes and distribution of benefits and costs for any given strategy, and hence the outcome in net terms, requires that mitigation is considered in three conceptually distinct stages. In Stage I, 'sustainment', the mitigation objective is to sustain a free or acceptable status by preventing an increase of a pathogen or eliminating it when it occurs. The role of surveillance is to document that the pathogen remains below a defined threshold, giving early warning of an increase in incidence or other significant changes in risk, and enabling early response. If a pathogen is not contained, the situation needs to be assessed as Stage II, 'investigation'. Here, surveillance obtains critical epidemiological information to decide on the appropriate intervention strategy to reduce or eradicate a disease in Stage III, 'implementation'. Stage III surveillance informs the choice, timing, and scale of interventions and documents the progress of interventions directed at prevalence reduction in the population. This article originates from a research project to develop a conceptual framework and practical tool for the economic evaluation of surveillance. Exploring the technical relationship between mitigation as a source of economic value and surveillance and intervention as sources of economic cost is crucial. A framework linking the key technical relationships is proposed. Three conceptually distinct stages of mitigation are identified. Avian influenza, salmonella, and foot and mouth disease are presented to illustrate the framework.