Genomic and phenotypic characterization of in vitro-generated Chlamydia trachomatis recombinants.
Pre-genomic and post-genomic studies demonstrate that chlamydiae actively recombine in vitro and in vivo, although the molecular and cellular biology of this process is not well understood. In this study, we determined the genome sequence of twelve Chlamydia trachomatis recombinants that were generated in vitro under antibiotic selection. These strains were used to explore the process of recombination in Chlamydia spp., including analysis of candidate recombination hotspots, and to correlate known C. trachomatis in vitro phenotypes with parental phenotypes and genotypes. Each of the 190 examined recombination events was the product of homologous recombination, and no candidate targeting motifs were identified at recombination sites. There was a single deletion event in one recombinant progeny that resulted in the removal of 17.1 kilobases between two rRNA operons. There was no evidence for preference for any specific region of the chromosome for recombination, and analyses of a total of over 200 individual recombination events do not provide any support for recombination hotspots in vitro. Two measurable phenotypes were analyzed in these studies. First, the efficiency of attachment to host cells in the absence of centrifugation was examined, and this property segregated to regions of the chromosome that carry the polymorphic membrane protein (Pmp) genes. Second, the formation of secondary inclusions within cells varied among recombinant progeny, but this did not cleanly segregate to specific regions of the chromosome. These experiments examined the process of recombination in C. trachomatis and identified tools that can be used to associate phenotype with genotype in recombinant progeny. There were no data supporting the hypothesis that particular nucleotide sequences are preferentially used for recombination in vitro. Selected phenotypes can be segregated by analysis of recombination, and this technology may be useful in preliminary analysis of the relationship of genetic variation to phenotypic variation in the chlamydiae.


Relations Between Toddler Sleep Characteristics, Sleep Problems, and Temperament.
Two sources of information (parent-reported sleep diaries and actigraph records) were used to investigate how toddler sleep characteristics (bed time/sleep onset, wake time/sleep offset, total nighttime sleep, and total sleep time) are related to sleep problems and temperament. There were 64 toddler participants in the study. Consistent with studies of older children, parent reports differed from actigraph-based records. The findings that parent-reported and actigraph-recorded sleep characteristics varied as a function of parent report of toddler sleep problems and temperament add needed information on toddler sleep. Such information may contribute to improving parents' awareness of their child's sleep characteristics and correlates of problem sleep.


Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum).
Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.


A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime.
Microorganisms show an astonishing versatility in energy metabolism. They can use a variety of different catabolic electron acceptors, but they use them according to a thermodynamic hierarchy, which is determined by the redox potential of the available electron acceptors. This hierarchy is reflected by a regulatory machinery that leads to the production of respiratory chains in dependence of the availability of the corresponding electron acceptors. In this study, we showed that the γ-proteobacterium Shewanella oneidensis produces several functional electron transfer chains simultaneously. Furthermore, these chains are interconnected, most likely with the aid of c-type cytochromes. The cytochrome pool of a single S. oneidensis cell consists of ca. 700 000 hemes, which are reduced in the absence on an electron acceptor, but can be reoxidized in the presence of a variety of electron acceptors, irrespective of prior growth conditions. The small tetraheme cytochrome (STC) and the soluble heme and flavin containing fumarate reductase FccA have overlapping activity and appear to be important for this electron transfer network. Double deletion mutants showed either delayed growth or no growth with ferric iron, nitrate, dimethyl sulfoxide or fumarate as electron acceptor. We propose that an electron transfer machinery that is produced irrespective of a thermodynamic hierarchy not only enables the organism to quickly release catabolic electrons to a variety of environmental electron acceptors, but also offers a fitness benefit in redox-stratified environments.


MicroRNA-214 protects the mouse heart from ischemic injury by controlling Ca²⁺ overload and cell death.
Early reperfusion of ischemic cardiac tissue remains the most effective intervention for improving clinical outcome following myocardial infarction. However, abnormal increases in intracellular Ca²⁺ during myocardial reperfusion can cause cardiomyocyte death and consequent loss of cardiac function, referred to as ischemia/reperfusion (IR) injury. Therapeutic modulation of Ca²⁺ handling provides some cardioprotection against the paradoxical effects of restoring blood flow to the heart, highlighting the significance of Ca²⁺ overload to IR injury. Cardiac IR is also accompanied by dynamic changes in the expression of microRNAs (miRNAs); for example, miR-214 is upregulated during ischemic injury and heart failure, but its potential role in these processes is unknown. Here, we show that genetic deletion of miR-214 in mice causes loss of cardiac contractility, increased apoptosis, and excessive fibrosis in response to IR injury. The cardioprotective roles of miR-214 during IR injury were attributed to repression of the mRNA encoding sodium/calcium exchanger 1 (Ncx1), a key regulator of Ca²⁺ influx; and to repression of several downstream effectors of Ca²⁺ signaling that mediate cell death. These findings reveal a pivotal role for miR-214 as a regulator of cardiomyocyte Ca²⁺ homeostasis and survival during cardiac injury.


RNF4-dependent hybrid SUMO-ubiquitin chains are signals for RAP80 and thereby mediate the recruitment of BRCA1 to sites of DNA damage.
The DNA repair function of the breast cancer susceptibility protein BRCA1 depends in part on its interaction with RAP80, which targets BRCA1 to DNA double-strand breaks (DSBs) through recognition of K63-linked polyubiquitin chains. The localization of BRCA1 to DSBs also requires sumoylation. We demonstrated that, in addition to having ubiquitin-interacting motifs, RAP80 also contains a SUMO-interacting motif (SIM) that is critical for recruitment to DSBs. In combination with the ubiquitin-binding activity of RAP80, this SIM enabled RAP80 to bind with nanomolar affinity to hybrid chains consisting of ubiquitin conjugated to SUMO. Furthermore, RNF4, a SUMO-targeted ubiquitin E3 ligase that synthesizes hybrid SUMO-ubiquitin chains, localized to DSBs and was critical for the recruitment of RAP80 and BRCA1 to sites of DNA damage. Our findings, therefore, connect ubiquitin- and SUMO-dependent DSB recognition, revealing that RNF4-synthesized hybrid SUMO-ubiquitin chains are recognized by RAP80 to promote BRCA1 recruitment and DNA repair.


Extra-germ cell expression of mouse nuclear receptor subfamily 6, group A, member 1 (NR6A1).
Nuclear receptor subfamily 6, group A, member 1 (NR6A1) is an orphan member of the nuclear receptor superfamily and is required for normal mouse embryonic development. In adult mice, NR6A1 is predominantly expressed in spermatogenic cells and growing oocytes of the gonads and has a role in female reproduction by modulating the transcription of the oocyte-specific genes bone morphogenetic protein 15 (Bmp15) and growth differentiation factor 9 (Gdf9). In our goal to further understand the functional role of NR6A1 during postnatal development, we generated a Nr6a1:beta-galactosidase (LacZ) knockin reporter (Nr6a1(LacZ/+)) mouse line in which the Nr6a1:LacZ fusion gene was expressed and then characterized Nr6a1 expression in these reporter mice by performing LacZ staining. Our RT-PCR analyses showed that Nr6a1 was expressed in a variety of somatic tissues (e.g., oviduct and lung) other than gonads of normal adult mice. In adult Nr6a1(LacZ/+) mice, robust LacZ staining was observed in the gametes of gonads. Strong positive LacZ staining was also observed in the sperm of the epididymis, epithelial cells of the oviduct, and bronchioles within the lung. In adult Nr6a1(LacZ/+) mice, positive LacZ staining was observed in other somatic tissues, including hippocampus, cerebral cortex, cerebellum, and thalamus of brain; pars intermedia and pars anterior of pituitary; parathyroid; and islet of pancreas. NR6A1 expression in sperm within the epididymis, epithelial cells in the oviduct, and bronchioles of the lung was further confirmed by immunohistochemical studies. Nr6a1 is expressed not only in the germ cells of mouse gonads but also in a variety of somatic tissues, including epididymis, oviduct, brain, and pituitary. The extra-germ cell expression of NR6A1 makes it a less attractive contraceptive.


Arabidopsis Myrosinase Genes AtTGG4 and AtTGG5 Are Root-Tip Specific and Contribute to Auxin Biosynthesis and Root-Growth Regulation.
Plant myrosinases (β-thioglucoside glucohydrolases) are classified into two subclasses, Myr I and Myr II. The biological function of Myr I has been characterized as a major biochemical defense against insect pests and pathogens in cruciferous plants. However, the biological function of Myr II remains obscure. We studied the function of two Myr II member genes AtTGG4 and AtTGG5 in Arabidopsis. RT-PCR showed that both genes were specifically expressed in roots. GUS-assay revealed that both genes were expressed in the root-tip but with difference: AtTGG4 was expressed in the elongation zone of the root-tip, while AtTGG5 was expressed in the whole root-tip. Moreover, myrosin cells that produce and store the Myr I myrosinases in aboveground organs were not observed in roots, and AtTGG4 and AtTGG5 were expressed in all cells of the specific region. A homozygous double mutant line tgg4tgg5 was obtained through cross-pollination between two T-DNA insertion lines, tgg4E8 and tgg5E12, by PCR-screening in the F2 and F3 generations. Analysis of myrosinase activity in roots of mutants revealed that AtTGG4 and AtTGG5 had additive effects and contributed 35% and 65% myrosinase activity in roots of the wild type Col-0, respectively, and myrosinase activity in tgg4tgg5 was severely repressed. When grown in Murashiege & Skoog (MS) medium or in soil with sufficient water, Col-0 had the shortest roots, and tgg4tgg5 had the longest roots, while tgg4E8 and tgg5E12 had intermediate root lengths. In contrast, when grown in soil with excessive water, Col-0 had the longest roots, and tgg4tgg5 had the shortest roots. These results suggested that AtTGG4 and AtTGG5 regulated root growth and had a role in flood tolerance. The auxin-indicator gene DR5::GUS was then introduced into tgg4tgg5 by cross-pollination. DR5::GUS expression patterns in seedlings of F1, F2, and F3 generations indicated that AtTGG4 and AtTGG5 contributed to auxin biosynthesis in roots. The proposed mechanism is that indolic glucosinolate is transported to the root-tip and converted to indole-3-acetonitrile (IAN) in the tryptophan-dependent pathways by AtTGG4 and AtTGG5, and IAN is finally converted to indole-3-acetic acid (IAA) by nitrilases in the root-tip. This mechanism guarantees the biosynthesis of IAA in correct cells of the root-tip and, thus, a correct auxin gradient is formed for healthy development of roots.


Development of advanced practice competency standards for dietetics in Australia.
This study aimed to explore the work roles, major tasks and core activities of advanced practice dietitians in Australia to define the Competency Standards for advanced practice. A qualitative approach was used to review advanced dietetic practice in Australia involving experienced professionals, mostly dietitians. Four focus groups were conducted with a total of 17 participants and an average of 20 years experience: 15 dietitian practitioners plus 2 employers (1 dietitian and 1 non-dietitian). The focus groups explored the key purpose, roles and outcomes of these practitioners. Data from the focus groups were confirmed with in-depth interviews about their core activities with a purposive sample of 10 individuals recently recognised as Advanced Accredited Practising Dietitians. Data from both focus groups and interviews were analysed adductively to identify key themes. The key theme that emerged to define advanced dietetics practice was leadership, with four subthemes that described in more detail the major work roles and outcomes of advanced practice. These subthemes identified that advanced practitioners were (i) outcome-focused, having impact; (ii) influence others and advocate; (iii) innovate and embrace change; and (iv) inspire others and are recognised for their practice. These outcomes were conceptualised within a broad generalist framework to generate revised Competency Standards. This study confirmed that leadership rather than specialist practice skills is the key determinant of advanced practice.


Laparoscopic apical mesh excision for deep dyspareunia caused by mesh banding in the vaginal apex.
Gynecare Prolift has been successfully used for pelvic floor repair with favorable objective and subjective outcomes. There have been, however, increasing reports of significant rates of postoperative dyspareunia and impairment of sexual function. We are presenting two cases of post Prolift dyspareunia. The patients underwent several vaginal revisions with excision of the apical bands. However, they returned soon with the same complaint. Ultimately, laparoscopic excision of the apical mesh was performed. Patients reported significant improvement in their intercourse pain after the procedure. Our experience shows that new onset dyspareunia is primarily caused by the apical component of the Prolift system with deep penetration pain reproduced by pressure on the fixed nondistensible apex. This problem can be treated laparoscopically with excision of the apical mesh.


An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort.
The Viking Health Study Shetland is a population-based research cohort of 2,122 volunteer participants with ancestry from the Shetland Isles in northern Scotland. The high kinship and detailed phenotype data support a range of approaches for associating rare genetic variants, enriched in this isolate population, with quantitative traits and diseases. As an exemplar, the c.1750G > A; p.Gly584Ser variant within the coding sequence of the KCNH2 gene implicated in Long QT Syndrome (LQTS), which occurred once in 500 whole genome sequences from this population, was investigated. Targeted sequencing of the KCNH2 gene in family members of the initial participant confirmed the presence of the sequence variant and identified two further members of the same family pedigree who shared the variant. Investigation of these three related participants for whom single nucleotide polymorphism (SNP) array genotypes were available allowed a unique shared haplotype of 1.22 Mb to be defined around this locus. Searching across the full cohort for this haplotype uncovered two additional apparently unrelated individuals with no known genealogical connection to the original kindred. All five participants with the defined haplotype were shown to share the rare variant by targeted Sanger sequencing. If this result were verified in a healthcare setting, it would be considered clinically actionable, and has been actioned in relatives ascertained independently through clinical presentation. The General Practitioners of four study participants with the rare variant were alerted to the research findings by letters outlining the phenotype (prolonged electrocardiographic QTc interval). A lack of detectable haplotype sharing between c.1750G > A; p.Gly584Ser chromosomes from previously reported individuals from Finland and those in this study from Shetland suggests that this mutation has arisen more than once in human history. This study showcases the potential value of isolate population-based research resources for genomic medicine. It also illustrates some challenges around communication of actionable findings in research participants in this context.


Mindfulness Broadens Awareness and Builds Eudaimonic Meaning: A Process Model of Mindful Positive Emotion Regulation.
Contemporary scholarship on mindfulness casts it as a form of purely non-evaluative engagement with experience. Yet, traditionally mindfulness was not intended to operate in a vacuum of dispassionate observation, but was seen as facilitative of eudaimonic mental states. In spite of this historical context, modern psychological research has neglected to ask the question of how the practice of mindfulness affects downstream emotion regulatory processes to impact the sense of meaning in life. To fill this lacuna, here we describe the Mindfulness-to-Meaning Theory, from which we derive a novel process model of mindful positive emotion regulation informed by affective science, in which mindfulness is proposed to introduce flexibility in the generation of cognitive appraisals by enhancing interoceptive attention, thereby expanding the scope of cognition to facilitate reappraisal of adversity and savoring of positive experience. This process is proposed to culminate in a deepened capacity for meaning-making and greater engagement with life.


Gamma-delta T lymphocytes and 25-hydroxy vitamin D levels as key factors in autoimmunity and inflammation: the case of zoledronic acid-induced acute phase reaction.
Zoledronic acid (ZA) infusion for osteoporosis is frequently associated with the onset of an acute phase reaction (APR) secondary to the activation of γδ T cell receptor (TCR) lymphocytes (γδ T cells) and to low vitamin D levels, similar to what is observed in chronic inflammation and autoimmunity. In this study we investigated whether the phenotype of γδ T cells is associated with APR and 25-OH vitamin D (25-OHvD) levels. For flow-cytometry analysis, peripheral blood samples were obtained from 52 osteoporotic women prior to 5 mg ZA intravenous infusion and from nine women (five with APR) one week later. Twenty-six/52 (50%) patients reported APR and APR+ cases had a higher percentage of central memory Th1-like γδ T cells. One week after ZA infusion, APR was associated with a decreased percentage of central memory Th1-like γδ T cells, an increase in the percentage and activation of effector memory Th1-like γδ T cells, and an increase in Th17-like γδ T cells. Lower 25-OHvD levels were significantly associated with APR, but no correlation was found between 25-OHvD level and γδ T cell percentage or subsets. In conclusion, patients experiencing APR related to ZA infusion have lower 25-OHvD levels and we suggest that the higher percentage of central memory Th1-like γδ T cells and the expansion of effector memory Th1-like and Th17-like γδ T cells are associated with the occurrence of APR.


Electronic cigarette use in youths: a position statement of the Forum of International Respiratory Societies.
Children and adolescents are highly susceptible to nicotine addiction, which affects their brain development, even in those who smoke infrequently. Young people who become addicted to nicotine are at greater risk of becoming lifelong tobacco consumers. The use of nicotine-delivering electronic cigarettes has risen dramatically among youths worldwide. In addition to physical dependence, adolescents are susceptible to social and environmental influences to use electronic cigarettes. The product design, flavours, marketing, and perception of safety and acceptability have increased the appeal of electronic cigarettes to young people, thus leading to new generations addicted to nicotine. Moreover, there is growing evidence that electronic cigarettes in children and adolescents serve as a gateway to cigarette smoking. There can be no argument for harm reduction in children. To protect this vulnerable population from electronic cigarettes and other nicotine delivery devices, we recommend that electronic cigarettes be regulated as tobacco products and included in smoke-free policies. Sale of electronic cigarettes should be barred to youths worldwide. Flavouring should be prohibited in electronic cigarettes, and advertising accessible by youths and young adults be banned. Finally, we recommend greater research on the health effects of electronic cigarettes and surveillance of use across different countries.


Sodium-glucose co-transporter-2 inhibitors in type 2 diabetes: Are clinical trial benefits for heart failure reflected in real-world clinical practice? A systematic review and meta-analysis of observational studies.
To determine the absolute risk reduction (ARR) of heart failure events in people treated with sodium-glucose co-transporter-2 (SGLT2) inhibitors. We searched PubMed, EMBASE, CINAHL and ISI Web of Science for observational studies published to 9 May 2022 that explored the association between SGLT2 inhibitors and any indication for heart failure (including new diagnosis or hospitalization for heart failure) in type 2 diabetes. Identified studies were independently screened by two reviewers and assessed for bias using the Newcastle-Ottawa scale. Eligible studies with comparable outcome data were pooled for meta-analysis using random-effects models, reporting hazard ratios (HRs) with 95% confidence intervals (CIs). The ARR per 100 person-years was determined overall, and in subgroups with and without baseline cardiovascular disease (CVD). From 43 eligible studies, with a total of 4 818 242 participants from 17 countries, 21 were included for meta-analysis. SGLT2 inhibitors were associated with a reduced risk of hospitalization for heart failure (HR 0.65, 95% CI 0.59-0.72) overall and both in those with CVD (HR 0.78, 95% CI 0.68-0.89) and without CVD (HR 0.53, 95% CI 0.39-0.71). Risk reduction for hospitalization for heart failure in people with a history of CVD (ARR 1.17, 95% CI 0.78-1.55) was significantly greater than for those without CVD (ARR 0.39, 95% CI 0.32-0.47). The number-needed-to-treat to prevent one event of hospitalization for heart failure was 86 (95% CI 65-128) person-years of treatment for the CVD group and 256 (95% CI 215-316) person-years for those without CVD. Real-world SGLT2 inhibitor use supports randomized trial data for the size effect of reduced hospitalization for heart failure in type 2 diabetes, although with a much lower ARR in people without CVD.


Estimating the functional form for the density dependence from life history data.
Two contrasting approaches to the analysis of population dynamics are currently popular: demographic approaches where the associations between demographic rates and statistics summarizing the population dynamics are identified; and time series approaches where the associations between population dynamics, population density, and environmental covariates are investigated. In this paper, we develop an approach to combine these methods and apply it to detailed data from Soay sheep (Ovis aries). We examine how density dependence and climate contribute to fluctuations in population size via age- and sex-specific demographic rates, and how fluctuations in demographic structure influence population dynamics. Density dependence contributes most, followed by climatic variation, age structure fluctuations and interactions between density and climate. We then simplify the density-dependent, stochastic, age-structured demographic model and derive a new phenomenological time series which captures the dynamics better than previously selected functions. The simple method we develop has potential to provide substantial insight into the relative contributions of population and individual-level processes to the dynamics of populations in stochastic environments.


A Systematic Review of the Cardiovascular Manifestations and Outcomes in the Setting of Coronavirus-19 Disease.
The impact of coronavirus disease, 2019 (COVID-19), has been profound. Though COVID-19 primarily affects the respiratory system, it has also been associated with a wide range of cardiovascular (CV) manifestations portending extremely poor prognosis. The principal hypothesis for CV involvement is through direct myocardial infection and systemic inflammation. We conducted a systematic review of the current literature to provide a foundation for understanding the CV manifestations and outcomes of COVID-19. PubMed and EMBASE databases were electronically searched from the inception of the databases through 27 April 2020. A second literature review was conducted to include major trials and guidelines that were published after the initial search but before submission. The inclusion criteria for studies to be eligible were case reports, case series, and observation studies reporting CV outcomes among patients with COVID-19 infection. This review of the current COVID-19 disease and CV outcomes literature revealed a myriad of CV manifestations with potential avenues for treatment and prevention. Future studies are required to understand on a more mechanistic level the effect of COVID-19 on the myocardium and thus provide avenues to improve mortality and morbidity.


Neutrophils but not eosinophils are involved in growth suppression of IL-4-secreting tumors.
Local expression of IL-4 by gene-modified tumor cells increases their immunogenicity by inducing an inflammatory response that is dominated by eosinophils. Eosinophils have been implicated as antitumor effector cells because the application of a granulocyte-depleting Ab inhibited rejection of IL-4 transfected tumors. This Ab did not discriminate between eosinophils and neutrophils and, therefore, this experiment could not exclude neutrophils as primary effector cells, whereas eosinophils were innocent bystander cells in IL-4 transfected tumors. We analyzed tumor growth suppression and granulocyte infiltration in IL-5-deficient (IL-5(-/-)) mice that had a deficiency of eosinophils, using two tumor lines (B16-F10 and MCA205) transfected to secrete IL-4. IL-4-expressing tumors were at least as efficiently rejected in IL-5(-/-) mice as in wild-type mice, despite an almost complete absence of tumor-infiltrating eosinophils. However, neutrophils were present in undiminished amounts and their depletion partially restored tumor growth. Furthermore, the growth of IL-5-secreting tumors was not impaired in either wild-type or IL-5(-/-) mice, even though it induced eosinophilia in both mouse strains. These findings demonstrate that eosinophils can be induced in IL-5(-/-) mice by exogenous IL-5 and argue against a compensatory effect of neutrophils in the absence of eosinophils. We conclude that 1) infiltration of IL-4 transfected tumors by eosinophils is completely IL-5 dependent, 2) eosinophils have no tumoricidal activity, and 3) neutrophils are responsible, at least in part, for tumor suppression.


Towards theory driven structure elucidation of complex natural products: mandelalides and coibamide A.
The effectiveness of computational tools in determining relative configurations of complex molecules is investigated, using natural products mandelalides A-D and coibamide A, towards a generalized recipe for the scientific community at large. Ultimately, continuing efforts in this vein will accelerate and strengthen relative structure elucidation of complex molecules, such as natural products. Molecular mechanics conformational search, quantum mechanical NMR chemical shift predictions, and DP4 analyses led to confirmation of the revised structures of mandelalides A-D and coibamide A. All chiral centers in the northern hemisphere of mandelalides A-D are inverted with respect to the originally proposed structures, in agreement with recent total syntheses of mandelalide A by Ye, Fürstner & Carter. In the case of coibamide A, it was found that Fang & Su's revision, in which both the macrocycle [MeAla(11)] and the side chain [HIV(2)] residues are inverted from l to d, was consistent with the authentic natural product and computations.


Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant.
Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients' phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical relevance of the deletion and the duplication causes a paradigm shift in (cyto)genetic counselling.


Australians' views on personal genomic testing: focus group findings from the Genioz study.
Personal genomic testing provides healthy individuals with access to information about their genetic makeup for purposes including ancestry, paternity, sporting ability and health. Such tests are available commercially and globally, with accessibility expected to continue to grow, including in Australia; yet little is known of the views/expectations of Australians. Focus groups were conducted within a multi-stage, cross-disciplinary project (Genioz) to explore this. In mid-2015, 56 members of the public participated in seven focus groups, allocated into three age groups: 18-24, 25-49, and ≥50 years. Three researchers coded transcripts independently and generated themes. Awareness of personal genomic testing was low, but most could deduce what "personal genomics" might entail. Very few had heard of the term "direct-to-consumer" testing, which has implications for organisations developing information to support individuals in their decision-making. Participants' understanding of genetics was varied and drawn from several sources. There were diverse perceptions of the relative influence of genetics and environment on health, mental health, behavior, talent, or personality. Views about having a personal genomic test were mixed, with greater interest in health-related tests if they believed there was a reason for doing so. However, many expressed scepticisms about the types of tests available, and how the information might be used; concerns were also raised about privacy and the potential for discrimination. These exploratory findings inform subsequent stages of the Genioz study, thereby contributing to strategies of supporting Australians to understand and make meaningful and well-considered decisions about the benefits, harms, and implications of personal genomic tests.


Improving the management of multimorbidity in general practice: protocol of a cluster randomised controlled trial (The 3D Study).
An increasing number of people are living with multimorbidity. The evidence base for how best to manage these patients is weak. Current clinical guidelines generally focus on single conditions, which may not reflect the needs of patients with multimorbidity. The aim of the 3D study is to develop, implement and evaluate an intervention to improve the management of patients with multimorbidity in general practice. This is a pragmatic two-arm cluster randomised controlled trial. 32 general practices around Bristol, Greater Manchester and Glasgow will be randomised to receive either the '3D intervention' or usual care. 3D is a complex intervention including components affecting practice organisation, the conduct of patient reviews, integration with secondary care and measures to promote change in practice organisation. Changes include improving continuity of care and replacing reviews of each disease with patient-centred reviews with a focus on patients' quality of life, mental health and polypharmacy. We aim to recruit 1383 patients who have 3 or more chronic conditions. This provides 90% power at 5% significance level to detect an effect size of 0.27 SDs in the primary outcome, which is health-related quality of life at 15 months using the EQ-5D-5L. Secondary outcome measures assess patient centredness, illness burden and treatment burden. The primary analysis will be a multilevel regression model adjusted for baseline, stratification/minimisation, clustering and important co-variables. Nested process evaluation will assess implementation, mechanisms of effectiveness and interaction of the intervention with local context. Economic analysis of cost-consequences and cost-effectiveness will be based on quality-adjusted life years. This study has approval from South-West (Frenchay) National Health Service (NHS) Research Ethics Committee (14/SW/0011). Findings will be disseminated via final report, peer-reviewed publications and guidance to healthcare professionals, commissioners and policymakers. ISRCTN06180958; Pre-results.


Changes in perceived stress and recovery in overreached young elite soccer players.
The aim of this study was to prospectively monitor sport-specific performance and assess the stress-recovery balance in overreached (OR) soccer players and controls. During two competitive seasons, 94 players participated in the study. The stress-recovery balance (RESTQ-Sport) and sport-specific performance (Interval Shuttle Run Test) were assessed monthly. Seven players with performance decrement of at least a month were classified as OR. Stress and recovery measures were assessed between groups (OR vs healthy players) and at different times within the OR group. An unfavorable total recovery score appeared 2 months before diagnosis when compared with the reference values of the healthy group established at the start of the season (P=0.009) and also over the two seasons (P=0.028). The scales Emotional Stress (P=0.044), Physical Recovery (P=0.009), General Well-being (P=0.001) and Sleep Quality (P=0.045) were sensitive to OR compared with the average of the healthy group over the two seasons. Finally, Fatigue and Being in Shape demonstrated the largest changes in stress and recovery within the OR players (effect size=1.14 and 1.50). The longitudinal monitoring of performance and changes in stress and recovery may be useful for the detection of OR in its earliest stage. The information obtained from these tests can be used to optimize individual training and recovery programs.


CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid.
In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate in-silico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. CaGrid selected Taverna as its workflow execution system of choice due to its integration with web service technology and support for a wide range of web services, plug-in architecture to cater for easy integration of third party extensions, etc. The caGrid Workflow Toolkit (or the toolkit for short), an extension to the Taverna workflow system, is designed and implemented to ease building and running caGrid workflows. It provides users with support for various phases in using workflows: service discovery, composition and orchestration, data access, and secure service invocation, which have been identified by the caGrid community as challenging in a multi-institutional and cross-discipline domain. By extending the Taverna Workbench, caGrid Workflow Toolkit provided a comprehensive solution to compose and coordinate services in caGrid, which would otherwise remain isolated and disconnected from each other. Using it users can access more than 140 services and are offered with a rich set of features including discovery of data and analytical services, query and transfer of data, security protections for service invocations, state management in service interactions, and sharing of workflows, experiences and best practices. The proposed solution is general enough to be applicable and reusable within other service-computing infrastructures that leverage similar technology stack.


Elastic properties of the forisome.
Forisomes are elongate Ca2+-responsive contractile protein bodies and act as flow blocking gates within the phloem of legumes. Because an understanding of their mechanical properties in vitro underpins understanding of their physiology in vivo, we undertook, using a microcantilever method, microscopic tensile tests (incremental stress-relaxation measurements) on forisomes from Canavalia gladiata (Jacq.) DC Akanata Mame and Vicia faba L. Witkiem Major. Viscoelastic properties of forisomes in their longitudinal direction were investigated before and after Ca2+-induced contraction, but in the radial direction only before contraction. Forisomes showed mechanical properties typical of a biological material with a unidirectional fibrous structure, i.e. the modulus of elasticity in the direction of their fibers is much greater than in the radial direction. Creep data were collected in all tensile tests and fit with a three parameter viscoelastic model. The pre-contraction longitudinal elastic moduli of the forisomes were not differentiable between the two species (V. faba, 660 ± 360 kPa; C. gladiata, 600 ± 360 kPa). Both species showed a direction-dependent mechanical response: the elastic modulus was dramatically smaller in the radial direction than in the longitudinal direction, suggesting a weak protein cross-linking amongst longitudinal protein fibers. Activation of forisomes decreased forisome stiffness longitudinally, as evidenced by the loss of toe-region in the stress strain curve, suggesting that the forisome may have dispersed or disordered its protein structure in a controlled fashion. Contractile forces generated by single forisomes undergoing activation were also measured for V. faba (510 ± 390 nN) and C. gladiata (570 ± 310 nN).


A controlled trial of sorbinil, an aldose reductase inhibitor, in chronic painful diabetic neuropathy.
A double-blind, randomized, placebo-controlled cross-over trial of the aldose reductase inhibitor sorbinil was undertaken in 15 patients (age 35-68 yr) with chronic painful diabetic neuropathy. Treatment was evaluated by subjective pain responses, clinical examination, vibration perception threshold, motor and sensory nerve electrophysiology, and cardiovascular reflex tests of autonomic nerve function. Among the many measurements, only pain, tendon reflex scores, and sural sensory potential amplitude improved significantly during sorbinil administration, while scores of clinical sensory examination deteriorated. Four patients experienced an idiosyncratic reaction that rapidly recovered on discontinuing the drug. This study suggests that aldose reductase inhibitor treatment with suggests that aldose reductase inhibitor treatment with sorbinil may have an effect on symptomatic diabetic neuropathy in man.


Assessing the use of magnetic resonance imaging virtopsy as an alternative to autopsy: a systematic review and meta-analysis.
The post mortem examination or autopsy is a trusted method of identifying the cause of death. Patients and their families may oppose an autopsy for a variety of reasons, including fear of mutilation or owing to religious and personal beliefs. Imaging alternatives to autopsy have been explored, which may provide a viable alternative. To explore the possibility of using MRI virtopsy to establish the cause of death as an alternative to the traditional post mortem examination or autopsy. Systematic review was carried out of all studies, without language restriction, identified from Medline, Cochrane (1960-2016) and Embase (1991-2016) up to December 2016. Further searches were performed using the bibliographies of articles and abstracts. All studies reporting the diagnosis of the cause of death by both MRI virtopsy and traditional autopsy were included. Five studies with 107 patients, contributed to a summative quantitative outcome in adults. The combined sensitivity of MRI virtopsy was 0.82 (95% CI 0.56 to 0.94) with a diagnostic odds ratio (DOR) of 11.1 (95% CI 2.2 to 57.0). There was no significant heterogeneity between studies (Q=1.96, df=4, p=0.75, I2=0). Eight studies, with 953 patients contributed to a summative quantitative outcome in children. The combined sensitivity of MRI virtopsy was 0.73 (95% CI 0.59 to 0.84) with a DOR of 6.44 (95% CI 1.36 to 30.51). There was significant heterogeneity between studies (Q=34.95, df=7, p<0.01, I2=80). MRI virtopsy may offer a viable alternative to traditional autopsy. By using MRI virtopsy, a potential cost reduction of at least 33% is feasible, and therefore ought to be considered in eligible patients.


RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells.
By using a protein-DNA cross-linking method (D. S. Gilmour and J. T. Lis, Mol. Cell. Biol. 5:2009-2018, 1985), we examined the in vivo distribution of RNA polymerase II on the hsp70 heat shock gene in Drosophila melanogaster Schneider line 2 cells. In heat shock-induced cells, a high level of RNA polymerase II was detected on the entire gene, while in noninduced cells, the RNA polymerase II was confined to the 5' end of the hsp70 gene, predominantly between nucleotides -12 and +65 relative to the start of transcription. This association of RNA polymerase II was apparent whether the cross-linking was performed by a 10-min UV irradiation of chilled cells with mercury vapor lamps or by a 40-microsecond irradiation of cells with a high-energy xenon flash lamp. We hypothesize that RNA polymerase II has access to, and a high affinity for, the promoter region of this gene before induction, and this poised RNA polymerase II may be critical in the mechanism of transcription activation.


An Agar-Based Method for Plating Marine Protozoan Parasites of the Genus Perkinsus.
The genus Perkinsus includes protozoan parasites of mollusks responsible for losses in the aquaculture industry and hampering the recovery of natural shellfish beds worldwide, and they are a key taxon for understanding intracellular parasitism adaptations. The ability to propagate the parasite in liquid media, in the absence of the host, has been crucial for improving understanding of its biology; however, alternative techniques to grow the parasite are needed to explore other basic aspects of the Perkinsus spp. biology. We optimized a DME: Ham's F12-5% FBS- containing solid agar medium for plating Perkinsus marinus. This solid medium supported trophozoite propagation both by binary fission and schizogony. Colonies were visible to the naked eye 17 days after plating. We tested the suitability of this method for several applications, including the following: 1) Subcloning P. marinus isolates: single discrete P. marinus colonies were obtained from DME: Ham's F12-5% FBS- 0.75% agar plates, which could be further propagated in liquid medium; 2) Subcloning engineered Perkinsus mediterraneus MOE[MOE]: GFP by streaking cultures on plates; 3) Chemical susceptibility: Infusing the DME: Ham's F12-5% FBS- 0.75% agar plates with triclosan resulted in inhibition of the parasite propagation in a dose-dependent manner. Altogether, our plating method has the potential for becoming a key tool for investigating diverse aspects of Perkinsus spp. biology, developing new molecular tools, and for biotechnological applications.


Invasion-inhibitory antibodies elicited by immunization with Plasmodium vivax apical membrane antigen-1 expressed in Pichia pastoris yeast.
In a recent vaccine trial performed with African children, immunization with a recombinant protein based on Plasmodium falciparum apical membrane antigen 1 (AMA-1) conferred a significant degree of strain-specific resistance against malaria. To contribute to the efforts of generating a vaccine against Plasmodium vivax malaria, we expressed the ectodomain of P. vivax AMA-1 (PvAMA-1) as a secreted soluble protein in the methylotrophic yeast Pichia pastoris. Recognized by a high percentage of sera from individuals infected by P. vivax, this recombinant protein was found to have maintained its antigenicity. The immunogenicity of this protein was evaluated in mice using immunization protocols that included homologous and heterologous prime-boost strategies with plasmid DNA and recombinant protein. We used the following formulations containing different adjuvants: aluminum salts (Alum), Bordetella pertussis monophosphoryl lipid A (MPLA), flagellin FliC from Salmonella enterica serovar Typhimurium, saponin Quil A, or incomplete Freund's adjuvant (IFA). The formulations containing the adjuvants Quil A or IFA elicited the highest IgG antibody titers. Significant antibody titers were also obtained using a formulation developed for human use containing MPLA or Alum plus MPLA. Recombinant PvAMA-1 produced under "conditions of good laboratory practice" provided a good yield, high purity, low endotoxin levels, and no microbial contaminants and reproduced the experimental immunizations. Most relevant for vaccine development was the fact that immunization with PvAMA-1 elicited invasion-inhibitory antibodies against different Asian isolates of P. vivax. Our results show that AMA-1 expressed in P. pastoris is a promising antigen for use in future preclinical and clinical studies.


Tead1 is required for maintaining adult cardiomyocyte function, and its loss results in lethal dilated cardiomyopathy.
Heart disease remains the leading cause of death worldwide, highlighting a pressing need to identify novel regulators of cardiomyocyte (CM) function that could be therapeutically targeted. The mammalian Hippo/Tead pathway is critical in embryonic cardiac development and perinatal CM proliferation. However, the requirement of Tead1, the transcriptional effector of this pathway, in the adult heart is unknown. Here, we show that tamoxifen-inducible adult CM-specific Tead1 ablation led to lethal acute-onset dilated cardiomyopathy, associated with impairment in excitation-contraction coupling. Mechanistically, we demonstrate Tead1 is a cell-autonomous, direct transcriptional activator of SERCA2a and SR-associated protein phosphatase 1 regulatory subunit, Inhibitor-1 (I-1). Thus, Tead1 deletion led to a decrease in SERCA2a and I-1 transcripts and protein, with a consequent increase in PP1-activity, resulting in accumulation of dephosphorylated phospholamban (Pln) and decreased SERCA2a activity. Global transcriptomal analysis in Tead1-deleted hearts revealed significant changes in mitochondrial and sarcomere-related pathways. Additional studies demonstrated there was a trend for correlation between protein levels of TEAD1 and I-1, and phosphorylation of PLN, in human nonfailing and failing hearts. Furthermore, TEAD1 activity was required to maintain PLN phosphorylation and expression of SERCA2a and I-1 in human induced pluripotent stem cell-derived (iPS-derived) CMs. To our knowledge, taken together, this demonstrates a nonredundant, novel role of Tead1 in maintaining normal adult heart function.


The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.
Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.


Like-charge interactions between colloidal particles are asymmetric with respect to sign.
Two-dimensional dispersions of colloidal particles with a range of surface chemistries and electrostatic potentials are characterized under a series of solution ionic strengths. A combination of optical imaging techniques are employed to monitor both the colloid structure and the electrostatic surface potential of individual particles in situ. We find that like-charge multiparticle interactions can be tuned from exclusively repulsive to long-range attractive by changing the particle surface composition. This behavior is strongly asymmetric with respect to the sign of the surface potential. Collective long-range attractive interactions are only observed among negatively charged particles.


Radiation induces changes in toll-like receptors of the uterine cervix of the rat.
Radiotherapy is an important therapeutic approach against cervical cancer but associated with adverse effects including vaginal fibrosis and dyspareunia. We here assessed the immunological and oxidative responses to cervical irradiation in an animal model for radiation-induced cervicitis. Rats were sedated and either exposed to 20 Gy of ionising radiation given by a linear accelerator or only sedated (controls) and euthanized 1-14 days later. The expressions of toll-like receptors (TLRs) and coupled intracellular pathways in the cervix were assessed with immunohistofluorescence and western blot. Expression of cytokines were analysed with the Bio-Plex Suspension Array System (Bio-Rad). We showed that TLRs 2-9 were expressed in the rat cervix and cervical irradiation induced up-regulation of TLR5, TRIF and NF-κB. In the irradiated cervical epithelium, TLR5 and TRIF were increased in concert with an up-regulation of oxidative stress (8-OHdG) and antioxidant enzymes (SOD-1 and catalase). G-CSF, M-CSF, IL-10, IL- 17A, IL-18 and RANTES expressions in the cervix decreased two weeks after cervical irradiation. In conclusion, the rat uterine cervix expresses the TLRs 2-9. Cervical irradiation induces immunological changes and oxidative stress, which could have importance in the development of adverse effects to radiotherapy.


Tumor markers in fine-needle aspiration washout for cervical lymphadenopathy in patients with known malignancy: preliminary study.
The purposes of our study were to assess whether tumor marker concentration in fine-needle aspiration (FNA) washout from cervical lymph nodes (LNs) differs between metastatic and nonmetastatic LNs and whether tumor marker concentrations in FNA washout can contribute to the diagnosis of metastatic LNs. Ultrasound-guided FNA was performed for 157 neck nodes in 157 patients, including 136 patients with known malignancy (28 breast, 34 lung, 41 head and neck, seven esophagus, nine cervix, 10 gastrointestinal [GI] tract, and seven ovary cancers) and 21 patients without known malignancy (control group). Immediately after an FNA cytology specimen was obtained, the needle was rinsed with 1 mL of normal saline solution, and variable tumor marker concentrations were measured in the washout: carcinoembryonic antigen (CEA) and cancer antigen (CA) 15-3 for breast; CEA and cytokeratin 19 fragment for lung; squamous cell antigen for head and neck, esophagus, and cervix; CEA and CA 19-9 for GI; CA 125 for ovarian cancer; and all the tumor marker concentrations for the control group. The tumor marker concentration was compared between the metastatic and nonmetastatic LNs in the control group and between the metastatic and nonmetastatic LNs in the known malignancy group, according to the known malignancy. At final diagnosis, 104 LNs were metastatic and 53 were nonmetastatic (including 21 LNs in the control group). The tumor marker concentrations of cases with negative or nondiagnostic cytologic results were evaluated. The sensitivity of FNA cytology alone was compared with the combined sensitivity of FNA cytology and tumor marker concentration. Metastatic LNs had higher corresponding FNA tumor marker concentrations than did nonmetastatic LNs in both the control and known malignancy groups (p < 0.05), except for CA 19-9 in GI cancer. Eight of 10 cases (80%) with negative or nondiagnostic cytologic results but metastatic LNs at final diagnosis showed elevated tumor marker concentrations. The sensitivity of FNA cytology (90.4%) increased to 98.1% when combined with tumor marker concentration (p < 0.05). Tumor marker concentrations in FNA washout with cervical metastatic LNs were elevated in comparison with those of nonmetastatic LNs. Evaluation of tumor marker concentrations in FNA washout could improve the detection of metastatic LNs in patients with known malignancy.


Development of an index to rank dairy females on expected lifetime profit.
The objective of this study was to develop an index to rank dairy females on expected profit for the remainder of their lifetime, taking cognizance of both additive and nonadditive genetic merit, permanent environmental effects, and current states of the animal including the most recent calving date and cow parity. The cow own worth (COW) index is intended to be used for culling the expected least profitable females in a herd, as well as inform purchase and pricing decisions for trading of females. The framework of the COW index consisted of the profit accruing from (1) the current lactation, (2) future lactations, and (3) net replacement cost differential. The COW index was generated from estimated performance values (sum of additive genetic merit, nonadditive genetic merit, and permanent environmental effects) of traits, their respective net margin values, and transition probability matrices for month of calving, survival, and somatic cell count; the transition matrices were to account for predicted change in a cow's state in the future. Transition matrices were generated from 3,156,109 lactation records from the Irish national database between the years 2010 and 2013. Phenotypic performance records for 162,981 cows in the year 2012 were used to validate the COW index. Genetic and permanent environmental effects (where applicable) were available for these cows from the 2011 national genetic evaluations and used to calculate the COW index and their national breeding index values (includes only additive genetic effects). Cows were stratified per quartile within herd, based on their COW index value and national breeding index value. The correlation between individual animal COW index value and national breeding index value was 0.65. Month of calving of the cow in her current lactation explained 18% of the variation in the COW index, with the parity of the cow explaining an additional 3 percentage units of the variance in the COW index. Females ranking higher on the COW index yielded more milk and milk solids and calved earlier in the calving season than their lower ranking contemporaries. The difference in phenotypic performance between the best and worst quartiles was larger for cows ranked on COW index than cows ranked on the national breeding index. The COW index is useful to rank females before culling or purchasing decisions on expected profit and is complementary to the national breeding index, which identifies the most suitable females for breeding replacements.


mRNA expression of programmed cell death ligand 1 and components of the phosphatidylinositol 3-kinase/AKT/phosphatase and tensin homolog pathway in epidermal growth factor receptor mutation-positive lung adenocarcinoma.
The objective of this study is to investigate the relationship between programmed cell death ligand 1 (PD-L1) expression and the mutation status of epidermal growth factor receptor (EGFR) in lung adenocarcinoma, as well as the correlation between the clinical features of patients and mRNA levels of PD-L1 and components of the phosphatidylinositol 3-kinase (PI3K)/ protein kinase B (AKT)/phosphatase and tensin homolog (PTEN) pathways. mRNA levels of PD-L1, PI3K, AKT, and PTEN in tumor and matched normal tissues of patients with EGFR mutation-positive lung adenocarcinoma were determined by real-time polymerase chain reaction. Twenty-three patients with EGFR mutation-positive lung adenocarcinoma were enrolled, and 46 samples (23 pairs of tumor and matched normal lung tissues) were collected. PD-L1 and AKT mRNA levels were higher in EGFR mutation-positive lung adenocarcinoma than in matched normal lung tissues (P = 0.047 and P = 0.046, respectively), whereas PI3K and PTEN mRNA levels were significantly lower in the cancerous tissues (P = 0.009 and P = 0.039, respectively). PD-L1 expression was positively correlated with PI3K/AKT signaling pathway activation. PD-L1 upregulation in lung adenocarcinoma was positively correlated with EGFR exon 19 mutations (P = 0.034). AKT mRNA upregulation was correlated with lymph node metastasis (P = 0.034). PTEN mRNA downregulation was correlated with high tumor staging and lymph node metastasis (P = 0.035 and P = 0.014, respectively). Elevated PD-L1 mRNA expression in lung adenocarcinoma is associated with EGFR mutation and may be mediated through the PI3K-AKT pathway. EGFR exon 19 mutations closely correlate with increased PD-L1 mRNA expression. Increased AKT mRNA expression correlates with lymph node metastasis, while decreased PTEN mRNA levels correlate with advanced tumor stage and lymph node metastasis.


First Passage Time Memory Lifetimes for Multistate, Filter-Based Synapses.
Models of associative memory with discrete state synapses learn new memories by forgetting old ones. In contrast to non-integrative models of synaptic plasticity, models with integrative, filter-based synapses exhibit an initial rise in the fidelity of recall of stored memories. This rise to a peak is driven by a transient process and is then followed by a return to equilibrium. In a series of papers, we have employed a first passage time (FPT) approach to define and study memory lifetimes, incrementally developing our methods, from both simple and complex binary-strength synapses to simple multistate synapses. Here, we complete this work by analyzing FPT memory lifetimes in multistate, filter-based synapses. To achieve this, we integrate out the internal filter states so that we can work with transitions only in synaptic strength. We then generalize results on polysynaptic generating functions from binary strength to multistate synapses, allowing us to examine the dynamics of synaptic strength changes in an ensemble of synapses rather than just a single synapse. To derive analytical results for FPT memory lifetimes, we partition the synaptic dynamics into two distinct phases: the first, pre-peak phase studied with a drift-only approximation, and the second, post-peak phase studied with approximations to the full strength transition probabilities. These approximations capture the underlying dynamics very well, as demonstrated by the extremely good agreement between results obtained by simulating our model and results obtained from the Fokker-Planck or integral equation approaches to FPT processes.


Water based synthesis of highly conductive GaxLi7-3xLa3Hf2O12 garnets with comparable critical current density to analogous GaxLi7-3xLa3Zr2O12 systems.
Next generation lithium ion batteries are envisaged as those which feature an all solid-state architecture. This will enable the higher energy density storage required to meet the demands of modern society, especially for the growing electric vehicle market. Solid state batteries have, however, proved troublesome to implement commercially due to the lack of a suitable solid-state electrolyte, which needs to be highly conductive, have a low interfacial resistance and a suitably wide electrochemical stability window. Garnet materials are potential contenders for these batteries, demonstrating many of the desired properties, although there remain challenges to overcome. Here we report a facile synthesis of Li7La3Hf2O12 and Ga/AlxLi7-3xLa3Hf2O12 garnets, with the synthesis of Ga0.2Li6.4La3Hf2O12 requiring only dissolution of precursors in water and heating to 700 °C. Ga0.2Li6.4La3Hf2O12 was shown to display a high room temperature conductivity (0.373 mS cm-1 at 28 °C). Moreover, in Li|garnet|Li cells, we observed a comparable critical current density compared to Ga0.2Lai6.4La3Zr2O12, despite a lower density and higher area specific resistance compared to literature values, suggesting Hf systems may be further engineered to deliver additional improvements for use in future solid state batteries.


HTR2A gene variants and psychiatric disorders: a review of current literature and selection of SNPs for future studies.
Variants at the gene encoding for the 5-hydrosytryptamine (serotonin) receptor 2A (HTR2A) have been associated with many psychiatric disorders such as schizophrenia, mood disorders, attention deficit hyperactivity disorder, suicide, anxiety disorders, obsessive-compulsive disorder, eating disorders, and Alzheimer's disease. The studied SNPs differ across studies, in the present review we focused on available evidence with the aim of identifying the overall phenotypic profile of HTR2A variant carriers. We then extensively analyzed all SNPs of the HTR2A gene with criteria of frequency, haplotype blocks, previous evidence, functionality in order to obtain a list of suitable SNPs for future studies that properly cover all possible genetic control of the HTR2A gene. Genetic association studies report conflicting and generally negative results. Most replicated data suggest C allele of the 102 T/C and Tyr452 variants as risk factor for psychosis and antipsychotic response, but the number of not replicating studies does not allow to draw any definite conclusion. Moreover their impact as risk factors is very small. In the other investigated psychiatric fields, evidence shows no involvement or at least a small and not replicated role for HTR2A gene variants. Conflicting and negative results could be due to a real marginal role of this receptor gene variants, or it could be caused by a lack of gene coverage of investigated SNPs. We suggest a wider investigation of the HTR2A gene to better understand its role in psychiatric disorders, preferably complemented with the use of proteomic or metabolomic approaches.


The distribution of axial length, anterior chamber depth, lens thickness, and vitreous chamber depth in an adult population of Shahroud, Iran.
Ocular biometric parameters can be influenced by race, ethnicity, and genetics; their differences across different populations can probably explain differences in refractive errors in these populations. The aim of this study is to determine the normal range of axial length, anterior chamber depth, lens thickness, and vitreous chamber depth in the population of Shahroud in the north of Iran. In the first phase of Shahroud Eye Cohort Study, the 40-64 year old population were sampled cross-sectionally; 6311 were invited and 5190 (82.2%) participated in the study. Biometric examinations were done using the LENSTAR/BioGraph (WaveLight AG, Erlangen, Germany) after vision tests and before cycloplegic refraction tests. Any type of eye surgery, extensive pterygium, and lack of cooperation were used as exclusion criteria, and analyses were done with data from 4869 eyes. We found a mean axial length of 23.14 mm (95% confidence interval [CI], 23.11-23.17), mean anterior chamber depth of 2.62 mm (95% CI, 2.60-2.63), mean lens thickness of 4.28 mm (95% CI, 4.27-4.29), and the mean vitreous chamber depth was 15.72 mm (95% CI, 15.70-15.75).Kolmogorov-Smirnov tests showed that the distribution of axial length, anterior chamber depth, lens thickness, and vitreous chamber depth significantly differed from normal; axial length and vitreous chamber depth demonstrated a leptokurtic distribution as well.Axial length, anterior chamber depth, and vitreous chamber depth significantly decreased with age, and lens thickness significantly increased with age (p < 0.001). All indices were significantly higher in men. The distributions of axial length, vitreous chamber depth, and lens thickness are reported for the first time in an Iranian adult population. Compared to other studies, axial length was in the mid range, nonetheless, studying axial length components showed that the Iranian population had smaller anterior chamber depth and lens thickness. Age and gender were significantly associated with all indices assessed in this study.


In vivo two-photon voltage-sensitive dye imaging reveals top-down control of cortical layers 1 and 2 during wakefulness.
Conventional methods of imaging membrane potential changes have limited spatial resolution, particularly along the axis perpendicular to the cortical surface. The laminar organization of the cortex suggests, however, that the distribution of activity in depth is not uniform. We developed a technique to resolve network activity of different cortical layers in vivo using two-photon microscopy of the voltage-sensitive dye (VSD) ANNINE-6. We imaged spontaneous voltage changes in the barrel field of the somatosensory cortex of head-restrained mice and analyzed their spatiotemporal correlations during anesthesia and wakefulness. EEG recordings always correlated more strongly with VSD signals in layer (L) 2 than in L1. Nearby (<200 mum) cortical areas were correlated with one another during anesthesia. Waking the mouse strongly desynchronized neighboring cortical areas in L1 in the 4- to 10-Hz frequency band. Wakefulness also slightly increased synchrony of neighboring territories in L2 in the 0.5- to 4.0-Hz range. Our observations are consistent with the idea that, in the awake animal, long-range inputs to L1 of the sensory cortex from various cortical and thalamic areas exert top-down control on sensory processing.


Proposed consensus definitions for new-onset refractory status epilepticus (NORSE), febrile infection-related epilepsy syndrome (FIRES), and related conditions.
We convened an international group of experts to standardize definitions of New-Onset Refractory Status Epilepticus (NORSE), Febrile Infection-Related Epilepsy Syndrome (FIRES), and related conditions. This was done to enable improved communication for investigators, physicians, families, patients, and other caregivers. Consensus definitions were achieved via email messages, phone calls, an in-person consensus conference, and collaborative manuscript preparation. Panel members were from 8 countries and included adult and pediatric experts in epilepsy, electroencephalography (EEG), and neurocritical care. The proposed consensus definitions are as follows: NORSE is a clinical presentation, not a specific diagnosis, in a patient without active epilepsy or other preexisting relevant neurological disorder, with new onset of refractory status epilepticus without a clear acute or active structural, toxic or metabolic cause. FIRES is a subcategory of NORSE, applicable for all ages, that requires a prior febrile infection starting between 2 weeks and 24 hours prior to onset of refractory status epilepticus, with or without fever at onset of status epilepticus. Proposed consensus definitions are also provided for Infantile Hemiconvulsion-Hemiplegia and Epilepsy syndrome (IHHE) and for prolonged, refractory and super-refractory status epilepticus. This document has been endorsed by the Critical Care EEG Monitoring Research Consortium. We hope these consensus definitions will promote improved communication, permit multicenter research, and ultimately improve understanding and treatment of these conditions.


DDPC: Dragon Database of Genes associated with Prostate Cancer.
Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc.kaust.edu.sa/ddpc/.


Micellar transitions in the aqueous solutions of a surfactant-like ionic liquid: 1-butyl-3-methylimidazolium octylsulfate.
We have observed dual transitions in various physical properties while investigating the surfactant-like behavior of the ionic liquid (IL) 1-butyl-3-methylimidazolium octylsulfate [C(4)mim][C(8)SO(4)] in aqueous media. Interestingly, in conductivity measurements, it was found that the second transition, which is comparatively weak in pure water, can be modulated and tuned to the desired concentration without affecting the first transition by the addition of a suitable electrolyte. Using an array of techniques, such as conductivity, ultrasonics, TEM, cryo-TEM, DLS, (1)H NMR and 2D (1)H-(1)H NOESY, it has been revealed that the first transition corresponds to the anionic aggregation with imidazolium cations adsorbed as counterions, and the second transition corresponds to the restructuring of the initially formed aggregates in a way that the alkyl chain of the imidazolium cation is incorporated towards the micellar core, leading to a unique mixed micelle-type structure in a single IL system.


Network modeling of BVD transmission.
Endemic diseases of cattle, such as bovine viral diarrhea, have significant impact on production efficiency of food of animal origin with consequences for animal welfare and climate change reduction targets. Many modeling studies focus on the local scale, examining the on-farm dynamics of this infectious disease. However, insight into prevalence and control across a network of farms ultimately requires a network level approach. Here, we implement understanding of infection dynamics, gained through these detailed on-farm modeling studies, to produce a national scale model of bovine viral diarrhea virus transmission. The complex disease epidemiology and on-farm dynamics are approximated using SIS dynamics with each farm treated as a single unit. Using a top down approach, we estimate on-farm parameters associated with contraction and subsequent clearance from infection at herd level. We examine possible control strategies associated with animal movements between farms and find measures targeted at a small number of high-movement farms efficient for rapid and sustained prevalence reduction.


Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia.
We developed a heterologous COVID-19 vaccine consisting of two components, a recombinant adenovirus type 26 (rAd26) vector and a recombinant adenovirus type 5 (rAd5) vector, both carrying the gene for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (rAd26-S and rAd5-S). We aimed to assess the safety and immunogenicity of two formulations (frozen and lyophilised) of this vaccine. We did two open, non-randomised phase 1/2 studies at two hospitals in Russia. We enrolled healthy adult volunteers (men and women) aged 18-60 years to both studies. In phase 1 of each study, we administered intramuscularly on day 0 either one dose of rAd26-S or one dose of rAd5-S and assessed the safety of the two components for 28 days. In phase 2 of the study, which began no earlier than 5 days after phase 1 vaccination, we administered intramuscularly a prime-boost vaccination, with rAd26-S given on day 0 and rAd5-S on day 21. Primary outcome measures were antigen-specific humoral immunity (SARS-CoV-2-specific antibodies measured by ELISA on days 0, 14, 21, 28, and 42) and safety (number of participants with adverse events monitored throughout the study). Secondary outcome measures were antigen-specific cellular immunity (T-cell responses and interferon-γ concentration) and change in neutralising antibodies (detected with a SARS-CoV-2 neutralisation assay). These trials are registered with ClinicalTrials.gov, NCT04436471 and NCT04437875. Between June 18 and Aug 3, 2020, we enrolled 76 participants to the two studies (38 in each study). In each study, nine volunteers received rAd26-S in phase 1, nine received rAd5-S in phase 1, and 20 received rAd26-S and rAd5-S in phase 2. Both vaccine formulations were safe and well tolerated. The most common adverse events were pain at injection site (44 [58%]), hyperthermia (38 [50%]), headache (32 [42%]), asthenia (21 [28%]), and muscle and joint pain (18 [24%]). Most adverse events were mild and no serious adverse events were detected. All participants produced antibodies to SARS-CoV-2 glycoprotein. At day 42, receptor binding domain-specific IgG titres were 14 703 with the frozen formulation and 11 143 with the lyophilised formulation, and neutralising antibodies were 49·25 with the frozen formulation and 45·95 with the lyophilised formulation, with a seroconversion rate of 100%. Cell-mediated responses were detected in all participants at day 28, with median cell proliferation of 2·5% CD4+ and 1·3% CD8+ with the frozen formulation, and a median cell proliferation of 1·3% CD4+ and 1·1% CD8+ with the lyophilised formulation. The heterologous rAd26 and rAd5 vector-based COVID-19 vaccine has a good safety profile and induced strong humoral and cellular immune responses in participants. Further investigation is needed of the effectiveness of this vaccine for prevention of COVID-19. Ministry of Health of the Russian Federation.


Retinal vascular caliber, iris color, and age-related macular degeneration in the Irish Nun Eye Study.
To evaluate the relationship between retinal vascular caliber (RVC), iris color, and age-related macular degeneration (AMD) in elderly Irish nuns. Data from 1233 participants in the cross-sectional observational Irish Nun Eye Study were assessed from digital photographs with a standardized protocol using computer-assisted software. Macular images were graded according to the modified Wisconsin Age-related Maculopathy Grading System. Regression models were used to assess associations, adjusting for age, mean arterial blood pressure, body mass index, refraction, and fellow RVC. In total, 1122 (91%) participants had gradable retinal images of sufficient quality for vessel assessment (mean age: 76.3 years [range, 56-100 years]). In an unadjusted analysis, we found some support for a previous finding that individuals with blue iris color had narrower retinal venules compared to those with brown iris color (P < 0.05), but this was no longer significant after adjustment. Age-related macular degeneration status was categorized as no AMD, any AMD, and late AMD only. Individuals with any AMD (early or late AMD) had significantly narrower arterioles and venules compared to those with no AMD in an unadjusted analysis, but this was no longer significant after adjustment. A nonsignificant reduced risk of any AMD or late AMD only was observed in association with brown compared to blue iris color, in both unadjusted and adjusted analyses. Retinal vascular caliber was not significantly associated with iris color or early/late AMD after adjustment for confounders. A lower but nonsignificant AMD risk was observed in those with brown compared to blue iris color.


Hepatitis C virus treatment for prevention among people who inject drugs: Modeling treatment scale-up in the age of direct-acting antivirals.
Substantial reductions in hepatitis C virus (HCV) prevalence among people who inject drugs (PWID) cannot be achieved by harm reduction interventions such as needle exchange and opiate substitution therapy (OST) alone. Current HCV treatment is arduous and uptake is low, but new highly effective and tolerable interferon-free direct-acting antiviral (DAA) treatments could facilitate increased uptake. We projected the potential impact of DAA treatments on PWID HCV prevalence in three settings. A dynamic HCV transmission model was parameterized to three chronic HCV prevalence settings: Edinburgh, UK (25%); Melbourne, Australia (50%); and Vancouver, Canada (65%). Using realistic scenarios of future DAAs (90% sustained viral response, 12 weeks duration, available 2015), we projected the treatment rates required to reduce chronic HCV prevalence by half or three-quarters within 15 years. Current HCV treatment rates may have a minimal impact on prevalence in Melbourne and Vancouver (<2% relative reductions) but could reduce prevalence by 26% in 15 years in Edinburgh. Prevalence could halve within 15 years with treatment scale-up to 15, 40, or 76 per 1,000 PWID annually in Edinburgh, Melbourne, or Vancouver, respectively (2-, 13-, and 15-fold increases, respectively). Scale-up to 22, 54, or 98 per 1,000 PWID annually could reduce prevalence by three-quarters within 15 years. Less impact occurs with delayed scale-up, higher baseline prevalence, or shorter average injecting duration. Results are insensitive to risk heterogeneity or restricting treatment to PWID on OST. At existing HCV drug costs, halving chronic prevalence would require annual treatment budgets of US $3.2 million in Edinburgh and approximately $50 million in Melbourne and Vancouver. Interferon-free DAAs could enable increased HCV treatment uptake among PWID, which could have a major preventative impact. However, treatment costs may limit scale-up, and should be addressed.


TNF-α increases the intrinsic excitability of cerebellar Purkinje cells through elevating glutamate release in Bergmann Glia.
For decades, the glial function has been highlighted not only as the 'structural glue', but also as an 'active participant' in neural circuits. Here, we suggest that tumor necrosis factor α (TNF-α), a key inflammatory cytokine, alters the neural activity of the cerebellar Purkinje cells (PCs) by facilitating gliotransmission in the juvenile male rat cerebellum. A bath application of TNF-α (100 ng/ml) in acute cerebellar slices elevates spiking activity of PCs with no alterations in the regularity of PC firings. Interestingly, the effect of TNF-α on the intrinsic excitability of PCs was abolished under a condition in which the type1 TNF receptor (TNFR1) in Bergmann glia (BG) was genetically suppressed by viral delivery of an adeno-associated virus (AAV) containing TNFR1-shRNA. In addition, we measured the concentration of glutamate derived from dissociated cerebellar cortical astrocyte cultures treated with TNF-α and observed a progressive increase of glutamate in a time-dependent manner. We hypothesised that TNF-α-induced elevation of glutamate from BGs enveloping the synaptic cleft may directly activate metabotropic glutamate receptor1 (mGluR1). Pharmacological inhibition of mGluR1, indeed, prevented the TNF-α-mediated elevation of the intrinsic excitability in PCs. Taken together, our study reveals that TNF-α triggers glutamate release in BG, thereby increasing the intrinsic excitability of cerebellar PCs in a mGluR1-dependent manner.


Interpretation of symptoms in chronic fatigue syndrome.
Chronic fatigue syndrome (CFS) is an illness characterised by fatigue and other symptoms. Both psychological and biological aetiological factors have been proposed, but the disorder is of uncertain origin. The aetiology of the symptoms is therefore ambiguous. It has been suggested (a) that patients with CFS tend to interpret their symptoms as indicating physical illness and (b) they tend not to interpret these symptoms in terms of negative emotion. In order to test these hypotheses we developed a self-report questionnaire to assess the interpretation of symptoms in patients with CFS. It was administered to patients with CFS, patients with depression, patients with multiple sclerosis (MS), and normal controls. Preliminary results suggest that the measure has acceptable psychometric properties. Patients with CFS were more likely than either depressed patients or normal controls to interpret symptoms (characteristic of CFS) in terms of physical illness, but did not differ in this from the MS patients. When compared with all three other groups (including the MS patients), the patients with CFS were least likely to interpret symptoms in terms of negative emotional states. The theoretical and clinical implications of the findings are discussed.


Anodic coupling reactions: exploring the generality of Curtin-Hammett controlled reactions.
Intramolecular anodic olefin coupling reactions can be compatible with the presence of dithioketal protecting groups even though the dithioketal oxidizes at a lower potential than either of the groups participating in the cyclization. In such cases, product formation is controlled by the Curtin-Hammett Principle. In this study, the generality of such reactions is examined along with the use of alternative reaction conditions to suppress unwanted side reactions.


Characteristics and determinants of sexual behavior among adolescents of migrant workers in Shangai (China).
China is facing a critical challenge of rapid and widespread human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) increase. Rural-to-urban migration plays a crucial role in shifting the HIV/sexual transmitted infection (STI) epidemic. The purpose of this study was to assess the prevalence of sexual behaviors and the correlates among the early adolescents of migrant workers in China. A cross-sectional study was conducted in 10 junior high schools from April to June of 2008. A total of 2821 adolescents aged 14.06 +/- 0.93 years (8.9% of migrant workers vs. 91.1% of general residents) participated in the survey. A self-administrated questionnaire was used to collect information on knowledge, attitude, and behaviors associated with increased risk for HIV/STI. The percentage of adolescents who ever had sexual intercourse or had sexual intercourse in last three months was 7.2% and 4.3% in adolescents of migrant workers, respectively; in contrast, 4.5% and 1.8% in their peers of general residents, respectively. 47.3% adolescents of migrant workers and 34.3% of those adolescents of general residents reported no condom use in sexual intercourse during last three months. Multivariate logistic regression analyses found that migration was a independent risk factor for sexual intercourse in last three months in our sampled adolescents (odds ratio [OR] = 1.23, 95% confidence interval [CI]: 1.01-1.72). In adolescents of migrant workers, factors such as lower family income (OR: 2.22, CI: 1.09-3.05 for low level; OR:1.25, CI: 1.04-1.59 for medium level), younger age at first sexual intercourse (OR: 1.24, CI: 1.09-1.57), lower knowledge on HIV/AIDS (OR: 0.93, CI: 0.90-0.97), and fewer communication on HIV/AIDS related issues (OR: 0.79, CI: 0.90-0.97) were related to sexual intercourse in last three months. Based on these results, we advocated that heightened concerns targeting the adolescents of migrant workers be particularly necessary, given their higher level of sexual experience, lower socioeconomic status, restricted reproductive health information, and vulnerability to HIV/STI.


The effect of changing patterns of obstetric care in Scotland (1980-2004) on rates of preterm birth and its neonatal consequences: perinatal database study.
Rates of preterm birth are rising worldwide. Studies from the United States and Latin America suggest that much of this rise relates to increased rates of medically indicated preterm birth. In contrast, European and Australian data suggest that increases in spontaneous preterm labour also play a role. We aimed, in a population-based database of 5 million people, to determine the temporal trends and obstetric antecedents of singleton preterm birth and its associated neonatal mortality and morbidity for the period 1980-2004. There were 1.49 million births in Scotland over the study period, of which 5.8% were preterm. We found a percentage increase in crude rates of both spontaneous preterm birth per 1,000 singleton births (10.7%, p<0.01) and medically indicated preterm births (41.2%, p<0.01), which persisted when adjusted for maternal age at delivery. The greater proportion of spontaneous preterm births meant that the absolute increase in rates of preterm birth in each category were similar. Of specific maternal complications, essential and pregnancy-induced hypertension, pre-eclampsia, and placenta praevia played a decreasing role in preterm birth over the study period, with gestational and pre-existing diabetes playing an increasing role. There was a decline in stillbirth, neonatal, and extended perinatal mortality associated with preterm birth at all gestation over the study period but an increase in the rate of prolonged hospital stay for the neonate. Neonatal mortality improved in all subgroups, regardless of obstetric antecedent of preterm birth or gestational age. In the 28 wk and greater gestational groups we found a reduction in stillbirths and extended perinatal mortality for medically induced but not spontaneous preterm births (in the absence of maternal complications) although at the expense of a longer stay in neonatal intensive care. This improvement in stillbirth and neonatal mortality supports the decision making behind the 34% increase in elective/induced preterm birth in these women. Although improvements in neonatal outcomes overall are welcome, preterm birth still accounts for over 66% of singleton stillbirths, 65% of singleton neonatal deaths, and 67% of infants whose stay in the neonatal unit is "prolonged," suggesting this condition remains a significant contributor to perinatal mortality and morbidity. In our population, increases in spontaneous and medically induced preterm births have made equal contributions to the rising rate of preterm birth. Despite improvements in related perinatal mortality, preterm birth remains a major obstetric and neonatal problem, and its frequency is increasing. Please see later in the article for the Editors' Summary.


Concentration variation and molecular characteristics of soluble (1,3;1,6)-β-D-glucans in submerged cultivation products of Ganoderma lucidum mycelium.
(1,3)-β-D-Glucans with (1,6)-β-D-glucosyl branches are bioactive polysaccharides in fruiting bodies and mycelia of Ganoderma lucidum, a mushroom used in traditional Chinese medicine. Submerged cultivation of mycelium is one of the more efficient means of generating polysaccharides from this fungus. Twelve mycelium samples examined in this study demonstrated the quantitative and qualitative molecular characteristics of soluble (1,3;1,6)-β-D-glucans. It was observed that the concentration of soluble (1,3;1,6)-β-D-glucan varied substantially from 1.3 to 79.9 mg/dL. (1,3;1,6)-β-D-Glucans also preserved their molecular characteristics with degrees of branching (DB) of 0.21-0.36 and molecular masses of 10(5)-10(6) g/mol for those samples with substantial quantities of β-D-glucan. Using the high aggregating tendency of these molecules, (1,3;1,6)-β-D-glucans were successfully purified via fractional precipitation with 35% (v/v) ethanol. (1,3;1,6)-β-D-Glucan was proposed as a putative bioactive marker for immunomodulation because it was the most abundant polysaccharide in G. lucidum mycelium products to stimulate macrophage RAW 264.7 cells to release TNF-α.


Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors.
The recent finding that reprogrammed human pluripotent stem cells can be derived by nuclear transfer into human oocytes as well as by induced expression of defined factors has revitalized the debate on whether one approach might be advantageous over the other. Here we compare the genetic and epigenetic integrity of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal, and adult origin. The two cell types showed similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs had comparable numbers of de novo coding mutations, but significantly more than parthenogenetic ESCs. As iPSCs, NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of derivation approach.


Pervasive domestication of defective prophages by bacteria.
Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the bacterial genome. We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. The size distribution of prophage elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic degradation. Accordingly, we observed a pervasive pattern of systematic counterselection of nonsynonymous mutations in prophage genes. Importantly, such patterns of purifying selection are observed not only on accessory regions but also in core phage genes, such as those encoding structural and lysis components. This suggests that bacterial hosts select for phage-associated functions. Several of these conserved prophages have gene repertoires compatible with described functions of adaptive prophage-derived elements such as bacteriocins, killer particles, gene transfer agents, or satellite prophages. We suggest that bacteria frequently domesticate their prophages. Most such domesticated elements end up deleted from the bacterial genome because they are replaced by analogous functions carried by new prophages. This puts the bacterial genome in a state of continuous flux of acquisition and loss of phage-derived adaptive genes.


Theoretical Modeling of Plasmon-Enhanced Raman Images of a Single Molecule with Subnanometer Resolution.
Under local plasmonic excitation, Raman images of single molecules can now surprisingly reach subnanometer resolution. However, its physical origin has not been fully understood. Here we report a quantum-mechanical description of the interaction between a molecule and a highly confined plasmonic field. We show that when the spatial distribution of the plasmonic field is comparable to the size of the molecule, the optical transition matrix of the molecule becomes dependent on the position and distribution of the plasmonic field, resulting in a spatially resolved high-resolution Raman image of the molecule. The resonant Raman image reflects the electronic transition density of the molecule. In combination with first-principles calculations, the simulated Raman image of a porphyrin derivative adsorbed on a silver surface nicely reproduces its experimental counterpart. The present theory provides the basic framework for describing linear and nonlinear responses of molecules under highly confined plasmonic fields.


Early experiences and predictors of recruitment success for the National Children's Study.
We aimed to describe 17 months of experience with household recruitment of live births for the National Children's Study in Queens, a highly urban, diverse borough of New York City (NYC), and to assess predictors of recruitment success. Recruitment data (enumeration, pregnancy screening of age-eligible women, identification of pregnancies, and consent) for the period of January 2009 through May 2010 were calculated. Geographic information systems were used to create 11 community-level variables for each of the 18 study segments where recruitment occurred, using US Census, NYC Office of Vital Statistics, NYC Department of City Planning, and NYC Police Department data. Recruitment yields were analyzed with respect to these variables at the segment level. Enumeration identified 4889 eligible women, of whom 4333 (88.6%) completed the pregnancy screener. At least 115 births were lost because of an inability of the pregnancy screener to identify pregnant women, whereas another 115 could be expected to be lost because of missed enumerations and pregnancy screeners. The consent rate was 60.3%. Segments with higher percentages of low birth weight had higher enumeration, pregnancy screening, and consent rates. In a highly immigrant, urban setting, households could be approached for recruitment of women to participate in the National Children's Study with consent rates equal to those experienced in clinical settings. Refinement of the pregnancy screener and other recruitment materials presents an opportunity to optimize recruitment, improve the representativeness of study participants, and improve the cost-effectiveness of study execution.