Binge Drinking, Cannabis Co-Consumption and Academic Achievement in First Year University Students in Spain: Academic Adjustment as a Mediator.
Little is known about how binge drinking or the combination of binge drinking and cannabis consumption affect academic achievement in students during the transition to university, or about the mechanisms that mediate this relationship. The purpose of this study was to evaluate the association between this pattern of alcohol/cannabis consumption and academic achievement, considering academic adjustment as a possible mediator. A total of 258 Spanish, first-year university students (145 females and 113 males), enrolled in undergraduate degree courses, were categorized into three groups on the basis of their patterns of alcohol/cannabis consumption: control, binge drinkers and co-consumers. The findings showed a significant effect of the combined binge drinking/cannabis consumption, but not of binge drinking alone, upon academic achievement and academic adjustment. Grade point average (GPA) and academic adjustment were lower in the co-consumers than in the other groups. Regarding the mediation effect, 34.33% of the impact of combined alcohol/cannabis use on GPA was mediated by academic adjustment. The combined consumption of alcohol and cannabis led to difficulties in adaptation to academic life, which in turn contributed to poorer performance at university. The implications of the findings are discussed.


Pomegranate extract inhibits the proliferation and viability of MMTV-Wnt-1 mouse mammary cancer stem cells in vitro.
Pomegranate (Punica granatum L.) is known to possess anticancer activities. The effects of a standardized extract of pomegranate (PE) on a mouse mammary cancer cell line (designated WA4) derived from mouse MMTV-Wnt-1 mammary tumors were examined in this study. The WA4 cell line has been previously characterized as containing a majority of cells possessing stem cell characteristics. PE inhibited the proliferation of WA4 cells in a time- and concentration-dependent manner. This was due to an arrest of cell cycle progression in the G0/G1 phase. PE was also cytotoxic to quiescent WA4 cells in a concentration-dependent manner at concentrations >10 microg/ml. PE treatment of WA4 cells resulted in an increase in caspase-3 enzyme activity in a time- and concentration-dependent manner, indicating that the cytotoxic effect of PE was due to the induction of apoptosis. We tested the effect of several individual phytochemicals derived from PE on WA4 cells. Ellagic acid, ursolic acid and luteolin caused a time- and concentration-dependent reduction of cell proliferation and viability, suggesting that they contribute to the inhibitory effect of PE, while caffeic acid had no effect. Cancer stem cells, which are highly resistant to conventional chemotherapeutic agents, are thought to be the origin of both primary and secondary breast tumors, and thus are a critical target in both breast cancer therapy and prevention. These data suggest that PE, which is a proven and safe dietary supplement, has promise as an treatment against breast cancer by preventing proliferation of cancer stem cells.


Predicting fatigue using countermovement jump force-time signatures: PCA can distinguish neuromuscular versus metabolic fatigue.
This study investigated the relationship between the ground reaction force-time profile of a countermovement jump (CMJ) and fatigue, specifically focusing on predicting the onset of neuromuscular versus metabolic fatigue using the CMJ. Ten recreational athletes performed 5 CMJs at time points prior to, immediately following, and at 0.5, 1, 3, 6, 24 and 48 h after training, which comprised repeated sprint sessions of low, moderate, or high workloads. Features of the concentric portion of the CMJ force-time signature at the measurement time points were analysed using Principal Components Analysis (PCA) and functional PCA (fPCA) to better understand fatigue onset given training workload. In addition, Linear Mixed Effects (LME) models were developed to predict the onset of fatigue. The first two Principal Components (PCs) using PCA explained 68% of the variation in CMJ features, capturing variation between athletes through weighted combinations of force, concentric time and power. The next two PCs explained 9.9% of the variation and revealed fatigue effects between 6 to 48 h after training for PC3, and contrasting neuromuscular and metabolic fatigue effects in PC4. fPCA supported these findings and further revealed contrasts between metabolic and neuromuscular fatigue effects in the first and second half of the force-time curve in PC3, and a double peak effect in PC4. Subsequently, CMJ measurements up to 0.5 h after training were used to predict relative peak CMJ force, with mean squared errors of 0.013 and 0.015 at 6 and 48 h corresponding to metabolic and neuromuscular fatigue. The CMJ was found to provide a strong predictor of neuromuscular and metabolic fatigue, after accounting for force, concentric time and power. This method can be used to assist coaches to individualise future training based on CMJ response to the immediate session.


Aldo-keto Reductase Metabolizes Glyphosate and Confers Glyphosate Resistance in Echinochloa colona.
Glyphosate, the most commonly used herbicide in the world, controls a wide range of plant species, mainly because plants have little capacity to metabolize (detoxify) glyphosate. Massive glyphosate use has led to world-wide evolution of glyphosate-resistant (GR) weed species, including the economically damaging grass weed Echinochloa colona An Australian population of E colona has evolved resistance to glyphosate with unknown mechanisms that do not involve the glyphosate target enzyme 5-enolpyruvylshikimate-3-P synthase. GR and glyphosate-susceptible (S) lines were isolated from this population and used for resistance gene discovery. RNA sequencing analysis and phenotype/genotype validation experiments revealed that one aldo-keto reductase (AKR) contig had higher expression and higher resultant AKR activity in GR than S plants. Two full-length AKR (EcAKR4-1 and EcAKR4-2) complementary DNA transcripts were cloned with identical sequences between the GR and S plants but were upregulated in the GR plants. Rice (Oryza sativa) calli and seedlings overexpressing EcAKR4-1 and displaying increased AKR activity were resistant to glyphosate. EcAKR4-1 expressed in Escherichia coli can metabolize glyphosate to produce aminomethylphosphonic acid and glyoxylate. Consistent with these results, GR E colona plants exhibited enhanced capacity for detoxifying glyphosate into aminomethylphosphonic acid and glyoxylate. Structural modeling predicted that glyphosate binds to EcAKR4-1 for oxidation, and metabolomics analysis of EcAKR4-1 transgenic rice seedlings revealed possible redox pathways involved in glyphosate metabolism. Our study provides direct experimental evidence of the evolution of a plant AKR that metabolizes glyphosate and thereby confers glyphosate resistance.


Attitudes toward E-Cigarettes, Reasons for Initiating E-Cigarette Use, and Changes in Smoking Behavior after Initiation: A Pilot Longitudinal Study of Regular Cigarette Smokers.
We examined 1) changes in smoking and vaping behavior and associated cotinine levels and health status among regular smokers who were first-time e-cigarette purchasers and 2) attitudes, intentions, and restrictions regarding e-cigarettes. We conducted a pilot longitudinal study with assessments of the aforementioned factors and salivary cotinine at weeks 0, 4, and 8. Eligibility criteria included being ≥18 years old, smoking ≥25 of the last 30 days, smoking ≥5 cigarettes per day (cpd), smoking regularly ≥1 year, and not having started using e-cigarettes. Of 72 individuals screened, 40 consented, 36 completed the baseline survey, and 83.3% and 72.2% were retained at weeks 4 and 8, respectively. Participants reduced cigarette consumption from baseline to week 4 and 8 (p's < 0.001); 23.1% reported no cigarette use in the past month at week 8. There was no significant decrease in cotinine from baseline to week 4 or 8 (p's = ns). At week 8, the majority reported improved health (65.4%), reduced smoker's cough (57.7%), and improved sense of smell (53.8%) and taste (50.0%). The majority believed that e-cigarettes versus regular cigarettes have fewer health risks (97.2%) and that e-cigarettes have been shown to help smokers quit (80.6%) and reduce cigarette consumption (97.2%). In addition, the majority intended to use e-cigarettes as a complete replacement for regular cigarettes (69.4%) and reported no restriction on e-cigarette use in the home (63.9%) or car (80.6%). Future research is needed to document the long-term impact on smoking behavior and health among cigarette smokers who initiate use of e-cigarettes.


Modulation of exon skipping and inclusion by heterogeneous nuclear ribonucleoprotein A1 and pre-mRNA splicing factor SF2/ASF.
The essential splicing factor SF2/ASF and the heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) modulate alternative splicing in vitro of pre-mRNAs that contain 5' splice sites of comparable strengths competing for a common 3' splice site. Using natural and model pre-mRNAs, we have examined whether the ratio of SF2/ASF to hnRNP A1 also regulates other modes of alternative splicing in vitro. We found that an excess of SF2/ASF effectively prevents inappropriate exon skipping and also influences the selection of mutually exclusive tissue-specific exons in natural beta-tropomyosin pre-mRNA. In contrast, an excess of hnRNP A1 does not cause inappropriate exon skipping in natural constitutively or alternatively spliced pre-mRNAs. Although hnRNP A1 can promote alternative exon skipping, this effect is not universal and is dependent, e.g., on the size of the internal alternative exon and on the strength of the polypyrimidine tract in the preceding intron. With appropriate alternative exons, an excess of SF2/ASF promotes exon inclusion, whereas an excess of hnRNP A1 causes exon skipping. We propose that in some cases the ratio of SF2/ASF to hnRNP A1 may play a role in regulating alternative splicing by exon inclusion or skipping through the antagonistic effects of these proteins on alternative splice site selection.


Regulation of gephyrin cluster size and inhibitory synaptic currents on Renshaw cells by motor axon excitatory inputs.
Renshaw cells receive a high density of inhibitory synapses characterized by large postsynaptic gephyrin clusters and mixed glycinergic/GABAergic inhibitory currents with large peak amplitudes and long decays. These properties appear adapted to increase inhibitory efficacy over Renshaw cells and mature postnatally by mechanisms that are unknown. We tested the hypothesis that heterosynaptic influences from excitatory motor axon inputs modulate the development of inhibitory synapses on Renshaw cells. Thus, tetanus (TeNT) and botulinum neurotoxin A (BoNT-A) were injected intramuscularly at postnatal day 5 (P5) to, respectively, elevate or reduce motor axon firing activity for approximately 2 weeks. After TeNT injections, the average gephyrin cluster areas on Renshaw cells increased by 18.4% at P15 and 28.4% at P20 and decreased after BoNT-A injections by 17.7% at P15 and 19.9% at P20. The average size differences resulted from changes in the proportions of small and large gephyrin clusters. Whole-cell recordings in P9-P15 Renshaw cells after P5 TeNT injections showed increases in the peak amplitude of glycinergic miniature postsynaptic currents (mPSCs) and the fast component of mixed (glycinergic/GABAergic) mPSCs compared with controls (60.9% and 78.9%, respectively). GABAergic mPSCs increased in peak amplitude to a smaller extent (45.8%). However, because of the comparatively longer decays of synaptic GABAergic currents, total current transfer changes after TeNT were similar for synaptic glycine and GABA(A) receptors (56 vs 48.9% increases, respectively). We concluded that motor axon excitatory synaptic activity modulates the development of inhibitory synapse properties on Renshaw cells, influencing recruitment of postsynaptic gephyrin and glycine receptors and, to lesser extent, GABA(A) receptors.


Effect of inoculum size, bacterial species, type of surfaces and contact time to the transfer of foodborne pathogens from inoculated to non-inoculated beef fillets via food processing surfaces.
The objective of the present study was to determine the factors affecting the transfer of foodborne pathogens from inoculated beef fillets to non-inoculated ones, through food processing surfaces. Three different levels of inoculation of beef fillets surface were prepared: a high one of approximately 107 CFU/cm2, a medium one of 105 CFU/cm2 and a low one of 103 CFU/cm2, using mixed-strains of Listeria monocytogenes, or Salmonella enterica Typhimurium, or Escherichia coli O157:H7. The inoculated fillets were then placed on 3 different types of surfaces (stainless steel-SS, polyethylene-PE and wood-WD), for 1 or 15 min. Subsequently, these fillets were removed from the cutting boards and six sequential non-inoculated fillets were placed on the same surfaces for the same period of time. All non-inoculated fillets were contaminated with a progressive reduction trend of each pathogen's population level from the inoculated fillets to the sixth non-inoculated ones that got in contact with the surfaces, and regardless the initial inoculum, a reduction of approximately 2 log CFU/g between inoculated and 1st non-inoculated fillet was observed. S. Typhimurium was transferred at lower mean population (2.39 log CFU/g) to contaminated fillets than E. coli O157:H7 (2.93 log CFU/g), followed by L. monocytogenes (3.12 log CFU/g; P < 0.05). Wooden surfaces (2.77 log CFU/g) enhanced the transfer of bacteria to subsequent fillets compared to other materials (2.66 log CFU/g for SS and PE; P < 0.05). Cross-contamination between meat and surfaces is a multifactorial process strongly depended on the species, initial contamination level, kind of surface, contact time and the number of subsequent fillet, according to analysis of variance. Thus, quantifying the cross-contamination risk associated with various steps of meat processing and food establishments or households can provide a scientific basis for risk management of such products.


Transitions in smartphone addiction proneness among children: The effect of gender and use patterns.
This study assessed the incidence of transitions in smartphone addiction proneness (SAP) among children and examined the effects of gender, use patterns (social networking sites (SNSs) use and smartphone gaming) and depression on smartphone addiction transitions. A representative sample of 2,155 children from Taipei completed longitudinal surveys in both 2015 (5th grade) and 2016 (6th grade). Latent transition analysis (LTA) was used to characterize transitions in SAP and to examine the effects of gender, use patterns and depression on SAP transitions. LTA identified four latent statuses of SAP: about half of the children were in non-SAP status, one-fifth were in tolerance status, one-sixth were in withdrawal status, and one-seventh were in high-SAP status. Both boys and girls had a higher prevalence of high-SAP and tolerance in 6th grade than in 5th grade, whereas in both grades boys had a higher prevalence of high-SAP and withdrawal, and girls had a higher prevalence of non-SAP and tolerance. Controlling for parents' education, family structure, and household income, higher use of SNSs by children, increasing use of mobile gaming and higher levels of depression were individually associated with increased odds of being in one of the three SAP statuses other than non-SAP. When all three covariates were jointly entered into the model, usage of SNSs and depression remained significant predictors. Both boys and girls tended to transition to tolerance or high-SAP statuses, while children's depression and their usage of SNSs increased the risk of smartphone addiction.


Spatial and space-time correlations in systems of subpopulations with genetic drift and migration.
The geographic distribution of genetic variation is an important theoretical and experimental component of population genetics. Previous characterizations of genetic structure of populations have used measures of spatial variance and spatial correlations. Yet a full understanding of the causes and consequences of spatial structure requires complete characterization of the underlying space-time system. This paper examines important interactions between processes and spatial structure in systems of subpopulations with migration and drift, by analyzing correlations of gene frequencies over space and time. We develop methods for studying important features of the complete set of space-time correlations of gene frequencies for the first time in population genetics. These methods also provide a new alternative for studying the purely spatial correlations and the variance, for models with general spatial dimensionalities and migration patterns. These results are obtained by employing theorems, previously unused in population genetics, for space-time autoregressive (STAR) stochastic spatial time series. We include results on systems with subpopulation interactions that have time delay lags (temporal orders) greater than one. We use the space-time correlation structure to develop novel estimators for migration rates that are based on space-time data (samples collected over space and time) rather than on purely spatial data, for real systems. We examine the space-time and spatial correlations for some specific stepping stone migration models. One focus is on the effects of anisotropic migration rates. Partial space-time correlation coefficients can be used for identifying migration patterns. Using STAR models, the spatial, space-time, and partial space-time correlations together provide a framework with an unprecedented level of detail for characterizing, predicting and contrasting space-time theoretical distributions of gene frequencies, and for identifying features such as the pattern of migration and estimating migration rates in experimental studies of genetic variation over space and time.


Coffee and fetal death: a cohort study with prospective data.
The authors conducted a cohort study within the Danish National Birth Cohort to determine whether coffee consumption during pregnancy is associated with late fetal death (spontaneous abortion and stillbirth). A total of 88,482 pregnant women recruited from March 1996 to November 2002 participated in a comprehensive interview on coffee consumption and potentially confounding factors in pregnancy. Information on pregnancy outcome was obtained from the National Hospital Discharge Register and medical records. The authors detected 1,102 fetal deaths. High levels of coffee consumption were associated with an increased risk of fetal death. Relative to nonconsumers of coffee, the adjusted hazard ratios for fetal death associated with coffee consumption of 1/2-3, 4-7, and > or =8 cups of coffee per day were 1.03 (95% confidence interval (CI): 0.89, 1.19), 1.33 (95% CI: 1.08, 1.63), and 1.59 (95% CI: 1.19, 2.13), respectively. Reverse causation due to unrecognized fetal demise may explain the association between coffee intake and risk of fetal death prior to 20 completed weeks' gestation but not the association with fetal loss following 20 completed weeks' gestation. Consumption of coffee during pregnancy was associated with a higher risk of fetal death, especially losses occurring after 20 completed weeks of gestation.


Investigation into the use of satellite data in aiding characterization of particulate air quality in the Atlanta, Georgia metropolitan area.
Poor air quality episodes occur often in metropolitan Atlanta, GA. The primary focus of this research is to assess the capability of satellites as a tool in characterizing air quality in Atlanta. Results indicate that intracity PM2.5 (particulate matter < or = 2.5 microm in aerodynamic diameter) concentrations show similar patterns as other U.S. urban areas, with the highest concentrations occurring within the city. PM2.5 and MODIS (Moderate Resolution Imaging Spectroradiometer) aerosol optical depth (AOD) have higher values in the summer than spring, yet MODIS AOD doubles in the summer unlike PM2.5. Most (80%) of the Ozone Monitoring Instrument aerosol index (AI) is below 0.5 with little differences between spring and summer. Using this value as a constraint of the carbonaceous aerosol signal in the urban area, aerosol transport events such as wildfire smoke associated with higher positive AI values can be identified. The results indicate that MODIS AOD is well correlated with PM2.5 on a yearly and seasonal basis with correlation coefficients as high as 0.8 for Terra and 0.7 for Aqua. A possible alternative view of the PM2.5 and AOD relationship is seen through the use of AOD thresholds. These probabilistic thresholds provide a means to describe the air quality index (AQI) through the use of multiyear AOD records for a specific area. The National Ambient Air Quality Standards (NAAQS) are used to classify the AOD into different AQI codes and probabilistically determine thresholds of AOD that represent most of a specific AQI category. For example, 80% of cases of moderate AQI days have AOD values between 0.5 and 0.6. The development of AOD thresholds provides a useful tool for evaluating air quality from the use of satellites in regions where there are sparse ground-based measurements of PM2.5.


Catheter-based adenovirus-mediated local intravascular gene delivery of a soluble TGF-beta type II receptor using an infiltrator in porcine coronary arteries: efficacy and complications.
Enhanced extracellular matrix (ECM) accumulation is an important finding in human restenotic arterial neointima after angioplasty. Transforming growth factor beta1(TGF-beta1) is known to regulate the synthesis and turnover of a variety of ECM components, and may play an important role in restenosis. Recombinant adenoviral vector expressing an ectodomain of the TGF-beta type II receptor fused to the human immunoglobulin Fc portion (AdTbeta-ExR) inhibits the action of TGF-beta probably either by adsorbing TGF-beta or by acting as a dominant negative receptor. We carried out a catheter-based local adenovirus mediated gene delivery using an Infiltrator in porcine coronary arteries to know the pattern of gene expression, efficacy and procedural complications. Twenty four coronary arteries in 13 pigs were used for intravascular gene delivery by intramural injection with either AdTbeta-ExR or adenovirus expressing beta-galactosidase (AdCALacZ). Direct immunofluorescent staining and reverse transcription polymerase chain reaction (RT-PCR) were used for detection of type II TGF-beta receptor and its mRNA respectively. X-Gal histochemistry was performed to identify beta-galactosidase. Both soluble TGF-beta receptor and beta-galactosidase were expressed locally in the media and adventita at injected arterial segments without any significant dissemination to remote area. Intravascular gene transfection performed with various titer of each adenoviral vector showed that AdTbeta-ExR of 5 x 10(8) pfu and AdCALacZ of 2.5 x 10(8) pfu were the minimum titer for the expression of each transgene. Infiltration of CD3 positive T cells was detected by immunohistochemical staining in the area of each transgene expression, and tends to decrease over time after gene delivery. Pathological study of 24 treated arteries showed complications such as disruption of external elastic lamina with hemorrhage (n = 4), minimal disruption of internal elastic lamina and endothelial layer, and medial thickening. In conclusion, catheter-based local intravascular gene delivery of adenoviral vector is feasible and effective in a selected artery, but must be undertaken with caution due to possible lethal complications. Local delivery of soluble TGF-beta type II receptor in this way may provide an effective intravascular gene therapy to inhibit TGF-beta signal pathway without any significant systemic side effect.


[A relational ethical model for the assessment of decision-making competence in psychiatry].
Nowadays, partly due to legislation, decision-making competence is playing an ever-increasing role in psychiatry. So far, however, there are no clear criteria for evaluating the actual competence of the procedure.
 AIM: To develop a relational ethical model, including criteria and methodology, which can be used to assess and enhance decision-making competence mainly from a relational and ethical perspective.
 METHOD: Combination of a review of the literature and ethical reflection. First of all, a limited study was made of the literature relating to the concept of and criteria for decision-making competence. On the basis of the literature and relational ethical reflection, ten criteria were developed for decision-making competence and a method was devised for assessing the procedure.
 RESULTS: The criteria that have to be satisfied can be summarised as follows: the persons involved must understand the information, and must be able to apply it to their own situation. They must be able to gain insight into their own situation and be able to weigh up the available options, and be able to estimate consequences for themselves, as well as for others. They must be able to motivate choices in a sensible and comprehensible manner without being subject to coercive influences coming from internal and external sources. Participants' choices should be motivated on the basis of their own personal values. The decision-making competence is assessed and enhanced by giving a score to the individual criteria and by making an overall evaluation. This is achieved by a dialogue including all the persons involved: the care seeker (as far as possible), close relatives and the care-providers.
 CONCLUSION: The persons involved can attain greater objectivity by exchanging views orally on the ten proposed criteria for decision-making competence.


Human glial chimeric mice reveal astrocytic dependence of JC virus infection.
Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease triggered by infection with the human gliotropic JC virus (JCV). Due to the human-selective nature of the virus, there are no animal models available to investigate JCV pathogenesis. To address this issue, we developed mice with humanized white matter by engrafting human glial progenitor cells (GPCs) into neonatal immunodeficient and myelin-deficient mice. Intracerebral delivery of JCV resulted in infection and subsequent demyelination of these chimeric mice. Human GPCs and astrocytes were infected more readily than oligodendrocytes, and viral replication was noted primarily in human astrocytes and GPCs rather than oligodendrocytes, which instead expressed early viral T antigens and exhibited apoptotic death. Engraftment of human GPCs in normally myelinated and immunodeficient mice resulted in humanized white matter that was chimeric for human astrocytes and GPCs. JCV effectively propagated in these mice, which indicates that astroglial infection is sufficient for JCV spread. Sequencing revealed progressive mutation of the JCV capsid protein VP1 after infection, suggesting that PML may evolve with active infection. These results indicate that the principal CNS targets for JCV infection are astrocytes and GPCs and that infection is associated with progressive mutation, while demyelination is a secondary occurrence, following T antigen-triggered oligodendroglial apoptosis. More broadly, this study provides a model by which to further assess the biology and treatment of human-specific gliotropic viruses.


Supramolecular control of transition metal complexes in water by a hydrophobic cavity: a bio-inspired strategy.
Supramolecular chemistry in water is a very challenging research area. In biology, water is the universal solvent where transition metal ions play major roles in molecular recognition and catalysis. In enzymes, it participates in substrate binding and/or activation in the heart of a pocket defined by the folded protein. The association of a hydrophobic cavity with a transition metal ion is thus a very appealing strategy for controlling the metal ion properties in the very competitive water solvent. Various systems based on intrinsically water-soluble macrocyclic structures such as cyclodextrins, cucurbituryls, and metallo-cages have been reported. Others use calixarenes and resorcinarenes functionalized with hydrophilic substituents. One approach for connecting a metal complex to these cavities is to graft a ligand for metal ion binding at their edge. Early work with cyclodextrins has shown Michaelis-Menten like catalysis displaying enhanced kinetics and substrate-selectivity. Remarkable examples of regio- and stereo-selective transformation of substrates have been reported as well. Dynamic two-phase systems for transition metal catalysis have also been developed. They rely on either water-transfer of the metal complex through ligand embedment or synergistic coordination of a metal ion and substrate hosting. Another strategy consists in using metallo-cages, which provide a well-defined hydrophobic space, to stabilize metal complexes in water. When the cages can host simultaneously a substrate and a reactive metal complex, size- and regio-selective catalysis was obtained. Finally, construction of a polydentate coordination site closely interlocked with a calixarene or resorcinarene macrocycle has been shown to be a very fruitful strategy for obtaining metal complexes with remarkable hosting properties. For each of these systems, the synergism resulting from the biomimetic association of a hydrophobic cavity and a metal ion is discussed within the objective of developing new tools for either selective molecular recognition (with analytical perspectives) or performant catalysis, in water.


Apremilast Is Effective in Lichen Planus Mucosae-Associated Stenotic Esophagitis.
A 74-year-old woman with extensive lichen planus mucosae (LPM) developed stenotic esophagitis that was refractory to intravenous glucocorticosteroids. Esophageal dilatations to 14 mm width were repeatedly performed without any lasting effect. After introducing oral apremilast, she experienced complete clinical remission within the first 4 weeks of treatment. Control esophagoscopy confirmed a marked recovery of the esophageal mucosa with no recurrence of the former stenosis. Our observation is in line with the case series of Paul et al. [J Am Acad Dermatol 2013;68: 255-261] who first reported on the benefit of apremilast in patients with extensive LPM. Ideally, the effectiveness of apremilast in LPM should be studied in a randomized controlled trial.


Clinical experience with 13C MRS in vivo.
13C MRS was installed on a clinical scanner at 1.5 T in order to facilitate integrated MR examinations of human brain disorders. Using a simplified protocol, (1-(13)C) glucose and/or (1-(13)C) acetate were administered orally or by intravenous infusion. (13)C spectra of diagnostic quality were acquired in more than 100 consecutive studies. Novel (13)C neurochemical data contributed to the understanding of Alzheimer's, Canavan's, mitochondrial and hepatic encephalopathy, epilepsy and normal brain development. (13)C MRS uncovered hitherto unknown disorders of NAA-synthesis, glutamate neurotransmission, TCA-cycle and glycolysis. Despite low inherent signal-to-noise, natural abundance (13)C MRS showed diagnostic promise. (13)C MRS is feasible in a clinical setting, at reasonable cost in neonates, children, adults and elderly patients.


Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS.
Cryptococcal meningitis is one of the most important HIV-related opportunistic infections, especially in the developing world. In order to help develop global strategies and priorities for prevention and treatment, it is important to estimate the burden of cryptococcal meningitis. Global burden of disease estimation using published studies. We used the median incidence rate of available studies in a geographic region to estimate the region-specific cryptococcal meningitis incidence; this was multiplied by the 2007 United Nations Programme on HIV/AIDS HIV population estimate for each region to estimate cryptococcal meningitis cases. To estimate deaths, we assumed a 9% 3-month case-fatality rate among high-income regions, a 55% rate among low-income and middle-income regions, and a 70% rate in sub-Saharan Africa, based on studies published in these areas and expert opinion. Published incidence ranged from 0.04 to 12% per year among persons with HIV. Sub-Saharan Africa had the highest yearly burden estimate (median incidence 3.2%, 720 000 cases; range, 144 000-1.3 million). Median incidence was lowest in Western and Central Europe and Oceania (</=0.1% each). Globally, approximately 957 900 cases (range, 371 700-1 544 000) of cryptococcal meningitis occur each year, resulting in 624 700 deaths (range, 125 000-1 124 900) by 3 months after infection. This study, the first attempt to estimate the global burden of cryptococcal meningitis, finds the number of cases and deaths to be very high, with most occurring in sub-Saharan Africa. Further work is needed to better define the scope of the problem and track the epidemiology of this infection, in order to prioritize prevention, diagnosis, and treatment strategies.


Protein-protein interactions in intracellular Ca2+-release channel function.
Release of Ca2+ ions from intracellular stores can occur via two classes of Ca2+-release channel (CRC) protein, the inositol 1,4, 5-trisphosphate receptors (InsP3Rs) and the ryanodine receptors (RyRs). Multiple isoforms and subtypes of each CRC class display distinct but overlapping distributions within mammalian tissues. InsP3Rs and RyRs interact with a plethora of accessory proteins which modulate the activity of their intrinsic channels. Although many aspects of CRC structure and function have been reviewed in recent years, the properties of proteins with which they interact has not been comprehensively surveyed, despite extensive current research on the roles of these modulators. The aim of this article is to review the regulation of CRC activity by accessory proteins and, wherever possible, to outline the structural details of such interactions. The CRCs are large transmembrane proteins, with the bulk of their structure located cytoplasmically. Intra- and inter-complex protein-protein interactions between these cytoplasmic domains also regulate CRC function. Some accessory proteins modulate channel activity of all CRC subtypes characterized, whereas other have class- or even isoform-specific effects. Certain accessory proteins exert both direct and indirect forms of regulation on CRCs, occasionally with opposing effects. Others are themselves modulated by changes in Ca2+ concentration, thereby participating in feedback mechanisms acting on InsP3R and RyR activity. CRCs are therefore capable of integrating numerous signalling events within a cell by virtue of such protein-protein interactions. Consequently, the functional properties of InsP3Rs and RyRs within particular cells and subcellular domains are 'customized' by the accessory proteins present.


Electrically driven phase transition in magnetite nanostructures.
Magnetite (Fe3O4), an archetypal transition-metal oxide, has been used for thousands of years, from lodestones in primitive compasses to a candidate material for magnetoelectronic devices. In 1939, Verwey found that bulk magnetite undergoes a transition at TV approximately 120 K from a high-temperature 'bad metal' conducting phase to a low-temperature insulating phase. He suggested that high-temperature conduction is through the fluctuating and correlated valences of the octahedral iron atoms, and that the transition is the onset of charge ordering on cooling. The Verwey transition mechanism and the question of charge ordering remain highly controversial. Here, we show that magnetite nanocrystals and single-crystal thin films exhibit an electrically driven phase transition below the Verwey temperature. The signature of this transition is the onset of sharp conductance switching in high electric fields, hysteretic in voltage. We demonstrate that this transition is not due to local heating, but instead is due to the breakdown of the correlated insulating state when driven out of equilibrium by electrical bias. We anticipate that further studies of this newly observed transition and its low-temperature conducting phase will shed light on how charge ordering and vibrational degrees of freedom determine the ground state of this important compound.


Angiopoietin-2 is related to tumor angiogenesis in gastric carcinoma: possible in vivo regulation via induction of proteases.
Tumor angiogenesis progresses by a dynamic balance between tumor vascular regression and growth. Angiopoietin (Ang)-2 (the natural antagonist for the angiogenic Tie-2 receptor) and vascular endothelial growth factor (VEGF) are thought to be critical regulators in this process; therefore, these may play a critical role in cancer aggressiveness. The aim of this study was to clarify the clinical and biological significance of the expression of Ang-2 in human gastric cancers and to investigate the relationship between Ang-2 together with VEGF and the induction of proteases such as matrix metalloproteinases (MMPs) in the process of tumor development. Eighty-five individuals with gastric cancer, who had undergone surgery without preoperative treatment, were studied. A stable transfectant of the human MKN-7 gastric cancer cell lines with an Ang-2 expression vector was used for the experimental study. First, we examined the relationship between the mRNA expression of Angs by Northern blot analysis and clinicopathological features. High Ang-2-expression cases showed more frequent vascular involvement and more advanced stages of disease compared with low Ang-2-expression cases (P < 0.05). With regard to prognosis, the survival time for patients in the high-Ang-2 mRNA group was significantly shorter (P < 0.05). When we examined the localization of Ang-2 in human gastric cancers, immunohistochemical analysis revealed that this protein was expressed predominantly in cancer tissues when compared with normal tissues. Interestingly it was expressed not only in endothelia cells (ECs) but also in cancer cells. Second, Ang-2-transfected cells were implanted in vivo into the gastric walls of nude mice. Ang-2-transfectant mice developed highly metastatic tumors with hypervascularity as compared with MKN-7 or control vector-transfectant tumors. There was a significant correlation between Ang-2 mRNA expression and lower grade of vessel maturation. Third, on the basis of the in vivo data, we focused on production of proteases such as MMPs to investigate possible mechanisms in these processes. MMP-1, MMP-9, and urokinase-type plasminogen activator in ECs were strongly up-regulated by Ang-2 in the presence of VEGF in vitro. These data suggest that production of Ang-2 is implicated in tumor development in human gastric cancers. Its production may contribute to tumor angiogenesis by induction of proteases in ECs, which may be enhanced in the presence of VEGF.


The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships.
Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra- and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred.


Predictors of survival from out-of-hospital cardiac arrest: a systematic review and meta-analysis.
Prior studies have identified key predictors of out-of-hospital cardiac arrest (OHCA), but differences exist in the magnitude of these findings. In this meta-analysis, we evaluated the strength of associations between OHCA and key factors (event witnessed by a bystander or emergency medical services [EMS], provision of bystander cardiopulmonary resuscitation [CPR], initial cardiac rhythm, or the return of spontaneous circulation). We also examined trends in OHCA survival over time. An electronic search of PubMed, EMBASE, Web of Science, CINAHL, Cochrane DSR, DARE, ACP Journal Club, and CCTR was conducted (January 1, 1950 to August 21, 2008) for studies reporting OHCA of presumed cardiac etiology in adults. Data were extracted from 79 studies involving 142 740 patients. The pooled survival rate to hospital admission was 23.8% (95% CI, 21.1 to 26.6) and to hospital discharge was 7.6% (95% CI, 6.7 to 8.4). Stratified by baseline rates, survival to hospital discharge was more likely among those: witnessed by a bystander (6.4% to 13.5%), witnessed by EMS (4.9% to 18.2%), who received bystander CPR (3.9% to 16.1%), were found in ventricular fibrillation/ventricular tachycardia (14.8% to 23.0%), or achieved return of spontaneous circulation (15.5% to 33.6%). Although 53% (95% CI, 45.0% to 59.9%) of events were witnessed by a bystander, only 32% (95% CI, 26.7% to 37.8%) received bystander CPR. The number needed to treat to save 1 life ranged from 16 to 23 for EMS-witnessed arrests, 17 to 71 for bystander-witnessed, and 24 to 36 for those receiving bystander CPR, depending on baseline survival rates. The aggregate survival rate of OHCA (7.6%) has not significantly changed in almost 3 decades. Overall survival from OHCA has been stable for almost 30 years, as have the strong associations between key predictors and survival. Because most OHCA events are witnessed, efforts to improve survival should focus on prompt delivery of interventions of known effectiveness by those who witness the event.


Evaluation and optimization of reduction and alkylation methods to maximize peptide identification with MS-based proteomics.
Mass spectrometry (MS) has become an increasingly important technique to analyze proteins. In popular bottom-up MS-based proteomics, reduction and alkylation are routine steps to facilitate peptide identification. However, incomplete reactions and side reactions may occur, which compromise the experimental results. In this work, we systematically evaluated the reduction step with commonly used reagents, i.e., dithiothreitol, 2-mercaptoethanol, tris(2-carboxyethyl)phosphine, or tris(3-hydroxypropyl)phosphine, and alkylation with iodoacetamide, acrylamide, N-ethylmaleimide, or 4-vinylpyridine. By using digested peptides from a yeast whole-cell lysate, the number of proteins and peptides identified were very similar using four different reducing reagents. The results from four alkylating reagents, however, were dramatically different with iodoacetamide giving the highest number of peptides with alkylated cysteine and the lowest number of peptides with incomplete cysteine alkylation and side reactions. Alkylation conditions with iodoacetamide were further optimized. To identify more peptides with cysteine, thiopropyl-sepharose 6B resins were used to enrich them, and the optimal conditions were employed for the reduction and alkylation. The enrichment resulted in over three times more cysteine-containing peptides than without enrichment. Systematic evaluation of the reduction and alkylation with different reagents can aid in a better design of bottom-up proteomic experiments.


Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.
The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5' phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.


Arboviral surveillance of field-collected mosquitoes reveals circulation of West Nile virus lineage 1 strains in Eastern Thrace, Turkey.
Arbovirus screening in invertebrate vectors is an important component of the vector-borne disease surveillance programs. Turkey has been shown to harbor medically important mosquito-borne arboviruses such as West Nile Virus (WNV). However, limited information about infections in vectors are currently available. This study was performed to provide preliminary data from Eastern Thrace region, Turkey, where no arbovirus vector surveillance has previously been performed. Mosquito sampling was undertaken at 23 sites in Edirne province during July, 2012. All specimens were identified morphologically, and selected individuals were subjected to DNA barcoding via cytochrome c oxidase I (COI) sequencing. Consensus PCR for Flavivirus, Alphavirus, and Phlebovirus genera and WNV-specific nested and real-time reverse transcription PCR were employed for mosquito pool screening and/or confirmation. Viral sequences detected in pools were characterized via sequencing. A total of 9261 mosquitoes were captured and distributed into 232 pools from the following species: Ochlerotatus caspius (90.9%), Culex pipiens sensu lato (s.l.) (4.7%), Anopheles pseudopictus (3%), and Anopheles maculipennis s.l. (1.3%). Specimens morphologically classified as Cx. pipiens s.l. were identified as Cx. pipiens pipiens via barcoding. Thirty-seven mosquito pools (15.9%) were positive in pan-flavivirus and WNV-specific assays. Viral sequences in positive pools were characterized as WNV lineage 1 clade 1a and demonstrated 1-4% divergence. No flavivirus sequences other than WNV were detected in the mosquito pools. WNV infection rates in Oc. caspius and Cx. pipiens s.l. pools were 15.6% and 36.3%, respectively. Comparison of current and previously identified WNV sequences from Turkey revealed 94.00-96.34% similarity. WNV RNA was identified for the first time in Cx. pipiens s.l. and Oc. caspius mosquitoes in Eastern Thrace, Turkey. Our findings indicate the circulation of WNV lineage 1 strains in potential vector species and provide an epidemiological link between WNV activity in mosquitoes and vertebrate infections.


Sleep apnea prevalence in acute myocardial infarction--the Sleep Apnea in Post-acute Myocardial Infarction Patients (SAPAMI) Study.
While sleep apnea (SA) might be a modifiable cardiovascular risk factor, recent data suggest that SA is severely underdiagnosed in patients after acute myocardial infarction (MI). There is limited evidence about day-night variation of onset of MI on dependence of having SA. We therefore investigated the prevalence of SA and examined the day-night variation of onset of MI in acute MI patients. We prospectively studied 782 consecutive patients admitted to the hospital with the diagnosis of acute MI. All subjects underwent sleep evaluations using a portable device after at least 48 h post-admission. Using the apnea-hypopnea index (AHI), groups were defined as patients without SA (<5 events/h), mild SA (5-15 events/h), moderate SA (15-30 events/h), and severe SA (≥ 30 events/h). Almost all patients (98%) underwent urgent coronary angiography and 91% of patients underwent primary PCI. Using a threshold of AHI ≥ 5 events/h, SA was present in 65.7% of patients after acute MI. Mild SA was present in 32.6%, moderate in 20.4% and severe in 12.7%. The day-night variation in the onset of MI in all groups of SA patients was similar to that observed in non-SA patients. From 6 AM to 12 PM, the frequency of MI was higher in both SA and non-SA patients, as compared to the interval from 12 AM to 6 AM (all p<0.05). There is a high prevalence of SA in patients presenting with acute MI. Peak time of MI onset in SA patients was between 6 AM and noon, similar to that in the general population. Whether diagnosis and treatment of SA after MI will significantly improve outcomes in these patients remains to be determined.


Bone mineral density in premenopausal women with systemic lupus erythematosus.
To study bone mineral density (BMD) in premenopausal women with systemic lupus erythematosus (SLE) and to evaluate the influence of disease activity and use of corticosteroids. A cross-sectional study on BMD of 118 premenopausal women with SLE. Patients were divided into 2 groups, 74 who had been treated with corticosteroids and 44 who had not. BMD at lumbar spine, femoral neck, and trochanter was measured. BMD in patients without and with corticosteroid treatment was 1.13 +/- 0.13 vs 1.05 +/- 0.14 g/cm2 (p = 0.005) at lumbar spine, 0.92 +/- 0.12 vs 0.86 +/- 0.12 g/cm2 (p = 0.005) at femoral neck, and 0.78 +/- 0.13 vs 0.72 +/- 0.12 g/cm2 (p = 0.014) at trochanter, respectively. Stepwise multilinear regression analysis showed that corticosteroid exposure was independently associated with decreased BMD in the corticosteroid treated patients (r2 = 7% for lumbar and 6.6% for trochanter model). No significant difference in BMD in corticosteroid treated patients appeared when they were subgrouped according to whether they were taking calcium supplements. Prevalence of osteoporosis at lumbar spine in corticosteroid treated patients was 1.4%, and was lower than reported for age and sex matched Caucasians. BMD measurements were significantly lower in premenopausal SLE patients who had had corticosteroid treatment than those who had not. There was a negative correlation between BMD and corticosteroid therapy, but not disease activity. Prevalence of osteoporosis, based on lumbar spine BMD, was lower than that reported in Caucasians.


In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA).
Lower Kane Cave, Wyoming (USA), has hydrogen sulfide-bearing springs that discharge into the cave passage. The springs and cave stream harbour white filamentous microbial mats dominated by Epsilonproteobacteria. Recently, novel 16S rRNA gene sequences from the phylum Acidobacteria, subgroup 7, were found in these cave mats. Although Acidobacteria are ubiquitously distributed in many terrestrial and marine habitats, little is known about their ecophysiology. To investigate this group in Lower Kane Cave in more detail, a full-cycle rRNA approach was applied based on 16S and 23S rRNA gene clone libraries and the application of novel probes for fluorescence in situ hybridization. The 16S and 23S rRNA gene clone libraries yielded seven and six novel acidobacterial operational taxonomic units (OTUs) respectively. The majority of the OTUs were affiliated with subgroups 7 and 8. One OTU was affiliated with subgroup 6, and one OTU could not be assigned to any of the present acidobacterial subgroups. Fluorescence in situ hybridization distinguished two morphologically distinct, rod-shaped cells of the acidobacterial subgroups 7 and 8. Although the ecophysiology of Acidobacteria from Lower Kane Cave will not be fully resolved until cultures are obtained, acidobacterial cells were always associated with the potentially chemolithoautotrophic epsilon- or gammaproteobacterial filaments, suggesting perhaps a lifestyle based on heterotrophy or chemoorganotrophy.


Clinical efficacy of home-use blue-light therapy for mild-to moderate acne.
Blue-light light-emitting diode (LED) therapy has become widely used for the treatment of inflammatory acne. In this study we evaluated the efficacy of a home use blue-light LED application in improving lesions and shortening their time to clearance. This was an IRB approved randomized self-control study. For each patient (n = 30), 2 similar lesions, one of each side of the face were chosen for treatment with either a blue-light LED hand-held or sham device. Treatments (n = 4) were conducted twice daily in the clinic and lesions were followed-up till resolution. Reduction in blemishes size and erythema and the overall improvement were evaluated by both the physician and the patients. Time to lesion resolution was recorded. There was a significant difference in the response of lesions to the blue-light LED application as opposed to the placebo in terms of reduction in lesion size and lesion erythema as well as the improvement in the overall skin condition (p < 0.025). Signs of improvement were observed as early as post 2 treatments. Time to resolution was significantly shorter for the blue-light LED therapy. The results support the effectiveness of using blue-light LED therapy on a daily basis for better improvement and faster resolution of inflammatory acne lesions.


Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.
Formation of nucleosome free region (NFR) accompanied by specific histone modifications at flanking nucleosomes is an important prerequisite for enhancer and promoter activity. Due to this process, active regulatory elements often exhibit a distinct shape of histone signal in the form of a peak-valley-peak (PVP) pattern. However, different features of PVP patterns and their robustness in predicting active regulatory elements have never been systematically analyzed. Here, we present PARE, a novel computational method that systematically analyzes the H3K4me1 or H3K4me3 PVP patterns to predict NFRs. We show that NFRs predicted by H3K4me1 and me3 patterns are associated with active enhancers and promoters, respectively. Furthermore, asymmetry in the height of peaks flanking the central valley can predict the directionality of stable transcription at promoters. Using PARE on ChIP-seq histone modifications from four ENCODE cell lines and four hematopoietic differentiation stages, we identified several enhancers whose regulatory activity is stage specific and correlates positively with the expression of proximal genes in a particular stage. In conclusion, our results demonstrate that PVP patterns delineate both the histone modification landscape and the transcriptional activities governed by active enhancers and promoters, and therefore can be used for their prediction. PARE is freely available at http://servers.binf.ku.dk/pare.


Autolysis parallels activation of mu-calpain.
The kinetics of autolysis and activation of mu-calpain were measured with microtubule-associated protein 2 (MAP2) as a very sensitive substrate. The initial rate of MAP2 hydrolysis was found to be a linear function of the autolysed 76 kDa form of mu-calpain large subunit at both 10 and 300 microM Ca2+, and both straight lines intersected the origin. This finding supports the view that native mu-calpain is an inactive proenzyme and that activation is accompanied by autolysis. The first-order rate constant of autolysis, K1(aut), was determined at different Ca2+ concentrations: the half-maximal value was at pCa2+ = 3.7 (197 microM Ca2+), whereas the maximal value was 1.52 s-1, at 30 degrees C. The Ca(2+)-induced activation process was then monitored by using our novel, continuous fluorimetric assay with labelled MAP2 as substrate. The first-order rate constant of activation, k1(act), was derived as the reciprocal of the lag phase ('transit time') at the initial part of the progress curve: half-maximum was at pCa2+ = 3.8 (158 microM Ca2+) and the maximum value was 2.15 s-1. The good agreement between the kinetic parameters of mu-calpain autolysis and activation is remarkable. We claim that this is the first kinetically correct determination of the rate constant of autolysis of mu-calpain. Pre-activated mu-calpain has a Ca2+ requirement that is almost three orders of magnitude smaller [half-maximal activation at pCa2+ = 6.22 (0.6 microM Ca2+)]. We cannot exclude the possibility that the activation process involves other mechanistic steps, e.g. the rapid dissociation of the mu-calpain heterodimer, but we state that in our conditions in vitro autolysis and activation run in close parallel.


TripNet: a method for constructing rooted phylogenetic networks from rooted triplets.
The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network.


Ultrasound confirmation of endotracheal tube position in neonates.
The placement of the endotracheal tube (ETT) in neonates is a challenging procedure that currently requires timely confirmation of tip placement by radiographic imaging. We sought to determine if bedside ultrasound (US) could demonstrate ETT tip location in preterm and term newborns and offer a quick alternative method of ETT positioning. We conducted a prospective pilot study of 30 newborns admitted to the UC San Diego Medical Center who had their ETT placement confirmed by chest radiographs. After a radiograph, each infant had a US exam with a 13-MHz linear transducer on a portable US machine. To assist localization, gentle longitudinal movement of the ETT of less than 0.5 cm was performed. Measurements from the tip of the ETT tip to the carina were made on chest radiograph and midsagittal US images. Study infants had a mean gestational age of 30.2 ± 4.9 (SD) weeks and mean birth weight of 1,595.2 ± 862 g. US images were taken a mean 2.9 ± 2.2 h after radiographs. Data from 2 infants were excluded for poor radiograph image quality and extreme outlier values. The ETT was visualized by US in all newborns examined. We observed a good correlation between ETT tip-to-carina distance on US and radiograph (r(2) = 0.68) with minimal bias. Each study took less than 5 min to obtain without any clinical deterioration. Bedside US can visualize the anatomic position of the ETT position in preterm and term infants but further validation is required before routine clinical implementation.


Small variable segments constitute a major type of diversity of bacterial genomes at the species level.
Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.


High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.
The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.


Maternal vitamin B-6 and folate status and risk of oral cleft birth defects in the Philippines.
Vitamin deficiencies induce oral clefts in animal experiments, but the role of specific nutrients in human oral clefts is uncertain. Associations between maternal vitamin B-6 and folate status and risk of nonsyndromic cleft lip, with or without cleft palate (CL/P), were examined in case-control studies at two sites in the Philippines--Negros Occidental and Davao. Cases were mothers of affected children and control mothers were those who had no children with oral clefts. The risk of having a CL/P-affected child increased with increasing tertile of vitamin B-6 deficiency in both Negros Occidental and Davao (odds ratios [ORs] and 95% confidence intervals [CIs] for sites combined = 1.0 [reference], OR, 2.94; 95% CI, 1.51-5.73; OR, 4.98; 95% CI, 2.56-9.67). Poor B-6 status had a stronger association with CL/P among mothers with lower versus higher plasma folate levels. Increasing tertiles of plasma folate were marginally associated with an increased risk of clefts in both sites combined (1.0 [reference]; OR, 1.58; 95% CI, 0.93-2.68; OR, 1.59; 95% CI, 0.94-2.70). Increasing tertiles of erythrocyte folate were associated with a decreased risk of CL/P in Negros Occidental (1.0 [reference]; OR, 0.34; 95% CI, 0.13-0.90; OR, 0.46; 95% CI, 0.20-1.09) and an increased risk in Davao (1.0 [reference]; OR, 1.23; 95% CI, 0.54-2.81; OR, 4.85; 95% CI, 2.24-10.50). The inconsistent associations between folate status and CL/P risk appeared to be a result of statistical interaction between folate, vitamin B-6, and case-control status that produced different results in study areas of higher versus lower prevalence of vitamin B-6 deficiency. Poor maternal vitamin B-6 status was consistently associated with an increased risk of CL/P at two sites in the Philippines. Folate-CL/P associations were inconsistent and may be related to the vitamin B-6 status or other characteristics of the populations under study.


Plant and soil responses to high and low diversity grassland restoration practices.
The USDA's Conservation Reserve Program (CRP) has predominantly used only a few species of dominant prairie grasses (CP2 practice) to reduce soil erosion, but recently has offered a higher diversity planting practice (CP25) to increase grassland habitat quality. We quantified plant community composition in CP25 and CP2 plantings restored for 4 or 8 years and compared belowground properties and processes among restorations and continuously cultivated soils in southeastern Nebraska, USA. Relative to cultivated soils, restoration increased soil microbial biomass (P = 0.033), specifically fungi (P < 0.001), and restored soils exhibited higher rates of carbon (C) mineralization (P = 0.010). High and low diversity plantings had equally diverse plant communities; however, CP25 plantings had greater frequency of cool-season (C(3)) grasses (P = 0.007). Older (8 year) high diversity restorations contained lower microbial biomass (P = 0.026), arbuscular mycorrhizal fungi (AMF) biomass (P = 0.003), and C mineralization rates (P = 0.028) relative to 8 year low diversity restorations; older plantings had greater root biomass than 4 year plantings in all restorations (P = 0.001). Low diversity 8 year plantings contained wider root C:N ratios, and higher soil microbial biomass, microbial community richness, AMF biomass, and C mineralization rate relative to 4 year restorations (P < 0.050). Net N mineralization and nitrification rates were lower in 8 year than 4 year high diversity plantings (P = 0.005). We attributed changes in soil C and N pools and fluxes to increased AMF associated with C(4) grasses in low diversity plantings. Thus, reduced recovery of AMF in high diversity plantings restricted restoration of belowground microbial diversity and microbially-mediated soil processes over time.


Real-world carbon nanoparticle exposures induce brain and gonadal alterations in zebrafish (Danio rerio) as determined by biospectroscopy techniques.
Carbon-based nanoparticles (CNPs) have emerged as novel man-made materials with diverse applications, which may present significant risks to organisms. To bridge the gap in our knowledge of nanotoxicology, a number of in vitro or in vivo studies have been carried out. However, toxicity data remains limited. Herein, we employed a biospectroscopy approach to assess CNP-induced effects in zebrafish (Danio rerio). Zebrafish were exposed to Fullerene (C60), long or short multi-walled carbon nanotubes (MWCNTs), or single-walled carbon nanotubes (SWCNTs) for 21 days at two concentrations: 0.1 mg L(-1) or 0.001 mg L(-1). Following exposure, the brain, gills, gonads and liver from zebrafish were interrogated by attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy. Computational analysis was then applied to the acquired infrared (IR) spectra, and distinct biochemical segregations between the exposed tissues vs. control were observed with spectral biomarkers of alterations identified. In addition, lipid-to-protein ratios in all four tissues were calculated by the IR spectra; unsaturated lipid levels in brain and gonad were assessed by Raman spectroscopy. Marked lipid alterations were observed. These findings show that biospectroscopy approaches have the potential to detect CNP-induced biochemical alterations in zebrafish.


[Molecular mechanisms of parthenolide's action: Old drug with a new face].
Parthenolide, a sesquiterpene lactone derived from the leaves of feverfew (Tanacetum parthenium), is considered a main bioactive component of this herb. Feverfew has been used orally or as an infusion for the treatment of migraine, arthritis, fever, and stomachache. Besides its anti-inflammatory and anti-migraine properties, parthenolide also shows anticancer activities in a variety of cell lines. It contains an alpha-methylene-gamma-lactone ring and an epoxide moiety which are able to interact with nucleophilic sites of biologically important molecules. Parthenolide modulates multiple targets, thereby contributing to its various in vitro and in vivo effects. Inhibition of NF-kappaB activity, constitutive in many types of cancers, via either interaction with IKK or more directly with the p65 subunit of NF-kappaB, is considered one of the main mechanisms of its action. In addition, inhibition of STAT and MAP kinase activities and the induction of sustained JNK activity as well as p53 activity via influencing MDM2 and HDAC1 levels lead to an increased susceptibility of cancer cells to chemo- and radiotherapy. At the epigenetic level, parthenolide reduces HDAC1 level and, by inhibiting DNMT2 activity, induces global hypomethylation of DNA, which can restore the expressions of some suppressor genes. Moreover, this compound reduces the cellular level of GSH in cancer cells, followed by ROS accumulation and apoptosis. A unique property of parthenolide is its ability to induce cell death mainly in cancer cells, while sparing healthy ones and it also protects normal cells from UVB and oxidative stress. More remarkably, it seems to have the potential to target some cancer stem cells. Its wide array of biological activity and low toxicity make parthenolide a very promising drug with multi-pharmacological potential, largely dependent on the cellular context.


Effects of mast cell growth factor, interleukin-3, and interleukin-6 on human primitive hematopoietic progenitors from bone marrow and cord blood.
Phycoerythrin (PE)-labeled murine monoclonal antibodies (MAB) to CD2, CD10, CD19, CD20, and CD33 were used as lineage markers, as were PE-labeled anti-DR MAB and fluorescein isothiocyanate (FITC)-conjugated MAB to CD34. One hundred CD34+Lin+DR+ or CD34+Lin-DR- cells were individually sorted and incubated without adherent cell layer in alpha-medium with or without cytokines such as 100 U/mL recombinant human interleukin-3 (rhIL-3), 100 U/mL rhIL-6, and/or 500 ng/mL mast cell growth factor (MGF). The incubated cells were harvested and cultured in medium containing methylcellulose every 2 weeks. The numbers of colonies from colony-forming units-granulocyte/macrophage (CFU-GM), burst-forming units-erythroid (BFU-E), and mixed colony-forming units (CFU-Mix) were scored on day 14. In the incubation, CD34+Lin-DR- cells from bone marrow and cord blood produced more CFU-GM and BFU-E, and for longer periods, than did CD34+Lin+DR+ cells. In addition, CD34+Lin-DR- from cord blood supplied more CFU-GM and BFU-E than did CD34+Lin-DR- from bone marrow. Although these data demonstrate that MGF, IL-3, and IL-6 synergistically stimulate the production of CFU-GM and BFU-E, this study indicates that CD34+Lin-DR- cells contain more primitive hematopoietic progenitors and that CD34+Lin-DR- cells are unable to maintain their self-renewal capacity in the presence of IL-3, IL-6, and MGF without adherent cell layer.


Perinatal common mental disorders among women and the social and emotional development of their infants in rural Vietnam.
Little is known about the effect of common mental disorders (CMD) among women in the perinatal period on infant development in low-income countries. The aim of this study was to examine the effect of exposures to maternal symptoms of ante- and post-natal CMD on infant social-emotional development in a low-income setting. A prospective community-based investigation in which a cohort of pregnant women was recruited in rural northern Vietnam and followed until 6 months postpartum. Psychosocial and biological data were collected in four assessment waves. The outcome was 6-month old infants' scores on the Bayley Scales of Infant and Toddler Development Social-Emotional Questionnaire. Direct and indirect effects of maternal CMD on the outcome were tested simultaneously with path analysis. Complete data were available for 378 mother-infant dyads. There were no direct effects of ante- or post-natal CMD on infant Social-Emotional scores. However, there was an indirect pathway (path coefficient -1.11, 95% CI -1.79 to -0.42) in which antenatal CMD were associated with increased likelihood of postnatal CMD, which were associated with reduced parenting self-efficacy and less affectionate and warm parenting practices, which were associated with lower infant social-emotional scores. Parenting self-efficacy and practices also mediated the adverse effects of a woman being young or of high parity or experiencing poverty, intimate partner violence, a poor relationship with her own mother, non-economic life adversity and insufficient breastmilk, on infant social-emotional development. We acknowledge some limitations including (1) a moderate rate of attrition, (2) the use of a screening test for perinatal CMD, (3) the Bayley scales are not yet validated for use in Vietnam and (4) possible response bias in which maternal perceptions of their infants were influenced by their mood. These data indicate that women's antenatal and postnatal mental health is a crucial but currently inadequately understood determinant of the social and emotional development of infants in low-income settings.


Organization of the Tgm family of transposable elements in soybean.
We have compared the organization of six Tgm elements that were selected from a genomic library of soybean DNA on the basis of hybridization with subcloned regions of Tgm 1 (transposon, Glycine max) from the seed lectin gene. These elements ranged in size from 1.6 kbp to greater than 12 kbp. Tgm2, Tgm3, Tgm4 and Tgm5 represent partial isolates in which the genomic clone contained a 3' but not a 5' terminus of the element; while Tgm6 and Tgm7, like Tgm1, were small isolates flanked by both 5' and 3' nonelement sequences. Cross-hybridization studies between subcloned portions of these seven elements identified regions of homology which suggest that the Tgm transposable elements of soybean form a family of deletion derivatives. In addition to internal deletion events, numerous deletions and base substitutions are also present within the borders of these elements which are comprised of the same tandemly repeated sequence. The 39% amino acid homology between a 1 kb portion of an open reading frame in Tgm4 and Tgm5 and ORF1, an open frame from the first intron of the maize Enhancer (Suppressor-mutator) transposable element, suggests that both elements encode a common function that requires a high degree of protein conservation.


Glucose-6-phosphatase mRNA and activity are increased to the same extent in kidney and liver of diabetic rats.
Using Northern blot with a specific glucose-6-phosphatase (Glc6Pase) cDNA probe and enzymatic activity determination, we studied the effect of streptozotocin-induced diabetes on Glc6Pase in rat gluconeogenic tissues. The Glc6Pase mRNA abundance was increased four to five times in both the liver and kidney of diabetic rats. This was correlated with a concomitant 130% increase in Glc6Pase catalytic subunit in both tissues. The elevated level of Glc6Pase mRNA was significantly corrected in both the liver and kidney of diabetic rats after a 12-h insulin treatment. We also studied Glc6Pase mRNA and activity in gluconeogenic tissues during the fed-fasted and fasted-refed transitions in normal rats. In the liver, the abundance of Glc6Pase mRNA was sharply increased about four times after 24 or 48 h of fasting. In the kidney, the Glc6Pase mRNA level was gradually increased some three and five times after 24 and 48 h of fasting, respectively. The increase of Glc6Pase mRNA in both organs was matched with a doubling of the activity of Glc6Pase catalytic subunit: rapid in the liver and gradual in the kidney. The liver Glc6Pase mRNA abundance in 48-h fasted rats was acutely and importantly decreased upon refeeding. The kidney Glc6Pase mRNA level was also significantly lowered under these conditions, albeit less rapidly. These data demonstrate that efficient control of Glc6Pase takes place in both gluconeogenic organs at the pretranslational level and suggest that insulin might play an important role in this control. In addition, using reverse transcription-polymerase chain reaction and Northern blot, we report that Glc6Pase mRNA is not detectable in several other tissues previously assumed to express the enzyme.


On the evolution of sport.
Sports have received little attention from evolutionary biologists. I argue that sport began as a way for men to develop the skills needed in primitive hunting and warfare, then developed to act primarily as a lek where athletes display and male spectators evaluate the qualities of potential allies and rivals. This hypothesis predicts that (1) the most popular modern male sports require the skills needed for success in male-male physical competition and primitive hunting and warfare; (2) champion male athletes obtain high status and thereby reproductive opportunities in ways that parallel those gained by successful primitive hunters and warriors; (3) men pay closer attention than do women to male sports so they can evaluate potential allies and rivals; and (4) male sports became culturally more important when opportunities to evaluate potential allies and rivals declined as both the survival importance of hunting and the proportion of men who experience combat decreased. The characteristics of primitive and modern sports are more consistent with these predictions than those generated by intersexual sexual selection theories of sport.


Changes in ecologically critical terrestrial climate conditions.
Terrestrial ecosystems have encountered substantial warming over the past century, with temperatures increasing about twice as rapidly over land as over the oceans. Here, we review the likelihood of continued changes in terrestrial climate, including analyses of the Coupled Model Intercomparison Project global climate model ensemble. Inertia toward continued emissions creates potential 21st-century global warming that is comparable in magnitude to that of the largest global changes in the past 65 million years but is orders of magnitude more rapid. The rate of warming implies a velocity of climate change and required range shifts of up to several kilometers per year, raising the prospect of daunting challenges for ecosystems, especially in the context of extensive land use and degradation, changes in frequency and severity of extreme events, and interactions with other stresses.


Fibroblast stimulation in schistosomiasis. XI. Purification to apparent homogeneity of fibroblast-stimulating factor-1, an acidic heparin-binding growth factor produced by schistosomal egg granulomas.
Liver fibrosis is the most serious complication of infection with Schistosoma mansoni and Schistosoma japonicum and is responsible for severe morbidity and mortality in hundreds of thousands of patients in many Third World nations. The pathogenesis of this condition remains to be elucidated. We proposed that certain cytokines produced by cells that comprise the chronic granulomas that surround the helminth eggs within the liver initiate hepatic fibrogenesis. We now report our successful purification to apparent homogeneity of the egg granuloma-derived fibroblast mitogen. The high affinity of this factor for heparin (elutes from heparin-Sepharose with 1.5 M NaCl) facilitates its purification by a two-step procedure, and identifies the cytokine as a heparin-binding growth factor (HBGF). Furthermore, because it has an isoelectric point approximately equal to 6.2, it has one of the characteristics of a class 1 (acidic) HBGF. We immunized rabbits with the purified factor and observed that the resulting antibodies (IgG) detected the factor but not acidic fibroblast growth factor (the prototypic class 1 HBGF) either by dot-blot ELISA or neutralization of biologic activity. The granuloma product and fibroblast growth factor also differ in target-cell specificity and amino acid composition. On the basis of these distinctions, we have designated the granuloma-derived mitogen fibroblast-stimulating factor-1. With the availability of purified fibroblast-stimulating factor-1 and the future analysis of its amino acid sequence, its structural relationship to other mesenchymal growth factors can be determined.


Comparisons of oncological and functional outcomes among radical retropubic prostatectomy, high dose rate brachytherapy, cryoablation and high-intensity focused ultrasound for localized prostate cancer.
To conduct a retrospective, single institutional and comparative study for radical retropubic prostatectomy (RRP), high dose rate brachytherapy (HDRBT), cryoablation and high-intensity focused ultrasound (HIFU) in localized prostate cancer with respect to oncological and functional outcomes. We reviewed 97, 161, 114 and 120 patients of RRP, HDRBT, cryoablation and HIFU respectively for localized prostate cancer from May 2008 to December 2013. PSA biochemical recurrence, salvage treatment-free rate, metastasis-free rate, and biochemical recurrence-free survival were analyzed for oncological outcomes. Functional outcomes included complications and serial IIEF-5 scores, IPSS and related QoL scores. During nearly 3 years of follow-up, the patients of HDRBT experienced higher PSA biochemical recurrence rate overall (54.7%), as well as D'Amico intermediate-risk (34.4%) and high-risk (61.8%) groups, lower salvage treatment-free rate (46.7%), and metastasis-free rate (90.7%). Besides, the patients of RRP demonstrated higher urethral stricture (29.9%) and urinary incontinence (11.3%). The patients of HIFU revealed lower de novo erectile dysfunction rate at 1 year (65.6%), higher serial IIEF-5 scores, lower IPSS and related QoL scores. The patients of HDRBT demonstrated worse oncological outcomes in D'Amico intermediate and high-risk groups. Besides, the patients of RRP had more complications rate in urethral stricture and urinary incontinence. Moreover, the patients of HIFU experienced better urinary function improvement and more possible sexual function preservation. In consideration of trifecta, HIFU may provide equivalent cancer control and better quality of life for patients of localized prostate cancer.


Translational control of nociception via 4E-binding protein 1.
Activation of the mechanistic/mammalian target of rapamycin (mTOR) kinase in models of acute and chronic pain is strongly implicated in mediating enhanced translation and hyperalgesia. However, the molecular mechanisms by which mTOR regulates nociception remain unclear. Here we show that deletion of the eukaryotic initiation factor 4E-binding protein 1 (4E-BP1), a major mTOR downstream effector, which represses eIF4E activity and cap-dependent translation, leads to mechanical, but not thermal pain hypersensitivity. Mice lacking 4E-BP1 exhibit enhanced spinal cord expression of neuroligin 1, a cell-adhesion postsynaptic protein regulating excitatory synapse function, and show increased excitatory synaptic input into spinal neurons, and a lowered threshold for induction of synaptic potentiation. Pharmacological inhibition of eIF4E or genetic reduction of neuroligin 1 levels normalizes the increased excitatory synaptic activity and reverses mechanical hypersensitivity. Thus, translational control by 4E-BP1 downstream of mTOR effects the expression of neuroligin 1 and excitatory synaptic transmission in the spinal cord, and thereby contributes to enhanced mechanical nociception.


Phenomenology and adapted physical activity: philosophy and professional practice.
Through the increased use of qualitative research methods, the term phenomenology has become a quite familiar notion for researchers in adapted physical activity (APA). In contrast to this increasing interest in phenomenology as methodology, relatively little work has focused on phenomenology as philosophy or as an approach to professional practice. Therefore, the purpose of this article is to examine the relevance of phenomenology as philosophy and as pedagogy to the field of APA. First, phenomenology as philosophy is introduced through three key notions, namely the first-person perspective, embodiment, and life-world. The relevance of these terms to APA is then outlined. Second, the concept of phenomenological pedagogy is introduced, and its application and potential for APA are discussed. In conclusion, it is argued that phenomenology can help theorize ways of understanding human difference in movement contexts and form a basis of action-oriented research aiming at developing professional practice.


Personality disorder symptomatology is associated with anomalies in striatal and prefrontal morphology.
Personality disorder symptomatology (PD-Sx) can result in personal distress and impaired interpersonal functioning, even in the absence of a clinical diagnosis, and is frequently comorbid with psychiatric disorders such as substance use, mood, and anxiety disorders; however, they often remain untreated, and are not taken into account in clinical studies. To investigate brain morphological correlates of PD-Sx, we measured subcortical volume and shape, and cortical thickness/surface area, based on structural magnetic resonance images. We investigated 37 subjects who reported PD-Sx exceeding DSM-IV Axis-II screening thresholds, and 35 age, sex, and smoking status-matched control subjects. Subjects reporting PD-Sx were then grouped into symptom-based clusters: N = 20 into Cluster B (reporting Antisocial, Borderline, Histrionic, or Narcissistic PD-Sx) and N = 28 into Cluster C (reporting Obsessive-Compulsive, Avoidant, or Dependent PD-Sx); N = 11 subjects reported PD-Sx from both clusters, and none reported Cluster A (Paranoid, Schizoid, or Schizotypal) PD-Sx. Compared to control, Cluster C PD-Sx was associated with greater striatal surface area localized to the caudate tail, smaller ventral striatum volumes, and greater cortical thickness in right prefrontal cortex. Both Cluster B and C PD-Sx groups also showed trends toward greater posterior caudate volumes and orbitofrontal surface area anomalies, but these findings did not survive correction for multiple comparisons. The results point to morphological abnormalities that could contribute to Cluster C PD-Sx. In addition, the observations parallel those in substance use disorders, pointing to the importance of considering PD-Sx when interpreting findings in often-comorbid psychiatric disorders.


A novel, specific interaction involving the Csk SH3 domain and its natural ligand.
C-terminal Src kinase (Csk) takes part in a highly specific, high affinity interaction via its Src homology 3 (SH3) domain with the proline-enriched tyrosine phosphatase PEP in hematopoietic cells. The solution structure of the Csk-SH3 domain in complex with a 25-residue peptide from the Pro/Glu/Ser/Thr-rich (PEST) domain of PEP reveals the basis for this specific peptide recognition motif involving an SH3 domain. Three residues, Ala 40, Thr 42 and Lys 43, in the SH3 domain of Csk specifically recognize two hydrophobic residues, Ile 625 and Val 626, in the proline-rich sequence of the PEST domain of PEP. These two residues are C-terminal to the conventional proline-rich SH3 domain recognition sequence of PEP. This interaction is required in addition to the classic polyproline helix (PPII) recognition by the Csk-SH3 domain for the association between Csk and PEP in vivo. NMR relaxation analysis suggests that Csk-SH3 has different dynamic properties in the various subsites important for peptide recognition.


Hematopoietic cell types: prototype for a revised cell ontology.
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. The CL is a candidate reference ontology of the OBO Foundry and requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. We have now addressed the specific content of one area of the CL, the section of the ontology dealing with hematopoietic cells. This section has been extensively revised to improve its content and eliminate multiple inheritance in the asserted hierarchy, and the groundwork has been laid for structuring the hematopoietic cell type terms as cross-products incorporating logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time.


Evaluation of invertebrate infection models for pathogenic corynebacteria.
For several pathogenic bacteria, model systems for host-pathogen interactions were developed, which provide the possibility of quick and cost-effective high throughput screening of mutant bacteria for genes involved in pathogenesis. A number of different model systems, including amoeba, nematodes, insects, and fish, have been introduced, and it was observed that different bacteria respond in different ways to putative surrogate hosts, and distinct model systems might be more or less suitable for a certain pathogen. The aim of this study was to develop a suitable invertebrate model for the human and animal pathogens Corynebacterium diphtheriae, Corynebacterium pseudotuberculosis, and Corynebacterium ulcerans. The results obtained in this study indicate that Acanthamoeba polyphaga is not optimal as surrogate host, while both Caenorhabtitis elegans and Galleria larvae seem to offer tractable models for rapid assessment of virulence between strains. Caenorhabtitis elegans gives more differentiated results and might be the best model system for pathogenic corynebacteria, given the tractability of bacteria and the range of mutant nematodes available to investigate the host response in combination with bacterial virulence. Nevertheless, Galleria will also be useful in respect to innate immune responses to pathogens because insects offer a more complex cell-based innate immune system compared with the simple innate immune system of C. elegans.


Implications of peptide assemblies in amyloid diseases.
Neurodegenerative disorders and type 2 diabetes are global epidemics compromising the quality of life of millions worldwide, with profound social and economic implications. Despite the significant differences in pathology - much of which are poorly understood - these diseases are commonly characterized by the presence of cross-β amyloid fibrils as well as the loss of neuronal or pancreatic β-cells. In this review, we document research progress on the molecular and mesoscopic self-assembly of amyloid-beta, alpha synuclein, human islet amyloid polypeptide and prions, the peptides and proteins associated with Alzheimer's, Parkinson's, type 2 diabetes and prion diseases. In addition, we discuss the toxicities of these amyloid proteins based on their self-assembly as well as their interactions with membranes, metal ions, small molecules and engineered nanoparticles. Through this presentation we show the remarkable similarities and differences in the structural transitions of the amyloid proteins through primary and secondary nucleation, the common evolution from disordered monomers to alpha-helices and then to β-sheets when the proteins encounter the cell membrane, and, the consensus (with a few exceptions) that off-pathway oligomers, rather than amyloid fibrils, are the toxic species regardless of the pathogenic protein sequence or physicochemical properties. In addition, we highlight the crucial role of molecular self-assembly in eliciting the biological and pathological consequences of the amyloid proteins within the context of their cellular environments and their spreading between cells and organs. Exploiting such structure-function-toxicity relationship may prove pivotal for the detection and mitigation of amyloid diseases.


Metabolism and disposition of diethylene glycol in rat and dog.
The disposition of carbon-14-labeled diethylene glycol (DEG) was determined in rats after oral, iv, and dermal administration, and in dogs after oral administration. Oral administration of DEG to rats was by gavage of 50 or 5000 mg/kg doses, or by provision of 0.3 1.0, and 3.0% in drinking water. Oral doses were well absorbed and excreted primarily (approximately 80%) in urine within 24 hr of administration. Greater than half of the dose was excreted unchanged, with 10-30% of the dose appearing as a single metabolite. The metabolite was isolated and characterized by 13C-NMR to be 2-(hydroxy) ethoxyacetic acid (HEAA). Confirmation of identity was provided by synthesis of HEAA and comparison of its NMR spectra and chromatographic behavior with those of the metabolite. Intravenous doses (50 mg/kg) were eliminated by the same routes and at the same rates as those administered orally and exhibited the same metabolic profile. The fate of oral doses of DEG administered to dogs (500 mg/kg) was similar to that of DEG in rats, with about 30% of the administered dose being excreted in urine as HEAA. DEG slowly penetrated the skin of rats after application of 50 mg to a 12-cm2 area. Only about 10% of the dose was absorbed in 72 hr of exposure, and the absorbed dose appeared to have the same fate as doses administered iv or orally. In all studies with rats, excretion of radiolabel in feces and persistence in tissues were low. The highest percentage of conversion to 14CO2 was 7%, found for doses of 0.3% DEG in drinking water.


Differential roles for cryptochromes in the mammalian retinal clock.
Cryptochromes 1 and 2 (CRY1/2) are key components of the negative limb of the mammalian circadian clock. Like many peripheral tissues, Cry1 and -2 are expressed in the retina, where they are thought to play a role in regulating rhythmic physiology. However, studies differ in consensus as to their localization and function, and CRY1 immunostaining has not been convincingly demonstrated in the retina. Here we describe the expression and function of CRY1 and -2 in the mouse retina in both sexes. Unexpectedly, we show that CRY1 is expressed throughout all retinal layers, whereas CRY2 is restricted to the photoreceptor layer. Retinal period 2::luciferase recordings from CRY1-deficient mice show reduced clock robustness and stability, while those from CRY2-deficient mice show normal, albeit long-period, rhythms. In functional studies, we then investigated well-defined rhythms in retinal physiology. Rhythms in the photopic electroretinogram, contrast sensitivity, and pupillary light response were all severely attenuated or abolished in CRY1-deficient mice. In contrast, these physiological rhythms are largely unaffected in mice lacking CRY2, and only photopic electroretinogram rhythms are affected. Together, our data suggest that CRY1 is an essential component of the mammalian retinal clock, whereas CRY2 has a more limited role.-Wong, J. C. Y., Smyllie, N. J., Banks, G. T., Pothecary, C. A., Barnard, A. R., Maywood, E. S., Jagannath, A., Hughes, S., van der Horst, G. T. J., MacLaren, R. E., Hankins, M. W., Hastings, M. H., Nolan, P. M., Foster, R. G., Peirson, S. N. Differential roles for cryptochromes in the mammalian retinal clock.