Prostate cancer screening in men aged 50 to 69 years (STHLM3): A prospective population-based diagnostic study. Grönberg H, Adolfsson J, Aly M, Nordström T, Wiklund P, Brandberg Y, Thompson J, Wiklund F, Lindberg J, Clements M, Egevad L, Eklund M.Lancet Oncol. 2015 Dec;16(16):1667-76. [Epub 2015 Nov 10]. doi: 10.1016/S1470-2045(15)00361-7.
The prostate-specific antigen (PSA) test is used to screen for prostate cancer but has a high false-positive rate that translates into unnecessary prostate biopsies and overdiagnosis of low-risk prostate cancers. We aimed to develop and validate a model to identify high-risk prostate cancer (with a Gleason score of at least 7) with better test characteristics than that provided by PSA screening alone. The Stockholm 3 (STHLM3) study is a prospective, population-based, paired, screen-positive, diagnostic study of men without prostate cancer aged 50 to 69 years randomly invited by date of birth from the Swedish Population Register kept by the Swedish Tax Agency. Men with prostate cancer at enrolment were excluded from the study. The predefined STHLM3 model (a combination of plasma protein biomarkers [PSA, free PSA, intact PSA, hK2, MSMB, MIC1], genetic polymorphisms [232 SNPs], and clinical variables [age, family, history, previous prostate biopsy, prostate exam]), and PSA concentration were both tested in all participants enrolled. The primary aim was to increase the specificity compared with PSA without decreasing the sensitivity to diagnose high-risk prostate cancer. The primary outcomes were number of detected high-risk cancers (sensitivity) and the number of performed prostate biopsies (specificity). The STHLM3 training cohort was used to train the STHLM3 model, which was prospectively tested in the STHLM3 validation cohort. Logistic regression was used to test for associations between biomarkers and clinical variables and prostate cancer with a Gleason score of at least 7. This study is registered with ISCRTN.com, number ISRCTN84445406. The STHLM3 model performed significantly better than PSA alone for detection of cancers with a Gleason score of at least 7 (P<0.0001), the area under the curve was 0·56 (95% CI: 0·55-0·60) with PSA alone and 0·74 (95% CI: 0·72-0·75) with the STHLM3 model. All variables used in the STHLM3 model were significantly associated with prostate cancers with a Gleason score of at least 7 (P<0·05) in a multiple logistic regression model. At the same level of sensitivity as the PSA test using a cutoff of≥3ng/ml to diagnose high-risk prostate cancer, use of the STHLM3 model could reduce the number of biopsies by 32% (95% CI: 24-39) and could avoid 44% (35-54) of benign biopsies. The STHLM3 model could reduce unnecessary biopsies without compromising the ability to diagnose prostate cancer with a Gleason score of at least 7, and could be a step towards personalised risk-based prostate cancer diagnostic programmes. Stockholm County Council (Stockholms Läns Landsting).


Validating and Improving Injury Burden Estimates Study: the Injury-VIBES study protocol.
Priority setting, identification of unmet and changing healthcare needs, service and policy planning, and the capacity to evaluate the impact of health interventions requires valid and reliable methods for quantifying disease and injury burden. The methodology developed for the Global Burden of Disease (GBD) studies has been adopted to estimate the burden of disease in national, regional and global projects. However, there has been little validation of the methods for estimating injury burden using empirical data. To provide valid estimates of the burden of non-fatal injury using empirical data. Data from prospective cohort studies of injury outcomes undertaken in the UK, USA, Australia, New Zealand and The Netherlands. Meta-analysis of deidentified, patient-level data from over 40 000 injured participants in six prospective cohort studies: Victorian State Trauma Registry, Victorian Orthopaedic Trauma Outcomes Registry, UK Burden of Injury study, Prospective Outcomes of Injury study, National Study on Costs and Outcomes of Trauma and the Dutch Injury Patient Survey. Data will be systematically analysed to evaluate and refine injury classification, development of disability weights, establishing the duration of disability and handling of cases with more than one injury in burden estimates. Developed methods will be applied to incidence data to compare and contrast various methods for estimating non-fatal injury burden. The findings of this international collaboration have the capacity to drive how injury burden is measured for future GBD estimates and for individual country or region-specific studies.


A multiscale computational model of spatially resolved calcium cycling in cardiac myocytes: from detailed cleft dynamics to the whole cell concentration profiles.
Mathematical modeling of excitation-contraction coupling (ECC) in ventricular cardiac myocytes is a multiscale problem, and it is therefore difficult to develop spatially detailed simulation tools. ECC involves gradients on the length scale of 100 nm in dyadic spaces and concentration profiles along the 100 μm of the whole cell, as well as the sub-millisecond time scale of local concentration changes and the change of lumenal Ca(2+) content within tens of seconds. Our concept for a multiscale mathematical model of Ca(2+) -induced Ca(2+) release (CICR) and whole cardiomyocyte electrophysiology incorporates stochastic simulation of individual LC- and RyR-channels, spatially detailed concentration dynamics in dyadic clefts, rabbit membrane potential dynamics, and a system of partial differential equations for myoplasmic and lumenal free Ca(2+) and Ca(2+)-binding molecules in the bulk of the cell. We developed a novel computational approach to resolve the concentration gradients from dyadic space to cell level by using a quasistatic approximation within the dyad and finite element methods for integrating the partial differential equations. We show whole cell Ca(2+)-concentration profiles using three previously published RyR-channel Markov schemes.


Micro-CT evaluation of tooth, calvaria and mechanical stress-induced tooth movement in adult Runx2/Cbfa1 heterozygous knock-out mice.
Runx2/Cbfa1 is essential for osteoblast differentiation and bone formation. Runx2 null mice (Runx2(-/-)) completely lack mineralized tissue and die soon after birth, whereas Runx2 heterozygous knock-out mice (Runx2(+/-)) stay alive but show morphological defects in the skeletal system as observed in cleidocranial dysplasia (CCD) in humans. The aim of this study is to elucidate the role of Runx2 in adult mineralized tissue and also to reveal the distinct features of heterozygous deletion of Runx2 in response to tooth movement. Therefore, we examined the cranium, tooth and the periodontium in adult Runx2(+/-) using soft X-ray and micro-CT. In addition, tooth movement induced by mechanical loading was evaluated. In adult Runx2(+/-), crown:root ratio of the first maxillary molar was significantly lower than that of wild type (WT). Irregularities in root morphology was also observed. The cranium was narrow with thin parietal bone compared to WT. Mechanical stress-induced tooth movement was similar between Runx2(+/-) and WT in terms of movement distance. However, while rotational movement between the first and third week was increased in WT, it was not altered in Runx2(+/-) mice. These data indicate that Runx2 plays a role in cranium and the tooth development in adulthood.


EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python.
The Empirical Mode Decomposition (EMD) package contains Python (>=3.5) functions for analysis of non-linear and non-stationary oscillatory time series. EMD implements a family of sifting algorithms, instantaneous frequency transformations, power spectrum construction and single-cycle feature analysis. These implementations are supported by online documentation containing a range of practical tutorials.


The role of biomechanics and inflammation in cartilage injury and repair.
Osteoarthritis is a painful and debilitating disease characterized by progressive degenerative changes in the articular cartilage and other joint tissues. Biomechanical factors play a critical role in the initiation and progression of this disease, as evidenced by clinical and animal studies of alterations in the mechanical environment of the joint caused by trauma, joint instability, disuse, or obesity. The onset of these changes after joint injury generally has been termed posttraumatic arthritis and can be accelerated by factors such as a displaced articular fracture. Within this context, there is considerable evidence that interactions between biomechanical factors and proinflammatory mediators are involved in the progression of cartilage degeneration in posttraumatic arthritis. In vivo studies have shown increased concentrations of inflammatory cytokines and mediators in the joint in mechanically induced models of osteoarthritis. In vitro explant studies confirm that mechanical load is a potent regulator of matrix metabolism, cell viability, and the production of proinflammatory mediators such as nitric oxide and prostaglandin E2. Knowledge of the interaction of inflammatory and biomechanical factors in regulating cartilage metabolism would be beneficial to an understanding of the etiopathogenesis of posttraumatic osteoarthritis and in the improvement of therapies for joint injury.


Outcomes for HIV-associated diffuse large B-cell lymphoma in the modern combined antiretroviral therapy era.
Non-Hodgkin's lymphoma (NHL) remains among the most frequent malignancies in persons living with HIV (PLWHIV). Survival among patients with HIV-associated diffuse large B-cell lymphoma (DLBCL), the most frequent NHL subtype, has improved markedly in recent years. We aimed to analyze characteristics and outcomes of DLBCL in HIV-infected patients in the era of modern combined antiretroviral therapy (cART). PLWHIV with lymphoma were prospectively enrolled in the French ANRS-CO16 Lymphovir cohort between 2008 and 2015. We compared the patients treated with R-CHOP) (rituximab, cyclophosphamide, daunorubicin, vin-cristine, prednisolone) with HIV-negative DLBCL patients enrolled simultaneously in the R-CHOP arms of Lymphoma Study Association trials. Among 110 PLWHIV with NHL, 52 (47%) had systemic DLBCL. These 52 cases had frequent extranodal disease (81%), poor performance status (35%) and advanced age-adjusted international prognostic index (aaIPI) (58%), and were mainly treated with R-CHOP (n = 44, 85%). Their median CD4 T-cell count was 233 cells/μl, and 79% of patients were on cART. The 2-year overall and progression-free survival rates were both 75% (95% confidence interval: 64%, 88%). Factors associated with progression or death in univariate analysis were poor performance status [hazard ratio: 3.3 (1.2, 8.9)], more than one extranodal site [hazard ratio: 3.4 (1.1, 10.5)] and an advanced aaIPI [hazard ratio: 3.7 (1.0, 13.1)]. Progression-free survival after R-CHOP therapy did not differ from that of the HIV-negative counterparts (P = 0.11). In the recent cART era, despite frequent high-risk features, the 2-year overall survival of HIV-DLBCL patients reaches 75%. Outcomes after R-CHOP therapy are similar to those of HIV-negative patients with similar aaIPI.


Effect of anthocyanin-rich blackberry juice on endoplasmic reticulum stress in streptozotocin-induced diabetic rats.
This study investigates blackberry juice's effects on glucose metabolism, oxidative stress, inflammation, and endoplasmic reticulum stress (ER) in streptozotocin (STZ)-induced diabetic rats. Fifty Wistar rats were distributed to five groups randomly of ten rats each: Normal control, diabetic control, 9 mL/kg body weight (b.wt) blackberry juice only, blackberry juice plus diabetes, and 500 mg/kg b.wt metformin plus diabetes. A single intraperitoneal injection of 50 mg/kg b.wt STZ induced diabetes in the rats. This animal study continued for 56 days after the confirmation of diabetes. The levels of liver function and renal function, as well as insulin, glucose-6-phosphatase, glucokinase, and malondialdehyde (MDA) levels, and the activities of catalase (CAT) and superoxide dismutase (SOD), were determined. Additionally, interleukin-6 (IL-6) levels, tumor necrosis factor-alpha (TNF-α), and activated transcription factor 4 (ATF4) expressions were examined in the liver homogenate of rats. Furthermore, the liver tissues were utilized for histopathological examination. The results showed that blackberry juice prevented drastic loss of body weight and reduced food consumption in diabetic rats. Additionally, the levels of blood glucose, total protein, aspartate aminotransferase (AST), albumin, alanine aminotransferase (ALT), uric acid, creatinine, and urea improved after the administration of blackberry juice in diabetic rats. Blackberry juice significantly increased glucose metabolism and antioxidant status while reducing ER stress and inflammation in diabetic rats. Moreover, blackberry juice improved glucose metabolism by increasing insulin levels and improving the dysregulated activities of glucose-metabolizing enzymes. The microstructure of liver tissues in diabetic rats was also improved with blackberry juice treatment. Therefore, blackberry juice has the potential to alleviate diabetes in rats and could be considered as a functional food for people with diabetes.


Sinus surgery and delivery method influence the effectiveness of topical corticosteroids for chronic rhinosinusitis: systematic review and meta-analysis.
Published randomized controlled trials (RCTs) on the efficacy of intranasal corticosteroid (INCS) in chronic rhinosinusitis (CRS) use either nasal delivery (nasal drop or nasal spray) or sinus delivery (sinus catheter or sinus irrigation) in patients with or without sinus surgery. This influences topical drug delivery and distribution. The effect of these factors on the published results of RCTs is assessed. This systematic review explores the strength of evidence supporting the influence of sinus surgery and delivery methods on the effectiveness of topical steroids in studies for CRS with meta-analyses. A systematic review was conducted of RCTs comparing INCS with either placebo or no intervention for treating CRS. Data were extracted for meta-analysis and subgroup analyses by sinus surgery status and topical delivery methods. Forty-eight studies (3961 patients) met the inclusion criteria. INCS improved overall symptoms (standardized mean difference [SMD], -0.49; p < 0.00001) and the proportion of responders (risk ratio [RR], 0.59; p < 0.00001) compared with placebo. It decreased nasal polyp size with a greater proportion of responders (RR, 0.48; p < 0.00001) and prevented polyp recurrence (RR, 0.59; p = 0.0004) compared with placebo. Reduction of polyp size was greater in patients with sinus surgery (RR, 0.31; 95% confidence interval [CI], 0.20, 0.48) than those without (RR, 0.61; 95% CI, 0.46, 0.81; p = 0.009). Greater symptom improvement occurred when sinus delivery methods (SMD, -1.32; 95% CI, -2.26, -0.38) were compared with nasal delivery methods (SMD, -0.38; 95% CI, -0.55, -0.22; p < 0.00001). INCS is effective for CRS. Prior sinus surgery and direct sinus delivery enhance the effectiveness of INCS in CRS.


On the safety assessment of human exposure in the proximity of cellular communications base-station antennas at 900, 1800 and 2170 MHz.
In this work, the procedures for safety assessment in the close proximity of cellular communications base-station antennas at three different frequencies (900, 1800 and 2170 MHz) are analysed. For each operating frequency, we have obtained and compared the distances to the antenna from the exposure places where electromagnetic fields are below reference levels and the distances where the specific absorption rate (SAR) values in an exposed person are below the basic restrictions, according to the European safety guidelines. A high-resolution human body model has been located, in front of each base-station antenna as a worst case, at different distances, to compute whole body averaged SAR and maximum 10 g averaged SAR inside the exposed body. The finite-difference time-domain method has been used for both electromagnetic fields and SAR calculations. This paper shows that, for antenna-body distances in the near zone of the antenna, the fact that averaged field values be below the reference levels could, at certain frequencies, not guarantee guidelines compliance based on basic restrictions.


Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting.
Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.


Artificial switchable catalysts.
Catalysis is key to the effective and efficient transformation of readily available building blocks into high value functional molecules and materials. For many years research in this field has largely focussed on the invention of new catalysts and the optimization of their performance to achieve high conversions and/or selectivities. However, inspired by Nature, chemists are beginning to turn their attention to the development of catalysts whose activity in different chemical processes can be switched by an external stimulus. Potential applications include using the states of multiple switchable catalysts to control sequences of transformations, producing different products from a pool of building blocks according to the order and type of stimuli applied. Here we outline the state-of-art in artificial switchable catalysis, classifying systems according to the trigger used to achieve control over the catalytic activity and stereochemical or other structural outcomes of the reaction.


Quantum interferences and electron transfer in photosystem I.
We have studied the electron transfer occurring in the photosystem I (PSI) reaction center from the special pair to the first iron-sulfur cluster. Electronic structure calculations performed at the DFT level were employed to determine the on-site energies of the fragments comprising PSI, as well as the charge transfer integrals between neighboring pairs. This electronic Hamiltonian was then used to compute the charge transfer dynamics, using the stochastic surrogate Hamiltonian approach to account for the coherent propagation of the electronic density but also for its energy relaxation and decoherence. These simulations give reasonable transfer time ranging from subpicoseconds to nanoseconds and predict coherent oscillations for several picoseconds. Due to these long-lasting coherences, the propagation of the electronic density can be enhanced or inhibited by quantum interferences. The impact of random fluctuations and asymmetries on these interferences is then discussed. Random fluctuations lead to a classical transport where both constructive and destructive quantum interferences are suppressed. Finally it is shown that an energy difference of 0.15 eV between the on-site energies of the phylloquinones leads to a highly efficient electron transfer even in presence of strong random fluctuations.


The use of human patient simulators: best practices with novice nursing students.
Only recently have nursing educators begun to consider the enormous implications of using high-fidelity human patient simulation in general nursing education. As a first step in exploring the potential of this new technology with novice nursing students, faculty conducted a quantitative and qualitative analysis of students' reactions to a simulation. In addition, from the analysis and the review of literature, the faculty identified specific best practices for using this educational methodology with novice nursing students.


Sensitivity analysis of discrete-time interregional population systems.
This paper shows analytically how (a) the long-run growth rate and (b) the long-run proportional distribution of an interregional population system with a time-homogeneous structural matrix are affected by small changes or errors in (a) the natural growth rates of individual regions and (b) the interregional migration rates. Furthermore, the analytic results are applied to an eight-region Canadian population system. Finally, it is claimed that the method introduced here can be easily applied to sensitivity analysis of both the intrinsic growth rate and the "stable" age-composition of the Leslie model with respect to changes in age-specific birth and survival rates.


Regulation of the dynamics of hsp90 action on the glucocorticoid receptor by acetylation/deacetylation of the chaperone.
It is known that inhibition of histone deacetylases (HDACs) leads to acetylation of the abundant protein chaperone hsp90. In a recent study, we have shown that knockdown of HDAC6 by a specific small interfering RNA leads to hyperacetylation of hsp90 and that the glucocorticoid receptor (GR), an established hsp90 "client" protein, is defective in ligand binding, nuclear translocation, and gene activation in HDAC6-deficient cells (Kovacs, J. J., Murphy, P. J. M., Gaillard, S., Zhao, X., Wu, J-T., Nicchitta, C. V., Yoshida, M., Toft, D. O., Pratt, W. B., and Yao, T-P. (2005) Mol. Cell 18, 601-607). Using human embryonic kidney wild-type and HDAC6 (small interfering RNA) knockdown cells transiently expressing the mouse GR, we show here that the intrinsic properties of the receptor protein itself are not affected by HDAC6 knockdown, but the knockdown cytosol has a markedly decreased ability to assemble stable GR.hsp90 heterocomplexes and generate stable steroid binding activity under cell-free conditions. HDAC6 knockdown cytosol has the same ability to carry out dynamic GR.hsp90 heterocomplex assembly as wild-type cytosol. Addition of purified hsp90 to HDAC6 knockdown cytosol restores stable GR.hsp90 heterocomplex assembly to the level of wild-type cytosol. hsp90 from HDAC6 knockdown cytosol has decreased ATP-binding affinity, and it does not assemble stable GR.hsp90 heterocomplexes when it is a component of a purified five-protein assembly system. Incubation of knockdown cell hsp90 with purified HDAC6 converts the hsp90 to wild-type behavior. Thus, acetylation of hsp90 results in dynamic GR.hsp90 heterocomplex assembly/disassembly, and this is manifest in the cell as a approximately 100-fold shift to the right in the steroid dose response for gene activation.


Searching for Paralympians: Characteristics of Participants Attending "Search" Events.
Initiatives have been designed to attract novice athletes and to enable transfer for experienced athletes. However, the authors have very little knowledge of the effectiveness of these programs. To further improve our understanding, this study explored the demographic and sporting careers of 225 participants attending one of the 10 Paralympian Search events held between 2016 and 2018. The sample consisted of participants with a wide range of impairments and sport experiential backgrounds. The majority of the participants reported having some experience in sports, suggesting that either the promotions reached athletes involved in sports already or the advertising appealed especially to this cohort. Athletes with impairments acquired at various stages of their lives (congenital, before adolescence, adolescence, early adulthood, and adulthood) displayed differences in their sporting trajectories, suggesting considerations for current developmental models. Furthermore, it should be considered to vary the testing locations of future events to increase the reach to rural areas and implement new methods to attract novice participants.


Serous cystadenoma of pancreas: A clinicopathologic experience of 23 cases from a major tertiary care center.
Serous cystadenomas of pancreas are rare benign epithelial neoplasms, which predominantly occur in the pancreatic body and tail of elderly females. Majority of these tumors have microcystic appearance. Macrocystic and solid variants have also been described. A number of more aggressive cystic pancreatic lesions are included in the differential diagnosis. Distinction from such lesions is important for optimal management. Our aim was to study the clinical and histological features of serous cystadenomas which would be helpful in making their correct diagnosis and understanding their behavior. We reviewed 23 cases of serous cystadenomas diagnosed in our institution between January 2001 and June 2018. Mean age at presentation was 53.43 years. Female to male ratio was 4.75:1. Over half (56.5%) of the cases were diagnosed incidentally. Abdominal pain was the most common symptom. Body and tail (either alone or in combination) were the most common locations. Tumor size ranged from 2 to 16 cm. Central scar was seen in 43.4% cases. Two cases were unilocular (macrocystic). Microscopically, all cases showed simple cuboidal to flattened epithelium with round, uniform nuclei, and glycogen-rich clear cytoplasm. Focal micropapillae formation was seen in eight cases (34.7%). Surgical resection was performed in 82.6% cases. Recurrence occurred in only one single case. Pancreatic serous cystadenomas are benign neoplasms with excellent prognosis. The tumors showed typical morphological features in all cases. Surgical resection was performed in the majority of cases in our study owing to lack of optimal and complete radiological workup pre-operatively and the concern for not missing and adequately treating pancreatic mucinous cystic neoplasms.


Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays.
A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity.


Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA.
Molecular evolution can be conceptualized as a walk over a "fitness landscape", or the function of fitness (e.g., catalytic activity) over the space of all possible sequences. Understanding evolution requires knowing the structure of the fitness landscape and identifying the viable evolutionary pathways through the landscape. However, the fitness landscape for any catalytic biomolecule is largely unknown. The evolution of catalytic RNA is of special interest because RNA is believed to have been foundational to early life. In particular, an essential activity leading to the genetic code would be the reaction of ribozymes with activated amino acids, such as 5(4 H)-oxazolones, to form aminoacyl-RNA. Here we combine in vitro selection with a massively parallel kinetic assay to map a fitness landscape for self-aminoacylating RNA, with nearly complete coverage of sequence space in a central 21-nucleotide region. The method (SCAPE: sequencing to measure catalytic activity paired with in vitro evolution) shows that the landscape contains three major ribozyme families (landscape peaks). An analysis of evolutionary pathways shows that, while local optimization within a ribozyme family would be possible, optimization of activity over the entire landscape would be frustrated by large valleys of low activity. The sequence motifs associated with each peak represent different solutions to the problem of catalysis, so the inability to traverse the landscape globally corresponds to an inability to restructure the ribozyme without losing activity. The frustrated nature of the evolutionary network suggests that chance emergence of a ribozyme motif would be more important than optimization by natural selection.


Cloning and expression of a human voltage-gated potassium channel. A novel member of the RCK potassium channel family.
We have isolated and characterized a human cDNA (HBK2) that is homologous to novel member (RCK2) of the K+ channel RCK gene family expressed in rat brain. RCK2 mRNA was detected predominantly in midbrain areas and brainstem. The primary sequences of the HBK2/RCK2 K+ channel proteins exhibit major differences to other members of the RCK gene family. The bend region between segments S1 and S2 is unusually long and does not contain the N-glycosylation site commonly found in this region. They might be O-glycosylated instead. Functional characterization of the HBK2/RCK2 K+ channels in Xenopus laevis oocytes following micro-injection in in vitro transcribed HBK2 or RCK2 cRNA showed that the HBK2/RCK2 proteins form voltage-gated K+ channels with novel functional and pharmacological properties. These channels are different to RCK1, RCK3, RCK4 and RCK5 K+ channels.


Bacillus clausii effect on gene expression pattern in small bowel mucosa using DNA microarray analysis.
Probiotics are widely used for the cure or prevention of several clinical conditions. However, clinical decisions need to be substantiated by an analysis of the complex bacteria-host interplay in the intestinal lumen. To identify the gene expression pattern induced by Bacillus clausii in the intestinal mucosa of healthy individuals. Six male patients (mean age 38+/-5 years) affected by endoscopically confirmed mild oesophagitis were treated for one month with esomeprazole, and were randomly selected to receive or not B. clausii (groups I and II, respectively). Duodenal biopsies were taken pre and post-treatment to identify the modification of gene expression, using the GeneChip Human U133A array. To validate the microarray analysis, real-time reverse transcriptase-polymerase chain reaction (PCR) of five target genes was performed. After B. clausii administration, a total of 158 and 265 genes were up and downregulated, respectively. Quantitative PCR confirmed the microarray data. B. clausii mainly affected the expression of genes involved in immune response and inflammation, apoptosis and cell growth, cell differentiation, cell-cell signalling, cell adhesion, signal transcription and transduction. Our data represent the first global analysis of B. clausii effects on the gene expression profile in normal intestine, and provide the basis to identify the mechanisms by which these agents interact with the host and exert their beneficial effects. Future studies are needed to clarify the B. clausii-induced gene pattern in the clinical disorders in which probiotics have proved to be effective.


Battle for the thermostat: Gender and the effect of temperature on cognitive performance.
This paper studies differences in the effect of temperature on cognitive performance by gender in a large controlled lab experiment (N = 543). We study performance in math, verbal and cognitive reflection tasks and find that the effects of temperature vary significantly across men and women. At higher temperatures, women perform better on a math and verbal task while the reverse effect is observed for men. The increase in female performance in response to higher temperature is significantly larger and more precisely estimated than the corresponding decrease in male performance. In contrast to math and verbal tasks, temperature has no impact on a measure of cognitive reflection for either gender. Our findings suggest that gender mixed workplaces may be able to increase productivity by setting the thermostat higher than current standards.


Temporal trends and black-white disparity in mortality among hospitalized persons living with HIV in the United States.
We sought to determine whether black-white gap in mortality exists among hospitalized HIV-positive patients in the United States (US). We hypothesized that in-hospital mortality (IHM) would be similar between black and white HIV-positive patients due to the nationwide availability of HIV services.Our analysis was restricted to hospitalized HIV-positive patients (15-49 years). We used the National Inpatient Sample (NIS) that covered the period from January 1, 2002 to December 31, 2014. We employed joinpoint regression to construct temporal trends in IHM overall and within subgroups over the study period. We applied multivariable survey logistic regression to generate adjusted odds ratios (OR) and 95% confidence intervals (CI).The total number of HIV-related hospitalizations and IHM decreased over time, with 6914 (3.9%) HIV-related in-hospital deaths in 2002 versus 2070 HIV-related in-hospital deaths (1.9%) in 2014, (relative reduction: 51.2%). HIV-related IHM among blacks declined at a slightly faster rate than in the general population (by 56.8%, from 4.4% to 1.9%). Among whites, the drop was similar to that of the general population (51.2%, from 3.9% to 1.9%). Although IHM rates did not differ between blacks and whites, being black with HIV was independently associated with a 17% elevated odds for IHM (OR = 1.17; 95% CI = 1.11-1.25).In-hospital HIV-related deaths continue to decline among both blacks and whites in the US. Among hospitalized HIV-positive patients black-white disparity still persists, but to a lesser extent than in the general HIV population. Improved access to HIV care is a key to eliminating black-white disparity in HIV-related mortality.


The paradigm model of distorted doctor-patient relationship in Southern Iran: a grounded theory study.
The doctor-patient relationship (DPR) is one of the most important subjects in medical sociology and health policy. Due to mutual understanding, undistorted DPRs not only result in satisfaction of both doctors and patients, but also help to reduce financial burdens for patients and the health care system. The purpose of this research was to identify a DPR based on the qualitative paradigm model which is called the grounded theory (GT) methodology. The data were collected from 3 focus groups, the participants of which consisted of 21 faculty members of Shiraz University of Medical Sciences, Shiraz, Iran. The content of the interviews, following the transcription stage, was organized based on open, axial, and selective coding. Results showed that DPR was distorted which was the consequence of an inefficient structure in the healthcare system which is related to several cultural barriers. In this situation, agency is determinant so the doctor's personality determines the direction of DPR. Consequences of such scenarios are the patient's distrust, patient's dissatisfaction, lack of mutual understanding, patient suppression, and patient deception. Therefore, the health care system should emphasize on reforming its inefficient infrastructures, so that, besides being controlled and surveyed, physicians are socialized ethically.


Oral lactoferrin treatment resolves amoebic intracecal infection in C3H/HeJ mice.
Entamoeba histolytica is a protozoan parasite that causes amoebiasis, an illness that affects many people around the world. We have previously reported that lactoferrin is able to kill E. histolytica in in vitro cultures. The aim of the present study was to evaluate the therapeutic effect of orally administered bovine lactoferrin in the control of intestinal amoebiasis of susceptible C3H/HeJ mice. The results showed that 20 mg lactoferrin/kg orally administered each day for 1 week was able to eliminate the infection in 63% of the mice, since neither trophozoites nor evidence of epithelial damage and (or) swelling were found in tissue sections of the cecum. The rest of the treated animals (37%) showed a decrease in trophozoite numbers and mucus secreted to the lumen, as compared with untreated and infected mice (p < 0.05). By immunohistochemistry, the profile of secreted cytokines in the cecum revealed that infected but untreated animals showed a mixed Th1/regulatory cytokines profile, whereas the cecum of mice treated (cured) showed a Th2 cytokine profile (IL-4) and expression of the multifunctional IL-6. In addition, cytokines and increasing cecal production of total IgA antibodies were found associated with little inflammation and disease control observed in the cecum of lactoferrin-treated animals. These results suggest that oral administration of lactoferrin can control intestinal amoebic infection probably by killing amoebas or favoring their removal and reestablish the antiinflammatory intestinal environment.


Seasonal changes in prescribing of long-acting beta-2-agonists-containing drugs.
For patients with asthma, COPD, or asthma-COPD overlap syndrome (ACOS), inter-country comparisons of seasonal changes in drug prescriptions are scarce or missing. Hence, we aimed to compare seasonal changes in prescription rates of long-acting beta-2-agonist (LABA) in four European countries. A common study protocol was applied to six health care databases (Germany, Spain, the Netherlands (2), and the UK (2)) to calculate age- and sex-standardized point prevalence rates (PPRs) of LABA-containing prescriptions by the 1st of March, June, September, and December of each year during the study period 2002-2009. Seasonal variation of PPRs was quantified using seasonal indexes (SIs; based on the ratio-to-moving-average-method) and SIs averaged over the study period (aSI) stratified by sex, age, and indication (asthma, COPD, or ACOS). There was a moderate seasonal change in LABA-containing prescriptions which was more pronounced in asthma or COPD patients compared to ACOS patients. For asthma and ACOS patients, highest seasonal variation was found for patients living in Spain (aSI: 87.3-110.7, aSI: 93.2-103.1) whereas for COPD highest seasonal variation was revealed for the NPCRD database (the Netherlands) (aSI: 92.2-105.6). Regarding age and sex, highest seasonal variation was found in Spanish boys under 10 years of age having a diagnosis of asthma. By applying a common analysis in six databases, we could observe moderate overall seasonal changes in LABA-containing prescription rates in patients with asthma, COPD, or ACOS.


Successful pregnancy and normal delivery after whole craniospinal irradiation in two patients.
Two cases of normal pregnancies and deliveries after whole craniospinal irradiation (WCSI) are described, and whether the ovaries can be left out of the WCSI field by identifying ovarian position using magnetic resonance imaging (MRI) is determined. The distance between the upper edge of the pubic symphysis and the central part of the ovary was measured on MRI in 17 women. The right ovary was located 20.3-68.4 mm to the right of and 33.7-113.5 mm above the upper edge of the pubic symphysis; the left ovary was located 26.2-72.5 mm to the left and 25.8-106.6 mm above this edge. The lower border of the spinal field in WCSI should be the caudal border of the thecal sac, i.e., S2-S4. The line of this location, which nearly approximates normal ovarian position, should be employed in radiotherapy planning to avoid irradiating at least one ovary with its thecal sac. Omitting this area from the WCSI field in women of childbearing age with a good long-term prognosis, preserves potential fertility. It appears that the ovaries might be excluded from the WCSI field, using appropriate techniques, so as to preserve female fertility.


Endothelin receptor in human astrocytoma U373MG cells: binding, dissociation, receptor internalization.
Endothelin (ET) receptor in human astrocytoma U373MG cells was characterized. ET-1, ET-3, sarafotoxin S6C, IRL1620, BQ788, Ro46-2005 and PD142893 inhibited specific [125I]ET-1 binding with Ki values of 0.03 0.06, 0.74, 5.01, 4.45, 2275 and 157 nM, respectively. ETA selective antagonists BQ123 and FR139317 at 1 microM did not block [125I]ET-1 binding. Reverse transcription-polymerase chain reaction confirmed the results from competition studies that U373 cells expressed predominantly ETB receptor. The Bmax and KD values of [125I]ET-1 binding were 0.15 pmol/1 x 10(6) cells and 0.23 nM. The molecular mass for the receptor was 45 kDa. ET-1 binding did not stimulate Ca+2 mobilization, phosphatidylinositol hydrolysis or arachidonic acid release, nor did it affect the intracellular cAMP or cGMP level. Interestingly, a majority of ET (> 80%) bound to the receptor was rapidly internalized, consistent with emerging evidence that a major function of ETB receptor is to clear ET. [125I]ET-1 binding was time-dependent and bound [125I]ET-1 was difficult to dissociate. In contrast, bound antagonists were much easier to dissociate. The results suggest that agonists and antagonists of the ET receptor exhibited different dissociation characteristics, with antagonist binding more reversible than agonist binding.


Review: Melatonin stimulates the synthesis and release of gonadotropin-inhibitory hormone in birds.
Gonadotropin-inhibitory hormone (GnIH), a neuropeptide that inhibits gonadotropin synthesis and release, was first identified in the quail hypothalamus. To understand the physiological role of GnIH, this review will demonstrate the mechanisms that regulate GnIH synthesis and release. Pinealectomy (Px) combined with orbital enucleation (Ex) decreased the synthesis of GnIH precursor mRNA and content of mature GnIH peptide in the diencephalon. Melatonin administration to Px plus Ex birds caused a dose-dependent increase in the synthesis of GnIH precursor mRNA and production of mature peptide. A melatonin receptor subtype, Mel(1c,) was expressed in GnIH-immunoreactive neurons, suggesting direct action of melatonin on GnIH neurons. Melatonin administration further increased GnIH release in a dose-dependent manner from hypothalamic explants in vitro. GnIH mRNA expression and GnIH release during the dark period were greater than those during the light period in explants from quail exposed to long-day photoperiods. Conversely, plasma luteinizing hormone (LH) concentration decreased during the dark period. This review summarizes that melatonin appears to act on GnIH neurons in stimulating not only GnIH synthesis but also its release, thus inhibiting plasma LH concentration in birds.


Linking out-of-body experience and self processing to mental own-body imagery at the temporoparietal junction.
The spatial unity of self and body is challenged by various philosophical considerations and several phenomena, perhaps most notoriously the "out-of-body experience" (OBE) during which one's visual perspective and one's self are experienced to have departed from their habitual position within one's body. Although researchers started examining isolated aspects of the self, the neurocognitive processes of OBEs have not been investigated experimentally to further our understanding of the self. With the use of evoked potential mapping, we show the selective activation of the temporoparietal junction (TPJ) at 330-400 ms after stimulus onset when healthy volunteers imagined themselves in the position and visual perspective that generally are reported by people experiencing spontaneous OBEs. Interference with the TPJ by transcranial magnetic stimulation (TMS) at this time impaired mental transformation of one's own body in healthy volunteers relative to TMS over a control site. No such TMS effect was observed for imagined spatial transformations of external objects, suggesting the selective implication of the TPJ in mental imagery of one's own body. Finally, in an epileptic patient with OBEs originating from the TPJ, we show partial activation of the seizure focus during mental transformations of her body and visual perspective mimicking her OBE perceptions. These results suggest that the TPJ is a crucial structure for the conscious experience of the normal self, mediating spatial unity of self and body, and also suggest that impaired processing at the TPJ may lead to pathological selves such as OBEs.


A prospective cohort study of postmenopausal hormone use and risk of breast cancer in US women.
The association between history of postmenopausal hormone use as of 1976 and breast cancer incidence during 1976-1980 was examined prospectively among 33,335 married, postmenopausal registered nurses aged 30-55 years at entry. Half the women reported postmenopausal hormone use, and one fourth had taken these drugs for over five years. During 1976-1980, 221 new cases of breast cancer were identified. The relative risk (RR) for those who had used postmenopausal hormones when compared with women who had never used them was 1.1 (95% confidence limits (CL) 0.8, 1.4); for current and past users, the relative risks were 1.0 (95% CL 0.7, 1.4) and 1.3 (95% CL 0.9, 1.8), respectively. These ratios were not substantially modified by whether or not a woman's ovaries had been removed or by other known breast cancer risk factors. No increase in breast cancer risk was apparent among women who had used postmenopausal hormones for less than five years (RR = 1.0, 95% CL 0.5, 1.6). An apparent effect among the subgroup of women who had used them for five to nine years (RR = 1.5, 95% CL 1.0, 2.2) was not present among the few women with longer-term use (RR = 0.9, 95% CL 0.4, 1.6). These findings are moderately reassuring, but since there are as yet few women in this cohort with long-term durations of use and, particularly, with long intervals since first use, continued follow-up of this and other cohorts will be required before firm conclusions can be drawn, especially among specific subgroups.


Runners in their forties dominate ultra-marathons from 50 to 3,100 miles.
This study investigated performance trends and the age of peak running speed in ultra-marathons from 50 to 3,100 miles. The running speed and age of the fastest competitors in 50-, 100-, 200-, 1,000- and 3,100-mile events held worldwide from 1971 to 2012 were analyzed using single- and multi-level regression analyses. The number of events and competitors increased exponentially in 50- and 100-mile events. For the annual fastest runners, women improved in 50-mile events, but not men. In 100-mile events, both women and men improved their performance. In 1,000-mile events, men became slower. For the annual top ten runners, women improved in 50- and 100-mile events, whereas the performance of men remained unchanged in 50- and 3,100-mile events but improved in 100-mile events. The age of the annual fastest runners was approximately 35 years for both women and men in 50-mile events and approximately 35 years for women in 100-mile events. For men, the age of the annual fastest runners in 100-mile events was higher at 38 years. For the annual fastest runners of 1,000-mile events, the women were approximately 43 years of age, whereas for men, the age increased to 48 years of age. For the annual fastest runners of 3,100-mile events, the age in women decreased to 35 years and was approximately 39 years in men. The running speed of the fastest competitors increased for both women and men in 100-mile events but only for women in 50-mile events. The age of peak running speed increased in men with increasing race distance to approximately 45 years in 1,000-mile events, whereas it decreased to approximately 39 years in 3,100-mile events. In women, the upper age of peak running speed increased to approximately 51 years in 3,100-mile events.


Learning curves in surgery: variables, analysis and applications.
Learning curves graphically represent the relationship between learning effort and learning outcome. Learning curves are increasingly used in research, the design of randomised controlled trials, the assessment of competency, healthcare education and training programme design. In this review we have outlined the principles behind plotting learning curves, described the common methods used to analyse learning curves, how to interpret learning curves, the multitude of learning models, their applications and potential pitfalls, and the importance of a mathematically rigorous approach to learning curve analytics.


Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods.
A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea-land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum-likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic-Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.


Does Muscle Mass Affect Running Times in Male Long-distance Master Runners?
The aim of the present study was to investigate associations between skeletal muscle mass, body fat and training characteristics with running times in master athletes (age > 35 years) in half-marathon, marathon and ultra-marathon. We compared skeletal muscle mass, body fat and training characteristics in master half-marathoners (n=103), master marathoners (n=91) and master ultra-marathoners (n=155) and investigated associations between body composition and training characteristics with race times using bi- and multi-variate analyses. After multi-variate analysis, body fat was related to half-marathon (β=0.9, P=0.0003), marathon (β=2.2, P<0.0001), and ultra-marathon (β=10.5, P<0.0001) race times. In master half-marathoners (β=-4.3, P<0.0001) and master marathoners (β=-11.9, P<0.0001), speed during training was related to race times. In master ultra-marathoners, however, weekly running kilometers (β=-1.6, P<0.0001) were related to running times. To summarize, body fat and training characteristics, not skeletal muscle mass, were associated with running times in master half-marathoners, master marathoners, and master ultra-marathoners. Master half-marathoners and master marathoners rather rely on a high running speed during training whereas master ultra-marathoners rely on a high running volume during training. The common opinion that skeletal muscle mass affects running performance in master runners needs to be questioned.


The impact of Theileria parva infections and other factors on calf mean daily weight gains in smallholder dairy farms in Murang'a District, Kenya.
The association between mean daily weight gain, Theileria parva infections, clinical East Coast fever and other possible determinants of weight gain were examined in a longitudinal observational study that was conducted in cohorts of female calves from five agro-ecological zone (AEZ)-grazing strata. The strata were upper-midlands (UM) 1 zero-grazing, UM 1 open-grazing, UM 2 zero-grazing, UM 4 zero-grazing and UM 4 open-grazing. In total, 225 calves on 188 smallholder dairy farms were visited within the first 2 weeks of life and thereafter at biweekly intervals up to the age of 6 months between March 1995 and August 1996. During each visit, the calves were weighed and other calf-management practices in the farm during the visit such as housing, feeding and tick control also were recorded. Other events such as morbidity and mortality between or during the visits were also recorded. The overall mean daily weight gains were 0.24-0.29 kg (S.D.=0.17-0.22 kg) and were lower than the recommended targets for smallholder farms of 0.40-0.50 kg. The major tendency in variability of daily weight gains was due to visit-to-visit variation (especially in calves >3 months old). Differences in mean daily gains were associated with AEZ-grazing strata and calf-level factors that included breed of calf, calf sickness, incidence of ECF, feeding of milk, concentrate feeds and minerals and interaction between calf age and AEZ-grazing strata (P<0.05). ECF and other calf sicknesses exerted a temporal effect on calf-growth at the height of illness and immediately after; calves later recovered the lost growth except where other factors such as poor calf nutrition prevailed. Improvement in calf-growth in Murang'a District is achievable and extension services should continue to target individual-calf-level management practices.


Aerosol infection model of tuberculosis in wistar rats.
We explored suitability of a rat tuberculosis aerosol infection model for investigating the pharmacodynamics of new antimycobacterial agents. Infection of rats via the aerosol route led to a reproducible course of M. tuberculosis infection in the lungs. The pulmonary bacterial load increased logarithmically during the first six weeks, thereafter, the infection stabilized for the next 12 weeks. We observed macroscopically visible granulomas in the lungs with demonstrable acid-fast bacilli and associated histopathology. Rifampicin (RIF) at a dose range of 30 to 270 mg/kg exhibited a sharp dose response while isoniazid (INH) at a dose range of 10 to 90 mg/kg and ethambutol (EMB) at 100 to 1000 mg/kg showed shallow dose responses. Pyrazinamide (PZA) had no dose response between 300 and 1000 mg/kg dose range. In a separate time kill study at fixed drug doses (RIF 90 mg/kg, INH 30 mg/kg, EMB 300 mg/kg, and PZA 300 mg/kg) the bactericidal effect of all the four drugs increased with longer duration of treatment from two weeks to four weeks. The observed infection profile and therapeutic outcomes in this rat model suggest that it can be used as an additional, pharmacologically relevant efficacy model to develop novel antitubercular compounds at the interface of discovery and development.


Increased ventilation does not impair maximal voluntary contractions of the elbow flexors.
Exercise performance is impaired by increased respiratory work, yet the mechanism for this is unclear. This experiment assessed whether neural drive to an exercising muscle was affected by cortically driven increases in ventilation. On each of 5 days, eight subjects completed a 2-min maximal voluntary contraction (MVC) of the elbow flexor muscles, followed by 4 min of recovery, while transcranial magnetic stimulation tested for suboptimal neural drive to the muscle. On 1 day, subjects breathed without instructions under normocapnia. During the 2-min MVC, ventilation was approximately 3.5 times that at rest. On another day, subjects breathed without instruction under hypercapnia. During the 2-min MVC, ventilation was approximately 1.5 times that on the normocapnic day. On another 2 days under normocapnia, subjects voluntarily matched their breathing to the uninstructed breathing under normocapnia and hypercapnia using target feedback of the rate and inspiratory volume. On a fifth day under normocapnia, the volume feedback was set to each subject's vital capacity. On this day, ventilation during the 2-min MVC was approximately twice that on the uninstructed normocapnic day (or approximately 7 times rest). The experimental manipulations succeeded in producing voluntary and involuntary hyperpnea. However, maximal voluntary force, fatigue and voluntary activation of the elbow flexor muscles were unaffected by cortically or chemically driven increases in ventilation. Results suggest that any effects of increased respiratory work on limb exercise performance are not due to a failure to drive both muscle groups optimally.


DYRK1A-dosage imbalance perturbs NRSF/REST levels, deregulating pluripotency and embryonic stem cell fate in Down syndrome.
Down syndrome (DS) is the most common cause of mental retardation. Many neural phenotypes are shared between DS individuals and DS mouse models; however, the common underlying molecular pathogenetic mechanisms remain unclear. Using a transchromosomic model of DS, we show that a 30%-60% reduced expression of Nrsf/Rest (a key regulator of pluripotency and neuronal differentiation) is an alteration that persists in trisomy 21 from undifferentiated embryonic stem (ES) cells to adult brain and is reproducible across several DS models. Using partially trisomic ES cells, we map this effect to a three-gene segment of HSA21, containing DYRK1A. We independently identify the same locus as the most significant eQTL controlling REST expression in the human genome. We show that specifically silencing the third copy of DYRK1A rescues Rest levels, and we demonstrate altered Rest expression in response to inhibition of DYRK1A expression or kinase activity, and in a transgenic Dyrk1A mouse. We reveal that undifferentiated trisomy 21 ES cells show DYRK1A-dose-sensitive reductions in levels of some pluripotency regulators, causing premature expression of transcription factors driving early endodermal and mesodermal differentiation, partially overlapping recently reported downstream effects of Rest +/-. They produce embryoid bodies with elevated levels of the primitive endoderm progenitor marker Gata4 and a strongly reduced neuroectodermal progenitor compartment. Our results suggest that DYRK1A-mediated deregulation of REST is a very early pathological consequence of trisomy 21 with potential to disturb the development of all embryonic lineages, warranting closer research into its contribution to DS pathology and new rationales for therapeutic approaches.


Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.
Characterizing protein flexibility is an important goal for understanding the physical-chemical principles governing biological function. This paper presents a Fragment Ensemble Method to capture the mobility of a protein fragment such as a missing loop and its extension into a Protein Ensemble Method to characterize the mobility of an entire protein at equilibrium. The underlying approach in both methods is to combine a geometric exploration of conformational space with a statistical mechanics formulation to generate an ensemble of physical conformations on which thermodynamic quantities can be measured as ensemble averages. The Fragment Ensemble Method is validated by applying it to characterize loop mobility in both instances of strongly stable and disordered loop fragments. In each instance, fluctuations measured over generated ensembles are consistent with data from experiment and simulation. The Protein Ensemble Method captures the mobility of an entire protein by generating and combining ensembles of conformations for consecutive overlapping fragments defined over the protein sequence. This method is validated by applying it to characterize flexibility in ubiquitin and protein G. Thermodynamic quantities measured over the ensembles generated for both proteins are fully consistent with available experimental data. On these proteins, the method recovers nontrivial data such as order parameters, residual dipolar couplings, and scalar couplings. Results presented in this work suggest that the proposed methods can provide insight into the interplay between protein flexibility and function.


Measuring school climate in high schools: a focus on safety, engagement, and the environment.
School climate has been linked to multiple student behavioral, academic, health, and social-emotional outcomes. The US Department of Education (USDOE) developed a 3-factor model of school climate comprised of safety, engagement, and environment. This article examines the factor structure and measurement invariance of the USDOE model. Drawing upon 2 consecutive waves of data from over 25,000 high school students (46% minority), a series of exploratory and confirmatory factor analyses examined the fit of the Maryland Safe and Supportive Schools Climate Survey with the USDOE model. The results indicated adequate model fit with the theorized 3-factor model of school climate, which included 13 subdomains: safety (perceived safety, bullying and aggression, and drug use); engagement (connection to teachers, student connectedness, academic engagement, school connectedness, equity, and parent engagement); environment (rules and consequences, physical comfort, and support, disorder). We also found consistent measurement invariance with regard to student sex, grade level, and ethnicity. School-level interclass correlation coefficients ranged from 0.04 to .10 for the scales. Findings supported the USDOE 3-factor model of school climate and suggest measurement invariance and high internal consistency of the 3 scales and 13 subdomains. These results suggest the 56-item measure may be a potentially efficient, yet comprehensive measure of school climate.


Glucose metabolism by Lactobacillus divergens.
Earlier studies on the fermentation of D-[1-14C]- and D-[3,4-14C]glucose by Lactobacillus divergens showed that lactate was the major fermentation product and that it was probably produced by glycolysis. It was therefore recommend that L. divergens be reclassified as a homofermentative organism. In the present investigation, products of D-[1-14C]-,D-[2-14C]- and D-[3,4-14C]glucose fermented by L. divergens were isolated, and their specific radioactivities and the distribution patterns of radioactivity in their C-atoms were determined. The positional labelling patterns of the fermentation products, their specific radioactivities and their concentrations confirmed that glucose is degraded via the glycolytic pathway. Some secondary decarboxylation/dissimilation of pyruvate to acetate, formate and CO2 was also observed. These results provide conclusive proof that L. divergens is indeed a homofermentative organism. Results obtained with D-[U-14C]glucose showed that approximately three-quarters of the lactate but less than 10% each of the formate and acetate were produced from glucose. The remainder was presumably derived to a varying degree from endogenous non-glucose sources such as fructose and/or amino acids.


Reproductive effort and value in different populations of the marine mussel, Mytilus edulis L.
Fecundity, reproductive effort (estimated both from production measurements and from physiological data), the energetic costs of reproduction and the reproductive value of different size classes were measured for mussels at different sites and related to age and to tissue weight. Variability between sites was considerable and differences as great as 10 x were recorded between minimum and maximum values for egg production, reproductive effort and reproductive value. However, similarities between mussels from different sites were also apparent, as regards egg size, the estimated metabolic costs of egg production (based on measurements of oxygen consumption), the relationship (isometric) between egg production and body size, the fact of an increase in reproductive effort with increase in size, and the age at which maximum residual reproductive values was expressed. These relationships are discussed in terms of the fundamental reproductive strategy of the species and the degree of environmental stress imposed on the mussels at the different sites.


Loss of interleukin-21 receptor activation in hypoxic endothelial cells impairs perfusion recovery after hindlimb ischemia.
Surgical hindlimb ischemia (HLI) in mice has become a valuable preclinical model to study peripheral arterial disease. We previously identified that the different phenotypic outcomes after HLI across inbred mouse strains is related to a region on the short arm of mouse chromosome 7. The gene coding the interleukin-21 receptor (IL-21R) lies at the peak of association in this region. With quantitative real-time polymerase chain reaction, we found that a mouse strain with a greater ability to upregulate IL-21R after HLI had better perfusion recovery than a strain with no upregulation after HLI. Immunofluorescent staining of ischemic hindlimb tissue showed IL-21R expression on endothelial cells (ECs) from C57BL/6 mice. An EC-enriched fraction isolated from ischemic hindlimb muscle showed higher Il-21R levels than an EC-enriched fraction from nonischemic limbs. In vitro, human umbilical vein ECs showed elevated IL-21R expression after hypoxia and serum starvation. Under these conditions, IL-21 treatment increased cell viability, decreased cell apoptosis, and augmented tube formation. In vivo, either knockout Il21r or blocking IL-21 signaling by treating with IL-21R-Fc (fusion protein that blocks IL-21 binding to its receptor) in C57BL/6 mice resulted in less perfusion recovery after HLI. Both in vitro and in vivo modulation of the IL-21/IL-21R axis under hypoxic conditions resulted in increased signal transducer and activator of transcription 3 phosphorylation and a subsequent increase in the B-cell lymphoma leukemia-2/BCL-2-associated X protein ratio. Our data indicate that IL-21R upregulation and ligand activation in hypoxic ECs may help perfusion recovery by limiting/preventing apoptosis and favoring cell survival and angiogenesis through the signal transducer and activator of transcription 3 pathway.


Cognitive behavioural therapy as an adjunct to pharmacotherapy for treatment resistant depression in primary care: the CoBalT randomised controlled trial protocol.
Antidepressants are often the first-line treatment for depression but only one third of patients respond fully to pharmacotherapy. This paper describes the protocol for a randomised controlled trial (RCT) designed to evaluate the clinical and cost effectiveness of cognitive behavioural therapy (CBT) as an adjunct to pharmacotherapy for patients with treatment resistant depression in primary care. CoBalT is a two parallel group multi-centre pragmatic RCT. Eligible participants were those who: (i) were aged 18-75years; (ii) were currently taking antidepressant medication (for at least 6weeks at an adequate dose); (iii) scored ≥14 on the Beck Depression Inventory (BDI-II); (iv) had adhered to their medication; and (v) met ICD-10 criteria for depression (assessed using the Clinical Interview Schedule - revised version). Those who gave written informed consent were randomised to one of two treatment groups: usual care or usual care plus CBT. The primary outcome is depressive symptoms assessed using the BDI-II at 6months post-randomisation. Secondary outcomes measured at 6 and 12months include quality of life, antidepressant use and health care utilisation. Outcomes will be analysed on an intention-to-treat basis. The CoBalT trial will provide evidence on the clinical and cost effectiveness of CBT as an adjunct to antidepressant medication in the treatment of depression that has not responded to pharmacotherapy. Given the move to widen access to 'talking therapies', the results of this study will be timely.


Underlying skills of oral and silent reading.
Many studies have examined reading and reading development. The majority of these studies, however, focused on oral reading rather than on the more dominant silent reading mode. Similarly, it is common practice to assess oral reading abilities rather than silent reading abilities in schools and in diagnosis of reading impairments. More important, insights gained through examinations of oral reading tend to be generalized to silent reading. In the current study, we examined whether such generalizations are justified. We directly compared oral and silent reading fluency by examining whether these reading modes relate to the same underlying skills. In total, 132 fourth graders read words, sentences, and text orally, and 123 classmates read the same material silently. As underlying skills, we considered phonological awareness, rapid naming, and visual attention span. All skills correlated significantly with both reading modes. Phonological awareness contributed equally to oral and silent reading. Rapid naming, however, correlated more strongly with oral reading than with silent reading. Visual attention span correlated equally strongly with both reading modes but showed a significant unique contribution only to silent reading. In short, we showed that oral and silent reading indeed are fairly similar reading modes, based on the relations with reading-related cognitive skills. However, we also found differences that warrant caution in generalizing findings across reading modes.


Advances in hydrogels applied to degenerative diseases.
Hydrogels are currently applied in the treatment of numerous degenerative diseases because of their three dimensional (3D) nature, high water content and wide range of polymers that can be used for their fabrication. Hydrogels have been investigated and commercialized, for example, as soft contact lens-based ophthalmic drug delivery systems. These novel devices improved the bioavailability of ophthalmic drugs and their residence time. Hydrogels are also being investigated to facilitate and augment targeted delivery of chemotherapeutic agents. This approach minimizes significantly the side effects associated with conventional administration of anti-cancer therapeutics. The application of hydrogels as 3D scaffold has recently gained momentum because they can mimic key features of the extracellular matrix. For this reason, hydrogels are representing a viable alternative to traditional tumor xenograft in cancer biology studies. This review highlights recent advances in the development of hydrogels that are applied in degenerative diseases such as ocular, cancer, spine and cartilage degenerative pathologies.


Challenges facing European agriculture and possible biotechnological solutions.
Agriculture faces many challenges to maximize yields while it is required to operate in an environmentally sustainable manner. In the present study, we analyze the major agricultural challenges identified by European farmers (primarily related to biotic stresses) in 13 countries, namely Belgium, Bulgaria, the Czech Republic, France, Germany, Hungary, Italy, Portugal, Romania, Spain, Sweden, UK and Turkey, for nine major crops (barley, beet, grapevine, maize, oilseed rape, olive, potato, sunflower and wheat). Most biotic stresses (BSs) are related to fungi or insects, but viral diseases, bacterial diseases and even parasitic plants have an important impact on yield and harvest quality. We examine how these challenges have been addressed by public and private research sectors, using either conventional breeding, marker-assisted selection, transgenesis, cisgenesis, RNAi technology or mutagenesis. Both national surveys and scientific literature analysis followed by text mining were employed to evaluate genetic engineering (GE) and non-GE approaches. This is the first report of text mining of the scientific literature on plant breeding and agricultural biotechnology research. For the nine major crops in Europe, 128 BS challenges were identified with 40% of these addressed neither in the scientific literature nor in recent European public research programs. We found evidence that the private sector was addressing only a few of these "neglected" challenges. Consequently, there are considerable gaps between farmer's needs and current breeding and biotechnology research. We also provide evidence that the current political situation in certain European countries is an impediment to GE research in order to address these agricultural challenges in the future. This study should also contribute to the decision-making process on future pertinent international consortia to fill the identified research gaps.


Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.


Evaluation of first night effect using ambulatory monitoring and automatic sleep stage analysis.
Home sleep recordings were conducted over three consecutive nights in 12 normal subjects using the Oxford Medilog 9000 system and automatic sleep stage analysis. The equipment was well tolerated and adequate sleep recordings were obtained on each test evening. The results showed that there was no significant differences over the three nights for any of the sleep parameters measured.


Fungi: the neglected allergenic sources.
Allergic diseases are considered the epidemics of the twentieth century estimated to affect more than 30% of the population in industrialized countries with a still increasing incidence. During the past two decades, the application of molecular biology allowed cloning, production and characterization of hundreds of recombinant allergens. In turn, knowledge about molecular, chemical and biologically relevant allergens contributed to increase our understanding of the mechanisms underlying IgE-mediated type I hypersensitivity reactions. It has been largely demonstrated that fungi are potent sources of allergenic molecules covering a vast variety of molecular structures including enzymes, toxins, cell wall components and phylogenetically highly conserved cross-reactive proteins. Despite the large knowledge accumulated and the compelling evidence for an involvement of fungal allergens in the pathophysiology of allergic diseases, fungi as a prominent source of allergens are still largely neglected in basic research as well as in clinical practice. This review aims to highlight the impact of fungal allergens with focus on asthma and atopic dermatitis.


Aptamer-enabled uptake of small molecule ligands.
The relative ease of isolating aptamers with high specificity for target molecules suggests that molecular recognition may be common in the folds of natural RNAs. We show here that, when expressed in cells, aptamers can increase the intracellular concentrations of their small molecule ligands. We have named these aptamers as DRAGINs (Drug Binding Aptamers for Growing Intracellular Numbers). The DRAGIN property, assessed here by the ability to enhance the toxicity of their ligands, was found for some, but not all, aminoglycoside aptamers. One aptamer protected cells against killing by its ligand. Another aptamer promoted killing as a singlemer and protected against killing as a tandemer. Based on a mathematical model, cell protection vs. killing is proposed as governed by aptamer affinity and access to the inner surface of the cell membrane, with the latter being a critical determinant. With RNA molecules proposed as the earliest functional polymers to drive the evolution of life, we suggest that RNA aptamer-like structures present in primitive cells might have selectively concentrated precursors for polymer synthesis. Riboswitches may be the evolved forms of these ancient aptamer-like "nutrient procurers". Aptamers with DRAGIN capability in the modern world could be applied for imaging cells, in synthetic cell constructs, or to draw drugs into cells to make "undruggable" targets accessible to small molecule inhibitors.


Multiple-channel optical signal processing with wavelength-waveform conversions, pulsewidth tunability, and signal regeneration.
A multiple-channel multiple-function optical signal processor (MCMF-OSP) including wavelength-waveform conversions, pulsewidth tunability, and signal regeneration is realized through AND logic gate based on optical parametric processing with a pulsewidth-tunable RZ clock pump. The proposed scheme simultaneously offers four signal processing functions which are useful in wavelength-division multiplexing (WDM) transmission systems, and at network nodes with the necessity for multiple-channel data processing. After the discussions on the concept of MCMF-OSP, a proof-of concept experiment is demonstrated on four 10 Gb/s nonreturn-to-zero (NRZ) data format channels using nonlinearities in semiconductor optical amplifier (SOA) and highly nonlinear fiber (HNLF). A wavelength and waveform conversions to return-to-zero (RZ) modulation format are obtained together with pulsewidth-tunable range from 20% to 80% duty cycles for all input signals. The converted signals inherit the timing and waveform of the RZ clock pump, thus resulting in a time regeneration and large tolerance to narrow-band optical filtering (NAOF) and fiber accumulated chromatic dispersion (CD).


The Cantwell-Ransley epispadias repair in exstrophy and epispadias: lessons learned.
We evaluated our experience with the Cantwell-Ransley epispadias repair to determine the lessons that have been learned with the increased experience and follow-up. A total of 75 boys (60 with bladder exstrophy and 15 with complete epispadias) underwent a Cantwell-Ransley epispadias repair at our institute in the last 6 years. Primary repair was performed in 58 boys (45 with exstrophy and 13 with epispadias), and secondary repair was performed after prior failed closure in 17 boys (12 at the secondary exstrophy closure, 3 with exstrophy, and 2 with complete epispadias). At a mean follow-up of 28 months, all patients had a horizontal or downward angled penis while standing. The incidence of urethrocutaneous fistulas in the immediate postoperative state was 21% and at 3 months was 15%. The incidence of urethrocutaneous fistulas was no more in those patients in whom paraexstrophy skin flaps were used at anterior closure than in those in whom the urethral plate was left intact. Two patients developed a urethral stricture at the proximal anastomotic area, and 4 patients had minor skin separation of the dorsal penile skin closure. Catheterization or cystoscopy, or both, has been performed in 60 patients and revealed an easily negotiable urethral channel in all. The Cantwell-Ransley epispadias repair offers a straighter urethra, better correction of chordee and cosmesis, and a lower fistula rate in the exstrophy or epispadias patient.


Scholarship and research in occupational therapy education.
OBJECTIVE. The purpose of this study was to identify a baseline or benchmark for faculty engagement and productivity in occupational therapy education scholarship and research. METHOD. A custom-designed survey was emailed to 2,225 faculty members. The survey included questions on basic demographic information and education scholarship (e.g., use of evidence to inform teaching, frequency and nature of involvement in education scholarship. RESULTS. A total of 520 faculty members (23%) completed the survey. Of these, 450 (86.5%) identified themselves as full-time core faculty, and only their responses were analyzed. Although 90% of the faculty respondents engaged in scholarly teaching, only 34% identified education as an area of content expertise, and only 16% reported frequent involvement with education scholarship. Instructional methods were the primary area of study. CONCLUSION. A need exists to build research capacity for education research and more diversification of education research topics, including professional socialization and competencies.


Embryonic Aneuploidy after Preimplantation Genetic Screening: Age- and Indication-Matched Comparative Study between Indian and Spanish Population.
Recent studies show that there are differences in female fertility in different ethnic groups with ovarian aging and IVF treatment outcomes. Advanced maternal age is a known risk factor for miscarriage, accounting largely due to genetically abnormal fetus. This study investigates if there are any differences in rates of embryo aneuploidy based on age and indications for preimplantation genetic screening (PGS) between Indian and Spanish women. This multicenter study was carried out at fertility centers in India and Spain. Data from autologous IVF cycles of women <45 years age (Spanish: 39.4 ± 3.8 years; Indian: 35.3 ± 4.6 years) were included. A total of 37,962 embryos from 7009 IVF cycles from Spain and 1894 embryos from 308 IVF cycles from India, having similar clinical indications, underwent similar IVF treatment protocol. The embryos were analyzed by PGS using either a day-3 or day-5/6 embryo biopsy. Both Indian and Spanish ethnic population showed a reduction in aneuploidy rate in day-5/6 biopsy compared with day-3 biopsy (Spanish: 53.3% vs. 81.1%, P < 0.01; Indian: 50% vs. 75%, P < 0.02). There was a significant decrease in highly abnormal or chaotic embryos in trophectoderm biopsies compared with day-3 biopsies (Spanish: 2% vs. 16.1%, P < 0.01; Indian: 2.5% vs. 17.7%, P < 0.01). Both the populations showed similar trend in aneuploidy rate with maternal age. The results showed no significance between aneuploidy rate compared within different age groups and indications. However, there was a significant reduction in the miscarriage rate in Spanish population in day-3 biopsy compared with Indian population (10.7% vs. 19.8%; P < 0.05; 95% confidence interval [0.0044-0.0712]). There were no differences in the clinical outcomes compared between the two populations. This study shows that the aneuploidy rates between Indian and Spanish women of the same age group undergoing IVF treatment do not differ. An in-depth analysis to compare the types of anomalies reported with PGS in both the population will be of much interest.


The contrecoup-coup phenomenon: a new understanding of the mechanism of closed head injury.
A common observation in closed head injuries is the contrecoup brain injury. As the in vivo brain is less dense than the cerebrospinal fluid (CSF), one hypothesis explaining this observation is that upon skull impact, the denser CSF moves toward the site of skull impact displacing the brain in the opposite direction, such that the initial impact of the brain parenchyma is at the contrecoup location. A simple model was developed consisting of a balloon filled with water of density 1.00 g/mL enclosed in a clear plastic jar containing salt water of density 1.04 g/mL, simulating the same relative densities of the CSF and brain. The initial movement of the balloon, modeling the brain, was toward the contrecoup location with subsequent movement toward the coup location. The pattern of brain injury in which the contrecoup injury is greater than the coup injury is a result of initial movement of the brain in the contrecoup location. During the process of closed head injury, the brain parenchyma is initially displaced away from the site of skull impact and toward the contrecoup site resulting in the more severe brain contusion.


Procalcitonin-guided therapy in intensive care unit patients with severe sepsis and septic shock--a systematic review and meta-analysis.
Procalcitonin (PCT) algorithms for antibiotic treatment decisions have been studied in adult patients from primary care, emergency department, and intensive care unit (ICU) settings, suggesting that procalcitonin-guided therapy may reduce antibiotic exposure without increasing the mortality rate. However, information on the efficacy and safety of this approach in the most vulnerable population of critically ill patients with severe sepsis and septic shock is missing. Two reviewers independently performed a systematic search in PubMed, Embase, ISI Web of Knowledge, BioMed Central, ScienceDirect, Cochrane Central Register of Controlled Trials, http://www.ClinicalTrials.gov and http://www.ISRCTN.org. Eligible studies had to be randomized controlled clinical trials or cohort studies which compare procalcitonin-guided therapy with standard care in severe sepsis patients and report at least one of the following outcomes: hospital mortality, 28-day mortality, duration of antimicrobial therapy, length of stay in the intensive care unit or length of hospital stay. Disagreements about inclusion of studies and judgment of bias were solved by consensus. Finally seven studies comprising a total of 1,075 patients with severe sepsis or septic shock were included in the meta-analysis. Both hospital mortality (RR [relative risk]: 0.91, 95%CI [confidence interval]: 0.61; 1.36) and 28-day mortality (RR: 1.02, 95%CI: 0.85; 1.23) were not different between procalcitonin-guided therapy and standard treatment groups. Duration of antimicrobial therapy was significantly reduced in favor of procalcitonin-guided therapy (HR [hazard ratio]: 1.27, 95%CI: 1.01; 1.53). Combined estimates of the length of stay in the ICU and in hospital did not differ between groups. Procalcitonin-guided therapy is a helpful approach to guide antibiotic therapy and surgical interventions without a beneficial effect on mortality. The major benefit of PCT-guided therapy consists of a shorter duration of antibiotic treatment compared to standard care. Trials are needed to investigate the effect of PCT-guided therapy on mortality, length of ICU and in-hospital stay in severe sepsis patients.


Investigation of possible transmission of a susceptible microorganism through a contaminated duodenoscope; a case report.
Despite compliance to extensive reprocessing protocols, duodenoscopes have been linked to outbreaks of susceptible and multi-drug resistant organisms (MDRO) due to persistent duodenoscope contamination. Duodenoscope-associated infections (DAIs) based on transmission of susceptible microorganisms are likely to be underreported due to detection bias. We describe the retrospective detection of a DAI case caused by a susceptible microorganism which at the time of clinical infection was not recognized as such. During 2017 and 2018, duodenoscopes were cultured on a daily basis due to research activities. While analyzing this data, it was found that a duodenoscope had been contaminated with Enterobacter cloacae complex over a period of 3 months. We checked whether patients treated with this duodenoscope had developed infections and found one patient with an E. cloacae cholangitis 3 months after the ERCP (Endoscopic retrograde cholangiopancreaticography) procedure. The isolates on the duodenoscope and in the patients' blood culture were indistinguishable by amplified fragment length polymorphism (AFLP). By classical multi-locus sequence typing (MLST), both strains were of the same (but novel) sequence type. Application of whole genome MLST showed 93 (out of 3757) allelic differences. This case report describes a plausible link between a contaminated duodenoscope and a patient infection with E. cloacae. Transmission of susceptible E. cloacae was highly suspected from AFLP and MLST results; by WGS, 93 allelic differences were found which proves closely related strains. This report shows that DAIs by susceptible microorganisms can be easily missed and therefore its true prevalence remains underscored.


Engineered Functional Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes.
Functional redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is considered as a source of genetic and functional innovation. In any case, genetically redundant genes are expected to show an acceleration in the rate of molecular evolution. Here, we tackle the role of functional redundancy in viral RNA genomes. To this end, we have evaluated the rates of compensatory evolution for deleterious mutations affecting an essential function, the suppression of RNA silencing plant defense, of tobacco etch potyvirus (TEV). TEV genotypes containing deleterious mutations in presence/absence of engineered functional redundancy were evolved and the pattern of fitness and pathogenicity recovery evaluated. Genetically redundant genotypes suffered less from the effect of deleterious mutations and showed relatively minor changes in fitness and pathogenicity. By contrast, nongenetically redundant genotypes had very low fitness and pathogenicity at the beginning of the evolution experiment that were fully recovered by the end. At the molecular level, the outcome depended on the combination of the actual mutations being compensated and the presence/absence of functional redundancy. Reversions to wild-type alleles were the norm in the nonredundant genotypes while redundant ones either did not fix any mutation at all or showed a higher nonsynonymous mutational load.


Electromagnetic hypersensitivity: biological effects of dirty electricity with emphasis on diabetes and multiple sclerosis.
Dirty electricity is a ubiquitous pollutant. It flows along wires and radiates from them and involves both extremely low frequency electromagnetic fields and radio frequency radiation. Until recently, dirty electricity has been largely ignored by the scientific community. Recent inventions of metering and filter equipment provide scientists with the tools to measure and reduce dirty electricity on electrical wires. Several case studies and anecdotal reports are presented. Graham/Stetzer (GS) filters have been installed in schools with sick building syndrome and both staff and students reported improved health and more energy. The number of students needing inhalers for asthma was reduced in one school and student behavior associated with ADD/ADHD improved in another school. Blood sugar levels for some diabetics respond to the amount of dirty electricity in their environment. Type 1 diabetics require less insulin and Type 2 diabetics have lower blood sugar levels in an electromagnetically clean environment. Individuals diagnosed with multiple sclerosis have better balance and fewer tremors. Those requiring a cane walked unassisted within a few days to weeks after GS filters were installed in their home. Several disorders, including asthma, ADD/ADHD, diabetes, multiple sclerosis, chronic fatigue, fibromyalgia, are increasing at an alarming rate, as is electromagnetic pollution in the form of dirty electricity, ground current, and radio frequency radiation from wireless devices. The connection between electromagnetic pollution and these disorders needs to be investigated and the percentage of people sensitive to this form of energy needs to be determined.


Surround optical fiber immunoassay (SOFIA): an ultra-sensitive assay for prion protein detection.
We describe the development of a new technology (SOFIA) and demonstrate its utility by establishing a sensitive and specific assay for PrP(Sc). SOFIA is a surround optical fiber immunoassay which is comprised of a set of specific monoclonal antibodies and comprehensive capture of high energy fluorescence emission. In its current format, this system is capable of detecting less than 10 attogram (ag) of hamster, sheep and deer recombinant PrP. Approximately 10 ag of PrP(Sc) from 263 K-infected hamster brains can be detected with similar lower limits of PrP(Sc) detection from the brains of scrapie-infected sheep and deer infected with chronic wasting disease. These detection limits allow protease treated and untreated material to be diluted beyond the point where PrP(C), non-specific proteins or other extraneous material may interfere with PrP(Sc) signal detection and/or specificity. This not only eliminates the issue of specificity of PrP(Sc) detection but also increases sensitivity since the possibility of partial PrP(Sc) proteolysis is no longer a concern. SOFIA will likely lead to early antemortem detection of transmissible encephalopathies and is also amenable for use with additional target amplification protocols. SOFIA represents a sensitive means for detecting specific proteins involved in disease pathogenesis and/or diagnosis that extends beyond the scope of the transmissible spongiform encephalopathies.


Highly wear-resistant and biocompatible carbon nanocomposite coatings for dental implants.
Diamond-like carbon coatings are increasingly used as wear-protective coatings for dental implants, artificial joints, etc. Despite their advantages, they may have several weak points such as high internal stress, poor adhesive properties or high sensitivity to ambient conditions. These weak points could be overcome in the case of a new carbon nanocomposite coating (CNC) deposited by using a C60 ion beam on a Co/Cr alloy. The structure of the coatings was investigated by Raman and XPS spectroscopy. The wear resistance was assessed by using a reciprocating tribotester under the loads up to 0.4 N in both dry and wet sliding conditions. Biocompatibility of the dental implants was tested in vivo on rabbits. Biocompatibility, bioactivity and mechanical durability of the CNC deposited on a Co/Cr alloy were investigated and compared with those of bulk Co/Cr and Ti alloys. The wear resistance of the CNC was found to be 250-650 fold higher compared to the Co/Cr and Ti alloys. Also, the CNC demonstrated much better biological properties with respect to formation of new tissues and absence of negative morphological parameters such as necrosis and demineralization. Development of the CNC is expected to aid in significant improvement of lifetime and quality of implants for dental applications.