Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds.
Birds are the most diverse living tetrapod group and are a model of large-scale adaptive radiation. Neontological studies suggest a radiation within the avian crown group, long after the origin of flight. However, deep time patterns of bird evolution remain obscure because only limited fossil data have been considered. We analyse cladogenesis and limb evolution on the entire tree of Mesozoic theropods, documenting the dinosaur-bird transition and immediate origins of powered flight. Mesozoic birds inherited constraints on forelimb evolution from non-flying ancestors, and species diversification rates did not accelerate in the earliest flying taxa. However, Early Cretaceous short-tailed birds exhibit both phenotypic release of the hindlimb and increased diversification rates, unparalleled in magnitude at any other time in the first 155 Myr of theropod evolution. Thus, a Cretaceous adaptive radiation of stem-group birds was enabled by restructuring of the terrestrial locomotor module, which represents a key innovation. Our results suggest two phases of radiation in Avialae: with the Cretaceous diversification overwritten by extinctions of stem-group birds at the Cretaceous-Palaeogene boundary, and subsequent diversification of the crown group. Our findings illustrate the importance of fossil data for understanding the macroevolutionary processes generating modern biodiversity.


Electrical stimulation promotes nerve cell differentiation on polypyrrole/poly (2-methoxy-5 aniline sulfonic acid) composites.
The purpose of this work was to investigate for the first time the potential biomedical applications of novel polypyrrole (PPy) composites incorporating a large polyelectrolyte dopant, poly (2-methoxy-5 aniline sulfonic acid) (PMAS). The physical and electrochemical properties were characterized. The PPy/PMAS composites were found to be smooth and hydrophilic and have low electrical impedance. We demonstrate that PPy/PMAS supports nerve cell (PC12) differentiation, and that clinically relevant 250 Hz biphasic current pulses delivered via PPy/PMAS films significantly promote nerve cell differentiation in the presence of nerve growth factor (NGF). The capacity of PPy/PMAS composites to support and enhance nerve cell differentiation via electrical stimulation renders them valuable for medical implants for neurological applications.


A microfluidic device for continuous sensing of systemic acute toxicants in drinking water.
A bioluminescent-cell-based microfluidic device for sensing toxicants in drinking water was designed and fabricated. The system employed Vibrio fischeri cells as broad-spectrum sensors to monitor potential systemic cell toxicants in water, such as heavy metal ions and phenol. Specifically, the chip was designed for continuous detection. The chip design included two counter-flow micromixers, a T-junction droplet generator and six spiral microchannels. The cell suspension and water sample were introduced into the micromixers and dispersed into droplets in the air flow. This guaranteed sufficient oxygen supply for the cell sensors. Copper (Cu2+), zinc (Zn2+), potassium dichromate and 3,5-dichlorophenol were selected as typical toxicants to validate the sensing system. Preliminary tests verified that the system was an effective screening tool for acute toxicants although it could not recognize or quantify specific toxicants. A distinct non-linear relationship was observed between the zinc ion concentration and the Relative Luminescence Units (RLU) obtained during testing. Thus, the concentration of simple toxic chemicals in water can be roughly estimated by this system. The proposed device shows great promise for an early warning system for water safety.


Involvement of the receptor-associated prorenin system in the pathogenesis of human conjunctival lymphoma.
Extranodal marginal zone B-cell lymphoma (EMZL) is the most common subtype of conjunctival lymphoma, though its molecular mechanisms of pathogenesis are largely unknown. We attempted to explore the association of the renin-angiotensin system (RAS) and (pro)renin receptor ([P]RR) in the pathogenesis of conjunctival lymphoma. Surgically removed conjunctiva EMZL samples were used for gene expression, and immunohistochemical and immunofluorescence analyses of (P)RR and RAS components. Human B-lymphoblast IM-9 cells were treated with prorenin or angiotensin II (Ang II), and gene expression levels were analyzed using real-time quantitative PCR (qPCR). In addition, immunofluorescence analysis of EMZL samples was used to evaluate the in vivo expression of those components. Gene expression and immunohistochemical analyses revealed the expression of RAS components, including (P)RR and angiotensin II type 1 receptor (AT1R), in EMZL tissues. Double-labeling analyses demonstrated that (P)RR and AT1R were detected in cells positive for CD20, a marker for B-cells, where they colocalized with prorenin and angiotensinogen, respectively. Prorenin stimulation of human B-lymphoblast IM-9 cells increased mRNA expression levels of fibroblast growth factor 2 (FGF2), while angiotensin II treatment upregulated the expression levels of basigin (BSG), matrix metallopeptidase (MMP)2, 9, and 14, which were abolished by (P)RR and AT1R blockades, respectively. Immunofluorescence analyses of clinical samples showed colocalizations of (P)RR and AT1R with the products of these upregulated genes. The present study suggests that activation of (P)RR and AT1R is associated with the pathogenesis of conjunctival EMZL by stimulating the production of FGF2 and MMPs.


Risk Factors for High Mortality on the Liver Transplant Waiting List in Times of Organ Shortage: A Single-Center Analysis.
BACKGROUND Germany has the highest rate of patients dying or becoming unfit for transplant while waitlisted within the Eurotransplant region. Therefore, the aim of the current study was to analyze mortality as well as risk factors for mortality of candidates listed for liver transplantation at our center. MATERIAL AND METHODS Between 01/2011 and 12/2013, 481 adult patients were listed for primary liver transplantation (LT) at a single German center. Clinical and laboratory parameters were prospectively collected and retrospectively analyzed by univariable and multivariable logistic regression and Cox proportional hazards. RESULTS The mean model for end-stage liver disease (MELD) score of all liver transplant waitlist registrants (52.4 years, 60.1% male) was 16.9 (±10.2) at time of listing, with 10% of the listed patients having a MELD score of >32. After waitlisting, 133 (27.7%) candidates died within the follow-up period. Three-month-survival after listing for transplantation was 89% for patients ultimately receiving LT vs. 71.2% that did not receive LT (p<0.001). Multivariable analysis identified clinical parameters such as ICU treatment, preceding abdominal surgery, variceal bleeding, and ascites, as well as hydropic decompensation, as independent risk factors for waitlist mortality. CONCLUSIONS Consideration of independent risk factors of mortality within the MELD-based allocation system potentially improves assessment of individual urgency and might improve utilization of available organs.


AglQ is a novel component of the Haloferax volcanii N-glycosylation pathway.
N-glycosylation is a post-translational modification performed by members of all three domains of life. Studies on the halophile Haloferax volcanii have offered insight into the archaeal version of this universal protein-processing event. In the present study, AglQ was identified as a novel component of the pathway responsible for the assembly and addition of a pentasaccharide to select Asn residues of Hfx. volcanii glycoproteins, such as the S-layer glycoprotein. In cells deleted of aglQ, both dolichol phosphate, the lipid carrier used in Hfx. volcanii N-glycosylation, and modified S-layer glycoprotein Asn residues only presented the first three pentasaccharide subunits, pointing to a role for AglQ in either preparing the third sugar for attachment of the fourth pentasaccharide subunit or processing the fourth sugar prior to its addition to the lipid-linked trisaccharide. To better define the precise role of AglQ, shown to be a soluble protein, bioinformatics tools were recruited to identify sequence or structural homologs of known function. Site-directed mutagenesis experiments guided by these predictions identified residues important for AglQ function. The results obtained point to AglQ acting as an isomerase in Hfx. volcanii N-glycosylation.


Muscular thin films for building actuators and powering devices.
We demonstrate the assembly of biohybrid materials from engineered tissues and synthetic polymer thin films. The constructs were built by culturing neonatal rat ventricular cardiomyocytes on polydimethylsiloxane thin films micropatterned with extracellular matrix proteins to promote spatially ordered, two-dimensional myogenesis. The constructs, termed muscular thin films, adopted functional, three-dimensional conformations when released from a thermally sensitive polymer substrate and were designed to perform biomimetic tasks by varying tissue architecture, thin-film shape, and electrical-pacing protocol. These centimeter-scale constructs perform functions as diverse as gripping, pumping, walking, and swimming with fine spatial and temporal control and generating specific forces as high as 4 millinewtons per square millimeter.


Prospective five-year study of ultrasound-guided foam sclerotherapy in the treatment of great saphenous vein reflux.
The purpose of this study was to determine the long-term efficacy, safety and rate of recurrence for varicose veins associated with great saphenous vein (GSV) reflux treated with ultrasound-guided foam sclerotherapy (UGFS). A five-year prospective study was performed, recording the effect on the GSV and saphenofemoral junction (SFJ) diameters, and reflux in the superficial venous system over time. UGFS was the sole treatment modality used in all cases, and repeat UGFS was performed where indicated following serial annual ultrasound. No serious adverse outcomes were observed - specifically no thromboembolism, arterial injection, anaphylaxis or nerve damage. There was a 4% clinical recurrence rate after five years, with 100% patient acceptance of success. Serial annual duplex ultrasound demonstrated a significant reduction in GSV and SFJ diameters, maintained over time. There was ultrasound recurrence in 27% at 12 months, and in 64% at five years, including any incompetent trunkal or tributary reflux even 1 mm in diameter being recorded. Thirty percent had pure ultrasound recurrence, 17% new vessel reflux and 17% combined new and recurrent vessels on ultrasound. Of all, 16.5% required repeat UGFS treatment between 12 and 24 months, but less than 10% in subsequent years. The safety and clinical efficacy of UGFS for all clinical, aetiological, anatomical and pathological elements classes of GSV reflux was excellent. The popularity of this outpatient technique with patients reflects ease of treatment, lower cost, lack of downtime and elimination of venous signs and symptoms. Patients accept that UGFS can be repeated readily if required for recurrence in this common chronic condition. The subclinical ultrasound evidence of recanalization or new vein incompetence needs to be considered in this light.


Assessment of safety and immunogenicity of two different lots of diphtheria, tetanus, pertussis, hepatitis B and Haemophilus influenzae type b vaccine manufactured using small and large scale manufacturing process.
Hib vaccine can be easily incorporated in EPI vaccination schedule as the immunization schedule of Hib is similar to that of DTP vaccine. To meet the global demand of Hib vaccine, SIIL scaled up the Hib conjugate manufacturing process. This study was conducted in Indian infants to assess and compare the immunogenicity and safety of DTwP-HB+Hib (Pentavac(®)) vaccine of SIIL manufactured at large scale with the 'same vaccine' manufactured at a smaller scale. 720 infants aged 6-8 weeks were randomized (2:1 ratio) to receive 0.5 ml of Pentavac(®) vaccine from two different lots one produced at scaled up process and the other at a small scale process. Serum samples obtained before and at one month after the 3rd dose of vaccine from both the groups were tested for IgG antibody response by ELISA and compared to assess non-inferiority. Neither immunological interference nor increased reactogenicity was observed in either of the vaccine groups. All infants developed protective antibody titres to diphtheria, tetanus and Hib disease. For hepatitis B antigen, one child from each group remained sero-negative. The response to pertussis was 88% in large scale group vis-à-vis 87% in small scale group. Non-inferiority was concluded for all five components of the vaccine. No serious adverse event was reported in the study. The scale up vaccine achieved comparable response in terms of the safety and immunogenicity to small scale vaccine and therefore can be easily incorporated in the routine childhood vaccination programme.


MRI-guided biopsies and minimally invasive therapy for prostate cancer.
Recent advances in multiparametric magnetic resonance imaging (mp-MRI) have led to a paradigm shift in the diagnosis and management of prostate cancer (PCa). Its sensitivity in detecting clinically significant cancer and the ability to localize the tumor within the prostate gland has opened up discussion on targeted diagnosis and therapy in PCa. Use of mp-MRI in conjunction with prostate-specific antigen followed by targeted biopsy allows for a better diagnostic pathway than transrectal ultrasound (TRUS) biopsy and improves the diagnosis of PCa. Improved detection of PCa by mp-MRI has also opened up opportunities for focal therapy within the organ while reducing the incidence of side-effects associated with the radical treatment methods for PCa. This review discusses the evidence and techniques for in-bore MRI-guided prostate biopsy and provides an update on the status of MRI-guided targeted focal therapy in PCa.


Design, synthesis, radiolabeling and in vivo evaluation of potential positron emission tomography (PET) radioligands for brain imaging of the 5-HT₇ receptor.
Here we describe the design, synthesis, and pharmacological evaluation of a set of compounds structurally related to the high affinity serotonin 5-HT7 receptor agonist N-(4-cyanophenylmethyl)-4-(2-diphenyl)-1-piperazinehexanamide (6, LP-211). Specific structural modifications were performed in order to maintain affinity for the target receptor and to improve the selectivity over 5-HT1A and adrenergic α1 receptors. The synthesized compounds have chemical features that could enable labeling with a positron emitter radioisotope (carbon-11 or fluorine-18) and lipophilicity within the range considered optimal for brain penetration and low non-specific binding. 4-[2-(4-Methoxyphenyl)phenyl]-N-(pyridin-4-ylmethyl)piperazinehexanamide (23a) and N-pyridin-4-ylmethyl-3-[4-[2-(4-methoxyphenyl)phenyl]piperazin-1-yl]ethoxy]propanamide (26a) were radiolabeled on the methoxy group with carbon-11. Positron emission tomography (PET) analysis revealed that [(11)C]-23a and [(11)C]-26a were P-glycoprotein (P-gp) substrates and rapidly metabolized, resulting in poor brain uptake. These features were not predicted by in vitro tests.


The role of the intracarotid amobarbital procedure in evaluation of patients for epilepsy surgery.
To examine the role of the intracarotid amobarbital procedure (IAP) in the presurgical evaluation of patients with medically refractory localization-related epilepsy. We retrospectively studied 111 patients who underwent cortical resective surgery at our center between 1991 and 1996. In patients with mesial temporal lobe epilepsy (mTLE), a presurgical determination of the epileptogenic zone was compared with localization based on IAP memory asymmetry scores, and with ultimate localization after resective surgery. In patients with neocortical or mesial frontal epilepsy, the IAP was evaluated for evidence of unilateral or bilateral poor memory performance. Of 68 patients with mTLE localized by noninvasive tests, 60 had concordant lateralized memory deficits on IAP. Eight patients had lateralized memory deficits on IAP that were discordant with noninvasive tests and with localization as determined by surgical outcome. All 11 mTLE patients requiring invasive EEG monitoring were correctly lateralized by IAP, including one patient in whom the noninvasive evaluation otherwise provided false lateralization. Of 32 patients with neocortical or mesial frontal lobe epilepsy, 21 displayed memory deficits on IAP. Of 10 patients with bilateral deficits, five had mesial frontal lobe epilepsy. In 13 patients with lateralized memory deficits, seven underwent electrode implantation in the mesial temporal lobe, and four ultimately underwent resection of an epileptogenic mesial temporal lobe in addition to a neocortical resection. In patients with mTLE, lateralized memory deficits on IAP usually confirm localization provided by noninvasive tests. However, in mTLE not well lateralized by the noninvasive evaluation, and in neocortical or mesial frontal epilepsy, the IAP may provide information regarding localization that ultimately alters surgical management.


Neuroimage signature from salient keypoints is highly specific to individuals and shared by close relatives.
Neuroimaging studies typically adopt a common feature space for all data, which may obscure aspects of neuroanatomy only observable in subsets of a population, e.g. cortical folding patterns unique to individuals or shared by close relatives. Here, we propose to model individual variability using a distinctive keypoint signature: a set of unique, localized patterns, detected automatically in each image by a generic saliency operator. The similarity of an image pair is then quantified by the proportion of keypoints they share using a novel Jaccard-like measure of set overlap. Experiments demonstrate the keypoint method to be highly efficient and accurate, using a set of 7536 T1-weighted MRIs pooled from four public neuroimaging repositories, including twins, non-twin siblings, and 3334 unique subjects. All same-subject image pairs are identified by a similarity threshold despite confounds including aging and neurodegenerative disease progression. Outliers reveal previously unknown data labeling inconsistencies, demonstrating the usefulness of the keypoint signature as a computational tool for curating large neuroimage datasets.


An HR-induced tobacco peroxidase gene is responsive to spermine, but not to salicylate, methyl jasmonate, and ethephon.
In Tobacco mosaic virus (TMV)-infected tobacco plants carrying the N resistance gene, a hypersensitive reaction or response (HR) occurs to enclose the virus in the infected tissue. Although a contribution of peroxidases to the resistance has been proposed, no evidence has been presented that tobacco peroxidase genes respond to HR. Here, we describe the HR-induced expression of a tobacco peroxidase gene (tpoxC1) whose induction kinetics were slightly different from those of acidic and basic tobacco pathogenesis-related (PR) protein genes. Interestingly, tpoxC1 was insensitive to the inducers of PR genes such as salicylic acid, methyl jasmonate, and ethephon. Spermine activated tpoxC1 gene expression at a low level and both acidic and basic PR gene expression at a considerably higher level. These results indicate that the induced expression of tpoxC1 is regulated differently from that of classical tobacco PR genes in the N gene-mediated self-defense system in tobacco plants.


From microbes to numbers: extracting meaningful quantities from images.
Light microscopy offers a unique window into the life and works of microbes and their interactions with hosts. Mere visualization of images, however, does not provide the quantitative information needed to reliably and accurately characterize phenotypes or test computational models of cellular processes, and is unfeasible in high-throughput screens. Algorithms that automatically extract biologically meaningful quantitative data from images are therefore an increasingly essential complement to the microscopes themselves. This paper reviews some of the computational methods developed to detect, segment and track cells, molecules or viruses, with an emphasis on their underlying assumptions, limitations, and the importance of validation.


Comparative effectiveness of empiric antibiotics for community-acquired pneumonia.
Narrow-spectrum antibiotics are recommended as the first-line agent for children hospitalized with community-acquired pneumonia (CAP). There is little scientific evidence to support that this consensus-based recommendation is as effective as the more commonly used broad-spectrum antibiotics. The objective was to compare the effectiveness of empiric treatment with narrow-spectrum therapy versus broad-spectrum therapy for children hospitalized with uncomplicated CAP. This multicenter retrospective cohort study using medical records included children aged 2 months to 18 years at 4 children's hospitals in 2010 with a discharge diagnosis of CAP. Patients receiving either narrow-spectrum or broad-spectrum therapy in the first 2 days of hospitalization were eligible. Patients were matched by using propensity scores that determined each patient's likelihood of receiving empiric narrow or broad coverage. A multivariate logistic regression analysis evaluated the relationship between antibiotic and hospital length of stay (LOS), 7-day readmission, standardized daily costs, duration of fever, and duration of supplemental oxygen. Among 492 patients, 52% were empirically treated with a narrow-spectrum agent and 48% with a broad-spectrum agent. In the adjusted analysis, the narrow-spectrum group had a 10-hour shorter LOS (P = .04). There was no significant difference in duration of oxygen, duration of fever, or readmission. When modeled for LOS, there was no difference in average daily standardized cost (P = .62) or average daily standardized pharmacy cost (P = .26). Compared with broad-spectrum agents, narrow-spectrum antibiotic coverage is associated with similar outcomes. Our findings support national consensus recommendations for the use of narrow-spectrum antibiotics in children hospitalized with CAP.


Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification.
Biologists increasingly use co-culture systems in which two or more cell types are grown in cell culture together in order to better model cells' native microenvironments. Co-cultures are often required for cell survival or proliferation, or to maintain physiological functioning in vitro. Having two cell types co-exist in culture, however, poses several challenges, including difficulties distinguishing the two populations during analysis using automated image analysis algorithms. We previously analyzed co-cultured primary human hepatocytes and mouse fibroblasts in a high-throughput image-based chemical screen, using a combination of segmentation, measurement, and subsequent machine learning to score each cell as hepatocyte or fibroblast. While this approach was successful in counting hepatocytes for primary screening, segmentation of the fibroblast nuclei was less accurate. Here, we present an improved approach that more accurately identifies both cell types. Pixel-based machine learning (using the software ilastik) is used to seed segmentation of each cell type individually (using the software CellProfiler). This streamlined and accurate workflow can be carried out using freely available and open source software.


Diagnostic accuracy of the MMSE in detecting probable and possible Alzheimer's disease in ethnically diverse highly educated individuals: an analysis of the NACC database.
To validate and extend the findings of a raised cut score of O'Bryant and colleagues (O'Bryant SE, Humphreys JD, Smith GE, et al. Detecting dementia with the mini-mental state examination in highly educated individuals. Arch Neurol. 2008;65(7):963-967.) for the Mini-Mental State Examination in detecting cognitive dysfunction in a bilingual sample of highly educated ethnically diverse individuals. Archival data were reviewed from participants enrolled in the National Alzheimer's Coordinating Center minimum data set. Data on 7,093 individuals with 16 or more years of education were analyzed, including 2,337 cases with probable and possible Alzheimer's disease, 1,418 mild cognitive impairment patients, and 3,088 nondemented controls. Ethnic composition was characterized as follows: 6,296 Caucasians, 581 African Americans, 4 American Indians or Alaska natives, 2 native Hawaiians or Pacific Islanders, 149 Asians, 43 "Other," and 18 of unknown origin. Diagnostic accuracy estimates (sensitivity, specificity, and likelihood ratio) of Mini-Mental State Examination cut scores in detecting probable and possible Alzheimer's disease were examined. A standard Mini-Mental State Examination cut score of 24 (≤23) yielded a sensitivity of 0.58 and a specificity of 0.98 in detecting probable and possible Alzheimer's disease across ethnicities. A cut score of 27 (≤26) resulted in an improved balance of sensitivity and specificity (0.79 and 0.90, respectively). In the cognitively impaired group (mild cognitive impairment and probable and possible Alzheimer's disease), the standard cut score yielded a sensitivity of 0.38 and a specificity of 1.00 while raising the cut score to 27 resulted in an improved balance of 0.59 and 0.96 of sensitivity and specificity, respectively. These findings cross-validate our previous work and extend them to an ethnically diverse cohort. A higher cut score is needed to maximize diagnostic accuracy of the Mini-Mental State Examination in individuals with college degrees.


Cell-free circulating tumor DNA in colorectal cancer: a proof of concept with simplified methodology.
Cell-free DNA analysis (cfDNA) holds promise for residual disease or tumor burden quantification in colorectal cancer, with reduced costs and diagnostic equipment compared to gold standard-specific tumor DNA (ctDNA) analysis. This prospective case-control study included 46 colorectal cancer patients and healthy controls to perform cfDNA quantification by fluorometry using Quantus Fluorometer (Promega, Madison, WI) and using cell-free DNA ScreenTape assay (Agilent) and 4200 TapeStation instrument (Agilent Technologies, Inc., Santa Clara, CA, USA). cfDNA quantification results were correlated with stage, clinical and histopathological features. 33 localized (8 stage I, 12 stage II, and 13 stage III) and 13 advanced colorectal cancer patients were included. No differences in cfDNA quantification by fluorometry were demonstrated depending on stage or histopathological features in localized disease patients. Differences in cfDNA quantification by fluorometry could be demonstrated in patients with advanced disease depending on the presence of liver metastases and synchronous or metachronous metastatic disease. Differences in cfDNA quantification by fluorometry could be demonstrated between advanced colorectal cancer patients and both localized disease patients and healthy controls. Secondary cfDNA analysis by electrophoresis, although showing more specificity to measure ctDNA in cfDNA values, could not improve the capacity to detect differences between analyzed a groups beyond previously achieved with fluorometry. This exploratory analysis of cfDNA based on fluorometry and electrophoresis methods showed promising results discriminating colorectal cancer and non-cancer patients, as well as different colorectal cancer stages and disease profiles. Further studies are needed to increase our knowledge and to help to overcome barriers to broader implementation and applications.


Interoceptive conditioning with nicotine using extinction and re-extinction to assess stimulus similarity with bupropion.
Bupropion is an atypical antidepressant that increases long-term quit rates of tobacco smokers. A better understanding of the relation between nicotine and this first-line medication may provide insight into improving treatment. For all experiments, rats first had nicotine (0.4 mg base/kg) and saline session intermixed; intermittent access to sucrose only occurred on nicotine session. Nicotine in this protocol comes to differentially control "anticipatory" dipper entries. To more closely examine the overlap in the interoceptive stimulus effects of nicotine and bupropion, we assessed whether subsequent prolonged and repeated non-reinforced (extinction) sessions with the bupropion stimulus could weaken responding to nicotine (i.e., transfer of extinction). We also examined whether retraining the discrimination after initial extinction and then conducting extinction again (i.e., re-extinction) with bupropion would affect responding. We found that bupropion (20 and 30 mg/kg) fully substituted for the nicotine stimulus in repeated 20-min extinction sessions. The extent of substitution in extinction did not necessarily predict performance in the transfer test (e.g., nicotine responding unchanged after extinction with 20 mg/kg bupropion). Generalization of extinction back to nicotine was not seen with 20 mg/kg bupropion even after increasing the number of extinction session from 6 to 24. Finally, there was evidence that learning in the initial extinction phase was retained in the re-extinction phase for nicotine and bupropion. These findings indicate that learning involving the nicotine stimuli are complex and that assessment approach for stimulus similarity changes conclusions regarding substitution by bupropion. Further research will be needed to identify whether such differences may be related to different facets of nicotine dependence and/or its treatment.


Pulse shaping of octave spanning femtosecond laser pulses.
Characterization and pulse shaping of octave spanning femtosecond lasers poses a significant challenge. We have constructed a grating-based pulse shaper for an ultra-broad-bandwidth (620-1020 nm)femtosecond laser, and used it to compensate the phase distortions of the laser, spatial-light modulator and optics within 0.1 rad accuracy accross the entire bandwidth using Multiphoton Intrapulse Interference Phase Scan (MIIPS) without a precompressor. The compensated transform limited pulses generated a second harmonic spectrum with a 12,260 cm(-1) spectral width. Binary phase modulation was introduced by this pulse shaping system to demonstrate high resolution control of the second harmonic generation spectrum.


Bio-inspired benzo[k,l]xanthene lignans: synthesis, DNA-interaction and antiproliferative properties.
In this work twelve benzo[k,l]xanthene lignans were synthesized by biomimetic, Mn-mediated oxidative coupling of caffeic esters and amides. These compounds, bearing different flexible pendants at position C1/C2 of the aromatic core, interact with DNA in a dual mode, as confirmed by DF-STD NMR analysis and molecular docking: the planar core acts as a base pair intercalant, whereas the flexible pendants act as minor groove binders. Their antiproliferative activity was evaluated on a panel of six tumor cell lines: HT-29, Caco-2, HCT-116 (human colon carcinoma), H226, A549 (human lung carcinoma), and SH-SY5Y (human neuroblastoma). All compounds under study, except 29, resulted in activity against one or more cell lines, and the markedly lipophilic esters 13 and 28 showed the highest activity. Compound 13 was more active than the anticancer drug 5-fluorouracil (5-FU) towards HCT-116 (colon, GI50 = 3.16 μM) and H226 (lung, GI50 = 4.33 μM) cell lines.


Comparison between deep breathing exercises and incentive spirometry after CABG surgery.
To compare the effects of deep breathing exercises (DBE) and the flow-oriented incentive spirometry (IS) in patients undergone coronary artery bypass grafting (CABG) through the following variables: forced vital capacity - FVC, forced expiratory volume in 1 second - FEV(1), maximal respiratory pressures and oxygen saturation. Thirty six patients in CABG postoperative period underwent thirty minutes of non-invasive ventilation during the first 24 hours after extubation and were randomly shared into two groups as following: DBE (n=18) and IS (n=18). The spirometric variables were assessed on the preoperative period and seventh postoperative day (POD). The respiratory muscle strength and oxygen saturation were assessed on the preoperative period, first, second and seventh POD. The groups were considered homogeneous in relation to the demographic and surgical variables. It has been noted fall in the values of FVC and FEV(1) between the preoperative period and the seventh POD, but without significant differences between groups. The maximal respiratory pressures showed drop in the first POD but with and partial recovery until the seventh POD, also without significant differences between groups. The oxygen saturation was the only variable that was completely recovered on the seventh POD, also without significant differences between groups. There were not observed significant differences in maximal respiratory pressures, spirometric variables and oxygen saturation in patients undergone deep breathing exercises and flow-oriented incentive spirometry after coronary artery bypass grafting.


Additional data in the debate on stage I non-small cell lung cancer: surgery versus stereotactic ablative radiotherapy.
Lobectomy has been the standard of care for patients with early stage non-small cell lung cancer (NSCLC), resulting in nearly universal local control and excellent overall survival. However, up to one-quarter of early stage patients are unable to undergo or refuse definitive resection. With the increasing adoption of stereotactic ablative radiotherapy (SABR) over conventionally fractionated radiotherapy among medical inoperable patients, tumor control and overall survival rates in this population have significantly improved. Trials demonstrating excellent outcomes among both medically inoperable and medical operable patients with stage I NSCLC have spurred interest in comparisons between surgery and SABR. The recent publication of the randomized STARS and ROSEL trials demonstrated fewer toxicities and an improvement in overall survival among patients treated with SABR compared with surgery. Based on these trials and retrospective comparisons between the modalities, definitive SABR now more firmly appears to be a viable first-line option for treating patients with operable stage I NSCLC.


A pre-specified analysis of the Dapagliflozin and Prevention of Adverse Outcomes in Chronic Kidney Disease (DAPA-CKD) randomized controlled trial on the incidence of abrupt declines in kidney function.
This pre-specified analysis of DAPA-CKD assessed the impact of sodium-glucose cotransporter 2 inhibition on abrupt declines in kidney function in high-risk patients based on having chronic kidney disease (CKD) and substantial albuminuria. DAPA-CKD was a randomized, double-blind, placebo-controlled trial that had a median follow-up of 2.4 years. Adults with CKD (urinary albumin-to-creatinine ratio 200-5000 mg/g and estimated glomerular filtration rate 25-75 mL/min/1.73m2) were randomized to dapagliflozin 10 mg/day matched to placebo (2152 individuals each). An abrupt decline in kidney function was defined as a pre-specified endpoint of doubling of serum creatinine between two subsequent study visits. We also assessed a post-hoc analysis of investigator-reported acute kidney injury-related serious adverse events. Doubling of serum creatinine between two subsequent visits (median time-interval 100 days) occurred in 63 (2.9%) and 91 (4.2%) participants in the dapagliflozin and placebo groups, respectively (hazard ratio 0.68 [95% confidence interval 0.49, 0.94]). Accounting for the competing risk of mortality did not alter our findings. There was no heterogeneity in the effect of dapagliflozin on abrupt declines in kidney function based on baseline subgroups. Acute kidney injury-related serious adverse events were not significantly different and occurred in 52 (2.5%) and 69 (3.2%) participants in the dapagliflozin and placebo groups, respectively (0.77 [0.54, 1.10]). Thus, in patients with CKD and substantial albuminuria, dapagliflozin reduced the risk of abrupt declines in kidney function.


American College of Physicians Ethics Manual. Third edition.
Medicine, law, and social values are not static and must be re-examined periodically. This edition of the ACP Ethics Manual covers emerging issues in medical ethics and revisits some old issues. The overview of the evolution of medical ethics, which appeared in previous editions of the Manual, has been eliminated to allow more space for the consideration of today's ethical dilemmas. Other changes include a revised chapter on end-of-life care, discussion of physician-assisted suicide, revised sections on conflicts of interest and on medical risk to the physician and patient, given developments in human immunodeficiency virus (HIV) infection and the acquired immunodeficiency syndrome (AIDS), and discussion of sexual contact between physician and patient. A statement on disclosure of errors and a section on care of the physician's family have also been added. The sections on confidential information told by a patient's family or friend to the physician; on physician-pharmaceutical industry relations; on physicians in training; and on the impaired physician have been expanded. Sections on advertising, peer review, and resource allocation have been revised. The literature of biomedical ethics expands at a rate that does not allow a bibliography to remain current, so an exhaustive list of references or suggested readings is not included in this manual. Instead, only cited references are listed.


Sulforaphane-induced metabolomic responses with epigenetic changes in estrogen receptor positive breast cancer cells.
Estrogen is a risk factor for breast cancer. The isothiocyanate sulforaphane (SFN), found in cruciferous vegetables, has been identified as an effective chemopreventive agent, and may prevent or treat breast cancer by reversing estrogen-induced metabolic changes. Here, we investigated metabolic changes in estrogen receptor-positive breast cancer (MCF-7) cells treated with estradiol (E2) and/or SFN to identify key metabolite panels that might provide new insights into the underlying mechanisms of the antitumor effects of SFN. Gas chromatography-mass spectrometry and ultra performance liquid chromatography-mass spectrometry (UPLC-Orbitrap- MS) were used to obtain the metabolic profiles of MCF-7 cells. The data were analyzed using Student's t-test and multivariate statistics, including principal component analysis and partial least squares discriminant analysis. Hydroxymethylation was detected by UPLC-Orbitrap- MS and verified by immunofluorescence assay. We report that significant changes in metabolites induced by E2 and SFN were associated with differences in glycolysis and energy metabolism, and also amino acid, purine, and folic acid metabolism. E2 may alter methylation and hydroxymethylation status via the folic acid pathway. We also identified biomarkers that may be of use in interpretation of the metabolic pathways evoked by the effects of E2 and SFN on breast cancer cells. The identified biomarkers associated with metabolic pathways provide new insight into the chemopreventive mechanisms of SFN.


Activated Src increases adhesion, survival and alpha2-integrin expression in human breast cancer cells.
Focal adhesion kinase (FAK) is an intracellular kinase that localizes to focal adhesions. FAK is overexpressed in human tumours, and FAK regulates both cellular adhesion and anti-apoptotic survival signalling. Disruption of FAK function by overexpression of the FAK C-terminal domain [FAK-CD, analogous to the FRNK (FAK-related non-kinase) protein] leads to loss of adhesion and apoptosis in tumour cells. We have shown that overexpression of an activated form of the Src tyrosine kinase suppressed the loss of adhesion induced by dominant-negative; adenoviral FAK-CD and decreased the apoptotic response in BT474 and MCF-7 breast cancer cell lines. This adhesion-dependent apoptosis was increased by the Src-family kinase inhibitor PP2 [4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine]. We have also shown that expression of activated Src in breast cancer cells increased the expression of alpha2-integrin and that overexpression of alpha2-integrin suppressed FAK-CD-mediated loss of adhesion. Our results suggest a model in which Src regulates adhesion and survival through enhanced expression of the alpha2-integrin. This provides a mechanism through which Src promotes cellular adhesion and alters the adhesive function of FAK.


Expression of mRNA's of cytokines and growth factors in experimental glomerulonephritis.
A variety of cytokines and growth factors have been recently shown to modulate the growth of mesangial cells and the synthesis of the mesangial matrix. We examined chronological change of mRNA expression of interleukin-1 beta (IL-1 beta), tumor necrosis factor-alpha (TNF-alpha), transforming growth factor beta 1 (TGF-beta 1), and the platelet-derived growth factor (PDGF)-B chain in glomeruli of nephrotoxic serum nephritis using reverse transcription and the polymerase chain reaction (RT-PCR) method. Expression of TNF-alpha mRNA increased immediately after induction of nephrotoxic serum nephritis. Levels of IL-1 beta and PDGF-B chain mRNAs increased at 24 hr and remained elevated for 4 weeks. TGF-beta 1 mRNA expression increased significantly at 24 hr, peaking at 2 weeks. The chronological changes of these cytokines and growth factors were associated with two phases of inflammation in this model. Among them, expression of PDGF-B chain mRNA preceded mesangial proliferation and expression of TGF-beta 1 preceded accumulation of mesangial matrix, indicating that these two growth factors contributed to these histological alterations.


Structural basis for pH gating of the two-pore domain K+ channel TASK2.
TASK2 (also known as KCNK5) channels generate pH-gated leak-type K+ currents to control cellular electrical excitability1-3. TASK2 is involved in the regulation of breathing by chemosensory neurons of the retrotrapezoid nucleus in the brainstem4-6 and pH homeostasis by kidney proximal tubule cells7,8. These roles depend on channel activation by intracellular and extracellular alkalization3,8,9, but the mechanistic basis for TASK2 gating by pH is unknown. Here we present cryo-electron microscopy structures of Mus musculus TASK2 in lipid nanodiscs in open and closed conformations. We identify two gates, distinct from previously observed K+ channel gates, controlled by stimuli on either side of the membrane. Intracellular gating involves lysine protonation on inner helices and the formation of a protein seal between the cytoplasm and the channel. Extracellular gating involves arginine protonation on the channel surface and correlated conformational changes that displace the K+-selectivity filter to render it nonconductive. These results explain how internal and external protons control intracellular and selectivity filter gates to modulate TASK2 activity.


Triglyceride-induced diabetes associated with familial lipoprotein lipase deficiency.
Raised plasma triglycerides (TGs) and nonesterified fatty acid (NEFA) concentrations are thought to play a role in the pathogenesis of insulin-resistant diabetes. We report on two sisters with extreme hypertriglyceridemia and overt diabetes, in whom surgical normalization of TGs cured the diabetes. In all of the family members (parents, two affected sisters, ages 18 and 15 years, and an 11-year-old unaffected sister), we measured oral glucose tolerance, insulin sensitivity (by the euglycemic-hyperinsulinemic clamp technique), substrate oxidation (indirect calorimetry), endogenous glucose production (by the [6,6-2H2]glucose technique), and postheparin plasma lipoprotein lipase (LPL) activity. In addition, GC-clamped polymerase chain reaction-amplified DNA from the promoter region and the 10 coding LPL gene exons were screened for nucleotide substitution. Two silent mutations were found in the father's exon 4 (Glu118 Glu) and in the mother's exon 8 (Thr361 Thr), while a nonsense mutation (Ser447 Ter) was detected in the mother's exon 9. Mutations in exons 4 and 8 were inherited by the two affected girls. At 1-2 years after the appearance of hyperchylomicronemia, both sisters developed hyperglycemia with severe insulin resistance. Because medical therapy (including high-dose insulin) failed to reduce plasma TGs or control glycemia, lipid malabsorption was surgically induced by a modified biliopancreatic diversion. Within 3 weeks of surgery, plasma TGs and NEFA and cholesterol levels were drastically lowered. Concurrently, fasting plasma glucose levels fell from 17 to 5 mmol/l (with no therapy), while insulin-stimulated glucose uptake, oxidation, and storage were all markedly improved. Throughout the observation period, plasma TG levels were closely correlated with both plasma glucose and insulin concentrations, as measured during the oral glucose tolerance test. These cases provide evidence that insulin-resistant diabetes can be caused by extremely high levels of TGs.


Dynamic ventrorostral displacement of the dorsal laryngeal mucosa in horses.
The objectives of this report were to describe the occurrence and features of dynamic ventrorostral displacement of the dorsal laryngeal mucosa (VRDDLM) in a group of Thoroughbred horses presented for investigation of poor performance and/or abnormal respiratory noise. Records from 600, dynamic, endoscopic examinations of the upper respiratory tract of horses were reviewed. Horses with VRDDLM were identified as those in which the dorsal laryngeal mucosa progressively obscured the interarytenoid notch and dorsoaxial portion of the corniculate processes of the arytenoid cartilages during high-speed exercise. The condition was recognised in 12 horses. Concurrent abnormalities of the respiratory tract of eight horses were also identified and included, axial deviation of the aryepiglottic folds, vocal cord prolapse, unilateral and bilateral ventromedial luxation of the apex of the corniculate process of the arytenoid cartilage, and intermittent dorsal displacement of the soft palate. VRDDLM is a rare abnormality of the upper portion of the respiratory tract of horses that may be associated with abnormal respiratory noise and potentially poor performance. The significance of the condition is not known, but the presence of this condition in combination with other, obstructive diseases of the equine airway warrants further investigation.


Vascular Occlusion and Sequential Compression for Recovery After Resistance Exercise.
The purpose of this study was to evaluate vascular occlusion (OCC) and sequential intermittent pneumatic compression (SIPC) as recovery strategies after fatiguing resistance exercise. Twelve strength-trained male participants (age: 24.0 ± 6.3 years, height: 180.4 ± 9.7 cm, and weight: 84.8 ± 9.6 kg) participated in a randomized cross-over study. Participants performed a fatiguing resistance exercise bout consisting of 10 sets with 10 repetitions of back squats at 70% 1 repetition maximum with 3-minute rest between sets. Outcome measures of perceived recovery status, muscle soreness, concentric peak isokinetic torque of the quadriceps, squat jump (SJ) height, and countermovement jump (CMJ) height were taken before the fatiguing resistance exercise bout and repeated immediately post, 1 hour, and 24 hours later. Immediately after the postexercise measures, participants undertook 1 of the 3 recovery strategies: OCC, SIPC, and a passive control (CON). Concentric peak isokinetic torque of the quadriceps was decreased significantly immediately post and 1 hour after the fatiguing resistance exercise bout compared with baseline values (p ≤ 0.05). Mean SJ and CMJ jump height decreased significantly immediately post and 1 hour compared with baseline measures, but only the SJ was significantly decreased at 24 hours. There were no significant differences between conditions for any of the postexercise measures (p > 0.05). In conclusion, this study indicates that OCC and SIPC are not effective for attenuating muscle performance loss after a fatiguing resistance exercise bout relative to passive recovery.


Lipoperoxidation induced by hydrogen peroxide in human erythrocyte membranes. 2. Comparison of the antioxidant effect of Ginkgo biloba extract (EGb 761) with those of water-soluble and lipid-soluble antioxidants.
An in vitro model using healthy human erythrocyte suspensions was used to compare the antioxidant effect of standardized Ginkgo biloba extract (EGb 761) with those of water-soluble (ascorbic acid, glutathione and uric acid) and lipid-soluble (alpha-tocopherol and retinol acetate) antioxidants. Lipid peroxidation was induced by hydrogen peroxide in the absence (control) and presence of antioxidants at low (25 micrograms/ml) and high (250 micrograms/ml) concentrations. Malondialdehyde production was determined as the indicator of lipid peroxidation during the incubation period. The results suggest that all of the antioxidants, except ascorbic acid, have antioxidant potential in this system in a concentration-dependent manner. When the antioxidants were compared, EGb 761 was found to be more effective than water-soluble antioxidants, and as effective as lipid-soluble antioxidants. Among the lipid-soluble antioxidants there was no significant difference in potency between alpha-tocopherol and retinol acetate, but uric acid was the most potent of the water-soluble antioxidants. The antioxidant potency of EGb 761 appears to be comparable with that of the well-known antioxidants alpha-tocopherol and retinol acetate.


Molecular monitoring in CML: how deep? How often? How should it influence therapy?
With the advent of tyrosine kinase inhibitors (TKIs), the goals of therapy in chronic myeloid leukemia (CML) are steadily shifting. Long-term disease control on TKI therapy has been the goal and expectation for most patients. More recently, treatment-free remission (TFR) has entered mainstream practice and is increasingly being adopted as the main goal of therapy. This therapeutic shift not only influences TKI selection but also, has necessitated the refinement and dissemination of highly sensitive and accurate molecular monitoring techniques. Measurement of BCR-ABL1 messenger RNA expression through reverse transcription quantitative polymerase chain reaction, reported according to the International Scale, has become the primary tool for response assessment in CML. Achieving specific time-dependent molecular milestones, as defined by global therapeutic guidelines, has been established as critical in maximizing optimal outcomes while identifying patients at risk of therapy failure. Depth and duration of a deep molecular response have become the new therapeutic targets in patients considered for TFR. Consequently, molecular monitoring in CML has become even more critical to ongoing response assessment, identifying patients with TKI resistance and poor drug adherence, and enabling TFR to be attempted safely and effectively.


Potential biodiversity benefits from international programs to reduce carbon emissions from deforestation.
Deforestation is the second largest anthropogenic source of carbon dioxide emissions and options for its reduction are integral to climate policy. In addition to providing potentially low cost and near-term options for reducing global carbon emissions, reducing deforestation also could support biodiversity conservation. However, current understanding of the potential benefits to biodiversity from forest carbon offset programs is limited. We compile spatial data on global forest carbon, biodiversity, deforestation rates, and the opportunity cost of land to examine biodiversity conservation benefits from an international program to reduce carbon emissions from deforestation. Our results indicate limited geographic overlap between the least-cost areas for retaining forest carbon and protecting biodiversity. Therefore, carbon-focused policies will likely generate substantially lower benefits to biodiversity than a more biodiversity-focused policy could achieve. These results highlight the need to systematically consider co-benefits, such as biodiversity in the design and implementation of forest conservation programs to support international climate policy.


Deletion of carboxy-terminal residues of murine granulocyte-macrophage colony-stimulating factor results in a loss of biologic activity and altered glycosylation.
A deletion mutant of murine granulocyte-macrophage colony-stimulating factor (GM-CSF) which differs in primary structure from native GM-CSF in the carboxy-terminal 11 amino acids was prepared. Four amino acid residues are mutated and the seven terminal residues including Cys-118 are deleted. Supernatants from COS-1 cells transfected with this deletion mutant (GM-CSF(del] showed a 3000-fold decrease in the ability to stimulate bone marrow stem cells to proliferate and differentiate into granulocytes and macrophages in vitro. Northern blot analysis using poly(A)+ RNA extracted from the transfected cells showed equal accumulations of GM-CSF and GM-CSF(del). Transfection with full-length GM-CSF followed by immunoprecipitation of metabolically labeled supernatant proteins with rabbit anti-rGM-CSF antiserum yielded predominantly the 23-kDa, fully glycosylated form and small amounts of both a 29-kDa form and the 18-kDa non-N-glycosylated form. Transfection of the GM-CSF(del) mutant and immunoprecipitation revealed a large, diffuse band on sodium dodecyl sulfate--polyacrylamide gel electrophoresis with a molecular weight of about 29 kDa. Digestion of the immunoprecipitated 29-kDa species with N-glycanase converted the 29-kDa form into two forms of about 23 and 18 kDa, suggesting that the increase in molecular weight of the deletion mutant protein resulted from hyperglycosylation. Adding tunicamycin to the culture medium of cells transfected with GM-CSF(del) also yielded a single non-N-glycosylated species of about 18 kDa, but secretion was at a significantly lower level than either the 29-kDa hyperglycosylated GM-CSF(del) protein from non-tunicamycin-treated cells or the 18-kDa non-N-glycosylated full-length GM-CSF from tunicamycin-treated cells. Since very recent scanning-deletion analysis indicates that there is a critical region for activity near Cys-118 and that Cys-118 is necessary for maximal activity, we conclude that the Cys-118 residue is necessary for proper glycosylation and maximal biologic activity of GM-CSF.


Multidrug-Resistant Acinetobacter baumannii - The Modern Menace: A Retrospective Study in a Tertiary Hospital in Mangalore.
Multidrug resistance in Acinetobacter baumannii is constantly on the rise. There has also been an increase in the morbidity and mortality of patients with infection by the same pathogen. This study aimed to assess the patterns of antibiotic resistance exhibited by various clinical isolates of Acinetobacter baumannii, examine the risk factors associated, and investigate the prevalence of co-infecting pathogens and the clinical outcomes of the patients. Retrospective cross-sectional study. Reports of 100 isolates of Acinetobacter baumannii obtained from patients admitted in two tertiary hospitals were used for the study. Identification and determination of antibiotic resistance patterns were done using Vitek2. The presence of probable risk factors was noted. The pattern of clinical outcomes of the patients and the prevalence of co-infecting pathogens were analyzed. Data analysis was done using descriptive statistics. More than 50% of isolates showed resistance independently to imipenem and meropenem. Higher rates of susceptibility were observed with tigecycline (55%). Isolates obtained from patients in the intensive care unit (ICU) showed resistance to a more number of antibiotics than those in the wards and operation theatre. Seventeen percent of the isolates were associated with a co-infecting pathogen such as Pseudomonas, Enterococcus, Klebsiella, 87% of the patients were discharged, 12% expired, and 1% were shifted. A positive correlation was found between the duration of hospital stay and number of antibiotics to which the isolate was resistant. Multidrug resistance in Acinetobacter baumannii continues to be a menace. In this study, a large number of isolates exhibited resistance to carbapenems such as imipenem, meropenem, and ertapenem, thereby signifying the need for further research and the use of other antibiotics such as tigecycline, to which higher susceptibility was observed.


Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases.
E. coli Par10 is a peptidyl-prolyl cis/trans isomerase (PPIase) from Escherichia coli catalyzing the isomerization of Xaa-Pro bonds in oligopeptides with a broad substrate specificity. The structure of E. coli Par10 has been determined by multidimensional solution-state NMR spectroscopy based on 1207 conformational constraints (1067 NOE-derived distances, 42 vicinal coupling-constant restraints, 30 hydrogen-bond restraints, and 68 phi/psi restraints derived from the Chemical Shift Index). Simulated-annealing calculations with the program ARIA and subsequent refinement with XPLOR yielded a set of 18 convergent structures with an average backbone RMSD from mean atomic coordinates of 0.50 A within the well-defined secondary structure elements. E. coli Par10 is the smallest known PPIase so far, with a high catalytic efficiency comparable to that of FKBPs and cyclophilins. The secondary structure of E. coli Par10 consists of four helical regions and a four-stranded antiparallel beta-sheet. The N terminus forms a beta-strand, followed by a large stretch comprising three alpha-helices. A loop region containing a short beta-strand separates these helices from a fourth alpha-helix. The C terminus consists of two more beta-strands completing the four-stranded anti-parallel beta-sheet with strand order 2143. Interestingly, the third beta-strand includes a Gly-Pro cis peptide bond. The curved beta-strand forms a hydrophobic binding pocket together with alpha-helix 4, which also contains a number of highly conserved residues. The three-dimensional structure of Par10 closely resembles that of the human proteins hPin1 and hPar14 and the plant protein Pin1At, belonging to the same family of highly homologous proteins.


Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.
The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.


Partitioning behaviour of 1-hexanol into lipid membranes as studied by deuterium NMR spectroscopy.
Deuterium nuclear magnetic resonance (NMR) spectroscopy was used to study the partitioning behaviour of 1-hexanol specifically deuterated in the alpha-position into model lipid bilayers. In all systems studied, the observed deuterium NMR lineshapes were time-dependent. Initially, 1-hexanol-d2 gave rise to an isotropic deuterium resonance with a different chemical shift from that of aqueous 1-hexanol-d2. After equilibration over a period of days, a broader spectral component characteristic of a spherically-averaged powder-pattern was observed. The quadrupole anisotropy of the 1-hexanol-d2 giving rise to the broad spectrum depended upon the cholesterol content of the membrane. From quantitation of the anisotropic to isotropic deuterium NMR spectra, the partition coefficients of 1-hexanol-d2 in a number of bilayer systems (asolectin and phosphatidylcholine bilayers (the latter with and without cholesterol] were determined. The partitioning of 1-hexanol-d2 into red blood cell membranes, and a suspension of lipids extracted from red blood cell membranes, was also examined. It is suggested that 1-hexanol, and probably other lipophiles, can partition to either the bilayer surface or the bilayer interior in a time-dependent manner.


Development of a safe and effective one-minute preoperative skin preparation.
Three consecutive controlled randomized clinical trials utilizing 1,324 patients were conducted to study the efficacy of incise drapes to prevent wound infections. When a polyester antimicrobial incise drape (loban 2 Antimicrobial Film) was applied to an operative area after a one-minute skin preparation using either 70% alcohol or 2% iodine in 90% alcohol, the clean wound infection rate (1.3%) and overall wound infection rate (2.5%) were comparable to those following a standard ten-minute skin preparation with Betadine (1.3% and 2.3%, respectively). During preliminary studies, it was demonstrated that separation of polyethylene antimicrobial incise drapes from the skin during operation was associated with a sixfold increase in infection rate when compared with operations in which the incise drape did not lift. Design of the drape and technique of application are important considerations in preventing lift from the skin.


Vagally mediated heart rate variability in headache patients--a systematic review and meta-analysis.
Vagal nerve activity-indexed by heart rate variability (HRV)-has been linked to altered pain processing and inflammation, both of which may underpin headache disorders and lead to cardiovascular disease (CVD). Here we examined the evidence for differences in parasympathetic (vagal) activity indexed by time- and frequency-domain measures of HRV in patients with headache disorders compared to healthy controls (HCs). A systematic review and meta-analysis was conducted on studies investigating group differences in vagally mediated HRV (vmHRV) including time- (root-mean-square of successive R-R-interval differences (RMSSD)) and frequency- (high-frequency HRV) domain measures. Studies eligible for inclusion were identified by a systematic search of the literature, based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Seven studies reporting a total of 10 comparisons of patients with headache disorders (HF-HRV n = 67, RMSSD n = 122) and HCs (HF-HRV n = 64, RMSSD n = 125) were eligible for inclusion. Random-effects meta-analysis revealed a significant main effect on RMSSD (Z = 2.03, p = 0.04; Hedges' g = -0.63; 95% CI (-1.24, -0.02); k = 6) and similar pooled effect size estimates for HF-HRV when breathing was controlled (g = -0.30; 95% CI (-0.69; 0.10)) but not when breathing was not controlled (g = 0.02; 95% CI (-0.69; 0.74)). Controlling for breathing had no effect on RMSSD. vmHRV is reduced in patients with headache disorders, findings associated with a medium effect size. Suggestions for future research in this area are provided, emphasizing a need to investigate the impact of headache disorders and commonly comorbid conditions-including mental disorders-as well as the investigation of the risk for CVD in migraine in particular. We further emphasize the need for large-scale studies to investigate HRV as a mechanism mediating the association of migraine and CVD.


Biased energy efficiency perception based on instantaneous consumption displays - Indication for heuristic energy information processing.
Instantaneous consumption displays (ICDs) can be used as central information source to perceive the energy efficiency of manoeuvre-level driving. A key question is whether drivers who use ICDs can accurately derive energy efficiency differences of different driving strategies based on ICDs. There is reason to assume that drivers' consumption judgements may be biased, similar to driving-related phenomena like the time-saving bias. Therefore, the aim of the present research was to examine drivers' accuracy in deriving average consumption from dynamic ICD sequences. Participants viewed videos of a schematic ICD in a controlled experiment where the maximum instantaneous consumption systematically varied over time. Participants (N = 55) overestimated the average consumption values. The empirical ranking of the sequences did significantly correlate with the heuristic but not with the correct efficiency ranking. The current study incorporated multilevel modelling due to the nested structure of the data. The estimation difference was greater with higher peak height and shorter peak duration. The effect of peak height on estimation difference weakened with longer peak duration. In sum, the results indicate that ICDs can create biased perceptions of energy efficiency and that drivers seem to use simplifying heuristics. Knowledge and affinity for technology interaction appear to relate to biased estimations, whereas the intensity of prior experience with consumption displays seems irrelevant. Further studies should test other interfaces with debiasing potential such as manoeuvre-based aggregation or fading-trace approaches. Moreover, studies are needed that enable modelling of the effects of more natural temporal-spatial visual attention distribution (e.g. in a driving simulator setting).


Minute vascular replacements.
Glutaraldehyde-tanned, mesh-reinforced, mandrel-grown ovine collagen conduits were compared with tanned human umbilical arteries and polytetrafluoroethylene (PTFE) grafts in the aorta of rat recipients. All grafts had 100% patency and became lined by a cellular neointima. The mean maximum thickness of the neointima of the tanned human umbilical artery, ovine collagen graft, and the PTFE grafts was 68, 57, and 13 micrometer, respectively. Neointimal proliferation was complete for the two biosynthetic grafts, but none was seen in the center of the PTFE grafts as late as ten weeks. The mean increase in lumen cross-sectional area was 49% for the umbilical artery grafts, 23% for ovine collagen conduits, and 4% for the PTFE grafts. Longer follow-up periods will be required before unqualified support can be given to clinical trials of these small-diameter prostheses; however, long-term patency for synthetic grafts of such a small caliber is encouraging for future microvascular applications and for study of host-prosthesis interactions.


On the use of random walk schemes in oil spill modelling.
In oil spill models, vertical mixing due to turbulence is commonly modelled by random walk. If the eddy diffusivity varies with depth, failing to take the derivative of the diffusivity into account in the random walk scheme will lead to incorrect results. Depending on the diffusivity profile, the result may be either over- or underprediction of the amount of surfaced oil. The importance of using consistent random walk schemes has been known for decades in, e.g., the plankton modelling community. However, it appears not to be common knowledge in the oil spill community, with inconsistent random walk schemes appearing even in recent publications. We demonstrate and quantify the error due to inconsistent random walk, using a simplified oil spill model, and two different diffusivity profiles. In the two cases considered, a commonly used inconsistent scheme predicts respectively 54% and 202% the amount of surface oil, compared to a consistent scheme.


Medical errors in primary care: results of an international study of family practice.
To describe errors Canadian family physicians found in their practices and reported to study investigators. To compare errors reported by Canadian family physicians with those reported by physicians in five other countries. Analytical study of reports of errors. The Linnaeus Collaboration was formed to study medical errors in primary care. General practitioners in six countries, including a new Canadian family practice research network (Nortren), anonymously reported errors in their practices between June and December 2001. An evolving taxonomy was used to describe the types of errors reported. Practices in Canada, Australia, England, the Netherlands, New Zealand, and the United States. Family physicians in the six countries. Types of errors reported. Differences in errors reported in different countries. In Canada, 15 family doctors reported 95 errors. In the other five countries, 64 doctors reported 413 errors. Although the absence of a denominator made it impossible to calculate rates of errors, Canadian doctors and doctors from the other countries reported similar proportions of errors arising from health system dysfunction and gaps in knowledge or skills. All countries reported similar proportions of laboratory and prescribing errors. Canadian doctors reported harm to patients from 39.3% of errors; other countries reported harm from 29.3% of errors. Canadian physicians considered errors "very serious" in 5.8% of instances; other countries thought them very serious in 7.1% of instances. Hospital admissions and death were among the consequences of errors reported in other countries, but these consequences were not reported in Canada. Serious errors occur in family practice and affect patients in similar ways in Canada and other countries. Validated studies that analyze errors and record error rates are needed to better understand ways of improving patient safety in family practice.


The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy.
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.


A hierarchy of proliferative cells exists in mouse lens epithelium: implications for lens maintenance.
To determine the distribution of slow-cycling cells, which are detected as label-retaining cells (LRCs), in mouse lens epithelium during postnatal development. Pregnant BALB/c mice were injected intraperitoneally (twice daily) with tritiated thymidine (3H-TdR), beginning at 17 days of gestation until birth. At birth, the in utero-labeled neonatal mice were injected subcutaneously with 3H-TdR (twice daily) for 3 days. Mice were killed weekly for the first month and then at 3-week intervals up to 18.5 weeks (chase periods). Eyes were removed and processed for autoradiography. In living mice, small scrape wounds were made on the anterior surface of the lens of mice that had been "chased" for 18.5 weeks. Twenty-four hours later, wounded mice received a single injection of BrdU. Immediately after the in utero/postnatal labeling period, 100% of the lens epithelial cells incorporated 3H-TdR, and all were heavily labeled. With time, the number of LRCs declined so that only 13% of the lens epithelial cells were labeled at 18.5 weeks. At this time the heaviest labeled cells were exclusively found in the central zone and represented 2% to 3% of the total LRCs. In contrast, lightly labeled cells were found in both the central and germinative zones. After wounding, the heavily labeled LRCs incorporated BrdU, indicating that these cells were healthy and could be recruited to proliferate. The heavily labeled LRCs, located exclusively in the central region, represent cells that divide very infrequently during homeostasis (putative stem cells); on perturbation, these cells can proliferate. The lightly labeled LRCs, located in the central and germinative zones, cycle more frequently than the heavily labeled ones. These LRCs may be phenotypically indistinguishable from stem cells and maintain the normal proliferative needs of the lens. A third population of actively cycling cells exists primarily in the germinative zone and represents the transit amplifying cells, which have a limited proliferative potential.


Analysis of Serological Biomarkers of SARS-CoV-2 Infection in Convalescent Samples From Severe, Moderate and Mild COVID-19 Cases.
Precision monitoring of antibody responses during the COVID-19 pandemic is increasingly important during large scale vaccine rollout and rise in prevalence of Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2) variants of concern (VOC). Equally important is defining Correlates of Protection (CoP) for SARS-CoV-2 infection and COVID-19 disease. Data from epidemiological studies and vaccine trials identified virus neutralising antibodies (Nab) and SARS-CoV-2 antigen-specific (notably RBD and S) binding antibodies as candidate CoP. In this study, we used the World Health Organisation (WHO) international standard to benchmark neutralising antibody responses and a large panel of binding antibody assays to compare convalescent sera obtained from: a) COVID-19 patients; b) SARS-CoV-2 seropositive healthcare workers (HCW) and c) seronegative HCW. The ultimate aim of this study is to identify biomarkers of humoral immunity that could be used to differentiate severe from mild or asymptomatic SARS-CoV-2 infections. Some of these biomarkers could be used to define CoP in further serological studies using samples from vaccination breakthrough and/or re-infection cases. Whenever suitable, the antibody levels of the samples studied were expressed in International Units (IU) for virus neutralisation assays or in Binding Antibody Units (BAU) for ELISA tests. In this work we used commercial and non-commercial antibody binding assays; a lateral flow test for detection of SARS-CoV-2-specific IgG/IgM; a high throughput multiplexed particle flow cytometry assay for SARS-CoV-2 Spike (S), Nucleocapsid (N) and Receptor Binding Domain (RBD) proteins); a multiplex antigen semi-automated immuno-blotting assay measuring IgM, IgA and IgG; a pseudotyped microneutralisation test (pMN) and an electroporation-dependent neutralisation assay (EDNA). Our results indicate that overall, severe COVID-19 patients showed statistically significantly higher levels of SARS-CoV-2-specific neutralising antibodies (average 1029 IU/ml) than those observed in seropositive HCW with mild or asymptomatic infections (379 IU/ml) and that clinical severity scoring, based on WHO guidelines was tightly correlated with neutralisation and RBD/S antibodies. In addition, there was a positive correlation between severity, N-antibody assays and intracellular virus neutralisation.


Chamomile (Matricaria recutita) may provide antidepressant activity in anxious, depressed humans: an exploratory study.
Anxiety and depression are the most commonly reported psychiatric conditions and frequently occur as comorbid disorders. While the advent of conventional drug therapies has simplified treatment, a large segment of the population goes untreated or declines conventional therapy for financial, cultural, or personal reasons. Therefore, the identification of inexpensive and effective alternative therapies for anxiety and depression is of relevance to public health. The current study explores data from a 2009 clinical chamomile trial in humans to determine if chamomile provides clinically meaningful antidepressant activity versus a placebo. In the 2009 randomized, double-blind, placebo-controlled study, the research team examined the antianxiety and antidepressant action of oral chamomile (Matricaria recutita) extract in participants with symptoms of comorbid anxiety and depression. In the 2009 study, all of participants' evaluations took place at the Depression Research Unit at the University of Pennsylvania. The study drew participants from patients at the Department of Family Medicine and Community Health's primary care clinic at the University of Pennsylvania, Philadelphia. Of the 57 participants in the 2009 trial, 19 had anxiety with comorbid depression; 16 had anxiety with a past history of depression; and 22 had anxiety with no current or past depression. The intervention and placebo groups in the 2009 trial received identically appearing 220-mg capsules containing either pharmaceutical-grade chamomile extract standardized to a content of 1.2% apigenin or a placebo (ie, lactose monohydrate NF), respectively. In the current study, the research team used generalized estimating equations analysis to identify clinically meaningful changes over time in scores from the Hamilton Depression Rating (HAM-D) questionnaire among treatment groups. In the current study, the research team observed a significantly greater reduction over time in total HAM-D scores for chamomile vs placebo in all participants (P < .05). The team also observed a clinically meaningful but nonsignificant trend for a greater reduction in total HAM-D scores for chamomile vs placebo in participants with current comorbid depression (P = .062). When the team examined the HAM-D core mood item scores, it observed a significantly greater reduction over time for chamomile vs placebo in all participants (P < .05) and a clinically meaningful but nonsignificant trend for a greater reduction over time for chamomile vs placebo in participants without current or past depression (P = .06). Chamomile may provide clinically meaningful antidepressant activity that occurs in addition to its previously observed anxiolytic activity.


CDH13 Polymorphisms are Associated with Adiponectin Levels and Metabolic Syndrome Traits Independently of Visceral Fat Mass.
Visceral fat accumulation contributes to the development of metabolic syndrome. As visceral fat accumulation increases, adiponectin levels decrease; therefore, adiponectin provides a link between visceral fat accumulation and metabolic disorders. Genome-wide association studies (GWASs) have identified genetic variations in the cadherin 13 (CDH13) gene that are associated with adiponectin levels. We investigated whether single nucleotide polymorphisms (SNPs) in CDH13 was associated with adiponectin levels and metabolic syndrome traits independent of the visceral fat area (VFA), as measured using computed tomography (CT) in 945 Japanese individuals. We found that three CDH13 SNPs reported by recent GWASs (i.e., rs3865188, rs4783244, and rs12051272) were significantly associated with higher adiponectin levels (P < 1 × 10 (-14)), even after adjustment for VFA. However, these adiponectin-inducing alleles of CDH13 SNPs were significantly associated with traits consistent with deteriorating metabolic symptoms, such as higher fasting insulin, homeostasis model assessment-insulin resistance (HOMA-IR) scores, and triglycerides and lower high-density lipoprotein (HDL)-cholesterol levels, similar to increasing VFA and decreasing adiponectin levels. These results suggested that CDH13 SNPs cause an adiponectin-resistant status to compensate for increasing adiponectin levels and could result in the deterioration of metabolic syndrome traits.


[Alterations in hypothalamus-adipose tissue axis in relation with the risk of coronary atherosclerosis].
Recent population studies in Southern Argentina have found a sharp rise in prevalence of overweight and obesity in both sexes and specially after fifty years of age. Hence, the obesity in itself was found associated with the presence of metabolic syndrome (MS) and coronary heart disease, which have been demonstrated by angiography studies. The regulation of energy homeostasis is controlled by interactions between the central nervous system (neurotransmitters and neuropeptides) and the peripheric system (hormones) through very complex mechanisms. Genetics or acquired alterations in these regulation systems can be the origin of obesity and specially of central obesity. The visceral adipose tissue can be considered a secretor organ and its mass increment could generate insulin-resistance (IR) state, which directly or indirectly, could develop into endothelial dysfunction and coronary atherosclerosis. Although some studies estimate that 40% of IR are of genetic origin, a high proportion of these are acquired by inadequate habits in life style (specially excess of food intake and low physical activity). Finally, a better knowledge of the central and peripheric regulations in alimentation habits and energetic balance could help to develop treatments to decrease the incidence of these metabolic alterations and, consequently the morbidity and mortality due to coronary atherosclerosis.


Research: Continuous Surveillance of Sleep Apnea Patients in a Medical-Surgical Unit.
This report consists of two separate studies on the use of continuous capnography monitoring conducted in an effort to improve patient safety at Virtua Health System. The desire for improved patient safety is motivating continuous monitoring and improved surveillance in clinical areas not traditionally equipped for such monitoring. We explored the use of remote monitoring of capnography, using enterprise middleware, in patients recovering from surgery in a medical-surgical unit. Continuous monitoring traditionally has been used in higher-acuity settings, such as intensive care units. Patients diagnosed or suspected to have obstructive or central sleep apnea may benefit from the increased surveillance afforded by continuous monitoring. Pain management in this cohort of patients, recovering from bariatric, joint replacement, or other major surgery, often involves administration of opioids (e.g., hydromorphone, morphine sulfate), which are known to increase risk of respiratory depression. Continuous monitoring of these patients increases the likelihood of detecting adverse clinical events. Our goal was to implement continuous monitoring in order to identify alarm conditions caused by adverse clinical events requiring intervention (e.g., opioid-induced respiratory depression) and artifacts related to patient movement, suspect measurements, or other medical device-generated alarm signals.


Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations.
The multimodular nature of many eukaryotic proteins underlies their temporal or spatial engagement in a range of protein cocomplexes. Using the multimodule protein testin (TES), we here report a proteomics approach to increase insight in cocomplex diversity. The LIM-domain containing and tumor suppressor protein TES is present at different actin cytoskeleton adhesion structures in cells and influences cell migration, adhesion and spreading. TES module accessibility has been proposed to vary due to conformational switching and variants of TES lacking specific domains target to different subcellular locations. By applying iMixPro AP-MS ("intelligent Mixing of Proteomes"-affinity purification-mass spectrometry) to a set of tagged-TES modular variants, we identified proteins residing in module-specific cocomplexes. The obtained distinct module-specific interactomes combine to a global TES interactome that becomes more extensive and richer in information. Applying pathway analysis to the module interactomes revealed expected actin-related canonical pathways and also less expected pathways. We validated two new TES cocomplex partners: TGFB1I1 and a short form of the glucocorticoid receptor. TES and TGFB1I1 are shown to oppositely affect cell spreading providing biological validity for their copresence in complexes since they act in similar processes.


Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate.
The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.


Physical activity as a strategy for maintaining tobacco abstinence: a randomized trial.
For smoking cessation, physical activity (PA) may help manage withdrawal symptoms, mood, stress, and weight; yet studies of PA as an aid for smoking cessation have been mixed. This study examined: (1) the impact of an extended relapse prevention program on increasing moderate to vigorous PA (MVPA) in adults enrolled in a tobacco cessation treatment trial; (2) whether changes in MVPA were associated with sustained abstinence from smoking; and (3) mechanisms by which MVPA may support sustained abstinence from smoking. In a randomized controlled trial conducted from 2003-2006 in San Francisco, California, 407 adult smokers received a 12 week group-based smoking cessation treatment with bupropion and nicotine patch with the quit date set at week 3. At week 12, participants were randomized to no further treatment or to 40 weeks of bupropion or placebo with or without an 11-session relapse prevention intervention of which 2 sessions (held at weeks 16 and 20) focused on PA. Participants receiving the PA intervention (n=163) received a pedometer, counseling to increase steps 10% biweekly towards a 10,000 steps/day goal, and personalized reports graphing progress with individualized goals. The International Physical Activity Questionnaire assessed weekly minutes of MVPA at baseline and weeks 12 and 24. Sustained abstinence from tobacco at week 24 was validated with expired carbon monoxide. In a repeated mixed model analysis, intervention participants significantly increased their MVPA relative to control participants, F(1,475)=3.95, p=.047. Pedometer step counts also increased significantly, t(23)=2.36, p=.027, though only 15% of intervention participants provided 6 weeks of pedometer monitoring. Controlling for treatment condition, increased MVPA predicted sustained smoking abstinence at week 24, odds ratio=1.84 (95% CI: 1.07, 3.05). Among participants with sustained abstinence, increased MVPA was associated with increased vigor (r=0.23, p=.025) and decreased perceived difficulty with staying smoke-free (r=-0.21, p=.038). PA promotion as an adjunct to tobacco treatment increases MVPA levels; changes in MVPA predict sustained abstinence, perhaps by improving mood and self-efficacy.


A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.
Novel RNA motif design is of great practical importance for technology and medicine. Increasingly, computational design plays an important role in such efforts. Our coarse-grained RAG (RNA-As-Graphs) framework offers strategies for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates. In RAG, RNA secondary structures are represented as tree or dual graphs. Graphs with known RNA structures are called "existing", and the others are labeled "hypothetical". By using simplified features for RNA graphs, we have clustered the hypothetical graphs into "RNA-like" and "non-RNA-like" groups and proposed RNA-like graphs as candidates for design. Here, we propose a new way of designing graph features by using Fiedler vectors. The new features reflect graph shapes better, and they lead to a more clustered organization of existing graphs. We show significant increases in K-means clustering accuracy by using the new features (e.g., up to 95% and 98% accuracy for tree and dual graphs, respectively). In addition, we propose a scoring model for top graph candidate selection. This scoring model allows users to set a threshold for candidates, and it incorporates weighing of existing graphs based on their corresponding number of known RNAs. We include a list of top scored RNA-like candidates, which we hope will stimulate future novel RNA design.


Inhibition of tumor growth in vivo with a soluble CD44-immunoglobulin fusion protein.
CD44H is the principal cell surface receptor for hyaluronate, which is a major glycosaminoglycan of the extracellular matrix. Expression of CD44H is enhanced in a variety of malignant tumors and correlates with tumor aggressiveness, supporting the notion that interaction between CD44H and hyaluronate may play an important role in tumor growth and dissemination. In this report we show that in vivo tumor formation by human lymphoma Namalwa cells, stably transfected with CD44H, can be suppressed by a soluble human CD44H-immunoglobulin fusion protein. Disruption of the interaction between CD44H and its physiologic ligands may provide a novel strategy for controlling tumor growth in vivo.


Barriers to Initiation of Pediatric HIV Treatment in Uganda: A Mixed-Method Study.
Although the advantages of early infant HIV diagnosis and treatment initiation are well established, children often present late to HIV programs in resource-limited settings. We aimed to assess factors related to the timing of treatment initiation among HIV-infected children attending three clinical sites in Uganda. Clinical and demographic determinants associated with early disease (WHO clinical stages 1-2) or late disease (stages 3-4) stage at presentation were assessed using multilevel logistic regression. Additionally, semistructured interviews with caregivers and health workers were conducted to qualitatively explore determinants of late disease stage at presentation. Of 306 children initiating first-line regimens, 72% presented late. Risk factors for late presentation were age below 2 years old (OR 2.83, P = 0.014), living without parents (OR 3.93, P = 0.002), unemployment of the caregiver (OR 4.26, P = 0.001), lack of perinatal HIV prophylaxis (OR 5.66, P = 0.028), and high transportation costs to the clinic (OR 2.51, P = 0.072). Forty-nine interviews were conducted, confirming the identified risk factors and additionally pointing to inconsistent referral from perinatal care, caregivers' unawareness of HIV symptoms, fear, and stigma as important barriers. The problem of late disease at presentation requires a multifactorial approach, addressing both health system and individual-level factors.


Anatomic fundoplication failure after laparoscopic antireflux surgery.
Anatomic fundoplication failure occurs after antireflux surgery and may be more common in the learning curve of laparoscopic antireflux surgery (LARS). The authors' aims were to assess the incidence, presentation, precipitating factors, and management of anatomic fundoplication failures after LARS. The advent of LARS has increased the frequency with which antireflux surgery is performed for the treatment of gastroesophageal reflux disease. Postoperative symptoms frequently occur and may result from physiologic abnormalities or anatomic failure of the fundoplication (e.g., displacement or disruption). Few data exist on the potential causes or best treatment of anatomic fundoplication failures. LARS was performed in 290 patients by one of the authors over a 6-year period. In the first 53 patients (group 1), the short gastric vessels were divided on a selective basis and the diaphragmatic crura were closed only when large hiatal hernias were present. In the subsequent 237 patients (group 2), the crura were always approximated posterior to the short gastric vessels and full fundic mobilization was performed. Clinical postoperative evaluation was performed on a regular basis, with detailed tests of anatomy and physiology when untoward symptoms developed. Postoperative foregut symptoms were reported by 26% of the patients, of whom 73% were found to have an intact fundoplication. In 7% of the entire group, anatomic failure of the fundoplication was demonstrated, with the majority exhibiting intrathoracic migration of the wrap with or without disruption of the fundoplication. New-onset postoperative epigastric or substernal chest pain frequently heralded fundoplication failure. Factors correlated with the development of anatomic fundoplication failure included presence in group 1, early postoperative vomiting, other diaphragm "stressors," and large hiatal hernias. Repeat operation has been performed in 8 of the 20 patients (40%), with 5 patients successfully treated using laparoscopic techniques. Anatomic fundoplication failure occurred in 7% of patients undergoing LARS, with the majority occurring in patients who underwent surgery during the learning curve. Anatomic failure is associated with technical shortcomings, large hiatal hernias, and early postoperative vomiting. Full esophageal mobilization and meticulous closure of the diaphragmatic crura posterior to the esophagus should minimize anatomic functional failure after LARS.


Identification, characterization and genetic mapping of TLR1 loci in rainbow trout (Oncorhynchus mykiss).
Induction of innate immune pathways is critical for early anti-microbial defense but there is limited understanding of how teleosts recognize microbial molecules and activate these pathways. In mammals, Toll-like receptors (TLR) 1 and 2 form a heterodimer involved in recognizing peptidoglycans and lipoproteins of microbial origin. Herein, we identify and describe the rainbow trout (Oncorhynchus mykiss) TLR1 gene ortholog and its mRNA expression. Two TLR1 loci were identified from a rainbow trout bacterial artificial chromosome (BAC) library using DNA sequencing and genetic linkage analyses. Full length cDNA clone and direct sequencing of four BACs revealed an intact omTLR1 open reading frame (ORF) located on chromosome 14 and a second locus on chromosome 25 that contains a TLR1 pseudogene. The duplicated trout loci exhibit conserved synteny with other fish genomes that extends beyond the TLR1 gene sequences. The omTLR1 gene includes a single large coding exon similar to all other described TLR1 genes, but unlike other teleosts it also has a 5' UTR exon and intron preceding the large coding exon. The omTLR1 ORF is predicted to encode an 808 amino-acid protein with 69% similarity to the Fugu TLR1 and a conserved pattern of predicted leucine-rich repeats (LRR). Phylogenetic analysis grouped omTLR1 with other fish TLR1 genes on a separate branch from the avian TLR1 and mammalian TLR1, 6 and 10. omTLR1 expression levels in rainbow trout anterior kidney leukocytes were not affected by the human TLR2/6 and TLR2/1 agonists diacylated lipoprotein (Pam(2)CSK(4)) and triacylated lipoprotein (Pam(3)CSK(4)). However, due to the lack of TLR6 and 10 genes in teleost genomes and up-regulation of TLR1 mRNA in response to LPS and bacterial infection in other fish species we hypothesize an important role for omTLR1 in anti-microbial immunity. Therefore, the identification of a TLR2 ortholog in rainbow trout and the development of assays to measure ligand binding and downstream signaling are critical for future elucidation of omTLR1 functions.