Structure and expression of an Otx5-related gene in the dogfish Scyliorhinus canicula: evidence for a conserved role of Otx5 and Crxgenes in the specification of photoreceptors.
We report the full-length coding sequence and the expression pattern during neurulation and early organogenesis of ScOtx5, a novel member of the Otx gene family in the dogfish Scyliorhinus canicula. Phylogenetic analyses confirm that ScOtx5 is closely related to the Xenopus XlOtx5/ 5bgenes, and also to the Crx genes characterized in mammals and zebrafish. This supports the hypothesis that these genes define a third gnathostome Otx orthology class. During neurulation, ScOtx5 transcripts are detected in the foregut diverticulum and the anterior neuroectoderm. At the onset of organogenesis, ScOtx5 is transcribed over a broad domain spanning the whole prosencephalon and mesencephalon, albeit with a much lower signal intensity than its paralogues Otx1 and Otx2. At later stages, four major expression sites are observed: the developing eye and epiphysis, the olfactory placodes and a broad epidermal domain in the dorsal part of the head. In the embryonic eye, the signal is first detected in the presumptive pigmented retina and slightly later in the adjacent outer layer of the neural retina, fated to photoreceptors. The comparison of this expression pattern with those of osteichthyan Otx genes suggests that a role in the specification of photoreceptors may correspond to a functional specialization of Otx5and Crx genes, fixed early in the gnathostome lineage, prior to the splitting of chondrichthyans and osteichthyans. In contrast, the roles played by ScOtx5 in the retinal pigmented epithelium or in the olfactory placodes may be fulfilled by different combinations of paralogous genes in other gnathostome taxa.


Stem cell therapy for autism.
Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions whose incidence is reaching epidemic proportions, afflicting approximately 1 in 166 children. Autistic disorder, or autism is the most common form of ASD. Although several neurophysiological alterations have been associated with autism, immune abnormalities and neural hypoperfusion appear to be broadly consistent. These appear to be causative since correlation of altered inflammatory responses, and hypoperfusion with symptology is reported. Mesenchymal stem cells (MSC) are in late phases of clinical development for treatment of graft versus host disease and Crohn's Disease, two conditions of immune dysregulation. Cord blood CD34+ cells are known to be potent angiogenic stimulators, having demonstrated positive effects in not only peripheral ischemia, but also in models of cerebral ischemia. Additionally, anecdotal clinical cases have reported responses in autistic children receiving cord blood CD34+ cells. We propose the combined use of MSC and cord blood CD34+cells may be useful in the treatment of autism.


Pachychoroid pigment epitheliopathy.
To report nine cases of pachychoroid pigment epitheliopathy. An observational case series of nine patients who underwent comprehensive ophthalmic examination, fundus photography, fundus autofluorescence, spectral-domain optical coherence tomography, and enhanced depth imaging optical coherence tomography. Eighteen eyes of 9 patients, aged 27 years to 89 years, were diagnosed with pachychoroid pigment epitheliopathy based on the characteristic funduscopic appearance of reduced fundus tessellation with overlying retinal pigment epithelial changes in one or both eyes, fundus autofluorescence abnormalities, and increased subfoveal choroidal thickness confirmed by enhanced depth imaging optical coherence tomography (mean, 460.2 μm). The five older patients had been previously diagnosed with age-related macular degeneration, while the four younger subjects were referred for possible inflammatory chorioretinitis, pattern dystrophy, or nonspecific drusen. No subjects had a history of or subsequently developed subretinal fluid. Pachychoroid pigment epitheliopathy falls within a spectrum of diseases associated with choroidal thickening that includes central serous chorioretinopathy and polypoidal choroidal vasculopathy, and it should be suspected in eyes with a characteristic fundus appearance related to choroidal thickening and associated retinal pigment epithelial abnormalities but no history of subretinal fluid. Enhanced depth imaging optical coherence tomography confirming an abnormally thick choroid and characteristic retinal pigment epithelial changes on fundus autofluorescence support the diagnosis. Because these patients are frequently misdiagnosed, the recognition of pachychoroid pigment epitheliopathy may avoid unnecessary diagnostic testing and interventions.


In vitro interaction of a polypeptide homologous to human Ro/SS-A antigen (calreticulin) with a highly conserved amino acid sequence in the cytoplasmic domain of integrin alpha subunits.
We endeavored to identify proteins interacting with KLGFFKR, a highly conserved motif in the cytoplasmic domain adjacent to the transmembrane domain of the alpha subunit of integrins. We found that affinity chromatography of cell extracts with this peptide followed by elution with EDTA resulted in the isolation of a 60-kDa protein (p60). The N-terminal amino acid sequence of this 60-kDa polypeptide was found to be highly homologous to the Ro/SS-A antigen, a 60-kDa protein homologous to calreticulin and Aplysia "memory molecule". The binding of p60 was found to be specific for the KLGFFKR sequence since this polypeptide did not bind to a peptide with a scrambled amino acid sequence (KLRFGFK), and it was also specifically eluted from the KLGFFKR affinity matrix ith soluble KLGFFKR peptide but not with the scrambled peptide. Solid phase in vitro binding assays demonstrated specific interaction of p60 with integrin alpha 3 and alpha 5 subunits but not with the beta 1 subunit. Furthermore, p60 could be copurified with alpha 3 beta 1 following coincubation in vitro. These interactions could be inhibited by KLGFFKR peptide and also by EDTA, indicating sequence-specific and divalent cation dependent binding. Despite the fact that calreticulin is thought to be localized in the endoplasmic reticulum, a pool of Ro/SS A antigen homologous 60-kDa polypeptide was found to be present in the soluble cytoplasm, indicating the feasibility of an interaction of p60 with the integrin alpha subunits. Our data suggest that p60 (Ro/SS-A Ag) can specifically bind to integrin alpha subunits via the highly conserved KLGFFKR amino acid sequence.


GSM base station electromagnetic radiation and oxidative stress in rats.
The ever increasing use of cellular phones and the increasing number of associated base stations are becoming a widespread source of nonionizing electromagnetic radiation. Some biological effects are likely to occur even at low-level EM fields. In this study, a gigahertz transverse electromagnetic (GTEM) cell was used as an exposure environment for plane wave conditions of far-field free space EM field propagation at the GSM base transceiver station (BTS) frequency of 945 MHz, and effects on oxidative stress in rats were investigated. When EM fields at a power density of 3.67 W/m2 (specific absorption rate = 11.3 mW/kg), which is well below current exposure limits, were applied, MDA (malondialdehyde) level was found to increase and GSH (reduced glutathione) concentration was found to decrease significantly (p < 0.0001). Additionally, there was a less significant (p = 0.0190) increase in SOD (superoxide dismutase) activity under EM exposure.


[Evaluation of neuropsychomotor development in first grade children and its relation with nutrition]
OBJECTIVE: To investigate the neurological performance of elementary school students from the city of Porto Alegre, state of Rio Grande do Sul, Brazil, in order to assess the association of neurological development and nutritional status. METHODS: We carried out an observational, analytical, and crosssectional study on a random and proportional population sample selected out of all first-grade students (n=35,521) in the city of Porto Alegre for a total of 484 children, out of which 64.7% were enrolled in state public schools, 11.9% in city public schools, and 23.4% in private schools. Our sample size allowed for a precision of -/+ 3% (95% confidence interval) for an estimated prevalence of 10% of cortical dysfunction. Children were submitted to individual examinations at the school. We collected data regarding sex, age, color of skin, nutritional status, and school of origin. An informed consent was obtained from the State and City Departments of Education and from the principals of the private schools. Statistical analysis was carried out using the chi-square test and ANOVA. RESULTS: From 11.4% to 38.2% of children presented ENE results lower than expected according to their age. The most affected factors were sensory activity and gnosia (38.2%), and the least affected factor was motor persistence (11.4%). There were no statistically significant differences between boys and girls. We observed an association of children with low height-for-age and weight-for-age and cortical dysfunction. CONCLUSIONS: Chronic malnutrition is a risk factor for brain function performance.


Epileptic encephalopathy with electrical status epilepticus during slow sleep: evaluation of treatment response from a tertiary center.
This study aimed to evaluate the clinical, electrophysiological, etiological features, and treatment response in children with epileptic encephalopathy with electrical status epilepticus during slow sleep (ESES). Clinical data, records of electroencephalograms (EEG), and brain magnetic resonance imaging (MRI) findings of 33 patients with ESES who were treated, and followed up for at least one year were retrospectively analyzed. Of all patients, 57.6% were male, and 42.4% were female. The mean age was 10.45 ± 2.88 years. At first admission, 90% of patients had seizures, and 10% had only school failure. Twelve patients had childhood focal epileptic syndrome. In etiology, asphyxia (n=6), hydrocephalus (n=2), polymicrogyria (n=1), and mesial temporal sclerosis (n=1) were determined. Neurological examination was abnormal in 27.2%, and brain MRI findings were pathological in 36.3% of the patients. During the ESES phase, the spike-wave index (SWI) on the non-rapid eye movement (NREM) sleep EEG was > 85% in 16 patients and 50-85% in 17 patients. Only one patient received one, and the others had at least two antiseizure medications. Benzodiazepines were found to be the most effective treatment. In the two-year follow-up, 24 patients (72.7%) were seizure-free, and nineteen patients (57.5%) had complete recovery of SWI on their NREM sleep EEG. There was a significant correlation with reduction of the SWI on the EEG and seizure control (p < 0.001). In addition, a significant correlation was found between neurocognitive and behavioral scores scored before and after treatment, seizure control, and EEG recovery. ESES is an epileptic encephalopathy that can be treated safely with antiseizure medications. Neurocognitive examinations and follow-up of EEG findings are valuable in terms of the treatment response. Benzodiazepines were found to be very effective in additional treatment.


Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate.
We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool. A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively. The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes. By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.


Update on clinical significance of coagulase-negative staphylococci.
The clinical significance of coagulase-negative Staphylococcus species (CNS) continues to increase as strategies in medical practice lead to more invasive procedures. Hospitalized patients that are immunocompromised and/or suffering from chronic diseases are the most vulnerable to infection. Since CNS are widespread on the human body and are capable of producing very large populations, distinguishing the etiologic agent(s) from contaminating flora is a serious challenge. For this reason, culture identification should proceed to the species and strain levels. A much stronger case can be made for the identification of a CNS etiologic agent if the same strain is repeatedly isolated from a series of specimens as opposed to the isolation of different strains of one or more species. Strain identity initially can be based on colony morphology, and then one or more molecular approaches can be used to gain information on the genotype. Many of the CNS species are commonly resistant to antibiotics that are being indicated for staphylococcal infections, with the exception of vancomycin. The widespread use of antibiotics in hospitals has provided a reservoir of antibiotic-resistant genes. The main focus on mechanisms of pathogenesis has been with foreign body infections and the role of specific adhesins and slime produced by Staphylococcus epidermidis. Slime can reduce the immune response and opsonophagocytosis, thereby interfering with host defense mechanisms. As we become more aware of the various strategies used by CNS, we will be in a better position to compromise their defense mechanisms and improve treatment.


Clustering and energy spectra in two-dimensional dusty gas turbulence.
We present direct numerical simulation of heavy inertial particles (dust) immersed in two-dimensional turbulent flow (gas). The dust particles are modeled as monodispersed heavy particles capable of modifying the flow through two-way coupling. By varying the Stokes number (St) and the mass-loading parameter (ϕ_{m}), we study the clustering phenomenon and the gas phase kinetic energy spectra. We find that the dust-dust correlation dimension (d_{2}) also depends on ϕ_{m}. In particular, clustering decreases as mass loading (ϕ_{m}) is increased. In the kinetic energy spectra of gas we show (i) the emergence of a different scaling regime and that (ii) the scaling exponent in this regime is not universal but a function of both St and ϕ_{m}. Using a scale-by-scale enstrophy budget analysis we show that in this emerged scaling regime, which we call the dust-dissipative range, viscous dissipation due to the gas balances the back-reaction from the dust.


Protective effects of quercetin and vitamin C against nicotine-induced toxicity in the blood of Wistar rats.
Nicotine is a potential inducer of oxidative stress, through which it can damage numerous biological molecules. The aim of our study was to investigate the prooxidative effects of nicotine and protective (additive or synergistic) effects of quercetin and vitamin C in the blood of experimental animals, to determine whether the combination of these antioxidants might be beneficial for clinical purposes. Wistar albino rats were receiving intraperitoneal nicotine injection (0.75 mg kg-1 per day) or saline (control group) or nicotine plus quercetin (40 mg kg-1 per day) and vitamin C (100 mg kg-1 per day) for three consecutive days. On day 4, we determined their blood lipid profile, liver enzymes, oxidative stress parameters, and antioxidative system parameters. Compared to untreated control, nicotine significantly increased total cholesterol, LDLcholesterol, triglycerides, liver enzymes (alanine transaminase, aspartate transaminase, and lactate dehydrogenase) and oxidative stress parameters (superoxide anion, hydrogen peroxide, and lipid peroxide) and decreased HDL-cholesterol, glutathione, and superoxide dismutase/catalase activity. Quercetin + vitamin C reversed these values significantly compared to the nicotine alone group. Our results confirm that nicotine has significant prooxidative effects that may disrupt the redox balance and show that the quercetin + vitamin C combination supports antioxidant defence mechanisms with strong haematoprotective activity against nicotine-induced toxicity. In practical terms, this means that a diet rich in vitamin C and quercetin could prevent nicotine-induced toxicity and could also be useful in the supportive care of people exposed to nicotine.


Predictive biomarkers of recovery in traumatic brain injury.
Recent advances in medicine, intensive care and diagnostic imaging modalities have led to a pronounced reduction in deaths and disability resulting from traumatic brain injury. However, there are not sufficient findings to evaluate and quantify the severity of the initial and secondary processes destructive and therefore there are not effective therapeutic measures to effectively predict the outcome. For this reason, in recent decades, researchers and clinicians have focused on specific markers of cellular brain injury to improve the diagnosis and the evaluation of outcome. Many proteins synthesized in the astroglia cells or in the neurons, such as neuron-specific enolase, S100 calcium binding protein B, myelin basic protein, creatine kinase brain isoenzyme, glial fibrillary acidic protein, plasma desoxyribonucleic acid, brain-derived neurotrophic factor, and ubiquitin carboxy-terminal hydrolase-L1, have been proposed as potential markers for cell damage in central nervous system. Usually, the levels of these proteins increase following brain injury and are found in increasing concentrations in the cerebrospinal fluid depending on the injury magnitude, and can also be found in blood stream because of a compromised blood-brain barrier. In this review, we examine the various factors that must be taken into account in the search for a reliable non-invasive biomarkers in traumatic brain injury and their role in the diagnosis and outcome evaluation.


Comparative risk of leptomeningeal disease after resection or stereotactic radiosurgery for solid tumor metastasis to the posterior fossa.
The authors tested the hypothesis that patients with metastatic posterior fossa lesions (MPFLs) treated with resection have a higher risk of leptomeningeal disease (LMD) than those with MPFLs treated with stereotactic radiosurgery (SRS). Between 1993 and 2004, 379 patients with MPFLs were treated with resection or SRS at The University of Texas M. D. Anderson Cancer Center. The authors' primary study outcome was the incidence of LMD, as diagnosed with cerebrospinal fluid cytological analysis and/or neuroimaging. Resection was performed in 260 patients, whereas 119 patients underwent SRS. The median patient age was 56 years, 51% of patients were male, and 93% had a Karnofsky Performance Scale score>or=70. The most common primary cancers were those of the lung, breast, and kidney, as well as melanoma. Leptomeningeal dissemination of cancer occurred in 33 patients: 26 in the resection group and 7 in the SRS group (resection group: rate ratio [RR] 2.06, 95% confidence interval [CI] 0.89-4.75, p=0.09). Piecemeal tumor resection (137 cases) was associated with a significantly higher risk of LMD than en bloc resection (123 cases; RR 3.4, 95% CI 1.43-8.12, p=0.006) or SRS (RR 3.37, 95% CI 1.41-8.04, p=0.006), and there was no significant difference in the risk for LMD between en bloc resection and SRS (en bloc resection: RR 0.98, 95% CI 0.34-2.81, p=0.98). The multivariate RR and significance associated with piecemeal resection, however, were consistent, with a strong effect (RR 2.45, 95% CI 1.19-5.02, p=0.02) and no indication of biases associated with tumor size, location, or cystic/necrotic appearance. There is an increased risk of LMD after piecemeal resection of an MPFL. This increase, although clinically and statistically significant, is not as alarming as previously reported and is absent when en bloc removal is achieved. Further assessment of the role of resection in a controlled prospective setting is warranted.


The Non-Vitamin K Antagonist Oral Anticoagulants in Heart Disease: Section V-Special Situations.
Non-vitamin K antagonist oral anticoagulants (NOACs) include dabigatran, which inhibits thrombin, and apixaban, betrixaban, edoxaban and rivaroxaban, which inhibit factor Xa. In large clinical trials comparing the NOACs with the vitamin K antagonist (VKA) warfarin, dabigatran, apixaban, rivaroxaban and edoxaban were at least as effective for stroke prevention in atrial fibrillation and for treatment of venous thromboembolism, but were associated with less intracranial bleeding. In addition, the NOACs are more convenient to administer than VKAs because they can be given in fixed doses without routine coagulation monitoring. Consequently, the NOACs are now replacing VKAs for these indications, and their use is increasing. Although, as a class, the NOACs have a favourable benefit-risk profile compared with VKAs, choosing among them is complicated because they have not been compared in head-to-head trials. Therefore, selection depends on the results of the individual trials, renal function, the potential for drug-drug interactions and preference for once- or twice-daily dosing. In addition, several 'special situations' were not adequately studied in the dedicated clinical trials. For these situations, knowledge of the unique pharmacological features of the various NOACs and judicious cross-trial comparison can help inform prescription choices. The purpose of this position article is therefore to help clinicians choose the right anticoagulant for the right patient at the right dose by reviewing a variety of special situations not widely studied in clinical trials.


Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
The structure of the class C ampC beta-lactamase (cephalosporinase) from Enterobacter cloacae strain P99 has been established by x-ray crystallography to 2-A resolution and compared to a class A beta-lactamase (penicillinase) structure. The binding site for beta-lactam (penicillinase) structure. The binding site for beta-lactam antibiotics is generally more open than that in penicillinases, in agreement with the ability of the class C beta-lactamases to better bind third-generation cephalosporins. Four corresponding catalytic residues (Ser-64/70, Lys-67/73, Lys-315/234, and Tyr-150/Ser-130 in class C/A) lie in equivalent positions within 0.4 A. Significant differences in positions and accessibilities of Arg-349/244 may explain the inability of clavulanate-type inhibitors to effectively inactivate the class C beta-lactamases. Glu-166, required for deacylation of the beta-lactamoyl intermediate in class A penicillinases, has no counterpart in this cephalosporinase; the nearest candidate, Asp-217, is 10 A from the reactive Ser-64. A comparison of overall tertiary folding shows that the cephalosporinase, more than the penicillinase, is broadly similar to the ancestral beta-lactam-inhibited enzymes of bacterial cell wall synthesis. On this basis, it is proposed that the cephalosporinase is the older of the two beta-lactamases, and, therefore, that a local refolding in the active site, rather than a simple point mutation, was required for the primordial class C beta-lactamase to evolve to the class A beta-lactamase having an improved ability to catalyze the deacylation step of beta-lactam hydrolysis.


Effects of the metabotropic glutamate receptor antagonist MCPG on phosphoinositide turnover and synaptic plasticity in visual cortex.
The neurotransmitter glutamate, in addition to activating ligand-gated ion channels, also stimulates phosphoinositide (PI) hydrolysis in neurons by activating a group of G-protein-coupled metabotropic glutamate receptors (mGluRs). A role for mGluRs in synaptic plasticity originally was hypothesized based on the observation that the developmental decline in glutamate-stimulated PI turnover is well correlated with the decline in experience-dependent synaptic plasticity in visual cortex. Over the past few years, the compound alpha-methyl-4-carboxyphenylglycine (MCPG) has been widely used to test the role of PI-coupled mGluRs in a number of types of synaptic plasticity, including long-term potentiation (LTP), long-term depression (LTD), ocular dominance plasticity in visual cortex, and the neural plasticity underlying learning and memory. The conclusions of most of these studies were based on the assumption that MCPG blocks the actions of glutamate at PI-coupled mGluRs in the cerebral cortex. Here we show that this assumption is not valid in visual cortex. Although MCPG does antagonize the actions of the synthetic mGluR agonist 1S, 3R-aminocyclopentane-1,3-dicarboxylic acid, it fails to block PI turnover and changes in spike adaptation stimulated by glutamate, the endogenous mGluR ligand. In addition, we find that MCPG fails to block the NMDA receptor-dependent forms of LTP, LTD, and depotentiation in visual cortex.


Tumor necrosis factor α-converting enzyme inhibition reverses hepatic steatosis and improves insulin sensitivity markers and surgical outcome in mice.
Hepatic steatosis is an established risk factor for complications following major hepatic resection. Pharmacological options to reverse steatosis prior to surgery, however, are lacking. We hypothesized that treatment with the pharmacologic tumor necrosis factor-α converting enzyme (TACE)-inhibitor Marimastat would reverse established steatosis, leading to improved outcome following hepatectomy. C57BL/6 male mice were fed a high fat diet for 9 weeks to establish obesity, hepatic steatosis and insulin resistance, and were administered either Marimastat or vehicle for an additional 2 or 4 weeks. Leptin deficient, hyperinsulinemic ob/ob mice were treated with Marimastat for 4 weeks. Hepatic steatosis was quantified by magnetic resonance spectroscopy and confirmed by histology. After two weeks, Marimastat-treated animals significantly improved surrogate markers for insulin sensitivity and liver histology, and experienced a 66% decrease in steatosis (P = 0.010). These findings were confirmed in ob/ob mice. Transcripts related to fatty acid synthesis were significantly downregulated in Marimastat-treated animals. Following pre-treatment with Marimastat or vehicle for two weeks, high fat fed C57BL/6 mice were subjected to two-thirds hepatectomy. Post-operative liver injury as quantified by serum aspartate aminotransferase levels and alanine aminotransferase levels was significantly decreased by 57% (P = 0.020) and 44% (P = 0.032) respectively, compared to controls. Treatment with the TACE-inhibitor Marimastat improved surrogate markers for insulin sensitivity and reversed steatosis in mouse models of diet-induced obesity and leptin deficiency, thereby attenuating post-operative injury following hepatectomy. This may suggest a potential therapeutic role in patients with fatty liver disease; especially those who need to undergo hepatic resection.


Screening for impaired glucose tolerance. Results from a population-based study in 21,057 individuals.
To study the distribution of fasting plasma glucose and impaired glucose tolerance (IGT) in a large general population and explore their possible implications for large-scale screening. The study focuses especially on the relation to age, obesity, and heredity background of diabetes. A total of 21,057 men and women aged 30-60 years were used for this cross-sectional study. Individuals with known diabetes and individuals with a fasting plasma glucose > or = 7 mmol/l were excluded. A physical examination, including blood sampling and an oral glucose tolerance test, was conducted. The relative risk for IGT increased more than fourfold among obese subjects compared with normal-weight subjects, yet only 25% of IGT subjects were obese. Similarly, IGT subjects more frequently reported having first-degree relatives with diabetes than did subjects with normal glucose tolerance. Nonetheless, > 70% of IGT subjects reported no heredity background of diabetes. Subjects with IGT showed higher mean values of BMI, blood pressure, and triglycerides. Only 13% of the men and 19% of the women having impaired fasting glucose (IFG) fulfilled the criteria of IGT. The present study shows that a high-risk screening strategy for IGT targeted solely toward subjects with obesity and/or heredity background of diabetes will fail to detect the majority of subjects with IGT in the general population. The new concept of IFG may not replace the concept of IGT as a risk marker for worsening to diabetes.


Mexican-American neighborhood's social capital and attitudes about violence.
Measurement of the effectiveness of violence prevention interventions is in a developmental phase. Social capital provides a framework within which to examine this topic from a community perspective. The purpose of this study was to examine the relationships among three measures of social capital and attitudes about violence among Mexican-Americans. A cross-sectional survey was conducted of households randomly selected by block in two adjacent Mexican-American communities. Demographics, attitudes about and experiences with violence, and three measures of social capital (collective efficacy, neighborhood block conditions, community integration) were assessed. Descriptive, bivariate, and logistic regression analyses were used to examine indicators of violence attitudes and experiences. Of the 473 respondents who completed the survey, 323 (68%) were female, 393 (83%) were Mexican-American, 395 (84%) were born in the US, and 346 (72%) owned their own homes. Participants with high measures of collective efficacy were 1.68 times more likely to have negative attitudes about violence (CI 1.06-2.65) and 15.25 times more likely to have negative attitudes about couple violence (CI 9.05-25.74). Participants with high scores on neighborhood block conditions were 2.33 times more likely to have negative attitudes about couple violence (CI 1.40-3.87). Scores on community integration were not significant indicators of participants' tolerance and experiences with violence. Two measures of social capital were positively associated with and predictive of negative attitudes toward violence. The results suggest that primary violence prevention programs in Mexican-American communities should focus on strengthening a sense of collective efficacy and improving neighborhood conditions.


Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs.
Transcription activator-like effector nucleases (TALENs) are powerful new research tools that enable targeted gene disruption in a wide variety of model organisms. Recent work has shown that TALENs can induce mutations in endogenous zebrafish genes, but to date only four genes have been altered, and larger-scale tests of the success rate, mutation efficiencies and germline transmission rates have not been described. Here, we constructed homodimeric TALENs to 10 different targets in various endogenous zebrafish genes and found that 7 nuclease pairs induced targeted indel mutations with high efficiencies ranging from 2 to 76%. We also tested obligate heterodimeric TALENs and found that these nucleases induce mutations with comparable or higher frequencies and have better toxicity profiles than their homodimeric counterparts. Importantly, mutations induced by both homodimeric and heterodimeric TALENs are passed efficiently through the germline, in some cases reaching 100% transmission. For one target gene sequence, we observed substantially reduced mutagenesis efficiency for a variant site bearing two mismatched nucleotides, raising the possibility that TALENs might be used to perform allele-specific gene disruption. Our results suggest that construction of one to two heterodimeric TALEN pairs for any given gene will, in most cases, enable researchers to rapidly generate knockout zebrafish.


Inhibitor SBFI26 suppresses the malignant progression of castration-resistant PC3-M cells by competitively binding to oncogenic FABP5.
Castration resistant-prostate cancer is largely impervious to feather hormonal therapy and hence the outlook for patients is grim. Here we use an approach to attach the recently discovered Achilles heel. The experimental treatment established in this study is based on the recent discovery that it is the FABP5-PPARγ-VEGF signalling axis, rather than the androgen receptor pathway, played a dominant role in promoting the malignant progression of castration resistant prostate cancer cells. Treatments have been established in mice by suppressing the biological activity of FABP5 using a chemical inhibitor SBFI26. The inhibitor significantly suppressed the proliferation, migration, invasiveness and colony formation of PC3-M cells in vitro. It also produced a highly significant suppression of both the metastases and the primary tumours developed from cancer cells implanted orthotopically into the prostate glands of the mice. The inhibitor SBFI26 interferes with the FABP5-PPARγ- signalling pathway at the initial stage of the signal transduction by binding competitively to FABP5 to inhibit cellular fatty acid uptake. This avoids the fatty-acid stimulation of PPARγ and prevents it activating the down-stream regulated cancer-promoting genes. This entirely novel experimental approach to treating castration- resistant prostate cancer is completely different from current treatments that are based on androgen-blockade therapy.


Dietary intake and human milk residues of hexachlorocyclohexane isomers in two Chinese cities.
Residues of hexachlorocyclohexane isomers (HCHs, including alpha-HCH, beta-HCH, gamma-HCH, and delta-HCH) in human milk of two populations from Beijing and Shenyang, China were studied. In addition to human milk samples from 76 women, 271 composite food samples covering major food categories were also collected for HCH analysis. The food consumption and social-demographic characteristics of the studied populations were investigated and dietary intakes of HCHs of the milk donors on an individual basis were calculated. The dependences of HCH concentration in the human milk on food consumption, dietary intake of HCHs, and demographic characteristics were studied. It was found that beta-HCH dominated the HCHs detected in the human milk. Although there were dramatic declines in HCHs in the human milk compared to historical data, the current levels (312 +/- 377 ng/g fat and 360 +/- 235 ng/g fat as the means and standard deviations for Beijing and Shenyang, respectively) were still much higher than those reported in other cities within China and around the world. It was revealed that the residual level of HCHs in the human milk was positively correlated (p < 0.001) to the quantities of food consumption. Milk, oil, vegetables, and fruits contributed a large portion of HCHs intake in Beijing, while cereals, milk, vegetables, oil, and meat were the most important dietary intake sources of HCHs in Shenyang. Both daily dietary intake of HCHs (p < 0.001) and body mass index (BMI, body weight divided by the squared height) (p < 0.01) were significantly correlated with human milk HCHs. A nonlinear model was developed to predict the residues of HCHs in human milk using both dietary intake and BMI as independent variables. Potential risk of the HCH exposure of breastfed infants is discussed.


Social relationships as a major determinant in the valuation of health states.
To empirically determine the impact of the capacity to sustain social relationships on valuing health states. 68 clinical experts conducted a health state valuation exercise in five sites using pairwise comparison, ranking, and person trade-off as elicitation methods. 23,840 pairwise comparisons of a total of 379 health states were analyzed by conditional logistic regression. Social relationships had a clear monotonic association with perceived disability: the more limited the capacity to sustain social relationships, the more disabling the resulting health state valuations. The highest level of limitations with respect to social relationships was associated with slightly lower impact on health state valuations compared to the highest level of limitations in physical functioning. Social relationships showed an independent contribution to health state valuations and should be included in health state measures.


Plant Growth Retardant B-995: A Possible Mode of Action.
Inhibition of shoot elongation in dwarf and tall peas by the 1,1-dimethylhydrazide of succinic acid (B-995) was correlated with the inhibition of the oxidation of tryptamine-2-C(14) to indoleacetaldehyde-2-C(14) in homogenates prepared from epicotyls of young plants treated with B-995. The growth-retarding action of B-995 is attributed to the formation of 1,1-dimethylhydrazine in vivo. This hydrazine strongly inhibited tryptamine oxidation by pea epicotyl homogenates.


The interactions between clinical informatics and bioinformatics: a case study.
For the past decade, Stanford Medical Informatics has combined clinical informatics and bioinformatics research and training in an explicit way. The interest in applying informatics techniques to both clinical problems and problems in basic science can be traced to the Dendral project in the 1960s. Having bioinformatics and clinical informatics in the same academic unit is still somewhat unusual and can lead to clashes of clinical and basic science cultures. Nevertheless, the benefits of this organization have recently become clear, as the landscape of academic medicine in the next decades has begun to emerge. The author provides examples of technology transfer between clinical informatics and bioinformatics that illustrate how they complement each other.


Reticular activation and the dynamics of neuronal networks.
It is postulated that during arousal the cortical system is driven by a spatially and temporally noisy signal arising from non-specific reticulo-cortical pathways. An elementary unit of cortical neuroanatomy is assumed, which permits non-linear dynamics to be represented by stochastic linear equations. Under these assumptions the resonant modes of the system of cortical dendrites approach thermodynamic equilibrium. Specific sensory signals perturb the dendritic system about equilibrium, generate low frequency, linear, non-dispersive waves corresponding to the EEG, which in turn regulate action potential sequences, and instantiate internal inputs to the dendritic field. A large and distributed memory capacity in axo-synaptic couplings, resistance to interference between functionally separate logical operations, and a very large next-state function set emerge as properties of the network. The model is able to explain the close association of the EEG with cognition, the channel of low capacity corresponding to the field of immediate attention, the low overall correlation of action potentials with EEG, and specificity of action potentials in some neurons during particular cognitive activity. Predictions made from hypothesis include features of thermal equilibrium in EEG (determinable by autoregression) and expectation that the cortical evoked response can be accounted for as the response to a sensory impulse of specific time characteristics.


Tuberculin skin testing in Vietnamese refugees with a history of BCG vaccination.
Among 50 Indo-Chinese children 18 years of age or younger who were screened at the Albany County (New York) Health Department, during 1979, 14 had a history of BCG vaccination. These patients were not intradermally tested with 5 TU of PPD because it was assumed that the reactions would not be interpretable. To test this hypothesis, nine patients were available for testing. Six patients had a negative reaction, two had a reaction greater than 10 mm of induration, and one had an equivocal reaction. Nine of the 36 patients without a history of BCG vaccination also had positive reactions to the same dose of PPD. All patients with positive reactions had normal chest x-ray films and received isoniazid prophylaxis, regardless of BCG history in accordance with Centers for Disease Control recommendations. A history of BCG vaccination should not preclude skin testing with PPD (given in tuberculin units), and a patient with a positive reaction should receive appropriate treatment.


The direct measurement of 3-beta-hydroxy butyrate enhances the management of diabetic ketoacidosis in children and reduces time and costs of treatment.
In this study the effectiveness of a quantitative test of beta-hydroxybutyrate (beta-HBA) against a commercial test for urine ketone bodies (UKB) in monitoring diabetic ketoacidosis (DKA) was evaluated to verify whether this ketone-testing method was able to reduce the monitoring costs and professional burden of nurses and physicians. Thirty-three children with severe (arterial pH < or = 7.2) or moderate (7.2 < pH < or = 7.3) DKA were studied. Sixteen patients were randomly monitored with blood beta-HBA (group 1) and 17 by UKB (group 2). Contrary to UKB, beta-HBA levels appeared correlated with: HbA1c values on admission (r = 0.99; p = 0.0001); latent period before diagnosis of diabetes (r = 0.95; p = 0.0001); changes in arterial pH (r = -0.82; p = 0.0001) and blood bicarbonate values (r = -0.63; p = 0.001) during the treatment for DKA. Required time to achieve the resolution of ketosis in group 1 patients was related to the values of beta-HBA on admission (r = 0.84; p < 0.001). Determination of beta-HBA showed that ketosis in group 1 patients cleared 4 to 9.5 hours earlier than in group 2. Due to this early normalization, the patients of group 1 left the Intensive Care Unit 6.5 +/- 1.5 hr earlier than those of group 2. This led to 22 hr saved for clinical assessment and 375 laboratory investigations for a total saving of 2940 euros including costs for laboratory tests (29.8%) and clinical assessment (70.2%). Quantitative determination of beta-HBA levels seems to offer useful information for monitoring DKA in newly-diagnosed diabetic children and for reducing time and costs in an Intensive Care Unit.


An in Vivo Nanosensor Measures Compartmental Doxorubicin Exposure.
Preclinical measurements of drug exposure to specific organs and tissues is normally performed by destructive methods. Tissue-specific measurements are important, especially for drugs with intractable dose-limiting toxicities, such as doxorubicin-mediated cardiotoxicity. We developed a method to rapidly quantify doxorubicin exposure to tissues within living organisms using an implantable optical nanosensor that can be interrogated noninvasively following surgical implantation. The near-infrared fluorescence of single-walled carbon nanotubes functionalized with DNA was found to respond to doxorubicin via a large and uniform red-shift. We found this to be common to DNA-intercalating agents, including anthracycline compounds such as doxorubicin. Doxorubicin was measured in buffer and serum, intracellularly, and from single nanotubes on a surface. Doxorubicin adsorption to the DNA-suspended nanotubes did not displace DNA but bound irreversibly. We incorporated the nanosensors into an implantable membrane which allowed cumulative detection of doxorubicin exposure in vivo. On implanting the devices into different compartments, such as subcutaneously and within the peritoneal cavity, we achieved real-time, minimally invasive detection of doxorubicin injected into the peritoneal cavity, as well as compartment-specific measurements. We measured doxorubicin translocation across the peritoneal membrane in vivo. Robust, minimally invasive pharmacokinetic measurements in vivo suggest the suitability of this technology for preclinical drug discovery applications.


Grating-coupled surface plasmon polaritons and waveguide modes in a silver-dielectric-silver structure.
A silver-dielectric-silver structure that supports both waveguide modes and surface plasmon polaritons is explored. The upper interface between the dielectric and the silver is periodically corrugated to allow coupling of visible photons to both types of mode. Such a metallic microcavity leads to plasmonic and waveguide self-interacting bandgaps at Brillouin zone boundaries. In addition there are found other bandgaps from mode crossings within the Brillouin zone. This results specifically in a very flat photonic band due to anticrossings between a surface plasmon polariton and waveguide modes. Characterization of the observed modes in terms of their resonant electromagnetic fields is achieved by using a multilayer, multishape differential grating theory.


Outcomes of triple-negative versus non-triple-negative breast cancers managed with breast-conserving therapy.
Triple negative breast cancer is associated with aggressive behavior and high risk of local and regional failure. Aggressive surgical intervention is considered suitable. This makes role of breast conserving therapy (BCT) debatable in these patients. The objective of this study was to compare outcome of BCT for triple negative versus non-triple negative breast cancer. Medical records of patients who underwent breast conserving therapy from 1999 to 2009 at Shaukat Khanum Cancer Hospital and had complete receptor status information were extracted. Patients were divided into triple negative breast cancer (TNBC) and non-TNBC. Patient characteristics, medical treatment modalities and adverse events were compared. Expected five year locoregional recurrence free, disease free and overall survival was calculated. The Cox proportional hazard model was used to identify independent predictors of outcome. A total of 194 patients with TNBC and 443 with non-TNBC were compared. Significant difference was present for age at presentation (p<0.0001), family history (p=0.005), grade (p<0.0001) and use of hormonal therapy (p<0.0001). The number of locoregional failures, distant failures and mortalities were not significantly different. No significant difference was present in 5 year locoregional recurrence free (96% vs 92%, p=0.3), disease free (75% vs 74%, p=0.7) and overall survival (78% vs 83%, p=0.2). On multivariate analysis, tumor size, nodal involvement and hormonal treatment were independent predictors of negative events. Breast conserving therapy has comparable outcomes for triple negative and non-triple negative breast cancers.


Breakdown of C3 after complement activation. Identification of a new fragment C3g, using monoclonal antibodies.
The physiological breakdown of C3 has been studied using monoclonal anti-C3 antibodies, and it has been found that the later stages of this process--the breakdown of C3bi--is more complex than had previously been recognized. C3bi is the reaction product produced from C3b by the action of factor I which, in the presence of factor H, produces a double cleavage in the alpha chain of C3b. It is here reported that, both on cells and in the fluid phase, the breakdown of C3bi in serum gives rise to two products: C3c and the product previously described as alpha 2D, which we now propose to designate C3d,g. Alpha 2D differs from C3d in that it contains an additional fragment of approximately 8,000 mol wt that carries the antigenic determinant for the clone 9 monoclonal anti-C3 antibody. C3g cannot be precipitated by anti-C3 antisera and therefore behaves as a uni- or bideterminant antigen. The cleavage of C3d,g to C3d and C3g does not occur in sterile serum. It is also still uncertain what enzyme cleaves C3bi to C3c and C3d,g in plasma. Plasmin can do so in vitro, but plasminogen-depleted serum can still produce the cleavage. The antigenic determinant recognized by clone 9 in C3 is not exposed in C3 or C3b, but appears as a neoantigen in C3bi (and in C3d,g). Anti-C3g therefore is a potentially useful ligand for detecting complement-activation products. C3g represents a new, highly anionic C3 fragment and seems not to be identical with the C3e fragment described by others.


B Cell-Intrinsic Role for IRF5 in TLR9/BCR-Induced Human B Cell Activation, Proliferation, and Plasmablast Differentiation.
Upon recognition of antigen, B cells undergo rapid proliferation followed by differentiation to specialized antibody secreting cells (ASCs). During this transition, B cells are reliant upon a multilayer transcription factor network to achieve a dramatic remodeling of the B cell transcriptional landscape. Increased levels of ASCs are often seen in autoimmune diseases and it is believed that altered expression of regulatory transcription factors play a role in this imbalance. The transcription factor interferon regulatory factor 5 (IRF5) is one such candidate as polymorphisms in IRF5 associate with risk of numerous autoimmune diseases and correlate with elevated IRF5 expression. IRF5 genetic risk has been widely replicated in systemic lupus erythematosus (SLE), and loss of Irf5 ameliorates disease in murine lupus models, in part, through the lack of pathogenic autoantibody secretion. It remains unclear, however, whether IRF5 is contributing to autoantibody production through a B cell-intrinsic function. To date, IRF5 function in healthy human B cells has not been characterized. Using human primary naive B cells, we define a critical intrinsic role for IRF5 in B cell activation, proliferation, and plasmablast differentiation. Targeted IRF5 knockdown resulted in significant immunoglobulin (Ig) D retention, reduced proliferation, plasmablast differentiation, and IgG secretion. The observed decreases were due to impaired B cell activation and clonal expansion. Distinct from murine studies, we identify and confirm new IRF5 target genes, IRF4, ERK1, and MYC, and pathways that mediate IRF5 B cell-intrinsic function. Together, these results identify IRF5 as an early regulator of human B cell activation and provide the first dataset in human primary B cells to map IRF5 dysfunction in SLE.


Antimicrobial susceptibility of Pseudomonas aeruginosa: results of a UK survey and evaluation of the British Society for Antimicrobial Chemotherapy disc susceptibility test.
A survey was conducted in 1999, first to establish the prevalence of antibiotic resistance among clinical isolates of Pseudomonas aeruginosa in the UK and secondly to test whether the use of the standardized British Society for Antimicrobial Chemotherapy (BSAC) disc testing method improved the accuracy of routine susceptibility testing for this organism. Twenty-five hospitals were each asked to collect up to 100 consecutive, clinically significant isolates of P. aeruginosa and to test their susceptibility to amikacin, gentamicin, ceftazidime, imipenem, meropenem, ciprofloxacin, piperacillin and piperacillin/tazobactam using the new BSAC disc method. A total of 2194 isolate reports were available for analysis and 10% of the isolates represented, plus those with unusual resistances, were re-tested centrally for quality control purposes. The zone distributions were essentially unimodal, indicating the absence of major populations with acquired resistance. The results indicated that resistance rates to the beta-lactam, aminoglycoside and quinolone agents tested in P. aeruginosa in the UK remain low (<12%), and were mostly unchanged since a previous survey conducted in 1993. High resistance rates were nevertheless reported for isolates from cystic fibrosis patients. The accuracy of susceptibility testing using the new BSAC disc testing method was better than in previous studies, when Stokes' method was most frequently used. Critically, the proportion of resistant isolates incorrectly reported as susceptible was reduced significantly; nevertheless, depending on the antibiotic, up to 49% of the isolates reported as intermediate or resistant were found susceptible on central re-testing.


Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein.
Mycobacterium tuberculosis (Mtb) mounts a stubborn defense against oxidative and nitrosative components of the immune response. Dihydrolipoamide dehydrogenase (Lpd) and dihydrolipoamide succinyltransferase (SucB) are components of alpha-ketoacid dehydrogenase complexes that are central to intermediary metabolism. We find that Lpd and SucB support Mtb's antioxidant defense. The peroxiredoxin alkyl hydroperoxide reductase (AhpC) is linked to Lpd and SucB by an adaptor protein, AhpD. The 2.0 angstrom AhpD crystal structure reveals a thioredoxin-like active site that is responsive to lipoamide. We propose that Lpd, SucB (the only lipoyl protein detected in Mtb), AhpD, and AhpC together constitute a nicotinamide adenine dinucleotide (reduced)-dependent peroxidase and peroxynitrite reductase. AhpD thus represents a class of thioredoxin-like molecules that enables an antioxidant defense.


Measurement of intracellular accumulation of anthracyclines in cancerous cells by direct injection of cell lysate in MEKC/LIF detection.
Anthracyclines are chemotherapeutic drugs that are broadly used in the treatment of various types of solid cancers and leukemia. Herein, we report on a novel analytical method for intracellular accumulation of anthracyclines using MEKC/LIF detection. An aqueous separation system permitted the injection of cell lysates directly into the capillary. The MEKC migrating solution was made up of borate buffer at pH 9.22 containing sodium taurodeoxycholate, (2-hydroxypropyl)-gamma-CD, and SDS. The anthracyclines, Doxorubicin (DOX) and epirubicin (EPI) were detected by LIF using a Nd:YAG laser (532 nm) or an argon ion laser (488 nm) for excitation. Two cell lines, human humerus tumor cells (RDES) and human lung tumor cells (A549), were treated with a mixture of the two anthracyclines for fixed periods of time, and then intracellular concentrations were determined by injecting cell lysates directly. Recovery values of 96.0-100.8% were obtained for DOX and EPI. Reproducibility quantified by RSD was less than 3.9% intraday and 6.7% interday at concentrations ranging between 50 and 500 nM. The uptake of EPI was found to be slightly less than that of DOX for A549, but higher levels of EPI were observed in RDES. Intracellular accumulation of anthracyclines was greater in RDES than in A549, but both types of cells excreted anthracyclines after 12 h. These results indicate that MEKC with an aqueous medium is useful for investigating intracellular uptake and accumulation of drugs, since cell lysates can be used directly with no pretreatment such as deproteination or solvent extraction of analytes.


Essential Oil of Cannabis sativa L: Comparison of Yield and Chemical Composition of 11 Hemp Genotypes.
Cannabis sativa L. is an annual species cultivated since antiquity for different purposes. While, in the past, hemp inflorescences were considered crop residues, at present, they are regarded as valuable raw materials with different applications, among which extraction of the essential oil (EO) has gained increasing interest in many fields. The aim of the present study is the evaluation of the yield and the chemical composition of the EO obtained by hydrodistillation from eleven hemp genotypes, cultivated in the same location for two consecutive growing seasons. The composition of the EOs was analyzed by GC-MS, and then subjected to multivariate statistical analysis. Sesquiterpenes represented the main class of compounds in all the EOs, both in their hydrocarbon and oxygenated forms, with relative abundances ranging from 47.1 to 78.5%; the only exception was the Felina 32 sample collected in 2019, in which cannabinoids predominated. Cannabinoids were the second most abundant class of compounds, of which cannabidiol was the main one, with relative abundances between 11.8 and 51.5%. The statistical distribution of the samples, performed on the complete chemical composition of the EOs, evidenced a partition based on the year of cultivation, rather than on the genotype, with the exception of Uso-31. Regarding the extraction yield, a significant variation was evidenced among both the genotypes and the years of cultivation.


Epidemiology of diarrheal disease outbreaks on cruise ships, 1986 through 1993.
To describe the epidemiology of cruise-associated diarrheal disease outbreaks from 1986 through 1993, to determine if the incidence had changed since 1985, and to determine the preventability of outbreaks that continue to occur. The numerator data were collated from Centers for Disease Control and Prevention (CDC) outbreak investigation reports from 1986 through 1993. The denominator data were summations of cruise ship data on the number of passengers and length of cruises collected during routine diarrheal illness surveillance, available only for the period 1989 through 1993. Cruise ships with outbreaks of diarrheal disease. Cruise ship passengers and crew of staff ho participated in the original investigations. The incidence of outbreaks during the study period, pathogens isolated, and vehicles of transmission implicated in investigations. Among cruises of 3 to 15 days, CDC staff investigated 1.4 outbreaks per 1000 cruises, or 2.3 outbreaks per 10 million passenger-days. An etiologic agent was implicated in 21 (68%) of 31 investigated outbreaks: bacterial in 12, viral in nine. A specific vehicle of transmission was identified in 16. The most common vehicles of transmission were undercooked scallops (three outbreaks caused by enterotoxigenic Escherichia coli), eggs (two outbreaks caused by Salmonella serotype Enteritidis, one by Norwalk-like virus), and food items provided by caterers during onshore excursions (three outbreaks, one caused by Shigella sonnei). Observance of two simple precautions could have prevented almost one third (5/16, or 31%) of the investigated outbreaks on cruise ships. Cruise lines have been reminded to cook seafoods thoroughly and to use pasteurized eggs for menu items calling for pooled eggs. Preventing food handlers from working while ill and not using onshore caterers for offship excursions might have prevented at least an additional one third (5/16) of these outbreaks.


scCAN: single-cell clustering using autoencoder and network fusion.
Unsupervised clustering of single-cell RNA sequencing data (scRNA-seq) is important because it allows us to identify putative cell types. However, the large number of cells (up to millions), the high-dimensionality of the data (tens of thousands of genes), and the high dropout rates all present substantial challenges in single-cell analysis. Here we introduce a new method, named single-cell Clustering using Autoencoder and Network fusion (scCAN), that can overcome these challenges to accurately segregate different cell types in large and sparse scRNA-seq data. In an extensive analysis using 28 real scRNA-seq datasets (more than three million cells) and 243 simulated datasets, we validate that scCAN: (1) correctly estimates the number of true cell types, (2) accurately segregates cells of different types, (3) is robust against dropouts, and (4) is fast and memory efficient. We also compare scCAN with CIDR, SEURAT3, Monocle3, SHARP, and SCANPY. scCAN outperforms these state-of-the-art methods in terms of both accuracy and scalability. The scCAN package is available at https://cran.r-project.org/package=scCAN . Data and R scripts are available at http://sccan.tinnguyen-lab.com/.


Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity.
Fusion genes can be oncogenic drivers in a variety of cancer types and represent potential targets for targeted therapy. The BRAF gene is frequently involved in oncogenic gene fusions, with fusion frequencies of 0.2%-3% throughout different cancers. However, BRAF fusions rarely occur in the same gene configuration, potentially challenging personalized therapy design. In particular, the impact of the wide variety of fusion partners on the oncogenic role of BRAF during tumor growth and drug response is unknown. Here, we used patient-derived colorectal cancer organoids to functionally characterize and cross-compare BRAF fusions containing various partner genes (AGAP3, DLG1, and TRIM24) with respect to cellular behavior, downstream signaling activation, and response to targeted therapies. We demonstrate that 5' fusion partners mainly promote canonical oncogenic BRAF activity by replacing the auto-inhibitory N-terminal region. In addition, the 5' partner of BRAF fusions influences their subcellular localization and intracellular signaling capacity, revealing distinct subsets of affected signaling pathways and altered gene expression. Presence of the different BRAF fusions resulted in varying sensitivities to combinatorial inhibition of MEK and the EGF receptor family. However, all BRAF fusions conveyed resistance to targeted monotherapy against the EGF receptor family, suggesting that BRAF fusions should be screened alongside other MAPK pathway alterations to identify patients with metastatic colorectal cancer to exclude from anti-EGFR-targeted treatment. IMPLICATIONS: Although intracellular signaling and sensitivity to targeted therapies of BRAF fusion genes are influenced by their 5' fusion partner, we show that all investigated BRAF fusions confer resistance to clinically relevant EGFR inhibition.


The Effect of Rev-erbα Agonist SR9011 on the Immune Response and Cell Metabolism of Microglia.
Microglia are the immune cells of the brain. Hyperactivation of microglia contributes to the pathology of metabolic and neuroinflammatory diseases. Evidence has emerged that links the circadian clock, cellular metabolism, and immune activity in microglia. Rev-erb nuclear receptors are known for their regulatory role in both the molecular clock and cell metabolism, and have recently been found to play an important role in neuroinflammation. The Rev-erbα agonist SR9011 disrupts circadian rhythm by altering intracellular clock machinery. However, the exact role of Rev-erbα in microglial immunometabolism remains to be elucidated. In the current study, we explored whether SR9011 also had such a detrimental impact on microglial immunometabolic functions. Primary microglia were isolated from 1-3 days old Sprague-Dawley rat pups. The expression of clock genes, cytokines and metabolic genes was evaluated using RT-PCR and rhythmic expression was analyzed. Phagocytic activity was determined by the uptake capacity of fluorescent microspheres. Mitochondria function was evaluated by measuring oxygen consumption rate and extracellular acidification rate. We found that key cytokines and metabolic genes are rhythmically expressed in microglia. SR9011 disturbed rhythmic expression of clock genes in microglia. Pro-inflammatory cytokine expression was attenuated by SR9011 during an immune challenge by TNFα, while expression of the anti-inflammatory cytokine Il10 was stimulated. Moreover, SR9011 decreased phagocytic activity, mitochondrial respiration, ATP production, and metabolic gene expression. Our study highlights the link between the intrinsic clock and immunometabolism of microglia. We show that Rev-erbα is implicated in both metabolic homeostasis and the inflammatory responses in microglia, which has important implications for the treatment of metabolic and neuroinflammatory diseases.


Economic burden of dengue in Indonesia.
Dengue is associated with significant economic expenditure and it is estimated that the Asia Pacific region accounts for >50% of the global cost. Indonesia has one of the world's highest dengue burdens; Aedes aegypti and Aedes albopictus are the primary and secondary vectors. In the absence of local data on disease cost, this study estimated the annual economic burden during 2015 of both hospitalized and ambulatory dengue cases in Indonesia. Total 2015 dengue costs were calculated using both prospective and retrospective methods using data from public and private hospitals and health centres in three provinces: Yogyakarta, Bali and Jakarta. Direct costs were extracted from billing systems and claims; a patient survey captured indirect and out-of-pocket costs at discharge and 2 weeks later. Adjustments across sites based on similar clinical practices and healthcare landscapes were performed to fill gaps in cost estimates. The national burden of dengue was extrapolated from provincial data using data from the three sites and applying an empirically-derived epidemiological expansion factor. Total direct and indirect costs per dengue case assessed at Yogyakarta, Bali and Jakarta were US$791, US$1,241 and US$1,250, respectively. Total 2015 economic burden of dengue in Indonesia was estimated at US$381.15 million which comprised US$355.2 million for hospitalized and US$26.2 million for ambulatory care cases. Dengue imposes a substantial economic burden for Indonesian public payers and society. Complemented with an appropriate weighting method and by accounting for local specificities and practices, these data may support national level public health decision making for prevention/control of dengue in public health priority lists.


Neutral Aminyl Radicals Derived from Azoimidazolium Dyes.
The synthesis and characterization of a new class of neutral aminyl radicals is reported. Monoradicals were obtained by reduction of azoimidazolium dyes with potassium. Structural, spectroscopic, and computational data suggest that the spin density is centered on one of the nitrogen atoms of the former azo group. The reduction of a dimeric dye with an octamethylbiphenylene bridge between the azo groups resulted in the formation of a biradical with largely independent unpaired electrons. Both the monoradicals and the biradical were found to display high stability in solution as well as in the solid state.


Cardiac parasympathetic activity in severe uncomplicated coronary artery disease.
Previous studies have suggested that coronary artery disease is independently associated with reduced cardiac parasympathetic activity, and that this is important in its pathophysiology. These studies included many patients with complications that might be responsible for the reported autonomic abnormalities. To measure cardiac parasympathetic activity in patients with uncomplicated coronary artery disease. 44 patients of mean (SD) age 56 (8) with severe uncomplicated coronary artery disease (symptoms uncontrolled on maximal medical treatment; > 70% coronary stenosis at angiography; normal ejection fraction; no evidence of previous infarction, diabetes, or hypertension). Heart rate variability was measured from 24 hour ambulatory electrocardiograms by counting the number of times successive RR intervals exceeded the preceding RR interval by > 50 ms, a previously validated sensitive and specific index of cardiac parasympathetic activity. Mean (range) of counts were: waking 112 (range 6-501)/h, sleeping 198 (0-812)/h, and total 3912 (151-14 454)/24 h. These mean results were unremarkable, and < 10% of patients fell below the lower 95% confidence interval for waking, sleeping, or total 24 hour counts in normal people. There was no relation between the severity of coronary artery disease or the use of concurrent antianginal drug treatment and cardiac parasympathetic activity. In contrast with previous reports no evidence of a specific independent association between coronary artery disease and reduced cardiac parasympathetic activity was found. The results of previous studies may reflect the inclusion of patients with complications and not the direct effect of coronary artery disease itself.


Change in psychosocial functioning and quality of life of patients with body dysmorphic disorder treated with fluoxetine: a placebo-controlled study.
In a 12-week placebo-controlled study of fluoxetine in the treatment of body dysmorphic disorder, the authors investigated change in psychosocial functioning and mental health-related quality of life in 60 subjects. The subjects were assessed with the LIFE-RIFT (a measure of impaired functioning), Social and Occupational Functioning Scale (SOFAS), and Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36) before and after receiving fluoxetine or placebo. At baseline, the patients had impaired psychosocial functioning and markedly poor mental health-related quality of life. Compared to placebo, fluoxetine was associated with significantly greater improvement in LIFE-RIFT and SOFAS scores and with improvement on the mental health subscale of the SF-36 that approached significance. Decrease in the severity of body dysmorphic disorder, as measured by the Yale-Brown Obsessive Compulsive Scale Modified for Body Dysmorphic Disorder, was significantly correlated with improvement in functioning and quality of life.


The effect of dental implant spacing on peri-implant bone using the rabbit (Oryctolagus cuniculus) tibia model.
This study investigated the effects of implant proximity on inter-implant bone height, density, and osseointegration using digital radiography and histology. After a feasibility study, a total of 80 endosteal implants were placed in 20 New Zealand White Rabbit tibias. With the aid of a surgical jig, four 8.5-mm implants were placed in the medial aspect of the tibial crest at inter-implant distances of approximately 1, 1.5, and 3 mm. Standardized digital radiographs using a paralleling device were made immediately after placement of implants. Implants were allowed to osseointegrate for 90 days. After this healing period, the animals were sacrificed, and the standardized radiographs were repeated. The tibias were harvested, processed, and invested in epoxy. Sagittal sections were made from each specimen for histologic evaluation. The initial and postmortem digital radiographs were evaluated for inter-implant distances, vertical bone height changes over time and between implant pairs, and bone density changes over time and between implant pairs using a computer image analysis program and computer statistics program. The actual inter-implant distances were consistent in a range of 0.2 mm. Bone height increased significantly from presurgical levels at all 3 locations (p < .0005). Repeated measures analysis of variance comparing change in bone height at the 3 implant pair distances showed significant differences among the 3 (p = .002). Paired t tests showed that the amount of bone growth at the 1-mm separation site was significantly greater than the 1.5-mm site (p = .026) and the 3-mm site (p = .001), whereas bone growth at the 1.5- and 3-mm sites did not show significant differences (p = .162). A repeated measures analysis of variance comparing change in bone density showed no significant differences (p > .05) among the 3 inter-implant distances for either the 8-mm position (approximately crestal bone height) or the 6-mm position (approximately 2 mm subcrestal). Within the limits of this study, it seems placing implants closely together does not adversely affect bone height or density. Conversely, it seems that placing implants closer together may increase bone growth.


A unique chromosomal rearrangement in the Cryptococcus neoformans var. grubii type strain enhances key phenotypes associated with virulence.
The accumulation of genomic structural variation between closely related populations over time can lead to reproductive isolation and speciation. The fungal pathogen Cryptococcus is thought to have recently diversified, forming a species complex containing members with distinct morphologies, distributions, and pathologies of infection. We have investigated structural changes in genomic architecture such as inversions and translocations that distinguish the most pathogenic variety, Cryptococcus neoformans var. grubii, from the less clinically prevalent Cryptococcus neoformans var. neoformans and Cryptococcus gattii. Synteny analysis between the genomes of the three Cryptococcus species/varieties (strains H99, JEC21, and R265) reveals that C. neoformans var. grubii possesses surprisingly few unique genomic rearrangements. All but one are relatively small and are shared by all molecular subtypes of C. neoformans var. grubii. In contrast, the large translocation peculiar to the C. neoformans var. grubii type strain is found in all tested subcultures from multiple laboratories, suggesting that it has possessed this rearrangement since its isolation from a human clinical sample. Furthermore, we find that the translocation directly disrupts two genes. The first of these encodes a novel protein involved in metabolism of glucose at human body temperature and affects intracellular levels of trehalose. The second encodes a homeodomain-containing transcription factor that modulates melanin production. Both mutations would be predicted to increase pathogenicity; however, when recreated in an alternate genetic background, these mutations do not affect virulence in animal models. The type strain of C. neoformans var. grubii in which the majority of molecular studies have been performed is therefore atypical for carbon metabolism and key virulence attributes. The fungal pathogen Cryptococcus is a major cause of mortality among the immunocompromised population, primarily in AIDS patients of sub-Saharan Africa. Most research into the particular variety of Cryptococcus responsible for the vast majority of infections, Cryptococcus neoformans var. grubii, is performed using the type strain isolated in 1978 from a Hodgkin's disease patient from North Carolina. We have determined that this particular isolate contains a chromosomal translocation that directly interrupts two genes, which all descendants of this strain from various research laboratories appear to possess. Disruption of these two genes affects multiple virulence factors of Cryptococcus, particularly the ability to grow at human body temperature, which could have wide-ranging implications for molecular genetic studies and virulence assays using this important strain.


Atomistic organization and characterization of tube-like assemblies comprising peptide-polymer conjugates: computer simulation studies.
The structure and stability of the nanotube obtained by assembling peptide-polymer conjugates consisting of two poly(n-butyl acrylate) blocks coupled to the cyclic (D-alt-L)-octapeptide cyc[(L-Gln-D-Ala-L-Lys-D-Ala)2], have been investigated at the molecular level using atomistic molecular dynamics simulations. The effect of the wrapping polymer shells in the tube-like core, which consists of stacked beta-sheet cyclopeptides, has been examined by simulating assemblies of both unsubstituted cyclopeptides, and conjugates in chloroform and N,N-dimethylformamide solutions. Furthermore, the influence of the environment has been investigated by comparing conjugate assemblies in solution with those deposited on mica. In addition, nanotubes stabilized by beta-sheet-like hydrogen bonds between both parallel and antiparallel oriented cyclopeptides have been considered in all cases. The results, which have been analysed in terms of energy contributions, partial radial distribution functions, inter-subunit distances, shape of the cyclopeptide ring, internal van der Waals diameters, and both height and width of the nanostructures deposited on mica, have provided important microscopic insights. For example, analysis of both the energy terms and the structural dynamics obtained for the different assemblies indicate that the mica surface interacts more favourably with the parallel assembly than with the antiparallel ones, whereas the only configuration that is structurally stable in solution is the latter. Furthermore, adsorption onto the solid substrate produces a small deformation of the cylindrical molecular system.


Hepatitis A among men who have sex with men in Barcelona, 1989-2010: insufficient control and need for new approaches.
Men who have sex with men (MSM) are a known group at risk for hepatitis A and outbreaks among this group are frequent. In Barcelona, vaccination for MSM has been recommended since 1994. In 1998 a vaccination campaign among preadolescents was implemented and an immunization program in gay bathhouses began in 2004. to asses the incidence of hepatitis A in adults in Barcelona from 1989 to 2010 and to evaluate the outbreaks among MSM including all genotypes involved. All cases of acute hepatitis A among young adults notified to the Public Health Agency of Barcelona from 1989 to 2010 were included for analyses. We calculated the annual incidence rate and the incidence ratio male-to-female (M:F) as a marker for MSM. Spearman's coefficient was used to evaluate trends. We also evaluated the outbreaks among MSM and compared their characteristics using Chi-squared and ANOVA test. Fragment amplification of the VP1/P2A region was used for genetic analysis. The median annual incidence for the period of study was 4.7/100000 among females and 11.7/100000 among males. The rate of hepatitis A for adult woman decreased over time (Spearman' coefficient = -0.63, p = 0.002), whereas there was no decrease for adult men (Spearman' coefficient = 0.097, p = 0.67). During the study period the M:F ratio increased (Spearman' coefficient = 0.73, p < 0.001).Three large outbreaks among MSM were detected. When comparing outbreaks, there was a decrease in the percentage of bathhouse users (from 47% to 19%, p = 0.0001) and sex workers (from 6.5% to 0%) while the percentage of HIV infected individuals did not change significantly (range: 21%-28%, p = 0.36). The isolated strains were closely related to those circulating in Europe. Annual incidences remain high among MSM without tendency to decrease. More strategies which effectively reach the whole MSM community are needed.


A comparative study of phosphate binders in patients with end stage kidney disease undergoing hemodialysis.
In the present study, a comparative evaluation of the effects of calcium acetate, calcium carbonate, sevelamer hydrochloride and lanthanum carbonate was carried out in 120 patients with end stage kidney disease (ESKD) undergoing hemodialysis. Biochemical parameters, like serum phosphorous, serum calcium and serum alkaline phosphatase level and intact parathyroid hormone level, were measured. A statistically significant reduction in serum phosphorous, serum calcium, calcium × phosphorous and serum alkaline phosphatase level were observed with all phosphate binders during 3 months of treatment. Reduction in serum phosphorous were observed with calcium acetate (1.5 mg/dL), calcium carbonate (1.3 mg/dL), sevelamer hydrochloride (2.1 mg/dL) and lanthanum carbonate (1.79 mg/dL). The reduction of serum alkaline phosphatase was observed more commonly with sevelamer (107.37 IU/L) and lanthanum (104.33 IU/L) treatments than with calcium acetate (93.9 IU/L) and calcium carbonate (86.57 IU/L). There was no statistically significant change in serum calcium observed with sevelamer and lanthanum treatments, while calcium-based phosphate binders caused a significant rise in the serum calcium level. Serum intact parathyroid hormone level was significantly reduced with all phosphate binder treatments. This decline was highest with sevelamer and lowest with calcium carbonate. All treatments were well tolerated and safety profiles were consistent with previous reports in hemodialysis patients. It is concluded that all phosphate binders are safe and effective for the treatment of hyperphosphatemia in patients with ESKD undergoing hemodialysis. However, sevelamer hydrochloride seems to be superior among all with lowering incidence of hypercalcemia.


Pectic polysaccharides from Biophytum petersianum Klotzsch, and their activation of macrophages and dendritic cells.
The Malian medicinal plant Biophytum petersianum Klotzsch (Oxalidaceae) is used as a treatment against various types of illnesses related to the immune system, such as joint pains, inflammations, fever, malaria, and wounds. A pectic polysaccharide obtained from a hot water extract of the aerial parts of B. petersianum has previously been reported to consist of arabinogalactans types I and II (AG-I and AG-II), probably linked to a rhamnogalacturonan backbone. We describe here further structural characteristics of the main polysaccharide fraction (BP1002) and fractions obtained by enzymatic degradations using endo-alpha-d-(1-->4)-polygalacturonase (BP1002-I to IV). The results indicate that in addition to previously reported structures, rhamnogalacturan type II and xylogalacturonan areas appear to be present in the pectic polymer isolated from the plant. Atomic force microscopy confirmed the presence of branched structures, as well as a polydisperse nature. We further tested whether the BP1002 main fraction or the enzymatically degraded products could induce immunomodulating activity through stimulation of subsets of leukocytes. We found that macrophages and dendritic cells were activated by BP1002 fractions, while there was little response of T cells, B cells, and NK cells. The enzymatic treatment of the BP1002 main fraction gave important information on the structure-activity relations. It seems that the presence of rhamnogalacturonan type I is important for the bioactivity, as the bioactivity decreases with the decreased amounts of rhamnose, galactose, and arabinose. The demonstration of bioactivity by the plant extracts might indicate the mechanisms behind the traditional medical use of the plant.


A systematic review of training interventions addressing sexual violence against marginalized at-risk groups of women.
Women from marginalized groups working in occupations such as domestic work are at increased risk for sexual violence. Scarce evidence exists about training interventions targeting such groups. The article aims to identify community and workplace-based training interventions aiming to increase capacity among marginalized at-risk women to deal with sexual violence. A systematic review was applied. Inclusion criteria were English language published between 2003 and 2013; reporting on delivery and/or evaluation; focusing on any form of sexual violence; delivered to professionals, affected or at-risk women; targeting migrant, at-risk women or domestic workers. Data were extracted on the setting, content, evaluation process and target population. Four studies which focused on prevention or responding to sexual violence were included. One study provided sexual violence training to vulnerable female and one provided a HIV prevention intervention to marginalized women. Learning objectives included increasing knowledge around issues of sexual violence and/or gender and human rights, prevention and response strategies. Two studies aimed to train trainers. All studies conducted an outcome evaluation and two a process evaluation. It seems there is a gap on participatory empowerment training for marginalized women. Community train-the-trainer interventions are imperative to protect themselves and deal with the risk of sexual violence.


Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study.
In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.


Review: Challenges in the histopathological classification of ganglioglioma and DNT: microscopic agreement studies and a preliminary genotype-phenotype analysis.
Low-grade epilepsy-associated brain tumours (LEAT) are the second most common cause for drug-resistant, focal epilepsy, that is ganglioglioma (GG) and dysembryoplastic neuroepithelial tumours (DNT). However, molecular pathogenesis, risk factors for malignant progression and their frequent association with drug-resistant focal seizures remain poorly understood. This contrasts recent progress in understanding the molecular-genetic basis and targeted treatment options in diffuse gliomas. The Neuropathology Task Force of the International League Against Epilepsy examined available literature to identify common obstacles in diagnosis and research of LEAT. Analysis of 10 published tumour series from epilepsy surgery pointed to poor inter-rater agreement for the histopathology diagnosis. The Task Force tested this hypothesis using a web-based microscopy agreement study. In a series of 30 LEAT, 25 raters from 18 countries agreed in only 40% of cases. Highest discordance in microscopic diagnosis occurred between GG and DNT variants, when oligodendroglial-like cell patterns prevail, or ganglion cells were difficult to discriminate from pre-existing neurons. Suggesting new terminology or major histopathological criteria did not satisfactorily increase the yield of histopathology agreement in four consecutive trials. To this end, the Task Force applied the WHO 2016 strategy of integrating phenotype analysis with molecular-genetic data obtained from panel sequencing and 450k methylation arrays. This strategy was helpful to distinguish DNT from GG variants in all cases. The Task Force recommends, therefore, to further develop diagnostic panels for the integration of phenotype-genotype analysis in order to reliably classify the spectrum of LEAT, carefully characterize clinically meaningful entities and make better use of published literature.


Enhancing the biofuel upgrade performance for Pd nanoparticles via increasing the support hydrophilicity of metal-organic frameworks.
In this work, the influence of the hydrophilic/hydrophobic nature of metal-organic framework (MOF) materials on the catalytic performance of supported Pd nanoparticles for biofuel upgrade was studied. We show that the introduction of hydrophilic groups on a MOF can greatly enhance the performance of the resultant catalyst. Specifically, Pd nanoparticles supported on MIL-101-SO3Na with superhydrophilicity (Pd/MIL-101-SO3Na) far outperforms pristine MIL-101 and the benchmark catalyst Pd/C in the hydrodeoxygenation reaction of vanillin, a model component of pyrolysis oil derived from the lignin fraction. This is attributed to a favorable mode of adsorption of the highly water soluble reactants on the more hydrophilic support in the vicinity of the catalytically active Pd nanoparticles, thereby promoting their transformation.


Integrating and annotating the interactome using the MiMI plugin for cytoscape.
The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported. MiMI plugin v3.0.1 can be installed from within Cytoscape 2.6 using the Cytoscape plugin manager in 'Network and Attribute I/0' category. The plugin is also preloaded when Cytoscape is launched using Java WebStart at http://mimi.ncibi.org by querying a gene and clicking 'View in MiMI Plugin for Cytoscape' link.


Effect of platelet-derived growth factor-BB on tissue integration of cross-linked and non-cross-linked collagen matrices in a rat ectopic model.
To test whether or not the network structure and the addition of recombinant human platelet-derived growth factor-BB (rhPDGF-BB) to a chemically cross-linked collagen matrix (CCM)- and a non-cross-linked collagen matrix (NCCM)-influenced tissue integration, angiogenesis, and matrix degradation. Four treatment modalities were randomly assigned to four unconnected pouches in the back of 50 rats: (i) CCM-S (soaked in saline), (ii) CCM-P (plus rhPDGF-BB), (iii) NCCM-S (soaked in saline), and (iv) NCCM-P (plus rhPDGF-BB). The animals were sacrificed at 2, 4, 8, 16, and 24 weeks. Descriptive histology and histomorphometric assessments were performed thereby evaluating matrix thickness, the number of vessels (angiogenesis), and connective tissue formation. Means and standard deviations were calculated. Robust linear mixed modeling was used to test the effect of group (NCCM vs CCM), rhPDGF-BB, and time point of sacrifice (2, 4, and 8 weeks). The thickness of NCCM groups revealed stability (range 440-570 μm) over 8 weeks, while the matrices were no longer present at 16 and 24 weeks. CCM matrices demonstrated a maximal thickness at 2 weeks (2689 ± 187 μm for CCM-S and 2693 ± 389 μm for CCM-P), a decrease of roughly 40% at 8 weeks, but were still present at 16 and 24 weeks. Vascularization of NCCM gradually increased over time with a peak (mean 17.0; SD 1.7) for NCCM-S and NCCM-P (22.0 ± 34.8) at 8 weeks. Angiogenesis in CCM was significantly more pronounced at early time points with a peak at 2 weeks (29.3 ± 16.8 for CCM-S and 30.3 ± 18.4 for CCM-P). No statistically significant effect of rhPDGF-BB was observed for any of the evaluated parameters (all P > 0.05). The compact layer (in NCCM) delayed angiogenesis and connective tissue formation, while the spongeous cross-linked matrix of CCM facilitated early vascularization and demonstrated network presence over a longer time span.


Nutrient sensor signaling pathways and cellular stress in fetal growth restriction.
Fetal growth restriction is one of the most common obstetrical complications resulting in significant perinatal morbidity and mortality. The most frequent etiology of human singleton fetal growth restriction is placental insufficiency, which occurs secondary to reduced utero-placental perfusion, abnormal placentation, impaired trophoblast invasion and spiral artery remodeling, resulting in altered nutrient and oxygen transport. Two nutrient-sensing proteins involved in placental development and glucose and amino acid transport are mechanistic target of rapamycin (mTOR) and O-linked N-acetylglucosamine transferase (OGT), which are both regulated by availability of oxygen. Impairment in either of these pathways is associated with fetal growth restriction and accompanied by cellular stress in the forms of hypoxia, oxidative and endoplasmic reticulum (ER) stress, metabolic dysfunction and nutrient starvation in the placenta. Recent evidence has emerged regarding the potential impact of nutrient sensors on fetal stress response, which occurs in a sexual dysmorphic manner, indicating a potential element of genetic gender susceptibility to fetal growth restriction. In this mini review, we focus on the known role of mTOR and OGT in placental development, nutrient regulation and response to cellular stress in human fetal growth restriction with supporting evidence from rodent models.


Improving literature based discovery support by genetic knowledge integration.
We present an interactive literature based biomedical discovery support system (BITOLA). The goal of the system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database Medline. To make the system more suitable for disease candidate gene discovery and to decrease the number of candidate relations, we integrate background knowledge about the chromosomal location of the starting disease as well as the chromosomal location of the candidate genes from resources such as LocusLink, HUGO and OMIM. The BITOLA system can be also used as an alternative way of searching the Medline database. The system is available at http://www.mf.uni-lj.si/bitola/.


Portosystemic pressure gradient during transjugular intrahepatic portosystemic shunt with Viatorr stent graft: what is the critical low threshold to avoid medically uncontrolled low pressure gradient related complications?
Inappropriately decreased portosystemic pressure gradient (PSG) during transjugular intrahepatic portosystemic shunt (TIPS) can cause fatal complications but the critical low threshold of PSG is still not clear. The aim of the present study was to evaluate the critical low threshold of PSG during TIPS. Sixty-six patients with cirrhosis who successfully underwent de novo TIPS with Viatorr stent grafts were studied. Medically uncontrolled low pressure gradient (LPR) complication was defined as when a patient died, or when acute transplantation or a TIPS reduction procedure was performed due to refractory encephalopathy or the deterioration of hepatic function within 3 months after the procedure. For the determination of the risk group for medically uncontrolled LPR complications, the Child-Pugh score and the model of end-stage liver disease (MELD) score showing a 100% negative predictive value was decided on as a threshold for each score. The risk group was defined when either of both scores was higher than its threshold. For the determination of a critical low post-TIPS PSG, a value of post-TIPS PSG showing the highest discrimination power on the receiver operating characteristic (ROC) curve in the risk group was decided on as a critical low threshold of PSG. The medically uncontrolled LPR complication rates of the patients with the determined threshold or lower were evaluated for the risk group. Medically uncontrolled LPR complications developed in nine patients (13.6%). Five patients died and four patients had TIPS reduction procedures. Patients with more than 10 on the Child-Pugh score or more than 14 on the MELD score were determined to be the risk group and 34 patients were included. The critical lower threshold of the post-TIPS PSG showing the highest discrimination power on the ROC curve was 5 mmHg (sensitivity 100%, specificity 72%), and the medically uncontrolled LPR complication rates of the patients with 5 mmHg or lower on the post-TIPS PSG were 56.3% (9/16) in the risk group. The critical threshold of the post-TIPS PSG to avoid the medically uncontrolled LPR complications of TIPS was >5 mmHg. The PSG should not be reduced below this level in the risk group.


Therapeutic limitations of argon laser trabeculoplasty.
Sixty-one patients (82 eyes) were studied after argon laser trabeculoplasty (ALT) to determine the lasting efficacy of such treatment. This investigation, now in its fourth year, was prospective, and the information derived was analysed with the aid of a computer. Success was defined as intraocular pressure (IOP) below baseline (22 mmHg). The mean follow-up time was 24.5 months, when the success rate was 74% compared with 75% at three months. Success declined to 45% at 42 months. No significant difference was noted when (a) first lasered eyes of all patients and those fellow eyes treated were analysed separately, (b) when right and left eyes were analysed separately, nor (c) when patients were divided into two treatment groups, (I) 100 burns at 1 W, and (II) 65 burns at 850 mW. Eight of 11 eyes showed progressive postlaser field loss despite below-baseline intraocular pressures. ALT is an alternative to carbonic anhydrase inhibitor therapy, with a success rate of 66.7% at two years. However, repeat ALT was successful in only 25% of patients seven months after treatment.


Light pollution: the possible consequences of excessive illumination on retina.
Light is the visible part of the electromagnetic radiation within a range of 380-780 nm; (400-700 on primates retina). In vertebrates, the retina is adapted to capturing light photons and transmitting this information to other structures in the central nervous system. In mammals, light acts directly on the retina to fulfill two important roles: (1) the visual function through rod and cone photoreceptor cells and (2) non-image forming tasks, such as the synchronization of circadian rhythms to a 24 h solar cycle, pineal melatonin suppression and pupil light reflexes. However, the excess of illumination may cause retinal degeneration or accelerate genetic retinal diseases. In the last century human society has increased its exposure to artificial illumination, producing changes in the Light/Dark cycle, as well as in light wavelengths and intensities. Although, the consequences of unnatural illumination or light pollution have been underestimated by modern society in its way of life, light pollution may have a strong impact on people's health. The effects of artificial light sources could have direct consequences on retinal health. Constant exposure to different wavelengths and intensities of light promoted by light pollution may produce retinal degeneration as a consequence of photoreceptor or retinal pigment epithelium cells death. In this review we summarize the different mechanisms of retinal damage related to the light exposure, which generates light pollution.