Search

Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determination, and design. In this work, we developed a glycan-modeling algorithm, GlycanTreeModeler, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) of common glycan conformations derived from data in the Protein Data Bank (PDB) and from quantum mechanics (QM) calculations. GlycanTreeModeler was benchmarked on a test set of glycan structures of varying lengths, or "trees". Structures predicted by GlycanTreeModeler agreed with native structures at high accuracy for both de novo modeling and experimental density-guided building. We employed these tools to design de novo glycan trees into a protein nanoparticle vaccine to shield regions of the scaffold from antibody recognition, and experimentally verified shielding. This work will inform glycoprotein model prediction, glycan masking, and further aid computational methods in experimental structure determination and refinement.

The objective of this study is to evaluate the performance of functional tests using a camera-based system and machine learning techniques. Specifically, we investigate whether OpenPose and any standard camera can be used to assess the quality of the Single Leg Squat Test and Step Down Test functional tests. We recorded these exercises performed by forty-six healthy subjects, extract motion data, and classify them to expert assessments by three independent physiotherapists using 15 binary parameters. We calculated ranges of movement in Keypoint-pair orientations, joint angles, and relative distances of the monitored segments and used machine learning algorithms to predict the physiotherapists' assessments. Our results show that the AdaBoost classifier achieved a specificity of 0.8, a sensitivity of 0.68, and an accuracy of 0.7. Our findings suggest that a camera-based system combined with machine learning algorithms can be a simple and inexpensive tool to assess the performance quality of functional tests.

In low- and middle-income countries, undernutrition often co-exists with intestinal parasites, especially Soil Transmitted Helminth (STH) infections in children. The collective impact of both conditions result in undernutrition and can exacerbate the general poor health status of children. A cross-sectional survey of 422 mother-child (12-59 months old) pairs from 14 villages in the District of Ndelele, East Region of Cameroon, was carried out to assess the magnitude and correlates of undernutrition and intestinal parasites. Socio-demographic data were collected from mothers and anthropometric data were collected from children. Parasitological assessment was performed using a combination of direct microscopy flotation, sedimentation and centrifugation techniques. Correlates of undernutrition and intestinal parasites were identified using multinomial logistic regression at individual and household levels. 83.77% of the children assessed for undernutrition were undernourished and 66.82% were positive for one or more intestinal parasites. It was not uncommon for the study participants to be concurrently infected with two or more intestinal parasites. The most common intestinal parasitic infections detected in the study were A. lumbricoides, E. histolytica/dispar and Hookworm infection. Multinomial logistic regression using Nutritional status as outcome showed that, children who were not exclusively breastfed were 106% (RR = 2.06; C.I = 1.12-3.80) more likely to be underweight compared to those who were exclusively breastfed. The household size of 4 to 6 persons also significantly impacted wasting (p-value = 0.007) at 7% (RR = 1.07, C.I = 0.49-2.32). Analysis by a logistic regression model with STH infection as outcome revealed that, Fingernail cleanness (p-value = 0.044; AOR = 1.75; CI = 1.09-2.78) and household size (p-value = 0.038; AOR = 0.55; CI = 0.32-0.92) were positively associated with intestinal parasite infection at the 5% significant level. This study reveals that intestinal helminthic parasitic infections (STH) and undernutrition are serious health problems in children below five in the study area. To address this dire situation, concerted efforts are needed to improve sanitation, hygiene education access, community deworming programs, and improve diets.

In low- and middle-income countries, undernutrition often co-exists with intestinal parasites, especially Soil Transmitted Helminth (STH) infections in children. The collective impact of both conditions result in undernutrition and can exacerbate the general poor health status of children. A cross-sectional survey of 422 mother-child (12–59 months old) pairs from 14 villages in the District of Ndelele, East Region of Cameroon, was carried out to assess the magnitude and correlates of undernutrition and intestinal parasites. Socio-demographic data were collected from mothers and anthropometric data were collected from children. Parasitological assessment was performed using a combination of direct microscopy flotation, sedimentation and centrifugation techniques. Correlates of undernutrition and intestinal parasites were identified using multinomial logistic regression at individual and household levels. 83.77% of the children assessed for undernutrition were undernourished and 66.82% were positive for one or more intestinal parasites. It was not uncommon for the study participants to be concurrently infected with two or more intestinal parasites. The most common intestinal parasitic infections detected in the study were A. lumbricoides, E. histolytica/dispar and Hookworm infection. Multinomial logistic regression using Nutritional status as outcome showed that, children who were not exclusively breastfed were 106% (RR = 2.06; C.I = 1.12–3.80) more likely to be underweight compared to those who were exclusively breastfed. The household size of 4 to 6 persons also significantly impacted wasting (p-value = 0.007) at 7% (RR = 1.07, C.I = 0.49–2.32). Analysis by a logistic regression model with STH infection as outcome revealed that, Fingernail cleanness (p-value = 0.044; AOR = 1.75; CI = 1.09–2.78) and household size (p-value = 0.038; AOR = 0.55; CI = 0.32–0.92) were positively associated with intestinal parasite infection at the 5% significant level. This study reveals that intestinal helminthic parasitic infections (STH) and undernutrition are serious health problems in children below five in the study area. To address this dire situation, concerted efforts are needed to improve sanitation, hygiene education access, community deworming programs, and improve diets.

BackgroundMalnutrition is a major public health problem because of the devastating consequences it has on children, their families, and society at large. Our study, therefore, sought to determine the prevalence of undernutrition and overweight/obesity and its associated factors among children aged 6-12 in the South Tongu District, Ghana.MethodsA school-based cross-sectional study was conducted among 423 school children aged 6-12 years in the South Tongu District of Ghana. A multistage sampling method was employed to recruit the school children for the study. A semi-structured questionnaire was used to collect data from the respondents. We used a dual-purpose (height and weight) measuring scale to obtain the anthropometric data. The World Health Organization's AnthroPlus software was used to generate the z-scores for determining the nutritional status. Percentages were used to present the results of the prevalence of undernutrition and overweight/obesity among school children. Bivariate and multivariable binary logistic regression were used to examine the factors associated with undernutrition and overweight/obesity among school children. The results were presented as crude odds ratios (CORs) and adjusted odds ratios (AORs), with their 95% confidence interval (CI). Statistical significance was set at pResultsThe overall prevalence of undernutrition and overweight/obesity were 21.5% (CI = 17.7, 25.7) and 24.8% (CI = 20.8, 29.2), respectively. Specifically, the prevalence of stunting, thinness, underweight, overweight, and obesity were 10.4%, 12.1%, 3.8%, 11.1%, and 13.7%, respectively. School children whose household used water from non-portable sources were more likely to be undernourished [AOR = 2.03, 95% CI = 1.13, 3.63]. The odds of overweight/obesity was higher among school children whose mothers had attained formal education [AOR = 2.10, 95% CI = 1.09, 4.06], those who consumed beverages between meals per day [AOR = 1.87, CI = 1.08, 3.24], and those who had adequate dietary diversity score [AOR = 1.65, 95% CI = 1.02, 2.67]. School children aged 10-12 were less likely to be overweight/obese [AOR = 0.58, 95% CI = 0.35, 0.94] compared to those aged 6-9.ConclusionThe study showed a relatively high prevalence of undernutrition and overweight/obesity among school children in the South Tongu District. The identified risk factor(s) for undernutrition was the usage of water from non-potable sources whilst those of overweight/obesity were age (10-12 years), maternal formal education, beverage consumption between meals per day, and adequate dietary diversity. The findings reaffirm that malnutrition is still prevalent among school children. Hence, there is a need for the Ministry of Health, Ghana Education Service, and other Non-Governmental Organizations to pay critical attention to these factors to achieve the Sustainable Development Goal 2, target 2.2. Nutritional behavioural change education should be carried out among parents and school children. School health service activities should be intensified with a special focus on nutritional screening.

HIV care provides an opportunity to integrate comprehensive sexual and reproductive healthcare, including sexually transmitted infection (STI) management. We describe STI prevalence and correlates among men living with HIV (MLWH) accessing safer conception care to conceive a child with an HIV-uninfected partner while minimizing HIV transmission risks. This study reflects an ongoing safer conception program embedded within a regional referral hospital HIV clinic in southwestern Uganda. We enrolled MLWH, planning for pregnancy with an HIV-uninfected partner and accessing safer conception care. Participants completed interviewer-administered questionnaires detailing socio-demographics, gender dynamics, and sexual history. Participants also completed STI laboratory screening for syphilis (immunochromatographic testing confirmed by rapid plasma reagin), and chlamydia, gonorrhea, trichomoniasis, and HIV-RNA via GeneXpert nucleic acid amplification testing. Bivariable associations of STI covariates were assessed using Fisher's exact test. Among the 50 men who completed STI screening, median age was 33 (IQR 31-37) years, 13/50 (26%) had ≥2 sexual partners in the prior three months, and 46/50 (92%) had HIV-RNA

In this study, the effects of sea ice and wind speed on the timing and composition of phytoplankton spring bloom in the central and southern Baltic Sea are investigated by a hydrodynamic-biogeochemical model and observational data. The modelling experiment compared the results of a reference run in the presence of sea ice with those of a run in the absence of sea ice, which confirmed that ecological conditions differed significantly for both the scenarios. It has been found that diatoms dominate the phytoplankton biomass in the absence of sea ice, whereas dinoflagellates dominate the biomass in the presence of thin sea ice. The study concludes that under moderate ice conditions (representing the last few decades), dinoflagellates dominate the spring bloom phytoplankton biomass in the Baltic Sea, whereas diatoms will be dominant in the future as a result of climate change i.e. in the absence of sea ice.

IntroductionOver the past two decades, there have been several global interventions including the Sustainable Development Goals (SDGs), aimed at improving health outcomes. Despite efforts by countries to achieve the SDG targets, mental health challenges remain major public health concerns globally. We examined the prevalence and predictors of depression, anxiety, and stress as well as the comorbidities of these mental health issues among adults.Materials and methodsThis was a community-based cross-sectional study conducted among 2456 adults in four districts of the Volta Region of Ghana using data from the UHAS-Yonsei University Partnership Project. We analysed the data using frequency, percentage, mean, standard deviation, correlation, and binary logistic regression.ResultsOverall, 51.8% of the participants had at least one of the mental health issues examined. The prevalence of a mental health issue was 25.2%, 53.3%, and 9.7% for depression, anxiety, and stress respectively. Participants constituting 8.3% experienced all three mental health issues as comorbidities. Participants' level of formal education and income significantly predicted depression, anxiety, and stress respectively at the multivariable level. Adults with a tertiary level of education were, for instance, 68% (AOR = 0.32, 95%CI = 0.15-0.66), 65% (AOR = 0.35, 95%CI = 0.17-0.73), and 50% (AOR = 0.50, 95%CI = 0.33-0.76) less likely to experience depression, anxiety, and stress, respectively compared with those who had no formal education.ConclusionThe majority of our study participants either experienced depression, anxiety, or stress. There were quite high comorbidities of the mental health issues among the adult population. To accelerate progress towards the achievement of SDG 3.4 target of promoting mental health and wellbeing for all by the year 2030, there is a need for effective implementation of the country's 2012 Mental Health Act which makes provisions for the establishment of a Mental Health Fund. This could improve the financial circumstances of indigenes as income has been realised in the present study as an important factor influencing depression, anxiety, and stress among the adult population.

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities.

Ultrasound has many uses, such as in medical imaging, monitoring of crystallization, characterization of emulsions and suspensions, and disruption of cell membranes in the food industry. It can also affect microbial cells by promoting or slowing their growth and increasing the production of some metabolites. However, the exact mechanism explaining the effect of ultrasound has not been identified yet. Most equipment employed to study the effect of ultrasound on microorganisms has been designed for other applications and then only slightly modified. This results in limited control over ultrasound frequency and input power, or pressure distribution in the reactor. The present study aimed to obtain a well-defined reactor by simulating the pressure distribution of a sonobioreactor. Specifically, we optimized a sonotrode to match the bottle frequency and compared it to measured results to verify the accuracy of the simulation. The measured pressure distribution spectrum presented the same overall trend as the simulated spectrum. However, the peaks were much less intense, likely due to non-linear events such as the collapse of cavitation bubbles. To test the application of the sonobioreactor in biological systems, two biotechnologically interesting microorganisms were assessed: an electroactive bacterium, Geobacter sulfurreducens, and a lignocellulose-degrading fungus, Fusarium oxysporum. Sonication resulted in increased malate production by G. sulfurreducens, but no major effect on growth. In comparison, morphology and growth of F. oxysporum were more sensitive to ultrasound intensity. Despite considerable morphological changes at 4 W input power, the growth rate was not adversely affected; however, at 12 W, growth was nearly halted. The above findings indicate that the novel sonobioreactor provides an effective tool for studying the impact of ultrasound on microorganisms.

A structural-bioinformatics-based computational methodology and framework have been developed for the design of antibodies to targets of interest. RosettaAntibodyDesign (RAbD) samples the diverse sequence, structure, and binding space of an antibody to an antigen in highly customizable protocols for the design of antibodies in a broad range of applications. The program samples antibody sequences and structures by grafting structures from a widely accepted set of the canonical clusters of CDRs (North et al., J. Mol. Biol., 406:228-256, 2011). It then performs sequence design according to amino acid sequence profiles of each cluster, and samples CDR backbones using a flexible-backbone design protocol incorporating cluster-based CDR constraints. Starting from an existing experimental or computationally modeled antigen-antibody structure, RAbD can be used to redesign a single CDR or multiple CDRs with loops of different length, conformation, and sequence. We rigorously benchmarked RAbD on a set of 60 diverse antibody-antigen complexes, using two design strategies-optimizing total Rosetta energy and optimizing interface energy alone. We utilized two novel metrics for measuring success in computational protein design. The design risk ratio (DRR) is equal to the frequency of recovery of native CDR lengths and clusters divided by the frequency of sampling of those features during the Monte Carlo design procedure. Ratios greater than 1.0 indicate that the design process is picking out the native more frequently than expected from their sampled rate. We achieved DRRs for the non-H3 CDRs of between 2.4 and 4.0. The antigen risk ratio (ARR) is the ratio of frequencies of the native amino acid types, CDR lengths, and clusters in the output decoys for simulations performed in the presence and absence of the antigen. For CDRs, we achieved cluster ARRs as high as 2.5 for L1 and 1.5 for H2. For sequence design simulations without CDR grafting, the overall recovery for the native amino acid types for residues that contact the antigen in the native structures was 72% in simulations performed in the presence of the antigen and 48% in simulations performed without the antigen, for an ARR of 1.5. For the non-contacting residues, the ARR was 1.08. This shows that the sequence profiles are able to maintain the amino acid types of these conserved, buried sites, while recovery of the exposed, contacting residues requires the presence of the antigen-antibody interface. We tested RAbD experimentally on both a lambda and kappa antibody-antigen complex, successfully improving their affinities 10 to 50 fold by replacing individual CDRs of the native antibody with new CDR lengths and clusters.

We evaluate the changes on the hydrological (temperature and salinity) and biogeochemical (phytoplankton biomass) characteristics of the Mediterranean Sea induced by freshwater flow modifications under two different scenarios for the end of the 21st century. An ensemble of four regional climate model realizations using different global circulation models at the boundary and different emission scenarios are used to force a single ocean model for the Mediterranean Sea. Freshwater flow is modified according to the simulated changes in the precipitation rates for the different rivers' catchment regions. To isolate the effect resulting from a change in freshwater flow, model results are evaluated against a 'baseline' simulation realized assuming a constant inflow equivalent to climatologic values. Our model results indicate that sea surface salinity could be significantly altered by freshwater flow modification in specific regions and that the affected area and the sign of the anomaly are highly dependent on the used climate model and emission scenario. Sea surface temperature and phytoplankton biomass, on the contrary, show no coherent spatial pattern but a rather widespread scattered response. We found in open-water regions a significant negative relationship between sea surface temperature anomalies and phytoplankton biomass anomalies. This indicates that freshwater flow modification could alter the vertical stability of the water column throughout the Mediterranean Sea, by changing the strength of vertical mixing and consequently upper water fertilization. In coastal regions, however, the correlation between sea temperature anomalies and phytoplankton biomass is positive, indicating a larger importance of the physiological control of growth rates by temperature.

MicroRNAs (miRNAs) are a class of approximately 22 nucleotides single-stranded non-coding RNA molecules that play crucial roles in gene expression. It has been reported that the plant miRNAs might enter mammalian bloodstream and have a functional role in human metabolism, indicating that miRNAs might be one of the hidden bioactive ingredients in medicinal plants. Viscum album L. (Loranthaceae, European mistletoe) has been widely used for the treatment of cancer and cardiovascular diseases, but its functional compounds have not been well characterized. We considered that miRNAs might be involved in the pharmacological activities of V. album. High-throughput Illumina sequencing was performed to identify the novel and conserved miRNAs of V. album. The putative human targets were predicted. In total, 699 conserved miRNAs and 1373 novel miRNAs have been identified from V. album. Based on the combined use of TargetScan, miRanda, PITA, and RNAhybrid methods, the intersection of 30697 potential human genes have been predicted as putative targets of 29 novel miRNAs, while 14559 putative targets were highly enriched in 33 KEGG pathways. Interestingly, these highly enriched KEGG pathways were associated with some human diseases, especially cancer, cardiovascular diseases and neurological disorders, which might explain the clinical use as well as folk medicine use of mistletoe. However, further experimental validation is necessary to confirm these human targets of mistletoe miRNAs. Additionally, target genes involved in bioactive components synthesis in V. album were predicted as well. A total of 68 miRNAs were predicted to be involved in terpenoid biosynthesis, while two miRNAs including val-miR152 and miR9738 were predicted to target viscotoxins and lectins, respectively, which increased the knowledge regarding miRNA-based regulation of terpenoid biosynthesis, lectin and viscotoxin expressions in V. album.

The characteristics of the human-animal bond may be influenced by both owner-related and dog-related factors. A study was designed to explore the existence of different dog ownership patterns and their related factors. We created an on line questionnaire that included demographic questions about the dog and the owner, a Spanish version of the Monash Dog Owner Relationship Scale (MDORS) and a validated measure of satisfaction with life (Cantril's ladder). We collected 1140 valid responses from adult dog owners, who were recruited using the client databases of Spanish veterinary practices. We explored the presence of groups within the population using Principal Components Analysis (PCA) of the MDORS variables combined with Hierarchical Cluster Analysis (HCA). Two groups were found; Group I having a higher level of emotional involvement with their dogs compared with Group II. Binary logistic regression was used to explore demographic factors that influenced group membership. Four variables were significantly associated with membership of Group I (p

To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250 mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.

Global surface temperature has been increasing since the beginning of the 20th century but with a highly variable warming rate, and the alternation of rapid warming periods with 'hiatus' decades is a constant throughout the series. The superimposition of a secular warming trend with natural multidecadal variability is the most accepted explanation for such a pattern. Since the start of the 21st century, the surface global mean temperature has not risen at the same rate as the top-of-atmosphere radiative energy input or greenhouse gas emissions, provoking scientific and social interest in determining the causes of this apparent discrepancy. Multidecadal natural variability is the most commonly proposed cause for the present hiatus period. Here, we analyze the HadCRUT4 surface temperature database with spectral techniques to separate a multidecadal oscillation (MDV) from a secular trend (ST). Both signals combined account for nearly 88% of the total variability of the temperature series showing the main acceleration/deceleration periods already described elsewhere. Three stalling periods with very little warming could be found within the series, from 1878 to 1907, from 1945 to 1969 and from 2001 to the end of the series, all of them coincided with a cooling phase of the MDV. Henceforth, MDV seems to be the main cause of the different hiatus periods shown by the global surface temperature records. However, and contrary to the two previous events, during the current hiatus period, the ST shows a strong fluctuation on the warming rate, with a large acceleration (0.0085°C year(-1) to 0.017°C year(-1)) during 1992-2001 and a sharp deceleration (0.017°C year(-1) to 0.003°C year(-1)) from 2002 onwards. This is the first time in the observational record that the ST shows such variability, so determining the causes and consequences of this change of behavior needs to be addressed by the scientific community.

OBJECTIVE: Although dobutamine is widely used in neonatal clinical practice, the evidence for its use in this specific population is not clear. We conducted a systematic review of the use of dobutamine in juvenile animals to determine whether the evidence from juvenile animal experiments with dobutamine supported the design of clinical trials in neonatal/paediatric population. METHODS: Studies were identified by searching MEDLINE (1946-2012) and EMBASE (1974-2012). Articles retrieved were independently reviewed by three authors and only those concerning efficacy and safety of the drug in juvenile animals were included. Only original articles published in English and Spanish were included. RESULTS: Following our literature search, 265 articles were retrieved and 24 studies were included in the review: 17 focused on neonatal models and 7 on young animal models. Although the aims and design of these studies, as well as the doses and ages analysed, were quite heterogeneous, the majority of authors agree that dobutamine infusion improves cardiac output in a dose dependent manner. Moreover, the cardiovascular effects of dobutamine are influenced by postnatal age, as well as by the dose used and the duration of the therapy. There is inadequate information about the effects of dobutamine on cerebral perfusion to draw conclusions. CONCLUSION: There is enough preclinical evidence to ensure that dobutamine improves cardiac output, however to better understand its effects in peripheral organs, such as the brain, more specific and well designed studies are required to provide additional data to support the design of clinical trials in a paediatric population.

OBJECTIVE: Aerosol delivery holds potential to release surfactant or perfluorocarbon (PFC) to the lungs of neonates with respiratory distress syndrome with minimal airway manipulation. Nevertheless, lung deposition in neonates tends to be very low due to extremely low lung volumes, narrow airways and high respiratory rates. In the present study, the feasibility of enhancing lung deposition by intracorporeal delivery of aerosols was investigated using a physical model of neonatal conducting airways. METHODS: The main characteristics of the surfactant and PFC aerosols produced by a nebulization system, including the distal air pressure and air flow rate, liquid flow rate and mass median aerodynamic diameter (MMAD), were measured at different driving pressures (4-7 bar). Then, a three-dimensional model of the upper conducting airways of a neonate was manufactured by rapid prototyping and a deposition study was conducted. RESULTS: The nebulization system produced relatively large amounts of aerosol ranging between 0.3±0.0 ml/min for surfactant at a driving pressure of 4 bar, and 2.0±0.1 ml/min for distilled water (H2Od) at 6 bar, with MMADs between 2.61±0.1 µm for PFD at 7 bar and 10.18±0.4 µm for FC-75 at 6 bar. The deposition study showed that for surfactant and H2Od aerosols, the highest percentage of the aerosolized mass (∼65%) was collected beyond the third generation of branching in the airway model. The use of this delivery system in combination with continuous positive airway pressure set at 5 cmH2O only increased total airway pressure by 1.59 cmH2O at the highest driving pressure (7 bar). CONCLUSION: This aerosol generating system has the potential to deliver relatively large amounts of surfactant and PFC beyond the third generation of branching in a neonatal airway model with minimal alteration of pre-set respiratory support.

A coupled hydrodynamic-biogeochemical model was implemented in order to estimate the effects of Major Baltic Inflows on the near-bottom hydrophysical and biogeochemical conditions in the northern Baltic Proper and the western Gulf of Finland during the period 1991-2009. We compared results of a realistic reference run to the results of an experimental run where Major Baltic Inflows were suppressed. Further to the expected overall decrease in bottom salinity, this modelling experiment confirms that in the absence of strong saltwater inflows the deep areas of the Baltic Proper would become more anoxic, while in the shallower areas (western Gulf of Finland) near-bottom average conditions improve. Our experiment revealed that typical estuarine circulation results in the sporadic emergence of short-lasting events of near-bottom anoxia in the western Gulf of Finland due to transport of water masses from the Baltic Proper. Extrapolating our results beyond the modelled period, we speculate that the further deepening of the halocline in the Baltic Proper is likely to prevent inflows of anoxic water to the Gulf of Finland and in the longer term would lead to improvement in near-bottom conditions in the Baltic Proper. Our results reaffirm the importance of accurate representation of salinity dynamics in coupled Baltic Sea models serving as a basis for credible hindcast and future projection simulations of biogeochemical conditions.

Background aimsPrimary sclerosing cholangitis predominantly affects males and is an important indication for liver transplantation. The rs738409 variant (I148M) of the PNPLA3 gene is associated with alcoholic and non-alcoholic liver disease and we evaluated its impact on the disease course of PSC.MethodsThe I148M polymorphism was genotyped in 121 German PSC patients of a long-term prospective cohort and 347 Norwegian PSC patients.ResultsIn the prospective German cohort, actuarial survival free of liver transplantation was significantly reduced for I148M carriers (p = 0.011) compared to wildtype patients. This effect was restricted to patients with severe disease, as defined by development of dominant stenosis (DS) requiring endoscopic intervention. DS patients showed markedly decreased survival (p = 0.004) when carrying the I148M variant (I148M: mean 13.8 years; 95% confidence interval: 11.6-16.0 vs. wildtype: mean 18.6 years; 95% confidence interval: 16.3-20.9) while there was no impact on survival in patients without a DS (p = 0.87). In line with previous observations of sex specific effects of the I148M polymorphism, the effect on survival was further restricted to male patients (mean survival 11.9 years; 95% confidence interval: 10.0-14.0 in I148M carriers vs. 18.8 years; 95% confidence interval: 16.2-21.5 in wildtype; pConclusionsIn male PSC patients with severe disease with bile duct stenosis requiring intervention, the common I148M variant of the PNPLA3 gene is a risk factor for reduced survival.

Helicobacter pylori are responsible for the induction of chronic gastric inflammation progressing to atrophy, metaplasia, and gastric cancer. The overexpression of Cathepsin X/Z (Ctsz) in H. pylori-infected mucosa and gastric cancer is mediated predominantly by an augmented migration of ctsz(-/-)positive macrophages and the up-regulation of Ctsz in tumor epithelium. To explore the Ctsz-function in the context of chronic inflammation and the development of preneoplastic lesions, we used Ctsz-deficient mice in a H. pylori gastritis model. Ctsz (-/-) and wild-type (wt) mice were infected with H. pylori strain SS1. The mice were sacrificed at 24, 36, and 50 weeks post infection (wpi). The stomach was removed, and gastric strips were snap-frozen or embedded and stained with H&E. Tissue sections were scored for epithelial lesions and inflammation. Ki-67 and F4/80 immunostaining were used to measure epithelial cell proliferation and macrophage infiltration, respectively. The upregulation of compensating cathepsins and cytokines were confirmed by Western blotting and quantitative RT-PCR. SS1-infected wt and ctsz (-/-) mice showed strong inflammation, foveolar hyperplasia, atrophy, and cystically-dilated glands. However, at 50 wpi, ctsz (-/-) mice developed significantly more severe spasmolytic polypeptide-expressing metaplasia (SPEM), showed enhanced epithelial proliferation, and higher levels of infiltrating macrophages. Induction of cytokines was higher and significantly prolonged in ctsz (-/-) mice compared to wt. Ctsz deficiency supports H. pylori-dependent development of chronic gastritis up to metaplasia, indicating a protective, but not proteolytic, function of Ctsz in inflammatory gastric disease.

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

BACKGROUND: In a previous study PCR analysis of clinical samples from suspected cases of Buruli ulcer disease (BUD) from Togo and external quality assurance (EQA) for local microscopy were conducted at an external reference laboratory in Germany. The relatively poor performance of local microscopy as well as effort and time associated with shipment of PCR samples necessitated the implementation of stringent EQA measures and availability of local laboratory capacity. This study describes the approach to implementation of a national BUD reference laboratory in Togo. METHODOLOGY: Large scale outreach activities accompanied by regular training programs for health care professionals were conducted in the regions "Maritime" and "Central," standard operating procedures defined all processes in participating laboratories (regional, national and external reference laboratories) as well as the interaction between laboratories and partners in the field. Microscopy was conducted at regional level and slides were subjected to EQA at national and external reference laboratories. For PCR analysis, sample pairs were collected and subjected to a dry-reagent-based IS2404-PCR (DRB-PCR) at national level and standard IS2404 PCR followed by IS2404 qPCR analysis of negative samples at the external reference laboratory. PRINCIPAL FINDINGS: The inter-laboratory concordance rates for microscopy ranged from 89% to 94%; overall, microscopy confirmed 50% of all suspected BUD cases. The inter-laboratory concordance rate for PCR was 96% with an overall PCR case confirmation rate of 78%. Compared to a previous study, the rate of BUD patients with non-ulcerative lesions increased from 37% to 50%, the mean duration of disease before clinical diagnosis decreased significantly from 182.6 to 82.1 days among patients with ulcerative lesions, and the percentage of category III lesions decreased from 30.3% to 19.2%. CONCLUSIONS: High inter-laboratory concordance rates as well as case confirmation rates of 50% (microscopy), 71% (PCR at national level), and 78% (including qPCR confirmation at external reference laboratory) suggest high standards of BUD diagnostics. The increase of non-ulcerative lesions, as well as the decrease in diagnostic delay and category III lesions, prove the effect of comprehensive EQA and training measures involving also procedures outside the laboratory.

BACKGROUND AND STUDY AIMS: Bile stones represent a highly prevalent condition and abnormalities of the biliary tree predispose to stone recurrence due to development of biliary stasis. In our study, we assessed the importance of an altered bile duct course for stone formation. PATIENTS AND METHODS: 1,307 patients with choledocholithiasis in the absence of any associated hepatobiliary disease who underwent endoscopic retrograde cholangiopancreatography (ERCP) between 2002 and 2009 were analysed. The angle enclosed between the horizontal portion of the common bile duct (CBD) and the horizontal plane was measured (angle α). Oblique common bile duct (OCBD) was defined as a CBD with angle α < 45°. RESULTS: 103 patients (7.9%) were found to harbour OCBD and these were compared to 104 randomly selected control subjects. Compared to controls, OCBD patients were (i) significantly older (72 ± 13 vs. 67 ± 13, p

Biotherapeutics are often produced in non-human host cells like Escherichia coli, yeast, and various mammalian cell lines. A major focus of any therapeutic protein purification process is to reduce host cell proteins to an acceptable low level. In this study, various E. coli host cell proteins were identified at different purifications steps by HPLC fractionation, SDS-PAGE analysis, and tryptic peptide mapping combined with online liquid chromatography mass spectrometry (LC-MS). However, no host cell proteins could be verified by direct LC-MS analysis of final drug substance material. In contrast, the application of affinity enrichment chromatography prior to comprehensive LC-MS was adequate to identify several low abundant host cell proteins at the final drug substance level. Bacterial alkaline phosphatase (BAP) was identified as being the most abundant host cell protein at several purification steps. Thus, we firstly established two different assays for enzymatic and immunological BAP monitoring using the cobas® technology. By using this strategy we were able to demonstrate an almost complete removal of BAP enzymatic activity by the established therapeutic protein purification process. In summary, the impact of fermentation, purification, and formulation conditions on host cell protein removal and biological activity can be conducted by monitoring process-specific host cell proteins in a GMP-compatible and high-throughput (> 1000 samples/day) manner.

Endothelial progenitor cells (EPCs) originate either directly from hematopoietic stem cells or from a subpopulation of monocytes. Controversial views about intracellular lipid traffic prompted us to analyze the uptake of human high density lipoprotein (HDL), and HDL-cholesterol in human monocytic EPCs. Fluorescence and electron microscopy were used to investigate distribution and intracellular trafficking of HDL and its associated cholesterol using fluorescent surrogates (bodipy-cholesterol and bodipy-cholesteryl oleate), cytochemical labels and fluorochromes including horseradish peroxidase and Alexa Fluor® 568. Uptake and intracellular transport of HDL were demonstrated after internalization periods from 0.5 to 4 hours. In case of HDL-Alexa Fluor® 568, bodipy-cholesterol and bodipy-cholesteryl oleate, a photooxidation method was carried out. HDL-specific reaction products were present in invaginations of the plasma membrane at each time of treatment within endocytic vesicles, in multivesicular bodies and at longer periods of uptake, also in lysosomes. Some HDL-positive endosomes were arranged in form of "strings of pearl"- like structures. HDL-positive multivesicular bodies exhibited intensive staining of limiting and vesicular membranes. Multivesicular bodies of HDL-Alexa Fluor® 568-treated EPCs showed multilamellar intra-vacuolar membranes. At all periods of treatment, labeled endocytic vesicles and organelles were apparent close to the cell surface and in perinuclear areas around the Golgi apparatus. No HDL-related particles could be demonstrated close to its cisterns. Electron tomographic reconstructions showed an accumulation of HDL-containing endosomes close to the trans-Golgi-network. HDL-derived bodipy-cholesterol was localized in endosomal vesicles, multivesicular bodies, lysosomes and in many of the stacked Golgi cisternae and the trans-Golgi-network Internalized HDL-derived bodipy-cholesteryl oleate was channeled into the lysosomal intraellular pathway and accumulated prominently in all parts of the Golgi apparatus and in lipid droplets. Subsequently, also the RER and mitochondria were involved. These studies demonstrated the different intracellular pathway of HDL-derived bodipy-cholesterol and HDL-derived bodipy-cholesteryl oleate by EPCs, with concomitant.

During the past two decades, Mediterranean waters have been warming at a rather high rate resulting in scientific and social concern. This warming trend is observed in satellite data, field data and model simulations, and affects both surface and deep waters throughout the Mediterranean basin. However, the warming rate is regionally different and seems to change with time, which has led to the question of what causes underlie the observed trends. Here, we analyze available satellite information on sea surface temperature (SST) from the last 25 years using spectral techniques and find that more than half of the warming tendency during this period is due to a non-linear, wave-like tendency. Using a state of the art hydrodynamic model, we perform a hindcast simulation and obtain the simulated SST evolution of the Mediterranean basin for the last 52 years. These SST results show a clear sinusoidal tendency that follows the Atlantic Multidecadal Oscillation (AMO) during the simulation period. Our results reveal that 58% of recent warming in Mediterranean waters could be attributed to this AMO-like oscillation, being anthropogenic-induced climate change only responsible for 42% of total trend. The observed acceleration of water warming during the 1990s therefore appears to be caused by a superimposition of anthropogenic-induced warming with the positive phase of the AMO, while the recent slowdown of this tendency is likely due to a shift in the AMO phase. It has been proposed that this change in the AMO phase will mask the effect of global warming in the forthcoming decades, and our results indicate that the same could also be applicable to the Mediterranean Sea. Henceforth, natural multidecadal temperature oscillations should be taken into account to avoid underestimation of the anthropogenic-induced warming of the Mediterranean basin in the future.

Although Attention-Deficit/Hyperactivity Disorder (ADHD) was initially regarded as a disorder exclusive to childhood, nowadays its prevalence in adulthood is well established. The development of novel techniques for quantifying the thickness of the cerebral mantle allows the further exploration of the neuroanatomical profiles underlying the child and adult form of the disorder. To examine the cortical mantle in children and adults with ADHD, we applied a vertex-wise analysis of cortical thickness to anatomical brain MRI scans acquired from children with (n = 43) and without ADHD (n = 41), as well as a group of adult neurotypical individuals (n = 31), adult patients with a history of stimulant treatment (n = 31) and medication-naïve adults with ADHD (n = 24). We observed several clusters of reduced laminar cortical thickness in ADHD patients in comparison to neurotypical individuals. These differences were primarily located in the dorsal attention network, including the bilateral inferior and superior parietal cortex and a section of the frontal cortex (centered on the superior frontal and precentral gyrus bilaterally). Further laminar thickness deficits were observed in the bilateral orbitofrontal cortex and medial occipital cortex. The deficits in the cortical surface were especially pronounced in the child sample, while adult patients showed a more typical laminar thickness across the cerebral mantle. These findings show that the neuroanatomical profile of ADHD, especially the childhood form of the disorder, involves robust alterations in the cortical mantle, which are most prominent in brain regions subserving attentional processing.

BACKGROUND: Since the early 1990s more than 1,800 patients with lesions suspicious for Buruli ulcer disease (BUD) have been reported from Togo. However, less than five percent of these were laboratory confirmed. Since 2007, the Togolese National Buruli Ulcer Control Program has been supported by the German Leprosy and Tuberculosis Relief Association (DAHW). Collaboration with the Department for Infectious Diseases and Tropical Medicine (DITM), University Hospital, Munich, Germany, allowed IS2404 PCR analysis of diagnostic samples from patients with suspected BUD during a study period of three years. METHODOLOGY/PRINCIPAL FINDINGS: The DAHW integrated active BUD case finding in the existing network of TB/Leprosy Controllers and organized regular training and outreach activities to identify BUD cases at community level. Clinically suspected cases were referred to health facilities for diagnosis and treatment. Microscopy was carried out locally, external quality assurance (EQA) at DITM. Diagnostic samples from 202 patients with suspected BUD were shipped to DITM, 109 BUD patients (54%) were confirmed by PCR, 43 (29.9%) by microscopy. All patients originated from Maritime Region. EQA for microscopy resulted in 62% concordant results. CONCLUSIONS/SIGNIFICANCE: This study presents a retrospective analysis of the first cohort of clinically suspected BUD cases from Togo subjected to systematic laboratory analysis over a period of three years and confirms the prevalence of BUD in Maritime Region. Intensified training in the field of case finding and sample collection increased the PCR case confirmation rate from initially less than 50% to 70%. With a PCR case confirmation rate of 54% for the entire study period the WHO standards (case confirmation rate ≥50%) have been met. EQA for microscopy suggests the need for intensified supervision and training. In January 2011 the National Hygiene Institute, Lomé, has assumed the role of a National Reference Laboratory for PCR confirmation and microscopy.

BACKGROUND/AIMS: Hepcidin (gene name HAMP), an IL-6-inducible acute phase peptide with antimicrobial properties, is the key negative regulator of iron metabolism. Liver is the primary source of HAMP synthesis, but it is also produced by other tissues such as kidney or heart and is found in body fluids such as urine or cerebrospinal fluid. While the role of hepcidin in biliary system is unknown, a recent study demonstrated that conditional gp130-knockout mice display diminished hepcidin levels and increased rate of biliary infections. METHODS: Expression and localization of HAMP in biliary system was analyzed by real time RT-PCR, in-situ hybridization, immunostaining and -blotting, while prohepcidin levels in human bile were determined by ELISA. RESULTS: Hepcidin was detected in mouse/human gallbladder and bile duct epithelia. Biliary HAMP is stress-inducible, in that it is increased in biliary cell lines upon IL-6 stimulation and in gallbladder mucosa of patients with acute cholecystitis. Hepcidin is also present in the bile and elevated prohepcidin levels were observed in bile of primary sclerosing cholangitis (PSC) patients with concurrent bacterial cholangitis compared to PSC subjects without bacterial infection (median values 22.3 vs. 8.9; p = 0.03). In PSC-cholangitis subjects, bile prohepcidin levels positively correlated with C-reactive protein and bilirubin levels (r = 0.48 and r = 0.71, respectively). In vitro, hepcidin enhanced the antimicrobial capacity of human bile (p

Negotiation and trade typically require a mutual interaction while simultaneously resting in uncertainty which decision the partner ultimately will make at the end of the process. Assessing already during the negotiation in which direction one's counterpart tends would provide a tremendous advantage. Recently, neuroimaging techniques combined with multivariate pattern classification of the acquired data have made it possible to discriminate subjective states of mind on the basis of their neuronal activation signature. However, to enable an online-assessment of the participant's mind state both approaches need to be extended to a real-time technique. By combining real-time functional magnetic resonance imaging (fMRI) and online pattern classification techniques, we show that it is possible to predict human behavior during social interaction before the interacting partner communicates a specific decision. Average accuracy reached approximately 70% when we predicted online the decisions of volunteers playing the ultimatum game, a well-known paradigm in economic game theory. Our results demonstrate the successful online analysis of complex emotional and cognitive states using real-time fMRI, which will enable a major breakthrough for social fMRI by providing information about mental states of partners already during the mutual interaction. Interestingly, an additional whole brain classification across subjects confirmed the online results: anterior insula, ventral striatum, and lateral orbitofrontal cortex, known to act in emotional self-regulation and reward processing for adjustment of behavior, appeared to be strong determinants of later overt behavior in the ultimatum game. Using whole brain classification we were also able to discriminate between brain processes related to subjective emotional and motivational states and brain processes related to the evaluation of objective financial incentives.

TGR5, the G protein-coupled bile acid receptor 1 (GPBAR1), has been linked to inflammatory pathways as well as bile homeostasis, and could therefore be involved in primary sclerosing cholangitis (PSC) a chronic inflammatory bile duct disease. We aimed to extensively investigate TGR5 sequence variation in PSC, as well as functionally characterize detected variants.Complete resequencing of TGR5 was performed in 267 PSC patients and 274 healthy controls. Six nonsynonymous mutations were identified in addition to 16 other novel single-nucleotide polymorphisms. To investigate the impact from the nonsynonymous variants on TGR5, we created a receptor model, and introduced mutated TGR5 constructs into human epithelial cell lines. By using confocal microscopy, flow cytometry and a cAMP-sensitive luciferase assay, five of the nonsynonymous mutations (W83R, V178M, A217P, S272G and Q296X) were found to reduce or abolish TGR5 function. Fine-mapping of the previously reported PSC and UC associated locus at chromosome 2q35 in large patient panels revealed an overall association between the TGR5 single-nucleotide polymorphism rs11554825 and PSC (odds ratio = 1.14, 95% confidence interval: 1.03-1.26, p = 0.010) and UC (odds ratio = 1.19, 95% confidence interval 1.11-1.27, p = 8.5 x 10(-7)), but strong linkage disequilibrium precluded demarcation of TGR5 from neighboring genes.Resequencing of TGR5 along with functional investigations of novel variants provided unique insight into an important candidate gene for several inflammatory and metabolic conditions. While significant TGR5 associations were detected in both UC and PSC, further studies are needed to conclusively define the role of TGR5 variation in these diseases.