Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons.
Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative d-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data.


Feline coronavirus serotypes 1 and 2: seroprevalence and association with disease in Switzerland.
To determine the prevalence of antibodies to feline coronavirus (FCoV) serotypes 1 and 2 in Switzerland and their association with different disease manifestations, a serological study based on immunofluorescence tests was conducted with Swiss field cats using transmissible gastroenteritis virus (TGEV), FCoV type 1 and FCoV type 2 as antigens. A total of 639 serum samples collected in the context of different studies from naturally infected cats were tested. The current study revealed that, with an apparent prevalence of 83%, FCoV serotype 1 is the most prevalent serotype in Switzerland. FCoV type 1 viruses induced higher antibody titers than FCoV type 2, and were more frequently associated with clinical signs and/or feline infectious peritonitis. The antibody development in seven cats experimentally infected with FCoV type 1 revealed that, with progressing duration of infection, antibodies to FCoV type 1 significantly increased over those to FCoV type 2. There was a significant relationship between antibody titers against TGEV, FCoV 1, and FCoV 2 and TGEV antigen detected the highest proportion of seropositive cats. We conclude that a vaccine against FCoV should be based on FCoV type 1-related antigens and that for serodiagnosis of FCoV infection TGEV should be used to attain the highest diagnostic efficiency. When serology is used in addition to clinical signs, hematology, and clinical chemistry results as an aid to diagnose clinical FIP, TGEV shows a diagnostic efficiency equal to that of a FCoV antigen.


Digitalizing multidisciplinary pulmonary rehabilitation in COPD with a smartphone application: an international observational pilot study.
Concerning COPD, pulmonary rehabilitation (PR) has a positive effect on disease progression and mortality, is cost-effective, and is a part of recommendations of international guidelines. Only a minority of patients profit from conventional PR due to a lack of resources, physicians' guideline adherence, or patients' motivation. Novel digital therapies like Kaia COPD, a smartphone application that digitizes PR in COPD, are promising solutions to fill this void. Kaia COPD provides a digital version of PR and is certified as a class-I medical device in the European Union. We investigated anonymized data from users of the Kaia COPD app on in-app retention and the change in health-related quality of life (COPD assessment test and Chronic Respiratory Disease Questionnaire [CRQ]) during a period of 20 exercise days with the app. Of 349 app downloads, 56 users fulfilled inclusion criteria and 34 (61%) had finished day 20 at the time of analysis and were included. Users took 33±11 days to complete the 20-day core program. Users finishing the program reduced their COPD assessment test scores (mean 2.5 units from 21.6±7.7 to 19.1±8.4 units, P=0.008). In finishers, there was a statistically significant effect above the minimum clinically important threshold of the CRQ score on the domains of fatigue, mastery, and emotional function. There was a statistically significant but not clinically relevant effect on the domain of dyspnea of CRQ. Digitalizing PR with a smartphone app is feasible and accepted by selected patients. The app leads to short-term improvement of health-related quality of life in patients completing a 20-day core program. Due to its observational character, this study has several methodological limitations and was intended to show the feasibility and to extrapolate effect sizes for planned prospective randomized-controlled trials to confirm these findings.


Gene silencing of translationally controlled tumor protein (TCTP) by siRNA inhibits cell growth and induces apoptosis of human prostate cancer cells.
Translationally controlled tumor protein (TCTP) is a novel anti apoptotic protein which is highly expressed in several cancer cell types including prostate cancer. However, studies investigating the role of TCTP in prostate cancer are scarce. Therefore, in this study we evaluated the effect of small interference RNA (siRNA) based knocking down of TCTP gene in prostate cancer cells. Cell proliferation and apoptosis were evaluated. Our results showed that TCTP is highly expressed in LNCaP cells compared to normal prostate epithelial cells. Transfection with TCTP siRNA specifically and drastically reduced the expression of both mRNA and protein levels of TCTP in LNCaP cells. The decreased expression of TCTP was associated with decreased viability of LNCaP cells. Further analysis of the transfected LNCaP cells showed that they undergo apoptosis via caspase-8 and caspase-3 dependent pathways. Results presented herein suggest a potential therapeutic application for prostate cancer by targeting TCTP gene using an siRNA approach.


Controlling a burn: outer-sphere gating of hydroxylamine oxidation by a distal base in cytochrome P460.
Ammonia oxidizing bacteria (AOB) use the cytotoxic, energetic molecule hydroxylamine (NH2OH) as a source of reducing equivalents for cellular respiration. Despite disproportionation or violent decomposition being typical outcomes of reactions of NH2OH with iron, AOB and anammox heme P460 proteins including cytochrome (cyt) P460 and hydroxylamine oxidoreductase (HAO) effect controlled, stepwise oxidation of NH2OH to nitric oxide (NO). Curiously, a recently characterized cyt P460 variant from the AOB Nitrosomonas sp. AL212 is able to form all intermediates of cyt P460 catalysis, but is nevertheless incompetent for NH2OH oxidation. We now show via site-directed mutagenesis, activity assays, spectroscopy, and structural biology that this lack of activity is attributable to the absence of a critical basic glutamate residue in the distal pocket above the heme P460 cofactor. This substitution is the only distinguishing characteristic of a protein that is otherwise effectively structurally and spectroscopically identical to an active variant. This highlights and reinforces a fundamental principal of metalloenzymology: metallocofactor inner-sphere geometric and electronic structures are in many cases insufficient for imbuing reactivity; a precisely defined outer coordination sphere contributed by the polypeptide matrix can be the key differentiator between a metalloenzyme and an unreactive metalloprotein.


Observation of Fine Time Structures in the Cosmic Proton and Helium Fluxes with the Alpha Magnetic Spectrometer on the International Space Station.
We present the precision measurement from May 2011 to May 2017 (79 Bartels rotations) of the proton fluxes at rigidities from 1 to 60 GV and the helium fluxes from 1.9 to 60 GV based on a total of 1×10^{9} events collected with the Alpha Magnetic Spectrometer aboard the International Space Station. This measurement is in solar cycle 24, which has the solar maximum in April 2014. We observed that, below 40 GV, the proton flux and the helium flux show nearly identical fine structures in both time and relative amplitude. The amplitudes of the flux structures decrease with increasing rigidity and vanish above 40 GV. The amplitudes of the structures are reduced during the time period, which started one year after solar maximum, when the proton and helium fluxes steadily increase. Above ∼3 GV the p/He flux ratio is time independent. We observed that below ∼3 GV the ratio has a long-term decrease coinciding with the period during which the fluxes start to rise.


Physical activity and sedentary leisure time and their associations with BMI, waist circumference, and percentage body fat in 0.5 million adults: the China Kadoorie Biobank study.
Few large studies in China have investigated total physical activity and sedentary leisure time and their associations with adiposity. We investigated determinants of physical activity and sedentary leisure time and their associations with adiposity in China. A total of 466,605 generally healthy participants (age: 30-79 y, 60% female) in the China Kadoorie Biobank were included in this cross-sectional analysis. Self-reported information on a range of activities was collected by interviewer-administered questionnaire. Physical activity was calculated as metabolic equivalent task hours per day (MET-h/d) spent on work, transportation, housework, and nonsedentary recreation. Sedentary leisure time was quantified as hours per day. Adiposity measures included BMI, waist circumference, and percentage body fat (by bioimpedance analysis). Associations were estimated by linear and logistic regression. The mean physical activity was 22 MET-h/d, and the mean sedentary leisure time was 3.0 h/d. For each sex, physical activity was about one-third lower among professionals/administrators than among factory workers, with intermediate levels for other occupational categories. A 1-SD (14 MET-h/d) greater physical activity was associated with a 0.15-unit (95% CI: 0.14, 0.16) lower BMI (in kg/m(2)), a 0.58-cm (95% CI: 0.55, 0.61) smaller waist circumference, and 0.48 (95% CI: 0.45, 0.50) percentage points less body fat. In contrast, a 1-SD (1.5 h/d) greater sedentary leisure time was associated with a 0.19-unit higher BMI (95% CI: 0.18, 0.20), a 0.57-cm larger waist circumference (95% CI: 0.54, 0.59), and 0.44 (95% CI: 0.42, 0.46) percentage points more body fat. For any given physical activity level, greater sedentary leisure time was associated with a greater prevalence of increased BMI, as was lower physical activity for any given sedentary leisure time. In adult Chinese, physical activity varies substantially by occupation, and lack of physical activity and excess sedentary leisure time are independently and jointly associated with greater adiposity.


How to define successful transition? An exploration of consensus indicators and outcomes in young adults with chronic conditions.
In this short report, we use data from a previous cohort study to explore the relationship between five out of eight consensus indicators for successful transition and patient-reported outcomes in young adulthood. Data came from a 6-year cohort study that consisted of a survey among 518 young adults with various chronic conditions and a review of their electronic patient records. Associations between five indicators for successful transition and background variables and patient-reported outcomes were explored with Spearman's r. Significant variables were included in stepwise (logistic) regression analyses with transition outcomes as dependent variables. The indicators relate to some extent to better healthcare-related transition outcomes, but not to autonomy in participation. The explained variance of the models varied from 9.7% to 26.4%. The change in explained variance after adding indicators varied from 2% to 16%. The challenge of translating the definition of transition into holistic indicators remains. The current consensus indicators are a good start, but there is more to transition than transfer.


Using the script concordance test to assess clinical reasoning skills in undergraduate and postgraduate medicine.
The script concordance test is a relatively new format of written assessment that is used to assess higher-order clinical reasoning and data interpretation skills in medicine. Candidates are presented with a clinical scenario, followed by the reveal of a new piece of information. The candidates are then asked to assess whether this additional information increases or decreases the probability or likelihood of a particular diagnostic, investigative, or management decision. To score these questions, the candidate's decision in each question is compared with that of a reference panel of expert clinicians. This review focuses on the development of quality script concordance questions, using expert panellists to score the items and set the passing score standard, and the challenges in the practical implementation (including pitfalls to avoid) of the written assessment.


Mammalian Mst1 and Mst2 kinases play essential roles in organ size control and tumor suppression.
Control of organ size by cell proliferation and survival is a fundamental developmental process, and its deregulation leads to cancer. However, the molecular mechanism underlying organ size control remains elusive in vertebrates. In Drosophila, the Hippo (Hpo) signaling pathway controls organ size by both restricting cell growth and proliferation and promoting cell death. Here we investigated whether mammals also require the Hpo pathway to control organ size and adult tissue homeostasis. We found that Mst1 and Mst2, the two mouse homologs of the Drosophila Hpo, control the sizes of some, but not all organs, in mice, and Mst1 and Mst2 act as tumor suppressors by restricting cell proliferation and survival. We show that Mst1 and Mst2 play redundant roles, and removal of both resulted in early lethality in mouse embryos. Importantly, tumors developed in the liver with a substantial increase of the stem/progenitor cells by 6 months after removing Mst1 and Mst2 postnatally. We show that Mst1 and Mst2 were required in vivo to control Yap phosphorylation and activity. Interestingly, apoptosis induced by TNFalpha was blocked in the Mst1 and Mst2 double-mutant cells both in vivo and in vitro. As TNFalpha is a pleiotropic inflammatory cytokine affecting most organs by regulating cell proliferation and cell death, resistance to TNFalpha-induced cell death may also contribute significantly to tumor formation in the absence of Mst1 and Mst2.


Regulation of macrophage inhibitory factor (MIF) by epidermal growth factor receptor (EGFR) in the MCF10AT model of breast cancer progression.
Genetic aberration of EGFR is one of the major molecular characteristics of breast cancer. However, the molecular changes associated with EGFR signaling during different stages of breast cancer development have not been studied. In this study, complementary two-dimensional-DIGE and iTRAQ technologies were used to profile the expression level of proteins in 4 isogenic cell lines in the MCF10AT model of breast cancer progression following a time course of EGF stimulation. A total of 80 proteins (67 from iTRAQ, 15 from DIGE, 2 common in both) were identified to be up- or down-regulated by EGF treatment. Following EGF stimulation, the expression level of MIF, a cytokine that has been implicated in many human cancers, was decreased in MCF10A1 normal breast mammary epithelial cells, increased in MCF10AT1k preneoplastic and MCF10CA1h low grade breast cancer cells, but showed no obvious difference in the MCF10CA1a high grade cancer cells. The increase in MIF expression level following EGF treatment could also be observed in A431 cervical cancer cells. EGF-induced increases of MIF expression levels in CA1h breast cancer cells were abrogated when MEK, but not PIK3CA, was knocked down. In addition, silencing of MIF diminished the proliferation of EGF-stimulated CA1h cells when compared to control cells. Taken together, our data suggested an EGFR --> MEK --> MIF proliferative pathway that has never been reported previously and that this pathway "evolves" during disease progression as modeled by the MCF10AT system. Revelation of the novel relationship between MIF and EGF may contribute to an integrated understanding of the roles of these oncogenic factors during breast cancer development.


Second-harmonic generation in single-mode and multimode fibers.
We report efficient second-harmonic generation in several commercially available telecommunication-grade single-mode and multimode optical fibers. We have investigated the effect of standard dopants such as germanium, phosphorous, and fluorine, and find that the efficient second-harmonic generation is associated with germaniarelated photosensitive color centers. We observed a 1.5% conversion efficiency in single-mode fibers with germanium-, phosphorous-, and fluorine-doped cores and high hydroxyl levels.


Green tea epigallocatechin gallate enhances therapeutic efficacy of temozolomide in orthotopic mouse glioblastoma models.
The alkylating agent temozolomide, in combination with surgery and radiation, is the current standard of care for patients with glioblastoma. However, despite this extensive therapeutic effort, the inclusion of temozolomide extends survival only by a few short months. Among the factors contributing to chemoresistance is elevated expression of the endoplasmic reticulum (ER) chaperone GRP78 (glucose-regulated protein 78; BiP), a key pro-survival component of the ER stress response system. Because the green tea component EGCG (epigallocatechin 3-gallate) had been shown to inhibit GRP78 function, we investigated whether this polyphenolic agent would be able to increase the therapeutic efficacy of temozolomide in preclinical models of glioblastoma. Mice with intracranially implanted human U87 (p53 wild type) or U251 (p53 mutant) glioblastoma cells were treated with temozolomide and EGCG, alone and in combination. We found that EGCG alone did not provide survival benefit, but significantly improved the existing therapeutic effect of temozolomide, i.e., life extension was substantially greater under combination therapy as compared to temozolomide therapy alone. Immunohistochemical analysis of tumor tissue revealed increased expression levels of GRP78 in temozolomide-treated animals, which was diminished when temozolomide was combined with EGCG. Parallel in vitro experiments with siRNA targeting GRP78 or its major pro-apoptotic antagonist CHOP (CCAAT/enhancer binding protein homologous protein/GADD153) further established a critical role of the ER stress response system, where si-GRP78 sensitized cells to treatment with temozolomide, and si-CHOP provided protection from drug-induced toxicity. Thus, ER stress-regulatory components affect the chemotherapeutic response of glioblastoma cells to treatment with temozolomide, and inclusion of EGCG is able to increase the therapeutic efficacy of this DNA-damaging agent.


Disproportionation of hypophosphite and phosphite.
The disproportionation of NaH2PO2, NaH2PO3, Na2HPO3 and their mixtures was studied by TG-DSC, XRD and 31P NMR. NaH2PO2 reacted in three steps to yield PH3, Na5P3O10 and H2 by disproportionation and oxidation with water released in condensation reactions. In the first step at 310 °C NaH2PO2 reacted to yield PH3, Na2H2P2O5, Na2HPO3, Na4P2O7 and H2. H2 rather than H2O was the coproduct of the disproportionation, because H2O oxidized hypophosphite and phosphite at elevated temperatures, in agreement with DFT results that show that the reaction of H3PO3 with H2O is exothermic. The oxidation of phosphite by H2O has a twofold effect on gas formation. First, it diminishes gas formation because water is not released and, second, because H2O oxidizes phosphite, less phosphite is available for disproportionation to phosphate and, thus, less PH3 is formed. As a consequence, the maximum PH3 efficiency in the disproportionation of NaH2PO2 was not 50% but 40%. Phosphate was never observed, only Na4P2O7, which appeared as a primary product of the oxidation of Na2H2P2O5 by H2O. Na2HPO3 did not react below 450 °C when heated alone, but in the presence of compounds which release H2O it was oxidized to Na4P2O7 below 400 °C. NaH2PO3 first reacted to yield PH3 and Na2H2P2O5 and then to Na5P3O10 and Na3P3O9. Heating a 1 : 1 mixture of NaH2PO3 and Na2HPO3 led to PH3, Na2H2P2O5 and Na2HPO3, then to Na4P2O7 and eventually to Na5P3O10 and Na3P3O9. In all cases some red phosphorus was formed by the decomposition of PH3, especially at higher temperatures.


Analysis of shared heritability in common disorders of the brain.
Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.


Estimating the impact of school closure on influenza transmission from Sentinel data.
The threat posed by the highly pathogenic H5N1 influenza virus requires public health authorities to prepare for a human pandemic. Although pre-pandemic vaccines and antiviral drugs might significantly reduce illness rates, their stockpiling is too expensive to be practical for many countries. Consequently, alternative control strategies, based on non-pharmaceutical interventions, are a potentially attractive policy option. School closure is the measure most often considered. The high social and economic costs of closing schools for months make it an expensive and therefore controversial policy, and the current absence of quantitative data on the role of schools during influenza epidemics means there is little consensus on the probable effectiveness of school closure in reducing the impact of a pandemic. Here, from the joint analysis of surveillance data and holiday timing in France, we quantify the role of schools in influenza epidemics and predict the effect of school closure during a pandemic. We show that holidays lead to a 20-29% reduction in the rate at which influenza is transmitted to children, but that they have no detectable effect on the contact patterns of adults. Holidays prevent 16-18% of seasonal influenza cases (18-21% in children). By extrapolation, we find that prolonged school closure during a pandemic might reduce the cumulative number of cases by 13-17% (18-23% in children) and peak attack rates by up to 39-45% (47-52% in children). The impact of school closure would be reduced if it proved difficult to maintain low contact rates among children for a prolonged period.


Upregulation of RASSF1A in Colon Cancer by Suppression of Angiogenesis Signaling and Akt Activation.
Silencing of tumor suppressor genes (TSGs) and promotion of angiogenesis are associated with tumor development and metastasis. However, little is known if angiogenic molecules directly control TSGs and vice versa. A regulatory link between angiogenesis and down regulation of TSGs was evaluated using an anti-cancer agent, andrographolide (AGP) in cancer cells, mouse xenograft tissues and patient derived organoids through gene/protein expression, gene silencing, and immunohistochemical analyses. AGP treatment demonstrated significant expression of RASSF1A and PTEN TSGs in colon cancer and other cancer cells, mouse tissues and organoids. Depletion of RASSF1A with siRNA limited cyclin D1 and BAX expression. SiRNA depletion of PTEN, upstream regulator of RASSF1A resulted in a 50% reduction in RASSF1A expression. Histopathological analysis of the AGP treated tumor sections showed significant reduction in vessel size, microvascular density and tumor mitotic index suggesting suppression of angiogenesis. This was corroborated by protein analysis demonstrating significant reductions in angiogenesis signaling pathway molecules VEGF165, FOXM1, and pAkt, but significant elevation of the endogenous angiogenesis inhibitor Tsp-2. Treatment of cells with exogenous VEGF prevented the suppression of angiogenesis signaling by AGP, resulting in sustained expression of pAkt, an upstream down-regulator of RASSF1A. RASSF1A expression remained low in VEGF treated cells despite the addition of AGP. Our results demonstrate for the first time that AGP induces RASSF1A expression in colon cancer cells and is dependent on angiogenesis signaling events. Therefore, our research may facilitate novel therapeutic options for advanced colon cancer therapy.


The Notch intracellular domain represses CRE-dependent transcription.
Members of the cyclic-AMP response-element binding protein (CREB) transcription factor family regulate the expression of genes needed for long-term memory formation. Loss of Notch impairs long-term, but not short-term, memory in flies and mammals. We investigated if the Notch-1 (N1) exerts an effect on CREB-dependent gene transcription. We observed that N1 inhibits CREB mediated activation of cyclic-AMP response element (CRE) containing promoters in a γ-secretase-dependent manner. We went on to find that the γ-cleaved N1 intracellular domain (N1ICD) sequesters nuclear CREB1α, inhibits cAMP/PKA-mediated neurite outgrowth and represses the expression of specific CREB regulated genes associated with learning and memory in primary cortical neurons. Similar transcriptional effects were observed with the N2ICD, N3ICD and N4ICDs. Together, these observations indicate that the effects of Notch on learning and memory are, at least in part, via an effect on CREB-regulated gene expression.


Prevalence and deteminants of obesity in Spanish children and young people.
Prevalence estimates of obesity in a national random sample of Spanish children and young people are presented in this paper, defined by age- and sex-specific BMI national reference standards for the 85th percentile (overweight) and 97th percentile (obesity), as well as by Cole et al. criteria. A random sample of 3534 people, aged 2-24 years, was interviewed between 1998 and 2000. The study protocol included personal data, data on education and socioeconomic status (SES) for the family, dietary assessment, anthropometric measurements and physical activity. The prevalence of obesity was 13.9 % (95 % CI 12.7, 15.1) considering Spanish reference standards as cut-offs. Obesity was significantly higher in boys (15.6 %) than in girls (12 %). The highest values were observed between 6 and 13 years of age. Using Cole's cut-offs, the estimated prevalence of obesity was 6.3 % (95 % CI 5.4, 7.5) with a similar pattern to that previously described by sex. Regarding sociodemographic factors, sex, age group, region, size of locality of residence, mother's level of education and family SES level were significant predictors for obesity in children and adolescents under 14 years. Among young people, the main sociodemographic predictors for obesity were geographical region and family SES level. Odds ratio for obesity was 1.27 for those with a more frequent consumption of buns, cakes and snacks, and 1.71 for those with more frequent consumption of sugared drinks. Adequate consumption of fruit and vegetables, usually having breakfast and regular sports practice had a protective effect. The available data show that obesity in Spain is a public health issue given its magnitude and increasing trends. Among Spanish children and young people, those at prepubertal age, particularly boys, can be identified as a group at higher risk for overweight and obesity, particularly children from lower SES families.


Development and Characterization of Mechanically Durable Silicone-Polythiourethane Composites Modified with Tetrapodal Shaped ZnO Particles for the Potential Application as Fouling-Release Coating in the Marine Sector.
Ecological considerations strongly necessitate the development of environmentally friendly antifouling paints. A promising alternative to biocide containing antifouling paints are fouling-release coatings, which are non-toxic and designed to prevent permanent attachment of marine organisms to the surface, due to their low surface energy. However, these coatings suffer from insufficient mechanical properties, which make them unsuitable for mechanically stressed surfaces e.g., on ship hulls. To overcome those obstacles, polydimethylsiloxane (PDMS)-polythiourethane (PTU) composites modified with tetrapodal shaped micro-nano ZnO particles (t-ZnO) were produced and characterized by evaluating the surface energy, mechanical properties, and fouling-release performance. Among all variations, PTU/1 wt.% PDMS composites with 1 wt.% t-ZnO particles possess superior properties for applications as fouling-release coatings for maritime purposes.


Cycling time trial performance may be impaired by whey protein and L-alanine intake during prolonged exercise.
Previous studies reported that adding protein (PRO) to carbohydrate (CHO) solutions enhances endurance performance. The ergogenic effect may be a function of additional protein/amino acid calories, but this has not been examined. In addition, although supplemental L-alanine (ALA) is readily oxidized during exercise, the subsequent impact on metabolism and prolonged endurance performance is unknown. The purpose of this investigation was to independently gauge the impact of whey PRO hydrolysate and ALA supplementation on performance and various physiological parameters. Eight cyclists (age: 22.3 ± 5.6 yr, weight: 70.0 ± 8.0 kg, VO2max: 59.4 ± 4.9 ml · kg(-1) · min(-1)) performed 120 min of constant-load cycling (55% of peak power) followed by a 30-km time trial (TT) under placebo (PLA), PRO, and ALA conditions. Magnitude-based qualitative inferences were applied to evaluate treatment differences and data are presented as percent difference between treatments ± 90% confidence limit. Both ALA (2.1 ± 2.7%) and PRO intake (-2.1 ± 2.2%) possibly harmed performance compared with PLA. Of interest, heart rate was possibly lower with ALA than PLA at 20- (-2.7 ± 3.4%) and 120-min (-1.7 ± 2.9%) of constant-load cycling and the serum interleukin-6 (IL-6) response to 120 min of cycling was likely attenuated with PRO compared with PLA (PLA, 6.6 ± 3.7 fold vs. PRO, 2.9 ± 1.8 fold). In addition, blood glucose levels were lower with PRO than PLA at 20- (-8.8 ± 2.3%; very likely) and 120-min (-4.9 ± 4.6%; likely) of constant-load cycling. Although ALA intake appears to lower HR and PRO ingestion dampens the IL-6 response to exercise, the ingestion of PRO (without CHO) or ALA does not enhance, and may actually impair, performance following prolonged cycling.


The relative merits of lean, enriched, and empowered offices: an experimental examination of the impact of workspace management strategies on well-being and productivity.
Principles of lean management encourage managers to exert tight control over office space and the people within it. Alternative, design-led approaches promote the value of offices that are enriched, particularly by plants and art. On the basis of a social identity perspective, we argue that both of these approaches may compromise organizational outcomes by disempowering workers and failing to give them input into the design of their office space. This hypothesis is tested in two experiments (ns = 112, 47). The first was conducted in an interior office in a psychology department, the second in a commercial city office. In 4 independent conditions we examine the impact of space management strategies in which the office is either (a) lean, (b) decorated by the experimenter (with plants and art), (c) self-decorated, or (d) self-decorated and then redecorated by the experimenter. We examine the impact of these conditions on organizational identification, well-being, and various forms of productivity (attention to detail, information processing, information management, and organizational citizenship). In both experiments, superior outcomes are observed when offices are decorated rather than lean. However, further improvements in well-being and productivity are observed when workers have input into office decoration. Moreover, these effects are attenuated if this input is overridden. Implications for theory and practice are discussed. In particular, findings point to the need to question assumptions about the merits of lean office space management that have been dominant throughout the last century.


SU-E-T-464: Impact of the Treatment Margin on Tumor Control and Normal Tissue Complication for Prostate Treatment.
To investigate the consequence of treatment margin reduction on normal tissue complication probability (NTCP) and tumor control probability (TCP) of prostate external beam treatment. Intensity modulated rotational radiotherapy plans were generated for 10 prostate patients with 6 different posterior margin sizes from 5mm to 0. The prescription dose is 80Gy for 40 treatment fractions. The dose distributions were recalculated with consideration of the intrafractional motion and the localization error. The statistical uncertainties of the intrafractional motion and the localization error were derived based on the motion tracking data recorded by the Calypso 4D localization system for a large patient population. The TCP and NTCP were calculated based on the dose volume histograms (DVH) of prostate and rectum for plans with different margins using an equivalent uniform dose (EUD) based biological model. The 50% tumor control dose (TCD50) of 60Gy for prostate and the median toxic dose (TD50) of 55Gy for rectum were used in the calculation. The minimum dose of the prostate and the mean dose of the rectum dropped with the decrease of the treatment margin. When the posterior treatment margin was reduced from 5mm to zero, the EUD of prostate decreased from 83Gy (±0.5Gy) to 81Gy (±0.5Gy) and the TCP dropped from 93.2% (±0.1%) to 91.7% (±0.1%), the EUD of the rectum decreased more significantly from 48.9Gy (±0.4Gy) to 32.5Gy (±0.5Gy) and the NTCP dropped from 13.3% (±1.5%) to 0.03% (± 0.01%). The treatment margin size affects the dose to the target and the nearby critical structure. More significant impact on NTCP has been observed than on TCP. This gives us some room to consider the quality of the patient's after-treatment life. A wise choice of treatment margin can be made based on physician's opinion and patient's preference on the tumor control and the quality of life.


Casp8p41: The Protean Mediator of Death in CD4 T-cells that Replicate HIV.
HIV cure is now the focus of intense research after Timothy Ray Brown (the Berlin patient) set the precedent of being the first and only person cured. A major barrier to achieving this goal on a meaningful scale is an elimination of the latent reservoir, which is thought to comprise CD4-positive cells that harbor integrated, replication-competent HIV provirus. These cells do not express viral proteins, are indistinguishable from uninfected CD4 cells, and are thought to be responsible for HIV viral rebound-that occurs within weeks of combination anti retroviral therapy (cART) interruption. Modalities to engineer transcriptional stimulation (reactivation) of this dormant integrated HIV provirus, leading to expression of cytotoxic viral proteins, are thought to be a specific way to eradicate the latently infected CD4 pool and are becoming increasingly relevant in the era of HIV cure. HIV protease is one such protein produced after HIV reactivation that cleaves procaspase-8 to generate a novel protein Casp8p41. Casp8p41 then binds to the BH3 domain of BAK, leading to BAK oligomerization, mitochondrial depolarization, and apoptosis. In central memory T cells (TCMs) from HIV-infected patients, an elevated Bcl-2/procaspase-8 ratio was observed, and Casp8p41 binding to Bcl-2 was associated with a lack of reactivation-induced cell death. This was reversed by priming cells with a specific Bcl-2 antagonist prior to reactivation, resulting in increased cell death and decreased HIV DNA in a Casp8p41-dependent pathway. This review describes the biology, clinical relevance, and implications of Casp8p41 for a potential cure.


Temporal windows in visual processing: "prestimulus brain state" and "poststimulus phase reset" segregate visual transients on different temporal scales.
Dynamic vision requires both stability of the current perceptual representation and sensitivity to the accumulation of sensory evidence over time. Here we study the electrophysiological signatures of this intricate balance between temporal segregation and integration in vision. Within a forward masking paradigm with short and long stimulus onset asynchronies (SOA), we manipulated the temporal overlap of the visual persistence of two successive transients. Human observers enumerated the items presented in the second target display as a measure of the informational capacity read-out from this partly temporally integrated visual percept. We observed higher β-power immediately before mask display onset in incorrect trials, in which enumeration failed due to stronger integration of mask and target visual information. This effect was timescale specific, distinguishing between segregation and integration of visual transients that were distant in time (long SOA). Conversely, for short SOA trials, mask onset evoked a stronger visual response when mask and targets were correctly segregated in time. Examination of the target-related response profile revealed the importance of an evoked α-phase reset for the segregation of those rapid visual transients. Investigating this precise mapping of the temporal relationships of visual signals onto electrophysiological responses highlights how the stream of visual information is carved up into discrete temporal windows that mediate between segregated and integrated percepts. Fragmenting the stream of visual information provides a means to stabilize perceptual events within one instant in time.


Automated quantification of microvascular perfusion.
Changes in microvascular perfusion have been reported in many diseases, yet the functional significance of altered perfusion is often difficult to determine. This is partly because commonly used techniques for perfusion measurement often rely on either indirect or by-hand approaches. We developed and validated a fully automated software technique to measure microvascular perfusion in videos acquired by fluorescence microscopy in the mouse gastrocnemius. Acute perfusion responses were recorded following intravenous injections with phenylephrine, SNP, or saline. Software-measured capillary flow velocity closely correlated with by-hand measured flow velocity (R2 = 0.91, P < 0.0001). Software estimates of capillary hematocrit also generally agreed with by-hand measurements (R2 = 0.64, P < 0.0001). Detection limits range from 0 to 2000 μm/s, as compared to an average flow velocity of 326 ± 102 μm/s (mean ± SD) at rest. SNP injection transiently increased capillary flow velocity and hematocrit and made capillary perfusion more steady and homogenous. Phenylephrine injection had the opposite effect in all metrics. Saline injection transiently decreased capillary flow velocity and hematocrit without influencing flow distribution or stability. All perfusion metrics were temporally stable without intervention. These results demonstrate a novel and sensitive technique for reproducible, user-independent quantification of microvascular perfusion.


Multimodal bacteriochlorophyll theranostic agent.
The complimentary ability of different noninvasive imaging technologies with therapeutic modalities can be used in tandem providing high-resolution and highly sensitive imaging of events at the molecular and cellular level providing a means for image-guided therapy. There is increasing interest in using porphyrin-based photosensitizers as theranostics to take advantages of their near-infrared fluorescent properties for imaging and their strong singlet oxygen generation abilities for photodynamic therapy. Here we report a targeted multimodal bacteriochlorophyll theranostic probe. This probe consists of a bacteriochlorophyll derivative, a pharmacokinetics modification peptide linker and folate for targeted delivery to folate receptor expressing cancer cells. We demonstrate its multimodal theranostic capability, its folate receptor targeting ability and its utility for both NIR fluorescence imaging and photodynamic therapy purposes both in vitro and in vivo.


Leaving no one behind: lessons from implementation of policies for universal HIV treatment to universal health coverage.
The third Sustainable Development Goal (SDG - 3) aims to ensure healthy lives and promote well-being for all at all ages. SDG-3 has a specific target on universal health coverage (UHC), which emphasizes the importance of all people and communities having access to quality health services without risking financial hardship. The objective of this study is to review progress towards UHC using antiretroviral treatment (ART) as a case study. We used a mixed-methods design including qualitative and quantitative approaches. We reviewed and synthesised the evidence on the evolution of the WHO HIV treatment guidelines between 2002 and 2019. We calculated ART coverage over time by gender, age group, and location. We also estimated ART coverage differences and ratios. ART guidelines have evolved from "treating the sickest" to "treating all". ART coverage increased globally from under 7% in 2005 to 62% in 2018. There have been successes in increasing ART coverage in all populations and locations. However, progress varies by population and location in many regions. There is inequity in ART coverage: women (68%) versus men (55%), and adults (62%) versus children (54%). This inequity has widened over time, and with expanded ART eligibility criteria. On the other hand, data from at least one high-burden country (Ethiopia) shows that inequity among regions has narrowed over time due to the improvements in the primary health care systems and implementation of the public health approach in the country. ART coverage has increased at global, regional and national levels to all population groups. However, the gains have not been equitable among locations and populations. Policies towards universality may widen the inequity in resource-limited settings unless countries take precautions and "put the last first". We argue that primary health care and public health approaches, with multi-sectoral actions and community engagement, are vital to minimize inequity, achieve UHC and leave no one behind.


Crayfish plague in Japan: A real threat to the endemic Cambaroides japonicus.
Global introductions of aquatic species and their associated pathogens are threatening worldwide biodiversity. The introduction of two North American crayfish species, Procambarus clarkii and Pacifastacus leniusculus, into Japan in 1927 seems to have negatively affected native Japanese crayfish populations of Cambaroides japonicus. Several studies have shown the decline of these native populations due to competition, predation and habitat colonization by the two invasive North American crayfish species. Here, we identify an additional factor contributing to this decline. We report the first crayfish plague outbreaks in C. japonicus populations in Japan, which were diagnosed using both histological and molecular approaches (analyses of the internal transcribed spacer region). Subsequent analyses of the mitochondrial ribosomal rnnS and rnnL regions of diseased specimens indicate that these outbreaks originated from a P. clarkii population and identify a novel haplotype of Aphanomyces astaci, d3-haplotype, hosted by P. clarkii. Overall, our findings demonstrate the first two cases of crayfish plague in Japan, and the first case in a non-European native crayfish species, which originated from the red swamp crayfish P. clarkii. This finding is a matter of concern for the conservation of the native freshwater species of Japan and also highlights the risk of introducing crayfish carrier species into biogeographic regions harboring species susceptible to the crayfish plague.


Nematode distributions as spatial null models for macroinvertebrate species richness across environmental gradients: A case from mountain lakes.
Nematode species are widely tolerant of environmental conditions and disperse passively. Therefore, the species richness distribution in this group might largely depend on the topological distribution of the habitats and main aerial and aquatic dispersal pathways connecting them. If so, the nematode species richness distributions may serve as null models for evaluating that of other groups more affected by environmental gradients. We investigated this hypothesis in lakes across an altitudinal gradient in the Pyrenees. We compared the altitudinal distribution, environmental tolerance, and species richness, of nematodes with that of three other invertebrate groups collected during the same sampling: oligochaetes, chironomids, and nonchironomid insects. We tested the altitudinal bias in distributions with t-tests and the significance of narrow-ranging altitudinal distributions with randomizations. We compared results between groups with Fisher's exact tests. We then explored the influence of environmental factors on species assemblages in all groups with redundancy analysis (RDA), using 28 environmental variables. And, finally, we analyzed species richness patterns across altitude with simple linear and quadratic regressions. Nematode species were rarely biased from random distributions (5% of species) in contrast with other groups (35%, 47%, and 50%, respectively). The altitudinal bias most often shifted toward low altitudes (85% of biased species). Nematodes showed a lower portion of narrow-ranging species than any other group, and differed significantly from nonchironomid insects (10% and 43%, respectively). Environmental variables barely explained nematode assemblages (RDA adjusted R2 = 0.02), in contrast with other groups (0.13, 0.19 and 0.24). Despite these substantial differences in the response to environmental factors, species richness across altitude was unimodal, peaking at mid elevations, in all groups. This similarity indicates that the spatial distribution of lakes across altitude is a primary driver of invertebrate richness. Provided that nematodes are ubiquitous, their distribution offers potential null models to investigate species richness across environmental gradients in other ecosystem types and biogeographic regions.


New-onset insomnia among cancer patients undergoing chemotherapy: prevalence, risk factors, and its correlation with other symptoms.
Although insomnia is common among cancer patients, its prevalence remains variable, and its risk factors and correlation with other cancer-related symptoms are not fully explored in the literature. This study aims to determine the prevalence and severity of insomnia as well as risk factors and sleep-related symptom clusters in a sample of cancer patients. A cross-sectional survey was conducted collecting data from 213 cancer patients undergoing chemotherapy (age = 53.1 ± 11.3 years, 60% female). Insomnia was measured using the Insomnia Severity Index, a sleep log, and Actigraph, while symptoms were assessed using the Memorial Symptom Assessment Scale and the Hospital Anxiety and Depression Scale. Quality of life was measured with the Functional Assessment of Cancer Therapy-General. Of the participants, 42.8% reported insomnia, with 31.9% of those with insomnia reporting severe insomnia. Insomnia occurrence and severity were not correlated with the participants' characteristics, cancer-related or treatment-related factors, only with the participants' anxiety/depression scores. Principal component analysis showed that insomnia, depression, and anxiety formed a symptom cluster (p < 0.001). There was no difference between sleep parameters measured by Actigraphy in insomnia and non-insomnia participants. This study demonstrated that the prevalence of insomnia was high and indicated a symptom cluster of insomnia, depression, and anxiety. Therefore, interventions to reduce this symptom cluster may benefit cancer patients who are trying to manage these symptoms.


The liquid-ordered phase in sphingomyelincholesterol membranes as detected by the discrimination by oxygen transport (DOT) method.
Membranes made from binary mixtures of egg sphingomyelin (ESM) and cholesterol were investigated using conventional and saturation-recovery EPR observations of the 5-doxylstearic acid spin label (5-SASL). The effects of cholesterol on membrane order and the oxygen transport parameter (bimolecular collision rate of molecular oxygen with the nitroxide spin label) were monitored at the depth of the fifth carbon in fluid- and gel-phase ESM membranes. The saturation-recovery EPR discrimination by oxygen transport (DOT) method allowed the discrimination of the liquid-ordered (l(o)), liquid-disordered (l(d)), and solid-ordered (s(o)) phases because the bimolecular collision rates of the molecular oxygen with the nitroxide spin label differ in these phases. Additionally, oxygen collision rates (the oxygen transport parameter) were obtained in coexisting phases without the need for their separation, which provides information about the internal dynamics of each phase. The addition of cholesterol causes a dramatic decrease in the oxygen transport parameter around the nitroxide moiety of 5-SASL in the l(o) phase, which at 50 mol% cholesterol becomes approximately 5 times smaller than in the pure ESM membrane in the l(d) phase, and approximately 2 times smaller than in the pure ESM membrane in the s(o) phase. The overall change in the oxygen transport parameter is as large as approximately 20-fold. Conventional EPR spectra show that 5-SASL is maximally immobilized at the phase boundary between regions with coexisting l(d) and l(o) phases or s(o) and l(o) phases and the region with a single l(o) phase. The obtained results allowed for the construction of a phase diagram for the ESM-cholesterol membrane.


Influence of rest and exercise at a simulated altitude of 4,000 m on appetite, energy intake, and plasma concentrations of acylated ghrelin and peptide YY.
The reason for high altitude anorexia is unclear but could involve alterations in the appetite hormones ghrelin and peptide YY (PYY). This study examined the effect of resting and exercising in hypoxia (12.7% O(2); ∼4,000 m) on appetite, energy intake, and plasma concentrations of acylated ghrelin and PYY. Ten healthy males completed four, 7-h trials in an environmental chamber in a random order. The four trials were control-normoxia, control-hypoxia, exercise-normoxia, and exercise-hypoxia. During exercise trials, participants ran for 60 min at 70% of altitude-specific maximal oxygen consumption (Vo(2max)) and then rested. Participants rested throughout control trials. A standardized meal was consumed at 2 h and an ad libitum buffet meal at 5.5 h. Area under the curve values for hunger (assessed using visual analog scales) tended to be lower during hypoxic trials than normoxic trials (repeated-measures ANOVA, P = 0.07). Ad libitum energy intake was lower (P = 0.001) in hypoxia (5,291 ± 2,189 kJ) than normoxia (7,718 ± 2,356 kJ; means ± SD). Mean plasma acylated ghrelin concentrations were lower in hypoxia than normoxia (82 ± 66 vs. 100 ± 69 pg/ml; P = 0.005) while PYY concentrations tended to be higher in normoxia (32 ± 4 vs. 30 ± 3 pmol/l; P = 0.059). Exercise suppressed hunger and acylated ghrelin and increased PYY but did not influence ad libitum energy intake. These findings confirm that hypoxia suppresses hunger and food intake. Further research is required to determine if decreased concentrations of acylated ghrelin orchestrate this suppression.


A linked spatial and temporal model of the chemical and biological status of a large, acid-sensitive river network.
Freshwater sensitivity to acidification varies according to geology, soils and land-use, and consequently it remains difficult to quantify the current extent of acidification, or its biological impacts, based on limited spot samples. The problem is particularly acute for river systems, where the transition from acid to circum-neutral conditions can occur within short distances. This paper links an established point-based long-term acidification model (MAGIC) with a landscape-based mixing model (PEARLS) to simulate spatial and temporal variations in acidification for a 256 km(2) catchment in North Wales. Empirical relationships are used to predict changes in the probability of occurrence of an indicator invertebrate species, Baetis rhodani, across the catchment as a function of changing chemical status. Results suggest that, at present, 27% of the river network has a mean acid neutralising capacity (ANC) below a biologically-relevant threshold of 20 microeq l(-1). At high flows, this proportion increases to 45%. The model suggests that only around 16% of the stream network had a mean ANC < 20 microeq l(-1) in 1850, but that this increased to 42% at the sulphur deposition peak around 1970. By 2050 recovery is predicted, but with some persistence of acid conditions in the most sensitive, peaty headwaters. Stream chemical suitability for Baetis rhodani is also expected to increase in formerly acidified areas, but for overall abundance to remain below that simulated in 1850. The approach of linking plot-scale process-based models to catchment mixing models provides a potential means of predicting the past and future spatial extent of acidification within large, heterogeneous river networks and regions. Further development of ecological response models to include other chemical predictor variables and the effects of acid episodes would allow more realistic simulation of the temporal and spatial dynamics of ecosystem recovery from acidification.


Channelopathies: decoding disease pathogenesis.
The deconvolution of corrupted biological pathways in disease and the translation of patient-specific molecular mechanisms into tailored management algorithms have begun to extend the reach of individualized medicine from principles to practice. A case in point is the emergent deciphering of the pathobiology underlying life-threatening human diseases caused by dysfunction in adenosine triphosphate (ATP)-sensitive potassium (K(ATP)) channels. In a recent paper in Science, researchers used humanized mouse models to recapitulate a pathogenic K(ATP) channel mutation and pinpoint tissue-restricted lesions that stratify the consequences of genetic variation on disease traits. Advances in the molecular medicine of K(ATP) channelopathies offer new perspectives for personalized diagnosis and therapy.


Primary structure of v-raf: relatedness to the src family of oncogenes.
A replication-defective, acute transforming retrovirus (murine sarcoma virus 3611) was isolated from mouse and molecularly cloned. The nucleotide sequence of 1.5 kilobases encompassing the transforming gene (v-raf) was determined. This sequence, which predicts the amino acid sequence of a gag-raf fusion protein, terminates 180 nucleotides from the 3' end of the acquired cellular sequence. Comparison of the predicted amino acid sequence of v-raf with the predicted amino acid sequences of other oncogenes reveals significant homologies to the src family of oncogenes. There is a lack of homology within the sequence of the tyrosine acceptor domain described for the phosphotyrosine kinase members of the src family of transforming proteins. Phylogenetic arrangement of this family of oncogenes suggests that tyrosine-specific phosphorylation may be a recently acquired activity.


Interim Futility Monitoring Assessing Immune Therapies With a Potentially Delayed Treatment Effect.
Purpose Introduction of new immune therapies that may have a delayed beneficial effect necessitates re-evaluation of traditional clinical trial designs in oncology. A key design feature of randomized trials is interim futility monitoring, which allows stopping early if the accruing data convincingly demonstrate that the experimental treatment is detrimental or is unlikely to be shown superior to the standard treatment. The appropriateness of futility monitoring is frequently questioned when the effect of the experimental treatment may be delayed (eg, in trials of many immune agents). We examine the advisability of using futility monitoring when there is potential for a delayed treatment effect and make recommendations concerning its use. Methods We evaluated the loss of statistical power when using some common futility interim monitoring rules and a new proposed conservative rule via simulation under varying amounts of treatment-effect delay and varying accrual periods. We also considered scenarios where the experimental treatment starts out being worse than the standard treatment but ends up being better, as may sometimes be the case when an immune therapy is compared with an active standard therapy. Results Some standard methods of futility monitoring can result in an unacceptable loss of power when there is a delayed treatment effect, especially if the accrual period is rapid or the experimental treatment is initially worse. The proposed conservative futility rule has a negligible loss of power in the situations considered. Conclusion Although care must be taken with the choice of futility monitoring when there is a delayed treatment effect, inclusion of appropriate rules can reduce the exposure of patients to ineffective therapies without reducing the probability of correctly identifying effective treatments.


Surface plasmon resonance of gold nanoparticles assemblies at liquid | liquid interfaces.
Surface plasmon resonance (SPR) was observed when a planar close-packed assembly of gold nanoparticles (Au NPs) is adsorbed at the water|1,2-dichloroethane interface. Aqueous gold nanoparticles, 13 or 16 nm in diameter, are deposited at the interface by adding methanol to form a close-packed film with a visible gold mirror reflectance. By total internal reflection of a light beam on the interface, the angular dependence of the interfacial reflectivity was measured in a pseudo-Kretschmann configuration and compared to Fresnel simulations for a homogeneous gold film. The experimental angles for minimum reflectivity were found to match the simulated values. Then, the fluorescence of dye molecules co-adsorbed within 13 and 16 nm gold nanoparticles assemblies at the liquid|liquid interface was measured. The fluorescence intensity under SPR is revealed to be much greater than under total internal reflection conditions, yielding an enhancement factor of approximately 30 and 50 for 13 and 16 nm Au NPs assemblies, respectively. Also, the fluorescence lifetime was found to decrease under SPR conditions.


Lack of chemopreventive efficacy of DL-selenomethionine in colon carcinogenesis.
Epidemiologic observations and laboratory research have suggested that dietary selenium reduces the risk of colon cancer. Selenium-enriched brewer's yeast as a dietary supplement reduces the incidence of and mortality from cancer of the colon in humans. It is not clear whether the observed inhibitory effect is due to selenomethionine, or to other forms of selenium, or to a mixture of the selenium compounds present in selenium-enriched brewer's yeast. Therefore, bioassay described in this study examined the chemopreventive efficacy of 10 and 15 ppm selenomethionine, equivalent to 3.6 and 5.4 ppm as selenium, against azoxymethane (AOM)-induced colon carcinogenesis. At five weeks of age, groups of male F344 rats were fed diets containing 0 (control diet), 10 or 15 ppm selenomethionine. At seven and eight weeks of age, all rats except those in vehicle-treated groups received s.c. injections of AOM at a dose rate of 15 mg/kg body wt. The rats were maintained on their respective diets for 52 weeks and were then sacrificed. Colon tumors were processed and evaluated histopathologically. Colon tumor incidence and multiplicity were analyzed statistically. No obvious toxic effects were observed following dietary administration of 10 or 15 ppm selenomethionine as indicated by body weight gain. Administration of 10 or 15 ppm selenomethionine had no significant effect on colon tumor incidence and multiplicity. This study suggests that i) selenomethionine lacks chemopreventive efficacy against AOM-induced colon carcinogenesis and ii) other forms of selenium or a mixture of selenium compounds present in selenium-enriched brewer's yeast need to be evaluated for their chemopreventive efficacy.


Mortality and morbidity of very low birth weight newborn infants assisted in Buenos Aires public hospitals.
The Neonatal Network of Public Hospitals in the city of Buenos Aires closely monitors the progress of newborn infants with a birth weight less than 1500 g (very low birth weight, VLBW) because it largely contributes to neonatal morbidity and mortality. To analyze the morbidity and mortality of VLBW infants and determine their riskadjusted mortality using the score of the South American Neonatal Network (Red Neonatal de los países del Conosur de América, NEOCOSUR). Live infants born in the network hospitals with a birth weight of 500-1499 g between 2008 and 2010 were included in the study. Data was recorded prospectively using a standardized methodology. Mortality, morbidity and risk-adjusted mortality rates according to the NEOCOSUR score were estimated. Results. There were 92,698 infants born during the study period. Of them, 1.26% weighed less than 1500 g at birth. Only 40.4% of these received a full course of antenatal corticosteroids. A total of 62.7% of these developed respiratory distress syndrome, 5.4% enterocolitis, 10.1% intracranial hemorrhage, and 13.4% severe retinopathy. Early sepsis was observed in 5.6%, and late sepsis in 9.6%. Bronchopulmonary dysplasia was present in 10.7% of the cases. Neonatal mortality was 29.2%, and the adjusted mortality with no major malformations was 25.4%. Survival of infants with a birth weight of =750 g and a gestational age of =26 weeks was 50%. The observed/expected mortality ratio was 1.04, with a large variability. The percentage of VLBW infants who received antenatal corticosteroids was low. The incidence of sepsis and the rate of infants with severe retinopathy of prematurity are high. The risk-adjusted mortality is higher than expected.


An in-silico human cell model reveals the influence of spatial organization on RNA splicing.
Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing, which readies mRNA for translation. This complex and highly dynamical chemical process involves assembly and disassembly of many molecules in multiple cellular compartments and their transport among compartments. Our goal is to model the effect of spatial organization of membrane-less organelles (specifically nuclear speckles) and of organelle heterogeneity on splicing particle biogenesis in mammalian cells. Based on multiple sources of complementary experimental data, we constructed a spatial model of a HeLa cell to capture intracellular crowding effects. We then developed chemical reaction networks to describe the formation of RNA splicing machinery complexes and splicing processes within nuclear speckles (specific type of non-membrane-bound organelles). We incorporated these networks into our spatially-resolved human cell model and performed stochastic simulations for up to 15 minutes of biological time, the longest thus far for a eukaryotic cell. We find that an increase (decrease) in the number of nuclear pore complexes increases (decreases) the number of assembled splicing particles; and that compartmentalization is critical for the yield of correctly-assembled particles. We also show that a slight increase of splicing particle localization into nuclear speckles leads to a disproportionate enhancement of mRNA splicing and a reduction in the noise of generated mRNA. Our model also predicts that the distance between genes and speckles has a considerable effect on the mRNA production rate, with genes located closer to speckles producing mRNA at higher levels, emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and sub-compartments, provides a flexible foundation to study other cellular processes that are strongly modulated by spatiotemporal heterogeneity.


Construction of a protease-deficient strain set for the fission yeast Schizosaccharomyces pombe, useful for effective production of protease-sensitive heterologous proteins.
One of the major problems hindering effective production and purification of heterologous proteins from the fission yeast Schizosaccharomyces pombe is proteolytic degradation of the recombinant gene products by host-specific proteases. As an initial solution to this problem, we constructed a protease-deficient disruptant set by respective disruption of 52 Sz. pombe protease genes. Functional screening of the resultant set was performed by observing secretory production of a proteolytically sensitive model protein, human growth hormone (hGH). The results indicated that some of the resultant disruptants were effective in reducing hGH degradation, as observed during the hGH expression procedure and mainly as a result of unknown serine- and/or cysteine-type proteases in the culture medium. These findings also demonstrated that construction of a protease-deficient strain set is not only useful for practical application in protein production, but also for functional screening, specification and modification of proteases in Sz. pombe, where further investigations of proteolytic processes and improvement through multiple gene manipulations are required.


Alveolar hydatid disease of the liver: a report on thirty-nine surgical cases in eastern Anatolia, Turkey.
The charts of 39 consecutive patients who underwent surgery between 1979 and 1989 with a diagnosis of alveolar hydatid disease (AHD) of the liver were reviewed. The analysis of these cases from eastern Anatolia, which is the endemic region in Turkey, was undertaken to determine the current experience for AHD lesions. Of these patients, 33 (84.6%) had unresectable disease and the remaining six patients (15.4%) were treated by hepatic resection of the primary lesion. In the unresectable cases, laparotomy with biopsy was the most commonly used surgical procedure (56.4%), followed by tube drainage of the necrotic cavity (18.0%), marsupialization (5.1%), and cystojejunostomy (5.1%). Diagnostic studies and operative findings were useful in detecting the AHD lesions. Differential diagnosis was established mainly by histopathologic examination of a biopsy specimen or resected tissue. Pulmonary metastases were seen in two cases, and mortality occurred due to brain metastases in two other cases. Mebendazole was administered postoperatively to 19 patients with indications for 1) advanced AHD, 2) adjuvant therapy to radical and palliative surgical procedures, and 3) recurrences of disease after hepatic resection. The patients were treated with daily doses of approximately 50 mg/kg for periods of one and six years (median 3.2 years). Encouraging results were obtained in 11 of nineteen patients. Five-year survival was seen in 8 of the patients with AHD in this series. There were 18 deaths (46.2%) in our 39 patients. Long-term follow-up was not possible in four cases, and 17 patients (43.6%) were still living. The causes of mortality were advanced AHD in 14 cases, brain metastases in two, and acute myocardial infarction in another two.(ABSTRACT TRUNCATED AT 250 WORDS)


Evaluation of disinfecting procedures for aseptic transfer in hospital pharmacy departments.
Current practice in National Health Service (NHS) hospitals employs 70% Industrial Methylated Spirit spray for surface disinfection of components required in Grade A pharmaceutical environments. This study seeks to investigate other agents and procedures that may provide more effective sanitisation. Several methods are available to test the efficacy of disinfectants against vegetative organisms. However, no methods currently available test the efficacy of disinfectants against spores on the hard surfaces encountered in the pharmacy aseptic processing environment. Therefore, a method has been developed to test the efficacy of disinfectants against spores, modified from British Standard 13697 and Association of Analytical Chemists standards. The testing procedure was used to evaluate alternative biocides and disinfection methods for transferring components into hospital pharmacy cleanrooms, and to determine which combinations of biocide and application method have the greatest efficacy against spores of Bacillus subtilis subspecies subtilis 168, Bacillus subtilis American Type Culture Collection (ATCC) 6633, and Bacillus pumilis ATCC 27142. Stainless steel carrier test plates were used to represent the hard surfaces in hospital pharmacy cleanrooms. Plates were inoculated with 10(7)-10(8) colony-forming units per milliliter (CFU/mL) and treated with the various biocide formulations, using different disinfection methods. Sporicidal activity was calculated as log reduction in CFU. Of the biocides tested, 6% hydrogen peroxide and a quaternary ammonium compound/chlorine dioxide combination were most effective compared to a Quat/biguanide, amphoteric surfactant, 70% v/v ethanol in deionised water and isopropyl alcohol in water for injection. Of the different application methods tested, spraying followed by wiping was the most effective, followed closely by wiping alone. Spraying alone was least effective.


Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone.
Plant cell wall composition is important for regulating growth rates, especially in roots. However, neither analyses of cell wall composition nor transcriptomes on their own can comprehensively reveal which genes and processes are mediating growth and cell elongation rates. This study reveals the benefits of carrying out multiple analyses in combination. Sections of roots from five anatomically and functionally defined zones in Arabidopsis thaliana were prepared and divided into three biological replicates. We used glycan microarrays and antibodies to identify the major classes of glycans and glycoproteins present in the cell walls of these sections, and identified the expected decrease in pectin and increase in xylan from the meristematic zone (MS), through the rapid and late elongation zones (REZ, LEZ) to the maturation zone and the rest of the root, including the emerging lateral roots. Other compositional changes included extensin and xyloglucan levels peaking in the REZ and increasing levels of arabinogalactan-proteins (AGP) epitopes from the MS to the LEZ, which remained high through the subsequent mature zones. Immuno-staining using the same antibodies identified the tissue and (sub)cellular localization of many epitopes. Extensins were localized in epidermal and cortex cell walls, while AGP glycans were specific to different tissues from root-hair cells to the stele. The transcriptome analysis found several gene families peaking in the REZ. These included a large family of peroxidases (which produce the reactive oxygen species (ROS) needed for cell expansion), and three xyloglucan endo-transglycosylase/hydrolase genes (XTH17, XTH18, and XTH19). The significance of the latter may be related to a role in breaking and re-joining xyloglucan cross-bridges between cellulose microfibrils, a process which is required for wall expansion. Knockdowns of these XTHs resulted in shorter root lengths, confirming a role of the corresponding proteins in root extension growth.


MSK1 regulates homeostatic and experience-dependent synaptic plasticity.
The ability of neurons to modulate synaptic strength underpins synaptic plasticity, learning and memory, and adaptation to sensory experience. Despite the importance of synaptic adaptation in directing, reinforcing, and revising the behavioral response to environmental influences, the cellular and molecular mechanisms underlying synaptic adaptation are far from clear. Brain-derived neurotrophic factor (BDNF) is a prime initiator of structural and functional synaptic adaptation. However, the signaling cascade activated by BDNF to initiate these adaptive changes has not been elucidated. We have previously shown that BDNF activates mitogen- and stress-activated kinase 1 (MSK1), which regulates gene transcription via the phosphorylation of both CREB and histone H3. Using mice with a kinase-dead knock-in mutation of MSK1, we now show that MSK1 is necessary for the upregulation of synaptic strength in response to environmental enrichment in vivo. Furthermore, neurons from MSK1 kinase-dead mice failed to show scaling of synaptic transmission in response to activity deprivation in vitro, a deficit that could be rescued by reintroduction of wild-type MSK1. We also show that MSK1 forms part of a BDNF- and MAPK-dependent signaling cascade required for homeostatic synaptic scaling, which likely resides in the ability of MSK1 to regulate cell surface GluA1 expression via the induction of Arc/Arg3.1. These results demonstrate that MSK1 is an integral part of a signaling pathway that underlies the adaptive response to synaptic and environmental experience. MSK1 may thus act as a key homeostat in the activity- and experience-dependent regulation of synaptic strength.


Dynamic effects of acid on Barrett's esophagus. An ex vivo proliferation and differentiation model.
Barrett's esophagus (BE), or specialized intestinal metaplasia, is a premalignant heterogeneous epithelium associated with reflux and an increased risk for adenocarcinoma. Since acid is a major component of refluxate, we investigated its effects ex vivo on cell differentiation as determined by villin expression; and on cell proliferation, as determined by tritiated thymidine incorporation and proliferating cell nuclear antigen expression. To mimic known physiological conditions, endoscopic biopsies of normal esophagus, BE, and duodenum were exposed, in organ culture, to acidified media (pH 3-5) either continuously, or as a 1-h pulse and compared with exposure to pH 7.4 for up to 24 h. Before culture, villin expression was noted in 25% of BE samples, and increased after 6 or 24 h of continuous acid to 50% or 83% of BE samples, respectively. Increased villin expression correlated with ultrastructural maturation of the brush border. In contrast, an acid-pulse followed by culture at pH 7.4, did not alter villin expression in BE. Moreover, continuous acid exposure blocked cell proliferation in BE, whereas, an acid-pulse enhanced cell proliferation, as compared to pH 7.4. Based on our ex vivo findings, we propose a model in which the diverse patterns of acid exposure in vivo may contribute to the observed heterogeneity and unpredictable progression to neoplasia of BE.


Enhanced export of beta-galactosidase fusion proteins in prlF mutants is Lon dependent.
We have used fusions of the outer membrane protein LamB to beta-galactosidase (encoded by lacZ) to study the protein export process. This LamB-LacZ hybrid protein blocks export when synthesized at high levels, as evidenced by inducer (maltose) sensitivity, a phenomenon termed LacZ hybrid jamming. The prlF1 mutation relieves LacZ hybrid jamming and allows localization of the fusion protein to a noncytoplasmic compartment. prlF1 and similar alleles are gain-of-function mutations. Null mutations in this gene confer no obvious phenotypes. Extragenic suppressors of a gain-of-function prlF allele have been isolated in order to understand how this gene product affects the export process. The suppressors are all lon null mutations, and they are epistatic to all prlF phenotypes tested. Lon protease activity has been measured in prlF1 cells and shown to be increased. However, the synthesis of Lon is not increased in a prlF1 background, suggesting a previously unidentified mechanism of Lon activation. Further analysis reveals that prlF1 activates degradation of cytoplasmically localized precursors in a Lon protease-dependent manner. It is proposed that accumulation of precursors during conditions of hybrid protein jamming titrates an essential export component(s), possibly a chaperone. Increased Lon-dependent precursor degradation would free this component, thus allowing increased protein export under jamming conditions.


The use of patients' stories by self-help groups: a survey of voluntary organizations in the UK on the register of the College of Health.
OBJECTIVE: First-hand accounts of illness experience are believed to provide important insights for other patients and their carers. We report the results of a survey that explored how patients' stories are being collected and used by self-help and voluntary groups. METHODS: The annual College of Health survey contacts 2 458 addresses, which includes many self-help groups and voluntary associations. A brief questionnaire for the self-help groups on the register was attached to the summer 1999 survey on behalf of the DIPEx (database of individual patient experience) project. RESULTS: DIPEx received replies from 309 organizations representing a wide range of interests and conditions. These indicated that 202 (65%) of the groups currently use patients' stories in various ways. A further 59 (19%) of the groups reported that although they are not currently using them, they would like to in the future. Organizations that use patients' stories were invited to describe how they use them and provide examples, if applicable. Content analysis of the free text descriptions revealed 22 distinct uses among the 202 organizations using patient stories. The most frequent uses are the inclusion of patient stories in interviews or articles for the group newsletter (74 or 37%) and the use of stories for inclusion in newspaper articles or media broadcasts (31 or 15%). Some form of database of patients' stories was maintained by 23 groups (12%). CONCLUSIONS: These findings suggest that patients' stories are widely collected and used to support a wide range of the recognized functions of self-help and voluntary groups. This is encouraging to the DIPEx project's efforts to collect and analyse accounts of illness experience, which will be presented with evidence-based information about the effects of treatments.


Developments in the field of allergy in 2011 through the eyes of Clinical and Experimental Allergy.
As in previous years, we felt it would be of value to our readership to summarize the new information provided by the authors who have published in Clinical and Experimental Allergy in 2011 and set this in the context of recent advances in our understanding of the pathogenesis and management of allergic disease in all its many manifestations. In 2011, about 210 articles were published in Clinical and Experimental Allergy including editorials, reviews, opinion articles, guidelines, letters, book reviews and of course at the heart of the journal, papers containing original data. As before, this review is divided into sections based on the way the journal is structured, although this year we have grouped together all the papers dealing with mechanisms of allergic disease, whether they involve patients (clinical mechanisms), pure in vitro studies (basic mechanisms) or animal models (experimental models), as we felt this was a more coherent way to deal with the subject. In the field of asthma and rhinitis, the relationship between airway inflammation and airway dysfunction was of perennial interest to investigators, as were phenotypes and biomarkers. Aspirin hypersensitivity appeared in studies in several papers and there was new interest in asthma in the elderly. The mechanisms involved in allergic disease describe advances in our understanding of T cell responses, the relationship between inflammation and disease, mast cell and basophil activation, steroid resistance and novel therapies. In the section dealing with epidemiology, studies seeking to identify risk factors for allergic disease including vitamin D are prominent, as once again are studies investigating gene-environment interactions. The clinical allergy section focuses on drug allergy, food allergy and immunotherapy. The area of oral immunotherapy for food allergy is well covered and we were grateful to Stephen Durham for guest editing an outstanding special issue on immunotherapy in the centenary year of Leonard Noon's pioneering work. Lastly, in the field of allergens, the interest in component-resolved diagnosis continues to grow and there are also articles describing important novel cultivars and the effect of food processing on the allergenic properties of foods. Another terrific year, full of important and high-quality work,which the journal has been proud to bring to the allergy community.


Expression of dengue virus NS3 protein in Drosophila alters its susceptibility to infection.
We developed a Drosophila model in which the dengue virus NS3 protein is expressed in a tissue specific and inducible manner. Dengue virus NS3 is a multifunctional protein playing a major role during viral replication. Both protease and helicase domains of NS3 are interacting with human and insect host proteins including innate immune components of the host machinery. We characterized the NS3 transgenic flies showing that NS3 expression did not affect fly development. To further study the links between NS3 and the innate immune response, we challenge the flies with gram-positive and gram-negative bacteria. Interestingly, the Drosophila transgenic flies expressing NS3 were more susceptible to bacterial infections than control flies. However ubiquitous or immune-specific NS3 expression affected neither the life span nor the response to a non-infectious stress of the flies. In conclusion, we generated a new in vivo system to study the functional impact of DENV NS3 protein on the innate immune response.


t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks.
Protein-protein interaction (PPI) networks provide insights into understanding of biological processes, function and the underlying complex evolutionary mechanisms of the cell. Modeling PPI network is an important and fundamental problem in system biology, where it is still of major concern to find a better fitting model that requires less structural assumptions and is more robust against the large fraction of noisy PPIs. In this paper, we propose a new approach called t-logistic semantic embedding (t-LSE) to model PPI networks. t-LSE tries to adaptively learn a metric embedding under the simple geometric assumption of PPI networks, and a non-convex cost function was adopted to deal with the noise in PPI networks. The experimental results show the superiority of the fit of t-LSE over other network models to PPI data. Furthermore, the robust loss function adopted here leads to big improvements for dealing with the noise in PPI network. The proposed model could thus facilitate further graph-based studies of PPIs and may help infer the hidden underlying biological knowledge. The Matlab code implementing the proposed method is freely available from the web site: http://home.ustc.edu.cn/~yzh33108/PPIModel.htm.


Principal polynomial analysis.
This paper presents a new framework for manifold learning based on a sequence of principal polynomials that capture the possibly nonlinear nature of the data. The proposed Principal Polynomial Analysis (PPA) generalizes PCA by modeling the directions of maximal variance by means of curves, instead of straight lines. Contrarily to previous approaches, PPA reduces to performing simple univariate regressions, which makes it computationally feasible and robust. Moreover, PPA shows a number of interesting analytical properties. First, PPA is a volume-preserving map, which in turn guarantees the existence of the inverse. Second, such an inverse can be obtained in closed form. Invertibility is an important advantage over other learning methods, because it permits to understand the identified features in the input domain where the data has physical meaning. Moreover, it allows to evaluate the performance of dimensionality reduction in sensible (input-domain) units. Volume preservation also allows an easy computation of information theoretic quantities, such as the reduction in multi-information after the transform. Third, the analytical nature of PPA leads to a clear geometrical interpretation of the manifold: it allows the computation of Frenet-Serret frames (local features) and of generalized curvatures at any point of the space. And fourth, the analytical Jacobian allows the computation of the metric induced by the data, thus generalizing the Mahalanobis distance. These properties are demonstrated theoretically and illustrated experimentally. The performance of PPA is evaluated in dimensionality and redundancy reduction, in both synthetic and real datasets from the UCI repository.


RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.
RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.


Photocrosslinkable Gelatin Hydrogels Modulate the Production of the Major Pro-inflammatory Cytokine, TNF-α, by Human Mononuclear Cells.
Hydrogels are an attractive class of biomaterials in tissue engineering due to their inherently compatible properties for cell culture. Gelatin methacryloyl (GelMA) has shown significant promise in the fields of tissue engineering and drug delivery, as its physical properties can be precisely tuned depending on the specific application. There is a growing appreciation for the interaction between biomaterials and cells of the immune system with the increasing usage of biomaterials for in vivo applications. Here, we addressed the current lack of information regarding the immune-modulatory properties of photocrosslinked GelMA. We investigated the ability of human mononuclear cells to mount inflammatory responses in the context of a GelMA hydrogel platform. Using lipopolysaccharide to stimulate a pro-inflammatory immune response, we found tumor necrosis factor-α (TNF-α) expression was suppressed in GelMA culture conditions. Our findings have important implications on the future use of GelMA, and potentially similar hydrogels, and highlight the significance of investigating the potential immune-modulatory properties of biomaterials.


Bridging scales through multiscale modeling: a case study on protein kinase A.
The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM), subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA) activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD) simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD) simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic, and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.


Information provision as evaluated by people with cancer and bereaved relatives: A cross-sectional survey of 34 specialist palliative care teams.
To explore how individuals with cancer and bereaved relatives evaluate information provision by specialist palliative care services (PCSs). A cross-sectional survey was conducted within four multidisciplinary palliative homecare teams (HCTs), 17 hospital-based palliative care units (PCUs) and 13 hospital-based mobile palliative support teams (PSTs) in Belgium. During four measurement periods, structured questionnaires were administered to people being guided by PCSs and relatives of patients who had died while under the care of PCSs. In total, 628 patients (80%) and 980 relatives (55%) responded; 73-82% and 75-77% respectively reported having received the right amount of information. Compared with those receiving care within a PCU, those being supported by a PST were more likely to report suboptimal information provision and decision-making. Relatives of those who had died while under the guidance of a PST were also more likely to report suboptimal information provision than their PCU counterparts. Although information provision to cancer patients and relatives being supported by PCSs is generally evaluated positively, evaluations depend on the type of service. Information provided within PCUs offering highly personalised, continuous care appears to both groups more satisfactory than that provided by palliative care teams mainly supporting care staff.


Visible and near infra-red up-conversion in Tm3+/Yb3+ co-doped silica fibers under 980 nm excitation.
The spectroscopic properties of Tm(3+)/Yb(3+) co-doped silica fibers under excitation at 980 nm are reported. Three distinct up-conversion fluorescence bands were observed in the visible to near infra-red regions. The blue and red fluorescence bands at 475 and 650 nm, respectively, were found to originate from the (1)G(4) level of Tm(3+). A three step up-conversion process was established as the populating mechanism for these fluorescence bands. The fluorescence band at 800 nm was found to originate from two possible transitions in Tm(3+); one being the transition from the (3)H(4) to (3)H(6) manifold which was found to dominate at low pump powers; the other being the transition from the (1)G(4) to (3)H(6) level which dominates at higher pump powers. The fluorescence lifetime of the (3)H(4) and (3)F(4) levels of Tm(3+) and (2)F(5/2) level of Yb(3+) were studied as a function of Yb(3+) concentration, with no significant energy back transfer from Tm(3+) to Yb(3+) observed.


Histological type and grade of breast cancer tumors by parity, age at birth, and time since birth: a register-based study in Norway.
Some studies have indicated that reproductive factors affect the risk of histological types of breast cancer differently. The long-term protective effect of a childbirth is preceded by a short-term adverse effect. Few studies have examined whether tumors diagnosed shortly after birth have specific histological characteristics. In the present register-based study, comprising information for 22,867 Norwegian breast cancer cases (20-74 years), we examined whether histological type (9 categories) and grade of tumor (2 combined categories) differed by parity or age at first birth. Associations with time since birth were evaluated among 9709 women diagnosed before age 50 years. Chi-square tests were applied for comparing proportions, whereas odds ratios (each histological type vs. ductal, or grade 3-4 vs. grade 1-2) were estimated in polytomous and binary logistic regression analyses. Ductal tumors, the most common histological type, accounted for 81.4% of all cases, followed by lobular tumors (6.3%) and unspecified carcinomas (5.5%). Other subtypes accounted for 0.4%-1.5% of the cases each. For all histological types, the proportions differed significantly by age at diagnoses. The proportion of mucinous and tubular tumors decreased with increasing parity, whereas Paget disease and medullary tumors were most common in women of high parity. An increasing trend with increasing age at first birth was most pronounced for lobular tumors and unspecified carcinomas; an association in the opposite direction was seen in relation to medullary and tubular tumors. In age-adjusted analyses, only the proportions of unspecified carcinomas and lobular tumors decreased significantly with increasing time since first and last birth. However, ductal tumors, and malignant sarcomas, mainly phyllodes tumors, seemed to occur at higher frequency in women diagnosed <2 years after first childbirth. The proportions of medullary tumors and Paget disease were particularly high among women diagnosed 2-5 years after last birth. The high proportion of poorly differentiated tumors in women with a recent childbirth was partly explained by young age. Our results support previous observations that reproductive factors affect the risk of histological types of breast cancer differently. Sarcomas, medullary tumors, and possible also Paget disease, may be particularly susceptible to pregnancy-related exposure.


Exclusion of close linkage of Tourette's syndrome to D1 dopamine receptor.
The authors' goal was to establish if a mutation in D1 dopamine receptor locus (DRD1), or one genetically close to it, could cause Gilles de la Tourette's syndrome. DRD1 and linked markers (D5S36, D5S61, and D5S62) were studied in a large Mennonite Tourette's syndrome kindred. Only individuals with the full Tourette's syndrome were considered to be affected in one series of analyses; in another series the diagnostic spectrum was broadened to include chronic multiple tics. Liability classes were defined to take into account age at onset and sex differences; dominant inheritance was assumed. The authors' version of the LINKMAP program of the LINKAGE package modified to run under distributed parallel processing (Linda LINKMAP) was used for the multipoint linkage analysis. Complete (theta = 0.0) linkage of Tourette's syndrome with DRD1 was ruled out (lod score of -10.1) when the disease was defined narrowly. The area of exclusion of linkage (lod score between -2 and -10.5) extended from map position -0.10 to map position 0.50. The authors conducted an additional (centromeric) multipoint analysis with D5S36 as well as glucocorticoid receptor (GRL) and D5S22, resulting in an overlapping area of exclusion to map position -0.30 when the disease was defined narrowly. This result provides strong evidence against linkage of the DRD1 D1 dopamine receptor locus with Tourette's syndrome. This exclusion extends the authors' earlier work with the dopamine system in Tourette's syndrome to exclude the two best characterized dopamine receptors from linkage with Tourette's syndrome.