ICESluvan, a 94-kilobase mosaic integrative conjugative element conferring interspecies transfer of VanB-type glycopeptide resistance, a novel bacitracin resistance locus, and a toxin-antitoxin stabilization system.
A 94-kb integrative conjugative element (ICESluvan) transferable to Enterococcus faecium and Enterococcus faecalis from an animal isolate of Streptococcus lutetiensis consists of a mosaic of genetic fragments from different Gram-positive bacteria. A variant of ICESluvan was confirmed in S. lutetiensis from a patient. A complete Tn5382/Tn1549 with a vanB2 operon is integrated into a streptococcal ICESde3396-like region harboring a putative bacteriophage exclusion system, a putative agglutinin receptor precursor, and key components of a type IV secretion system. Moreover, ICESluvan encodes a putative MobC family mobilization protein and a relaxase and, thus, in total has all genetic components essential for conjugative transfer. A 9-kb element within Tn5382/Tn1549 encodes, among others, putative proteins similar to the TnpX site-specific recombinase in Faecalibacterium and VanZ in Paenibacillus, which may contribute to the detected low-level teicoplanin resistance. Furthermore, ICESluvan encodes a novel bacitracin resistance locus that is associated with reduced susceptibility to bacitracin when transferred to E. faecium. The expression of a streptococcal pezAT toxin-antitoxin-encoding operon of ICESluvan in S. lutetiensis, E. faecium, and E. faecalis was confirmed by reverse transcription (RT)-PCR, indicating an active toxin-antitoxin system which may contribute to stabilizing ICESluvan within new hosts. Junction PCR and DNA sequencing confirmed that ICESluvan excised to form a circular intermediate in S. lutetiensis, E. faecalis, and E. faecium. Transfer between E. faecalis cells was observed in the presence of helper plasmid pIP964. Sequence analysis of the original S. lutetiensis donor and enterococcal transconjugants showed that ICESluvan integrates in a site-specific manner into the C-terminal end of the chromosomal tRNA methyltransferase gene rumA.


Distinction between short-segment Barrett's esophageal and cardiac intestinal metaplasia.
To investigate the roles of mucin histochemistry, cytokeratin 7/20 (CK7/20) immunoreactivity, clinical characteristics and endoscopy to distinguish short-segment Barrett's esophageal (SSBE) from cardiac intestinal metaplasia (CIM). High iron diamine/Alcian blue (HID/AB) mucin-histochemical staining and immunohistochemical staining were used to classify intestinal metaplasia (IM) and to determine CK7/20 immunoreactivity pattern in SSBE and CIM, respectively, and these results were compared with endoscopical diagnosis and the positive rate of gastroesophageal reflux disease (GERD) symptoms and H pylori infection. Long-segment Barrett's esophageal and IM of gastric antrum were designed as control. The prevalence of type III IM was significantly higher in SSBE than in CIM (63.33% vs 23.08%, P< 0.005). The CK7/20 immunoreactivity in SSBE showed mainly Barrett's pattern (76.66%), and the GERD symptoms in most cases which showed Barrett's pattern were positive, whereas H pylori infection was negative. However, the CK7/20 immunoreactivity in CIM was gastric pattern preponderantly (61.54%), but there were 23.08% cases that showed Barrett's pattern. H pylori infection in all cases which showed gastric pattern was significantly higher than those which showed Barrett's pattern (63.83% vs 19.30%, P< 0.005), whereas the GERD symptoms in gastric pattern were significantly lower than that in Barrett's pattern (21.28% vs 85.96%, P< 0.005). Distinction of SSBE from CIM should not be based on a single method; however, the combination of clinical characteristics, histology, mucin histochemistry, CK7/20 immunoreactivity, and endoscopic biopsy should be applied. Type III IM, presence of GERD symptoms, and Barrett's CK7/20 immunoreactivity pattern may support the diagnosis of SSBE, whereas non-type III IM, positive H pylori infection, and gastric CK7/20 immunoreactivity pattern may imply CIM.


Targeting the Liver-Brain Axis with Hop-Derived Flavonoids Improves Lipid Metabolism and Cognitive Performance in Mice.
Sphingolipids including ceramides are implicated in the pathogenesis of obesity and insulin resistance. Correspondingly, inhibition of pro-inflammatory and neurotoxic ceramide accumulation prevents obesity-mediated insulin resistance and cognitive impairment. Increasing evidence suggests the farnesoid X receptor (FXR) is involved in ceramide metabolism, as bile acid-FXR crosstalk controls ceramide levels along the gut-liver axis. The authors previously reported that FXR agonist xanthohumol (XN), the principal prenylated flavonoid in hops (Humulus lupulus), and its hydrogenated derivatives, α,β-dihydroxanthohumol (DXN), and tetrahydroxanthohumol (TXN), ameliorated obesity-mediated insulin resistance, and cognitive impairment in mice fed a high-fat diet. To better understand how the flavonoids improve both, lipid and bile acid profiles in the liver are analyzed, sphingolipid relative abundance in the hippocampus is measured, and linked them to metabolic and neurocognitive performance. XN, DXN, and TXN (30 mg kg-1 BW per day) decrease ceramide content in liver and hippocampus; the latter is linked to improvements in spatial learning and memory. In addition, XN, DXN, and TXN decrease hepatic cholesterol content by enhancing de novo synthesis of bile acids. These observations suggest that XN, DXN, and TXN may alleviate obesity-induced metabolic and neurocognitive impairments by targeting the liver-brain axis.


Urinary phytoestrogen levels in young women from a multiethnic population.
Phytoestrogens include several classes of chemical compounds (i.e., isoflavones, coumestans, and lignans) which are structurally similar to endogenous estrogens. In biological systems, they have both estrogenic and antiestrogenic effects and may reduce the risk of developing certain types of hormonally related diseases. However, little information is available on population differences in exposure to phytoestrogens. To examine racial/ethnic differences in urinary phytoestrogen levels, 50 young women (ages 20-40 years) were randomly selected from participants in a previous epidemiological study in which 24-h urine specimens and a dietary assessment were obtained. Subjects were members of the Kaiser Permanente Medical Care Program of northern California. Selection was stratified on race/ethnicity. Urinary levels of seven phytoestrogens were measured using high-performance liquid chromatography-mass spectrometry. Substantial variation in phytoestrogen levels was observed and racial/ethnic differences are described. The highest levels of coumestrol and the lignans were observed in white women and the lowest levels in Latina and African American women. Genistein levels, however, were highest in Latina women; other isoflavone levels did not differ significantly by race/ethnicity.


Global Mapping of the Macrophage-HIV-1 Transcriptome Reveals that Productive Infection Induces Remodeling of Host Cell DNA and Chromatin.
It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. To shed light on this important issue, we performed comparative analyses of mRNA expression levels of host genes in uninfected bystander and HIV-1-infected human macrophages using an infectious reporter virus construct coupled with a large-scale RNA sequencing approach. We observed a rapid differential expression of several host factors in the productively infected macrophage population including genes regulating DNA replication factors and chromatin remodeling. A siRNA-mediated screening study to functionally identify host determinants involved in HIV-1 biology has provided new information on the virus molecular regulation in macrophages.


Partner notification for gonorrhoea: a comparative study with a provincial and a metropolitan UK clinic.
To compare partner notification practice and outcomes at a provincial and a metropolitan clinic. Prospective study, following standardisation of partner notification policy. Sheffield Department of Genitourinary Medicine, Royal Hallamshire Hospital and Jefferiss Wing Centre for Sexual Health, St Mary's Hospital, London. Consecutive patients with culture positive gonorrhoea between October 1994 and March 1996 who were interviewed by a health adviser. In Sheffield, 235 cases reported 659 outstanding contacts, of whom 129 (20%) were subsequently screened, and 65 (50%) had gonorrhoea. At St Mary's 510 cases reported 2176 outstanding contacts, of whom 98 (5%) were known to have been screened, and 53 (54%) had gonorrhoea. Patient or provider referral agreements appeared more productive in Sheffield, where 60% resulted in contact attendance, compared with 13% at St Mary's. Provider referral was used more frequently in Sheffield, for 44% of referrals, compared with 1% at St Mary's. Multivariate analysis showed that partner notification was less effective for casual and short term (< 7 days) partnerships in both centres, and for homosexual men at St Mary's. Partner notification outcomes were better in the provincial setting where contact attendance could be recorded more reliably and provider referral was used more extensively. The high proportion of contacts who remained untraced in both settings indicates the need for complementary screening and prevention initiatives.


Cell cycle regulation in the freeze tolerant wood frog, Rana sylvatica.
The wood frog (Rana sylvatica) is one of only a few vertebrate species that can survive extensive freezing of its body fluids during the winter. The mechanisms of natural freeze tolerance include metabolic rate depression to conserve energy and the implementation of cryoprotective strategies, especially the synthesis of huge amounts of glucose as a cryoprotectant. Liver is the main source of glucose production/export (and other cryoprotective actions) and plays a central role in freezing survival of the whole animal. Freezing is a multi-component stress that includes anoxia/ischemia due to the cessation of blood flow and dehydration of cells caused by ice accumulation in extracellular spaces. To help endure these stresses, cells need to suppress and reprioritize ATP-expensive cell functions. One of these is cell growth and proliferation, and we hypothesized that cell cycle arrest would be key to freezing survival. The present study examines the responses by key cell cycle components to freezing, anoxia and dehydration stresses in wood frog liver. Immunoblotting was used to investigate protein expression of Cdc 2, Cdks (2, 4, 6), and cyclins (A, B1, D1, E) as well as the phosphorylation states of Cdks (Thr14/Tyr15), the phosphatases Cdc25a (Ser76) and Cdc25c (Ser216) and the CIP/KIP Cdk inhibitors p21 (Thr145) and p27 (Thr187). Responses to 24 h freezing, 24 h anoxia and 40% dehydration as well as recovery from these stresses were analyzed. The results showed very similar responses by cell cycle components to anoxia or dehydration and were consistent with cell cycle suppression under stress and reversal during recovery. Freezing showed elements of cell cycle suppression, including reduced protein levels of Cdks and cyclins A and B1, but also showed unique responses by cyclin D1, Cdc25 phosphatases and p21/p27. These may be linked with alternative actions by these proteins that contribute to cryoprotection; e.g., an alternative action of cyclin D1 as a transcription factor may contribute to the upregulation of glucose-6-phosphatase, a key enzyme needed for the export of glucose cryoprotectant.


Divergence of the yellow gene between Drosophila melanogaster and D. subobscura: recombination rate, codon bias and synonymous substitutions.
The yellow (y) gene maps near the telomere of the X chromosome in Drosophila melanogaster but not in D. subobscura. Thus the strong reduction in the recombination rate associated with telomeric regions is not expected in D. subobscura. To study the divergence of a gene whose recombination rate differs between two species, the y gene of D. subobscura was sequenced. Sequence comparison between D. melanogaster and D. subobscura revealed several elements conserved in noncoding regions that may correspond to putative cis-acting regulatory sequences. Divergence in the y gene coding region between D. subobscura and D. melanogaster was compared with that found in other genes sequenced in both species. Both, yellow and scute exhibit an unusually high number of synonymous substitutions per site (ps). Also for these genes, the extent of codon bias differs between both species, being much higher in D. subobscura than in D. melanogaster. This pattern of divergence is consistent with the hitchhiking and background selection models that predict an increase in the fixation rate of slightly deleterious mutations and a decrease in the rate of fixation of slightly advantageous mutations in regions with low recombination rates such as in the y-sc gene region of D. melanogaster.


CD99 drives terminal differentiation of osteosarcoma cells by acting as a spatial regulator of ERK 1/2.
Differentiation therapy is an attractive treatment for osteosarcoma (OS). CD99 is a cell surface molecule expressed in mesenchymal stem cells and osteoblasts that is maintained during osteoblast differentiation while lost in OS. Herein, we show that whenever OS cells regain CD99, they become prone to reactivate the terminal differentiation program. In differentiating conditions, CD99-transfected OS cells express osteocyte markers, halt proliferation, and largely die by apoptosis, resembling the fate of mature osteoblasts. CD99 induces ERK activation, increasing its membrane-bound/cytoplasmic form rather than affecting its nuclear localization. Through cytoplasmic ERK, CD99 promotes activity of the main osteogenic transcriptional factors AP1 and RUNX2, which in turn enhance osteocalcin and p21(WAF1/CIP1) , leading to G0 /G1 arrest. These data underscore the alternative positions of active ERK into distinct subcellular compartments as key events for determining OS fate.


Effectiveness of a scalable group-based education and monitoring program, delivered by health workers, to improve control of hypertension in rural India: A cluster randomised controlled trial.
New methods are required to manage hypertension in resource-poor settings. We hypothesised that a community health worker (CHW)-led group-based education and monitoring intervention would improve control of blood pressure (BP). We conducted a baseline community-based survey followed by a cluster randomised controlled trial of people with hypertension in 3 rural regions of South India, each at differing stages of epidemiological transition. Participants with hypertension, defined as BP ≥ 140/90 mm Hg or taking antihypertensive medication, were advised to visit a doctor. In each region, villages were randomly assigned to intervention or usual care (UC) in a 1:2 ratio. In intervention clusters, trained CHWs delivered a group-based intervention to people with hypertension. The program, conducted fortnightly for 3 months, included monitoring of BP, education about hypertension, and support for healthy lifestyle change. Outcomes were assessed approximately 2 months after completion of the intervention. The primary outcome was control of BP (BP < 140/90 mm Hg), analysed using mixed effects regression, clustered by village within region and adjusted for baseline control of hypertension (using intention-to-treat principles). Of 2,382 potentially eligible people, 637 from 5 intervention clusters and 1,097 from 10 UC clusters were recruited between November 2015 and April 2016, with follow-up occurring in 459 in the intervention group and 1,012 in UC. Mean age was 56.9 years (SD 13.7). Baseline BP was similar between groups. Control of BP improved from baseline to follow-up more in the intervention group (from 227 [49.5%] to 320 [69.7%] individuals) than in the UC group (from 528 [52.2%] to 624 [61.7%] individuals) (odds ratio [OR] 1.6, 95% CI 1.2-2.1; P = 0.001). In secondary outcome analyses, there was a greater decline in systolic BP in the intervention than UC group (-5.0 mm Hg, 95% CI -7.1 to -3.0; P < 0.001) and a greater decline in diastolic BP (-2.1 mm Hg, 95% CI -3.6 to -0.6; P < 0.006), but no detectable difference in the use of BP-lowering medications between groups (OR 1.2, 95% CI 0.8-1.9; P = 0.34). Similar results were found when using imputation analyses that included those lost to follow-up. Limitations include a relatively short follow-up period and use of outcome assessors who were not blinded to the group allocation. While the durability of the effect is uncertain, this trial provides evidence that a low-cost program using CHWs to deliver an education and monitoring intervention is effective in controlling BP and is potentially scalable in resource-poor settings globally. The trial was registered with the Clinical Trials Registry-India (CTRI/2016/02/006678).


Orientia tsutsugamushi selectively stimulates the C-type lectin receptor Mincle and type 1-skewed proinflammatory immune responses.
Orientia tsutsugamushi is an obligately intracellular bacterium and the etiological agent of scrub typhus. The lung is a major target organ of infection, displaying type 1-skewed proinflammatory responses. Lung injury and acute respiratory distress syndrome are common complications of severe scrub typhus; yet, their underlying mechanisms remain unclear. In this study, we investigated whether the C-type lectin receptor (CLR) Mincle contributes to immune recognition and dysregulation. Following lethal infection in mice, we performed pulmonary differential expression analysis with NanoString. Of 671 genes examined, we found 312 significantly expressed genes at the terminal phase of disease. Mincle (Clec4e) was among the top 5 greatest up-regulated genes, accompanied with its signaling partners, type 1-skewing chemokines (Cxcr3, Ccr5, and their ligands), as well as Il27. To validate the role of Mincle in scrub typhus, we exposed murine bone marrow-derived macrophages (MΦ) to live or inactivated O. tsutsugamushi and analyzed a panel of CLRs and proinflammatory markers via qRT-PCR. We found that while heat-killed bacteria stimulated transitory Mincle expression, live bacteria generated a robust response in MΦ, which was validated by indirect immunofluorescence and western blot. Notably, infection had limited impact on other tested CLRs or TLRs. Sustained proinflammatory gene expression in MΦ (Cxcl9, Ccl2, Ccl5, Nos2, Il27) was induced by live, but not inactivated, bacteria; infected Mincle-/- MΦ significantly reduced proinflammatory responses compared with WT cells. Together, this study provides the first evidence for a selective expression of Mincle in sensing O. tsutsugamushi and suggests a potential role of Mincle- and IL-27-related pathways in host responses to severe infection. Additionally, it provides novel insight into innate immune recognition of this poorly studied bacterium.


Bacterial Infections Change Natural History of Cirrhosis Irrespective of Liver Disease Severity.
We assessed the prognostic significance of infections in relation to current prognostic scores and explored if infection could be considered per se a distinct clinical stage in the natural history of cirrhosis. We included consecutive patients with cirrhosis admitted to a tertiary referral liver unit for at least 48 h over a 2-year period. Diagnosis of infection was based on positive cultures or strict established criteria. We used competing risk analysis and propensity score matching for data analysis. 501 patients (63% male, 48% alcoholic liver disease, median Model of End-stage Liver Disease (MELD)=17) underwent 781 admissions over the study period. Portal hypertensive bleeding and complicated ascites were the commonest reasons of admission. The incidence of proven bacterial infection was 25.6% (60% community acquired and 40% nosocomial). Survival rates at 3, 6, 12, and 30 months were 83%, 77%, 71%, and 62% in patients without diagnosis of infection, vs. 50%, 46%, 41%, and 34% in patients with diagnosis of infection. Overall survival was independently associated with MELD score (hazards ratio (HR) 1.099), intensive care (ITU) stay (HR 1.967) and bacterial infection (HR 2.226). Bacterial infection was an independent predictor of survival even when patients who died within the first 30 days were excluded from the analysis in Cox regression (HR 2.013) and competing risk Cox models in all patients (HR 1.46) and propensity risk score-matched infected and non-infected patients (HR 1.67). Infection most likely represents a distinct prognostic stage of cirrhosis, which affects survival irrespective of disease severity, even after recovery from the infective episode.


Grid cells use HCN1 channels for spatial scaling.
Entorhinal grid cells have periodic, hexagonally patterned firing locations that scale up progressively along the dorsal-ventral axis of medial entorhinal cortex. This topographic expansion corresponds with parallel changes in cellular properties dependent on the hyperpolarization-activated cation current (Ih), which is conducted by hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. To test the hypothesis that grid scale is determined by Ih, we recorded grid cells in mice with forebrain-specific knockout of HCN1. We find that, although the dorsal-ventral gradient of the grid pattern was preserved in HCN1 knockout mice, the size and spacing of the grid fields, as well as the period of the accompanying theta modulation, was expanded at all dorsal-ventral levels. There was no change in theta modulation of simultaneously recorded entorhinal interneurons. These observations raise the possibility that, during self-motion-based navigation, Ih contributes to the gain of the transformation from movement signals to spatial firing fields.


Effectiveness of Chinese prescription Kangen-karyu for dyslipi-demia, using 3T3-L1 adipocytes and type 2 diabetic mice.
The Chinese prescription Kangen-karyu, comprised of six crude drugs, has received much attention due to its numerous biological activities. The present study was conducted to examine whether Kangen-karyu has an ameliorative effect on dyslipidemia. The effect of Kangen-karyu was evaluated using 3T3-L1 adipocytes, and also db/db mice as an experimental model for diabetic dyslipidemia. Kangen-karyu significantly inhibited adipocyte differentiation and lipid accumulation. Kangen-karyu also down-regulated the mRNA levels of peroxisome proliferator-activated receptor (PPAR)γ, sterol regulatory element-binding protein (SREBP)-1c, and fatty acid synthase, and the protein levels of aP2 and PPARγ, which indicates that Kangen-karyu inhibited adipogenesis during adipocyte differentiation, and may have potential anti-dyslipidemia effects. In addition, the administration of Kangen-karyu reduced hyperlipidemia in db/db type 2 diabetic mice through a decline in the serum levels of lipids, and an improvement of lipoprotein profiles. The enhanced hepatic triglyceride level of the db/db mice was significantly reduced by Kangen-karyu administration through the down-regulation of SREBP-1 and lipogenic enzymes in the liver. These findings indicate that Kangen-karyu exerts anti-dyslipidemia effects in adipocytes and type 2 diabetic db/db mice.


Dual-rotor tool path generation and removal error analysis in active feed polishing.
High-quality ultrasmooth surface is needed in modern optics, while the existing ultrasmooth surface processing methods are difficult to meet the requirement of the surface figure. In order to solve this problem, the active feed polishing (AFP) is taken as the research object, and the dual-rotor tool path is put forward for this technology. This tool path is generated based on the motion synthesis principle, which realizes smooth connection between different sections. At the same time, the eccentricity, the speed ratio, the velocity, and other parameters can be modified easily, avoiding using the complicated dual-rotor polishing mechanism. In order to further analyze the removal error, the removal amount calculation method for the dual-rotor path is researched and proposed. The simulation analysis results show that the greatest influence factor for the removal error is the sampling interval, the influence of the eccentricity and the speed ratio is less, and the velocity has little impact on it. In addition, the removal error can be controlled within acceptable range by reasonable selection of process parameters. Finally, through a processing experiment of a 100 mm plane lens, the feasibility and effectiveness of this path is verified. This experimental result shows that the AFP technology using the dual-rotor tool path can effectively correct the surface shape while reducing the surface roughness.


On the use of magnitude of reduction in HIV-1 RNA in clinical trials: statistical analysis and potential biases.
Clinical trials endpoints based on magnitude of reduction in HIV-1 RNA levels provide an important complement to endpoints based on either virologic failure or a proportion of patients having HIV-1 RNA levels below a threshold value. However, reductions in HIV-1 RNA often are not completely observed, because many patients have HIV-1 RNA levels below the limit of quantification at the primary follow-up visit. The crude method of analyzing such data is to define all HIV-1 RNA levels that fall below the limit of quantification as being equal to that limit of quantification. This method is widely used even though the underestimation inherent in such a method may also lead to underestimation of treatment difference in terms of HIV-1 RNA reduction. Analyses based on Kaplan-Meier method and censored regression can be used to estimate such a reduction. When a high percentage of patients have HIV-1 RNA levels below the limit of quantification at the time of primary follow-up, which corresponds to censored observations, the Kaplan-Meier method does not always provide an estimate of the median HIV-1 RNA reduction. We discuss a statistical method to provide lower and upper limits of such median reduction or of other percentiles of reduction. We found that when the percentage of censoring is high, the censored method may overestimate the HIV-1 RNA reduction and then may also overestimate the treatment difference. Although the censored method is preferable to the crude method, when the level of censoring is high, we suggest computation of the upper and lower limits either to provide a range of potential values of HIV-1 RNA reduction or to detect overestimation by the censored method.


Influence of agr on fibrinogen binding in Staphylococcus aureus Newman.
The ability of Staphylococcus aureus to bind fibrinogen is believed to be important in promoting bacterial adherence to both intravascular catheters and host tissues during infection. We investigated the influence of the global regulator agr on the fibrinogen binding capacity and its relationship to the expression of coagulase (encoded by coa) and clumping factor (encoded by clfA) in strain Newman. Strains were obtained by transducing site-specific mutations of clfA, coa, and agr into strain Newman to obtain single, double, and triple mutants of the respective genes. As expected, the clfA mutant bound less soluble 125I-labeled fibrinogen than the corresponding coa mutant in agr+ strains; however, with agr mutant strains, the upregulation in fibrinogen binding capacity correlated mostly with the increased expression and transcription of coagulase as shown by Western (immunoblot) and Northern (RNA) blot analysis. In particular, the coa agr double mutant resulted in a significant reduction in fibrinogen binding compared with that of the agr mutant. The contribution of clfA to fibrinogen binding in agr-negative strains was less than that of coa (32,740 +/- 1,189 versus 18,141 +/- 334 and 38,919 +/- 1,021 cpm for clfA agr, coa agr, and the single agr mutant, respectively). Thus, coagulase is a major binding protein for soluble fibrinogen in the agr-negative background. In in vitro microtiter and catheter adherence assays with solid-phase fibrinogen, clumping factor, but not coagulase, plays a major role in binding to immobilized fibrinogen. coa transcription was negatively modulated by agr and occurred mainly during the exponential growth phase. In contrast, clfA transcription was agr independent and was strongest during the postexponential phase. Although an agr coa clfA triple mutant bound less soluble fibrinogen than the agr coa double mutant (8,504 +/- 831 versus 18,141 +/- 334 cpm), significant residual fibrinogen binding capacity remained in the triple mutant, thus suggesting an additional fibrinogen binding component. By using direct ligand affinity blotting with 125I-fibrinogen, we could identify coagulase and an additional unidentified 52-kDa protein as a fibrinogen binding component in cell extracts. This band was absent in the extract of the coa clfA double mutant.


Spontaneous uveal amelanotic melanoma in transgenic Tyr-RAS+ Ink4a/Arf-/- mice.
To characterize a murine model of spontaneous amelanotic melanoma arising in the uvea of transgenic mice bearing a targeted deletion of the Ink4a/Arf tumor suppressor locus (exons 2 and 3) and expressing human H-ras controlled by the human tyrosinase promoter. Ocular lesions developed in 20 (15.7%) of 127 male albino Tyr-RAS+ Ink4a/Arf-/- transgenic FVB/N mice within 6 months, and were evaluated histologically and ultrastructurally. Uveal melanomas were locally invasive but confined to the eye, with no evidence of metastasis. Tumor cells exhibited epithelioid and spindle-shaped morphological features and closely resembled the human counterpart. Melan-A, S100 and neuron-specific enolase expression were detected immunohistochemically. Melanosomal structures were detected using electron microscopy. The retinal pigment epithelium was intact above small melanomas, and electron microscopy of the tumors failed to show the presence of basement membrane formation or desmosomes. Spontaneous uveal malignant melanomas occurring in male Tyr-RAS+ Ink4a/Arf-/- transgenic mice arise within the choroid or ciliary body and share histopathological features characteristic of human uveal melanoma. Uveal melanoma research has benefited from xenograft models, but engineered mouse models of spontaneous uveal amelanotic melanoma will undoubtedly further our understanding of the genetic underpinning for this disease.


Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS.
The primary structural information of proteins employed as biotherapeutics is essential if one wishes to understand their structure-function relationship, as well as in the rational design of new therapeutics and for quality control. Given both the large size (around 150 kDa) and the structural complexity of intact immunoglobulin G (IgG), which includes a variable number of disulfide bridges, its extensive fragmentation and subsequent sequence determination by means of tandem mass spectrometry (MS) are challenging. Here, we applied electron transfer dissociation (ETD), implemented on a hybrid Orbitrap Fourier transform mass spectrometer (FTMS), to analyze a commercial recombinant IgG in a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) top-down experiment. The lack of sensitivity typically observed during the top-down MS of large proteins was addressed by averaging time-domain transients recorded in different LC-MS/MS experiments before performing Fourier transform signal processing. The results demonstrate that an improved signal-to-noise ratio, along with the higher resolution and mass accuracy provided by Orbitrap FTMS (relative to previous applications of top-down ETD-based proteomics on IgG), is essential for comprehensive analysis. Specifically, ETD on Orbitrap FTMS produced about 33% sequence coverage of an intact IgG, signifying an almost 2-fold increase in IgG sequence coverage relative to prior ETD-based analysis of intact monoclonal antibodies of a similar subclass. These results suggest the potential application of the developed methodology to other classes of large proteins and biomolecules.


Benefit of cup medialization in total hip arthroplasty is associated with femoral anatomy.
Medialization of the cup with a respective increase in femoral offset has been proposed in THA to increase abductor moment arms. Insofar as there are potential disadvantages to cup medialization, it is important to ascertain whether the purported biomechanical benefits of cup medialization are large enough to warrant the downsides; to date, studies regarding this question have disagreed. The purpose of this study was to quantify the effect of cup medialization with a compensatory increase in femoral offset compared with anatomic reconstruction for patients undergoing THA. We tested the hypothesis that there is a (linear) correlation between preoperative anatomic parameters and muscle moment arm increase caused by cup medialization. Fifteen patients undergoing THA were selected, covering a typical range of preoperative femoral offsets. For each patient, a finite element model was built based on a preoperative CT scan. The model included the pelvis, femur, gluteus minimus, medius, and maximus. Two reconstructions were compared: (1) anatomic position of the acetabular center of rotation, and (2) cup medialization compensated by an increase in the femoral offset. Passive abduction-adduction and flexion-extension were simulated in the range of normal gait. Muscle moment arms were evaluated and correlated to preoperative femoral offset, acetabular offset, height of the greater trochanter (relative to femoral center of rotation), and femoral antetorsion angle. The increase of muscle moment arms caused by cup medialization varied among patients. Muscle moment arms increase by 10% to 85% of the amount of cup medialization for abduction-adduction and from -35% (decrease) to 50% for flexion-extension. The change in moment arm was inversely correlated (R(2) = 0.588, p = 0.001) to femoral antetorsion (anteversion), such that patients with less femoral antetorsion gained more in terms of hip muscle moments. No linear correlation was observed between changes in moment arm and other preoperative parameters in this series. The benefit of cup medialization is variable and depends on the individual anatomy. Cup medialization with compensatory increase of the femoral offset may be particularly effective in patients with less femoral antetorsion. However, cup medialization must be balanced against its tradeoffs, including the additional loss of medial acetabular bone stock, and eventual proprioceptive implications of the nonanatomic center of rotation and perhaps joint reaction forces. Clinical studies should better determine the relevance of small changes of moment arms on function and joint reaction forces.


When the law meets organ transplantation: the experience from the United kingdom.
Because the availability of organs falls short of the numbers of people who might benefit from transplantation, there has to be rationing of this resource. As organs donated from deceased donors are considered a national resource, there needs to be clear and transparent selection and allocation policies. There is the potential for a conflict between public and clinical priorities with legal requirements and this may lead to challenge in the courts. For example, both healthcare professionals and the general public may wish to give priority in allocation to children but this approach could be challenged on the basis of equity of access. We, therefore, recommend that selection and allocation policies should give clarity over the aims and assumptions, be evidence-based where possible or justify the assumptions where no evidence exists, have transparency of implementation and be supported by relevant stakeholders.


Who let the cats out? A global meta-analysis on risk of parasitic infection in indoor versus outdoor domestic cats ( Felis catus).
Parasitic infection risks in domestic animals may increase as a result of outdoor activities, often leading to transmission events to and from owners, other domestic animals and wildlife. Furthermore, outdoor access has not been quantified in domestic animals as a risk factor with respect to latitude or parasite transmission pathway. Cats are an ideal model to test parasitic infection risk in outdoor animals because there have been many studies analysing this risk factor in this species; and there is a useful dichotomy in cat ownership between indoor-only cats and those with outdoor access. Thus, we used meta-analysis to determine whether outdoor access is a significant risk factor for parasitic infection in domestic pet cats across 19 different pathogens including many relevant to human, domestic animal and wildlife health, such as Toxoplasma gondii and Toxocara cati. Cats with outdoor access were 2.77 times more likely to be infected with parasites than indoor-only cats. Furthermore, absolute latitude trended towards significance such that each degree increase in absolute latitude increased infection likelihood by 4%. Thus, restricting outdoor access can reduce the risk of parasitic infection in cats and reduce the risk of zoonotic parasite transmission, spillover to sympatric wildlife and negative impacts on feline health.


Metabolic and permeability changes caused by thiamine deficiency in immortalized rat brain microvessel endothelial cells.
The possible involvement of blood-brain barrier (BBB) breakdown in the pathogenesis of thiamine deficiency encephalopathy was investigated in RBE4 cells, an immortalized rat brain endothelial cell line. The effects of thiamine deficiency produced by addition of pyrithiamine and by reduction of thiamine in the culture medium, on the metabolism and permeability of the RBE4 monolayer was examined. Pyrithiamine treatment in low thiamine medium (M199) for 7 days caused cytotoxic effects on RBE4 cells at all concentrations (10-50 microg/ml). Pyrithiamine caused a concentration- and time-dependent decrease in MTT reduction and a significant increase in glucose consumption and lactate production compared to controls. Pyrithiamine treatment for 3 days caused a significant decrease in MTT reduction at 50 microg/ml only. In contrast, increased glucose consumption and lactate production by the RBE4 cells was observed after treatment for 3 days with concentrations of 25 microg/ml pyrithiamine and above. The permeability of RBE4 cell monolayers to [14C]sucrose (Mw 342), but not FITC-dextran (Mw 4000) was significantly increased by treatment with pyrithiamine concentrations of 25 microg/ml and above for 3 days. These effects were not accompanied by detectable changes in F-actin distribution or content, although F-actin content was significantly reduced by 7 days exposure to pyrithiamine. These results suggest that metabolic and permeability changes in thiamine-deficient RBE4 cells may be important early events in thiamine-deficiency encephalopathy. The relative role of the BBB in the pathogenesis of thiamine deficiency is discussed.


Different configurations of specific thyroid hormone response elements mediate opposite effects of thyroid hormone and GC-1 on gene expression.
T3 regulates transcription of the rat sarcoendoplasmic reticulum calcium ATPase in the heart. The T3 effect is mediated by three differently configured T3 response elements (TREs). Here we report the mutation of each individual TRE in the promoter and the contribution of each TRE on gene expression. Mutation of TRE1, a direct repeat element, exerted the strongest T3 response, compared with TRE2 and TRE3, which are inverted palindromes. The isolated TRE2 and TRE3, which showed no response (TRE2) or were weakly positive with T3 (TRE3), became strong negative regulatory elements with the T3 analog GC-1. We found that TRE1 recruits corepressor complexes containing nuclear receptor corepressor and histone deacetylase 3 in the absence of ligand, and steroid receptor coactivator-1-containing coactivator complexes with both T3 and GC-1. TRE3 bound the same corepressor complexes without ligand but showed only a weak association with steroid receptor coactivator-1 with T3 and a strong association with corepressor complexes with GC-1. Thus, GC-1 appears to control cofactor association differentially on these two sarcoendoplasmic reticulum calcium ATPase TREs, which could be the mechanism of ligand-dependent transcriptional activation and repression observed with the isolated TRE1 and TRE3 elements. Because the x-ray crystal structures of GC-1 and T3 complexed with the TR ligand binding domain are superimposable, the results imply that GC-1 and T3 induce differential effects on the receptor that are not evident in the static structures but must occur in the dynamic setting of receptor function. These results have implications for selective modulation of receptor function by agonist ligands.


A highly conserved effector in Fusarium oxysporum is required for full virulence on Arabidopsis.
Secreted-in-xylem (SIX) proteins of the vascular wilt pathogen Fusarium oxysporum f. sp. lycopersici are secreted during infection of tomato and function in virulence or avirulence. F. oxysporum formae speciales have specific host ranges but the roles of SIX proteins in diverse hosts are unknown. We identified homologs of F. oxysporum f. sp. lycopersici SIX1, SIX4, SIX8, and SIX9 in the genome of Arabidopsis infecting isolate Fo5176. A SIX4 homolog (termed Fo5176-SIX4) differed from that of F. oxysporum f. sp. lycopersici (Fol-SIX4) by only two amino acids, and its expression was induced during infection of Arabidopsis. Transgenic Arabidopsis plants constitutively expressing Fo5176-SIX4 had increased disease symptoms with Fo5176. Conversely, Fo5176-SIX4 gene knock-out mutants (Δsix4) had significantly reduced virulence on Arabidopsis, and this was associated with reduced fungal biomass and host jasmonate-mediated gene expression, the latter known to be essential for host symptom development. Full virulence was restored by complementation of Δsix4 mutants with either Fo5176-SIX4 or Fol-SIX4. Thus, Fo5176-SIX4 contributes quantitatively to virulence on Arabidopsis whereas, in tomato, Fol-SIX4 acts in host specificity as both an avirulence protein and a suppressor of other race-specific resistances. The strong sequence conservation for SIX4 in F. oxysporum f. sp. lycopersici and Fo5176 suggests a recent common origin.


In vivo molecular mediators of cancer growth suppression and apoptosis by selenium in mammary and prostate models: lack of involvement of gadd genes.
We used acute selenium (Se) treatments (i.e., daily single oral gavage of 2 mg Se per kilogram of body weight for 3 days) of female Sprague-Dawley rats bearing 1-methyl-1-nitrosourea-induced mammary carcinomas to increase the probability of detecting in vivo apoptosis and the associated gene/protein changes in the cancerous epithelial cells. The results show that whereas control carcinomas doubled in volume in 3 days, Se-methylselenocysteine and selenite treatments regressed approximately half of the carcinomas, accompanied by a 3- to 4-fold increase of morphologically observable apoptosis and approximately 40% inhibition of 5-bromo-2'-deoxyuridine index of the cancerous epithelial cells. The mRNA levels of growth arrest-DNA damage inducible 34 (gadd34), gadd45, and gadd153 genes were, contrary to expectation, not higher in the Se-treated carcinomas than in the gavage or diet restriction control groups. The gadd34 and gadd153 proteins were localized in the nonepithelial cells and not induced in the cancer epithelial cells of the Se-treated carcinomas. On the other hand, both Se forms decreased the expression of cyclin D1 and increased levels of P27Kip1 and c-Jun NH2-terminal kinase activation in a majority of the mammary carcinomas. Furthermore, the lack of induction of gadd genes in vivo by methylseleninic acid was confirmed in a human prostate xenograft model in athymic nude mice. In summary, these experiments showed the induction of cancer epithelial cell apoptosis and inhibition of cell proliferation by Se in vivo through the potential involvement of cyclin D1, P27Kip1, and c-Jun NH2-terminal kinase pathways. They cast doubt on the three gadd genes as mediators of Se action in vivo.


Immunosuppressive factors secreted by human amniotic epithelial cells.
Amniotic membrane has been applied to the ocular surface to restore corneal function. The beneficial effect of amniotic membrane transplantation may be due to the immunosuppressive effects of amniotic epithelial cells. The purpose of this study was to determine whether amniotic epithelial cells (AECs) secrete anti-inflammatory and antiproliferative factors that affect the chemotaxis of neutrophils and macrophages and suppress both T- and B-cell proliferation in vitro. Human amniotic cells were isolated from human amniotic membrane and cultured in vitro. The supernatants from AEC cultures were collected after 48 hours of incubation. Neutrophil and macrophage chemotactic activity was tested in the presence of AEC supernatant, using 24-well migration assay chambers. Lymphocyte proliferation was tested by H(3)-thymidine incorporation. Apoptosis was examined by caspase-3 and annexin V assays, and expression of cytokines was assessed by RT-PCR. AEC supernatant significantly inhibited the chemotactic activity of neutrophils and macrophages toward macrophage inflammatory protein (MIP)-2 (P < 0.05). The supernatant significantly reduced the proliferation of both T and B cells after mitogenic stimulation (P < 0.05). Caspase-3 assays revealed that the supernatant induced apoptosis of T and B cells, but not of corneal epithelial cells and liver cells. In contrast to lymphocytes, macrophages and neutrophils were resistant to apoptosis induced by AEC supernatant. The AECs expressed message for TNFalpha, Fas ligand (FasL), TRAIL (tumor necrosis factor-related apoptosis-inducing ligand), TGFbeta, and macrophage migration-inhibitory factor (MIF). However, AEC induction of apoptosis was inhibited (50%) by anti-FasL antibody but not by anti-TRAIL or anti-TNFalpha antibodies. Moreover, AEC supernatant inhibited macrophage migration in vitro. AECs secrete soluble factors that inhibit cells in both the innate and adaptive immune systems.


Export of toxic chemicals - a review of the case of uncontrolled electronic-waste recycling.
This paper reviews the concentrations of persistent organic pollutants such as flame retardants (PBDEs), dioxins/furans (PCDD/Fs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals/metalloid concentrations of different environmental media at Guiyu, a traditional rice-growing village located in southeastern Guangdong Province (PR China), which has turned into an intensive electronic-waste (e-waste) recycling site. Incomplete combustion of e-waste in open air and dumping of processed materials are the major sources of various toxic chemicals. By comparing with existing data available in other areas and also guidelines adopted in different countries, it is obvious that the environment is highly contaminated by these toxic chemicals derived from the recycling processes. For example, the monthly concentration of the sum of 22 PBDE congeners contained in PM(2.5) (16.8ngm(-3)) of air samples at Guiyu was 100 times higher than published data. In order to safeguard the environment and human health, detailed investigations are urgently needed, especially on tracking the exposure pathways of different toxic chemicals which may affect the workers and local residents especially mothers, infants and children.


HPA and SAM axis responses as correlates of self- vs parental ratings of anxiety in boys with an Autistic Disorder.
Anxiety and Autistic Disorder (AD) are both neurological conditions and both disorders share some features that make it difficult to precisely allocate specific symptoms to each disorder. HPA and SAM axis activities have been conclusively associated with anxiety, and may provide a method of validating anxiety rating scale assessments given by parents and their children with AD about those children. Data from HPA axis (salivary cortisol) and SAM axis (salivary alpha amylase) responses were collected from a sample of 32 high-functioning boys (M age=11yr) with an Autistic Disorder (AD) and were compared with the boys' and their mothers' ratings of the boys' anxiety. There was a significant difference between the self-ratings given by the boys and ratings given about them by their mothers. Further, only the boys' self-ratings of their anxiety significantly predicted the HPA axis responses and neither were significantly related to SAM axis responses. Some boys showed cortisol responses which were similar to that previously reported in children who had suffered chronic and severe anxiety arising from stressful social interactions. As well as suggesting that some boys with an AD can provide valid self-assessments of their anxiety, these data also point to the presence of very high levels of chronic HPA-axis arousal and consequent chronic anxiety in these boys.


Immunolocalisation studies on six matrix metalloproteinases and their inhibitors, TIMP-1 and TIMP-2, in synovia from patients with osteo- and rheumatoid arthritis.
To assess the likely importance of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) in the arthritic process. Synovial samples from seven joints with rheumatoid arthritis and three osteoarthritic joints were analysed by indirect immunofluorescence microscopy. Using specific human antisera, we documented the frequencies and distributions of collagenase, stromelysins 1 and 2, matrilysin, gelatinases A and B, TIMP-1, and TIMP-2. Stromelysin 1 was found in all synovia, bound to extracellular matrix, within cells, or both, indicating stromelysin synthesis. Matrilysin was present in only one active inflammatory synovium, and focal synthesis of collagenase and gelatinase A was seen in four synovia. Stromelysin 2 and TIMP-2 were not observed, but TIMP-1 synthesis was seen in five synovia, and in two active synovia the distribution of TIMP-1 positive cells was more widespread than that of MMPs. The presence of stromelysin 1 in all synovia clearly implicates this enzyme in joint damage. Collagenase, gelatinase A and matrilysin may also have a role in rheumatoid arthritis, but are not significant in osteoarthritis. However, marked regional variations were found in the synthesis of these MMPs, indicating not only that these diseases are episodic but that control of enzyme synthesis is focal. Only TIMP-1 may be considered an inhibitory factor.


Soda and cell aging: associations between sugar-sweetened beverage consumption and leukocyte telomere length in healthy adults from the National Health and Nutrition Examination Surveys.
We tested whether leukocyte telomere length maintenance, which underlies healthy cellular aging, provides a link between sugar-sweetened beverage (SSB) consumption and the risk of cardiometabolic disease. We examined cross-sectional associations between the consumption of SSBs, diet soda, and fruit juice and telomere length in a nationally representative sample of healthy adults. The study population included 5309 US adults, aged 20 to 65 years, with no history of diabetes or cardiovascular disease, from the 1999 to 2002 National Health and Nutrition Examination Surveys. Leukocyte telomere length was assayed from DNA specimens. Diet was assessed using 24-hour dietary recalls. Associations were examined using multivariate linear regression for the outcome of log-transformed telomere length. After adjustment for sociodemographic and health-related characteristics, sugar-sweetened soda consumption was associated with shorter telomeres (b = -0.010; 95% confidence interval [CI] = -0.020, -0.001; P = .04). Consumption of 100% fruit juice was marginally associated with longer telomeres (b = 0.016; 95% CI = -0.000, 0.033; P = .05). No significant associations were observed between consumption of diet sodas or noncarbonated SSBs and telomere length. Regular consumption of sugar-sweetened sodas might influence metabolic disease development through accelerated cell aging.


Morphology control, spectrum modification and extended optical applications of rare earth ion doped phosphors.
Rare earth ion (RE3+) doped nano-phosphors with controllable morphologies have a wide range of applications in laser crystals, LEDs, bio-probes, photo-catalysis, three-dimensional displays, sensors, and flash memories. This review summarizes the morphology control strategy, phase transfer theory, spectrum modulation, and extended optical applications of RE3+-doped phosphors. The roles of surfactants in the morphology control in the liquid-solid-solution phase transfer process for RE3+-doped fluorides, oxides and other compounds are discussed. The relevant mechanisms of controlling morphologies are illustrated. The size- and shape-dependent optical properties of RE3+ doped phosphors, including the emission intensities, intensity ratios of adjacent emission bands, decay times and thermal stability, are analyzed. The extended optical applications and main challenges of RE3+-doped phosphors are also discussed.


Nano-optical investigations of the metal-insulator phase behavior of individual VO(2) microcrystals.
Despite the relatively simple stoichiometry and structure of VO(2), many questions regarding the nature of its famous metal-insulator transition (MIT) remain unresolved. This is in part due to the prevailing use of polycrystalline film samples and the limited spatial resolution in most studies, hindering access to and control of the complex phase behavior and its inevitable spatial inhomogeneities. Here, we investigate the MIT and associated nanodomain formation in individual VO(2) microcrystals subject to substrate stress. We employ symmetry-selective polarization Raman spectroscopy to identify crystals that are strain-stabilized in either the monoclinic M1 or M2 insulating phase at room-temperature. Raman measurements are further used to characterize the phase dependence on temperature, identifying the appearance of the M2 phase during the MIT. The associated formation and spatial evolution of rutile (R) metallic domains is studied with nanometer-scale spatial resolution using infrared scattering-scanning near-field optical microscopy (s-SNOM). We deduce that even for small crystals of VO(2), the MIT is influenced by the competition between the R, M1, and M2 crystal phases with their different lattice constants subjected to the external substrate-induced stress. The results have important implications for the interpretation of the investigations of conventional polycrystalline thin films where the mutual interaction of constituent crystallites may affect the nature of the MIT in VO(2).


Proteomic identification of M. tuberculosis protein kinase substrates: PknB recruits GarA, a FHA domain-containing protein, through activation loop-mediated interactions.
Genes for functional Ser/Thr protein kinases (STPKs) are ubiquitous in prokaryotic genomes, but little is known about their physiological substrates and their actual involvement in bacterial signal transduction pathways. We report here the identification of GarA (Rv1827), a Forkhead-associated (FHA) domain-containing protein, as a putative physiological substrate of PknB, an essential Ser/Thr protein kinase from Mycobacterium tuberculosis. Using a global proteomic approach, GarA was found to be the best detectable substrate of the PknB catalytic domain in non-denatured whole-cell protein extracts from M. tuberculosis and the saprophyte Mycobacterium smegmatis. Enzymological and binding studies of the recombinant proteins demonstrate that docking interactions between the activation loop of PknB and the C-terminal FHA domain of GarA are required to enable efficient phosphorylation at a single N-terminal threonine residue, Thr22, of the substrate. The predicted amino acid sequence of the garA gene, including both the N-terminal phosphorylation motif and the FHA domain, is strongly conserved in mycobacteria and other related actinomycetes, suggesting a functional role of GarA in putative STPK-mediated signal transduction pathways. The ensuing model of PknB-GarA interactions suggests a substrate recruitment mechanism that might apply to other mycobacterial kinases bearing multiple phosphorylation sites in their activation loops.


Biometric Attendance and Big Data Analysis for Optimizing Work Processes.
Although biometric attendance management is available, large healthcare organizations have difficulty in big data analysis for optimization of work processes. The aim of this project was to assess the implementation of a biometric attendance system and its utility following big data analysis. In this prospective study the implementation of biometric system was evaluated over 3 month period at our institution. Software integration with other existing systems for data analysis was also evaluated. Implementation of the biometric system could be successfully done over a two month period with enrollment of 10,000 employees into the system. However generating reports and taking action this large number of staff was a challenge. For this purpose software was made for capturing the duty roster of each employee and integrating it with the biometric system and adding an SMS gateway. This helped in automating the process of sending SMSs to each employee who had not signed in. Standalone biometric systems have limited functionality in large organizations unless it is meshed with employee duty roster.


Genome evolution in polyploids.
Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.


[The chronic care model in Swiss primary care].
The care of patients with chronic disease is one of the most urgent medical challenges of actual society. The chronic care model (CCM) is an organizational, proactive approach for chronic disease in primary care. The system creates practical, supportive, evidence-based interactions between an informed, activated patient and a proactive practice team. CCM identifies six essential elements of high-quality health care: community; health system; self-management support; delivery system design; decision support, and clinical information systems. The article summarizes the evidence on the CCM, the adoption and implications for successful implementation into the Swiss health care system.


Pharmacotherapies for alcoholism: the old and the new.
Alcoholism and other alcohol use disorders are major public health problems, and the success rates of non-pharmacological treatment of these disorders such as psychotherapy, cognitive-behavioral therapy, group therapy, or residential treatment programs,remain only modest at best. High rates of recidivism (relapse) in alcoholics attempting to remain abstinent are prevalent worldwide. In recent years abundant evidence has accumulated demonstrating that alcoholism is a complex and multifaceted disease of the brain caused by numerous genetic, neurobiological, developmental, environmental, and socioeconomic factors that are still not yet fully understood.There is thus a great need to improve the success rates of all forms of treatment of alcoholism not only in preventing relapse, but curbing active alcohol consumption and craving. The development of improved pharmacotherapies that could be used as adjuncts to the aforementioned non-pharmacological treatment approaches is one avenue of great interest to the scientific community and the general public. Currently there are only three medications approved by the U.S. Food and Drug Administration (FDA) for use in the treatment of alcohol abuse and alcoholism--disulfiram, naltrexone, and acamprosate. Yet medication compliance issues and the modest efficacy of these compounds leave substantial room for improvement. This special issue is devoted to reviewing the current status of these FDA approved medications in the treatment of alcoholism. In addition, preclinical and clinical evidence suggesting that other classes of medications might also be of potential use are reviewed, including anticonvulsants, GABAB receptor agonists, cholinergic receptor partial agonists, corticotropin-releasing factor and cannabinoid CB1 receptor antagonists, nociceptin receptor ligands, and the novel antipsychotic aripiprazole.


Autologous bone marrow-derived mesenchymal stromal cells for the treatment of allograft rejection after renal transplantation: results of a phase I study.
Despite excellent short-term results, long-term survival of transplanted kidneys has not improved accordingly. Although alloimmune responses and calcineurin inhibitor-related nephrotoxicity have been identified as main drivers of fibrosis, no effective treatment options have emerged. In this perspective, mesenchymal stromal cells (MSCs) are an interesting candidate because of their immunosuppressive and regenerative properties. Of importance, no other clinical studies have investigated their effects in allograft rejection and fibrosis. We performed a safety and feasibility study in kidney allograft recipients to whom two intravenous infusions (1 million cells per kilogram) of autologous bone marrow (BM) MSCs were given, when a protocol renal biopsy at 4 weeks or 6 months showed signs of rejection and/or an increase in interstitial fibrosis/tubular atrophy (IF/TA). Six patients received MSC infusions. Clinical and immune monitoring was performed up to 24 weeks after MSC infusions. MSCs fulfilled the release criteria, infusions were well-tolerated, and no treatment-related serious adverse events were reported. In two recipients with allograft rejection, we had a clinical indication to perform surveillance biopsies and are able to report on the potential effects of MSCs in rejection. Although maintenance immunosuppression remained unaltered, there was a resolution of tubulitis without IF/TA in both patients. Additionally, three patients developed an opportunistic viral infection, and five of the six patients displayed a donor-specific downregulation of the peripheral blood mononuclear cell proliferation assay, not reported in patients without MSC treatment. Autologous BM MSC treatment in transplant recipients with subclinical rejection and IF/TA is clinically feasible and safe, and the findings are suggestive of systemic immunosuppression.


2016 AAHA/IAAHPC End-of-Life Care Guidelines.
End-of-life (EOL) care and decisionmaking embody the critical final stage in a pet's life and are as important and meaningful as the sum of the clinical care provided for all prior life stages. EOL care should focus on maximizing patient comfort and minimizing suffering while providing a collaborative and supportive partnership with the caregiver client. Timely, empathetic, and nonjudgmental communication is the hallmark of effective client support. Veterinarians should not allow an EOL patient to succumb to a natural death without considering the option of euthanasia and ensuring that other measures to alleviate discomfort and distress are in place. Animal hospice care addresses the patient's unique emotional and social needs as well as the physical needs traditionally treated in clinical practice. An EOL treatment plan should consist of client education; evaluating the caregiver's needs and goals for the pet; and a collaborative, personalized, written treatment plan involving the clinical staff and client. Primary care practices should have a dedicated team to implement palliative and hospice care for EOL patients. How the healthcare team responds to a client's grief after the loss of a pet can be a key factor in the client's continued loyalty to the practice. Referral to professional grief-support counseling can be a helpful option in this regard.


Outcome of noncardiac and nonvascular surgery in patients with mechanical heart valves.
There is a tendency to avoid noncardiac surgery in patients with mechanical heart valves (MHVs) owing to the increased risk of perioperative thromboembolism, infective endocarditis, and bleeding. We aimed to determine the risk of cardiac and noncardiac complications in patients with MHVs who underwent noncardiothoracic, nonvascular surgery. A total of 140 patients with MHVs (77 aortic, 46 mitral, and 17 double valve) and 1,200 patients with native valves (control group) were prospectively followed up for a minimum of 3 months after noncardiothoracic and nonvascular surgery. Patients with bioprostheses were excluded. Those patients aged >18 years who underwent an elective, non-outpatient, open surgical procedure were enrolled. Subcutaneous enoxaparin 1 mg/kg, twice daily, was used as bridging anticoagulation. The demographics, co-morbidities, and preoperative (medications, echocardiographic findings, laboratory results) and postoperative data were evaluated for their association with the occurrence of perioperative adverse events. The incidence of perioperative adverse cardiovascular (10.8% vs 10.7%, p = 0.985) and noncardiovascular (11.9% vs 11.4%, p = 0.989) events was similar in those patients with and without MHVs. Bleeding (18.6% vs 14.2%, p = 0.989), thromboembolism (3.6% vs 2%, p = 0.989), and mortality at 3 months (1.4% vs 1.3%, p = 0.825) were also similar for the 2 groups. In conclusion, with close follow-up and strict adherence to the guidelines, patients with MHVs and patients with native heart valves undergoing noncardiac and nonvascular surgery have a similar risk of mortality and morbidity.


Pharmacotherapies for chronic obstructive pulmonary disease: a multiple treatment comparison meta-analysis.
Most patients with moderate and severe chronic obstructive pulmonary disease (COPD) receive long-acting bronchodilators (LABA) for symptom control. It is, however, unclear if and what drug treatments should be added to LABAs to reduce exacerbations, which is an important goal of COPD management. Since current guidelines cannot make strong recommendations yet, our aim was to determine the relative efficacy of existing treatments and combinations to reduce the risk for COPD exacerbations. We included randomized clinical trials (RCTs) evaluating long-acting β(2) agonists (LABA), long-acting muscarinic antagonists (LAMA), inhaled glucocorticosterioids (ICS), and the phosphodiesterase-4 (PDE4) inhibitor roflumilast, and combinations of these interventions in moderate to severe COPD populations. Our primary outcome was the event rate of exacerbations. We conducted a random-effects Bayesian mixed-treatment comparison (MTC) and applied several sensitivity analyses. In particular, we confirmed our findings using a binomial MTC analysis examining whether a patient experienced at least one exacerbation event or not during the trial. We also used an additive assumption to calculate the combined effects of treatments that were not included in the systematic review. Twenty-six studies provided data on the total number of exacerbations and/or the mean annual rate of exacerbations among a combined 36,312 patients. There were a total of 10 treatment combinations in the MTC and 15 in the additive analysis. Compared with all other treatments, the combination of roflumilast plus LAMA exhibited the largest treatment effects, and had the highest probability (45%) of being the best first-line treatment. This was consistent whether applying the incidence rate analysis or the binomial analysis. When applying the additive assumption, most point estimates suggested that roflumilast may provide additional benefit by further reducing exacerbations. Using various meta-analytic approaches, our study demonstrates that depending on the choice of drug, combined treatments offer a therapeutic advantage.


Changing governance of the world's forests.
Major features of contemporary forest governance include decentralization of forest management, logging concessions in publicly owned commercially valuable forests, and timber certification, primarily in temperate forests. Although a majority of forests continue to be owned formally by governments, the effectiveness of forest governance is increasingly independent of formal ownership. Growing and competing demands for food, biofuels, timber, and environmental services will pose severe challenges to effective forest governance in the future, especially in conjunction with the direct and indirect impacts of climate change. A greater role for community and market actors in forest governance and deeper attention to the factors that lead to effective governance, beyond ownership patterns, is necessary to address future forest governance challenges.


The impact of the method of consent on response rates in the ISAAC time trends study.
Centres in Phases I and III of the International Study of Asthma and Allergies in Childhood (ISAAC) programme used the method of consent (passive or active) required by local ethics committees. Retrospectively, relationships between achieved response rates and method of consent for 13-14 and 6-7-year-olds (adolescents and children, respectively), were examined between phases and between English and non-English language centres. Information was obtained for 113 of 115 centres for adolescents and 72/72 centres for children. Both age groups: most centres using passive consent achieved high response rates (>80% adolescents and >70% children). English language centres using active consent showed a larger decrease in response rate. Adolescents: seven centres changed from passive consent in Phase I to active consent in Phase III (median decrease of 13%), with five centres showing lower response rates (as low as 34%). Children: no centre changed consent method between phases. Centres using active consent had lower median response rates (lowest response rate 45%). The requirement for active consent for population school-based questionnaire studies can impact negatively on response rates, particularly English language centres, thus adversely affecting the validity of the data. Ethics committees need to consider this issue carefully.


Experimental hyperphenylalaninemia in the pregnant guinea pig: possible phenylalanine teratogenesis and p-chlorophenylalanine embryotoxicity.
Maternal hyperphenylalaninemia (HPH) due to deficient phenylalanine (Phe) hydroxylation is a recognized human teratogen associated with an increased incidence of intrauterine growth retardation, microcephaly, congenital heart disease, and mental retardation. There are no previous reports of experimental HPH during organogenesis. Sustained HPH was produced in pregnant guinea pigs by adding 3.5% Phe and 1.0% parachlorophenylalanine (pCPA), an inhibitor of Phe hydroxylase, to standard guinea pig chow. Animals consumed the supplemented test diets from gestation day 1 until killed on gestation day 17. Examination of day 17 embryos revealed that embryonic mortality was associated only with maternal pCPA administration and was independent of the degree of maternal HPH. Embryonic malformation was associated with maternal HPH as well as maternal pCPA administration. Both maternal HPH and pCPA administration were associated with embryonic growth retardation. There was no association between maternal food intake or plasma tyrosine levels and embryonic abnormality or mortality. Both Phe and tyrosine were found to be concentrated in gestation day 17 yolk sac fluid when compared to maternal plasma Phe and tyrosine. The association of embryonic malformation and maternal HPH is consistent with human data. The embryotoxicity of pCPA requires further study and highlights the necessity of appropriate controls in models of experimental HPH.


NTP Toxicology and Carcinogenesis Studies of Telone II(R) (Technical-Grade 1,3-Dichloropropene [CAS No. 542-75-6] Containing 1.0% Epichlorohydrin as a Stabilizer) in F344/N Rats and B6C3F1 Mice (Gavage Studies).
Toxicology and carcinogenesis studies of Telone II(R) (a soil fumigant containing approximately 89% cis- and trans-1,3-dichloropropene, 2.5% 1,2-dichloropropane, 1.5% of a trichloropropene isomer, and 1.0% epichlorohydrin) were conducted by administering the commercial-grade formulation in corn oil by gavage to groups of 52 male and 52 female F344/N rats at doses of 0, 25, or 50 mg/kg and to groups of 50 male and 50 female B6C3F1 mice at doses of 0, 50, or 100 mg/kg. Doses were administered three times per week for 104 weeks. Ancillary studies were conducted in which dose groups containing five male and five female rats were killed after receiving Telone II(R) for 9, 16, 21, 24, or 27 months. Mean body weights of high dose male rats were about 5% lower than those for the vehicle control and low dose male rats; no differences in body weights were observed among groups of female rats. Survival was comparable for the different groups of male and female rats. For male and female mice, the dosed groups initially weighed 6%-22% less than did the vehicle controls; the weight differential decreased to 5%-9% by the end of the studies. Twenty-five vehicle control male mice died during weeks 48-51 from suppurative inflammation of the heart (myocarditis). At the end of the studies, the survival of male mice was as follows: vehicle control, 8/50; low dose, 28/50; high dose 31/50. Survival of female mice was lower (P<0.05) in the high dose group than in the vehicle controls (46/50; 45/50; 36/50). The primary organs affected were the forestomach (rats and mice), urinary bladder (mice), lung (mice), and liver (rats). Compound-related nonneoplastic lesions included basal cell or epithelial hyperplasia of the forestomach (rats and mice), epithelial hyperplasia of the urinary bladder (mice), and kidney hydronephrosis (mice). Neoplastic lesions associated with administration of Telone II(R) included squamous cell papillomas of the forestomach (male rats: 1/52; 1/52; 9/52; female rats: 0/52; 2/52; 3/52; female mice: 0/50; 1/50; 2/50), squamous cell carcinomas of the forestomach (male rats: 0/52; 0/52; 4/52; female mice: 0/50; 0/50; 2/50), transitional cell carcinomas of the urinary bladder (female mice: 0/50; 8/50; 21/48), alveolar/bronchiolar adenomas (female mice: 0/50; 3/50; 8/50), and neoplastic nodules of the liver (male rats: 1/52; 6/52; 7/52). Although the study in male mice was considered inadequate due to the deaths at weeks 48-51 of 25/50 vehicle control animals, 2/50 of the high dose males had transitional cell carcinomas of the urinary bladder. Furthermore, increases were seen in the incidences of alveolar/bronchiolar neoplasms of the lung (1/50; 13/50; 12/50) and of squamous cell papillomas of the forestomach (0/50; 2/50; 3/50). These findings plus the finding of nonneoplastic lesions in two of these organs (basal cell or epithelial hyperplasia of the forestomach: 0/50; 0/50; 4/50; epithelial hyperplasia of the urinary bladder: 0/50; 9/50; 18/50) suggest that Telone II(R) may have been responsible for the development of these lesions in male mice. Development of lesions of the forestomach (basal cell hyperplasia and squamous cell papilloma) was observed to be time dependent. The results of the scheduled kills supported the findings of the carcinogenesis studies. When the results from the scheduled kills at all time points were pooled with those of the 24-month carcinogenesis studies, the incidences were as follows: basal cell or epithelial hyperplasia of the forestomach-- male rats: 3/77; 13/77; 31/77; female rats: 1/75; 5/77; 35/77; squamous cell papilloma of the forestomach-- male rats: 1/77; 1/77; 13/77; female rats: 0/75; 2/77; 8/77; neoplastic nodules of the liver--male rats: 1/77; 6/76; 8/77; female rats: 6/75; 8/77; 12/77. cis- and trans-1,3- Dichloropropane are the principle components (89%) in Telone II(R), but the 1.0% epichlorohydrin, a direct-acting mutagen and carcinogen added as a stabilizer, may have influenced the development of the forestomach lesions. 1,3-Dichloropropene was mutagenic in Salmonella typhimuriumnt of the forestomach lesions. 1,3-Dichloropropene was mutagenic in Salmonella typhimurium strains TA98, TA100, and TA1535 without metabolic activation and in TA100 and TA1535 with metabolic activation by Aroclor-induced male Sprague-Dawley rat and Syrian hamster liver S9. No mutagenic response was seen in TA1537. Sex-linked recessive lethal mutations were observed in Drosophila melanogaster, and 1,3-dichloropropene did not induce reciprocal translocations in D. melanogaster. A data audit was conducted on the Telone II® 2-year carcinogenesis studies in rats and mice and the ancillary studies in rats. Except for the already known problem of survival of male vehicle control mice, no other discrepancies or problems that would compromise the validity of the findings or alter the interpretations of these studies were found. Under the conditions of these gavage studies, there was clear evidence of carcinogenicity for male F344/N rats, as indicated by Telone II®-related increased incidences of squamous cell papillomas and carcinomas of the forestomach, as well as an increased incidence of neoplastic nodules of the liver. In female F344/N rats, there was some evidence of carcinogenicity because Telone II® caused an increased incidence of squamous cell papillomas of the forestomach. The experiment in male B6C3F1 mice was considered to be an inadequate study of carcinogenicity because of reduced survival in the vehicle control group. However, there was some indication in the male mice of Telone II®-related increases of transitional cell carcinomas of the urinary bladder, squamous cell papillomas of the forestomach, and alveolar/bronchiolar adenomas and carcinomas of the lung. There was clear evidence of carcinogenicity for female B6C3F1 mice, since Telone II® caused increased incidences of transitional cell carcinomas of the urinary bladder; Telone II® also increased the incidences of alveolar/bronchiolar adenomas of the lung and of squamous cell papillomas or carcinomas of the forestomach in the female mice. Telone II®-related nonneoplastic lesions included basal cell or epithelial cell hyperplasia in the forestomach of male and female rats and male and female mice and epithelial hyperplasia of the urinary bladder in male and female mice. Synonyms: cis,trans-1,3-dichloropropene, D-D® Soil Fumigant; Telone® Soil Fumigants; Vorlex® Soil Fumigants


Enhanced electronic properties in mesoporous TiO2 via lithium doping for high-efficiency perovskite solar cells.
Perovskite solar cells are one of the most promising photovoltaic technologies with their extraordinary progress in efficiency and the simple processes required to produce them. However, the frequent presence of a pronounced hysteresis in the current voltage characteristic of these devices arises concerns on the intrinsic stability of organo-metal halides, challenging the reliability of technology itself. Here, we show that n-doping of mesoporous TiO2 is accomplished by facile post treatment of the films with lithium salts. We demonstrate that the Li-doped TiO2 electrodes exhibit superior electronic properties, by reducing electronic trap states enabling faster electron transport. Perovskite solar cells prepared using the Li-doped films as scaffold to host the CH3NH3PbI3 light harvester produce substantially higher performances compared with undoped electrodes, improving the power conversion efficiency from 17 to over 19% with negligible hysteretic behaviour (lower than 0.3%).


Soft tissue augmentation of ridge defects in the maxillary anterior area using two different methods: a randomized controlled clinical trial.
To test whether or not vascularized interpositional periosteal-connective tissue grafts are as successful as free subepithelial connective tissue grafts in augmenting volume defects in the anterior maxilla. Twenty subjects with Seibert class 1 ridge defects in the anterior maxilla were randomly, equally assigned to augmentation by vascularized interpositional periosteal-connective tissue graft (test) or free subepithelial connective tissue graft (control). Clinical periodontal parameters at teeth adjacent to the gap were recorded, and conventional impressions were taken prior to surgery (baseline = t(0)) and 1 (t(1)), 3 (t(3)) and 6 (t(6)) months after surgery. The casts were optically scanned, digitized and analyzed for ridge contour changes in the augmented area. Data were subjected to nonparametric statistics. The contour changes in labial distance between baseline and follow-up for the control group were (median, range) 1 mm, 0.37-1.45 (t(0)-t(1)); 1.18 mm, 0.39-1.40 (t(0)-t(3)); and 0.63 mm, 0.28-1.22 (t(0)-t(6)) and for test group 1.21 mm, 0.74-2.47 (t(0)-t(1)); 1.26 mm, 0.50-1.71 (t(0)-t(3)); and 1.18 mm, 0.16-1.75 (t(0)-t(6)). Significantly less shrinkage of the graft was observed in the test group after 6 months (P = 0.03). Clinical periodontal parameters at the neighboring teeth were stable over the follow-up period and did not differ between groups. Augmentation of single tooth gaps with moderate ridge defects in the anterior maxilla was successfully performed using both techniques. However, after 6 months, sites treated by the pediculated graft were superior in maintaining the initially augmented volume and showed less shrinkage of the graft. This could be attributed to better perfusion of the pediculated graft.


Centre-surround interactions in response to natural scene stimulation in the primary visual cortex.
Centre-surround interaction in the primary visual cortex (area V1) has been studied extensively using artificial, abstract stimulus patterns, such as bars, gratings and simple texture patterns. In this experiment, we extend the study of centre-surround interaction by using natural scene images. We systematically varied the contrast of natural image surrounds presented outside the classical receptive field (CRF), and recorded neuronal response to a natural image patch presented within the CRF in area V1 of awake, fixating macaques. For the majority of neurons (67 out of 111), the natural image surrounds profoundly modulated, mainly by suppressing, neuronal responses to CRF images. These modulatory effects started at the earliest stage of neuronal responses, and often depended on the contrast and higher-order structures of the surrounds. For 47 out of 67 neurons, randomising the phases of the Fourier spectrum of the natural image surround diminished the centre-surround interaction. Our results suggest that the centre-surround interaction in area V1 can be extended to natural vision, and is sensitive to the higher-order structures of natural scene images, such as image contours.


Biosynthesis of high density lipoprotein by chicken liver: intracellular transport and proteolytic processing of nascent apolipoprotein A-1.
To study the in vivo processing and secretion of Apolipoprotein A-I (Apo A-I), young chickens were administered individual L-[3H]amino acids intravenously and the time of intracellular transport of nascent Apo A-I from rough endoplasmic reticulum (RER) to the Golgi apparatus was measured. Within 3 to 9 min there was maximal incorporation of radioactivity into Apo A-I in both the RER and the Golgi cell fractions. By contrast, the majority of radioactive albumin was also present in the RER by 3 to 9 min, but did not reach peak amounts in the Golgi fraction until 9 to 25 min. Both radioactive Apo A-I and albumin appeared in the blood at about the same time (between 20 and 30 min). NH2-terminal amino acid sequence analysis of nascent intracellular Apo A-I showed that it contains a pro-hexapeptide extension identical to that of human Apo A-I. After 30 min of administration of radioactive amino acids radioactive Apo A-I was isolated by immunoprecipitation from the liver and serum. NH2-terminal sequence analysis of 20 amino acids indicated that chicken liver contained an equal mixture of nascent pro-Apo A-I and fully processed Apo A-I, whereas the serum only contained processed Apo A-I. Further studies showed that the RER only contained pro-Apo A-I, whereas a mixture of pro-Apo A-I and processed Apo A-I was found in the Golgi complex. These results indicate that, in chicken hepatocytes, there is a more rapid transport of Apo A-I than of albumin from the RER to the Golgi cell fractions, and that Apo A-I remains in the Golgi apparatus for a longer period of time before it is secreted into the blood. In addition these studies show that the in vivo proteolytic processing of chicken pro-Apo A-I to Apo A-I occurs in the Golgi cell fractions.


Lectin histochemistry of human leukaemic mast cells (HMC-1) transplanted into severe combined immunodeficient (scid) mice.
It is difficult to isolate and impossible to propagate human mast cells in tissue culture. As an alternative to the use of human differentiated mast cells, a human leukaemic mast cell line (HMC-1), which can be propagated in vitro, has been employed in a number of studies. Carbohydrate binding proteins, lectins, have been used to characterise the terminal sugar residues of human mast cells in situ. The aim of the present study is to characterise the lectin binding sites of HMC-1 cells transplanted into severe combined immunodeficient (scid) mice. Lectins specific for the complex carbohydrates, neuraminic acid and N-acetylglucosamine residues showed generally a strong uniform binding pattern, whereas mannose and glucose specific yielded lectins a greater heterogeneity. This glycotope expression pattern has some similarities with those of human mast cells in situ, and therefore HMC-1 cells grown in scid mice constitute a valuable model system for the study of carbohydrate expression in human mast cells.


Irritable bowel syndrome.
The prevalence of irritable bowel syndrome (IBS) varies depending on the criteria used to diagnose it, but it ranges from about 5% to 20%. IBS is associated with abnormal gastrointestinal motor function and enhanced visceral perception, as well as psychosocial and genetic factors. People with IBS often have other bodily and psychiatric symptoms, and have an increased likelihood of having unnecessary surgery compared with people without IBS. We conducted a systematic review and aimed to answer the following clinical question: What are the effects of treatments in people with IBS? We searched: Medline, Embase, The Cochrane Library, and other important databases up to July 2009 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). We found 18 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. In this systematic review we present information relating to the effectiveness and safety of the following interventions: 5HT(3) receptor antagonists (alosetron and ramosetron); 5HT(4) receptor agonists (tegaserod); antidepressants (tricyclic antidepressants and selective serotonin reuptake inhibitors [SSRIs]); antispasmodics (including peppermint oil); cognitive behavioural therapy (CBT); hypnotherapy; soluble and insoluble fibre supplementation; and loperamide.


Fresh and pickled vegetable consumption and gastric cancer in Japanese and Korean populations: a meta-analysis of observational studies.
It is widely known that vegetable consumption contributes to reducing the risk of gastric cancer (GC). However, the incidence rates of GC remain high in both Japanese and Korean populations, even though they have a high consumption of total vegetables. This may be due to the fact that Japanese and Koreans mainly consume processed vegetables, such as cooked, salted, or pickled vegetables, rather than fresh vegetables. To determine whether the intakes of fresh and pickled vegetables have different effects on the risk of GC in Japanese and Korean populations, we carried out a meta-analysis of published epidemiological reports. Eight studies on the consumption of fresh vegetables and 14 studies on the consumption of pickled vegetables related to GC risk were included in this meta-analysis. Four studies exploring differences in GC risk in men and women were considered separately. We observed that a high intake of fresh vegetables was significantly associated with a decreased risk of GC (overall summary OR = 0.62, 95% CI = 0.46-0.85) but that a high intake of pickled vegetables was significantly associated with an increased risk of GC (overall summary OR = 1.28, 95% CI = 1.06-1.53). The results of this meta-analysis provide evidence that a high intake of pickled vegetables may increase GC risk and suggest that a high consumption of fresh vegetables, rather than a large total amount of vegetables including pickled vegetables, is important to reduce GC risk.


Diverse CRISPR-Cas responses and dramatic cellular DNA changes and cell death in pKEF9-conjugated Sulfolobus species.
The Sulfolobales host a unique family of crenarchaeal conjugative plasmids some of which undergo complex rearrangements intracellularly. Here we examined the conjugation cycle of pKEF9 in the recipient strain Sulfolobus islandicus REY15A. The plasmid conjugated and replicated rapidly generating high average copy numbers which led to strong growth retardation that was coincident with activation of CRISPR-Cas adaptation. Simultaneously, intracellular DNA was extensively degraded and this also occurred in a conjugated Δcas6 mutant lacking a CRISPR-Cas immune response. Furthermore, the integrated forms of pKEF9 in the donor Sulfolobus solfataricus P1 and recipient host were specifically corrupted by transposable orfB elements, indicative of a dual mechanism for inactivating free and integrated forms of the plasmid. In addition, the CRISPR locus of pKEF9 was progressively deleted when conjugated into the recipient strain. Factors influencing activation of CRISPR-Cas adaptation in the recipient strain are considered, including the first evidence for a possible priming effect in Sulfolobus The 3-Mbp genome sequence of the donor P1 strain is presented.


Unsupervised genome-wide recognition of local relationship patterns.
Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion. We developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems. Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro's utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.


Prolonged self-paced exercise in the heat - environmental factors affecting performance.
In this review we examine how self-paced performance is affected by environmental heat stress factors during cycling time trial performance as well as considering the effects of exercise mode and heat acclimatization. Mean power output during prolonged cycling time trials in the heat (≥30°C) was on average reduced by 15% in the 14 studies that fulfilled the inclusion criteria. Ambient temperature per se was a poor predictor of the integrated environmental heat stress and 2 of the prevailing heat stress indices (WBGT and UTCI) failed to predict the environmental influence on performance. The weighing of wind speed appears to be too low for predicting the effect for cycling in trained acclimatized subjects, where performance may be maintained in outdoor time trials at ambient temperatures as high as 36°C (36°C UTCI; 28°C WBGT). Power output during indoor trials may also be maintained with temperatures up to at least 27°C when humidity is modest and wind speed matches the movement speed generated during outdoor cycling, whereas marked reductions are observed when air movement is minimal. For running, representing an exercise mode with lower movement speed and higher heat production for a given metabolic rate, it appears that endurance is affected even at much lower ambient temperatures. On this basis we conclude that environmental heat stress impacts self-paced endurance performance. However, the effect is markedly modified by acclimatization status and exercise mode, as the wind generated by the exercise (movement speed) or the environment (natural or fan air movement) exerts a strong influence.


Variable conductivity and embolism in roots and branches of four contrasting tree species and their impacts on whole-plant hydraulic performance under future atmospheric CO₂ concentration.
Anatomical and physiological acclimation to water stress of the tree hydraulic system involves trade-offs between maintenance of stomatal conductance and loss of hydraulic conductivity, with short-term impacts on photosynthesis and long-term consequences to survival and growth. Here, we study the role of variations in root and branch maximum hydraulic specific conductivity (k(s-max)) under high and low soil moisture in determining whole-tree hydraulic conductance (K(tree)) and in mediating stomatal control of gas exchange in four contrasting tree species growing under ambient and elevated CO₂ (CO₂(a) and CO₂(e)). We hypothesized that K(tree) would adjust to CO₂(e) through an increase in root and branch k(s-max) in response to anatomical adjustments. However, physiological changes observed under CO₂(e) were not clearly related to structural change in the xylem of any of the species. The only large effect of CO₂(e) occurred in branches of Liquidambar styraciflua L. and Cornus florida L. where an increase in k(s-max) and a decrease in xylem resistance to embolism (-P₅₀) were measured. Across species, embolism in roots explained the loss of K(tree) and therefore indirectly constituted a hydraulic signal involved in stomatal regulation and in the reduction of G(s-ref), the sap-flux-scaled mean canopy stomatal conductance at a reference vapour pressure deficit of 1 kPa. Across roots and branches, the increase in k(s-max) was associated with a decrease in -P₅₀, a consequence of structural acclimation such as larger conduits, lower pit resistance and lower wood density. Across species, treatment-induced changes in K(tree) translated to similar variation in G(s-ref). However, the relationship between G(s-ref) and K(tree) under CO₂(a) was steeper than under CO₂(e), indicating that CO₂(e) trees have lower G(s-ref) at a given K(tree) than CO₂(a) trees. Under high soil moisture, CO₂(e) greatly reduced G(s-ref). Under low soil moisture, CO₂(e) reduced G(s-ref) of only L. styraciflua and Ulmus alata. In some species, higher xylem dysfunction under CO₂(e) might impact tree performance in a future climate when increased evaporative demand could cause a greater loss of hydraulic function. The results contributed to our knowledge of the physiological and anatomical mechanisms underpinning the responses of tree species to drought and more generally to global change.