Isotope Shift Measurements of Stable and Short-Lived Lithium Isotopes for Nuclear Charge Radii Determination

Changes in the mean-square nuclear charge radii along the lithium isotopic chain were determined using a combination of precise isotope shift measurements and theoretical atomic structure calculations. Nuclear charge radii of light elements are of high interest due to the appearance of the nuclear halo phenomenon in this region of the nuclear chart. During the past years we have developed a new laser spectroscopic approach to determine the charge radii of lithium isotopes which combines high sensitivity, speed, and accuracy to measure the extremely small field shift of an 8 ms lifetime isotope with production rates on the order of only 10,000 atoms/s. The method was applied to all bound isotopes of lithium including the two-neutron halo isotope Li-11 at the on-line isotope separators at GSI, Darmstadt, Germany and at TRIUMF, Vancouver, Canada. We describe the laser spectroscopic method in detail, present updated and improved values from theory and experiment, and discuss the results.Comment: 34 pages, 24 figures, 14 table

Nuclear Charge Radius of Li-9, Li-11: Halo Neutron: the influence of Halo Neutrons

The nuclear charge radius of Li-11 has been determined for the first time by high precision laser spectroscopy. On-line measurements at TRIUMF-ISAC yielded a Li-7 - Li-11 isotope shift (IS) of 25101.23(13) MHz for the Doppler-free 2s - 3s transition. IS precision for all other bound Li isotopes was also improved. Differences from calculated mass-based IS yield values for change in charge radius along the isotope chain. The charge radius decreases monotonically from Li-6 to Li-9, and then increases from 2.217(35) fm to 2.467(37) fm for Li-11. This is compared to various models, and it is found that a combination of halo neutron correlation and intrinsic core excitation best reproduces the experimental results.Comment: 5 pages, 2 figure

Perioperative strategy in colonic surgery; LAparoscopy and/or FAst track multimodal management versus standard care (LAFA trial)

BACKGROUND: Recent developments in large bowel surgery are the introduction of laparoscopic surgery and the implementation of multimodal fast track recovery programs. Both focus on a faster recovery and shorter hospital stay. The randomized controlled multicenter LAFA-trial (LAparoscopy and/or FAst track multimodal management versus standard care) was conceived to determine whether laparoscopic surgery, fast track perioperative care or a combination of both is to be preferred over open surgery with standard care in patients having segmental colectomy for malignant disease. METHODS/DESIGN: The LAFA-trial is a double blinded, multicenter trial with a 2 × 2 balanced factorial design. Patients eligible for segmental colectomy for malignant colorectal disease i.e. right and left colectomy and anterior resection will be randomized to either open or laparoscopic colectomy, and to either standard care or the fast track program. This factorial design produces four treatment groups; open colectomy with standard care (a), open colectomy with fast track program (b), laparoscopic colectomy with standard care (c), and laparoscopic surgery with fast track program (d). Primary outcome parameter is postoperative hospital length of stay including readmission within 30 days. Secondary outcome parameters are quality of life two and four weeks after surgery, overall hospital costs, morbidity, patient satisfaction and readmission rate. Based on a mean postoperative hospital stay of 9 +/- 2.5 days a group size of 400 patients (100 each arm) can reliably detect a minimum difference of 1 day between the four arms (alfa = 0.95, beta = 0.8). With 100 patients in each arm a difference of 10% in subscales of the Short Form 36 (SF-36) questionnaire and social functioning can be detected. DISCUSSION: The LAFA-trial is a randomized controlled multicenter trial that will provide evidence on the merits of fast track perioperative care and laparoscopic colorectal surgery in patients having segmental colectomy for malignant disease

Accounting For Alignment Uncertainty in Phylogenomics

Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy

Developmental Hippocampal Neuroplasticity in a Model of Nicotine Replacement Therapy during Pregnancy and Breastfeeding

The influence of developmental nicotine exposure on the brain represents an important health topic in light of the popularity of nicotine replacement therapy (NRT) as a smoking cessation method during pregnancy.In this study, we used a model of NRT during pregnancy and breastfeeding to explore the consequences of chronic developmental nicotine exposure on cerebral neuroplasticity in the offspring. We focused on two dynamic lifelong phenomena in the dentate gyrus (DG) of the hippocampus that are highly sensitive to the environment: granule cell neurogenesis and long-term potentiation (LTP).Pregnant rats were implanted with osmotic mini-pumps delivering either nicotine or saline solutions. Plasma nicotine and metabolite levels were measured in dams and offspring. Corticosterone levels, DG neurogenesis (cell proliferation, survival and differentiation) and glutamatergic electrophysiological activity were measured in pups.Juvenile (P15) and adolescent (P41) offspring exposed to nicotine throughout prenatal and postnatal development displayed no significant alteration in DG neurogenesis compared to control offspring. However, NRT-like nicotine exposure significantly increased LTP in the DG of juvenile offspring as measured in vitro from hippocampal slices, suggesting that the mechanisms underlying nicotine-induced LTP enhancement previously described in adult rats are already functional in pups.These results indicate that synaptic plasticity is disrupted in offspring breastfed by dams passively exposed to nicotine in an NRT-like fashion

Analysis of Common and Specific Mechanisms of Liver Function Affected by Nitrotoluene Compounds

BACKGROUND: Nitrotoluenes are widely used chemical manufacturing and munitions applications. This group of chemicals has been shown to cause a range of effects from anemia and hypercholesterolemia to testicular atrophy. We have examined the molecular and functional effects of five different, but structurally related, nitrotoluenes on using an integrative systems biology approach to gain insight into common and disparate mechanisms underlying effects caused by these chemicals. METHODOLOGY/PRINCIPAL FINDINGS: Sprague-Dawley female rats were exposed via gavage to one of five concentrations of one of five nitrotoluenes [2,4,6-trinitrotoluene (TNT), 2-amino-4,6-dinitrotoluene (2ADNT) 4-amino-2,6-dinitrotoulene (4ADNT), 2,4-dinitrotoluene (2,4DNT) and 2,6-dinitrotoluene (2,6DNT)] with necropsy and tissue collection at 24 or 48 h. Gene expression profile results correlated well with clinical data and liver histopathology that lead to the concept that hematotoxicity was followed by hepatotoxicity. Overall, 2,4DNT, 2,6DNT and TNT had stronger effects than 2ADNT and 4ADNT. Common functional terms, gene expression patterns, pathways and networks were regulated across all nitrotoluenes. These pathways included NRF2-mediated oxidative stress response, aryl hydrocarbon receptor signaling, LPS/IL-1 mediated inhibition of RXR function, xenobiotic metabolism signaling and metabolism of xenobiotics by cytochrome P450. One biological process common to all compounds, lipid metabolism, was found to be impacted both at the transcriptional and lipid production level. CONCLUSIONS/SIGNIFICANCE: A systems biology strategy was used to identify biochemical pathways affected by five nitroaromatic compounds and to integrate data that tie biochemical alterations to pathological changes. An integrative graphical network model was constructed by combining genomic, gene pathway, lipidomic, and physiological endpoint results to better understand mechanisms of liver toxicity and physiological endpoints affected by these compounds

Achieving a cure for HIV infection: do we have reasons to be optimistic?

The introduction of highly active antiretroviral therapy (HAART) in 1996 has transformed a lethal disease to a chronic pathology with a dramatic decrease in mortality and morbidity of AIDS-related symptoms in infected patients. However, HAART has not allowed the cure of HIV infection, the main obstacle to HIV eradication being the existence of quiescent reservoirs. Several other problems have been encountered with HAART (such as side effects, adherence to medication, emergence of resistance and cost of treatment), and these motivate the search for new ways to treat these patients. Recent advances hold promise for the ultimate cure of HIV infection, which is the topic of this review. Besides these new strategies aiming to eliminate the virus, efforts must be made to improve current HAART. We believe that the cure of HIV infection will not be attained in the short term and that a strategy based on purging the reservoirs has to be associated with an aggressive HAART strategy

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs

Background A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the alignment used, and neglecting the uncertainty in the alignment can lead to significant bias in the resulting inference. In recent years, a number of approaches have been developed for probabilistic sampling of alignments, rather than simply generating a single optimum. However, this type of probabilistic information is currently not widely used in the context of downstream inference, since most existing algorithms are set up to make use of a single alignment. Results In this work we present a framework for representing a set of sampled alignments as a directed acyclic graph (DAG) whose nodes are alignment columns; each path through this DAG then represents a valid alignment. Since the probabilities of individual columns can be estimated from empirical frequencies, this approach enables sample-based estimation of posterior alignment probabilities. Moreover, due to conditional independencies between columns, the graph structure encodes a much larger set of alignments than the original set of sampled MSAs, such that the effective sample size is greatly increased. Conclusions The alignment DAG provides a natural way to represent a distribution in the space of MSAs, and allows for existing algorithms to be efficiently scaled up to operate on large sets of alignments. As an example, we show how this can be used to compute marginal probabilities for tree topologies, averaging over a very large number of MSAs. This framework can also be used to generate a statistically meaningful summary alignment; example applications show that this summary alignment is consistently more accurate than the majority of the alignment samples, leading to improvements in downstream tree inference. Implementations of the methods described in this article are available at http://statalign.github.io/WeaveAlign webcite