Developing a powerful in silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome.
Caspases are a family of cysteinyl proteases that regulate apoptosis and other biological processes. Caspase-3 is considered the central executioner member of this family with a wide range of substrates. Identification of caspase-3 cellular targets is crucial to gain further insights into the cellular mechanisms that have been implicated in various diseases including: cancer, neurodegenerative, and immunodeficiency diseases. To date, over 200 caspase-3 substrates have been identified experimentally. However, many are still awaiting discovery. Here, we describe a powerful bioinformatics tool that can predict the presence of caspase-3 cleavage sites in a given protein sequence using a Position-Specific Scoring Matrix (PSSM) approach. The present tool, which we call CAT3, was built using 227 confirmed caspase-3 substrates that were carefully extracted from the literature. Assessing prediction accuracy using 10 fold cross validation, our method shows AUC (area under the ROC curve) of 0.94, sensitivity of 88.83%, and specificity of 89.50%. The ability of CAT3 in predicting the precise cleavage site was demonstrated in comparison to existing state-of-the-art tools. In contrast to other tools which were trained on cleavage sites of various caspases as well as other similar proteases, CAT3 showed a significant decrease in the false positive rate. This cost effective and powerful feature makes CAT3 an ideal tool for high-throughput screening to identify novel caspase-3 substrates. The developed tool, CAT3, was used to screen 13,066 human proteins with assigned gene ontology terms. The analyses revealed the presence of many potential caspase-3 substrates that are not yet described. The majority of these proteins are involved in signal transduction, regulation of cell adhesion, cytoskeleton organization, integrity of the nucleus, and development of nerve cells. CAT3 is a powerful tool that is a clear improvement over existing similar tools, especially in reducing the false positive rate. Human proteome screening, using CAT3, indicate the presence of a large number of possible caspase-3 substrates that exceed the anticipated figure. In addition to their involvement in various expected functions such as cytoskeleton organization, nuclear integrity and adhesion, a large number of the predicted substrates are remarkably associated with the development of nerve tissues.


Virus-induced airway hyperresponsiveness in man.
Airway hyperresponsiveness is the most prominent functional abnormality in asthma. Although its aetiology is still unclear, it is well-known that allergen exposure and virus infections can temporarily induce or aggravate airway hyperresponsiveness. Among these environmental factors, virus infections appear to be clinically most relevant, since recent epidemiological studies have shown that most asthma exacerbations in children are associated with positive nasopharyngeal viral identification. The pathogenesis of virus-induced airway hyperresponsiveness has been investigated by experimental virus infections in animals and in man. Intranasal inoculation and/or inhalation of live attenuated influenza virus, or certain strains of rhinovirus, have been shown to induce airway hyperresponsiveness to various bronchoconstrictor stimuli in man. This indicates that experimental virus-infection, like allergen challenge, is an appropriate investigational model of asthma. The mechanisms of virus-induced airway hyperresponsiveness are still unclear, but may, in part, be similar to those involved in the pathogenesis of asthma. Currently investigated hypothesis include: epithelial damage or dysfunction, immunological responses, inflammatory mediator release, cholinergic and/or noncholinergic reflexes, and impaired beta-adrenoceptor function. Careful experimental studies, using modern laboratory techniques, are needed to unravel the role of viruses in the development of airway hyperresponsiveness. The results of such studies can potentially lead to an improvement of future asthma management.


Dermorphin-based potential affinity labels for mu-opioid receptors.
Dermorphin and [Lys7]dermorphin, selective micro -opioid receptor ligands originating from amphibian skin, have been modified with various electrophiles in either the 'message' or 'address' sequences as potential peptide-based affinity labels for micro -receptors. Introduction of the electrophilic isothiocyanate and bromoacetamide groups on the para position of Phe3 and Phe5 was accomplished by incorporating Fmoc-Phe(p-NHAlloc) into the peptide followed by selective deprotection and modification. The corresponding amine-containing peptides were also prepared. The pure peptides were evaluated in radioligand binding experiments using Chinese hamster ovary (CHO) cells expressing micro - and delta-opioid receptors. In dermorphin, introduction of the electrophilic groups in the 'message' domain lowered the binding affinity by > 1000-fold; only [Phe(p-NH2)3]dermorphin retained nanomolar affinity for micro -receptors. Modifications in the 'address' region of both dermorphin and [Lys7]dermorphin were relatively well tolerated. In particular, [Phe(p-NH2)5,Lys7]dermorphin showed similar affinity to dermorphin, with almost 2-fold higher selectivity for micro -receptors. [Phe(p-NHCOCH2Br)5]- and [Phe(p-NHCOCH2Br)5,Lys7]dermorphin exhibited relatively high affinity (IC50 = 27.7 and 15.1 nm, respectively) for micro -receptors. However, neither of these peptides inhibited [3H]DAMGO binding in a wash-resistant manner.


The DNA scanning mechanism of T4 endonuclease V. Effect of NaCl concentration on processive nicking activity.
T4 endonuclease V is a pyrimidine dimer-specific endonuclease which generates incisions in DNA at the sites of pyrimidine dimers by a processive reaction mechanism. A model is presented in which the degree of processivity is directly related to the efficacy of the one-dimensional diffusion of endonuclease V on DNA by which the enzyme locates pyrimidine dimers. The modulation of the processive nicking activity of T4 endonuclease V on superhelical covalently closed circular DNA (form I) which contains pyrimidine dimers has been investigated as a function of the ionic strength of the reaction. Agarose gel electrophoresis was used to separate the three topological forms of the DNA which were generated in time course reactions of endonuclease V with dimer-containing form I DNA in the absence of NaCl, and in 25, 50, and 100 mM NaCl. The degree of processivity was evaluated in terms of the mass fraction of form III (linear) DNA which was produced as a function of the fraction of form I DNA remaining. Processivity is maximal in the absence of NaCl and decreases as the NaCl concentration is increased. At 100 mM NaCl, processivity is abolished and endonuclease V generates incisions in DNA at the site of dimers by a distributive reaction mechanism. The change from the distributive to a processive reaction mechanism occurs at NaCl concentrations slightly below 50 mM. The high degree of processivity which is observed in the absence of NaCl is reversible to the distributive mechanism, as demonstrated by experiments in which the NaCl concentration was increased during the time course reaction. In addition, unirradiated DNA inhibited the incision of irradiated DNA only at NaCl concentrations at which processivity was observed.


Plugfest 2009: Global Interoperability in Telerobotics and Telemedicine.
Despite the great diversity of teleoperator designs and applications, their underlying control systems have many similarities. These similarities can be exploited to enable inter-operability between heterogeneous systems. We have developed a network data specification, the Interoperable Telerobotics Protocol, that can be used for Internet based control of a wide range of teleoperators. In this work we test interoperable telerobotics on the global Internet, focusing on the telesurgery application domain. Fourteen globally dispersed telerobotic master and slave systems were connected in thirty trials in one twenty four hour period. Users performed common manipulation tasks to demonstrate effective master-slave operation. With twenty eight (93%) successful, unique connections the results show a high potential for standardizing telerobotic operation. Furthermore, new paradigms for telesurgical operation and training are presented, including a networked surgery trainer and upper-limb exoskeleton control of micro-manipulators.


GROOLS: reactive graph reasoning for genome annotation through biological processes.
High quality functional annotation is essential for understanding the phenotypic consequences encoded in a genome. Despite improvements in bioinformatics methods, millions of sequences in databanks are not assigned reliable functions. The curation of protein functions in the context of biological processes is a way to evaluate and improve their annotation. We developed an expert system using paraconsistent logic, named GROOLS (Genomic Rule Object-Oriented Logic System), that evaluates the completeness and the consistency of predicted functions through biological processes like metabolic pathways. Using a generic and hierarchical representation of knowledge, biological processes are modeled in a graph from which observations (i.e. predictions and expectations) are propagated by rules. At the end of the reasoning, conclusions are assigned to biological process components and highlight uncertainties and inconsistencies. Results on 14 microbial organisms are presented. GROOLS software is designed to evaluate the overall accuracy of functional unit and pathway predictions according to organism experimental data like growth phenotypes. It assists biocurators in the functional annotation of proteins by focusing on missing or contradictory observations.


Reducing Anxiety and Improving Engagement in Health Care Providers Through an Auricular Acupuncture Intervention.
Stress and anxiety are experienced by health care providers as a consequence of caregiving and may result in physical, emotional, and psychological outcomes that negatively impact work engagement. The purpose of this study was to determine whether auricular acupuncture can reduce provider anxiety and improve work engagement. Study participants received 5 auricular acupuncture sessions within a 16-week period utilizing the National Acupuncture Detoxification Association protocol for treating emotional trauma. Each participant completed the State-Trait Anxiety Inventory and the Utrecht Work Engagement Scale (UWES-9) prior to their first session and again after their fifth treatment. Significant reductions were found in state and trait anxiety (State-Trait Anxiety Inventory), as well as significant increases in the overall scores on the UWES as compared with baseline. Only the dedication subcategory of the UWES showed significant improvement. Engagement has been linked to increased productivity and well-being and improved patient and organizational outcomes. Providing effective strategies such as auricular acupuncture to support health care providers in reducing anxiety in the workplace may improve engagement.


A quantitative method for measuring phototoxicity of a live cell imaging microscope.
Fluorescence-based imaging regimes require exposure of living samples under study to high intensities of focused incident illumination. An often underestimated, overlooked, or simply ignored fact in the design of any experimental imaging protocol is that exposure of the specimen to these excitation light sources must itself always be considered a potential source of phototoxicity. This can be problematic, not just in terms of cell viability, but much more worrisome in its more subtle manifestation where phototoxicity causes anomalous behaviors that risk to be interpreted as significant, whereas they are mere artifacts. This is especially true in the case of microbial pathogenesis, where host-pathogen interactions can prove especially fragile to light exposure in a manner that can obscure the very processes we are trying to observe. For these reasons, it is important to be able to bring the parameter of phototoxicity into the equation that brings us to choose one fluorescent imaging modality, or setup, over another. Further, we need to be able to assess the risk that phototoxicity may occur during any specific imaging experiment. To achieve this, we describe here a methodological approach that allows meaningful measurement, and therefore relative comparison of phototoxicity, in most any variety of different imaging microscopes. In short, we propose a quantitative approach that uses microorganisms themselves to reveal the range over which any given fluorescent imaging microscope will yield valid results, providing a metrology of phototoxic damage, distinct from photobleaching, where a clear threshold for phototoxicity is identified. Our method is widely applicable and we show that it can be adapted to other paradigms, including mammalian cell models.


Cell mitotic cycle synthesis of NIL hamster glycolipids including the Forssman antigen.
The synthesis of phospholipids and glycolipids during the cell mitotic cycle of an established hamster line, NIL, has been studied. Cells were synchronized with excess thymidine and mitotically harvested by shaking. Cells were radioactively labeled for 4 h with palmitate, glucosamine, or galactose. Lipids were analyzed by thin-layer chromatography. As cells progressed through the mitotic cycle, incorporation into phospholipids increased but the fraction represented by each remained constant. Similarly, ceramide monohexoside, dihexoside, and hematoside were labeled equally in all phases. Ceramide trihexoside and tetrahexoside were labeled only during G(1) and S. Ceramide pentahexoside (the Forssman antigen) shows density-dependent synthesis, accumulation, and reactivity. Ceramide pentahexoside was labeled during all phases of the mitotic cycle but the rate of incorporation decreased in S and G(2). The total amount of lipid assayed immunologically in cell extracts gradually increased. Exposure of the Forssman antigen in untreated or trypsin-treated cells was studied using binding of chemically labeled antiForssman antiserum. The amount of antigen detected in trypsinized cells increased during G(1) and early S but then remained constant. Mitotic cells exposed all detectable antigen. As cells progressed through the mitotic cycle, a large fraction of the Forssman antigen became cryptic.


Acoustic emissions generated in aged dental composites using a laser thermoacoustic technique.
The heating up of dental composites by laser will produce acoustic emissions (AEs) that may be related to fracture mechanisms in the composites. It has been proved that the mechanical properties of dental composites are affected by storage in food simulating liquids, i.e. 75% ethanol, which has a solubility parameter approximating to that of bisphenol glycidyl dimethacrylate (BisGMA) resin. A new method was innovated to evaluate the laser-induced AEs in dental composites aged by 75% ethanol solution. Model systems (50/50 BisGMA/TEGDMA resin filled with 0% and 75 wt.% 5-10 microm silanized BaSiO6) as well as three commercial composites (Marathon One, Z100 and Herculite XRV) were used in this study. Nine samples acting as the control group were tested to establish the correlation of AEs to laser power. The effect of ageing by immersion in 75% ethanol on AEs and diametral tensile strength (DTS) was then evaluated. A quasi-continuous wave CO2 laser was used to heat up the composites. AEs of frequency 100-200 kHz were collected, filtered, recorded and processed using a 4610 Smart Acoustic Monitor. Burst patterns, which formally were assumed to be correlated to fracture mechanisms, were also identified from the data obtained at laser power > or = 5 W for commercial composites and > or = 4 W for model systems. Higher laser powers cause the AE to increase for all composites except unfilled model resin. AEs as a function of power for all aged systems were flat (< 100 events) below 4 W. Emissions then rose sharply to > 1000 events at 7.1 W. Statistically significant differences were found between the AEs obtained at 5 W (commercial composites) and those at 4.3 W (model systems) for material systems and storage times. Marathon One was less affected by the laser and an abrupt change in AE was found between days 0 and 7 of storage for all commercial composites. The AE value from the unfilled model resin was found to be significantly different from that of the model composites. However, they showed an increase in AEs with length of storage time, which was inversely associated with the decreased tendency of their immersed DTS values. Laser-induced AEs may be a valuable adjunct to conventional mechanical testing.


ArmA methyltransferase in a monophasic Salmonella enterica isolate from food.
The 16S rRNA methyltransferase ArmA is a worldwide emerging determinant that confers high-level resistance to most clinically relevant aminoglycosides. We report here the identification and characterization of a multidrug-resistant Salmonella enterica subspecies I.4,12:i:- isolate recovered from chicken meat sampled in a supermarket on February 2009 in La Reunion, a French island in the Indian Ocean. Susceptibility testing showed an unusually high-level resistance to gentamicin, as well as to ampicillin, expanded-spectrum cephalosporins and amoxicillin-clavulanate. Molecular analysis of the 16S rRNA methyltransferases revealed presence of the armA gene, together with bla(TEM-1), bla(CMY-2), and bla(CTX-M-3). All of these genes could be transferred en bloc through conjugation into Escherichia coli at a frequency of 10(-5) CFU/donor. Replicon typing and S1 pulsed-field gel electrophoresis revealed that the armA gene was borne on an ~150-kb broad-host-range IncP plasmid, pB1010. To elucidate how armA had integrated in pB1010, a PCR mapping strategy was developed for Tn1548, the genetic platform for armA. The gene was embedded in a Tn1548-like structure, albeit with a deletion of the macrolide resistance genes, and an IS26 was inserted within the mel gene. To our knowledge, this is the first report of ArmA methyltransferase in food, showing a novel route of transmission for this resistance determinant. Further surveillance in food-borne bacteria will be crucial to determine the role of food in the spread of 16S rRNA methyltransferase genes worldwide.


Home monitoring program reduces interstage mortality after the modified Norwood procedure.
From 2002 to 2005, the interstage mortality after a modified Norwood procedure was 7% in our program. An interstage home monitoring program (HMP) was established to identify Norwood procedure patients at increased risk of decompensation and to reduce interstage mortality. Results of the first 5 years of the Norwood HMP were reviewed retrospectively. Interstage was defined as the time between Norwood hospital discharge and admission for second stage surgical palliation. In the HMP, families documented oxygen saturation, heart rate, weight, and feedings daily. Nurse practitioners called each family at least weekly, and when issues arose, action plans were determined based on symptom severity. Between October 2005 and October 2010 there were 46 Norwood procedure patients who survived to hospital discharge. All were enrolled in the HMP. Forty-five patients had a Norwood procedure with right ventricle to pulmonary artery conduit, and 1 patient had a modified Blalock-Taussig shunt. Interstage survival was 100%. Nineteen patients (41%) were admitted interstage; 5 patients were admitted twice, 1 patient was admitted 4 times. Seventeen patients (37%) required interstage interventions. Eight patients (17%) required major interventions: conduit stenting, aortic arch balloon angioplasty, emergent shunt, or early Glenn surgery. Minor interventions included supplemental oxygen, blood transfusion, intravenous hydration, diuresis, anti-arrhythmic therapy, or feeding adjustments. In the first 5 years of the HMP, all infants discharged after a modified Norwood procedure survived the interstage period. The HMP altered clinical management in 37% of patients. Home monitoring of oxygen saturation, heart rate, weight, and feedings, along with comprehensive care coordination, allowed timely interventions and reduced interstage mortality from 7% to 0%.


Hunter syndrome with late age of presentation: clinical description of a case and review of the literature.
Hunter syndrome is an X linked recessive mucopolysaccharidosis (type II) caused by the deficiency of iduronate 2-sulfatase. This in turn leads to the accumulation of glycosaminoglycans, dermatan and heparan sulfate. The intracellular and extracellular accumulation of these substances lead to multisystemic organ abnormality. It is a rare syndrome with a very low prevalence of 1.3:100,000 male live births. Usual presentation is in early childhood although milder variants have been documented to present at a later age. We present a rare case of Hunter syndrome in a 24-year-old male patient who presented with joint contractures and recent onset hoarseness of voice. X-rays were suggestive of dysostosis multiplex. Clinical diagnosis of Hunter syndrome was confirmed by enzyme assay and further by mutational analysis.


Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo.
Embryonic development starts with cleavages, a rapid sequence of reductive divisions that result in an exponential increase of cell number without changing the overall size of the embryo. In Drosophila, the final four rounds of cleavages occur at the surface of the embryo and give rise to ∼6000 nuclei under a common plasma membrane. We use live imaging to study the dynamics of this process and to characterize the emergent nuclear packing in this system. We show that the characteristic length scale of the internuclear interaction scales with the density, which allows the densifying embryo to sustain the level of structural order at progressively smaller length scales. This is different from nonliving materials, which typically undergo disorder-order transition upon compression. To explain this dynamics, we use a particle-based model that accounts for density-dependent nuclear interactions and synchronous divisions. We reproduce the pair statistics of the disordered packings observed in embryos and recover the scaling relation between the characteristic length scale and the density both in real and reciprocal space. This result reveals how the embryo can robustly preserve the nuclear-packing structure while being densified. In addition to providing quantitative description of self-similar dynamics of nuclear packings, this model generates dynamic meshes for the computational analysis of pattern formation and tissue morphogenesis.


Spectrum and Immediate Outcome of Acute Kidney Injury in a Pediatric Intensive Care Unit: A Snapshot Study from Indian Subcontinent.
Acute kidney injury (AKI) became an important cause of mortality and morbidity in critically ill children, despite advancement in its management. In developing countries etiology of AKI are different from that of developed countries. This observational study was carried out in pediatric intensive care unit (PICU) in 2 months to18 years of critically ill children. Kidney injury was defined and categorized by the pRIFLE criteria. Out of 361children, 86 children (23.8%) developed AKI at some point during admission, 275 children (age and sex matched) who did not develop kidney injury during hospitalization served as non-AKI children. Maximum cases of AKI were seen in 1-5 years of age. Maximum children of AKI were of viral encephalitis (n = 43, 50.0%) followed by scrub typhus (n = 14, 16.3%). Risk factors for the development of AKI were shock, PRISM score and longer hospital stay. In our study the mortality in AKI children (n = 30, 34.8%) was significantly higher (p = 0.005) as compared to non-AKI children (n = 56, 20.3%)). Duration on mechanical ventilation, PICU stay and hospital stay were also significantly (p = 0.001) higher in AKI children. AKI is common in critically ill children and associated with high mortality and morbidity. Bharat A, Mehta A, Tiwari HC, Sharma B, Singh A, Singh V. Spectrum and Immediate Outcome of Acute Kidney Injury in a Pediatric Intensive Care Unit: A Snapshot Study from Indian Subcontinent. Indian J Crit Care Med 2019;23(8):352-355.


Cluster analysis of dynamic contrast enhanced MRI reveals tumor subregions related to locoregional relapse for cervical cancer patients.
Solid tumors are known to be spatially heterogeneous. Detection of treatment-resistant tumor regions can improve clinical outcome, by enabling implementation of strategies targeting such regions. In this study, K-means clustering was used to group voxels in dynamic contrast enhanced magnetic resonance images (DCE-MRI) of cervical cancers. The aim was to identify clusters reflecting treatment resistance that could be used for targeted radiotherapy with a dose-painting approach. Eighty-one patients with locally advanced cervical cancer underwent DCE-MRI prior to chemoradiotherapy. The resulting image time series were fitted to two pharmacokinetic models, the Tofts model (yielding parameters Ktrans and νe) and the Brix model (ABrix, kep and kel). K-means clustering was used to group similar voxels based on either the pharmacokinetic parameter maps or the relative signal increase (RSI) time series. The associations between voxel clusters and treatment outcome (measured as locoregional control) were evaluated using the volume fraction or the spatial distribution of each cluster. One voxel cluster based on the RSI time series was significantly related to locoregional control (adjusted p-value 0.048). This cluster consisted of low-enhancing voxels. We found that tumors with poor prognosis had this RSI-based cluster gathered into few patches, making this cluster a potential candidate for targeted radiotherapy. None of the voxels clusters based on Tofts or Brix parameter maps were significantly related to treatment outcome. We identified one group of tumor voxels significantly associated with locoregional relapse that could potentially be used for dose painting. This tumor voxel cluster was identified using the raw MRI time series rather than the pharmacokinetic maps.


Allergy to human seminal fluid: cross-reactivity with dog dander.
Human seminal plasma (HSP) allergy is uncommon, with symptoms ranging from vulvovaginal pruritus to life-threatening anaphylaxis. Although several seminal plasma allergens have been reported and their molecular masses have been estimated to range between 12 and 75 kd, the prostate-specific antigen (PSA) has recently been identified as a causative allergen. Given that in a large number of cases symptoms appeared during or after the first intercourse, a cross-reactivity phenomenon might be implicated. We sought to assess the presence of IgE cross-reactivity among proteins from dog epithelium and HSP and to attempt to identify the allergens involved. Forty-one patients with dog epithelium allergy were selected. One of them experienced anaphylaxis in contact with her husband's seminal plasma. Skin prick tests, serum specific IgE measurements, SDS-PAGE immunoblotting, and inhibition tests were performed to study the pattern of IgE-binding proteins and the potential cross-reactivity between HSP and dog epithelium. Mass spectrometry was carried out to identify the protein involved in allergy reactions. Twenty-four percent of the sera from patients with dog epithelium allergy recognized an IgE-binding band of 28 kd in HSP immunoblotting. Mass spectrometry identified this band as the PSA. SDS-PAGE immunoblotting-inhibition showed a complete IgE-binding inhibition when sera from these patients were preincubated with dog dander extract. IgE cross-reactivity among proteins from dog dander and human PSA is demonstrated.


Rabbit and human atherosclerotic lesions contain IgG that recognizes epitopes of oxidized LDL.
Atherosclerotic lesions contain relatively large quantities of IgG. We have previously shown that both human and rabbit sera contain autoantibodies against epitopes of oxidized (Ox) low-density lipoprotein (LDL) and that LDL isolated from atherosclerotic lesions contains small amounts of tightly bound IgG. However, it is not known whether IgG isolated from atherosclerotic lesions recognizes epitopes present in native LDL or Ox-LDL. IgG was isolated from Watanabe heritable hyperlipidemic (WHHL) rabbit atherosclerotic lesions by sequential salt extractions, purified by fast protein liquid chromatography on protein G, and used in a solid-phase radioimmunoassay. IgG and immune complexes were also isolated from the saline extracts of human lesions by adsorption onto latex beads coated with anti-human IgG antibodies or protein A. IgG isolated from rabbit lesions showed significant titers against malondialdehyde (MDA)-modified LDL and LDL oxidized by copper ions for 4 and 18 hours but not against native LDL. On Western blots, lesion IgG stained MDA-LDL and fragments of Ox-LDL. Western blots of immune complexes isolated from human lesions revealed the presence in the isolated complexes of both apoprotein B and apoprotein B fragments, which reacted with antibodies to MDA-lysine. Furthermore, rabbit lesion IgG immunostained epitopes of Ox-LDL present in human atherosclerotic lesions. Immunostains obtained with rabbit lesion IgG were similar to those obtained with a monoclonal antibody specific for MDA-lysine. The results show that human and rabbit atherosclerotic lesions contain IgG that recognizes epitopes characteristic of Ox-LDL. These data suggest that immunologic processes may be an important component of the atherogenic process.


Study subjects and ordinary patients.
Clinical trials of treatment agents impose strict and often necessary inclusion and exclusion criteria, while patients presenting to physicians for treatment frequently exhibit complicating features that would have excluded them from entry into study. To quantify the degree of discordance between ordinary patients and study subjects, a retrospective chart review was carried out of all new patients with osteoporosis seen in an academic medical center within a consecutive 40-month period, meeting clinical treatment criteria. Each patient chart was reviewed for the inclusion and exclusion criteria of four large, multicenter study protocols. There were 120 consecutive female patients seeking health care, with bone density T-scores below -2.0 and/or with one or more low-trauma fractures. The four trials would have accepted 4, 5, 25 and 8 of our 120 patients. The trial with the most liberal inclusion criteria would have taken only 21% of the total. Principal reasons for ineligibility were comorbidity, prior treatment with bone-active agents, and current therapy with glucocorticoids, anticoagulants and anticonvulsants. Some of these exclusions inevitably reflect the patient mix of a referral center; nevertheless, comorbidity and its therapy are common in the age range in which osteoporosis is prevalent and would, therefore, be expected to be present in patients in general medical practice as well. Thus a large fraction, perhaps the majority, of patients with diagnoses of osteoporosis who are candidates for treatment by their physicians, are not eligible for entry into typical treatment trials. The results of such trials may, therefore, have uncertain applicability to types of patients excluded, both for safety and for efficacy.


A simple protocol to routinely assess the uniformity of proteomics analyses.
Mass-spectrometry-based proteomic approaches are increasingly applied to biological and clinical studies. Initially used by specialized laboratories, the technology has matured and gained acceptance by the community, using various analytical processes and platforms. To facilitate data comparison and integration across laboratories, there is a need to harmonize analytical processes to ensure the generation of reliable proteomic data sets. This is especially critical in the context of large initiatives, such as the Human Proteome Project promoted by the Human Proteome Organization (HUPO). Quality control is a first step toward the harmonization of proteomics data sets. We have developed a procedure to routinely assess the uniformity of proteomics analyses. It relies on a simple protocol based on three proteins and two sets of isotopically labeled peptides, one being added prior to tryptic digestion and the second one prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The proposed method evaluates in a single step both the sample preparation, by measuring the relative amounts of endogenous peptides and their isotopically labeled counterparts, and the LC-MS platform performance, by monitoring the main LC-MS attributes for reference peptides. The procedure is simple and easy to implement into routine workflows typically employed by the proteomics community.


Substrate deformation regulates DRM2-mediated DNA methylation in plants.
DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.


Changes in body weight and food choice in those attempting smoking cessation: a cluster randomised controlled trial.
Fear of weight gain is a barrier to smoking cessation and significant cause of relapse for many people. The provision of nutritional advice as part of a smoking cessation programme may assist some in smoking cessation and perhaps limit weight gain. The aim of this study was to determine the effect of a structured programme of dietary advice on weight change and food choice, in adults attempting smoking cessation. Cluster randomised controlled design. Classes randomised to intervention commenced a 24-week intervention, focussed on improving food choice and minimising weight gain. Classes randomised to control received "usual care". Twenty-seven classes in Greater Glasgow were randomised between January and August 2008. Analysis, including those who continued to smoke, showed that actual weight gain and percentage weight gain was similar in both groups. Examination of data for those successful at giving up smoking showed greater mean weight gain in intervention subjects (3.9 (SD 3.1) vs. 2.7 (SD 3.7) kg). Between group differences were not significant (p = 0.23, 95% CI -0.9 to 3.5). In comparison to baseline improved consumption of fruit and vegetables and breakfast cereal were reported in the intervention group. A higher percentage of control participants continued smoking (74% vs. 66%). The intervention was not successful at minimising weight gain in comparison to control but was successful in facilitating some sustained improvements in the dietary habits of intervention participants. Improved quit rates in the intervention group suggest that continued contact with advisors may have reduced anxieties regarding weight gain and encouraged cessation despite weight gain. Research should continue in this area as evidence suggests that the negative effects of obesity could outweigh the health benefits achieved through reductions in smoking prevalence.


Cognitive interviews guide design of a new CAM patient expectations questionnaire.
No consistent relationship exists between pre-treatment expectations and therapeutic benefit from various complementary and alternative medicine (CAM) therapies in clinical trials. However, many different expectancy measures have been used in those studies, with no validated questionnaires clearly focused on CAM and pain. We undertook cognitive interviews as part of a process to develop and validate such a questionnaire. We reviewed questions about expectations of benefits of acupuncture, chiropractic, massage, or yoga for pain. Components of the questions - verbs, nouns, response options, terms and phrases describing back pain - were identified. Using seven different cognitive interview scripts, we conducted 39 interviews to evaluate how individuals with chronic low back pain understood these individual components in the context of expectancy questions for a therapy they had not yet received. Chosen items were those with the greatest agreement and least confusion among participants, and were closest to the meanings intended by the investigators. The questionnaire drafted for psychometric evaluation had 18 items covering various domains of expectancy. "Back pain" was the most consistently interpreted descriptor for this condition. The most understandable response options were 0-10 scales, a structure used throughout the questionnaire, with 0 always indicating no change, and 10 anchored with an absolute descriptor such as "complete relief". The use of words to describe midpoints was found to be confusing. The word "expect" held different and shifting meanings for participants. Thus paired items comparing "hope" and "realistically expect" were chosen to evaluate 5 different aspects of treatment expectations (back pain; back dysfunction and global effects; impact of back pain on specific areas of life; sleep, mood, and energy; coping). "Impact of back pain" on various areas of life was found to be a consistently meaningful concept, and more global than "interference". Cognitive interviews identified wordings with considerable agreement among both participants and investigators. Some items widely used in clinical studies had different meanings to participants than investigators, or were confusing to participants. The final 18-item questionnaire is undergoing psychometric evaluation with goals of streamlining as well as identifying best items for use when questionnaire length is constrained.


Population structure of morphological traits in Clarkia dudleyana. I. Comparison of FST between allozymes and morphological traits.
Studies of genetic variation at allozyme loci, assumed to be selectively neutral, have provided valuable insights into the genetic structure of numerous populations. The degree to which population structure of allozyme variation reflects that of quantitative traits, however, is not well resolved. Here, we compare estimates of population differentiation (FST) of 11 populations for allozymes with those for nine discrete and nine continuous morphological traits. Overall, the allozymes have the lowest FST estimates, indicating relatively little population differentiation. Excepting two traits, petal width and long internode length, the continuous morphological traits have estimates similar to those from allozymes. The discrete morphological traits tend to have the highest estimates. On a single trait basis, estimates of FST for four discrete and two continuous traits are higher than those for allozymes. A more detailed (narrow-sense quantitative) genetic study of two populations suggests that these estimates of FST may underestimate the true value because of dominance. Clustering analyses show that the pattern of differentiation for the discrete morphological traits strongly reflects the geographical distribution of the populations, whereas the patterns for the continuous traits and allozymes do not. These results suggest that selection has been occurring on the discrete morphological traits, selecting toward a common optimum within each geographic group, and optima differing among geographic groups.


Assessment of chemically separated carbon nanotubes for nanoelectronics.
It remains an elusive goal to obtain high performance single-walled carbon-nanotube (SWNT) electronics such as field effect transistors (FETs) composed of single- or few-chirality SWNTs, due to broad distributions in as-grown materials. Much progress has been made by various separation approaches to obtain materials enriched in metal or semiconducting nanotubes or even in single chiralties. However, research in validating SWNT separations by electrical transport measurements and building functional electronic devices has been scarce. Here, we performed length, diameter, and chirality separation of DNA functionalized HiPco SWNTs by chromatography methods, and we characterized the chiralities by photoluminescence excitation spectroscopy, optical absorption spectroscopy, and electrical transport measurements. The use of these combined methods provided deeper insight to the degree of separation than either technique alone. Separation of SWNTs by chirality and diameter occurred at varying degrees that decreased with increasing tube diameter. This calls for new separation methods capable of metallicity or chirality separation of large diameter SWNTs (in the approximately 1.5 nm range) needed for high performance nanoelectronics. With most of the separated fractions enriched in semiconducting SWNTs, nanotubes placed in parallel in short-channel (approximately 200 nm) electrical devices fail to produce FETs with high on/off switching, indicating incomplete elimination of metallic species. In rare cases with a certain separated SWNT fraction, we were able to fabricate FET devices composed of small-diameter, chemically separated SWNTs in parallel, with high on-/off-current (I(on)/I(off)) ratios up to 105 owing to semiconducting SWNTs with only a few (n,m) chiralities in the fraction. This was the first time that chemically separated SWNTs were used for short channel, all-semiconducting SWNT electronics dominant by just a few (n,m)'s. Nevertheless, the results suggest that much improved chemical separation methods are needed to produce nanotube electronics at a large scale.


The VICI-trial: high frequency oscillation versus conventional mechanical ventilation in newborns with congenital diaphragmatic hernia: an international multicentre randomized controlled trial.
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly of the diaphragm resulting in pulmonary hypoplasia and pulmonary hypertension. It is associated with a high risk of mortality and pulmonary morbidity. Previous retrospective studies have reported high frequency oscillatory ventilation (HFO) to reduce pulmonary morbidity in infants with CDH, while others indicated HFO to be associated with worse outcome. We therefore aimed to develop a randomized controlled trial to compare initial ventilatory treatment with high-frequency oscillation and conventional ventilation in infants with CDH. This trial is designed as a multicentre trial in which 400 infants (200 in each arm) will be included. Primary outcome measures are BPD, described as oxygen dependency by day 28 according to the definition of Jobe and Bancalari, and/or mortality by day 28. All liveborn infants with CDH born at a gestational age of over 34 weeks and no other severe congenital anomalies are eligible for inclusion. Parental informed consent is asked antenatally and the allocated ventilation mode starts within two hours after birth. Laboratory samples of blood, urine and tracheal aspirate are taken at the first day of life, day 3, day 7, day 14 and day 28 to evaluate laboratory markers for ventilator-induced lung injury and pulmonary hypertension. To date, randomized clinical trials are lacking in the field of CDH. The VICI-trial, as the first randomized clinical trial in the field of CDH, may provide further insight in ventilation strategies in CDH patient. This may hopefully prevent mortality and morbidity. Netherlands Trial Register (NTR): NTR1310.


Mapping a gene involved in regulating dietary cholesterol absorption. The sitosterolemia locus is found at chromosome 2p21.
The molecular mechanisms regulating the amount of dietary cholesterol retained in the body as well as the body's ability to selectively exclude other dietary sterols are poorly understood. Studies of the rare autosomal recessively inherited disease sitosterolemia (OMIM 210250) may shed some light on these processes. Patients suffering from this disease appear to hyperabsorb both cholesterol and plant sterols from the intestine. Additionally, there is failure of the liver's ability to preferentially and rapidly excrete these non-cholesterol sterols into bile. Consequently, people who suffer from this disease have very elevated plasma plant sterol levels and develop tendon and tuberous xanthomas, accelerated atherosclerosis, and premature coronary artery disease. Identification of this gene defect may therefore throw light on regulation of net dietary cholesterol absorption and lead to an advancement in the management of this important cardiovascular risk factor. By studying 10 well-characterized families with this disorder, we have localized the genetic defect to chromosome 2p21, between microsatellite markers D2S1788 and D2S1352 (maximum lodscore 4.49, theta = 0.0).


Potential of information technology in dental education.
The use of information technology (IT) in dentistry is far ranging. In order to produce a working document for the dental educator, this paper focuses on those methods where IT can assist in the education and competence development of dental students and dentists (e.g. e-learning, distance learning, simulations and computer-based assessment). Web pages and other information-gathering devices have become an essential part of our daily life, as they provide extensive information on all aspects of our society. This is mirrored in dental education where there are many different tools available, as listed in this report. IT offers added value to traditional teaching methods and examples are provided. In spite of the continuing debate on the learning effectiveness of e-learning applications, students request such approaches as an adjunct to the traditional delivery of learning materials. Faculty require support to enable them to effectively use the technology to the benefit of their students. This support should be provided by the institution and it is suggested that, where possible, institutions should appoint an e-learning champion with good interpersonal skills to support and encourage faculty change. From a global prospective, all students and faculty should have access to e-learning tools. This report encourages open access to e-learning material, platforms and programs. The quality of such learning materials must have well defined learning objectives and involve peer review to ensure content validity, accuracy, currency, the use of evidence-based data and the use of best practices. To ensure that the developers' intellectual rights are protected, the original content needs to be secure from unauthorized changes. Strategies and recommendations on how to improve the quality of e-learning are outlined. In the area of assessment, traditional examination schemes can be enriched by IT, whilst the Internet can provide many innovative approaches. Future trends in IT will evolve around improved uptake and access facilitated by the technology (hardware and software). The use of Web 2.0 shows considerable promise and this may have implications on a global level. For example, the one-laptop-per-child project is the best example of what Web 2.0 can do: minimal use of hardware to maximize use of the Internet structure. In essence, simple technology can overcome many of the barriers to learning. IT will always remain exciting, as it is always changing and the users, whether dental students, educators or patients are like chameleons adapting to the ever-changing landscape.


Grade of the inner cell mass, but not trophectoderm, predicts live birth in fresh blastocyst single transfers.
Debate continues over which morphological parameter is most important in selecting blastocysts for transfer. We aimed to investigate which parameter more accurately predicts the occurrence of a live birth by designing a retrospective cohort study of 1084 fresh elective single blastocyst transfers. Primary outcome was live birth rate (LBR) and secondary outcomes were implantation, clinical pregnancy and early pregnancy loss rates. Blastocyst expansion and inner cell mass (ICM), but not trophoectoderm, were associated with LBR in the definitive multivariable regression analysis. When ICM grade dropped from A to C the likelihood of achieving a live birth was reduced by 55% (OR= 0.45, 95% CI 0.26-0.79, p = .005). These results were similar for clinical pregnancy rates. Early pregnancy loss rates of embryos with ICM grade C were more than double (38.0%) compared to those of grades A (15.95%) and B (17.17%, p = .002). The transfer of an embryo with an optimal inner cell mass reduces early pregnancy loss and increases the likelihood of a live birth. We did not find any significant association between trophectoderm and LBR in the multivariable analysis in contrast with recent studies.


Evaluation of deficiencies in current discharge summaries for dialysis patients in Canada.
Deficits in the transfer of information between inpatient and outpatient physicians are common and pose a patient safety risk. This is particularly the case for vulnerable populations such as patients with end-stage renal disease requiring dialysis. These patients have unique and complex health care needs that may not be effectively communicated on standard discharge summaries, which may result in potential medical errors and adverse events. To evaluate Canadian dialysis center directors' perceptions of deficiencies in the content and quality of hospital discharge summaries for dialysis patients. A web-based, cross-sectional survey of Canadian dialysis center directors was performed between September and November 2010. The survey consisted of three parts. The first part was designed to assess dialysis center directors' attitudes on the quality of discharge summaries they receive. The second part was designed to elicit respondents' preferences for discharge summary content, and the third part consisted of questions regarding demographic and practice information. Of 79 dialysis center directors, 21 (27%) completed the survey. Sixty-two percent felt that current discharge summaries inadequately communicate dialysis-specific information. Receipt of antibiotics for line sepsis or peritonitis, modifications to vascular access, and changes in target weight/dialysis prescription were rated as essential dialysis-specific information to include in discharge summaries by respondents. Over three quarters of dialysis center directors find the current practice of transferring discharge information for hospitalized dialysis patients grossly inadequate. The inclusion of dialysis-specific information may improve the quality of discharge summaries for dialysis patients.


A clinical analysis of two indolent lymphoma entities: mantle cell lymphoma and marginal zone lymphoma (including the mucosa-associated lymphoid tissue and monocytoid B-cell subcategories): a Southwest Oncology Group study.
The objectives of this study were (1) to determine the clinical presentation and natural history associated with two newly recognized pathologic entities termed mantle cell lymphoma (MCL) and marginal zone lymphoma (MZL), including the mucosa-associated lymphoid tissue (MALT) and monocytoid B-cell subcategories, and (2) to determine whether these entities differ clinically from the other relatively indolent non-Hodgkin's lymphomas with which they have been previously classified. We reviewed the conventional pathology and clinical course of 376 patients who had no prior therapy; had stage III/IV disease; were classified as Working Formulation categories A, B, C, D, or E; and received cyclophosphamide, doxorubicin, vincristine, prednisone (CHOP) on Southwest Oncology Group (SWOG) studies no. 7204, 7426, or 7713. All slides were reviewed by the three pathologists who reached a consensus diagnosis. Age, sex, performance status, bone marrow and/or gastrointestinal involvement, failure-free survival, and overall survival were compared among all the categories. We found that (1) MCL and MZL each represent approximately 10% of stage III or IV patients previously classified as Working Formulation categories A through E and treated with CHOP on SWOG clinical trials; (2) the failure-free survival and overall survival of patients with MZL is the same as that of patients with Working Formulation categories A through E, but the failure-free survival and overall survival of the monocytoid B-cell patients were higher than that of the MALT lymphoma patients (P = .009 and .007, respectively); and (3) the failure-free survival and overall survival of patients with MCL is significantly worse than that of patients with Working Formulation categories A through E (P = .0002 and .0001, respectively). In conclusion, patients with advanced stage MALT lymphomas may have a more aggressive course than previously recognized. Patients with MCL do not have an indolent lymphoma and are candidates for innovative therapy.


ACTH responses to somatostatin, valproic acid and dexamethasone in Nelson's syndrome.
Pituitary tumours occurring in patients bilaterally adrenalectomized because of Cushing's disease (Nelson's syndrome) are frequently invasive and a complete their resection is not possible in most of them. Administration of the drugs decreasing ACTH secretion could be helpful in such unresectable tumours. We tried to evaluate the influence of somatostatin and valproic acid, compared to dexamethasone, in short-term studies, on plasma ACTH levels in Nelson's syndrome (NS). Basal ACTH levels were determined within 18 h after last dose of hydrocortisone and next, 1 and 2 hours following oral administration of 20 mg of hydrocortisone. Somatostatin was injected s.c. in two patients with NS while sodium valproate and dexamethasone were administered orally for three days in three patients with NS (two with an invasive pituitary tumour and one with a localized, intrasellar adenoma). The blood for ACTH and cortisol determination was drawn before the tests (two hours after 20 mg of hydrocortisone ingestion) as well as 1 and 2 hours following somatostatin injection and after 3 days of valproic acid or dexamethasone administration. High plasma ACTH levels were found before the tests. Somatostatin lowered ACTH levels in both patients, more effectively in the patient with non-invasive pituitary adenoma. Valproic acid decreased moderately ACTH concentration in two patients, while following dexamethasone administration a fall in ACTH levels was observed in all three patients, the most evident in the patient with a non-invasive Nelson's adenoma. Somatostatin seemed to be more effective in its inhibitory action on ACTH secretion than valproic acid, thus its administration in invasive cases of NS could be tried as a supplementary method to neurosurgery. The response to dexamethasone administration indicates that a feed-back regulation, although impaired, exists in these cases.


Elevated serum sialic acid concentration in NIDDM and its relationship to blood pressure and retinopathy.
In view of the possible link between serum sialic acid and cardiovascular disease in the general population, we investigated whether serum total and lipid-associated sialic concentrations are elevated in NIDDM patients compared with normal subjects. We also investigated how sialic acid levels relate to glycemic control, blood pressure, microalbuminuria, retinopathy, and serum lipid levels. We selected 20 NIDDM patients at random and matched them for age and sex with 20 normal subjects. The patients also had a similar BMI as the control subjects. A first morning blood sample was taken for sialic acid, glucose, fructosamine, and lipid analysis, as was a first morning urine sample for assessment of microalbuminuria. Retinopathy was assessed by fundoscopy. Both total and lipid-associated sialic acid levels were elevated in the NIDDM patients compared with control subjects (mean +/- SD, total: 0.74 +/- 0.11 vs. 0.60 +/- 0.22 g/L, P < 0.02; lipid-associated: 0.18 +/- 0.04 vs 0.12 +/- 0.04 g/L, P < 0.001). Total serum sialic acid was correlated with systolic blood pressure (r = 0.58, P < 0.01) and diastolic blood pressure (r = 0.58, P < 0.02). There was no significant relationship of total sialic acid with age, duration of diabetes, BMI, microalbuminuria, serum triglyceride, blood glucose, or serum fructosamine. A relationship of lipid-associated sialic acid levels and systolic blood pressure did not reach significance (P = 0.09). In 9 patients with background retinopathy with or without maculopathy, the total serum sialic acid concentration was higher than in those without retinopathy (0.81 +/- 0.09 vs. 0.69 +/- 0.10 g/L, P < 0.008). Lipid-associated sialic acid levels were similar in those with and without retinopathy. (The conversion factor for standard units to SI units is 1 gL = 3.2 mM.) Total serum sialic acid levels were significantly elevated in a relatively small group of NIDDM patients and were correlated with hypertension and retinopathy. A larger study of circulating sialic acid concentrations as a risk factor for the development or marker of diabetic angiopathy is therefore justified.


Proton beam therapy utilization in adults with primary brain tumors in the United States.
The utilization of proton beam therapy (PBT) as the primary treatment of adults with primary brain tumors (APBT) was evaluated through query of the National Cancer Database (NCDB) between the years 2004 and 2015. International Classification of Diseases for Oncology code for each patient was stratified into six histology categories; high-grade gliomas, medulloblastomas, ependymomas, other gliomas, other malignant tumors, or other benign intracranial tumors. Demographics of the treatment population were also analyzed. A total of 1,296 patients received PBT during the 11-year interval for treatment of their primary brain tumor. High-grade glioma, medulloblastoma, ependymoma, other glioma, other malignant, and other benign intracranial histologies made up 39%, 20%, 13%, 12%, 13%, and 2% of the cohort, respectively. The number of patients treated per year increased from 34 to 300 in years 2004 to 2015. Histologies treated with PBT varied over the 11-year interval with high-grade gliomas comprising 75% and 45% at years 2004 and 2015, respectively. The majority of the patient population was 18-29 years of age (59%), Caucasian race (73%), had median reported income of over $63,000 (46%), were privately insured (68%), and were treated at an academic institution (70%). This study characterizes trends of malignant and benign APBT histologies treated with PBT. Our data from 2004 through 2015 illustrates a marked increase in the utilization of PBT in the treatment of APBT and shows variability in the tumor histology treated over this time.


Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3.
Intestinal mucosal integrity is dependent on epithelial function and a regulated immune response to injury. Fucosyltransferase VII (Fuc-TVII) is an essential enzyme required for the expression of the functional ligand for E- and P-selectin. Trefoil factor 3 (TFF3) is involved in both protecting the intestinal epithelium against injury as well as aiding in wound repair following injury. The aim of the present study was to assess the interplay between barrier function and leukocyte recruitment in intestinal inflammation. More specifically, we aimed to examine how targeted disruption of Fuc-TVII either in wild-type or TFF3(-/-) mice would alter their susceptibility to colonic injury. TFF3 and Fuc-TVII double-knockout mice (TFF3/Fuc-TVII(-/-) mice) were generated by mating TFF3(-/-) and Fuc-TVII(-/-) mice. Colitis was induced by administration of dextran sodium sulfate (DSS) (2.5% wt/vol) in the drinking water. Changes in baseline body weight, diarrhea, and fecal blood were assessed daily. Upon euthanasia, extents of colonic inflammation were assessed macroscopically, microscopically, and through quantification of myeloperoxidase (MPO) activity. Colonic lymphocyte subpopulations were assessed at 6 days after administration of DSS by flow cytometry and immunohistochemistry. No baseline intestinal inflammation was found in TFF3/Fuc-TVII(-/-), TFF3(-/-), Fuc-TVII(-/-), or wild-type mice. Loss of Fuc-TVII resulted in a reduction in disease severity whereas TFF3(-/-) mice were markedly more susceptible to DSS-induced colitis. Remarkably, the loss of Fuc-TVII in TFF3(-/-) mice markedly decreased the severity of DSS-induced colitis as evidenced by reduced weight loss, diarrhea, decreased colonic MPO levels and improved survival. Furthermore, the loss of TFF3 resulted in increased severity of spontaneous colitis in IL-2/beta-microglobulin-deficient mice. These studies highlight the importance of the interplay between factors involved in the innate immune response, mucosal barrier function, and genes involved in regulating leukocyte recruitment and other aspects of the immune response.


A meta-analysis of the Dark Triad and work behavior: a social exchange perspective.
We reviewed studies of the Dark Triad (DT) personality traits--Machiavellianism, narcissism, and psychopathy-and meta-analytically examined their implications for job performance and counterproductive work behavior (CWB). Relations among the DT traits and behaviors were extracted from original reports published between 1951 and 2011 of 245 independent samples (N = 43,907). We found that reductions in the quality of job performance were consistently associated with increases in Machiavellianism and psychopathy and that CWB was associated with increases in all 3 components of the DT, but that these associations were moderated by such contextual factors as authority and culture. Multivariate analyses demonstrated that the DT explains moderate amounts of the variance in counterproductivity, but not job performance. The results showed that the 3 traits are positively related to one another but are sufficiently distinctive to warrant theoretical and empirical partitioning.


Emotional conditioning to masked stimuli and modulation of visuospatial attention.
Two studies investigated the effects of conditioning to masked stimuli on visuospatial attention. During the conditioning phase, masked snakes and spiders were paired with a burst of white noise, or paired with an innocuous tone, in the conditioned stimulus (CS)+ and CS- conditions, respectively. Attentional allocation to the CSs was then assessed with a visual probe task, in which the CSs were presented unmasked (Experiment 1) or both unmasked and masked (Experiment 2), together with fear-irrelevant control stimuli (flowers and mushrooms). In Experiment 1, participants preferentially allocated attention to CS+ relative to control stimuli. Experiment 2 suggested that this attentional bias depended on the perceived aversiveness of the unconditioned stimulus and did not require conscious recognition of the CSs during both acquisition and expression.


Role of a Candida albicans P1-type ATPase in resistance to copper and silver ion toxicity.
Copper ion homeostasis is complicated in that copper is an essential element needed for a variety of cellular processes but is toxic at excess levels. To identify Candida albicans genes that are involved in resistance to copper ion toxicity, a library containing inserts of C. albicans genomic DNA was used to complement the copper sensitivity phenotype of a Saccharomyces cerevisiae cup1Delta strain that is unable to produce Cup1p, a metallothionein (MT) responsible for high-level copper ion resistance. A P1-type ATPase (CPx type) that is closely related to the human Menkes and Wilson disease proteins was cloned. The gene encoding this pump was termed CRD1 (for copper resistance determinant). A gene encoding a 76-amino-acid MT similar to higher eukaryotic MTs in structure was also cloned, and the gene was termed CRD2. Transcription of the CRD1 gene was found to increase upon growth with increasing copper levels, while the CRD2 mRNA was expressed at a constant level. Strains with the CRD1 gene disrupted were extremely sensitive to exogenous copper and failed to grow in medium containing 100 microM CuSO(4). These crd1 strains also exhibited increased sensitivity to silver and cadmium, indicating that Crd1p is somewhat promiscuous with respect to metal ion transport. Although strains with the CRD2 gene disrupted showed reduced growth rate with increasing copper concentration, the crd2 mutants eventually attained wild-type levels of growth, demonstrating that CRD2 is less important for resistance to copper ion toxicity. Crd1p is the first example of a eukaryotic copper pump that provides the primary source of cellular copper resistance, and its ability to confer silver resistance may enhance the prevalence of C. albicans as a nosocomial pathogen.


Real-time fMRI paradigm control, physiology, and behavior combined with near real-time statistical analysis.
This study presents an integrated approach to on-line fMRI data processing that combines real-time paradigm control and real-time MR image statistical analysis with nearly real-time integration of fMRI behavioral and physiological data. The real-time paradigms involve accurate timing control of multiple independent processing streams for stimulus presentation, physiological monitoring, behavioral response recording, and scanner synchronization. The real-time image analysis provides high resolution MR image reconstruction, head motion detection, translational motion correction, and t test statistical activation maps for either block design or single-trial based paradigms. The near real-time analysis allows physiological and behavioral data collected during a paradigm to be combined with the MR time series and provides extended data filtering and statistical processing within a few minutes after the end of the scan. This integrated approach improves fMRI reliability for both clinical and research studies.


Optical properties of deep ice at the South Pole: absorption.
We discuss recent measurements of the wavelength-dependent absorption coefficients in deep South Pole ice. The method uses transit-time distributions of pulses from a variable-frequency laser sent between emitters and receivers embedded in the ice. At depths of 800-1000 m scattering is dominated by residual air bubbles, whereas absorption occurs both in ice itself and in insoluble impurities. The absorption coefficient increases approximately exponentially with wavelength in the measured interval 410-610 nm. At the shortest wavelength our value is approximately a factor 20 below previous values obtained for laboratory ice and lake ice; with increasing wavelength the discrepancy with previous measurements decreases. At ~415 to ~500 nm the experimental uncertainties are small enough for us to resolve an extrinsic contribution to absorption in ice: submicrometer dust particles contribute by an amount that increases with depth and corresponds well with the expected increase seen near the Last Glacial Maximum in Vostok and Dome C ice cores. The laser pulse method allows remote mapping of gross structure in dust concentration as a function of depth in glacial ice.


Alcohol and heightened aggression in individual mice.
The objective of the current research was to study the large individual differences in alcohol effects on aggressive behavior under systematically varied conditions in experimental protocols with mice. Three experiments were conducted with outbred Swiss-Webster derived mice that identified those individuals whose aggressive behavior was reliably heightened by low acute alcohol doses. In all experimental protocols, low alcohol doses were orally administered to a "resident" male mouse that subsequently confronted an "intruder" opponent for 5 min while all salient elements of aggressive behavior and motor activities were quantified. In all three experiments, alcohol (1.0 g/kg) heightened aggressive behavior by at least two standard deviations of the individual's water vehicle control mean in 27% of the mice. In 64% of mice, no reliable change in aggressive behavior was detected after the identical alcohol treatment, and in 9% of the mice alcohol decreased aggressive behavior. Experiments differed in protocol indicating that these aggression-heightening effects were evident in resident mice that were either maintained at restricted or unlimited amounts of food, housed singly or in breeding pairs with a female partner, and conditioned to perform daily a food-reinforced task or remained undisturbed. The first experiment found the aggression-heightening effects to persist during weekly challenges for at least 2 months (n = 8 of 30). The second experiment showed these effects at intervals from 5 to 60 min after alcohol administration. Blood alcohol concentrations reached peak level within 5 to 10 min after oral administration in mice that had confronted an intruder. Those mice in whom alcohol heightened aggressive behavior (n = 21) did not differ from those that showed suppressed levels (n = 9) in terms of blood alcohol concentrations (79.6 vs. 82.4 mg%), suggesting that the intensity and frequency of aggressive behavior after alcohol were not directly dependent on the amount of alcohol in the circulation. The third experiment revealed that alcohol's (0.1 to 5.6 g/kg) effects on heightened aggressive behavior (n = 11) are dissociated from those on concurrently measured high- or low-rate operant performance as engendered by a multiple FR 30-FI 600 sec schedule of reinforcement. Current results indicate that this alcohol effect is relatively specific to aggressive behavior in individual animals, offering the opportunity for neuropharmacological and molecular characterization.


Toward understanding social cues and signals in human-robot interaction: effects of robot gaze and proxemic behavior.
As robots are increasingly deployed in settings requiring social interaction, research is needed to examine the social signals perceived by humans when robots display certain social cues. In this paper, we report a study designed to examine how humans interpret social cues exhibited by robots. We first provide a brief overview of perspectives from social cognition in humans and how these processes are applicable to human-robot interaction (HRI). We then discuss the need to examine the relationship between social cues and signals as a function of the degree to which a robot is perceived as a socially present agent. We describe an experiment in which social cues were manipulated on an iRobot Ava(TM) mobile robotics platform in a hallway navigation scenario. Cues associated with the robot's proxemic behavior were found to significantly affect participant perceptions of the robot's social presence and emotional state while cues associated with the robot's gaze behavior were not found to be significant. Further, regardless of the proxemic behavior, participants attributed more social presence and emotional states to the robot over repeated interactions than when they first interacted with it. Generally, these results indicate the importance for HRI research to consider how social cues expressed by a robot can differentially affect perceptions of the robot's mental states and intentions. The discussion focuses on implications for the design of robotic systems and future directions for research on the relationship between social cues and signals.


Methane emissions abatement by multi-ion-exchanged zeolite A prepared from both commercial-grade zeolite and coal fly ash.
The performance of multimetal-(Cu, Cr, Zn, Ni, and Co)-ion-exchanged zeolite A prepared from both a commercial-grade sample and one produced from coal fly ash in methane emissions abatement was evaluated in this study. The ion-exchange process was used to load the metal ions in zeolite A samples. The methane conversion efficiency by the samples was studied under various parameters including the amount of metal loading (7.3-19.4 wt%), reaction temperature (25-500 degrees C), space velocity (8400-41 900 h(-1)), and methane concentration (0.5-3.2 vol %). At 500 degrees C, the original commercial-grade zeolite A catalyzed 3% of the methane only, whereas the addition of different percentages of metals in the sample enhanced the methane conversion efficiency by 40-85%. Greater methane conversion was observed by increasing the percentage of metals added to the zeolite even though the BET surface area of the zeolite consequently decreased. Higher percentage methane conversion over the multi-ion-exchanged samples was observed at lower space velocities indicating the importance of the mass diffusion of reactants and products in the zeolite. Compared to the multi-ion-exchanged zeolite A prepared from the commercial-grade zeolite, the one produced from coal fly ash demonstrated similar performances in methane emissions abatement, showing the potential use of this low cost recycled material in gaseous pollutant treatment.


Filamentary switching: synaptic plasticity through device volatility.
Replicating the computational functionalities and performances of the brain remains one of the biggest challenges for the future of information and communication technologies. Such an ambitious goal requires research efforts from the architecture level to the basic device level (i.e., investigating the opportunities offered by emerging nanotechnologies to build such systems). Nanodevices, or, more precisely, memory or memristive devices, have been proposed for the implementation of synaptic functions, offering the required features and integration in a single component. In this paper, we demonstrate that the basic physics involved in the filamentary switching of electrochemical metallization cells can reproduce important biological synaptic functions that are key mechanisms for information processing and storage. The transition from short- to long-term plasticity has been reported as a direct consequence of filament growth (i.e., increased conductance) in filamentary memory devices. In this paper, we show that a more complex filament shape, such as dendritic paths of variable density and width, can permit the short- and long-term processes to be controlled independently. Our solid-state device is strongly analogous to biological synapses, as indicated by the interpretation of the results from the framework of a phenomenological model developed for biological synapses. We describe a single memristive element containing a rich panel of features, which will be of benefit to future neuromorphic hardware systems.


Exposure to widespread environmental endocrine disrupting chemicals and human sperm sex ratio.
In recent years, a trend toward a declining proportion of male births has been noted in several, but not all, industrialized countries. The underlying reason for the drop in the sex ratio is unclear, but one theory states that widespread environmental endocrine disrupting chemicals affecting the male reproductive system in a negative manner could be part of the explanation. The present study was designed to investigate whether the urinary phthalate, pyrethroids and polycyclic aromatic hydrocarbons metabolites concentrations were associated with sperm Y:X ratio. The study population consisted of 194 men aged under 45 years of age who attended infertility clinic in Lodz, Poland for diagnostic purposes with normal semen concentration of 20-300 mln/ml or with slight oligozoospermia (semen concentration of 15-20 mln/ml) (WHO, 1999). The Y:X ratio was assessed by fluorescent in situ hybridization. Urinary concentrations of 1-hydroxypyrene were measured by high performance liquid chromatography, phthalate metabolites were analyzed using a procedure based on the LC-MS/MS methods and metabolites of synthetic pyrethroids were assessed by gas chromatography ion-tap mass spectrometry method. After adjustment for potential confounders (past diseases, age, abstinence, smoking, alcohol consumption, sperm concentration, motility, morphology) 5OH MEHP, CDCCA to TDCCA and 1-OHP was negatively related to Y:X sperm chromosome ratio (p = 0.033, p < 0.001, p = 0.047 respectively). As this is the first study to elucidate the association between the level of metabolites of widespread environmental endocrine disrupting chemicals (phthalates, synthetic pyrethroids, polycyclic aromatic hydrocarbons) on sex chromosome ratio in sperm therefore, these findings require further replication in other populations.


RNA interference dynamics in juvenile Fasciola hepatica are altered during in vitro growth and development.
For over a decade RNA interference (RNAi) has been an important molecular tool for functional genomics studies in parasitic flatworms. Despite this, our understanding of RNAi dynamics in many flatworm parasites, such as the temperate liver fluke (Fasciola hepatica), remains rudimentary. The ability to maintain developing juvenile fluke in vitro provides the opportunity to perform functional studies during development of the key pathogenic life stage. Here, we investigate the RNAi competence of developing juvenile liver fluke. Firstly, all life stages examined possess, and express, core candidate RNAi effectors encouraging the hypothesis that all life stages of F. hepatica are RNAi competent. RNAi effector analyses supported growing evidence that parasitic flatworms have evolved a separate clade of RNAi effectors with unknown function. Secondly, we assessed the impact of growth/development during in vitro culture on RNAi in F. hepatica juveniles and found that during the first week post-excystment liver fluke juveniles exhibit quantitatively lower RNAi mediated transcript knockdown when maintained in growth inducing media. This did not appear to occur in older in vitro juveniles, suggesting that rapidly shifting transcript dynamics over the first week following excystment alters RNAi efficacy after a single 24 h exposure to double stranded (ds)RNA. Finally, RNAi efficiency was found to be improved through use of a repeated dsRNA exposure methodology that has facilitated silencing of genes in a range of tissues, thereby increasing the utility of RNAi as a functional genomics tool in F. hepatica.


Assignment of a locus for dominantly inherited venous malformations to chromosome 9p.
Venous malformation is the most common type of vascular anomaly. Depending upon size and location, these slow-flow anomalies may cause pain, anatomic distortion, or threaten life. Most venous malformations occur sporadically and present as solitary lesions. They also occur in several syndromes, some of which demonstrate Mendelian inheritance. We have mapped the locus for an autosomal dominant disorder in a three generation family that manifests as multiple cutaneous and mucosal venous malformations. This locus lies within a 24 cM interval on chromosome 9p, defined by the markers D9S157 and D9S163. The alpha and beta interferon gene cluster and the putative tumor suppressor genes MTS1 and MTS2 are also in this region. Characterization of the gene responsible for this disorder should yield insights into the precise pathogenic mechanisms for venous malformations.


Histone variant HTZ1 shows extensive epistasis with, but does not increase robustness to, new mutations.
Biological systems produce phenotypes that appear to be robust to perturbation by mutations and environmental variation. Prior studies identified genes that, when impaired, reveal previously cryptic genetic variation. This result is typically interpreted as evidence that the disrupted gene normally increases robustness to mutations, as such robustness would allow cryptic variants to accumulate. However, revelation of cryptic genetic variation is not necessarily evidence that a mutationally robust state has been made less robust. Demonstrating a difference in robustness requires comparing the ability of each state (with the gene perturbed or intact) to suppress the effects of new mutations. Previous studies used strains in which the existing genetic variation had been filtered by selection. Here, we use mutation accumulation (MA) lines that have experienced minimal selection, to test the ability of histone H2A.Z (HTZ1) to increase robustness to mutations in the yeast Saccharomyces cerevisiae. HTZ1, a regulator of chromatin structure and gene expression, represents a class of genes implicated in mutational robustness. It had previously been shown to increase robustness of yeast cell morphology to fluctuations in the external or internal microenvironment. We measured morphological variation within and among 79 MA lines with and without HTZ1. Analysis of within-line variation confirms that HTZ1 increases microenvironmental robustness. Analysis of between-line variation shows the morphological effects of eliminating HTZ1 to be highly dependent on the line, which implies that HTZ1 interacts with mutations that have accumulated in the lines. However, lines without HTZ1 are, as a group, not more phenotypically diverse than lines with HTZ1 present. The presence of HTZ1, therefore, does not confer greater robustness to mutations than its absence. Our results provide experimental evidence that revelation of cryptic genetic variation cannot be assumed to be caused by loss of robustness, and therefore force reevaluation of prior claims based on that assumption.


The protein kinase complement of the human genome.
We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.


The Value of Diffusion-Weighted Imaging in Combination With Conventional Magnetic Resonance Imaging for Improving Tumor Detection for Early Cervical Carcinoma Treated With Fertility-Sparing Surgery.
This study aimed to investigate the value of diffusion-weighted imaging (DWI) in combination with conventional magnetic resonance imaging (MRI) for improving tumor detection in young patients treated with fertility-sparing surgery because of early cervical carcinoma. Fifty-four patients with stage Ia or Ib1 cervical carcinoma were enrolled into this study. Magnetic resonance examinations were performed for these patients using conventional MRI (including T1-weighted imaging, T2-weighted imaging, and dynamic contrast-enhanced MRI) and DWI. The apparent diffusion coefficient (ADC) values of cervical carcinoma were analyzed quantitatively and compared with that of adjacent epithelium. Sensitivity, positive predictive value, and accuracy of 2 sets of MRI sequences were calculated on the basis of histologic results, and the diagnostic ability of conventional MRI/DWI combinations was compared with that of conventional MRI. The mean ADC value from cervical carcinoma (mean, 786 × 10 mm/s ± 100) was significantly lower than that from adjacent epithelium (mean, 1352 × 10 mm/s ± 147) (P = 0.01). When the threshold ADC value set as 1010 × 10 mm/s, the sensitivity and specificity for differentiating cervical carcinoma from nontumor epithelium were 78.2% and 67.2%, respectively. The sensitivity and accuracy of conventional MRI for tumor detection were 76.0% and 70.4%, whereas the sensitivity and accuracy of conventional MRI/DWI combinations were 91.7% and 90.7%, respectively. Conventional MRI/DWI combinations revealed a positive predictive value of 97.8% and only 4 false-negative findings. The addition of DWI to conventional MRI considerably improves the sensitivity and accuracy of tumor detection in young patients treated with fertility-sparing surgery, which supports the inclusion quantitative analysis of ADC value in routine MRI protocol before fertility-sparing surgery.


Coagulation and fibrinolysis during lung surgery:an experimental study.
Postoperative thromboembolism is a serious complication, but the incidence following surgery for lung cancer appears to be much lower compared with other surgical specialties. The reason is unknown and one may speculate that the lungs are reservoirs of anticoagulants or fibrinolytic substances, which are released by manipulation of the lung parenchyma during surgery. Standardized lung manipulation, single-lung ventilation and pneumonectomy were performed in 10 anaesthetized pigs. Baseline and serial postmanipulation intravenous and intra-arterial blood samples were analysed for a wide range of fibrinolytic substances as well as pro- and anticoagulant factors. We found a transient but significant decrease in activated partial thromboplastin time (aPTT) and plasminogen activator inhibitor following manipulation of the lungs. Pneumonectomy resulted in minor but significant decrease in antithrombin and a significant increase in aPTT. All other measured substances were virtually constant. A wide range of fibrinolytic and anticoagulant substances remained unchanged during experimental lung manipulation. Minor changes were transient and not considered clinically relevant. Future studies should be initiated in humans because we have no deeper understanding why thromboembolic complications are relatively uncommon after general thoracic surgery compared with other surgical specialties.


Creating a continuum of care: integrating obstetricians and gynecologists in the care of young cancer patients.
Cancer therapy can be lifesaving but significantly diminish female reproductive potential. This review provides an overview of the deleterious effects of cancer treatments on reproductive function, the fertility preservation options currently available for young women, and the outcomes of pregnancy after cancer treatment. In addition, special considerations for women who are diagnosed with cancer during pregnancy are discussed. To optimize the continuum of care for the patient, new corridors of communication between obstetricians, gynecologists, and oncology specialists must be developed to ensure the best outcomes for the patient, both in terms of cancer treatment and fertility preservation.


Coinfection with hepatitis C virus and schistosomiasis: fibrosis and treatment response.
To assess whether schistosomiasis coinfection with chronic hepatitis C virus (HCV) influences hepatic fibrosis and pegylated-interferon/ribavirin (PEG-IFN/RIB) therapy response. This study was designed as a retrospective analysis of 3596 chronic HCV patients enrolled in the Egyptian National Program for HCV treatment with PEG-IFN/RIB. All patients underwent liver biopsy and anti-schistosomal antibodies testing prior to HCV treatment. The serology results were used to categorize the patients into group A (positive schistosomal serology) or group B (negative schistosomal serology). Patients in group A were given oral antischistosomal treatment (praziquantel, single dose) at four weeks prior to PEG-IFN/RIB. All patients received a 48-wk course of PEG-IFN (PEG-IFNα2a or PEG-IFNα2b)/RIB therapy. Clinical and laboratory follow-up examinations were carried out for 24 wk after cessation of therapy (to week 72). Correlations of positive schistosomal serology with fibrosis and treatment response were assessed by multiple regression analysis. Schistosomal antibody was positive in 27.3% of patients (15.9% females and 84.1% males). The patients in group A were older (P = 0.008) and had a higher proportion of males (P = 0.002) than the patients in group B. There was no significant association between fibrosis stage and positive schistosomal serology (P = 0.703). Early virological response was achieved in significantly more patients in group B than in group A (89.4% vs 86.5%, P = 0.015). However, significantly more patients in group A experienced breakthrough at week 24 than patients in group B (36.3% vs 32.3%, P = 0.024). End of treatment response was achieved in more patients in group B than in group A (62.0% vs 59.1%) but the difference did not reach statistical significance (P = 0.108). Sustained virological response occurred in significantly more patients in group B than in group A (37.6% vs 27.7%, P = 0.000). Multivariate logistic regression analysis of patient data at treatment weeks 48 and 72 showed that positive schistosomal serology was associated with failure of response to treatment at week 48 (OR = 1.3, P = 0.02) and at week 72 (OR = 1.7, P < 0.01). Positive schistosomal serology has no effect on fibrosis staging but is significantly associated with failure of response to HCV treatment despite antischistosomal therapy.


Integration of Medicare and Medicaid for dually eligible beneficiaries: A focus group study examining beneficiaries' early experiences in California's dual financial alignment demonstration.
In 2014 California implemented a federal dual alignment demonstration used a capitated managed healthcare model called Cal MediConnect (CMC) to integrate medical care and long term services and supports (LTSS) for beneficiaries with both Medicare and Medicaid. These beneficiaries often have complex care needs, including multiple chronic conditions and disabilities. By 2016, 120,000 eligible beneficiaries were enrolled in the program. Focus groups with enrolled beneficiaries were conducted to gather rich data about their early experiences with quality of care, access to care, and coordination of care in CMC plans and to identify recommendations for program improvement. Evaluators conducted 14 focus groups with 104 beneficiaries enrolled in CMC plans in 6 demonstration counties. The passive enrollment process did not provide adequate information about certain aspects of CMC, leaving many beneficiaries unaware of new benefits such as care coordination, transportation, and managed LTSS. Most beneficiaries who were using the CMC care coordination benefit reported increased access to specialty care, medical equipment, and other LTSS. Changing providers and having trouble with authorization for specialty services, prescriptions, or medical equipment were common reasons for dissatisfaction. Many beneficiaries reported that early disruptions in care due to the transition of delivery system improved with time. Similar to other studies that examine beneficiaries' experiences with delivery system change, participants were confused about the passive enrollment process and demonstrated a lack of understanding of many aspects of Cal MediConnect. Analysis identified areas where beneficiaries noted improvement in their quality of care, access, and coordination of care, but also areas for improvement. Streamlining the authorization processes and extending continuity of care provisions would improve access to providers. Increasing beneficiaries' awareness of CMC plans' role in LTSS is key to improving their access to home- and community-based services.


Optical properties of injection molded subwavelength gratings.
We have fabricated injection molded subwavelength gratings for anti-reflection purposes superimposed upon a blazed grating structure in polycarbonate. The gratings are initially formed by electron-beam lithography and subsequently replicated using injection molding. There are several problems when trying to optically characterize a component such as a blazed transmittance grating. Standard spectrophotometers are not well suited for measuring transmittance in the different diffraction orders individually. Our sample size of 0.8x0.8 mm(2) is also a problem for standard instruments. First order transmittance has been measured for blazed gratings with single and double-sided AR-treatment and is transmittance is compared with with higher diffraction orders. Double-sided AR-treatment not only increase the total transmittance but also widens the wavelength range with high effectiveness of the first order diffraction.


Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers.
Chromosome 8q24 is the most commonly amplified region across multiple cancer types, and the typical length of the amplification suggests that it may target additional genes to MYC. To explore the roles of the genes most frequently included in 8q24 amplifications, we analyzed the relation between copy number alterations and gene expression in three sets of endometrial cancers (N = 252); and in glioblastoma, ovarian, and breast cancers profiled by TCGA. Among the genes neighbouring MYC, expression of the bromodomain-containing gene ATAD2 was the most associated with amplification. Bromodomain-containing genes have been implicated as mediators of MYC transcriptional function, and indeed ATAD2 expression was more closely associated with expression of genes known to be upregulated by MYC than was MYC itself. Amplifications of 8q24, expression of genes downstream from MYC, and overexpression of ATAD2 predicted poor outcome and increased from primary to metastatic lesions. Knockdown of ATAD2 and MYC in seven endometrial and 21 breast cancer cell lines demonstrated that cell lines that were dependent on MYC also depended upon ATAD2. These same cell lines were also the most sensitive to the histone deacetylase (HDAC) inhibitor Trichostatin-A, consistent with prior studies identifying bromodomain-containing proteins as targets of inhibition by HDAC inhibitors. Our data indicate high ATAD2 expression is a marker of aggressive endometrial cancers, and suggest specific inhibitors of ATAD2 may have therapeutic utility in these and other MYC-dependent cancers.


Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues.
To elucidate the genetic architecture of gene expression in pancreatic tissues. We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10-8) and tumour-derived (p=8.3×10-5) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the 'O' mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO 'O' mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.


Diagnostic value of serum gamma-glutamyl-transferase activity and mean corpuscular volume in alcoholic patients with or without cirrhosis.
In an attempt to assess the diagnostic values of serum gamma-glutamyltransferase (GGT) and mean corpuscular volume (MCV) variations as markers of liver disease and of abstinence in alcoholic patients, we compared 174 patients with alcoholic cirrhosis, 175 with noncirrhotic alcoholic liver disease and 67 patients with nonalcoholic cirrhosis. GGT and MCV values were checked three times, the day of admission, 7 days later, and on the last sample available during follow-up (1 to 12 months), and were compared according to the liver disease and abstinence. A decrease of GGT activity during the 1st week of hospitalization was noted in alcoholics with (-9 IU/liter) or without (-13 IU/liter) cirrhosis and not in nonalcoholic cirrhosis (+8 IU/liter), without MCV variations. During follow-up, median GGT activity was strikingly different in abstinent patients with (27 IU/liter) or without (21 IU/liter) cirrhosis and in nonabstinent patients (99 IU/liter and 123 IU/liter, respectively) (p less than 0.001). MCV decrease was noted in alcoholics whatever their abstinence or not, contrasting with the absence of decrease in nonalcoholic patients. For the diagnosis of alcoholism in cirrhotic patients, the positive predictive value (PPV) of a GGT or a MCV decrease during the 1st week of hospitalization was 0.82 and 0.78, respectively, and the negative predictive value (NPV) was 0.33 and 0.70, respectively. For abstinence during follow-up, the PPV of a GGT activity less than 50 IU/liter was 0.92 and the NPV was 0.65.(ABSTRACT TRUNCATED AT 250 WORDS)