Oregano essential oil vapour prevents Plasmopara viticola infection in grapevine (Vitis Vinifera) and primes plant immunity mechanisms.
The reduction of synthetic fungicides in agriculture is necessary to guarantee a sustainable production that protects the environment and consumers' health. Downy mildew caused by the oomycete Plasmopara viticola is the major pathogen in viticulture worldwide and responsible for up to 60% of pesticide treatments. Alternatives to reduce fungicides are thus utterly needed to ensure sustainable vineyard-ecosystems, consumer health and public acceptance. Essential oils (EOs) are amongst the most promising natural plant protection alternatives and have shown their antibacterial, antiviral and antifungal properties on several agricultural crops. However, the efficiency of EOs highly depends on timing, application method and the molecular interactions between the host, the pathogen and EO. Despite proven EO efficiency, the underlying processes are still not understood and remain a black box. The objectives of the present study were: a) to evaluate whether a continuous fumigation of a particular EO can control downy mildew in order to circumvent the drawbacks of direct application, b) to decipher molecular mechanisms that could be triggered in the host and the pathogen by EO application and c) to try to differentiate whether essential oils directly repress the oomycete or act as plant resistance primers. To achieve this a custom-made climatic chamber was constructed that enabled a continuous fumigation of potted vines with different EOs during long-term experiments. The grapevine (Vitis vinifera) cv Chasselas was chosen in reason of its high susceptibility to Plasmopara viticola. Grapevine cuttings were infected with P. viticola and subsequently exposed to continuous fumigation of different EOs at different concentrations, during 2 application time spans (24 hours and 10 days). Experiments were stopped when infection symptoms were clearly observed on the leaves of the control plants. Plant physiology (photosynthesis and growth rate parameters) were recorded and leaves were sampled at different time points for subsequent RNA extraction and transcriptomics analysis. Strikingly, the Oregano vulgare EO vapour treatment during 24h post-infection proved to be sufficient to reduce downy mildew development by 95%. Total RNA was extracted from leaves of 24h and 10d treatments and used for whole transcriptome shotgun sequencing (RNA-seq). Sequenced reads were then mapped onto the V. vinifera and P. viticola genomes. Less than 1% of reads could be mapped onto the P. viticola genome from treated samples, whereas up to 30% reads from the controls mapped onto the P. viticola genome, thereby confirming the visual observation of P. viticola absence in the treated plants. On average, 80% of reads could be mapped onto the V. vinifera genome for differential expression analysis, which yielded 4800 modulated genes. Transcriptomic data clearly showed that the treatment triggered the plant's innate immune system with genes involved in salicylic, jasmonic acid and ethylene synthesis and signaling, activating Pathogenesis-Related-proteins as well as phytoalexin synthesis. These results elucidate EO-host-pathogen interactions for the first time and indicate that the antifungal efficiency of EO is mainly due to the triggering of resistance pathways inside the host plants. This is of major importance for the production and research on biopesticides, plant stimulation products and for resistance-breeding strategies.


Differences in EMG-moment relationships between ACL-injured and uninjured adults during a weight-bearing multidirectional force control task.
Anterior cruciate ligament injury (ACLi) reduces mechanical knee joint stability. Differences in muscle activation patterns are commonly identified between ACLi individuals and uninjured controls (CON); however, how and which of these differences are adaptations to protect the knee or adversely increase risk of joint instability remain unclear. Since the neuromuscular system integrates activity of all muscles crossing the knee to create a moment-of-force that opposes an external load, this study sought to quantify differences in individual muscle electromyography (EMG)-moment relationships between ACLi and CON. Participants isometrically modulated ground reaction forces during a standing force matching protocol to elicit combinations of sagittal, frontal and transverse plane moments. Partial least squares regressions determined which internal joint moment(s) predicted activation of 10 leg muscles for each group. Compared to CON, ACLi demonstrated greater contribution of rectus femoris to knee extension, semitendinosus and gastrocnemii to knee flexion, and lateral gastrocnemii to knee external rotation moments. ACLi also showed lower contributions of biceps femoris to knee flexion, medial gastrocnemius to internal rotation, and varied hip muscle contributions to frontal plane hip moments. Between group differences in EMG-moment relationships during static conditions suggest neuromuscular contributions to sagittal plane stability increases after ACL injury, while knee stability during knee abduction and external rotation is reduced. Clinical Significance: Clinical assessments of ACLi should account for deficits in frontal and rotational plane stability by including tasks that elicit such loads. Improving hamstring muscle balance, hip abductor and gastrocnemius function may benefit ACLi rehabilitation interventions and should be studied further. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.


EAE/ASE recommendations for the use of echocardiography in new transcatheter interventions for valvular heart disease.
The introduction of devices for transcatheter aortic valve implantation, mitral repair, and closure of prosthetic paravalvular leaks has led to a greatly expanded armamentarium of catheter-based approaches to patients with regurgitant as well as stenotic valvular disease. Echocardiography plays an essential role in identifying patients suitable for these interventions and in providing intra-procedural monitoring. Moreover, echocardiography is the primary modality for post-procedure follow-up. The echocardiographic assessment of patients undergoing transcatheter interventions places demands on echocardiographers that differ from those of the routine evaluation of patients with native or prosthetic valvular disease. Consequently, the European Association of Echocardiography in partnership with the American Society of Echocardiography has developed the recommendations for the use of echocardiography in new transcatheter interventions for valvular heart disease. It is intended that this document will serve as a reference for echocardiographers participating in any or all stages of new transcatheter treatments for patients with valvular heart disease.


Long-term modulation of A-type K(+) conductances in hippocampal CA1 interneurons in rats after chronic intermittent ethanol exposure during adolescence or adulthood.
Chronic alcohol use, especially exposure to alcohol during adolescence or young adulthood, is closely associated with cognitive deficits that may persist into adulthood. Therefore, it is essential to identify possible neuronal mechanisms underlying the observed deficits in learning and memory. Hippocampal interneurons play a pivotal role in regulating hippocampus-dependent learning and memory by exerting strong inhibition on excitatory pyramidal cells. The function of these interneurons is regulated not only by synaptic inputs from other types of neurons but is also precisely governed by their own intrinsic membrane ionic conductances. The voltage-gated A-type potassium current (IA ) regulates the intrinsic membrane properties of neurons, and disruption of IA is responsible for many neuropathological processes including learning and memory deficits. Thus, it represents a previously unexplored cellular mechanism whereby chronic ethanol (EtOH) may alter hippocampal memory-related functioning. Using whole-cell electrophysiological recording methods, we investigated the enduring effects of chronic intermittent ethanol (CIE) exposure during adolescence or adulthood on IA in rat CA1 interneurons. We found that the mean peak amplitude of IA was significantly reduced after CIE in either adolescence or adulthood, but IA density was attenuated after CIE in adolescence but not after CIE in adulthood. In addition, the voltage-dependent steady-state activation and inactivation of IA were altered in interneurons after CIE. These findings suggest that CIE can cause long-term changes in IA channels in interneurons and thus may alter their inhibitory influences on memory-related local hippocampal circuits, which could be, in turn, responsible for learning and memory impairments observed after chronic EtOH exposure.


A broadband and omnidirectional electromagnetic wave concentrator with gradient woodpile structure.
We present the first realized three-dimensional (3D) practical implementation of the so called "optical black hole" in microwave frequencies, an electromagnetic (EM) concentrator. The 3D EM wave concentrator was designed with non-resonant gradient index (GRIN) 3D woodpile photonic crystals (PCs) structure in metamaterial regime, and fabricated by Stereolithography (SL) process. Omnidirectional EM wave capture and absorbing ability of the device in a broad bandwidth (12GHz-15GHz) were validated by full-wave simulation and experiments. Such devices may have applications in microwave energy harvesting and radiation detector.


Common Interests Without Common Expertise: Reflections on Early-career Experiences in Cross-disciplinary Research.
Cross-disciplinary research enables us to tackle complex problems that require expertise from different fields. Such collaborations involve researchers who have different perspectives, communication styles, and knowledge bases, and can produce results far greater than the sum of their parts. However, in an era of increasing scientific specialization, there exist many barriers for students and early career researchers (ECRs) interested in training in and undertaking interdisciplinary research endeavors. This perspective examines the challenges that students and ECRs perceive and experience in cross-disciplinary work and proposes pathways to create more inclusive and welcoming research environments. This work emerges from a National Science Foundation (NSF)-funded workshop held during the Society for Integrative and Comparative Biology (SICB) Annual Meeting in January 2023 in Austin, TX. The workshop brought together seasoned interdisciplinary scientists with undergraduate and graduate students to identify and discuss perceived challenges through small group discussions and experience sharing. Through summarizing a range of student concerns about embarking on careers as interdisciplinary scientists and identifying ways to dismantle institutional and lab management-level barriers, we aim to promote an inclusive and collaborative problem-solving environment for scientists of all experience levels.


Bulk motion-independent analyses of water diffusion changes in the brain during the cardiac cycle.
We evaluated dynamic changes in water diffusion in the brain during the cardiac cycle by using cine diffusion MRI. On a 1.5-T MRI, ECG-triggered single-shot diffusion echo planar imaging was used with sensitivity encoding, halfscan, and rectangular field of view techniques for minimizing bulk motion effects such as brain pulsation, with a data-sampling window of 3 ms. The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) in the white matter zone were determined in ten healthy volunteers and then compared with the intracranial volume change (ICVC) revealed by phase-contrast cine MRI during the cardiac cycle. In addition, a frequency analysis of these waveforms was performed. ADC and FA values changed significantly during the cardiac cycle, despite minimizing the effect of bulk motion, i.e., independent of bulk motion. The ADC was synchronized with the ICVC during the cardiac cycle. A significant positive correlation was noted among their amplitudes. Analysis of the dynamic change of water diffusion by use of cine diffusion MRI facilitates the assessment of intracranial conditions.


Assessing the minimal important difference in symptoms: a comparison of two techniques.
We have developed a method for estimating the minimally important difference (MID) for health status measures. Whereas the conventional approach requires patients to judge themselves relative to their memories, our method requires patients to judge themselves relative to others with the same condition. In this study we examined whether our method (based on between-patient differences) and the conventional method (based on within-patient changes) provides comparable estimates of the MID for one health status measure: the Chronic Respiratory Questionnaire. Patients with chronic obstructive pulmonary disease who were participating in a supervised respiratory rehabilitation program were included if they were in stable health (n = 112). Their mean score per question in the Chronic Respiratory Questionnaire was 4.5 (range, 1 to 7; where bigger values indicate better health). Our method estimated that the MID was 0.5 (95% confidence interval 0.4 to 0.7). This estimate was similar to the MID previously found using the conventional method. These observations support the role of the Chronic Respiratory Questionnaire for measuring patient's symptoms, the validity of our approach for assessing the MID, and an estimate on the order of 0.5 as the threshold for this particular health status measure.


1.76Tb/s Nyquist PDM 16QAM signal transmission over 714km SSMF with the modified SCFDE technique.
Nyquist pulse shaping is a promising technique for high-speed optical fiber transmission. We experimentally demonstrate the generation and transmission of a 1.76Tb/s, polarization-division-multiplexing (PDM) 16 quadrature amplitude modulation (QAM) Nyquist pulse shaping super-channel over 714km standard single-mode fiber (SSMF) with Erbium-doped fiber amplifier (EDFA) only amplification. The superchannel consists of 40 subcarriers tightly spaced at 6.25GHz with a spectral efficiency of 7.06b/s/Hz. The experiment is successfully enabled with the modified single carrier frequency domain estimation and equalization (SCFDE) scheme by performing training sequence based channel estimation in frequency domain and subsequent channel equalization in time domain. After 714km transmission, the bit-error-rate (BER) of all subcarriers are lower than the forward error correction limit of 3.8 × 10(-3).


Is the NICE traffic light system fit-for-purpose for children presenting with undifferentiated acute illness in primary care?
The National Institute of Clinical Excellence (NICE) traffic light system uses children's symptoms and signs to categorise acute infections into red, amber and green. To our knowledge, no study has described the proportion of children with acute undifferentiated illness who fall into these categories in primary care, which is important since red and amber children are considered at higher risk of serious illness requiring urgent secondary care assessment. To estimate the proportion of acutely unwell children presenting to primary care classified by the NICE traffic light system as red, amber or green, and to describe their initial management. Secondary analysis of the Diagnosis of Urinary Tract infection in Young children prospective cohort study. 6797 children under 5 years presenting to 225 general practices with acute undifferentiated illness were retrospectively mapped to the NICE traffic light system by a panel of general practitioners. 6406 (94%) children were classified as NICE red (32%) or amber (62%) with 1.6% red and 0.3%, respectively, referred the same day for hospital assessment; and 46% and 31%, respectively, treated with antibiotics. The remaining 385 (6%) were classified green, with none referred and 27% treated with antibiotics. Results were robust to sensitivity analyses. The majority of children presenting to UK primary care with acute undifferentiated illness meet red or amber NICE traffic light criteria,with only 6% classified as low risk, making it unfit for use in general practice. Research is urgently needed to establish as triage system suitable for general practice.


Predisposing factors to bacterial colonization in chronic obstructive pulmonary disease.
The aim of this prospective observational study was to determine those factors influencing bacterial colonization in patients with stable chronic obstructive pulmonary disease (COPD). Eighty-eight outpatients with stable COPD and 20 patients with normal spirometry and chest radiography (controls) had a fibreoptic bronchoscopy performed with topical aerosol anaesthesia. Bacterial colonization was determined using the protected specimen brush (PSB) with a cut-off > or = 10(3) colony-forming units (CFU x mL(-1)). The influence of age, degree of airflow obstruction, smoking habit, pack-yrs of smoking, and chest radiographic findings on bacterial colonization were assessed by univariate and multivariate analysis. Significant bacterial growth was found in 40% of patients and in none of the controls. Haemophilus influenzae, Streptococcus viridans, S. pneumoniae and Moraxella catarrhalis were the most frequent pathogens. After adjustment for other variables, severe airflow limitation (odds ratio (OR) 5.11, 95% confidence interval (CI) 1.45-17.9) and current smoking (OR 3.17, 95% CI 2.5-8) remained associated with positive bacterial cultures. When only potentially pathogenic micro-organisms were considered, significant bacterial growth was found in 30.7% of patients, with severe airflow obstruction (OR 9.28, 95% CI 2.19-39.3) being the only variable independently associated with positive bacterial cultures. Our results show that stable chronic obstructive pulmonary disease patients have a high prevalence of bacterial colonization of distal airways which is mainly related to the degree of airflow obstruction and cigarette smoking.


Robot-Based Assessment of HIV-Related Motor and Cognitive Impairment for Neurorehabilitation.
There is a pressing need for strategies to slow or treat the progression of functional decline in people living with HIV. This paper explores a novel rehabilitation robotics approach to measuring cognitive and motor impairment in adults living with HIV, including a subset with stroke. We conducted a cross-sectional study with 21 subjects exhibiting varying levels of cognitive and motor impairment. We tested three robot-based tasks - trajectory tracking, N-back, and spatial span - to assess if metrics derived from these tasks were sensitive to differences in subjects with varying levels of executive function and upper limb motor impairments. We also examined how well these metrics could estimate clinical cognitive and motor scores. The results showed that the average sequence length on the robot-based spatial span task was the most sensitive to differences between various cognitive and motor impairment levels. We observed strong correlations between robot-based measures and clinical cognitive and motor assessments relevant to the HIV population, such as the Color Trails 1 (rho = 0.83), Color Trails 2 (rho = 0.71), Digit Symbol - Coding (rho = 0.81), Montreal Cognitive Assessment - Executive Function subscore (rho = 0.70), and Box and Block Test (rho = 0.74). Importantly, our results highlight that gross motor impairment may be overlooked in the assessment of HIV-related disability. This study shows that rehabilitation robotics can be expanded to new populations beyond stroke, namely to people living with HIV and those with cognitive impairments.


Anti-borreliae efficacy of selected organic oils and fatty acids.
Borrelia sp. is a causative pathogen of Lyme disease which has become a worldwide health concern. Non-toxic approaches especially directed toward latent persistent forms of this pathogen are desired. Lipids in the form of volatile and non-volatile oils, and fatty acids with proven anti-borreliae efficacy could become an additional support or an alternative for consideration in treatment approaches. In this study we investigated 47 lipids (30 volatile and non-volatile oils, and 17 fatty acids) of plant and animal origin against typical motile, knob/round-shaped persisters, and biofilm-like aggregates of Borrelia burgdorferi s.s. and Borrelia garinii, which are identified as pathogenic factors of Lyme disease in the USA and Europe, using direct microscopic counting and spectrofluorometric measurements. Out of all examined lipids, 5 oils (Bay leaf oil, Birch oil, Cassia oil, Chamomile oil German, and Thyme oil) at or below 0.25%, and 3 fatty acids (13Z,16Z Docosadienoic acid, erucic acid, and petroselinic acid) at or below 0.75 mg/ml, showed bactericidal activity against typical motile spirochetes and knob/round-shaped persisters. Only Bay leaf oil and Cassia oil, including their major constituents, eugenol and cinnamaldehyde, showed to target biofilm-like aggregates of both tested Borrelia spp. at the same concentration, although with 20-30% eradication mark. Based on obtained results, volatile oils were more potent than non-volatile oils, and unsaturated fatty acids were more effective than saturated fatty acids. Among all tested oils, Bay leaf oil and Cassia oil, with their major components eugenol and cinnamaldehyde, seem to have the highest anti-borreliae efficacy.


De novo assembly of highly diverse viral populations.
Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.


Control of bacterial motility by environmental factors in polarly flagellated and peritrichous bacteria isolated from Lake Baikal.
Despite numerous studies on bacterial motility, little is known about the regulation of this process by environmental factors in natural isolates. In this study we investigated the control of bacterial motility in response to environmental parameters in two strains isolated from the natural habitat of Lake Baikal. Morphological characterization, carbon source utilization, fermentation analysis, and sequence comparison of 16S rRNA genes showed that these strains belong to two distinct genera, i.e., Enterobacter and Pseudomonas; they were named strains 22 and Y1000, respectively. Both strains swarmed at 25 degrees C and remained motile at low temperatures (4 degrees C), especially the Pseudomonas strain, which further supports the psychrotrophic characteristics of this strain. In contrast, a strong inhibition of motility was observed at above 30 degrees C and with a high NaCl concentration. The existence of flagellar regulatory proteins FlhDC and FleQ was demonstrated in Enterobacter strain 22 and Pseudomonas strain Y1000, respectively, and environmental conditions reduced the expression of the structural genes potentially located at the first level in the flagellar cascade in both organisms. Finally, as in Enterobacter strain 22, a strong reduction in the transcription of the master regulatory gene fleQ was observed in Pseudomonas strain Y1000 in the presence of novobiocin, a DNA gyrase inhibitor, suggesting a link between DNA supercoiling and motility control by environmental factors. Thus, striking similarities observed in the two organisms suggest that these processes have evolved toward a similar regulatory mechanism in polarly flagellated and laterally flagellated (peritrichous) bacteria.


Postprandial colonic transit and motor activity in chronic constipation.
The aim of this study was to correlate colonic motility and transit in patients with constipation and symptoms of the irritable bowel syndrome. Studies were performed in 16 patients with constipation and compared with the results in 12 healthy subjects. Intraluminal pressure was measured with perfused catheter ports in the transverse colon, splenic flexure, and descending and sigmoid colon. Movement of the luminal contents was measured by following the movement of Technetium-99m-DTPA that was instilled as a bolus in the splenic flexure. In both healthy subjects and patients with constipation there was no movement of the intraluminal tracer and no increase in intraluminal pressure during fasting. After eating a meal, healthy subjects and one group of the constipated patients had an increase in the radioactive marker in the transverse colon (p less than 0.03) and in the sigmoid colon (p less than 0.03). The movement of the intraluminal contents was associated with a positive pressure gradient between the descending colon and the transverse and sigmoid colon. There was no retrograde movement of the intraluminal contents and no postprandial increase in intraluminal pressure in the second group of patients with constipation. In healthy subjects, propagating contractions, which were associated with the rapid movement of intraluminal contents, began 60 min after eating. There were no propagating contractions in patients with constipation. These studies suggest that (a) the movement of intraluminal contents in healthy and constipated patients is determined by the postprandial pressure gradients within the colon, and (b) the propagating contraction is necessary for a normal bowel habit.


Sociodemographic Factors, Sexual Behaviors, and Alcohol and Recreational Drug Use Associated with HIV Among Men Who Have Sex with Men in Southern Vietnam.
A total of 2768 MSM participated in a survey in southern Vietnam. Univariate and multivariate logistic regression analyses were performed to determine predictors of HIV infection. The prevalence of HIV among MSM was 2.6 %. HIV infection was more likely in MSM who were older, had a religion, had engaged in anal sex with a foreigner in the past 12 months, previously or currently used recreational drugs, perceived themselves as likely or very likely to be infected with HIV, and/or were syphilis seropositive. MSM who had ever married, were exclusively or frequently receptive, sometimes consumed alcohol before sex, and/or frequently used condoms during anal sex in the past 3 months were less likely to be infected with HIV. Recreational drug use is strongly associated with HIV infection among MSM in southern Vietnam. HIV interventions among MSM should incorporate health promotion, condom promotion, harm reduction, sexually transmitted infection treatment, and address risk behaviors.


The global health network on alcohol control: successes and limits of evidence-based advocacy.
Global efforts to address alcohol harm have significantly increased since the mid-1990 s. By 2010, the World Health Organization (WHO) had adopted the non-binding Global Strategy to Reduce the Harmful Use of Alcohol. This study investigates the role of a global health network, anchored by the Global Alcohol Policy Alliance (GAPA), which has used scientific evidence on harm and effective interventions to advocate for greater global public health efforts to reduce alcohol harm. The study uses process-tracing methodology and expert interviews to evaluate the accomplishments and limitations of this network. The study documents how network members have not only contributed to greater global awareness about alcohol harm, but also advanced a public health approach to addressing this issue at the global level. Although the current network represents an expanding global coalition of like-minded individuals, it faces considerable challenges in advancing its cause towards successful implementation of effective alcohol control policies across many low- and middle-income countries (LMICs). The analysis reveals a need to transform the network into a formal coalition of regional and national organizations that represent a broader variety of constituents, including the medical community, consumer groups and development-focused non-governmental organizations. Considering the growing harm of alcohol abuse in LMICs and the availability of proven and cost-effective public health interventions, alcohol control represents an excellent 'buy' for donors interested in addressing non-communicable diseases. Alcohol control has broad beneficial effects for human development, including promoting road safety and reducing domestic violence and health care costs across a wide variety of illnesses caused by alcohol consumption.


Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo.
Cell lines are often regarded as clonal, even though this simplifies what is known about mutagenesis, transformation and other processes that destabilize them over time. Monitoring these clonal dynamics is important for multiple areas of biomedical research, including stem cell and cancer biology. Tracking the contributions of individual cells to large populations, however, has been constrained by limitations in sensitivity and complexity. We utilize cellular barcoding methods to simultaneously track the clonal contributions of tens of thousands of cells. We demonstrate that even with optimal culturing conditions, common cell lines including HeLa, K562 and HEK-293 T exhibit ongoing clonal dynamics. Starting a population with a single clone diminishes but does not eradicate this phenomenon. Next, we compare lentiviral and zinc-finger nuclease barcode insertion approaches, finding that the zinc-finger nuclease protocol surprisingly results in reduced clonal diversity. We also document the expected reduction in clonal complexity when cells are challenged with genotoxic stress. Finally, we demonstrate that xenografts maintain clonal diversity to a greater extent than in vitro culturing of the human non-small-cell lung cancer cell line HCC827. We demonstrate the feasibility of tracking and quantifying the clonal dynamics of entire cell populations within multiple cultured cell lines. Our results suggest that cell heterogeneity should be considered in the design and interpretation of in vitro culture experiments. Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents.


Palmoplantar exfoliation due to chloroquine.
Chloroquine is the drug very frequently used for the treatment of malaria. It is also used in amebiasis, rheumatoid arthritis, and various dermatological conditions. Chloroquine can cause muscle problems, loss of appetite, and diarrhea as a side effect. Cutaneous toxicity includes pruritus, hair loss, photosensitivity, and color changes. Exfoliation of skin over palms and soles is caused by chemotherapeutic drugs such as axitinib, fluorouracil, idarubicin, doxorubicin, sunitinib, sorafenib, and paclitaxel. Here, a case of a 40-year-old female is presented who developed palmoplantar exfoliation with depigmentation after taking chloroquine. Although not life-threatening, this side effect of a commonly used drug may cause anxiety and functional impairment which in turn affects the quality of life of an individual.


Hypertensive Disorders of Pregnancy in Relation to Coffee and Tea Consumption: The Japan Environment and Children's Study.
The association between coffee/tea intake and hypertensive disorders of pregnancy (HDP) remains unclear. This study aimed to investigate the association of caffeine, coffee, and tea intake during pregnancy with the risk of HDP. We assessed this association in 85,533 singleton pregnant women with live births in the Japan Environment and Children's Study, a prospective cohort in Japan that included women from early pregnancy onward. Caffeinated and decaffeinated coffee and tea (green, oolong, and black) consumption during pregnancy was assessed using a validated food frequency questionnaire conducted at mid-pregnancy, and caffeine intake was calculated based on coffee and tea consumption. Multivariable logistic regression was used to assess the association with the risk of HDP. HDP developed in 2222 women (2.6%). Caffeine intake was weakly associated with increased risk of HDP; the multivariable odds ratio of HDP for the highest versus the lowest quartile was 1.26 (95% confidence interval: 1.11, 1.43). Coffee drinkers of two or more cups per day showed a decreased risk compared with non-drinkers (multivariable odds ratio 0.79; 0.62, 0.99) even after adjustment for total caffeine intake. Tea consumption was not associated with the risk of HDP. Our study suggests that higher caffeine intake may increase HDP risk, while coffee drinkers had a lower risk. Further high-quality studies are needed to replicate these findings, and to elucidate if other substances in coffee may be protective against HDP.


25 years of the WHO essential medicines lists: progress and challenges.
The first WHO essential drugs list, published in 1977, was described as a peaceful revolution in international public health. The list helped to establish the principle that some medicines were more useful than others and that essential medicines were often inaccessible to many populations. Since then, the essential medicines list (EML) has increased in size; defining an essential medicine has moved from an experience to an evidence-based process, including criteria such as public-health relevance, efficacy, safety, and cost-effectiveness. High priced medicines such as antiretrovirals are now included. Differences exist between the WHO model EML and national EMLs since countries face varying challenges relating to costs, drug effectiveness, morbidity patterns, and rationality of prescribing. Ensuring equitable access to and rational use of essential medicines has been promoted through WHO's revised drug strategy. This approach has required an engagement by WHO on issues such as the effect of international trade agreements on access to essential medicines and research and development to ensure availability of new essential medicines.


PanCareLIFE: The scientific basis for a European project to improve long-term care regarding fertility, ototoxicity and health-related quality of life after cancer occurring among children and adolescents.
Survival after cancer diagnosed during childhood or adolescence continues to improve with new treatments and supportive therapies. Optimal long-term care requires that risks to vulnerable organs are clearly defined and translated into guidelines that are implemented into practice. PanCareLIFE is a pan-European consortium that addresses survivorship issues comprising fertility, hearing impairment and quality of life. This article describes the scientific basis of PanCareLIFE's studies. PanCareLIFE involves 17 partner institutions from eight European countries, with additional 11 data providers from five other countries. Study designs and methods include molecular genetic, cohort and case-control studies, a longitudinal study and an intervention study. Ethics and data protection issues have been taken into account from the beginning. PanCareLIFE will investigate the way that treatment impairs female fertility, by evaluating anti-Müllerian hormone levels and the underlying genetic susceptibility to loss of fertility. For our fertility studies, more than 6000 survivors have completed questionnaires, more than 1500 provided serum samples and more than 400 case-control triads have been identified. Fertility preservation guidelines for boys and girls will be developed. More than 2000 survivors have contributed audiograms for the ototoxicity study. Almost 1000 samples were sent for genetic analysis related to ototoxicity and gonadal reserve. The SF-36 questionnaire will measure quality of life in more than 10,000 survivors. The large number of subjects enrolled in PanCareLIFE and the detailed information accumulated will allow in-depth evaluation of important outcomes. Fertility preservation guidelines will help patients and their families make informed decisions and contribute to their long-term well-being.


Direct determination of urinary creatinine by reactive-thermal desorption-extractive electrospray-ion mobility-tandem mass spectrometry.
A direct, ambient ionization method has been developed for the determination of creatinine in urine that combines derivatization and thermal desorption with extractive electrospray ionization and ion mobility-mass spectrometry. The volatility of creatinine was enhanced by a rapid on-probe aqueous acylation reaction, using a custom-made thermal desorption probe, allowing thermal desorption and ionization of the monoacylated derivative. The monoacyl creatinine [M + H](+) ion (m/z 156) was subjected to mass-to-charge selection and collision induced dissociation to remove the acyl group, generating the protonated creatinine [M + H](+) product ion at m/z 114 before an ion mobility separation was applied to reduce chemical noise. Stable isotope dilution using creatinine-d3 as internal standard was used for quantitative measurements. The direct on-probe derivatization allows high sample throughput with a typical cycle time of 1 min per sample. The method shows good linearity (R(2) = 0.986) and repeatability (%RSD 8-10%) in the range of 0.25-2.0 mg/mL. The creatinine concentrations in diluted urine samples from a healthy individual were determined to contain a mean concentration of 1.44 mg/mL creatinine with a precision (%RSD) of 9.9%. The reactive ambient ionization approach demonstrated here has potential for the determination of involatile analytes in urine and other biofluids.


Real-time, high-accuracy 3D imaging and shape measurement.
In spite of the recent advances in 3D shape measurement and geometry reconstruction, simultaneously achieving fast-speed and high-accuracy performance remains a big challenge in practice. In this paper, a 3D imaging and shape measurement system is presented to tackle such a challenge. The fringe-projection-profilometry-based system employs a number of advanced approaches, such as: composition of phase-shifted fringe patterns, externally triggered synchronization of system components, generalized system setup, ultrafast phase-unwrapping algorithm, flexible system calibration method, robust gamma correction scheme, multithread computation and processing, and graphics-processing-unit-based image display. Experiments have shown that the proposed system can acquire and display high-quality 3D reconstructed images and/or video stream at a speed of 45 frames per second with relative accuracy of 0.04% or at a reduced speed of 22.5 frames per second with enhanced accuracy of 0.01%. The 3D imaging and shape measurement system shows great promise of satisfying the ever-increasing demands of scientific and engineering applications.


Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure.
Inherited bone marrow failure syndromes, such as Fanconi anemia (FA) and Shwachman-Diamond syndrome (SDS), feature progressive cytopenia and a risk of acute myeloid leukemia (AML). Using deep phenotypic analysis of early progenitors in FA/SDS bone marrow samples, we revealed selective survival of progenitors that phenotypically resembled granulocyte-monocyte progenitors (GMP). Whole-exome and targeted sequencing of GMP-like cells in leukemia-free patients revealed a higher mutation load than in healthy controls and molecular changes that are characteristic of AML: increased G>A/C>T variants, decreased A>G/T>C variants, increased trinucleotide mutations at Xp(C>T)pT, and decreased mutation rates at Xp(C>T)pG sites compared with other Xp(C>T)pX sites and enrichment for Cancer Signature 1 (X indicates any nucleotide). Potential preleukemic targets in the GMP-like cells from patients with FA/SDS included SYNE1, DST, HUWE1, LRP2, NOTCH2, and TP53. Serial analysis of GMPs from an SDS patient who progressed to leukemia revealed a gradual increase in mutational burden, enrichment of G>A/C>T signature, and emergence of new clones. Interestingly, the molecular signature of marrow cells from 2 FA/SDS patients with leukemia was similar to that of FA/SDS patients without transformation. The predicted founding clones in SDS-derived AML harbored mutations in several genes, including TP53, while in FA-derived AML the mutated genes included ARID1B and SFPQ. We describe an architectural change in the hematopoietic hierarchy of FA/SDS with remarkable preservation of GMP-like populations harboring unique mutation signatures. GMP-like cells might represent a cellular reservoir for clonal evolution.


Foraging strategy of wasps - optimisation of intake rate or energetic efficiency?
In endothermic wasps, foraging is an expensive activity. To maximise the benefit for the colony, wasps can optimise either the intake rate or energetic efficiency of a foraging trip. We investigated the foraging behaviour of vespine wasps under variable environmental and reward conditions. We trained them to forage for 0.5 mol l-1 sucrose solution from an artificial flower in a flow-through respiratory measurement chamber, and simultaneously measured their body temperature using infrared thermography to investigate interactions between thermoregulation and energetics. Measurement of carbon dioxide release (for energetic calculations) and load mass enabled the direct determination of foraging efficiency. An unlimited reward increased the wasps' energetic effort to increase the suction speed through high body temperatures. With reduced reward (limited flow), when an increased body temperature could not increase suction speed, the wasps decreased their body temperature to reduce the metabolic effort. Solar heat gain was used differently, either to increase body temperature without additional metabolic effort or to save energy. The foraging efficiency was mainly determined by the flow rate, ambient temperature and solar heat gain. In shade, an unlimited sucrose flow and a high ambient temperature yielded the highest energetic benefit. A limited flow reduced foraging efficiency in the shade, but only partly in sunshine. Solar radiation boosted the efficiency at all reward rates. Wasps responded flexibly to varying reward conditions by maximising intake rate at unlimited flow and switching to the optimisation of foraging efficiency when the intake rate could not be enhanced due to a limited flow rate.


Application of media literacy education for changing attitudes about self-medication of slimming supplements.
Background: Self-medication of slimming supplements has increased, and media advertising has a role in this. The present study aimed at determining the effect of media literacy educational intervention on attitudes about self-medication of slimming supplements among the female students at dormitories of Iran University of Medical Sciences. Methods: In this quasi-experimental study with a control group, 98 students were selected by multistage cluster sampling method and were randomly divided into 2 equal groups of test and control. The data collecting instrument was a researcher-made questionnaire about media literacy and attitude on self-medication of slimming pills. Based on the results obtained from the early completion of the questionnaires, an appropriate educational intervention was designed and implemented. Data were analyzed 1 and 3 months after the intervention using the following statistical methods: repeated measurements, Friedman test, Chi square, independent T-test and MannWhitney test. Results: Before the intervention, the mean scores of attitude and dimensions of media literacy were moderate in both groups, and there was no significant difference between them. However, positive correlations were observed among attitude and knowledge (r=0.99, p= 0.001), critical thinking (r= 0.61, p= 0.001), and analysis (r= 0.37, p= 0.009) in the experimental group. The mean scores of attitudes and dimensions of media literacy were found to be significant in both groups 1 and 3 months after the intervention (p<0.05). Conclusion: Media literacy education was effective in promoting a positive attitude about slimming supplements.


Genome sequence of a 45,000-year-old modern human from western Siberia.
We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.


Gene expression profiling of tolerant barley in response to Diuraphis noxia (Hemiptera: Aphididae) feeding.
Aphids are, arguably, the single most damaging group of agricultural insect pests throughout the world. Plant tolerance, which is a plant response to an insect pest, is viewed as an excellent management strategy. Developing testable hypotheses based on genome-wide and more focused methods will help in understanding the molecular underpinnings of plant tolerance to aphid herbivory. As a first step in this process, we undertook transcript profiling with Affymetrix GeneChip Barley Genome arrays using RNA extracted from tissues of tolerant and susceptible genotypes collected at three hours, three days and six days after Diuraphis noxia introduction. Acquired data were compared to identify changes unique to the tolerant barley at each harvest date. Transcript abundance of 4086 genes was differentially changed over the three harvest dates in tolerant and susceptible barley in response to D. noxia feeding. Across the three harvest dates, the greatest number of genes was differentially expressed in both barleys at three days after aphid introduction. A total of 909 genes showed significant levels of change in the tolerant barley in response to D. noxia feeding as compared to susceptible plants infested with aphids. Many of these genes could be assigned to specific metabolic categories, including several associated with plant defense and scavenging of reactive oxygen species (ROS). Interestingly, two peroxidase genes, designated HvPRXA1 and HvPRXA2, were up-regulated to a greater degree in response to D. noxia feeding on tolerant barley plants, indicating that specific peroxidases could be important for the tolerance process. These findings suggest that the ability to elevate and sustain levels of ROS-scavenging enzymes could play an important role in the tolerant response.


Differences in the effects of simulated sea aerosol on water relations, salt content, and leaf ultrastructure of rock-rose plants.
White-leaf rock-rose (Cistus albidus L.) and Montpellier rock-rose (C. monspeliensis L.) plants were sprayed 2 to 3 min per day over a 7-d period, in an unheated plastic greenhouse, with different aqueous solutions containing deionized water alone (control); an anionic surfactant (sodium dodecylbenzenesulfonate 82.5%, 50 mg L(-1)) (S1); a solution simulating the composition of sea aerosol (S2); and a solution simulating sea aerosol with anionic surfactant (S3). White-leaf rock-rose was more sensitive to sea aerosol, showing greater leaf damage and markedly decreased growth, and the presence of surfactant enhanced the phytotoxic effect leading to greater increases in mortality. Montpellier rock-rose did not appear to be more adversely affected when surfactant was used in combination with sea aerosol, and manifested slight or less severe symptoms than white-leaf rock-rose. There was a significant increase in leaf turgor potential in the plants treated with both sea aerosol treatments by osmotic adjustment effect. The decrease in photosynthesis level seems to be due to both stomatal and nonstomatal factors. The results of microscopical analysis of Montpellier rock-rose plants show that sea aerosol treatment caused alterations in the chloroplast structure, reducing the starch grain and swelling the thylakoid membranes. The results of this study indicated that Montpellier rock-rose was more tolerant to sea aerosol than white-leaf rock-rose, showing a lower reduction in plant growth and less leaf damage, probably because of its ability to compartmentalize the toxic ions at the intracellular level.


A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo.
The paper describes a mechanical model of epithelial tissue development in Drosophila embryos to investigate a buckling phenomenon called invagination. The finite element method is used to model this ventral furrow formation in 3D by decomposing the total deformation into two parts: an imposed active deformation, and an elastic passive deformation superimposed onto the latter. The model imposes as boundary conditions (i) a constant yolk volume and (ii) a sliding contact condition of the cells against the vitelline membrane, which is interpolated as a B-Spline surface. The active deformation simulates the effects of apical constriction and apico-basal elongation of cells. This set of local cellular mechanisms leads to global shape changes of the embryo which are associated with known gene expressions. Using the model we have tested different plausible hypotheses postulated to account for the mechanical behaviour of epithelial tissues. In particular, we conclude that only certain combinations of local cell shape change can successfully reproduce the invagination process. We have quantitatively compared the model with a 2D model and shown that it exhibits a more robust invagination phenomenon. The 3D model has also revealed that invagination causes a yolk flow from the central region to the anterior and posterior ends of the embryo, causing an accordion-like global compression and expansion wave to move through the embryo. Such a phenomenon cannot be described by 2D models.


Atopic dermatitis, melatonin, and sleep disturbance.
Sleep disturbance is common in patients with atopic dermatitis (AD). However, studies have largely been questionnaire-based, and the pathophysiology remains unclear. The aims of this study were to determine objective characteristics of sleep disturbance in children with AD and explore contributing factors and clinical predictors. Sleep parameters were measured by actigraphy and polysomnography in 72 patients with AD and 32 controls ages 1 to 18 years. Urinary 6-sulfatoxymelatonin levels, serum cytokines, and total and allergen-specific immunoglobulin E (IgE) levels were also measured. The patients with AD had significantly reduced sleep efficiency, longer sleep onset latency, more sleep fragmentation, and less nonrapid eye movement sleep. Results from actigraphy correlated well with those from polysomnography. The AD disease severity was associated with sleep disturbance (r = 0.55-0.7), and a Scoring Atopic Dermatitis index of ≥48.7 predicted poor sleep efficiency with a sensitivity of 83.3% and a specificity of 75% (area under the curve = 0.81, P = .001). Lower nocturnal melatonin secretion was significantly associated with sleep disturbance in the patients with AD. Other correlates of sleep disturbance included pruritus, scratching movements, higher total serum IgE levels, and allergic sensitization to dust mite and staphylococcal enterotoxins. Poor sleep efficiency is common in children with AD and can be predicted by the Scoring Atopic Dermatitis index. Melatonin and IgE might play a role in the sleep disturbance. Further studies are required to explore the mechanisms and clinical implications, and actigraphy could serve as a useful evaluating tool.


Immune status of free-ranging green turtles with fibropapillomatosis from Hawaii.
Cell-mediated and humoral immune status of free-ranging green turtles (Chelonia mydas) in Hawaii (USA) with and without fibropapillornatosis (FP) were assessed. Tumored and non-tumored turtles from Kaneohe Bay (KB) on the island of Oahu and from FP-free areas on the west (Kona/Kohala) coast of the island of Hawaii were sampled from April 1998 through February 1999. Turtles on Oahu were grouped (0-3) for severity of tumors with 0 for absence of tumors, 1 for light, 2 for moderate, and 3 for most severe. Turtles were weighed, straight carapace length measured and the regression slope of weight to straight carapace length compared between groups (KB0, KB1, KB2, KB3, Kona). Blood was assayed for differential white blood cell count, hematocrit, in vitro peripheral blood mononuclear cell (PBMC) proliferation in the presence of concanavalin A (ConA) and phytohaemagglutinin (PHA), and protein electrophoresis. On Oahu, heterophil/lymphocyte ratio increased while eosinophil/monocyte ratio decreased with increasing tumors score. Peripheral blood mononuclear cell proliferation indices for ConA and PHA were significantly lower for turtles with tumor scores 2 and 3. Tumor score 3 turtles (KB3) had significantly lower hematocrit, total protein, alpha 1, alpha 2, and gamma globulins than the other four groups. No significant differences in immune status were seen between non-tumored (or KB1) turtles from Oahu and Hawaii. There was no significant difference between groups in regression slopes of body condition to carapace length. We conclude that turtles with severe FP are imunosuppressed. Furthermore, the lack of significant difference in immune status between non-tumored (and KB1) turtles from Oahu and Kona/Kohala indicates that immunosuppression may not be a prerequisite for development of FP.


Socially-assigned race and health: a scoping review with global implications for population health equity.
Self-identified race/ethnicity is largely used to identify, monitor, and examine racial/ethnic inequalities. A growing body of work underscores the need to consider multiple dimensions of race - the social construction of race as a function of appearance, societal interactions, institutional dynamics, stereotypes, and social norms. One such multidimensional measure is socially-assigned race, the perception of one's race by others, that may serve as the basis for differential or unfair treatment and subsequently lead to deleterious health outcomes. We conducted a scoping review to systematically appraise the socially-assigned race and health literature. A systematic search of the PubMed, Web of Science, 28 EBSCO databases and 24 Proquest databases up to September 2019 was conducted and supplemented by a manual search of reference lists and grey literature. Quantitative and qualitative studies that examined socially-assigned race and health or health-related outcomes were considered for inclusion. Eighteen articles were included in the narrative synthesis. Self-rated health and mental health were among the most frequent outcomes studied. The majority of studies were conducted in the United States, with fewer studies conducted in New Zealand, Canada, and Latin America. While most studies demonstrate a positive association between social assignment as a disadvantaged racial or ethnic group and poorer health, some studies did not document an association. We describe key conceptual and methodological considerations that should be prioritized in future studies examining socially-assigned race and health. Socially-assigned race can provide additional insight into observed differential health outcomes among racial/ethnic groups in racialized societies based upon their lived experiences. Studies incorporating socially-assigned race warrants further investigation and may be leveraged to examine nuanced patterns of racial health advantage and disadvantage.


Spontaneous Bone Regeneration After Large Craniectomy in Pediatric Patient.
In children, decompressive craniectomy is commonly performed in cases of increased intracranial pressure that is not medically managed. Currently, it is standard practice to perform cranioplasty after decompressive craniectomy, although optimal timing for the procedure remains controversial. To date, few studies have reported spontaneous cranial bone regeneration in children without intervention. A 7-year-old female presented with frontotemporal bone fractures accompanied by dura mater lacerations and brain edema after a motor vehicle accident. She underwent a large decompressive craniectomy and repair of the lacerated dura with a collagen dural substitute. The patient was discharged from the hospital and did not present for follow-up until 10 months after surgery. At that time, computed tomography imaging revealed remarkable spontaneous bone regeneration. With conservative management, she developed enough bone regeneration in the calvarial defect area that cranioplasty surgery was deemed unnecessary. To this date, the patient has no aesthetic deformation of the skull bone and does not exhibit any residual cognitive impairment or motor deficits. This case report shows that cranial bone regeneration is possible in children older than 6 years old, bypassing the need for cranioplasty after decompressive craniectomy. On the basis of this observation, we recommend that more studies should be performed to identify the factors involved in spontaneous skull bone regeneration in the pediatric population.


Complexity analysis of resting-state MEG activity in early-stage Parkinson's disease patients.
The aim of the present study was to analyze resting-state brain activity in patients with Parkinson's disease (PD), a degenerative disorder of the nervous system. Magnetoencephalography (MEG) signals were recorded with a 151-channel whole-head radial gradiometer MEG system in 18 early-stage untreated PD patients and 20 age-matched control subjects. Artifact-free epochs of 4 s (1250 samples) were analyzed with Lempel-Ziv complexity (LZC), applying two- and three-symbol sequence conversion methods. The results showed that MEG signals from PD patients are less complex than control subjects' recordings. We found significant group differences (p-values <0.01) for the 10 major cortical areas analyzed (e.g., bilateral frontal, central, temporal, parietal, and occipital regions). In addition, using receiver-operating characteristic curves with a leave-one-out cross-validation procedure, a classification accuracy of 81.58% was obtained. In order to investigate the best combination of LZC results for classification purposes, a forward stepwise linear discriminant analysis with leave-one out cross-validation was employed. LZC results (three-symbol sequence conversion) from right parietal and temporal brain regions were automatically selected by the model. With this procedure, an accuracy of 84.21% (77.78% sensitivity, 90.0% specificity) was achieved. Our findings demonstrate the usefulness of LZC to detect an abnormal type of dynamics associated with PD.


Adverse drug events caused by serious medication administration errors.
To determine how often serious or life-threatening medication administration errors with the potential to cause harm (potential adverse drug events) result in actual harm (adverse drug events (ADEs)) in the hospital setting. Retrospective chart review of clinical events following observed medication administration errors. Medication errors are common at the medication administration stage for inpatients. While many errors can cause harm, it is unclear exactly how often. In a previous study where 14 041 medication administrations were directly observed, 1271 medication administration errors were discovered, of which 133 had the potential to cause serious or life-threatening harm and were considered serious or life-threatening potential adverse drug events. As a follow-up, clinical reviewers conducted detailed chart review of serious or life-threatening potential ADEs to determine if they caused an ADE. Reviewers assessed severity of the ADE and attribution to the error. Ten (7.5% (95% CI 6.98 to 8.01)) actual ADEs resulted from the 133 serious and life-threatening potential ADEs, of which 6 resulted in significant, three in serious, and one life threatening injury. Therefore 4 (3% (95% CI 2.12 to 3.6)) of serious or life threatening potential ADEs led to serious or life threatening ADEs. Half of the ADEs were caused by dosage or monitoring errors for anti-hypertensives. Unintercepted potential ADEs at the medication administration stage can cause serious patient harm. At hospitals where 6 million doses are administered per year, about 4000 preventable ADEs would be attributable to medication administration errors annually.


Scoping review on search queries and social media for disease surveillance: a chronology of innovation.
The threat of a global pandemic posed by outbreaks of influenza H5N1 (1997) and Severe Acute Respiratory Syndrome (SARS, 2002), both diseases of zoonotic origin, provoked interest in improving early warning systems and reinforced the need for combining data from different sources. It led to the use of search query data from search engines such as Google and Yahoo! as an indicator of when and where influenza was occurring. This methodology has subsequently been extended to other diseases and has led to experimentation with new types of social media for disease surveillance. The objective of this scoping review was to formally assess the current state of knowledge regarding the use of search queries and social media for disease surveillance in order to inform future work on early detection and more effective mitigation of the effects of foodborne illness. Structured scoping review methods were used to identify, characterize, and evaluate all published primary research, expert review, and commentary articles regarding the use of social media in surveillance of infectious diseases from 2002-2011. Thirty-two primary research articles and 19 reviews and case studies were identified as relevant. Most relevant citations were peer-reviewed journal articles (29/32, 91%) published in 2010-11 (28/32, 88%) and reported use of a Google program for surveillance of influenza. Only four primary research articles investigated social media in the context of foodborne disease or gastroenteritis. Most authors (21/32 articles, 66%) reported that social media-based surveillance had comparable performance when compared to an existing surveillance program. The most commonly reported strengths of social media surveillance programs included their effectiveness (21/32, 66%) and rapid detection of disease (21/32, 66%). The most commonly reported weaknesses were the potential for false positive (16/32, 50%) and false negative (11/32, 34%) results. Most authors (24/32, 75%) recommended that social media programs should primarily be used to support existing surveillance programs. The use of search queries and social media for disease surveillance are relatively recent phenomena (first reported in 2006). Both the tools themselves and the methodologies for exploiting them are evolving over time. While their accuracy, speed, and cost compare favorably with existing surveillance systems, the primary challenge is to refine the data signal by reducing surrounding noise. Further developments in digital disease surveillance have the potential to improve sensitivity and specificity, passively through advances in machine learning and actively through engagement of users. Adoption, even as supporting systems for existing surveillance, will entail a high level of familiarity with the tools and collaboration across jurisdictions.


Arabidopsis thaliana NIP7;1: an anther-specific boric acid transporter of the aquaporin superfamily regulated by an unusual tyrosine in helix 2 of the transport pore.
Plant nodulin-26 intrinsic proteins (NIPs) are members of the aquaporin superfamily that serve as multifunctional transporters of uncharged metabolites. In Arabidopsis thaliana, a specific NIP pore subclass, known as the NIP II proteins, is represented by AtNIP5;1 and AtNIP6;1, which encode channel proteins expressed in roots and leaf nodes, respectively, that participate in the transport of the critical cell wall nutrient boric acid. Modeling of the protein encoded by the AtNIP7;1 gene shows that it is a third member of the NIP II pore subclass in Arabidopsis. However, unlike AtNIP5;1 and AtNIP6;1 proteins, which form constitutive boric acid channels, AtNIP7;1 forms a channel with an extremely low intrinsic boric acid transport activity. Molecular modeling and molecular dynamics simulations of AtNIP7;1 suggest that a conserved tyrosine residue (Tyr81) located in transmembrane helix 2 adjacent to the aromatic arginine (ar/R) pore selectivity region stabilizes a closed pore conformation through interaction with the canonical Arg220 in ar/R region. Substitution of Tyr81 with a Cys residue, characteristic of established NIP boric acid channels, results in opening of the AtNIP7;1 pore that acquires a robust, transport activity for boric acid as well as other NIP II test solutes (glycerol and urea). Substitution of a Phe for Tyr81 also opens the channel, supporting the prediction from MD simulations that hydrogen bond interaction between the Tyr81 phenol group and the ar/R Arg may contribute to the stabilization of a closed pore state. Expression analyses show that AtNIP7;1 is selectively expressed in developing anther tissues of young floral buds of A. thaliana, principally in developing pollen grains of stage 9-11 anthers. Because boric acid is both an essential nutrient as well as a toxic compound at high concentrations, it is proposed that Tyr81 modulates transport and may provide an additional level of regulation for this transporter in male gametophyte development.


Patients' Experiences of Living with Atrial Fibrillation: A Mixed Methods Study.
Awareness of epidemiological and clinical consequences of atrial fibrillation (AF) has increased, as have disease-related costs. Less attention has been paid to patient-related issues, such as understanding how symptoms, different therapies, and lifestyle adjustments affect daily life. We aimed to describe patients' experiences of living with AF. The study design used a parallel convergent mixed methods approach. Patients with AF were included in the SMURF study and referred for catheter ablation. Patients completed questionnaires on symptoms, health-related quality of life, depression, anxiety, and perceived control and were interviewed. The datasets were analysed separately using inductive content analysis and descriptive statistics. Data were merged to obtain a final interpretation. Nineteen patients were interviewed and 18 completed questionnaires. Twelve of the patients were male, mean age 60 years (45-75 years). Inductive qualitative analysis revealed three categories: (i) symptoms and concerns limiting life, (ii) dimensions of worries, and (iii) strategies for management. The most common symptoms were tiredness, weakness/fatigue, and breathlessness during activities, and the most pronounced negative impacts on health-related quality of life (HRQOL) were physically related, shown in the ASTA questionnaire. The most negative SF-36 scores were found in role limitations due to physical health problems and vitality. HADS revealed five patients with some degree of anxiety and four with some degree of depression. Patients had lower scores on perceived control than perceived helplessness in CAS. Patients' perceived control was higher than their families', and families experienced more helplessness. The mixed methods design deepens our understanding of challenges faced by patients. Patients experienced a limited ability to perform activities of daily living due to AF which created different kinds of worries that encouraged the use of various strategies to manage their lives. Healthcare providers need to be aware that relationships between patients and their relatives can change, and therefore they need to be supported and integrated into the care system.


Risk estimations, risk factors, and genetic variants associated with Alzheimer's disease in selected publications from the Framingham Heart Study.
The study of Alzheimer's disease (AD) in the Framingham Heart Study (FHS), a multi-generational, community-based population study, began nearly four decades ago. In this overview, we highlight findings from seven prior publications that examined lifetime risk estimates for AD, environmental risk factors for AD, circulating and imaging markers of aging-related brain injury, and explorations on the genetics underlying AD. First, we describe estimations of the lifetime risk of AD. These estimates are distinguished from other measures of disease burden and have substantial public health implications. We then describe prospective studies of environmental AD risk factors: one examined the association between plasma levels of omega-3 fatty-acid and risk of incident AD, the other explored the association of diabetes to this risk in subsamples with specific characteristics. With evidence of inflammation as an underlying mechanism, we also describe findings from a study that compared the effects of serum cytokines and spontaneous production of peripheral blood mononuclear cell cytokines on AD risk. Investigating AD related endophenotypes increases sensitivity in identifying risk factors and can be used to explore pathophysiologic pathways between a risk factor and the disease. We describe findings of an association between large volume of white matter hyperintensities and a specific pattern of cognitive deficits in non-demented participants. Finally, we summarize our findings from two genetic studies: The first used genome-wide association (GWA) and family-based association methods to explore the genetic basis of cognitive and structural brain traits. The second is a large meta-analysis GWA study of AD, in which novel loci of AD susceptibility were found. Together, these findings demonstrate the FHS multi-directional efforts in investigating dementia and AD.


Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.
Advances in high throughput sequencing technology have enabled the identification of transcription factor (TF) binding sites in genome scale. TF binding studies are important for medical applications and stem cell research. Somatic cells can be reprogrammed to a pluripotent state by the combined introduction of factors such as Oct4, Sox2, c-Myc, Klf4. These reprogrammed cells share many characteristics with embryonic stem cells (ESCs) and are known as induced pluripotent stem cells (iPSCs). The signaling requirements for maintenance of human and murine embryonic stem cells (ESCs) differ considerably. Genome wide ChIP-seq TF binding maps in mouse stem cells include Oct4, Sox2, Nanog, Tbx3, Smad2 as well as group of other factors. ChIP-seq allows study of new candidate transcription factors for reprogramming. It was shown that Nr5a2 could replace Oct4 for reprogramming. Epigenetic modifications play important role in regulation of gene expression adding additional complexity to transcription network functioning. We have studied associations between different histone modification using published data together with RNA Pol II sites. We found strong associations between activation marks and TF binding sites and present it qualitatively. To meet issues of statistical analysis of genome ChIP-sequencing maps we developed computer program to filter out noise signals and find significant association between binding site affinity and number of sequence reads. The data provide new insights into the function of chromatin organization and regulation in stem cells.


Cognitive impairment and neurogenotoxic effects in rats exposed to low-intensity microwave radiation.
The health hazard of microwave radiation (MWR) has become a recent subject of interest as a result of the enormous increase in mobile phone usage. The present study aimed to investigate the effects of chronic low-intensity microwave exposure on cognitive function, heat shock protein 70 (HSP70), and DNA damage in rat brain. Experiments were performed on male Fischer rats exposed to MWR for 180 days at 3 different frequencies, namely, 900, 1800 MHz, and 2450 MHz. Animals were divided into 4 groups: group I: sham exposed; group II: exposed to MWR at 900 MHz, specific absorption rate (SAR) 5.953 × 10(-4) W/kg; group III: exposed to 1800 MHz, SAR 5.835 × 10(-4) W/kg; and group IV: exposed to 2450 MHz, SAR 6.672 × 10(-4) W/kg. All the rats were tested for cognitive function at the end of the exposure period and were subsequently sacrificed to collect brain. Level of HSP70 was estimated by enzyme-linked immunotarget assay and DNA damage was assessed using alkaline comet assay in all the groups. The results showed declined cognitive function, elevated HSP70 level, and DNA damage in the brain of microwave-exposed animals. The results indicated that, chronic low-intensity microwave exposure in the frequency range of 900 to 2450 MHz may cause hazardous effects on the brain.


Genetic mapping of IS200 copies in Salmonella typhimurim strain LT2.
The wild-type Salmonella typhimurium strain LT2 contains six copies of the insertion sequence element IS200 which is unique to Salmonella. We have determined the chromosomal locations of all six copies of IS200 in strain LT2. This was done by mapping the positions of Tn10 elements inserted near each copy of IS200. Such Tn10 insertions were detected by Southern hybridization as IS200-containing restriction fragments with altered electrophoretic mobility. The copies are located at quite evenly spaced sites in the chromosome. Some are found in regions with many known genes; others are in regions with few known functions. There is no indication of a possible function for IS200. The method described here should be applicable to the mapping of IS elements in general.


Understanding the value of local ecological knowledge and practices for habitat restoration in human-altered floodplain systems: a case from Bangladesh.
Worldwide there is a declining trend in natural fish catch (FAO, The state of world fisheries and aquaculture. http://www.fao.org/documents/show_cdr.asp?url_file=/docrep/007/y5600e/y5600e00.htm , 2002) and Bangladesh is no exception. The vast inland fisheries of Bangladesh have been declining over the years, largely a result of human alteration of the aquatic habitats arising from human interventions in the floodplain systems such as the establishment of water control structures which favor agricultural production but reduce fish habitats. It can be assumed that conventional management measures are not adequate to conserve natural fisheries and exploring alternative knowledge systems to complement existing management is warranted. This paper focuses on local ecological knowledge and several other local practices held by fishers engaging directly with floodplain ecosystems. These knowledge systems and practices may be valuable tools for understanding ecosystems processes and related changes and developing local level responses to avert negative consequences of such changes. This may help in devising alternatives to ecosystem management and the conservation of floodplain fish habitats of Bangladesh and elsewhere in the world. This study was conducted in a natural depression (locally called beel) and its surrounding floodplain system located in north central Bangladesh which has become highly degraded. The results of the study indicate that the fishers and local users of the floodplain ecosystems are rich in local ecological knowledge concerning the hydrology of the floodplains and small lakes, the habitat preferences of fish, the role of agricultural crops on fish habitats, and the impact of habitat human interventions in aquatic ecosystems. Given the apparent inadequacy of the present management regime, this article argues for an inclusion of local knowledge and practices into habitat management as a more holistic approach to floodplain habitat restoration and conservation that encourages multi-level cooperation and which builds on diversified knowledge systems.


Filamin A is reduced and contributes to the CASR sensitivity in human parathyroid tumors.
Parathyroid tumors display reduced sensitivity to extracellular calcium ([Ca2+]o). [Ca2+]o activates calcium-sensing receptor (CASR), which interacts with the scaffold protein filamin A (FLNA). The study aimed to investigate: (1) the FLNA expression in human parathyroid tumors, (2) its effects on the CASR mRNA and protein expression, and (3) on ERK signaling activation, (4) the effect of the carboxy-terminal CASR variants and (5) of the treatment with the CASR agonist R568 on FLNA-mediated ERK phosphorylation in HEK293 cells. Full-length FLNA immunostaining was variably reduced in parathyroid tumors. Immunofluorescence showed that FLNA localized in membrane and cytoplasm and co-localized with CASR in parathyroid adenomas (PAds)-derived cells. Cleaved C-terminus FLNA fragment could also be detected in PAds nuclear protein fractions. In HEK293 cells transfected with 990R-CASR or 990G-CASR variants, silencing of endogenous FLNA reduced CASR mRNA levels and total and membrane-associated CASR proteins. In agreement, FLNA mRNA levels positively correlated with CASR expression in a series of 74 PAds; however, any significant correlation with primary hyperparathyroidism severity could be detected and FLNA transcript levels did not differ between PAds harboring 990R or 990G CASR variants. R568 treatment was efficient in restoring 990R-CASR and 990G-CASR sensitivity to [Ca2+]o in the absence of FLNA. In conclusion, FLNA is downregulated in parathyroid tumors and parallels the CASR expression levels. Loss of FLNA reduces CASR mRNA and protein expression levels and the CASR-induced ERK phosphorylation. FLNA is involved in receptor expression, membrane localization and ERK signaling activation of both 990R and 990G CASR variants.


Closo-Carboranyl- and Metallacarboranyl [1,2,3]triazolyl-Decorated Lapatinib-Scaffold for Cancer Therapy Combining Tyrosine Kinase Inhibition and Boron Neutron Capture Therapy.
One of the driving forces of carcinogenesis in humans is the aberrant activation of receptors; consequently, one of the most promising mechanisms for cancer treatment is receptor inhibition by chemotherapy. Although a variety of cancers are initially susceptible to chemotherapy, they eventually develop multi-drug resistance. Anti-tumor agents overcoming resistance and acting through two or more ways offer greater therapeutic benefits over single-mechanism entities. In this study, we report on a new family of bifunctional compounds that, offering the possibility of dual action (drug + radiotherapy combinations), may result in significant clinical benefits. This new family of compounds combines two fragments: the drug fragment is a lapatinib group, which inhibits the tyrosine kinase receptor activity, and an icosahedral boron cluster used as agents for neutron capture therapy (BNCT). The developed compounds were evaluated in vitro against different tyrosine kinase receptors (TKRs)-expressing tumoral cells, and in vitro-BNCT experiments were performed for two of the most promising hybrids, 19 and 22. We identified hybrid 19 with excellent selectivity to inhibit cell proliferation and ability to induce necrosis/apoptosis of glioblastoma U87 MG cell line. Furthermore, derivative 22, bearing a water-solubility-enhancing moiety, showed moderate inhibition of cell proliferation in both U87 MG and colorectal HT-29 cell lines. Additionally, the HT-29 cells accumulated adequate levels of boron after hybrids 19 and 22 incubations rendering, and after neutron irradiation, higher BNCT-effects than BPA. The attractive profile of developed hybrids makes them interesting agents for combined therapy.


Patient participation in decision making: views of health professionals caring for people with colorectal cancer.
The aim of this study was to explore views on patient participation in decision making, as described by health professionals caring for people with colorectal cancer. Patient participation in health-care decision making is on the policy agenda at an international level. However, many aspects of cancer care and treatment are complex and it is unclear how health professionals view their role as promoters of patient participation. A qualitative exploratory study. In depth interviews with 35 health professionals in clinical practice. Data were analysed using thematic content analysis, assisted by a computer software package for analysis of qualitative data (N-VIVO). Choices in relation to surgical treatment were viewed as limited. Although it was perceived that patients could be more involved in decisions related to adjuvant treatment, providing information on various chemotherapy regimes was challenging. It was acknowledged that patients could be involved in treatment choices but there was far less clarity concerning aspects of physical and psychological care. Age was a factor when determining which patients should be offered treatment choices. The availability and presentation of choices to patients is context specific and tailored to the preferences of individuals. If health professionals focus only on aspects of decision making related to treatment, the potential for shared partnerships with patients in relation to choices about physical and psychological care may be lost. This may be particularly pertinent for nurses and allied professions who engage with patients throughout the illness trajectory. Policy makers should arguably appreciate that health professionals have an awareness of current thinking on patient participation, but may find policy recommendations challenging to implement in clinical practice when faced with the individual needs and preferences of patients and the complexities and uncertainties of disease management.


Dissection of the Burkholderia intracellular life cycle using a photothermal nanoblade.
Burkholderia pseudomallei and Burkholderia thailandensis are related pathogens that invade a variety of cell types, replicate in the cytoplasm, and spread to nearby cells. We have investigated temporal and spatial requirements for virulence determinants in the intracellular life cycle, using genetic dissection and photothermal nanoblade delivery, which allows efficient placement of bacterium-sized cargo into the cytoplasm of mammalian cells. The conserved Bsa type III secretion system (T3SS(Bsa)) is dispensable for invasion, but is essential for escape from primary endosomes. By nanoblade delivery of B. thailandensis we demonstrate that all subsequent events in intercellular spread occur independently of T3SS(Bsa) activity. Although intracellular movement was essential for cell-cell spread by B. pseudomallei and B. thailandensis, neither BimA-mediated actin polymerization nor the formation of membrane protrusions containing bacteria was required for B. thailandensis. Surprisingly, the cryptic (fla2) flagellar system encoded on chromosome 2 of B. thailandensis supported rapid intracellular motility and efficient cell-cell spread. Plaque formation by both pathogens was dependent on the activity of a type VI secretion system (T6SS-1) that functions downstream from T3SS(Bsa)-mediated endosome escape. A remarkable feature of Burkholderia is their ability to induce the formation of multinucleate giant cells (MNGCs) in multiple cell types. By infection and nanoblade delivery, we observed complete correspondence between mutant phenotypes in assays for cell fusion and plaque formation, and time-course studies showed that plaque formation represents MNGC death. Our data suggest that the primary means for intercellular spread involves cell fusion, as opposed to pseudopod engulfment and bacterial escape from double-membrane vacuoles.


Undirected, Homogeneous C-H Bond Functionalization: Challenges and Opportunities.
The functionalization of C-H bonds has created new approaches to preparing organic molecules by enabling new strategic "disconnections" during the planning of a synthetic route. Such functionalizations also have created the ability to derivatize complex molecules by modifying one or more of the many C-H bonds. For these reasons, researchers are developing new types of functionalization reactions of C-H bonds and new applications of these processes. These C-H bond functionalization reactions can be divided into two general classes: those directed by coordination to an existing functional group prior to the cleavage of the C-H bond (directed) and those occurring without coordination prior to cleavage of the C-H bond (undirected). The undirected functionalizations of C-H bonds are much less common and more challenging to develop than the directed reactions. This outlook will focus on undirected C-H bond functionalization, as well as related reactions that occur by a noncovalent association of the catalyst prior to C-H bond cleavage. The inherent challenges of conducting undirected functionalizations of C-H bonds and the methods for undirected functionalization that are being developed will be presented, along with the factors that govern selectivity in these reactions. Finally, this outlook discusses future directions for research on undirected C-H functionalization, with an emphasis on the limitations that must be overcome if this type of methodology is to become widely used in academia and in industry.


Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization.
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.


An evaluation of mass absorption cross-section for optical carbon analysis on Teflon filter media.
Black carbon (BC) or elemental carbon (EC) is a by-product of incomplete fuel combustion, and contributes adversely to human health, visibility, and climate impacts. Previous studies have examined nondestructive techniques for particle light attenuation measurements on Teflon® filters to estimate BC. The incorporation of an inline Magee Scientific OT21 transmissometer into the MTL AH-225 robotic weighing system provides the opportunity to perform optical transmission measurements on Teflon filters at the same time as the gravimetric mass measurement. In this study, we characterize the performance of the inline OT21, and apply it to determine the mass absorption cross-section (MAC) of PM2.5 BC across the United States. We analyzed 5393 archived Teflon® filters from the Chemical Speciation Network (CSN) collected during 2010-2011 and determined MAC by comparing light attenuation on Teflon® filters to corresponding thermal EC on quartz-fiber filters. Results demonstrated the importance of the initial transmission (I0) value used in light attenuation calculations. While light transmission varied greatly within filter lots, the average I0 of filter blanks during the sampling period provided an estimate for archived filters. For newly collected samples, it is recommended that filter-specific I0 measurements be made (i.e., same filter before sample collection). The estimated MAC ranged from 6.9 to 9.4 m2/g and varied by region and season across the United States, indicating that using a default value may lead to under- or overestimated BC concentrations. An analysis of the chemical composition of these samples indicated good correlation with EC for samples with higher EC content as a fraction of total PM2.5 mass, while the presence of light-scattering species such as crustal elements impacted the correlation affecting the MAC estimate. Overall, the method is demonstrated to be a quick, cost-effective approach to estimate BC from archived and newly sampled Teflon® filters by combining both gravimetric and BC measurements. Robotic optical analysis is a valid, cost-effective means to obtain a vast amount of BC data from archived and current routine filters. A tailored mass absorption cross-section by region and season is necessary for a more representative estimate of BC. Initial light transmission measurements play an important role due to the variability in blank filter transmission. Combining gravimetric mass and BC analysis on a single Teflon® filter reduces costs for monitoring agencies and maximizes data collection.


Context-specific, scenario-based risk scales.
Reacting to an emergency requires quick decisions under stressful and dynamic conditions. To react effectively, responders need to know the right actions to take given the risks posed by the emergency. While existing research on risk scales focuses primarily on decision making in static environments with known risks, these scales may be inappropriate for conditions where the decision maker's time and mental resources are limited and may be infeasible if the actual risk probabilities are unknown. In this article, we propose a method to develop context-specific, scenario-based risk scales designed for emergency response training. Emergency scenarios are used as scale points, reducing our dependence on known probabilities; these are drawn from the targeted emergency context, reducing the mental resources required to interpret the scale. The scale is developed by asking trainers/trainees to rank order a range of risk scenarios and then aggregating these orderings using a Kemeny ranking. We propose measures to assess this aggregated scale's internal consistency, reliability, and validity, and we discuss how to use the scale effectively. We demonstrate our process by developing a risk scale for subsurface coal mine emergencies and test the reliability of the scale by repeating the process, with some methodological variations, several months later.


New simian immunodeficiency virus infecting De Brazza's monkeys (Cercopithecus neglectus): evidence for a cercopithecus monkey virus clade.
Nearly complete sequences of simian immunodeficiency viruses (SIVs) infecting 18 different nonhuman primate species in sub-Saharan Africa have now been reported; yet, our understanding of the origins, evolutionary history, and geographic distribution of these viruses still remains fragmentary. Here, we report the molecular characterization of a lentivirus (SIVdeb) naturally infecting De Brazza's monkeys (Cercopithecus neglectus). Complete SIVdeb genomes (9,158 and 9227 bp in length) were amplified from uncultured blood mononuclear cell DNA of two wild-caught De Brazza's monkeys from Cameroon. In addition, partial pol sequences (650 bp) were amplified from four offspring of De Brazza's monkeys originally caught in the wild in Uganda. Full-length (9068 bp) and partial pol (650 bp) SIVsyk sequences were also amplified from Sykes's monkeys (Cercopithecus albogularis) from Kenya. Analysis of these sequences identified a new SIV clade (SIVdeb), which differed from previously characterized SIVs at 40 to 50% of sites in Pol protein sequences. The viruses most closely related to SIVdeb were SIVsyk and members of the SIVgsn/SIVmus/SIVmon group of viruses infecting greater spot-nosed monkeys (Cercopithecus nictitans), mustached monkeys (Cercopithecus cephus), and mona monkeys (Cercopithecus mona), respectively. In phylogenetic trees of concatenated protein sequences, SIVdeb, SIVsyk, and SIVgsn/SIVmus/SIVmon clustered together, and this relationship was highly significant in all major coding regions. Members of this virus group also shared the same number of cysteine residues in their extracellular envelope glycoprotein and a high-affinity AIP1 binding site (YPD/SL) in their p6 Gag protein, as well as a unique transactivation response element in their viral long terminal repeat; however, SIVdeb and SIVsyk, unlike SIVgsn, SIVmon, and SIVmus, did not encode a vpu gene. These data indicate that De Brazza's monkeys are naturally infected with SIVdeb, that this infection is prevalent in different areas of the species' habitat, and that geographically diverse SIVdeb strains cluster in a single virus group. The consistent clustering of SIVdeb with SIVsyk and the SIVmon/SIVmus/SIVgsn group also suggests that these viruses have evolved from a common ancestor that likely infected a Cercopithecus host in the distant past. The vpu gene appears to have been acquired by a subset of these Cercopithecus viruses after the divergence of SIVdeb and SIVsyk.


A new in situ hybridization and immunohistochemistry with a novel antibody to detect small T-antigen expressions of Merkel cell polyomavirus (MCPyV).
Approximately 80% of Merkel cell carcinomas (MCCs) harbor Merkel cell polyomavirus (MCPyV) which monoclonally integrates into the genome and has prognostic significance. The presence or absence of MCPyV is usually diagnosed using CM2B4 immunohistochemistry (IHC) for MCPyV-large T antigen (LT) protein. However, this method poses a risk of misdiagnosis. In this study, we determined MCPyV infection in MCCs using real-time PCR for MCPyV-LT DNA and prepared 16 cases of MCPyV-DNA-positive and -negative groups. Diagnostic sensitivity and specificity of conventional PCR for MCPyV-small T antigen (MCPyV-ST), IHC using a newly developed polyclonal antibody (ST-1) for MCPyV-ST protein (MCPyV-ST) (aa: 164-177), and in situ hybridization (ISH) as well as real-time PCR for MCPyV-ST mRNA were compared against CM2B4-IHC for sensitivity (0.94, 15/16) and specificity (0.94, 15/16). The followings are the respective sensitivity and specificity results from examinations for MCPyV-ST gene: conventional PCR for the MCPyV-ST (0.94, 1.0), ST-1-IHC (0.69, 1.0), real-time PCR for ST mRNA (1.0, no data), ST mRNA ISH (0.94, 1.0). Each of the MCPyV-pseudonegative (1/16) and -pseudopositive (1/16) diagnoses evaluated using CM2B4-IHC were accurately corrected by examinations for MCPyV-ST or its expression as well as real-time PCR for MCPyV-LT. Sensitivity of CM2B4-IHC (0.94) was superior to that of ST-1-IHC (0.69) but equal to that of ST mRNA-ISH (0.94). Specificities of ST-1-IHC (1.0) and ST mRNA-ISH (1.0) were superior to that of CM2B4-IHC (0.94). Therefore, combined application of ST mRNA-ISH and ST-IHC as well as CM2B4-IHC is recommended and will contribute to the diagnostic accuracy for MCPyV infection in MCCs. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9966295741144834.