Phosphoenolpyruvate synthetase and pyruvate, phosphate dikinase of Thermoproteus tenax: key pieces in the puzzle of archaeal carbohydrate metabolism.
The interconversion of phosphoenolpyruvate and pyruvate represents an important control point of the Embden-Meyerhof-Parnas (EMP) pathway in Bacteria and Eucarya, but little is known about this site of regulation in Archaea. Here we report on the coexistence of phosphoenolpyruvate synthetase (PEPS) and the first described archaeal pyruvate, phosphate dikinase (PPDK), which, besides pyruvate kinase (PK), are involved in the catalysis of this reaction in the hyperthermophilic crenarchaeote Thermoproteus tenax. The genes encoding T. tenax PEPS and PPDK were cloned and expressed in Escherichia coli, and the enzymic and regulatory properties of the recombinant gene products were analysed. Whereas PEPS catalyses the unidirectional conversion of pyruvate to phosphoenolpyruvate, PPDK shows a bidirectional activity with a preference for the catabolic reaction. In contrast to PK of T. tenax, which is regulated on transcript level but exhibits only limited regulatory potential on protein level, PEPS and PPDK activities are modulated by adenosine phosphates and intermediates of the carbohydrate metabolism. Additionally, expression of PEPS is regulated on transcript level in response to the offered carbon source as revealed by Northern blot analyses. The combined action of the differently regulated enzymes PEPS, PPDK and PK represents a novel way of controlling the interconversion of phosphoenolpyruvate and pyruvate in the reversible EMP pathway, allowing short-term and long-term adaptation to different trophic conditions. Comparative genomic analyses indicate the coexistence of PEPS, PPDK and PK in other Archaea as well, suggesting a similar regulation of the carbohydrate metabolism in these organisms.


Human cytomegalovirus (HCMV) immediate-early enhancer/promoter specificity during embryogenesis defines target tissues of congenital HCMV infection.
Congenital human cytomegalovirus (HCMV) infection is a common cause of deafness and neurological disabilities. Many aspects of this prenatal infection, including which cell types are infected and how infection proceeds, are poorly understood. Transcription of HCMV immediate-early (IE) genes is required for expression of all other HCMV genes and is dependent on host cell transcription factors. Cell type-specific differences in levels of IE transcription are believed to underlie differences in infection permissivity. However, DNA transfection experiments have paradoxically suggested that the HCMV major IE enhancer/promoter is a broadly active transcriptional element with little cell type specificity. In contrast, we show here that expression of a lacZ gene driven by the HCMV major IE enhancer/promoter -524 to +13 segment is restricted in transgenic mouse embryos to sites that correlate with known sites of congenital HCMV infection in human fetuses. This finding suggests that the IE enhancer/promoter is a major determinant of HCMV infection sites in humans and that transcription factors responsible for its regulation are cell type-specifically conserved between humans and mice. The lacZ expression patterns of these transgenic embryos yield insight into congenital HCMV pathogenesis by providing a spatiotemporal map of the sets of vascular, neural, and epithelial cells that are likely targets of infection. These transgenic mice may constitute a useful model system for investigating IE enhancer/promoter regulation in vivo and for identifying factors that modulate active and latent HCMV infections in humans.


Quinolinic alkaloids from Galipea longiflora Krause suppress production of proinflammatory cytokines in vitro and control inflammation in vivo upon Leishmania infection in mice.
An antileishmanial activity of quinolinic alkaloids from Galipea longiflora Krause, known as Evanta, has been demonstrated. We have previously shown that, apart from its leishmanicidal effect, in vitro pretreatment of spleen cells with an alkaloid extract of Evanta (AEE) interfered with the proliferation and interferon-γ production in lymphocytes polyclonally activated either with concanavalin A or anti-CD3. In the present study, we investigated if AEE could interfere with antigen-specific lymphocyte activation. We found that in vitro and in vivo treatment reduced recall lymphocyte responses, as measured by IFN-γ production (55% and 63% reduction compared to untreated cells, respectively). Apart from IFN-γ, the production of IL-12 and TNF was also suppressed. No effects were observed for meglumine antimoniate (SbV), the conventional drug used to treat leishmaniasis. When mice infected with Leishmania braziliensis promastigotes in the hind footpad were treated with AEE, the dynamics of the infection changed and the footpath thickness was efficiently controlled. The parasite load was also reduced but to a lesser extent than upon treatment with SbV. Combined treatment efficiently controlled both the thickness and parasite load as smaller lesions during the entire course of the infection were seen in the mice treated with AEE plus SbV compared with AEE or SbV alone. We discuss the benefits of combined administration of AEE plus SbV.


Ten-year Nationwide Population-based Survey on the Characteristics of Children with Henoch-Schӧnlein Purpura in Korea.
Henoch-Schӧnlein purpura (HSP) is a common vasculitis of childhood. Though HSP is usually self-limiting, severe complications can occur. The management for this condition has not been established yet. Thus, this nationwide study aimed at investigating epidemiological characteristics of children with HSP in Korea. The patterns of clinical practice with regard to the complications of the condition were also investigated. This is a national population-based study that used the National Health Insurance Database. Children below 18 years who were diagnosed with HSP in Korea between 2006 and 2015 were enrolled. Data, such as age, sex, yearly and monthly distribution of HSP, hospitalization, re-hospitalization, comorbidities, and interventions were obtained. The use of steroids was also analyzed. A total of 56,841 children were enrolled. The annual incidence of HSP was 55.9 per 100,000 children. The peak age was 5 years. Spring was the most prevalent season. Sex (male) and young age (< 9 years) were risk factors of hospitalization. Younger children were more likely to be re-hospitalized and suspected with intussusception, arthritis, and nephritis. Only 4 children received laparotomy. In total, 57% were managed with steroids, and mean durations of medication were 4-5 days. Children who were hospitalized and those with comorbidities used steroids more frequently (P < 0.001). The annual incidence of HSP is 55.9 per 100,000 children which is higher in Korea than that in other countries. Younger children can have a more severe clinical course. This nationwide survey provides valuable information to understand HSP in children and to inspire further research on HSP.


MOF membrane synthesis in the confined space of a vertically aligned LDH network.
MOF membranes have gained widespread attention due to their unprecedented gas separation performance. Relying on physical interactions, we successfully deposited MOF seeds on a substrate modified with a network of vertically aligned LDH walls before secondary growth of the MOF layer. ZIF-8 membranes thus prepared show considerable H2 permeance with high H2-CH4 selectivity. This approach is in general suitable for the deposition of nanoparticles on solid surface and their subsequent growth into a dense layer.


Local rotational symmetry in the packing of uniform spheres.
Local rotational symmetry (LRS) of a particulate system is important for understanding its structure and phase transition. However, how to properly characterize LRS for this system is still a challenge as the system normally includes both ordered and disordered local structures. Herein, based on the so-called common neighbour subcluster (CNS), we proposed a method to characterize the LRS of uniform spheres packings with the packing fraction ρ ranging within 0.20 and 0.74. It was found that different fold LRSs coexist in most packings, and their maximum degree increases at ρ < 0.64, except for the 2-fold LRS held by 6-sphere CNS that continuously increases to form the fcc crystal at ρ = 0.74. The overall LRS involving all the CNSs monotonically increases with two critical changes at ρ = (0.35-0.40) and 0.64; the evolution of individual LRSs held by specific CNS groups critically changes at ρ ≈ (0.35-0.40), 0.50, 0.55-0.60, and 0.64. The physics corresponding to these critical changes has also been discussed. The findings will significantly enrich the understanding of the structural symmetry of materials including atoms and particles.


Ocean acidification refugia in variable environments.
Climate change refugia in the terrestrial biosphere are areas where species are protected from global environmental change and arise from natural heterogeneity in landscapes and climate. Within the marine realm, ocean acidification, or the global decline in seawater pH, remains a pervasive threat to organisms and ecosystems. Natural variability in seawater carbon dioxide (CO2 ) chemistry, however, presents an opportunity to identify ocean acidification refugia (OAR) for marine species. Here, we review the literature to examine the impacts of variable CO2 chemistry on biological responses to ocean acidification and develop a framework of definitions and criteria that connects current OAR research to management goals. Under the concept of managing vulnerability, the most likely mechanisms by which OAR can mitigate ocean acidification impacts are by reducing exposure to harmful conditions or enhancing adaptive capacity. While local management options, such as OAR, show some promise, they present unique challenges, and reducing global anthropogenic CO2 emissions must remain a priority.


Natural history of relapsed myeloma, refractory to immunomodulatory drugs and proteasome inhibitors: a multicenter IMWG study.
Introduction of new myeloma therapies offers new options for patients refractory to immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs). In this multicenter study, patients with relapsed multiple myeloma, who have received at least three prior lines of therapy, are refractory to both an IMiD (lenalidomide or pomalidomide) and a PI (bortezomib or carfilzomib), and have been exposed to an alkylating agent were identified. The time patients met the above criteria was defined as time zero (T0). Five hundred and forty-three patients diagnosed between 2006 and 2014 were enrolled in this study. Median age at T0 was 62 years (range 31-87); 61% were males. The median duration between diagnosis and T0 was 3.1 years. The median number of lines of therapy before T0 was 4 (range 3-13). The median overall survival (OS) from T0 for the entire cohort was 13 (95% confidence interval (CI) 11, 15) months. At least one regimen recorded after T0 in 462 (85%) patients, with a median (95% CI) progression-free survival and OS from T0 of 5 (4, 6), and 15.2 (13, 17) months, respectively. The study provides the expected outcome of relapsed multiple myeloma that is refractory to a PI and an IMiD, a benchmark for comparison of new therapies being evaluated.


Dose-Optimized Computed Tomography for Screening and Follow-Up of Solid Pulmonary Nodules in Obesity: A Phantom Study.
To determine the lowest CT radiation dose-level at maintained image-quality and high sensitivity for detection of pulmonary-nodules in obesity. Single-energy CT with tin-filtration was performed in a chest-phantom with solid pulmonary-nodules simulating over-weight and obesity. CTDIvol of the standard-protocol was 0.41 mGy, subsequent scans were obtained at 1/2 and 1/4 dose-levels. Images were reconstructed using FBP and advanced-modeled iterative reconstruction (ADMIRE). Noise, image-quality, and sensitivity for nodule-detection were assessed. Noise was significantly reduced with ADMIRE (standard-dose: 73%; 1/2 dose: 73%; 1/4 dose: 71.2%; p < 0.001) compared to FBP. Image-quality was diagnostic for all images reconstructed with ADMIRE5. Sensitivity for nodule-detection was 100% at 1/2 and 1/4 dose-level for the phantom simulating over-weight and 97.37% (1/2 dose-level) and 81.58% (1/4 dose-level) for the phantom simulating obesity using ADMIRE5. In conclusion, single-energy CT with tin-filtration and ADMIRE shows potential for dose reduction in a phantom experiment down to 0.1 mGy in over-weight and 0.21 mGy obese subjects, while image quality and sensitivity for detection of solid pulmonary nodules remains high.


Transcriptomics and proteomics analyses of the PACAP38 influenced ischemic brain in permanent middle cerebral artery occlusion model mice.
The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) is considered to be a potential therapeutic agent for prevention of cerebral ischemia. Ischemia is a most common cause of death after heart attack and cancer causing major negative social and economic consequences. This study was designed to investigate the effect of PACAP38 injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with corresponding SHAM control that used 0.9% saline injection. Ischemic and non-ischemic brain tissues were sampled at 6 and 24 hours post-treatment. Following behavioral analyses to confirm whether the ischemia has occurred, we investigated the genome-wide changes in gene and protein expression using DNA microarray chip (4x44K, Agilent) and two-dimensional gel electrophoresis (2-DGE) coupled with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), respectively. Western blotting and immunofluorescent staining were also used to further examine the identified protein factor. Our results revealed numerous changes in the transcriptome of ischemic hemisphere (ipsilateral) treated with PACAP38 compared to the saline-injected SHAM control hemisphere (contralateral). Previously known (such as the interleukin family) and novel (Gabra6, Crtam) genes were identified under PACAP influence. In parallel, 2-DGE analysis revealed a highly expressed protein spot in the ischemic hemisphere that was identified as dihydropyrimidinase-related protein 2 (DPYL2). The DPYL2, also known as Crmp2, is a marker for the axonal growth and nerve development. Interestingly, PACAP treatment slightly increased its abundance (by 2-DGE and immunostaining) at 6 h but not at 24 h in the ischemic hemisphere, suggesting PACAP activates neuronal defense mechanism early on. This study provides a detailed inventory of PACAP influenced gene expressions and protein targets in mice ischemic brain, and suggests new targets for thereaupetic interventions.


Scleral spur and ciliary muscle in man and monkey.
The development of the human scleral spur and the role of the scleral spur in human and monkey eyes were studied by measuring the height of the scleral spur, the thickness of the uveal meshwork and the thickness of the longitudinal ciliary muscle. In an attempt to study how the tension of the ciliary muscle is transmitted to the inner wall of the Schlemm's canal, interconnections within the trabecular meshwork were also studied. The results indicate that after 40 weeks of gestation there is little or no further change with aging in the height of the scleral spur but there is a change in shape. The scleral spur is much less developed in monkey eyes than in human eyes. The corneoscleral meshwork predominates over the uveal meshwork in most human eyes while in monkey eyes the situation is the opposite. In man the thickness of the meridional part of the ciliary muscle attached to the scleral spur varies greatly in eyes with a well developed scleral spur. Interconnecting trabecular beams composed of elastic-like fiber were observed in the uveal and corneoscleral meshwork, as well as in the juxtacanalicular meshwork, extending to the cells of the inner wall of the Schlemm's canal. These findings and the dense structure of the scleral spur suggest that in monkey eyes, and at least in some human eyes, contraction of the ciliary muscle causes unfolding of the trabecular meshwork, not so much through the movement of the scleral spur as by movement of the interconnecting trabecular beams and fibers. One important role of the scleral spur is probably to keep the corneoscleral meshwork open when the ciliary muscle relaxes, and another is to enable inward-forward movement of the circular part of the ciliary muscle by pulling the posterior tip of the ciliary muscle anteriorly when the ciliary muscle contracts. A rigid scleral spur is an advantage for these two functions.


A Bayesian network model for integrative river rehabilitation planning and management.
As rehabilitation of previously channelized rivers becomes more common worldwide, flexible integrative modeling tools are needed to help predict the morphological, hydraulic, economic, and ecological consequences of the rehabilitation activities. Such predictions can provide the basis for planning and long-term management efforts that attempt to balance the diverse interests of river system stakeholders. We have previously reported on a variety of modeling methods and decision support concepts that can assist with various aspects of the river rehabilitation process. Here, we bring all of these tools together into a probability network model that links management actions, through morphological and hydraulic changes, to the ultimate ecological and economic consequences. Although our model uses a causal graph representation common to Bayesian networks, we do not limit ourselves to discrete-valued nodes or conditional Gaussian distributions as required by most Bayesian network implementations. This precludes us from carrying out easy probabilistic inference but gives us the advantages of functional and distributional flexibility and enhanced predictive accuracy, which we believe to be more important in most environmental management applications. We exemplify model application to a large, recently completed rehabilitation project in Switzerland.


Abortion Surveillance - United States, 2012.
Since 1969, CDC has conducted abortion surveillance to document the number and characteristics of women obtaining legal induced abortions in the United States. 2012. Each year, CDC requests abortion data from the central health agencies of 52 reporting areas (the 50 states, the District of Columbia, and New York City). The reporting areas provide this information voluntarily. For 2012, data were received from 49 reporting areas. For trend analysis, abortion data were evaluated from 47 areas that reported data every year during 2003-2012. Census and natality data, respectively, were used to calculate abortion rates (number of abortions per 1,000 women) and ratios (number of abortions per 1,000 live births). A total of 699,202 abortions were reported to CDC for 2012. Of these abortions, 98.4% were from the 47 reporting areas that provided data every year during 2003-2012. Among these same 47 reporting areas, the abortion rate for 2012 was 13.2 abortions per 1,000 women aged 15-44 years, and the abortion ratio was 210 abortions per 1,000 live births. From 2011 to 2012, the total number and ratio of reported abortions decreased 4% and the abortion rate decreased 5%. From 2003 to 2012, the total number, rate, and ratio of reported abortions decreased 17%, 18%, and 14%, respectively, and reached their lowest level in 2012 for the entire period of analysis (2003-2012). In 2012 and throughout the period of analysis, women in their 20s accounted for the majority of abortions and had the highest abortion rates; women in their 30s and older accounted for a much smaller percentage of abortions and had lower abortion rates. In 2012, women aged 20-24 and 25-29 years accounted for 32.8% and 25.4% of all abortions, respectively, and had abortion rates of 23.3 and 18.9 abortions per 1,000 women aged 20-24 and 25-29 years, respectively. In contrast, women aged 30-34, 35-39, and ≥40 years accounted for 16.4%, 9.1%, and 3.7% of all abortions, respectively, and had abortion rates of 12.4, 7.3, and 2.8 abortions per 1,000 women aged 30-34 years, 35-39 years, and ≥40 years, respectively. Throughout the period of analysis, abortion rates decreased among women aged 20-24, 25-29, and 30-34 years by 24%, 18%, and 10%, respectively, whereas they increased among women aged ≥40 years by 8%. In 2012, adolescents aged <15 and 15-19 years accounted for 0.4% and 12.2% of all abortions, respectively, and had abortion rates of 0.8 and 9.2 abortions per 1,000 adolescents aged <15 and 15-19 years, respectively. From 2003 to 2012, the percentage of abortions accounted for by adolescents aged 15-19 years decreased 27% and their abortion rate decreased 40%. These decreases were greater than the decreases for women in any older age group. In contrast to the percentage distribution of abortions and abortion rates by age, abortion ratios in 2012 and throughout the entire period of analysis were highest among adolescents aged ≤19 years and lowest among women aged 30-39 years. Abortion ratios decreased from 2003 to 2012 for women in all age groups. In 2012, the majority (65.8%) of abortions were performed by ≤8 weeks' gestation, and nearly all (91.4%) were performed by ≤13 weeks' gestation. Few abortions (7.2%) were performed between 14-20 weeks' gestation or at ≥21 weeks' gestation (1.3%). From 2003 to 2012, the percentage of all abortions performed at ≤8 weeks' gestation increased 7%; the percentage performed at >13 weeks remained consistently low (≤9.0%). In 2012, among the 40 reporting areas that included medical (nonsurgical) abortion on their reporting form, a total of 69.4% of abortions were performed by curettage at ≤13 weeks' gestation, 20.8% were performed by early medical abortion (a nonsurgical abortion at ≤8 weeks' gestation), and 8.7% were performed by curettage at >13 weeks' gestation; all other methods were uncommon. Among abortions performed at ≤8 weeks' gestation that were eligible on the basis of gestational age for early medical abortion, 30.8% were completed by this method. The percentage of abortions reported as early medical abortions increased 10% from 2011 to 2012. Deaths of women associated with complications from abortions for 2012 are being investigated as part of CDC's Pregnancy Mortality Surveillance System. In 2011, the most recent year for which data were available, two women were identified to have died as a result of complications from known legal induced abortions. No reported deaths were associated with known illegal induced abortions. Among the 47 areas that reported data every year during 2003-2012, the notable decreases that occurred during 2008-2011 in the total number, rate, and ratio of reported abortions continued from 2011 to 2012 and resulted in historic lows for all three measures of abortion. The data in this report can help to identify groups of women at greatest risk for abortion and can be used to guide and evaluate prevention efforts. Because unintended pregnancy is the major contributor to abortion, and unintended pregnancies are rare among women who use the most effective methods of contraception, increasing access to and use of these methods can help further reduce the number of unintended pregnancies, and therefore abortions, performed in the United States.


A Circle Has No End: Role of Cyclic Topology and Accompanying Structural Reorganization on the Hole Distribution in Cyclic and Linear Poly-p-phenylene Molecular Wires.
π-Conjugated organic oligomers/polymers hold great promise as long-range charge-transfer materials for modern photovoltaic applications. However, a set of criteria for the rational design of functional materials is not yet available, in part because of a lack of understanding of charge distribution in extended π-conjugated systems of different topologies, and concomitant effects on redox and optical properties. Herein we demonstrate the role of cyclic versus linear topology in controlling the redox/optical properties and hole distribution in poly-p-phenylenes (PPs) with the aid of experiment, computation, and our recently developed multistate parabolic model (MPM). It is unequivocally shown that the hole distribution in both cyclic and linear poly-p-phenylene (n ≥ 7) cation radicals is limited to seven p-phenylene units, despite the very different topologies. However, the effect of topology is evidenced in the very different trends in oxidation potentials of cyclic versus linear PPs, which are shown to originate largely from the geometrical distortion of individual p-phenylene units in cyclic PPs. The presence of additional pairwise electronic coupling element in cyclic PPs, absent in linear PPs, plays a significant role only in smaller cyclic PP5 and PP6. This study provides a detailed conceptual description of cyclic and linear poly-p-phenylene cation radicals and demonstrates the versatility and predictive power of MPM, an important new tool for the design and synthesis of novel and efficient charge-transfer materials for molecular electronics and photovoltaic applications, an area of widespread interest.


Group 6 transition metal dichalcogenide nanomaterials: synthesis, applications and future perspectives.
Group 6 transition metal dichalcogenides (G6-TMDs), most notably MoS2, MoSe2, MoTe2, WS2 and WSe2, constitute an important class of materials with a layered crystal structure. Various types of G6-TMD nanomaterials, such as nanosheets, nanotubes and quantum dot nano-objects and flower-like nanostructures, have been synthesized. High thermodynamic stability under ambient conditions, even in atomically thin form, made nanosheets of these inorganic semiconductors a valuable asset in the existing library of two-dimensional (2D) materials, along with the well-known semimetallic graphene and insulating hexagonal boron nitride. G6-TMDs generally possess an appropriate bandgap (1-2 eV) which is tunable by size and dimensionality and changes from indirect to direct in monolayer nanosheets, intriguing for (opto)electronic, sensing, and solar energy harvesting applications. Moreover, rich intercalation chemistry and abundance of catalytically active edge sites make them promising for fabrication of novel energy storage devices and advanced catalysts. In this review, we provide an overview on all aspects of the basic science, physicochemical properties and characterization techniques as well as all existing production methods and applications of G6-TMD nanomaterials in a comprehensive yet concise treatment. Particular emphasis is placed on establishing a linkage between the features of production methods and the specific needs of rapidly growing applications of G6-TMDs to develop a production-application selection guide. Based on this selection guide, a framework is suggested for future research on how to bridge existing knowledge gaps and improve current production methods towards technological application of G6-TMD nanomaterials.


Interplay of the PtsN (EIIA(Ntr)) protein of Pseudomonas putida with its target sensor kinase KdpD.
The nitrogen phosphotransferase system (PTS(Ntr) ) of Pseudomonas putida is a multi-component regulatory device that participates in controlling a variety of physiological processes in a post-translational fashion. A general survey of genes regulated by PtsN exposed transcription of the kdpFABC operon is most conspicuously affected. Measurements of kdpFp promoter activity in different pts mutants showed that PtsN is responsible for repression of kdpFABC transcription. This effect could be assigned mainly to PtsN∼P, depending on the external K(+) concentration. Bacterial two-hybrid assays demonstrated that kdpFp regulation is implemented through direct interaction of the PtsN protein with the sensor kinase KdpD of the KdpD/KdpE two-component system. Interaction between KdpD and PtsN was detectable with a PtsN variant that imitates the non-phosphorylated form as well as with a PtsN type mimicking the phosphorylated form of PtsN. These results raise a regulatory scenario in which the Kdp system is regulated by the action of PtsN through direct interaction with the sensor kinase KdpD, and the outcome of such an interaction depends on the phosphorylation state of PtsN as well as on the external K(+) concentration.


Aorto-atrial fistula formation and closure: a systematic review.
Blood flow between the aorta and atrium is a rare but complex pathological condition, also known as aorto-atrial fistula (AAF). The exact incidence of this condition is unknown, as are the major precipitating factors and best treatment options. We carried out a systematic review of the available case report literature reporting AAF. We systematically reviewed literature on AAF formation and closure. Separate Medline (PubMed), EMBASE, and Cochrane database queries were performed. The following MESH headings were used: atrium, ventricle, fistula, cardiac, shunts, aortic, aorto-atrial tunnels and coronary cameral fistula. All papers were considered for analysis irrespective of their quality, or the journal in which they were published. Fistula formation from the ascending aorta to the atria occurred more often in the right atrium compared to the left. Endocarditis was the major cause of AAF formation, whilst congenital causes were responsible for nearly 12%. In a number of cases fistula formation occurred secondary to cardiac surgery, whilst chest traumas were a relatively rare cause of AAF. Correction via an open surgical approach occurred in 73.5% of cases, whilst percutaneous intervention was utilised in 10% of patients. In 74.3% of all studied cases the fistula repair was successful and patients survived the procedures. In 14.7% of the cases patients did not survive. Similar outcomes were observed between percutaneous and surgical interventions. Data from larger populations with AAF is lacking, meaning that specific data regarding incidence and prevalence does currently not exist.


The incidence of consecutive manifestations in Von Hippel-Lindau disease.
Von Hippel-Lindau (VHL) disease is an autosomal dominant rare tumor syndrome characterized by high penetrance. VHL mutation carriers develop numerous manifestations in multiple organs during life. The natural course of development of new and growth of existing VHL-related manifestations is still unclear. In this study we aimed to gain insight into the development of subsequent manifestations in VHL disease. We retrospectively scored each new VHL-related manifestation as detected by standard follow-up (retina, central nervous system, kidneys and pancreas, excluding adrenal and endolymfatic sac manifestations) in 75 VHL mutation carriers. The Kaplan-Meier method was used to plot the cumulative proportions of all consecutive manifestations in each organ against age. The cumulative average number of manifestations in all organs during life was calculated by summating these cumulative proportions. Poisson model parameters were used to calculate average time to the detection of consecutive VHL manifestations in each organ. Consecutive VHL-related kidney and retina manifestations during life occur linearly according to Poisson distribution model. The total number of VHL manifestations rises linearly, with an average of seven VHL-related lesions at age 60 years. The incidence of consecutive VHL-related manifestations is constant during life in VHL mutation carriers. Our data is consistent with the notion that somatic inactivation of the remaining allele (Knudson's "two-hit" hypothesis) is the determining factor in developing new VHL-related manifestations.


Quantification of viral DNA and liver enzymes in plasma improves early diagnosis and management of herpes simplex virus hepatitis.
Herpes simplex virus (HSV) hepatitis is a rare and potential life-threatening disease. The diagnosis of HSV hepatitis is hampered by its indifferent clinical presentation, which necessitates confirmatory laboratory data to identify HSV in the affected liver. However, liver biopsies are often contraindicated in the context of coagulopathy, are prone to sampling errors and have low sensitivity in mild HSV hepatitis cases. There is an unmet need for less invasive diagnostic tools. The diagnostic and therapeutic value of HSV DNA load and liver enzyme level kinetics was determined in five patients with HSV hepatitis and twenty disease controls with HSV-DNAemia without hepatitis. At time of hospitalization, patients with HSV hepatitis had a higher median (± interquartile range) HSV DNA load (6.0 × 10(6) ± 1.2 × 10(9)) compared to disease controls (171 ± 2845). Viral DNA load correlated with liver transaminase levels and disease severity. Antiviral treatment led to rapid decline of HSV DNA load and improvement of liver function of patients with HSV hepatitis. The data advocate the prompt and consecutive quantification of the HSV DNA load and liver enzyme levels in plasma of patients suspected of HSV hepatitis as well as those under antiviral treatment.


Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics.
We performed a metagenomic survey (6.6 Gbp of 454 sequence data) of Southern Ocean (SO) microorganisms during the austral summer of 2007-2008, examining the genomic signatures of communities across a latitudinal transect from Hobart (44°S) to the Mertz Glacier, Antarctica (67°S). Operational taxonomic units (OTUs) of the SAR11 and SAR116 clades and the cyanobacterial genera Prochlorococcus and Synechococcus were strongly overrepresented north of the Polar Front (PF). Conversely, OTUs of the Gammaproteobacterial Sulfur Oxidizer-EOSA-1 (GSO-EOSA-1) complex, the phyla Bacteroidetes and Verrucomicrobia and order Rhodobacterales were characteristic of waters south of the PF. Functions enriched south of the PF included a range of transporters, sulfur reduction and histidine degradation to glutamate, while branched-chain amino acid transport, nucleic acid biosynthesis and methionine salvage were overrepresented north of the PF. The taxonomic and functional characteristics suggested a shift of primary production from cyanobacteria in the north to eukaryotic phytoplankton in the south, and reflected the different trophic statuses of the two regions. The study provides a new level of understanding about SO microbial communities, describing the contrasting taxonomic and functional characteristics of microbial assemblages either side of the PF.


Differences in subjective response to alcohol by gender, family history, heavy episodic drinking, and cigarette use: refining and broadening the scope of measurement.
Subjective response to alcohol (SR) has been shown to differ by gender, family history of alcoholism, drinking status, and cigarette smoking status. However, the requisite statistical basis for making mean-level comparisons (scalar measurement invariance; MI) has not been established for any SR measure, making it impossible to determine whether observed differences reflect true differences or measurement bias. Secondary data analyses were conducted to evaluate (a) MI of the Subjective Effects of Alcohol Scale (SEAS) by gender, family history, heavy drinking status, and cigarette smoking status using multigroup confirmatory factor analysis; and (b) the impact of these group-level variables on SR using multivariate general linear modeling. A central strength, the SEAS assesses novel high arousal negative (HIGH-; e.g., aggressive) and low arousal positive effects (LOW+; e.g., relaxed) in addition to commonly assessed high arousal positive [HIGH+; e.g., sociable] and low arousal negative effects [LOW-; e.g., woozy]). A total of 215 young adults reported on SR during a placebo-controlled alcohol administration study in a simulated bar setting (target blood alcohol concentration = .08%). Scalar MI was achieved for each group. After consuming alcohol, family history-positive individuals reported stronger HIGH- effects and female smokers reported weaker LOW+ effects than their counterparts. Heavy episodic drinkers and family history-positive females reported weaker LOW- effects than their counterparts. The SEAS permits meaningful SR comparisons within several important groups. SR differences largely were observed on the novel SEAS subscales, highlighting the importance of assessing a full range of SR.


Is Rumination a Risk and a Protective Factor?
High trait positive affect (PA) protects against depressive symptoms through cognitive responses such as rumination. However, how rumination in response to positive emotions (positive rumination) protects against depressive symptoms while rumination in response to negative emotions (brooding) predicts depressive symptoms is poorly understood. We hypothesized that (a) positive rumination and brooding represent a shared cognitive process of affect amplification on distinct affective content and (b) less brooding and greater positive rumination would distinctly mediate greater trait PA in predicting fewer depressive symptoms. Our prospective design among 321 adults first compared three confirmatory factor analysis models of the relationship between brooding and positive rumination. We then utilized structural equation modeling to examine whether brooding and positive rumination mediated the relationship between trait PA and depressive symptoms, controlling for baseline depressive symptoms, trait negative affect (NA), and the distinct effects of each mediator. Results supported a conceptualization of brooding and positive rumination as distinct but related constructs, represented as a common process of affect amplification to explain how rumination may amplify resilience or risk in predicting depressive symptoms (χ = 195.07, Δχ = 8.78, p < .001, CFI = .91, RMSEA = .07). Furthermore, positive rumination and brooding were distinctly predicted by trait PA, suggesting that trait PA exerts distinct effects on protective and risk forms of rumination. Less brooding mediated the relationship between greater trait PA and fewer depressive symptoms (β = -.04, p = .012), but positive rumination did not (β = .02, p = .517). Rumination may represent a protective and a risk factor, which may better enable individuals who brood to redirect their rumination on positive content and thereby reduce their risk of depressive symptoms.


Tracking a sample of patients lost to follow-up has a major impact on understanding determinants of survival in HIV-infected patients on antiretroviral therapy in Africa.
To date, data regarding the determinants of mortality in HIV-infected patients starting antiretroviral therapy (ART) in Africa have been primarily derived from routine clinical care settings practicing the public health approach. Losses to follow-up, however, are high in these settings and may lead to bias in understanding the determinants of mortality. We evaluated HIV-infected adults initiating ART between January 1, 2004 and September 30th, 2007 in an ART clinic in southwestern Uganda. Clinical and demographic characteristics were obtained through routine clinical care. In evaluating determinants of mortality, a 'naïve' analysis used only deaths known through routine processes. A 'sample-corrected' approach incorporated, through probability weights, outcomes from a representative sample of patients lost to follow-up whose vital status was ascertained through tracking in the community. In 3,628 patients followed for up to 3.75 years after ART initiation, the 'naïve' approach identified male sex and lower pre-ART CD4 count as independent determinants of mortality. The 'sample-corrected' approach found lower pre-ART CD4 count, older age, lower weight and calendar year of ART initiation, but not male sex, to be independent determinants of mortality. Analyses to identify determinants of mortality in HIV-infected patients on ART in Africa that do not account for losses to follow-up can identify spurious associations and miss actual relationships - both with the potential to mislead public health efforts. A sampling-based approach to account for losses to follow-up represents a feasible and potentially scalable method to strengthen the evidence available for implementation of ART delivery in Africa.


Benchmark simulation models, quo vadis?
As the work of the IWA Task Group on Benchmarking of Control Strategies for wastewater treatment plants (WWTPs) is coming to an end, it is essential to disseminate the knowledge gained. For this reason, all authors of the IWA Scientific and Technical Report on benchmarking have come together to provide their insights, highlighting areas where knowledge may still be deficient and where new opportunities are emerging, and to propose potential avenues for future development and application of the general benchmarking framework and its associated tools. The paper focuses on the topics of temporal and spatial extension, process modifications within the WWTP, the realism of models, control strategy extensions and the potential for new evaluation tools within the existing benchmark system. We find that there are major opportunities for application within all of these areas, either from existing work already being done within the context of the benchmarking simulation models (BSMs) or applicable work in the wider literature. Of key importance is increasing capability, usability and transparency of the BSM package while avoiding unnecessary complexity.


Invasive histiocytoma in the ear canal of a dog.
Cutaneous histiocytomas (CH) are derived from epidermal Langerhans cells. Single CH are generally associated with a good prognosis in dogs because most undergo spontaneous remission. However, aggressive behaviour and lymph node metastasis have been reported in a small number of dogs with single CH. To describe the clinical presentation, treatment and disease progression of an aggressive CH located in the ear canal of a dog. An 8-year-old intact male Rottweiler dog. A unilateral ear canal mass was identified as a CH on routine haematoxylin and eosin stained samples. The diagnosis was confirmed by the demonstration of markers associated with Langerhans cells (Iba-1, E-cadherin and CD18) and the absence of markers associated with B cells (CD79a, CD20, Pax5), T cells (CD3), plasma cells (Mum-1) and macrophages (CD11d, CD204). A total ear canal ablation was performed, but tumour cells extended throughout the horizontal canal and to the deep surgical margin. Due to the locally invasive nature of the mass and incomplete excision, adjunctive chemotherapy with CCNU was pursued. No measurable local disease was appreciable at the time of the last treatment. At 250 days post-surgery the dog was euthanized owing to the development of multiple abdominal masses. No evidence of local tumour recurrence was noted. Although single CH are typically associated with benign behaviour, the mass in this dog demonstrated locally invasive behaviour. Cutaneous histiocytomas in the ear canals of dogs may represent a particularly aggressive variant of the condition.


Multiscale nuclear magnetic relaxation dispersion of complex liquids in bulk and confinement.
The nuclear magnetic relaxation dispersion (NMRD) technique consists of measurement of the magnetic-field dependence of the longitudinal nuclear-spin-lattice relaxation rate 1/T1. Usually, the acquisition of the NMRD profiles is made using a fast field cycling (FFC) NMR technique that varies the magnetic field and explores a very large range of Larmor frequencies (10 kHz < ω0/(2π) <40 MHz). This allows extensive explorations of the fluctuations to which nuclear spin relaxation is sensitive. The FFC technique thus offers opportunities on multiple scales of both time and distance for characterizing the molecular dynamics and transport properties of complex liquids in bulk or embedded in confined environments. This review presents the principles, theories and applications of NMRD for characterizing fundamental properties such as surface correlation times, diffusion coefficients and dynamical surface affinity (NMR wettability) for various confined liquids. The basic longitudinal and transverse relaxation equations are outlined for bulk liquids. The nuclear relaxation of a liquid confined in pores is considered in detail in order to find the biphasic fast exchange relations for a liquid at proximity of a solid surface. The physical-chemistry of liquids at solid surfaces induces striking differences between NMRD profiles of aprotic and protic (water) liquids embedded in calibrated porous disordered materials. A particular emphasis of this review concerns the extension of FFC NMR relaxation to industrial applications. For instance, it is shown that the FFC technique is sufficiently rapid for following the progressive setting of cement-based materials (plasters, cement pastes, concretes). The technique also allows studies of the dynamics of hydrocarbons in proximity of asphaltene nano-aggregates and macro-aggregates in heavy crude oils as a function of the concentration of asphaltenes. It also gives new information on the wettability of petroleum fluids (brine and oil) embedded in shale oil rocks. It is useful for understanding the relations and correlations between NMR relaxation times T1 and T2, diffusion coefficients D, and viscosity η of heavy crude oils. This is of particular importance for interpreting T1, T2, 2D T1-T2 and D-T2 correlation spectra that could be obtained down-hole, thus giving a valuable tool for investigating in situ the molecular dynamics of petroleum fluids. Another domain of interest concerns biological applications. This is of particular importance for studying the complex dynamical spectrum of a folded polymeric structure that may span many decades in frequency or time. A direct NMRD characterization of water diffusional dynamics is presented at the protein interface. NMR experiments using a shuttle technique give results well above the frequency range accessible via the FFC technique; examples of this show protein dynamics over a range from fast and localized motions to slow and delocalized collective motions involving the whole protein. This review ends by an interpretation of the origin of the proton magnetic field dependence of T1 for different biological tissues of animals; this includes a proposal for interpreting in vivo MRI data from human brain at variable magnetic fields, where the FFC relaxation analysis suggests that brain white-matter is distinct from grey-matter, in agreement with diffusion-weighted MRI imaging.


Early Social-Emotional Functioning and Public Health: The Relationship Between Kindergarten Social Competence and Future Wellness.
We examined whether kindergarten teachers' ratings of children's prosocial skills, an indicator of noncognitive ability at school entry, predict key adolescent and adult outcomes. Our goal was to determine unique associations over and above other important child, family, and contextual characteristics. Data came from the Fast Track study of low-socioeconomic status neighborhoods in 3 cities and 1 rural setting. We assessed associations between measured outcomes in kindergarten and outcomes 13 to 19 years later (1991-2000). Models included numerous control variables representing characteristics of the child, family, and context, enabling us to explore the unique contributions among predictors. We found statistically significant associations between measured social-emotional skills in kindergarten and key young adult outcomes across multiple domains of education, employment, criminal activity, substance use, and mental health. A kindergarten measure of social-emotional skills may be useful for assessing whether children are at risk for deficits in noncognitive skills later in life and, thus, help identify those in need of early intervention. These results demonstrate the relevance of noncognitive skills in development for personal and public health outcomes.


Randomized Controlled Trial of Urokinase versus Placebo for Nondraining Malignant Pleural Effusion.
Patients with malignant pleural effusion experience breathlessness, which is treated by drainage and pleurodesis. Incomplete drainage results in residual dyspnea and pleurodesis failure. Intrapleural fibrinolytics lyse septations within pleural fluid, improving drainage. To assess the effects of intrapleural urokinase on dyspnea and pleurodesis success in patients with nondraining malignant effusion. We conducted a prospective, double-blind, randomized trial. Patients with nondraining effusion were randomly allocated in a 1:1 ratio to intrapleural urokinase (100,000 IU, three doses, 12-hourly) or matched placebo. Co-primary outcome measures were dyspnea (average daily 100-mm visual analog scale scores over 28 d) and time to pleurodesis failure to 12 months. Secondary outcomes were survival, hospital length of stay, and radiographic change. A total of 71 subjects were randomized (36 received urokinase, 35 placebo) from 12 U.K. centers. The baseline characteristics were similar between the groups. There was no difference in mean dyspnea between groups (mean difference, 3.8 mm; 95% confidence interval [CI], -12 to 4.4 mm; P = 0.36). Pleurodesis failure rates were similar (urokinase, 13 of 35 [37%]; placebo, 11 of 34 [32%]; adjusted hazard ratio, 1.2; P = 0.65). Urokinase was associated with decreased effusion size visualized by chest radiography (adjusted relative improvement, -19%; 95% CI, -28 to -11%; P < 0.001), reduced hospital stay (1.6 d; 95% CI, 1.0 to 2.6; P = 0.049), and improved survival (69 vs. 48 d; P = 0.026). Use of intrapleural urokinase does not reduce dyspnea or improve pleurodesis success compared with placebo and cannot be recommended as an adjunct to pleurodesis. Other palliative treatments should be used. Improvements in hospital stay, radiographic appearance, and survival associated with urokinase require further evaluation. Clinical trial registered with ISRCTN (12852177) and EudraCT (2008-000586-26).


Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans.
Marine algae convert a substantial fraction of fixed carbon dioxide into various polysaccharides. Flavobacteriia that are specialized on algal polysaccharide degradation feature genomic clusters termed polysaccharide utilization loci (PULs). As knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia and obtained 400 PULs. Bioinformatic PUL annotations suggest usage of a large array of polysaccharides, including laminarin, α-glucans, and alginate as well as mannose-, fucose-, and xylose-rich substrates. Many of the PULs exhibit new genetic architectures and suggest substrates rarely described for marine environments. The isolates' PUL repertoires often differed considerably within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD-like transporter complexes. Respective protein trees revealed clustering according to polysaccharide specificities predicted by PUL annotations. Using the trees, we analyzed expression of SusC/D homologs in multiyear phytoplankton bloom-associated metaproteomes and found indications for profound changes in microbial utilization of laminarin, α-glucans, β-mannan, and sulfated xylan. We hence suggest the suitability of SusC/D-like transporter protein expression within heterotrophic bacteria as a proxy for the temporal utilization of discrete polysaccharides.


Design and other methodological considerations for the construction of human fetal and neonatal size and growth charts.
This paper discusses the features of study design and methodological considerations for constructing reference centile charts for attained size, growth, and velocity charts with a focus on human growth charts used during pregnancy. Recent systematic reviews of pregnancy dating, fetal size, and newborn size charts showed that many studies aimed at constructing charts are still conducted poorly. Important design features such as inclusion and exclusion criteria, ultrasound quality control measures, sample size determination, anthropometric evaluation, gestational age estimation, assessment of outliers, and chart presentation are seldom well addressed, considered, or reported. Many of these charts are in clinical use today and directly affect the identification of at-risk newborns that require treatment and nutritional strategies. This paper therefore reiterates some of the concepts previously identified as important for growth studies, focusing on considerations and concepts related to study design, sample size, and methodological considerations with an aim of obtaining valid reference or standard centile charts. We discuss some of the key issues and provide more details and practical examples based on our experiences from the INTERGROWTH-21st Project. We discuss the statistical methodology and analyses for cross-sectional studies and longitudinal studies in a separate article in this issue.


Infection and inflammation in induced sputum from preschool children with chronic airways diseases.
We hypothesized airway inflammation can be detected non-invasively by induced sputum (IS) or peripheral blood eosinophilia, and IS can detect bacterial and viral infection in preschool children with airway disease, with results comparable to broncho-alveolar lavage (BAL). Preschool children with cystic fibrosis, recurrent wheeze, or wet cough underwent IS with nebulized hypertonic saline, chest physiotherapy, and oropharyngeal suction. Samples were analyzed for inflammation by cytology and bacterial culture, viral detection by PCR. Results were compared to BAL and blood in a sub-group undergoing clinically indicated bronchoscopy. 64 children (median age 33 [7-76] months) underwent IS without adverse events. IS was obtained from 61/64. Twenty out of sixty-four underwent BAL and IS, no IS was obtained in 2/23. Thirteen out of twenty-one (62%) had matching bacteria and viruses, 4/21 had positive BAL bacterial growth with negative IS, and 3/21 had negative BAL growth with positive IS. 67% of sputum samples were processed for cytology, 46% had <80% squamous cells; the proportion of squamous cells reduced with increasing age (r = -0.55, P < 0.01). IS was significantly more neutrophilic and less eosinophilic than BAL; 2/21 IS samples contained eosinophils compared to 17/23 BAL. There was a positive correlation between blood and BAL eosinophilia (r = 0.75, P < 0.01). IS from preschool children can be used to assess infection. BAL and IS culture concurred in approximately two-thirds. However, inflammation was measureable in only one-third of IS samples and the cell differential was predominantly neutrophilic compared to BAL. Blood eosinophils may provide a better reflection of lower airway eosinophilia in this age group. Pediatr Pulmonol. 2016;51:778-786. © 2015 WileyPeriodicals, Inc.


Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants.
Celiac disease (CD) is a unique autoimmune disorder in which the genetic factors (DQ2/DQ8) and the environmental trigger (gluten) are known and necessary but not sufficient for its development. Other environmental components contributing to CD are poorly understood. Studies suggest that aspects of gluten intake might influence the risk of CD occurrence and timing of its onset, i.e., the amount and quality of ingested gluten, together with the pattern of infant feeding and the age at which gluten is introduced in the diet. In this study, we hypothesize that the intestinal microbiota as a whole rather than specific infections dictates the switch from tolerance to immune response in genetically susceptible individuals. Using a sample of infants genetically at risk of CD, we characterized the longitudinal changes in the microbial communities that colonize infants from birth to 24 months and the impact of two patterns of gluten introduction (early vs. late) on the gut microbiota and metabolome, and the switch from gluten tolerance to immune response, including onset of CD autoimmunity. We show that infants genetically susceptible to CD who are exposed to gluten early mount an immune response against gluten and develop CD autoimmunity more frequently than at-risk infants in which gluten exposure is delayed until 12 months of age. The data, while derived from a relatively small number of subjects, suggest differences between the developing microbiota of infants with genetic predisposition for CD and the microbiota from infants with a non-selected genetic background, with an overall lack of bacteria of the phylum Bacteriodetes along with a high abundance of Firmicutes and microbiota that do not resemble that of adults even at 2 years of age. Furthermore, metabolomics analysis reveals potential biomarkers for the prediction of CD. This study constitutes a definite proof-of-principle that these combined genomic and metabolomic approaches will be key to deciphering the role of the gut microbiota on CD onset.


Pregnancy, time to pregnancy and obstetric outcomes among female childhood cancer survivors: results of the DCOG LATER-VEVO study.
To evaluate pregnancy rates, time to pregnancy (TTP) and obstetric outcomes in female childhood cancer survivors (CCSs) and to identify specific diagnosis- and treatment-related factors associated with these outcomes. The study is part of the DCOG LATER-VEVO study, a nationwide multicenter cohort study evaluating fertility among long-term Dutch female CCSs. Data were collected by questionnaire. The current study included 1095 CCSs and 812 controls, consisting of sisters of CCSs and a random sample of women from the general population. Among the subgroup of women who ever had the desire to become pregnant, the chance of becoming pregnant was significantly lower for CCSs than controls (OR 0.5, 95%CI 0.4-0.8). Moreover, TTP was 1.1 times longer for CCSs compared to controls (p = 0.09) and was significantly longer in survivors of CNS and renal tumours. Overall, no differences were found between CCSs and controls regarding the probability of ever having had a miscarriage, still birth, or induced abortion. However, CCSs had a significantly increased risk of delivering preterm (OR 2.2, 95%CI 1.3-3.7) and delivering via caesarean section (OR 1.8, 95%CI 1.2-2.6). Treatment with lower abdominal/pelvic radiotherapy was strongly associated with several adverse obstetric outcomes. CCSs are less likely to have ever been pregnant. Among those who do become pregnant, certain subgroups of CCSs are at increased risk of longer TTP. Moreover, as pregnant CCSs, especially those treated with lower abdominal/pelvic radiotherapy, are more likely to develop various adverse obstetric outcomes, appropriate obstetric care is highly advocated.


40Ar/39Ar Age of the Lathrop Wells Volcanic Center, Yucca Mountain, Nevada.
Paleomagnetic and (40)Ar/(39)Ar analyses from the Lathrop Wells volcanic center, Nevada, indicate that two eruptive events have occurred there. The ages (136 +/- 8 and 141 +/- 9 thousand years ago) for these two events are analytically indistinguishable. The small angular difference (4.7 degrees ) between the paleomagnetic directions from these two events suggests they differ in age by only about 100 years. These ages are consistent with the chronology of the surficial geological units in the Yucca Mountain area. These results contradict earlier interpretations of the cinder-cone geomorphology and soil-profile data that suggest that at least five temporally discrete eruptive events occurred at Lathrop Wells approximately 20,000 years ago.


Health Service Impact from Mass Gatherings: A Systematic Literature Review.
During a mass gathering, some participants may receive health care for injuries or illnesses that occur during the event. In-event first responders provide initial assessment and management at the event. However, when further definitive care is required, municipal ambulance services provide additional assessment, treatment, and transport of participants to acute care settings, such as hospitals. The impact on both ambulance services and hospitals from mass-gathering events is the focus of this literature review. Aim This literature review aimed to develop an understanding of the impact of mass gatherings on local health services, specifically pertaining to in-event and external health services. This research used a systematic literature review methodology. Electronic databases were searched to find articles related to the aim of the review. Articles focused on mass-gathering health, provision of in-event health services, ambulance service transportation, and hospital utilization. Twenty-four studies were identified for inclusion in this review. These studies were all case-study-based and retrospective in design. The majority of studies (n=23) provided details of in-event first responder services. There was variation noted in reporting of the number and type of in-event health professional services at mass gatherings. All articles reported that patients were transported to hospital by the ambulance service. Only nine articles reported on patients presenting to hospital. However, details pertaining to the impact on ambulance and hospital services were not reported. There is minimal research focusing on the impact of mass gatherings on in-event and external health services, such as ambulance services and hospitals. A recommendation for future mass-gathering research and evaluation is to link patient-level data from in-event mass gatherings to external health services. This type of study design would provide information regarding the impact on health services from a mass gathering to more accurately inform future health planning for mass gatherings across the health care continuum. Ranse J , Hutton A , Keene T , Lenson S , Luther M , Bost N , Johnston ANB , Crilly J , Cannon M , Jones N , Hayes C , Burke B . Health service impact from mass gatherings: a systematic literature review. Prehosp Disaster Med. 2017;32(1):71-77.


Randomised controlled trials (RCTs) in sports injury research: authors-please report the compliance with the intervention.
In randomised controlled trials (RCTs) of interventions that aim to prevent sports injuries, the intention-to-treat principle is a recommended analysis method and one emphasised in the Consolidated Standards of Reporting Trials (CONSORT) statement that guides quality reporting of such trials. However, an important element of injury prevention trials-compliance with the intervention-is not always well-reported. The purpose of the present educational review was to describe the compliance during follow-up in eight large-scale sports injury trials and address compliance issues that surfaced. Then, we discuss how readers and researchers might consider interpreting results from intention-to-treat analyses depending on the observed compliance with the intervention. Data from seven different randomised trials and one experimental study were included in the present educational review. In the trials that used training programme as an intervention, we defined full compliance as having completed the programme within ±10% of the prescribed running distance (ProjectRun21 (PR21), RUNCLEVER, Start 2 Run) or time-spent-running in minutes (Groningen Novice Running (GRONORUN)) for each planned training session. In the trials using running shoes as the intervention, full compliance was defined as wearing the prescribed running shoe in all running sessions the participants completed during follow-up. In the trials that used a running programme intervention, the number of participants who had been fully compliant was 0 of 839 (0%) at 24-week follow-up in RUNCLEVER, 0 of 612 (0%) at 14-week follow-up in PR21, 12 of 56 (21%) at 4-week follow-up in Start 2 Run and 8 of 532 (1%) at 8-week follow-up in GRONORUN. In the trials using a shoe-related intervention, the numbers of participants who had been fully compliant at the end of follow-up were 207 of 304 (68%) in the 21 week trial, and 322 of 423 (76%), 521 of 577 (90%), 753 of 874 (86%) after 24-week follow-up in the other three trials, respectively. The proportion of runners compliant at the end of follow-up ranged from 0% to 21% in the trials using running programme as intervention and from 68% to 90% in the trials using running shoes as intervention. We encourage sports injury researchers to carefully assess and report the compliance with intervention in their articles, use appropriate analytical approaches and take compliance into account when drawing study conclusions. In studies with low compliance, G-estimation may be a useful analytical tool provided certain assumptions are met.


Synergistic Antimycobacterial Actions of Knowltonia vesicatoria (L.f) Sims.
Euclea natalensis A.DC., Knowltonia vesicatoria (L.f) Sims, and Pelargonium sidoides DC. are South African plants traditionally used to treat tuberculosis. Extracts from these plants were used in combination with isoniazid (INH) to investigate the possibility of synergy with respect to antimycobacterial activity. The ethanol extract of K. vesicatoria was subjected to fractionation to identify the active compounds. The activity of the Knowltonia extract remained superior to the fractions with a minimum inhibitory concentration (MIC) of 625.0 μg/mL against Mycobacterium smegmatis and an MIC of 50.00 μg/mL against M. tuberculosis. The K. vesicatoria extract was tested against two different drug-resistant strains of M. tuberculosis, which resulted in an MIC of 50.00 μg/mL on both strains. The combination of K. vesicatoria with INH exhibited the best synergistic antimycobacterial activity with a fractional inhibitory concentration index of 0.25 (a combined concentration of 6.28 μg/mL). A fifty percent inhibitory concentration of this combination against U937 cells was 121.0 μg/mL. Two compounds, stigmasta-5,23-dien-3-ol (1) and 5-(hydroxymethyl)furan-2(5H)-one (2), were isolated from K. vesicatoria as the first report of isolation for both compounds from this plant and the first report of antimycobacterial activity. Compound (1) was active against drug-sensitive M. tuberculosis with an MIC of 50.00 μg/mL.


Control of T lymphocyte morphology by the GTPase Rho.
Rho family GTPase regulation of the actin cytoskeleton governs a variety of cell responses. In this report, we have analyzed the role of the GTPase Rho in maintenance of the T lymphocyte actin cytoskeleton. Inactivation of the GTPase Rho in the human T lymphocytic cell line HPB-ALL does not inhibit constitutively high adhesion to the integrin beta1 substrate fibronectin. It did however result in the aberrant extension of finger-like dendritic processes on the substrates VCAM-1, Fn, and mAb specific to beta1 integrins. Time-lapse video microscopy demonstrated that C3 induced extensions were primarily the result of an altered pseudopod elongation rather than retraction. Once the stellate pseudopodia extended, none retracted, and cells became completely immobile. Filipodial structures were absent and the dendritic-like processes in C3 treated cells were rich in filamentous actin. Immunolocalization of RhoA in untreated HPB-ALL cells spreading on fibronectin demonstrated a diffuse staining pattern within the pseudopodia. In C3 treated cells, clusters of RhoA were pronounced and localized within the altered extensions. GTPase Rho is actively involved in the regulation of T lymphocyte morphology and motility.


Genetic variation in the interleukin-28B gene is not associated with fibrosis progression in patients with chronic hepatitis C and known date of infection.
Polymorphisms in the interleukin-28B (IL28B) region are associated with spontaneous and treatment-induced viral clearance in hepatitis C virus (HCV) infection. Nevertheless, it is unknown whether genetic variation at the IL28B locus influences the natural history of chronic HCV infection. Thus, we asked whether an association between IL28B polymorphisms and liver fibrosis progression existed. We studied 247 consecutive patients with chronic HCV, an accurate estimate of the date of infection, and a liver biopsy performed before any treatment. No patient had a history of alcohol abuse or coinfection with other viruses. We assessed the role of rs8099917 and rs12979860 polymorphisms and the effect of host and environmental factors on fibrosis progression. Blood transfusion (75%) was the main modality of infection. Median age at infection was 21 years, and median interval between infection and liver biopsy was 25 years. One hundred twenty-nine patients (52%) were infected by HCV-1, 74 (30%) by HCV-2, 34 (14%) by HCV-3, and 10 (4%) by HCV-4. Bridging fibrosis/cirrhosis (Ishak ≥ 4) was detected in 24% of patients. Age at infection had a marked effect on fibrosis progression by both a linear model and Cox proportional-hazard regression (P < 2E-16). A 12.1% increase in the hazard of advanced fibrosis was estimated for each additional year at infection, suggesting that this was the major explanatory variable in this cohort. Male gender (P < 0.05), HCV genotype 3 (P < 0.001) and steatosis (P < 0.05) were also associated with faster fibrosis progression. Conversely, the two IL28B polymorphisms had no impact on fibrosis progression. In HCV patients with a known date of infection, IL28B genotype was not associated with fibrosis progression rate or with the risk of developing advanced liver fibrosis.


Urine Culture on Admission Impacts Antibiotic Use and Length of Stay: A Retrospective Cohort Study.
OBJECTIVETo examine the impact of urine culture testing on day 1 of admission on inpatient antibiotic use and hospital length of stay (LOS).DESIGNWe performed a retrospective cohort study using a national dataset from 2009 to 2014.SETTINGThe study used data from 230 hospitals in the United States.PARTICIPANTSAdmissions for adults 18 years and older were included in this study. Hospitalizations were matched with coarsened exact matching by facility, patient age, gender, Medicare severity-diagnosis related group (MS-DRG), and 3 measures of disease severity.METHODSA multilevel Poisson model and a multilevel linear regression model were used to determine the impact of an admission urine culture on inpatient antibiotic use and LOS.RESULTSMatching produced a cohort of 88,481 patients (n=41,070 with a culture on day 1, n=47,411 without a culture). A urine culture on admission led to an increase in days of inpatient antibiotic use (incidence rate ratio, 1.26; P<.001) and resulted in an additional 36,607 days of inpatient antibiotic treatment. Urine culture on admission resulted in a 2.1% increase in LOS (P=.004). The predicted difference in bed days of care between admissions with and without a urine culture resulted in 6,071 additional bed days of care. The impact of urine culture testing varied by admitting diagnosis.CONCLUSIONSPatients with a urine culture sent on day 1 of hospital admission receive more days of antibiotics and have a longer hospital stay than patients who do not have a urine culture. Targeted interventions may reduce the potential harms associated with low-yield urine cultures on day 1.Infect Control Hosp Epidemiol 2018;39:547-554.


Radiotherapy Treatment plannINg study Guidelines (RATING): A framework for setting up and reporting on scientific treatment planning studies.
Radiotherapy treatment planning studies contribute significantly to advances and improvements in radiation treatment of cancer patients. They are a pivotal step to support and facilitate the introduction of novel techniques into clinical practice, or as a first step before clinical trials can be carried out. There have been numerous examples published in the literature that demonstrated the feasibility of such techniques as IMRT, VMAT, IMPT, or that compared different treatment methods (e.g. non-coplanar vs coplanar treatment), or investigated planning approaches (e.g. automated planning). However, for a planning study to generate trustworthy new knowledge and give confidence in applying its findings, then its design, execution and reporting all need to meet high scientific standards. This paper provides a 'quality framework' of recommendations and guidelines that can contribute to the quality of planning studies and resulting publications. Throughout the text, questions are posed and, if applicable to a specific study and if met, they can be answered positively in the provided 'RATING' score sheet. A normalised weighted-sum score can then be calculated from the answers as a quality indicator. The score sheet can also be used to suggest how the quality might be improved, e.g. by focussing on questions with high weight, or by encouraging consideration of aspects given insufficient attention. Whilst the overall aim of this framework and scoring system is to improve the scientific quality of treatment planning studies and papers, it might also be used by reviewers and journal editors to help to evaluate scientific manuscripts reporting planning studies.


Extracellular vesicles derived from injured vascular tissue promote the formation of tertiary lymphoid structures in vascular allografts.
Tertiary lymphoid structures (TLS) accumulate at sites of chronic injury where they function as an ectopic germinal center, fostering local autoimmune responses. Vascular injury leads to the release of endothelial-derived apoptotic exosome-like vesicles (ApoExo) that contribute to rejection in transplanted organs. The purpose of the study was to evaluate the impact of ApoExo on TLS formation in a model of vascular allograft rejection. Mice transplanted with an allogeneic aortic transplant were injected with ApoExo. The formation of TLS was significantly increased by ApoExo injection along with vascular remodeling and increased levels of antinuclear antibodies and anti-perlecan/LG3 autoantibodies. ApoExo also enhanced allograft infiltration by γδT17 cells. Recipients deficient in γδT cells showed reduced TLS formation and lower autoantibodies levels following ApoExo injection. ApoExo are characterized by proteasome activity, which can be blocked by bortezomib. Bortezomib treated ApoExo reduced the recruitment of γδT17 cells to the allograft, lowered TLS formation, and reduced autoantibody production. This study identifies vascular injury-derived extracellular vesicles (ApoExo), as initiators of TLS formation and demonstrates the pivotal role of γδT17 in coordinating TLS formation and autoantibody production. Finally, our results suggest proteasome inhibition with bortezomib as a potential option for controlling TLS formation in rejected allografts.


Low-dose UV radiation before running wheel access activates brown adipose tissue.
In previous preclinical studies, low (non-burning) doses of UV radiation (UVR) limited weight gain and metabolic dysfunction in mice fed with a high-fat diet. Here, we explored the effects of low-dose UVR on physical activity and food intake and mechanistic pathways in interscapular brown adipose tissue (iBAT). Young adult C57Bl/6J male mice, housed as individuals, were fed a high-fat diet and exposed to low-dose UVR (sub-oedemal, 1 kJ/m2 UVB, twice-a-week) or 'mock' treatment, with or without running wheel access (2 h, for 'moderate' physical activity) immediately after phototherapy. There was no difference in distance run in mice exposed to UVR or mock-treated over 12 weeks of exposure to running wheels (P = 0.14). UVR (alone) did not significantly affect food intake, adiposity, or signs of glucose dysfunction. Access to running wheels increased food intake (after 10 weeks, P ≤ 0.02) and reduced gonadal white adipose tissue and iBAT mass (P ≤ 0.03). Body weight and hepatic steatosis were lowest in mice exposed to UVR with running wheel access. In the iBAT of mice exposed to UVR and running wheels, elevated Atgl, Cd36, Fasn, Igf1, Pparγ, and Ucp1 mRNAs and reduced CD11c on F4-80 + MHC class II+ macrophages were observed, while renal Sglt2 mRNA levels were increased, compared to high-fat diet alone (P ≤ 0.03). Blood levels of 25-hydroxyvitamin D were not increased by exposure to UVR and/or access to running wheels. In conclusion, when combined with physical activity, low-dose UVR may more effectively limit adiposity (specifically, body weight and hepatic steatosis) and modulate metabolic and immune pathways in iBAT.


A Multi-Site, Multi-Wavelength PPG Platform for Continuous Non-Invasive Health Monitoring in Hospital Settings.
This article presents a novel PPG acquisition platform capable of synchronous multi-wavelength signal acquisition from two measurement locations with up to 4 independent wavelengths from each in parallel. The platform is fully configurable and operates at 1ksps, accommodating a wide variety of transmitters and detectors to serve as both a research tool for experimentation and a clinical tool for disease monitoring. The sensing probes presented in this work acquire 4 PPG channels from the wrist and 4 PPG channels from the fingertip, with wavelengths such that surrogates for pulse wave velocity and haematocrit can be extracted. For conventional PPG sensing, we have achieved the mean error of 4.08 ± 3.72 bpm for heart-rate and a mean error of 1.54 ± 1.04% for SpO 2 measurement, with the latter lying within the FDA limits for commercial pulse oximeters. We have further evaluated over 700 individual peak-to-peak time differences between wrist and fingertip signals, achieving a normalized weighted average PWV of 5.80 ± 1.58 m/s, matching with values of PWV found for this age group in literature. Lastly, we introduced and computed a haematocrit ratio ( Rhct) between the deep IR and deep red wavelength from the fingertip sensor, finding a significant difference between male and female values (median of 1.9 and 2.93 respectively) pointing to devices sensitivity to Hct.


Computed tomography reference values for visceral obesity and increased metabolic risk in a Caucasian cohort.
Visceral obesity is associated with the metabolic syndrome. The metabolic risk differs per ethnicity, but reference values for visceral obesity for body composition analyses using Computed Tomography (CT) scans in the Caucasian population are lacking. Therefore, the aim of this study was to define gender specific reference values for visceral obesity in a Caucasian cohort based upon the association between the amount of visceral adipose tissue (VAT) and markers of increased metabolic risk. Visceral Adipose Tissue Area Index (VATI cm2/m2) at the level of vertebra L3 was analyzed using CT scans of 416 healthy living kidney donor candidates. The use of antihypertensive drugs and/or statins was used as an indicator for increased metabolic risk. Gender specific cut-off values for VATI with a sensitivity ≥80% were calculated using receiver operating characteristic (ROC) curves. In both men and women who used antihypertensive drugs, statins or both, VATI was higher than in those who did not use these drugs (p ≤ 0.013). In males and females respectively, a value of VATI of ≥38.7 cm2/m2 and ≥24.9 cm2/m2 was associated with increased metabolic risk with a sensitivity of 80%. ROC analysis showed that VATI was a better predictor of increased metabolic risk than BMI (area under ROC curve (AUC) = 0.702 vs AUC = 0.556 in males and AUC = 0.757 vs AUC = 0.630 in females). Gender and ethnicity specific cut-off values for visceral obesity are important in body composition research, although further validation is needed. This study also showed that quantification of VATI is a better predictor for metabolic risk than BMI.


Chemiluminescent microparticle immunoassay based detection and prevalence of HCV infection in district Peshawar Pakistan.
Due to the high rate of asymptomatic infections an advanced screening assay is of prompt importance to be used for the clinical diagnosis of HCV. Early detection of anti HCV is the first step in the management of chronic hepatitis and in the selection of patients needing treatments. In the current study we have first time used the advanced serological diagnostic technique i.e. Chemiluminescent Microparticle Immuno Assay (CMIA) for the detection of HCV infection in Peshawar Pakistan. A total number of 982 samples were collected among the general public belongs to the different areas of district Peshawar. The samples were centrifuged at high speed to obtain a clear supernatant serum. All the samples were run on Architect system a fully automated immuno analyzer CMIA base technology. Out of 982 blood samples analyzed in this study, 160 (15.9%) were confirmed to be positive for active HCV infection. The overall prevalence was found to be 13.4%. Gender wise prevalence was recorded to be higher in male (19.1%) than female (12.7%). The age group 21-30 years was identified as the highest risk group among the studied population. Among the tested samples, overall prevalence of active HCV infection was found to be 13.4% in the general population of Peshawar Pakistan. The young middle aged population of this region was at higher risk of HCV ailments compared to the other age groups.


Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans.
The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2. We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.


Development of Saccharomyces cerevisiae as a model pathogen. A system for the genetic identification of gene products required for survival in the mammalian host environment.
Saccharomyces cerevisiae, a close relative of the pathogenic Candida species, is an emerging opportunistic pathogen. An isogenic series of S. cerevisiae strains, derived from a human clinical isolate, were used to examine the role of evolutionarily conserved pathways in fungal survival in a mouse host. As is the case for the corresponding Candida albicans and Cryptococcus neoformans mutants, S. cerevisiae purine and pyrimidine auxotrophs were severely deficient in survival, consistent with there being evolutionary conservation of survival traits. Resistance to the antifungal drug 5-fluorocytosine was not deleterious and appeared to be slightly advantageous in vivo. Of mutants in three amino acid biosynthetic pathways, only leu2 mutants were severely deficient in vivo. Unlike the glyoxylate cycle, respiration was very important for survival; however, the mitochondrial genome made a respiration-independent contribution to survival. Mutants deficient in pseudohyphal formation were tested in vivo; flo11Delta mutants were phenotypically neutral while flo8Delta, tec1Delta, and flo8Delta tec1Delta mutants were slightly deficient. Because of its ease of genetic manipulation and the immense S. cerevisiae database, which includes the best annotated eukaryotic genome sequence, S. cerevisiae is a superb model system for the identification of gene products important for fungal survival in the mammalian host environment.


Germline variants and advanced colorectal adenomas: adenoma prevention with celecoxib trial genome-wide association study.
Identification of single-nucleotide polymorphisms (SNP) associated with development of advanced colorectal adenomas. Discovery phase: 1,406 Caucasian patients (139 advanced adenoma cases and 1,267 controls) from the Adenoma Prevention with Celecoxib (APC) trial were included in a genome-wide association study (GWAS) to identify variants associated with postpolypectomy disease recurrence. Genome-wide significance was defined as false discovery rate less than 0.05, unadjusted P = 7.4 × 10(-7). Validation phase: results were further evaluated using 4,175 familial colorectal adenoma cases and 5,036 controls from patients of European ancestry [COloRectal Gene Identification consortium (CORGI), Scotland, Australia, and VQ58]. Our study identified eight SNPs associated with advanced-adenoma risk in the APC trial (rs2837156, rs7278863, rs2837237, rs2837241, rs2837254, rs741864 at 21q22.2, and rs1381392 and rs17651822 at 3p24.1, at P < 10(-7) level with OR > 2). Five variants in strong pairwise linkage disequilibrium (rs7278863, rs2837237, rs741864, rs741864, and rs2837241; r(2) = 0.8-1) are in or near the coding region for the tight junction adhesion protein, IGSF5. An additional variant associated with advanced adenomas, rs1535989 [minor allele frequency, 0.11; OR, 2.09; 95% confidence interval (CI), 1.50-2.91], also predicted colorectal cancer development in a validation analysis (P = 0.019) using a series of adenoma cases or colorectal cancer (CORGI study) and 3 sets of colorectal cancer cases and controls (Scotland, VQ58, and Australia; N = 9,211). Our results suggest that common polymorphisms contribute to the risk of developing advanced adenomas and might also contribute to the risk of developing colorectal cancer. The variant at rs1535989 may identify patients whose risk for neoplasia warrants increased colonoscopic surveillance.


Aging alters intraocular but not interocular foveal center surround contrast suppression.
Numerous previous studies have shown that healthy aging results in increased foveal center surround contrast suppression when the center and surround patterns are presented to both eyes. The mechanistic cause of this observation is not well established. Neurophysiological and psychophysical studies have shown that different mechanisms of parafoveal center surround suppression can be tapped by manipulating viewing conditions to present the center and surround to the same eye (intraocular viewing) or to different eyes (interocular viewing), or by manipulating stimulus parameters such as duration. Here, we tested intraocular and interocular foveal center surround contrast suppression for stimuli of 40 ms and 200 ms duration in 18 younger and 18 older adults. For both groups, foveal intraocular center surround contrast suppression decreased with longer stimulus duration whereas interocular surround suppression did not, confirming contributions from separate mechanisms to these forms of suppression. Intraocular center surround contrast suppression was increased in older adults compared to younger adults; however, interocular suppression was similar in both groups. Our results indicate that aging differentially affects distinct forms of suppression arising at various levels of the visual pathway.


Energy deprivation and a deficiency in downstream metabolic target genes during the onset of embryonic heart failure in RXRalpha-/- embryos.
RXRalpha null mutant mice display ocular and cardiac malformations, liver developmental delay, and die from cardiac failure around embryonic day (E) 14.5 pc. To dissect the molecular basis of the RXRalpha-associated cardiomyopathy, we performed subtractive hybridization and systematically characterized putative downstream target genes that were selectively lacking in the mutant embryos, both at early (E10.5) and late (E13.5) stages of mouse embryonic development. Approximately 50% of the subtracted clones (61/115) encoded proteins involved in intermediary metabolism and electron transport, suggesting an energy deficiency in the RXRalpha-/- embryos. In particular, clone G1, which encodes subunit 14.5b of the NADH-ubiquinone dehydrogenase complex, displayed a dose-dependent expression in the wild-type, heterozygous and RXRalpha mutant mice. This gene was also downregulated in a retinoid-deficient rat embryo model. ATP content and medium Acyl-CoA dehydrogenase mRNA were lower in RXRalpha mutant hearts compared to wild-type mice. Ultrastructural studies showed that the density of mitochondria per myocyte was higher in the RXRalpha mutant compared to wild-type littermates. We propose a model whereby defects in intermediary metabolism may be a causative factor of the RXRalpha-/- phenotype and resembles an embryonic form of dilated cardiomyopathy.


Errors inherent in the primed infusion method for the measurement of the rate of glucose appearance in man when uptake is not forced by glucose or insulin infusion.
1. My aim was to investigate, by mathematical simulation, the errors inherent in the measurement by the primed infusion method of the rate of appearance of glucose in man when turnover was as low or lower than in overnight-fasted normal subjects (control subjects). The simulations were based on published data for means and variances of turnover rates and concentrations in nondiabetic subjects and diabetic patients. 2. Systematic errors (bias) were shown to be considerable whether or not the Steele equation was used, unless run-times were longer than is customary. Errors were greater the lower the turnover rate, and were greatest in patients with diabetes, owing to insulin resistance. Studies of, for example, control subjects, age, obesity, exercise, sepsis and injury, are, however, all likely to be affected. 3. Estimates of variance, within-group means, between-group differences and slopes of rate-concentration relationships were all biased. Entirely spurious results appeared statistically significant. 4. When the Steele equation was not used, run-times had to exceed 3 h in control subjects and 10 h in some diabetic patients to reduce bias to acceptable levels. The nature of the bias depended on how the priming dose/infusion rate ratio was chosen. Each choice implies a particular hypothesis about the values of the rate of appearance of glucose, their variance, and how they are related to concentration. The bias was always such as to favour that hypothesis. 5. When the Steele equation was used, the accessible glucose space (pool fraction x distribution volume) had to be correct to 20-30 ml to avoid unacceptable bias in some patients in runs 4 h long. The space is not known this accurately. Theoretically, in the near-steady metabolic states considered, the pool fraction should be near 1.00, i.e. the accessible space should be near the glucose distribution volume of 200-300 mg/kg. There is some confirmatory experimental evidence. 6. Large random errors from variance of specific (radio)activity measurements when the Steele equation is used can be reduced by a suitable choice of protocols. 7. The propagation of errors is too complex to permit correction of results. It is essential to choose protocols that can be shown to give results that are acceptably bias-free. Ways of doing this are discussed.


Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly.
Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max) genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS). Here the aim was to use BAC end sequences (BES) derived from three minimum tile paths (MTP) to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results show that when sequence divergence was 1-10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs) were single nucleotide polymorphisms (SNPs; 89%) and single nucleotide indels (SNIs 10%). Larger indels were rare but present (1%). Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5-10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de-convolution and positioning of sequence scaffolds (see BES_scaffolds section of SoyGD). This approach will assist genome annotation for paleopolyploid and true polyploid genomes such as soybean and many important cereal and fruit crops.


Development and Validation of the PREMM5 Model for Comprehensive Risk Assessment of Lynch Syndrome.
Purpose Current Lynch syndrome (LS) prediction models quantify the risk to an individual of carrying a pathogenic germline mutation in three mismatch repair (MMR) genes: MLH1, MSH2, and MSH6. We developed a new prediction model, PREMM5, that incorporates the genes PMS2 and EPCAM to provide comprehensive LS risk assessment. Patients and Methods PREMM5 was developed to predict the likelihood of a mutation in any of the LS genes by using polytomous logistic regression analysis of clinical and germline data from 18,734 individuals who were tested for all five genes. Predictors of mutation status included sex, age at genetic testing, and proband and family cancer histories. Discrimination was evaluated by the area under the receiver operating characteristic curve (AUC), and clinical impact was determined by decision curve analysis; comparisons were made to the existing PREMM1,2,6 model. External validation of PREMM5 was performed in a clinic-based cohort of 1,058 patients with colorectal cancer. Results Pathogenic mutations were detected in 1,000 (5%) of 18,734 patients in the development cohort; mutations included MLH1 (n = 306), MSH2 (n = 354), MSH6 (n = 177), PMS2 (n = 141), and EPCAM (n = 22). PREMM5 distinguished carriers from noncarriers with an AUC of 0.81 (95% CI, 0.79 to 0.82), and performance was similar in the validation cohort (AUC, 0.83; 95% CI, 0.75 to 0.92). Prediction was more difficult for PMS2 mutations (AUC, 0.64; 95% CI, 0.60 to 0.68) than for other genes. Performance characteristics of PREMM5 exceeded those of PREMM1,2,6. Decision curve analysis supported germline LS testing for PREMM5 scores ≥ 2.5%. Conclusion PREMM5 provides comprehensive risk estimation of all five LS genes and supports LS genetic testing for individuals with scores ≥ 2.5%. At this threshold, PREMM5 provides performance that is superior to the existing PREMM1,2,6 model in the identification of carriers of LS, including those with weaker phenotypes and individuals unaffected by cancer.


Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.
Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism. The transcriptome assembly has been submitted to NCBI Transcriptome Shotgun Assembly Sequence Database(http://www.ncbi.nlm.nih.gov/genbank/TSA.html) under accession numbers JI163767–JI182837 and JI210738–JI257410.


Two-dimensional population map of cortical connections in the human internal capsule.
To exploit diffusion imaging tractography to produce a two-dimensional (xy) probabilistic population map of the cortical connections within the human internal capsule (IC). Diffusion tensor imaging (DTI) was carried out on 11 healthy volunteers. We parceled an axial section of the IC according to its connections to the prefrontal, premotor, primary motor, primary somatosensory, posterior parietal, and occipital cortices using our locally developed probabilistic algorithm. A consistent topographical organization was generated that was consistent with our anatomical knowledge of the IC. In addition, our study shows that in humans the anterior half of the IC is occupied by the prefrontal cortex. This map may be of clinical use for correlating neurological deficit with hemispheric lesions, particularly those that affect sensorimotor function.