Comparison of stool microbiota compositions, stool alpha1-antitrypsin and calprotectin concentrations, and diarrhoeal morbidity of Indonesian infants fed breast milk or probiotic/prebiotic-supplemented formula.
The composition of faecal microbiota of babies is known to be influenced by diet. Faecal calprotectin and α1-antitrypsin concentrations may be associated with mucosal permeability and inflammation. We aimed to assess whether there was any difference after consumption of a probiotic/prebiotic formula on faecal microbiota composition, calprotectin and α1-antitrypsin levels, and diarrhoea in comparison with breast milk-fed Indonesian infants. One hundred sixty infants, 2 to 6 weeks old, were recruited to the study. They were either breastfed or formula fed (80 per group). Faecal samples were collected at recruitment and 3 months later. Bacterial groups characteristic of the human faecal microbiota were quantified in faeces by quantitative polymerase chain reaction. Calprotectin and α1-antitrypsin concentrations were measured using commercial kits. Details of diarrhoeal morbidity were documented and rated for severity. The compositions of the faecal microbiota of formula-fed compared with breast milk-fed children were similar except that the probiotic strain Bifidobacterium animalis subsp. lactis DR10 was more abundant after 3 months consumption of the formula. Alpha1-antitrypsin levels were higher in breastfed compared with formula-fed infants. The occurrence of diarrhoea did not differ between the groups of babies. Feeding Indonesian babies with a probiotic/prebiotic formula did not produce marked differences in the composition of the faecal microbiota in comparison with breast milk. Detrimental effects of formula feeding on biomarkers of mucosal health were not observed.


Diversity and composition of demersal fishes along a depth gradient assessed by baited remote underwater stereo-video.
Continental slopes are among the steepest environmental gradients on earth. However, they still lack finer quantification and characterisation of their faunal diversity patterns for many parts of the world. Changes in fish community structure and diversity along a depth gradient from 50 to 1200 m were studied from replicated stereo baited remote underwater video deployments within each of seven depth zones at three locations in north-eastern New Zealand. Strong, but gradual turnover in the identities of species and community structure was observed with increasing depth. Species richness peaked in shallow depths, followed by a decrease beyond 100 m to a stable average value from 700 to 1200 m. Evenness increased to 700 m depth, followed by a decrease to 1200 m. Average taxonomic distinctness △(+) response was unimodal with a peak at 300 m. The variation in taxonomic distinctness Λ(+) first decreased sharply from 50 to 300 m, then increased beyond 500 m depth, indicating that species from deep samples belonged to more distant taxonomic groups than those from shallow samples. Fishes with northern distributions progressively decreased in their proportional representation with depth whereas those with widespread distributions increased. This study provides the first characterization of diversity patterns for bait-attracted fish species on continental slopes in New Zealand and is an imperative primary step towards development of explanatory and predictive ecological models, as well as being fundamental for the implementation of efficient management and conservation strategies for fishery resources.


Integrity and function of the Saccharomyces cerevisiae spindle pole body depends on connections between the membrane proteins Ndc1, Rtn1, and Yop1.
The nuclear envelope in Saccharomyces cerevisiae harbors two essential macromolecular protein assemblies: the nuclear pore complexes (NPCs) that enable nucleocytoplasmic transport, and the spindle pole bodies (SPBs) that mediate chromosome segregation. Previously, based on metazoan and budding yeast studies, we reported that reticulons and Yop1/DP1 play a role in the early steps of de novo NPC assembly. Here, we examined if Rtn1 and Yop1 are required for SPB function in S. cerevisiae. Electron microscopy of rtn1Δ yop1Δ cells revealed lobular abnormalities in SPB structure. Using an assay that monitors lateral expansion of the SPB central layer, we found that rtn1Δ yop1Δ SPBs had decreased connections to the NE compared to wild type, suggesting that SPBs are less stable in the NE. Furthermore, large budded rtn1Δ yop1Δ cells exhibited a high incidence of short mitotic spindles, which were frequently misoriented with respect to the mother-daughter axis. This correlated with cytoplasmic microtubule defects. We found that overexpression of the SPB insertion factors NDC1, MPS2, or BBP1 rescued the SPB defects observed in rtn1Δ yop1Δ cells. However, only overexpression of NDC1, which is also required for NPC biogenesis, rescued both the SPB and NPC associated defects. Rtn1 and Yop1 also physically interacted with Ndc1 and other NPC membrane proteins. We propose that NPC and SPB biogenesis are altered in cells lacking Rtn1 and Yop1 due to competition between these complexes for Ndc1, an essential common component of both NPCs and SPBs.


Complex systems modeling for obesity research.
The obesity epidemic has grown rapidly into a major public health challenge, in the United States and worldwide. The scope and scale of the obesity epidemic motivate an urgent need for well-crafted policy interventions to prevent further spread and (potentially) to reverse the epidemic. Yet several attributes of the epidemic make it an especially challenging problem both to study and to combat. This article shows that these attributes--the great breadth in levels of scale involved, the substantial diversity of relevant actors, and the multiplicity of mechanisms implicated--are characteristic of a complex adaptive system. It argues that the obesity epidemic is driven by such a system and that lessons and techniques from the field of complexity science can help inform both scientific study of obesity and effective policies to combat obesity. The article gives an overview of modeling techniques especially well suited to study the rich and complex dynamics of obesity and to inform policy design.


A safe protocol for amalgam removal.
Today's environment has different impacts on our body than previous generations. Heavy metals are a growing concern in medicine. Doctors and individuals request the removal of their amalgam (silver mercury) restorations due to the high mercury content. A safe protocol to replace the silver mercury filling will ensure that there is minimal if any absorption of materials while being removed. Strong alternative white composite and lab-processed materials are available today to create a healthy and functioning mouth. Preparation of the patient prior to the procedure and after treatment is vital to establish the excretion of the mercury from the body.


Heated, humidified air for the common cold.
Heated, humidified air is used by common cold sufferers since the invention of the steam kettle. There is scientific literature available investigating this mode of therapy using a rhinotherm. The present reviews addresses to the use of hot, humid air in common cold. To assess the effects of inhaling heated water vapour with the help of a rhinotherm (an equipment designed to deliver heated water vapour to a person's nasal cavity), in the treatment of the common cold by comparing a. symptoms b. viral shedding c. nasal resistance after a natural or experimentally induced common cold. We searched MEDLINE with MeSH headings: common cold, rhinopharyngitis, inhalation, steam, heated vapour, rhinothermy, till July 1999. EMBASE, Current Contents, review articles, cross references were also searched. Attempts were also made to contact the manufacturers for any unpublished data. Randomized trials using heated water vapour in a standardized way in patients with the common cold or volunteers with experimental induction of rhinovirus infection were included in the review. All the articles retrieved were initially subjected to a review for inclusion / exclusion criteria. Review articles, editorials, abstracts with inadequate outcome description were excluded. Studies selected for inclusion were subjected to a methodological assessment. The results of a systematic review of six trials with 319 participants, support the use of warm vapour inhalations in the common cold in terms of relief of symptoms (Odds Ratio with 95 % CI 0.31, 0.16-0.60, Relative risk 0.56, 0.4-0.79). Results on symptom score indices were equivocal. None of the studies demonstrated a worsening of clinical symptom scores. One study demonstrated increased nasal resistance one week after steam inhalation in contrast to an earlier study which showed improvement in the nasal resistance. There was no evidence of decreased viral shedding measured by virus isolation in the nasal secretions or measurement of viral titres in nasal washings among treatment group. The rhinovirus titres in the nasal washings from the treatment group were the same as those of the placebo group on day one prior to the treatment and on all four days after the treatment. The area under curve was also similar in the placebo and treatment groups for titres of virus in the nasal washings as were the average viral titres across five days of follow up, the maximum values after treatment, and viral shedding velocity i.e. amount of virus shed per day. Minor side effects due to thermal stress were reported in all the studies. Three trials demonstrated beneficial effects on the symptoms of the common cold. One study from Israel showed a decrease in nasal resistance measured by peak nasal expiratory and inspiratory flow rate. Studies done in North America failed to show any objective improvement in outcome measures with the study intervention. A multi-centre double blind randomised controlled trial testing this therapy with uniform outcome measures is recommended.


The velocity and energy profiles of elite cross-country skiers executing downhill turns with different radii.
This study examined the influence of turn radius on velocity and energy profiles when skidding and step turning during more and less effective downhill turns while cross-country skiing. Thirteen elite female cross-country skiers performed single turns with a 9- or 12-m radius using the skidding technique and a 12- or 15-m radius with step turning. Mechanical parameters were monitored using a real-time kinematic Global Navigation Satellite System and video analysis. Step turning was more effective during all phases of a turn, leading to higher velocities than skidding (P < .05). With both techniques, a greater radius was associated with higher velocity (P < .05), but the quality of turning, as assessed on the basis of energy characteristics, was the same. More effective skidding turns involved more pronounced deceleration early in the turn and maintenance of higher velocity thereafter, while more effective step turning involved lower energy dissipation during the latter half of the turn. In conclusion, the single-turn analysis employed here reveals differences in the various techniques chosen by elite cross-country skiers when executing downhill turns of varying radii and can be used to assess the quality of such turns.


Creation of vortex lattices by a wavefront division.
The Young's double-slit experiment is one of the most popular stories in the history of physics. This paper, like many others, has emerged from the Young's idea. It investigates the diffraction of the plane or spherical wave produced by three or four small holes in an opaque screen. It was noticed that the interference field contained a lattice of optical vortices which were equivalent to those produced in optical vortex interferometer. The vortex lattice generated by the three holes possessed some unique properties from which the analytical formulae for vortex points position were derived. We also pointed out the differences between our case and the double-slit experiment. Finally, some remarks on possible applications of our arrangement are discussed briefly. These theoretical considerations are illustrated with the use of experimental results.


Dietary Onion or Ginger Modulates the Stress Response and Susceptibility to Vibrio harveyi JML1 Infection in Brown-marbled Grouper Epinephelus fuscoguttatus Juveniles.
Onion Allium cepa and ginger Zingiber officinale have health-promoting properties that qualify them as functional foods. The effect of repeated acute stressors was examined in juvenile Brown-marbled Grouper Epinephelus fuscoguttatus that were fed four diets supplemented with onion at 1.8%, ginger at 1.8%, vitamin C at 0.86%, and β-glucan at 0.8% of the diet. The non-supplemented diet served as the control. After 12 weeks of feeding, fish were exposed to stressors and were experimentally infected with a fish pathogen, the bacterium Vibrio harveyi JML1. After repeated exposure to hypoxia, cortisol levels rose significantly in the non-supplemented fish compared to those fed onion, ginger, β-glucan, or vitamin C. Within groups, postexposure cortisol levels in the onion-, ginger-, and vitamin C-fed fish did not change relative to pre-stress levels, whereas significant increases in poststress values were observed in the control and β-glucan groups. The net cortisol increase was also significantly greater in the non-supplemented group compared to the supplemented groups. The net cortisol increase did not vary among the supplemented groups except that the β-glucan-fed group exhibited a higher net increase than the onion-fed group. Similarly, repeated acute exposure to osmotic stress significantly increased the plasma cortisol level in the non-supplemented group compared to groups that received supplements; no differences were found in the supplemented groups except the β-glucan group. Within groups, significant increases in poststress values relative to pre-stress levels were found only in the control and β-glucan groups. Repeated acute exposure to hypoxia significantly increased cumulative mortality in the control group compared to the supplemented groups (except the β-glucan group), whereas repeated exposure to acute osmotic stress significantly increased cumulative mortality only in the control group 10 d after infection with V. harveyi JML1. Based on our collective results, most of the supplemented groups performed better than the control, but the best supplements were onion and ginger in terms of enhancing stress tolerance and increasing survival of Brown-marbled Grouper upon infection with V. harveyi JML1.


Roles of the Contralateral Efferent Reflex in Hearing Demonstrated with Cochlear Implants.
Our two ears do not function as fixed and independent sound receptors; their functioning is coupled and dynamically adjusted via the contralateral medial olivocochlear efferent reflex (MOCR). The MOCR possibly facilitates speech recognition in noisy environments. Such a role, however, is yet to be demonstrated because selective deactivation of the reflex during natural acoustic listening has not been possible for human subjects up until now. Here, we propose that this and other roles of the MOCR may be elucidated using the unique stimulus controls provided by cochlear implants (CIs). Pairs of sound processors were constructed to mimic or not mimic the effects of the contralateral MOCR with CIs. For the non-mimicking condition (STD strategy), the two processors in a pair functioned independently of each other. When configured to mimic the effects of the MOCR (MOC strategy), however, the two processors communicated with each other and the amount of compression in a given frequency channel of each processor in the pair decreased with increases in the output energy from the contralateral processor. The analysis of output signals from the STD and MOC strategies suggests that in natural binaural listening, the MOCR possibly causes a small reduction of audibility but enhances frequency-specific inter-aural level differences and the segregation of spatially non-overlapping sound sources. The proposed MOC strategy could improve the performance of CI and hearing-aid users.


Development of polymorphic microsatellite markers for the livebearing fish Poecilia parae.
We developed 16 novel polymorphic tetranucleotide microsatellite markers for Poecilia parae, a livebearing fish used in evolutionary studies because of its Y-linked colour and size polymorphism. A set of 199 clones was sequenced out of an enriched genomic library, and we achieved an enrichment efficiency of nearly 80%. Primers were designed for 16 pure repeats, and 59 P. parae were screened for polymorphism. Cross-amplification was tested on Poecilia picta and Poecilia reticulata, the guppy. The new microsatellite markers showed an exceptionally high allelic diversity and low stutter formation, proving their suitability for a broad range of applications in these species.


Clinical laboratory reference values amongst children aged 4 weeks to 17 months in Kilifi, Kenya: A cross sectional observational study.
Reference intervals for clinical laboratory parameters are important for assessing eligibility, toxicity grading and management of adverse events in clinical trials. Nonetheless, haematological and biochemical parameters used for clinical trials in sub-Saharan Africa are typically derived from industrialized countries, or from WHO references that are not region-specific. We set out to establish community reference values for haematological and biochemical parameters amongst children aged 4 weeks to 17 months in Kilifi, Kenya. We conducted a cross sectional study nested within phase II and III trials of RTS, S malaria vaccine candidate. We analysed 10 haematological and 2 biochemical parameters from 1,070 and 423 community children without illness prior to experimental vaccine administration. Statistical analysis followed Clinical and Laboratory Standards Institute EP28-A3c guidelines. 95% reference ranges and their respective 90% confidence intervals were determined using non-parametric methods. Findings were compared with published ranges from Tanzania, Europe and The United States. We determined the reference ranges within the following age partitions: 4 weeks to <6 months, 6 months to less than <12 months, and 12 months to 17 months for the haematological parameters; and 4 weeks to 17 months for the biochemical parameters. There were no gender differences for all haematological and biochemical parameters in all age groups. Hb, MCV and platelets 95% reference ranges in infants largely overlapped with those from United States or Europe, except for the lower limit for Hb, Hct and platelets (lower); and upper limit for platelets (higher) and haematocrit(lower). Community norms for common haematological and biochemical parameters differ from developed countries. This reaffirms the need in clinical trials for locally derived reference values to detect deviation from what is usual in typical children in low and middle income countries.


Temperature response of litter and soil organic matter decomposition is determined by chemical composition of organic material.
The global soil carbon pool is approximately three times larger than the contemporary atmospheric pool, therefore even minor changes to its integrity may have major implications for atmospheric CO2 concentrations. While theory predicts that the chemical composition of organic matter should constitute a master control on the temperature response of its decomposition, this relationship has not yet been fully demonstrated. We used laboratory incubations of forest soil organic matter (SOM) and fresh litter material together with NMR spectroscopy to make this connection between organic chemical composition and temperature sensitivity of decomposition. Temperature response of decomposition in both fresh litter and SOM was directly related to the chemical composition of the constituent organic matter, explaining 90% and 70% of the variance in Q10 in litter and SOM, respectively. The Q10 of litter decreased with increasing proportions of aromatic and O-aromatic compounds, and increased with increased contents of alkyl- and O-alkyl carbons. In contrast, in SOM, decomposition was affected only by carbonyl compounds. To reveal why a certain group of organic chemical compounds affected the temperature sensitivity of organic matter decomposition in litter and SOM, a more detailed characterization of the (13) C aromatic region using Heteronuclear Single Quantum Coherence (HSQC) was conducted. The results revealed considerable differences in the aromatic region between litter and SOM. This suggests that the correlation between chemical composition of organic matter and the temperature response of decomposition differed between litter and SOM. The temperature response of soil decomposition processes can thus be described by the chemical composition of its constituent organic matter, this paves the way for improved ecosystem modeling of biosphere feedbacks under a changing climate.


Face masks effectively limit the probability of SARS-CoV-2 transmission.
Airborne transmission by droplets and aerosols is important for the spread of viruses. Face masks are a well-established preventive measure, but their effectiveness for mitigating SARS-CoV-2 transmission is still under debate. We show that variations in mask efficacy can be explained by different regimes of virus abundance and related to population-average infection probability and reproduction number. For SARS-CoV-2, the viral load of infectious individuals can vary by orders of magnitude. We find that most environments and contacts are under conditions of low virus abundance (virus-limited) where surgical masks are effective at preventing virus spread. More advanced masks and other protective equipment are required in potentially virus-rich indoor environments including medical centers and hospitals. Masks are particularly effective in combination with other preventive measures like ventilation and distancing.


Climate change and long-term fire management impacts on Australian savannas.
Tropical savannas cover a large proportion of the Earth's land surface and many people are dependent on the ecosystem services that savannas supply. Their sustainable management is crucial. Owing to the complexity of savanna vegetation dynamics, climate change and land use impacts on savannas are highly uncertain. We used a dynamic vegetation model, the adaptive dynamic global vegetation model (aDGVM), to project how climate change and fire management might influence future vegetation in northern Australian savannas. Under future climate conditions, vegetation can store more carbon than under ambient conditions. Changes in rainfall seasonality influence future carbon storage but do not turn vegetation into a carbon source, suggesting that CO₂ fertilization is the main driver of vegetation change. The application of prescribed fires with varying return intervals and burning season influences vegetation and fire impacts. Carbon sequestration is maximized with early dry season fires and long fire return intervals, while grass productivity is maximized with late dry season fires and intermediate fire return intervals. The study has implications for management policy across Australian savannas because it identifies how fire management strategies may influence grazing yield, carbon sequestration and greenhouse gas emissions. This knowledge is crucial to maintaining important ecosystem services of Australian savannas.


Biogeography of a plant invasion: plant-herbivore interactions.
Theory predicts that native plant species should exhibit latitudinal gradients in the strength of their interactions with herbivores. We hypothesize that if an invasive plant species exhibits a different latitudinal gradient in response to herbivores (e.g., a nonparallel gradient), it can create large-scale heterogeneities in community resistance/susceptibility to the invasive species. We conducted a study of latitudinal variation in the strength of herbivory and defenses of native genotypes of Phragmites australis in North America (NA) and Europe (EU) and European invasive genotypes in NA. Within NA, we tested whether (1) invasive genotypes are better defended and suffer less herbivory than co-occurring native genotypes, (2) herbivory and defenses of native P. australis decreases with increasing latitude; and (3) invasive genotypes exhibit either no latitudinal gradient, or a nonparallel latitudinal gradient in herbivory and defenses compared to native genotypes. For the European genotypes, we tested two additional hypotheses: (4) defenses, nutritional condition, and herbivory would differ between the native (EU) and invasive ranges (NA) and (5) latitudinal gradients in defenses and herbivory would be similar between ranges. Within NA, chewing damage, internal stem-feeding incidence, and aphid abundance were 650%, 300%, and 70% lower, respectively, on invasive than native P. australis genotypes. Genotypes in NA also differed in nutritional condition (percent N, C:N ratio), but there was little support for invasive genotypes being better defended than native genotypes. For the European genotypes, herbivory was significantly lower in the invaded than native range, supporting the enemy-release hypothesis. Defense levels (leaf toughness and total phenolics) and tissue percent C and percent N were higher in the invaded than native range for European genotypes. Overall, latitudinal gradients in P. australis nutritional condition, defenses, and herbivory were common. Interestingly, chewing damage and stem-feeder incidence decreased with latitude for native P. australis genotypes in NA and EU, but no latitudinal gradients in response to herbivores were evident for invasive genotypes in NA. Nonparallel latitudinal gradients in herbivory between invasive and native P. australis suggest that the community may be more susceptible to invasion at lower than at higher latitudes. Our study points to the need for invasion biology to include a biogeographic perspective.


Impact of vessel size on angiographic and clinical outcomes of revascularization with biolimus-eluting stent with biodegradable polymer and sirolimus-eluting stent with durable polymer the LEADERS trial substudy.
We assessed the impact of vessel size on outcomes of stenting with biolimus-eluting degradable polymer stent (BES) and sirolimus-eluting permanent polymer stent (SES) within a randomized multicenter trial (LEADERS). Stenting of small vessels might be associated with higher rates of adverse events. "All-comer" patients (n = 1,707) were randomized to BES and SES. Post-hoc-stratified analysis of angiographic and clinical outcomes at 9 months and 1 year, respectively, was performed for vessels with reference diameter <or=2.75 mm versus >2.75 mm. Of 1,707 patients, 429 patients in the BES group with 576 lesions and 434 patients in the SES group with 557 lesions had only small vessels treated (50.6% of the patient cohort). In patients with small vessels there was no significant difference in overall major adverse cardiac events (MACE) rate (12.1% vs. 11.8%; p = 0.89) or target lesion revascularization (TLR) rate (9.6% vs. 7.4%; p = 0.26) between BES and SES. The MACE and TLR rates in the small-vessel patient population were higher than in the large-vessel population. The TLR rate was 9.6% versus 2.6%, and MACE rate was 12.1% versus 7.1% for small versus large vessels in the BES arm (TLR: hazard ratio [HR] = 3.724, p = 0.0013; MACE: HR = 1.720, p = 0.0412). In the SES arm, TLR was 7.4% versus 5.1%, and MACE was 11.8% versus 10.3% in small versus large vessels (TLR: HR = 1.435, p = 0.2594; MACE: HR = 1.149, p = 0.5546). Prevalence of small vessel disease is high in an "all-comer" population with higher TLR and MACE rates. The BES and SES seem equivalent in treatment outcomes of small vessels in this "all-comer" patient population.


Clinical assessment to screen for the detection of oral cavity cancer and potentially malignant disorders in apparently healthy adults.
The early detection and excision of potentially malignant disorders (PMD) of the lip and oral cavity that require intervention may reduce malignant transformations (though will not totally eliminate malignancy occurring), or if malignancy is detected during surveillance, there is some evidence that appropriate treatment may improve survival rates. To estimate the diagnostic accuracy of conventional oral examination (COE), vital rinsing, light-based detection, biomarkers and mouth self examination (MSE), used singly or in combination, for the early detection of PMD or cancer of the lip and oral cavity in apparently healthy adults. We searched MEDLINE (OVID) (1946 to April 2013) and four other electronic databases (the Cochrane Diagnostic Test Accuracy Studies Register, the Cochrane Oral Health Group's Trials Register, EMBASE (OVID), and MEDION) from inception to April 2013. The electronic databases were searched on 30 April 2013. There were no restrictions on language in the searches of the electronic databases. We conducted citation searches, and screened reference lists of included studies for additional references. We selected studies that reported the diagnostic test accuracy of any of the aforementioned tests in detecting PMD or cancer of the lip or oral cavity. Diagnosis of PMD or cancer was made by specialist clinicians or pathologists, or alternatively through follow-up. Two review authors independently screened titles and abstracts for relevance. Eligibility, data extraction and quality assessment were carried out by at least two authors independently and in duplicate. Studies were assessed for methodological quality using QUADAS-2. We reported the sensitivity and specificity of the included studies. Thirteen studies, recruiting 68,362 participants, were included. These studies evaluated the diagnostic accuracy of COE (10 studies), MSE (two studies). One randomised controlled of test accuracy trial directly evaluated COE and vital rinsing. There were no eligible diagnostic accuracy studies evaluating light-based detection or blood or salivary sample analysis (which tests for the presence of bio-markers of PMD and oral cancer). Given the clinical heterogeneity of the included studies in terms of the participants recruited, setting, prevalence of target condition, the application of the index test and reference standard and the flow and timing of the process, the data could not be pooled. For COE (10 studies, 25,568 participants), prevalence in the diagnostic test accuracy sample ranged from 1% to 51%. For the eight studies with prevalence of 10% or lower, the sensitivity estimates were highly variable, and ranged from 0.50 (95% confidence interval (CI) 0.07 to 0.93) to 0.99 (95% CI 0.97 to 1.00) with uniform specificity estimates around 0.98 (95% CI 0.97 to 1.00). Estimates of sensitivity and specificity were 0.95 (95% CI 0.92 to 0.97) and 0.81 (95% CI 0.79 to 0.83) for one study with prevalence of 22% and 0.97 (95% CI 0.96 to 0.98) and 0.75 (95% CI 0.73 to 0.77) for one study with prevalence of 51%. Three studies were judged to be at low risk of bias overall; two were judged to be at high risk of bias resulting from the flow and timing domain; and for five studies the overall risk of bias was judged as unclear resulting from insufficient information to form a judgement for at least one of the four quality assessment domains. Applicability was of low concern overall for two studies; high concern overall for three studies due to high risk population, and unclear overall applicability for five studies. Estimates of sensitivity for MSE (two studies, 34,819 participants) were 0.18 (95% CI 0.13 to 0.24) and 0.33 (95% CI 0.10 to 0.65); specificity for MSE was 1.00 (95% CI 1.00 to 1.00) and 0.54 (95% CI 0.37 to 0.69). One study (7975 participants) directly compared COE with COE plus vital rinsing in a randomised controlled trial. This study found a higher detection rate for oral cavity cancer in the conventional oral examination plus vital rinsing adjunct trial arm. The prevalence of the target condition both between and within index tests varied considerably. For COE estimates of sensitivity over the range of prevalence levels varied widely. Observed estimates of specificity were more homogeneous. Index tests at a prevalence reported in the population (between 1% and 5%) were better at correctly classifying the absence of PMD or oral cavity cancer in disease-free individuals that classifying the presence in diseased individuals. Incorrectly classifying disease-free individuals as having the disease would have clinical and financial implications following inappropriate referral; incorrectly classifying individuals with the disease as disease-free will mean PMD or oral cavity cancer will only be diagnosed later when the disease will be more severe. General dental practitioners and dental care professionals should remain vigilant for signs of PMD and oral cancer whilst performing routine oral examinations in practice.


Perceptual organization in the tilt illusion.
The tilt illusion is a paradigmatic example of contextual influences on perception. We analyze it in terms of a neural population model for the perceptual organization of visual orientation. In turn, this is based on a well-found treatment of natural scene statistics, known as the Gaussian Scale Mixture model. This model is closely related to divisive gain control in neural processing and has been extensively applied in the image processing and statistical learning communities; however, its implications for contextual effects in biological vision have not been studied. In our model, oriented neural units associated with surround tilt stimuli participate in divisively normalizing the activities of the units representing a center stimulus, thereby changing their tuning curves. We show that through standard population decoding, these changes lead to the forms of repulsion and attraction observed in the tilt illusion. The issues in our model readily generalize to other visual attributes and contextual phenomena, and should lead to more rigorous treatments of contextual effects based on natural scene statistics.


Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector.
Legionella pneumophila is an intracellular pathogen responsible for Legionnaires' disease. This bacterium uses the Dot/Icm type IV secretion system to inject a large number of bacterial proteins into host cells to facilitate the biogenesis of a phagosome permissive for its intracellular growth. Like many highly adapted intravacuolar pathogens, L. pneumophila is able to maintain a neutral pH in the lumen of its phagosome, particularly in the early phase of infection. However, in all cases, the molecular mechanisms underlying this observation remain unknown. In this report, we describe the identification and characterization of a Legionella protein termed SidK that specifically targets host v-ATPase, the multi-subunit machinery primarily responsible for organelle acidification in eukaryotic cells. Our results indicate that after being injected into infected cells by the Dot/Icm secretion system, SidK interacts with VatA, a key component of the proton pump. Such binding leads to the inhibition of ATP hydrolysis and proton translocation. When delivered into macrophages, SidK inhibits vacuole acidification and impairs the ability of the cells to digest non-pathogenic E. coli. We also show that a domain located in the N-terminal portion of SidK is responsible for its interactions with VatA. Furthermore, expression of sidK is highly induced when bacteria begin to enter new growth cycle, correlating well with the potential temporal requirement of its activity during infection. Our results indicate that direct targeting of v-ATPase by secreted proteins constitutes a virulence strategy for L. pneumophila, a vacuolar pathogen of macrophages and amoebae.


Propolis relieves the cardiotoxicity of chlorpyrifos in diabetic rats via alleviations of paraoxonase-1 and xanthine oxidase genes expression.
Pesticides cardiotoxicity in case of diabetic-induced cardiac complications is unidentified. The probable amelioration role of propolis is gauged against the cardiotoxic effects of chlorpyrifos in the diabetic rats through paraoxonase-1 (PON1) and xanthine oxidase (XO) genes dysregulation. Fifty-six male rats were distributed (n = 7) into eight groups. The first one saved as control whereas the 2nd, 3rd, and 4th were kept for propolis aqueous extract (100 mg/kg), diabetes (60 mg/kg streptozotocin) and chlorpyrifos (2.5 mg/kg), respectively. The 5th was diabetes/chlorpyrifos combination, while 6th, 7th, and 8th were intubated with propolis for four weeks after diabetic induction, chlorpyrifos intoxication, and their combination, respectively. The plasma glucose, lipid profiles, cardiac enzymes and interleukin-6 (IL-6) significantly elevated, while insulin decreased in the diabetic and combination groups. Although the cardiac acetylcholinesterase, total thiols, and PON1 significantly reduced after diabetic and/or chlorpyrifos gavage, the protein carbonyl, superoxide dismutase, catalase, and XO significantly elevated. The mRNA genes expression of PON1 and XO have also confirmed the enzymatic activities. Interestingly, propolis significantly restored the hyperglycemia, hypoinsulinemia, hyperlipidemia, IL-6 elevations, and antioxidant defense system disorder. These records revealed that the immunomodulatory, anti-diabetic and antioxidant tasks are fine pointers for the cardiovascular defender of propolis especially during diabetes and/or pesticides exposure.


Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.
Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.


Incidence and risk factors for liver enzyme elevation during highly active antiretroviral therapy in HIV-HCV co-infected patients: results from the Italian EPOKA-MASTER Cohort.
The risk of hepatotoxicity associated with different highly active antiretroviral therapy (HAART) regimens (containing multiple-protease inhibitors, single-protease inhibitors or non nucleoside reverse transcriptase inhibitors) in HIV-HCV co-infected patients has not been fully assessed. Retrospective analysis of a prospective cohort of 1,038 HIV-HCV co-infected patients who commenced a new HAART in the Italian MASTER database. Patients were stratified into naïve and experienced to antiretroviral therapy before starting the study regimens. Time to grade > or =III hepatotoxicity (as by ACTG classification) was the primary outcome. Secondary outcome was time to grade IV hepatotoxicity. Incidence of grade > or =III hepatotoxicity was 17.71 per 100 patient-years (p-yr) of follow up in naïve patient group and 8.22 per 100 p-yrs in experienced group (grade IV: 4.13 per 100 p-yrs and 1.08 per 100 p-yrs, respectively). In the latter group, the only independent factors associated with shorter time to the event at proportional hazards regression model were: previous liver transaminase elevations to grade > or =III, higher baseline alanine amino-transferase values, and use of a non nucleoside reverse transcriptase inhibitor based regimen. In the naive group, baseline aspartate transaminase level was associated with the primary outcome. Use of a single or multiple protease inhibitor based regimen was not associated with risk of hepatotoxicity in either naïve or experienced patient groups to a statistically significant extent. A cautious approach with strict monitoring should be applied in HIV-HCV co-infected experienced patients with previous liver transaminase elevations, higher baseline alanine amino-transferase values and who receive regimens containing non nucleoside reverse transcriptase inhibitors.


Characterization of M Cells in Tear Duct-Associated Lymphoid Tissue of Mice: A Potential Role in Immunosurveillance on the Ocular Surface.
The ocular mucosal tissues are exposed to potentially harmful foreign antigens in the air and tear fluid. The tear duct-associated lymphoid tissue (TALT) may contribute to immune surveillance in the eye region. Follicle-associated epithelium (FAE) of TALTs is classified as stratified squamous epithelium and consists of squamous epithelial cells arranged in layers on the basement membrane. In contrast, most mucosa-associated lymphoid tissue is covered by a monolayer of epithelium containing microfold (M) cells. Therefore, antigen uptake and the presence of M cells in TALT are not fully understood. The present study found that a small population of FAE cells in the TALT expressed intestinal M-cell markers, namely Sox8, Tnfaip2, GP2, and OPG. This cell population was identified as functional M cells because of their uptake capacity of luminal nanoparticles. In addition, RANKL, which is essential for M-cell differentiation, was expressed by stroma-like cells at the subepithelial region and its receptor RANK by the FAE in the TALT. The administration of RANKL markedly increased the number of Sox8+ M cells. In contrast, deficiency in OPG, an endogenous inhibitor of RANKL, increased the number of M cells in the TALT. These data demonstrate that the RANKL-RANK axis is essential for M-cell differentiation in the TALT. Furthermore, immunization via eye drops elicited the production of antigen-specific antibodies in tears, which was enhanced by RANKL administration. Thus, TALT M cells play an important role in the immunosurveillance of the eye region.


Mitochondrial energetics and therapeutics.
Mitochondrial dysfunction has been linked to a wide range of degenerative and metabolic diseases, cancer, and aging. All these clinical manifestations arise from the central role of bioenergetics in cell biology. Although genetic therapies are maturing as the rules of bioenergetic genetics are clarified, metabolic therapies have been ineffectual. This failure results from our limited appreciation of the role of bioenergetics as the interface between the environment and the cell. A systems approach, which, ironically, was first successfully applied over 80 years ago with the introduction of the ketogenic diet, is required. Analysis of the many ways that a shift from carbohydrate glycolytic metabolism to fatty acid and ketone oxidative metabolism may modulate metabolism, signal transduction pathways, and the epigenome gives us an appreciation of the ketogenic diet and the potential for bioenergetic therapeutics.


Exploring patient perspectives of prediabetes and diabetes severity: a qualitative study.
Objective: This qualitative study sought to identify and describe patients' variant perceptions of disease severity after receiving a type 2 diabetes (T2DM) or prediabetes (preDM) diagnosis. Design: Researchers interviewed 29 patients from two US medical centers to ascertain perceptions of severity. We used the constant comparative method from a grounded theory approach to identify themes from patients' perspectives that inform their disease severity. This approach was used to help translate research to practice and ultimately identify intervention strategies informed by authentic experiences of preDM and T2DM patients. Results: Perceptions of disease severity fell into two groups: high and low severity. Patients diagnosed with T2DM and preDM emerged in both groups and were comparative in terms of sample size, gender, and ethnic diversity. Several factors contributed to patients' beliefs, including what they were told about the disease, observations from experiences within their own social network, and information from formal diabetes classes and their own research. The two perspectives diverged when patients described how their belief was informed by three thematic properties or personal factors: (i) fears; (ii) clinician communication; and (iii) social comparisons. Conclusions: Beliefs about severity are influenced by patients' fears, interactions with clinicians, and experiences within their social networks. These findings show that when interacting with patients with T2DM or preDM, clinicians should elicit patient perceptions of disease severity so they may then tailor the discussion to address these perceptions and help patients grasp the severity of these conditions.


Climate correlates of 20 years of trophic changes in a high-elevation riparian system.
The consequences of climate change for ecosystem structure and function remain largely unknown. Here, I examine the ability of climate variation to explain long-term changes in bird and plant populations, as well as trophic interactions in a high-elevation riparian system in central Arizona, USA, based on 20 years of study. Abundances of dominant deciduous trees have declined dramatically over the 20 years, correlated with a decline in overwinter snowfall. Snowfall can affect overwinter presence of elk, whose browsing can significantly impact deciduous tree abundance. Thus, climate may affect the plant community indirectly through effects on herbivores, but may also act directly by influencing water availability for plants. Seven species of birds were found to initiate earlier breeding associated with an increase in spring temperature across years. The advance in breeding time did not affect starvation of young or clutch size. Earlier breeding also did not increase the length of the breeding season for single-brooded species, but did for multi-brooded species. Yet, none of these phenology-related changes was associated with bird population trends. Climate had much larger consequences for these seven bird species by affecting trophic levels below (plants) and above (predators) the birds. In particular, the climate-related declines in deciduous vegetation led to decreased abundance of preferred bird habitat and increased nest predation rates. In addition, summer precipitation declined over time, and drier summers also were further associated with greater nest predation in all species. The net result was local extinction and severe population declines in some previously common bird species, whereas one species increased strongly in abundance, and two species did not show clear population changes. These data indicate that climate can alter ecosystem structure and function through complex pathways that include direct and indirect effects on abundances and interactions of multiple trophic components.


Myofiber orientation and electrical activation in human and sheep atrial models.
Anatomically realistic computational models provide a powerful platform for investigating mechanisms that underlie atrial rhythm disturbances. In recent years, novel techniques have been developed to construct structurally-detailed, image-based models of 3D atrial anatomy. However, computational models still do not contain full descriptions of the atrial intramural myofiber architecture throughout the entire atria. To address this, a semi-automatic rule-based method was developed for generating multi-layer myofiber orientations in the human atria. The rules for fiber generation are based on the careful anatomic studies of Ho, Anderson and co-workers using dissection, macrophotography and visual tracing of fiber tracts. Separately, a series of high color contrast images were obtained from sheep atria with a novel confocal surface microscopy method. Myofiber orientations in the normal sheep atria were estimated by eigen-analyis of the 3D image structure tensor. These data have been incorporated into an anatomical model that provides the quantitative representation of myofiber architecture in the atrial chambers. In this study, we attempted to compare the two myofiber generation approaches. We observed similar myo-bundle structure in the human and sheep atria, for example in Bachmann's bundle, atrial septum, pectinate muscles, superior vena cava and septo-pulmonary bundle. Our computational simulations also confirmed that the preferential propagation pathways of the activation sequence in both atrial models is qualitatively similar, largely due to the domination of the major muscle bundles.


Peripheral arterial disease--what do we need to know?
Peripheral artery disease (PAD) results from progressive narrowing of arteries secondary to atherosclerosis and is defined as an Ankle Brachial Index of <0.9. PAD is highly prevalent and is an increasing burden on both the economy and the patient, especially given the rapid shift in demographics in the United States. Despite its prevalence and association with cardiovascular disease, PAD is still underdiagnosed and undertreated. This may, in part, be related to lack of recognition from the physician's side or paucity of evidence from clinical trials. It has been shown that medical therapy approved for cardiovascular disease is effective in the treatment of PAD and decreases cardiovascular events. Various revascularization strategies are also available for improving symptoms and quality of life in these patients, yet they are underutilized. In an attempt to increase its recognition, PAD has been considered a coronary artery disease equivalent. This article reviews the diagnosis and management of PAD. © 2011 Wiley Periodicals, Inc. The authors have no funding, financial relationships, or conflicts of interest to disclose.


Investigating the role of Cu-oxo species in Cu-nitrate formation over Cu-CHA catalysts.
The speciation of framework-interacting CuII sites in Cu-chabazite zeolite catalysts active in the selective catalytic reduction of NOx with NH3 is studied, to investigate the influence of the Al content on the copper structure and their reactivity towards a NO/O2 mixture. To this aim, three samples with similar Cu densities and different Si/Al ratios (5, 15 and 29) were studied using in situ X-ray absorption spectroscopy (XAS), FTIR and diffuse reflectance UV-Vis during pretreatment in O2 followed by the reaction. XAS and UV-Vis data clearly show the main presence of Z2CuII sites (with Z representing a framework negative charge) at a low Si/Al ratio, as predicted. EXAFS wavelet transform analysis showed a non-negligible fraction of proximal Z2CuII monomers, possibly stabilized into two 6-membered rings within the same cage. These sites are not able to form Cu-nitrates by interaction with NO/O2. By contrast, framework-anchored Z[CuII(NO3)] complexes with a chelating bidentate structure are formed in samples with a higher Si/Al ratio, by reaction of NO/O2 with Z[CuII(OH)] sites or structurally similar mono- or multi-copper Zx[CuIIxOy] sites. Linear combination fit (LCF) analysis of the XAS data showed good agreement between the fraction of Z[CuII(OH)]/Zx[CuIIxOy] sites formed during activation in O2 and that of Z[CuII(NO3)] complexes formed by reaction with NO/O2, further confirming the chemical inertia of Z2CuII towards these reactants in the absence of solvating NH3 molecules.


Predicting and scaling hens' preferences for topographically different responses.
Six hens were exposed to several concurrent (second-order) variable-interval schedules in which the response requirements on the alternatives were varied. The response requirements were one key peck versus five key pecks, one key peck versus one door push, and five key pecks versus one door push. Response- and time-allocation ratios undermatched the obtained reinforcement ratios but were well described by the generalized matching law. Time and response bias estimates from two pairs of response requirements were used to predict bias in the third pairing. The predicted values were close to those obtained; this result supports the notion that both numerically and topographically different responses act as constant sources of bias within the generalized matching law. The differences between the response and time biases could be accounted for by the different times needed to complete each response requirement. The results also suggest that the door push is a useful operant for research with domestic hens.


Urban particulate matter activates Akt in human lung cells.
The normally picturesque Cache Valley in northern Utah is frequently reported to have the worst particulate (PM) air pollution in the United States. Numerous epidemiological studies conducted elsewhere have associated PM exposure to a variety of cardiovascular diseases and early mortality. We have previously shown that Cache Valley PM (CVPM) is pro-inflammatory, through a variety of mechanisms involving the release of inflammatory cytokines, unfolded protein response, ER stress, and C-reactive protein (CRP). This study was undertaken to determine whether Cache Valley PM (CVPM) would activate Akt, an upstream mechanism common to these events. Human lung (BEAS-2B) cells were treated with either fine (PM(2.5)) or coarse (PM(10)) particles (12.5 and 25 μg/ml) for periods up to 24 h. PM-exposed cells exhibited Akt activation as evidenced by phosphorylation at Thr(308) and Ser(473). Events downstream of Akt activation such as NF-κB activation were observed at 1 and 24 h, but IκB phosphorylation occurred only at 24 h, indicating that mechanisms of PM-mediated NF-κB activation are time dependent. Akt and NF-κB related inflammatory cytokine IL-1α, and IL-6 and the chemokine IL-8 were upregulated in treated cells at 6 and 24 h. The calpain inhibitor leupeptin limited Akt phosphorylation to Ser(473) and reduced release of IL-1α, IL-6, and IL-8, indicating that calpain or similar protease(s) are involved in PM-induced activation of Akt and subsequent release of inflammatory cytokines. Our data indicate that PM activates Akt, which may play a role in the pro-inflammatory response to PM exposure.


CSF biomarkers in Olmsted County: Evidence of 2 subclasses and associations with demographics.
We studied interrelationships between CSF biomarkers and associations with APOE ε4 genotype, demographic variables, vascular variables, and clinical diagnosis in Olmsted County, Minnesota. We included 774 Mayo Clinic Study of Aging participants (693 cognitively unimpaired [CU]; 71 with mild cognitive impairment [MCI]). CSF β-amyloid 42 (Aβ42), total tau (t-tau), and hyperphosphorylated tau (p-tau) were analyzed using Aβ42 CSF, t-tau CSF, and p-tau (181P) CSF electrochemiluminescence immunoassays. Bivariate mixture models were used to evaluate latent classes. We used linear regression models to evaluate independent associations of APOE ε4, demographic factors, cardiovascular risk, and diagnosis with CSF biomarker levels. Results were weighted back to the Olmsted County population. Interrelationships between CSF Aβ42 and p-tau/t-tau were consistent with 2 latent classes in the general population. In subgroup 1 (n = 547 [71%]), we found a strong positive correlation between Aβ42 and p-tau (ρ = 0.81), while the correlation was much smaller in group 2 (ρ = 0.26, n = 227 [29%]). Group 2 was associated with older age, APOE ε4 genotype, a diagnosis of MCI, and elevated amyloid PET. Overall, APOE ε4 genotype and MCI were associated with Aβ42, while age was associated with p-tau/t-tau. There were no associations with sex, education, or vascular risk. We hypothesize the population without dementia can be subdivided into participants with and without biological Alzheimer disease (AD) based on the combination of CSF Aβ42 and p-tau/t-tau (represented also by the p-tau/t-tau/Aβ42 ratio). In those without biological AD, common factors such as CSF dynamics may cause a positive correlation between CSF Aβ42 and p-tau/t-tau, while AD leads to dissociation of these proteins.


Various applications of TALEN- and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome.
Modifying the genomes of many organisms is becoming as easy as manipulating DNA in test tubes, which is made possible by two recently developed techniques based on either the customizable DNA binding protein, TALEN, or the CRISPR/Cas9 system. Here, we describe a series of efficient applications derived from these two technologies, in combination with various homologous donor DNA plasmids, to manipulate the Drosophila genome: (1) to precisely generate genomic deletions; (2) to make genomic replacement of a DNA fragment at single nucleotide resolution; and (3) to generate precise insertions to tag target proteins for tracing their endogenous expressions. For more convenient genomic manipulations, we established an easy-to-screen platform by knocking in a white marker through homologous recombination. Further, we provided a strategy to remove the unwanted duplications generated during the "ends-in" recombination process. Our results also indicate that TALEN and CRISPR/Cas9 had comparable efficiency in mediating genomic modifications through HDR (homology-directed repair); either TALEN or the CRISPR/Cas9 system could efficiently mediate in vivo replacement of DNA fragments of up to 5 kb in Drosophila, providing an ideal genetic tool for functional annotations of the Drosophila genome.


Comparison of ICD-10R, DSM-IV-TR and DSM-5 in an adult autism spectrum disorder diagnostic clinic.
An Autism Spectrum Disorder (ASD) diagnosis is often used to access services. We investigated whether ASD diagnostic outcome varied when DSM-5 was used compared to ICD-10R and DSM-IV-TR in a clinical sample of 150 intellectually able adults. Of those diagnosed with an ASD using ICD-10R, 56 % met DSM-5 ASD criteria. A further 19 % met DSM-5 (draft) criteria for Social Communication Disorder. Of those diagnosed with Autistic Disorder/Asperger Syndrome on DSM-IV-TR, 78 % met DSM-5 ASD criteria. Sensitivity of DSM-5 was significantly increased by reducing the number of criteria required for a DSM-5 diagnosis, or by rating 'uncertain' criteria as 'present', without sacrificing specificity. Reduced rates of ASD diagnosis may mean some ASD individuals will be unable to access clinical services.


Low level of self-reported physical activity in ambulatory patients new to dialysis.
Physical inactivity contributes to the frailty and the decline in function that develops over time among patients with end-stage renal disease. We assessed physical activity among 1547 ambulatory patients new to dialysis in the United States Renal Data System Comprehensive Dialysis Study. We used a self-reporting Human Activity Profile that included Maximal and Adjusted Activity Scores and compared results to established norms by age and gender. Physical activity was found to be extremely low with scores for all age and gender categories below the 5th percentile of healthy individuals and 95% of patients had scores consonant with low fitness. Older age, female gender, diabetes, atherosclerotic disease, and a low level of education were associated with lower activity scores assessed by univariate and multivariable linear regression analysis. Higher serum albumin, creatinine, and lower body mass index, but not hemoglobin levels, were associated with greater physical activity. By multivariable analysis, patients on hemodialysis using a catheter reported lower levels of physical activity compared to those on peritoneal dialysis, hemodialysis using an arteriovenous fistula, or with a graft. Lower Maximal and Adjusted Activity Scores were associated with poor physical function and mental health. Hence, physical activity is distressingly low among patients new to dialysis. Thus, strategies to enhance activity in these patients should be explored.


Justified paternalism: the nature of beneficence in the care of dementia patients.
The issue of patient autonomy in cases of permanent dementia has recently received a great deal of philosophical attention. Specifically, many have worried about ethical issues surrounding advance directives in which people specify how they shall be treated when they are no longer competent to make their own medical decisions. Ronald Dworkin has been a staunch defender of what he calls precedent autonomy in these cases, believing persons have a right to control, to some degree, how their lives will end, despite the common intuition that the principle of beneficence requires us to improve the experiential quality of patients' lives. Objections have been brought against Dworkin on a number of fronts, including worries about personal identity theory and informed consent. Here, I offer an objection to Dworkin's assessment of the nature of paternalism as it relates to cases of permanent dementia.


Colorectal cancer screening with faecal occult blood test within a multiple disease screening programme: an experience from Keelung, Taiwan.
Given increasing rates of colorectal cancer (CRC) in countries with intermediate incidence rates, the decision to implement population-based screening must consider the trade-off between high costs and a relatively low yield. In Taiwan, we proposed community-based CRC screening using faecal occult blood tests (FOBT) within a multiple disease screening programme. Based on early results from the screening programme, we aimed to compare the projected efficacies, in terms of reductions in CRC mortality, achieved with multiple disease screening, single disease screening and no screening programmes. Annual FOBT has been included in the Keelung multiple disease screening programme. A total of 26,008 subjects were offered screening. Early indicators have been estimated to assess the potential effectiveness of this programme, including the Dukes' stage distribution of screen-detected cases, the proportionate incidence and the prevalence/incidence ratio. Transition rates according to adenoma size and Dukes' stage have been estimated from an eight-state Markov model. The projected mortality reductions based on this disease natural history have been estimated using Markov Chain Monte Carlo simulation for both multiple screening and single screening. The overall attendance rate was 82% at the first screen and 87% at the second screen. At the first screen, 70% of screen-detected cases were localized (i.e. Dukes' stage A or B). The corresponding figure for the second screen was 80%. Approximately three-quarters of detected adenomas were smaller than 1 cm. The estimated mean transition times from diminutive adenoma to small adenoma, from small adenoma to large adenoma and from large adenoma to pre-clinical Dukes' A or B invasive carcinoma were 14.4, 5.4 and 5.6 years, respectively. Estimated reductions in CRC mortality, based on annual screening, are 23 and 33% for the single and multiple disease screening programmes, respectively. Multiple screening with an annual screening regime may lead to a further 13% reduction in mortality when compared to conventional single screening. Early indications suggest that population-based screening for CRC with FOBT, implemented through a multi-disease screening programme, is both feasible and efficacious. Further evaluation of the programme, through longer follow-up and cost-effectiveness analysis, is now required.


A new diaryl urea compound, D181, induces cell cycle arrest in the G1 and M phases by targeting receptor tyrosine kinases and the microtubule skeleton.
Receptor tyrosine kinases (RTKs) modulate a variety of cellular events, including cell proliferation, differentiation, mobility and apoptosis. In addition, RTKs have been validated as targets for cancer therapies. Microtubules are another class of proven targets for many clinical anticancer drugs. Here, we report that 1-(4-chloro-3-(trifluoromethyl) phenyl)-3-(2-cyano-4-hydroxyphenyl)urea (D181) functions as both a receptor tyrosine kinase inhibitor and a tubulin polymerization enhancer. D181 displayed potent inhibitory activities against a panel of RTKs, including Flt3, VEGFR, cKit, FGFR1 and PDGFRβ. D181 also enhanced tubulin polymerization and modified the secondary structure of tubulin proteins to disrupt their dynamic instability. Because of synergistic cooperation, D181 strongly inhibited the proliferation of various cancer cell lines, induced LoVo cell cycle arrest in the G1 and M phases and suppressed tumor growth in nude mice bearing human LoVo and HT29 xenografts. Our studies have provided a new, promising lead compound and novel clues for multi-target anticancer drug design and development.


TNM classification system for primary cutaneous lymphomas other than mycosis fungoides and Sezary syndrome: a proposal of the International Society for Cutaneous Lymphomas (ISCL) and the Cutaneous Lymphoma Task Force of the European Organization of Research and Treatment of Cancer (EORTC).
Currently availabel staging systems for non-Hodgkin lymphomas are not useful for clinical staging classification of most primary cutaneous lymphomas. The tumor, node, metastases (TNM) system used for mycosis fungoides (MF) and Sézary syndrome (SS) is not appropriate for other primary cutaneous lymphomas. A usable, unified staging system would improve the communication about the state of disease, selection of appropriate management, standardization of enrollment/response criteria in clinical trials, and collection/analysis of prospective survival data. Toward this goal, during the recent meetings of the International Society for Cutaneous Lymphomas (ISCL) and the cutaneous lymphoma task force of the European Organization of Research and Treatment of Cancer (EORTC), the representatives have established a consensus proposal of a TNM classification system applicable for all primary cutaneous lymphomas other than MF and SS. Due to the clinical and pathologic heterogeneity of the cutaneous lymphomas, the currently proposed TNM system is meant to be primarily an anatomic documentation of disease extent and not to be used as a prognostic guide.


Calculated reciprocity after all: computation behind token transfers in orang-utans.
Transfers and services are frequent in the animal kingdom. However, there is no clear evidence in animals that such transactions are based on weighing costs and benefits when giving or returning favours and keeping track of them over time (i.e. calculated reciprocity). We tested two orang-utans (Pongo pygmaeus abelii) in a token-exchange paradigm, in which each individual could exchange a token for food with the experimenter but only after first obtaining the token from the other orang-utan. Each orang-utan possessed tokens valuable to their partner but useless to themselves. Both orang-utans actively transferred numerous tokens (mostly partner-valuable) to their partner. One of the orang-utans routinely used gestures to request tokens while the other complied with such requests. Although initially the transfers were biased in one direction, they became more balanced towards the end of the study. Indeed, data on the last three series produced evidence of reciprocity both between and within trials. We observed an increase in the number and complexity of exchanges and alternations. This study is the first experimental demonstration of the occurrence of direct transfers of goods based on calculated reciprocity in non-human-primates.


Psychiatric Comorbidity Is Associated Prospectively with Diminished Opioid Analgesia and Increased Opioid Misuse in Patients with Chronic Low Back Pain.
Opioids are frequently prescribed for chronic low back pain (CLBP), but there are little prospective data on which patient subgroups may benefit. Psychiatric comorbidity, such as high levels of depression and anxiety symptoms (termed comorbid negative affect [NA]), is a common presentation and may predict diminished opioid analgesia and/or increased opioid misuse. The authors conducted a 6½-month prospective cohort study of oral opioid therapy, with an active drug/placebo run-in period, in 81 CLBP patients with low, moderate, and high levels of NA. Treatment included an opioid titration phase with a prescribing physician blinded to NA group assignment and a 4-month continuation phase, during which subjects recorded daily pain levels using an electronic diary. The primary outcome was the percent improvement in average daily pain, summarized weekly. There was an overall 25% dropout rate. Despite the high NA group being prescribed a higher average daily dose of morphine equivalents, linear mixed model analysis revealed that the 24 study completers in each of the high NA and low NA groups had an average 21 versus 39% improvement in pain, respectively (P < 0.01). The high NA group also had a significantly greater rate of opioid misuse (39 vs. 8%, P < 0.05) and significantly more and intense opioid side effects (P < 0.01). These results indicate that the benefit and risk considerations in CLBP patients with high NA versus low NA are distinctly different. Thus, NA is an important phenotypic variable to characterize at baseline, before deciding whether to prescribe opioids for CLBP.


Differential expression of epithelial–mesenchymal transition and stem cell markers in intrinsic subtypes of breast cancer.
The transcription factors SLUG and SOX9 have been shown to define mammary stem cell state. Similarly, epithelial–mesenchymal transition (EMT) markers (E-Cadherin, mTOR) have been shown to play a role in tumor-progression and metastatic potential in breast cancer. Finally, SOX10 is known to be expressed in breast cancer as well. The overexpressions of EMT and stem cell markers have been shown to correlate with poor overall survival. In this study, we examined whether the expression of these markers correlates with intrinsic subtypes of breast cancer and whether there is a prognostic difference in their expression-profile. We analyzed 617 breast cancer samples from two tissue micro arrays. Breast cancer samples were categorized into three groups according to hormone receptor expression and HER2-status as Luminal A/B, HER2-positive, and triple negative subgroup. Immunohistochemical expressions of SLUG, SOX9, SOX10, E-Cadherin, and mTOR were semi-quantitatively analyzed using a two-tiered and three-tiered scoring system in which cytoplasmic and nuclear stains were considered. Strong nuclear expression of SLUG was observed preferentially in triple negative but not in Luminal A/B or HER2-positive cases (24 vs. 3 and 0 %, p < 0.001). Loss of SOX9 in the nuclear stain was less frequent in triple negative than in Luminal A/B or HER2-positive cases (4 vs. 9 vs. 13 %, p < 0.001). Expression of nuclear SOX10 was lower in triple negative than in Luminal A/B and HER2-positive cases (67 vs.78 and 79 %, p = 0.012). E-Cadherin loss was observed only in Luminal A/B tumors (p = 0.016), no difference in the mTOR expression was seen between any of the three groups. No correlation to conventional histopathological-parameters or stage could be established in our cohort. Our study shows an inversed preferential nuclear expression of SLUG, SOX10, and SOX9 in triple negative and non-triple negative cases. This information is important in understanding the biology of triple negative breast cancer, also in terms of future studies dealing with targeted therapies based on the alterations of EMT and stem cell markers.


NUMB phosphorylation destabilizes p53 and promotes self-renewal of tumor-initiating cells by a NANOG-dependent mechanism in liver cancer.
Stem cell populations are maintained through self-renewing divisions in which one daughter cell commits to a particular fate whereas the other retains the multipotent characteristics of its parent. The NUMB, a tumor suppressor, in conjunction with another tumor-suppressor protein, p53, preserves this property and acts as a barrier against deregulated expansion of tumor-associated stem cells. In this context, NUMB-p53 interaction plays a crucial role to maintain the proper homeostasis of both stem cells, as well as differentiated cells. Because the molecular mechanism governing the assembly and stability of the NUMB-p53 interaction/complex are poorly understood, we tried to identify the molecule(s) that govern this process. Using cancer cell lines, tumor-initiating cells (TICs) of liver, the mouse model, and clinical samples, we identified that phosphorylations of NUMB destabilize p53 and promote self-renewal of TICs in a pluripotency-associated transcription factor NANOG-dependent manner. NANOG phosphorylates NUMB by atypical protein kinase C zeta (aPKCζ), through the direct induction of Aurora A kinase (AURKA) and the repression of an aPKCζ inhibitor, lethal (2) giant larvae. By radioactivity-based kinase activity assays, we showed that NANOG enhances kinase activities of both AURKA and aPKCζ, an important upstream process for NUMB phosphorylation. Phosphorylation of NUMB by aPKCζ destabilizes the NUMB-p53 interaction and p53 proteolysis and deregulates self-renewal in TICs. Post-translational modification of NUMB by the NANOG-AURKA-aPKCζ pathway is an important event in TIC self-renewal and tumorigenesis. Hence, the NANOG-NUMB-p53 signaling axis is an important regulatory pathway for TIC events in TIC self-renewal and liver tumorigenesis, suggesting a therapeutic strategy by targeting NUMB phosphorylation. Further in-depth in vivo and clinical studies are warranted to verify this suggestion.


Depression and bipolar support alliance consensus statement on the unmet needs in diagnosis and treatment of mood disorders in children and adolescents.
To focus attention on the critical unmet needs of children and adolescents with mood disorders and to make recommendations for future research and allocation of healthcare resources. The 36-member Consensus Development Panel consisted of experts in child/adolescent or adult psychiatry and psychology, pediatrics, and mental health advocacy. Reviews of the literature concerning youth mood disorders were performed on the subjects of risk factors, prevention, diagnosis, treatment, and services delivery, and opinions and experiences of mental health advocates were obtained. The Consensus Development Panel listened to presentations and participated in discussions. Independent workgroups of clinicians, scientists, and mental health advocates considered the evidence and prepared preliminary statements. Workgroup leaders presented drafts for discussion by the Consensus Development Panel. The final document was reviewed by the entire group and edited to incorporate input from all participants. Evidence suggests high rates of unmet needs for children and adolescents with depression or bipolar disorder. Training is largely limited to child mental health specialists; general psychiatrists, pediatricians, and other primary care physicians receive little or no training. As a result, treatment patterns may reflect adult treatment plans that are not validated for youths. Effective treatments have been identified and some preliminary prevention models have been developed, but they are not yet widely applied. Patients experience limited exposure to clinicians adequately trained to address their problems and little information to guide care decisions, particularly concerning bipolar disorder. National efforts are required to restructure healthcare delivery and provider training and to immediately develop more advanced research on pathophysiology, prevention, and services delivery effectiveness.


Greenland subglacial drainage evolution regulated by weakly connected regions of the bed.
Penetration of surface meltwater to the bed of the Greenland Ice Sheet each summer causes an initial increase in ice speed due to elevated basal water pressure, followed by slowdown in late summer that continues into fall and winter. While this seasonal pattern is commonly explained by an evolution of the subglacial drainage system from an inefficient distributed to efficient channelized configuration, mounting evidence indicates that subglacial channels are unable to explain important aspects of hydrodynamic coupling in late summer and fall. Here we use numerical models of subglacial drainage and ice flow to show that limited, gradual leakage of water and lowering of water pressure in weakly connected regions of the bed can explain the dominant features in late and post melt season ice dynamics. These results suggest that a third weakly connected drainage component should be included in the conceptual model of subglacial hydrology.


Translocation joins c-myc and immunoglobulin gamma 1 genes in a Burkitt lymphoma revealing a third exon in the c-myc oncogene.
Recombinant DNA clones have been used to directly demonstrate that the Burkitt lymphoma cell line Raji, t(8;14) (q24;q32), has a rearranged copy of the c-myc gene adjacent to the gamma 1 constant region gene of the human immunoglobulin heavy-chain locus; the genes are arranged in the opposite direction for transcription. At least one further 5' exon has been detected in the normal c-myc gene by analysis of RNA transcripts, and the occurrence of high levels of two c-myc mRNA size classes, both apparently initiating in this exon, is described.


The feasibility of preventing mother-to-child transmission of HIV using peer counselors in Zimbabwe.
Prevention of mother-to-child transmission of HIV (PMTCT) is a major public health challenge in Zimbabwe. Using trained peer counselors, a nevirapine (NVP)-based PMTCT program was implemented as part of routine care in urban antenatal clinics. Between October 2002 and December 2004, a total of 19,279 women presented for antenatal care. Of these, 18,817 (98%) underwent pre-test counseling; 10,513 (56%) accepted HIV testing, of whom 1986 (19%) were HIV-infected. Overall, 9696 (92%) of women collected results and received individual post-test counseling. Only 288 men opted for HIV testing. Of the 1807 HIV-infected women who received posttest counseling, 1387 (77%) collected NVP tablet and 727 (40%) delivered at the clinics. Of the 1986 HIV-infected women, 691 (35%) received NVPsd at onset of labor, and 615 (31%) infants received NVPsd. Of the 727 HIV-infected women who delivered in the clinics, only 396 women returned to the clinic with their infants for the 6-week follow-up visit; of these mothers, 258 (59%) joined support groups and 234 (53%) opted for contraception. By the end of the study period, 209 (53%) of mother-infant pairs (n = 396) came to the clinic for at least 3 follow-up visits. Despite considerable challenges and limited resources, it was feasible to implement a PMTCT program using peer counselors in urban clinics in Zimbabwe.


The theory of surface-enhanced Raman scattering on semiconductor nanoparticles; toward the optimization of SERS sensors.
We present an expression for the lowest order nonzero contribution to the surface-enhanced Raman spectrum obtained from a system of a molecule adsorbed on a semiconductor nanoparticle. Herzberg-Teller vibronic coupling of the zero-order Born-Oppenheimer states results in an expression which may be regarded as an extension of the Albrecht A-, B-, and C-terms to SERS substrates. We show that the SERS enhancement is caused by combinations of several types of resonances in the combined system, namely, surface, exciton, charge-transfer, and molecular resonances. These resonances are coupled by terms in the numerator, which provide selection rules that enable various tests of the theory and predict the relative intensities of the Raman lines. Furthermore, by considering interactions of the various contributions to the SERS enhancement, we are able to develop ways to optimize the enhancement factor by tailoring the semiconductor nanostructure, thereby adjusting the locations of the various contributing resonances. This provides a procedure by which molecular sensors can be constructed and optimized. We provide several experimental examples on substrates such as monolayer MoS2 and GaN nanorods.


The validity and reliability of the 'Cancer Caregiving Tasks, Consequences and Needs Questionnaire' (CaTCoN).
Caregivers are often involved in and affected by the patient's disease. The questionnaire 'Cancer Caregiving Tasks, Consequences and Needs Questionnaire' (CaTCoN) was developed to measure caregivers' experiences. The aim of this study is to evaluate the construct validity and reliability of the multi-item scales in the CaTCoN using psychometric analyses as well as tests of convergent and discriminant validity with the existing instruments FAMCARE and Family Inventory of Needs (FIN). Based on theoretical considerations, a subscale structure in the CaTCoN was hypothesized, and the subscales were tested by item-item correlations, followed by factor analysis, calculation of internal consistency by Cronbach's alpha, and multitrait-scaling analysis. Further, theoretically based hypotheses about convergence and divergence between CaTCoN and FAMCARE/FIN (sub)scales were formulated and tested. Analyses were based on 590 caregivers' responses. Initially, 11 CaTCoN subscales were hypothesized. The item-item correlations and factor analysis lead to some revisions, but the analyses confirmed the hypothesized subscales to a large extent, resulting in nine CaTCoN subscales (Cronbach's alpha range 0.65-0.95). The hypothesized convergent CaTCoN and FAMCARE/FIN subscales correlated 0.59-0.74, and hypothesized divergent CaTCoN and FAMCARE/FIN subscales correlated -0.11-0.25, thus confirming the hypotheses concerning convergent and discriminant validity between CaTCoN and the existing questionnaires FAMCARE and FIN. Taken together the psychometric analyses and tests of convergent and discriminant validity indicate that the validity and reliability of the CaTCoN are satisfactory.


Mesenchymal stem cells as a source of Schwann cells: their anticipated use in peripheral nerve regeneration.
Schwann cells form myelin, sustain axons and provide the microenvironment for nerve fibers, thereby playing a key role in the peripheral nervous system (PNS). Schwann cells also provide support for the damaged PNS by producing factors that strongly promote axonal regrowth and contribute to remyelination, which is crucial for the recovery of neural function. These advantages are not confined to the PNS and also apply to the central nervous system. Many diseases, including peripheral nerve injury, neuropathy, multiple sclerosis and spinal cord injury, are targets for Schwann cell therapy. The collection of Schwann cells, however, causes new damage to other peripheral nerve segments. Furthermore, the doubling time of Schwann cells is not very fast, and thus adequate amounts of Schwann cells for clinical use cannot be collected within a reasonable amount of time. Mesenchymal stem cells, which are highly proliferative, are easily accessible from various types of mesenchymal tissues, such as the bone marrow, umbilical cord and fat tissue. Because these cells have the ability to cross oligolineage boundaries between mesodermal to ectodermal lineages, they are capable of differentiating into Schwann cells with step-by-step cytokine stimulation. In this review, we summarize the properties of mesenchymal stem cell-derived Schwann cells, which are comparable to authentic Schwann cells, and discuss future perspectives.


A Survey and Analysis of the American Public's Perceptions and Knowledge About Antibiotic Resistance.
Background. Little is known about the American public's perceptions or knowledge about antibiotic-resistant bacteria or antibiotic misuse. We hypothesized that although many people recognize antibiotic resistance as a problem, they may not understand the relationship between antibiotic consumption and selection of resistant bacteria. Methods. We developed and tested a survey asking respondents about their perceptions and knowledge regarding appropriate antibiotic use. Respondents were recruited with the Amazon Mechanical Turk crowdsourcing platform. The survey, carefully designed to assess a crowd-sourced population, asked respondents to explain "antibiotic resistance" in their own words. Subsequent questions were multiple choice. Results. Of 215 respondents, the vast majority agreed that inappropriate antibiotic use contributes to antibiotic resistance (92%), whereas a notable proportion (70%) responded neutrally or disagreed with the statement that antibiotic resistance is a problem. Over 40% of respondents indicated that antibiotics were the best choice to treat a fever or a runny nose and sore throat. Major themes from the free-text responses included that antibiotic resistance develops by bacteria, or by the infection, or the body (ie, an immune response). Minor themes included antibiotic overuse and antibiotic resistance caused by bacterial adaptation or an immune response. Conclusions. Our findings indicate that the public is aware that antibiotic misuse contributes to antibiotic resistance, but many do not consider it to be an important problem. The free-text responses suggest specific educational targets, including the difference between an immune response and bacterial adaptation, to increase awareness and understanding of antibiotic resistance.


Inter-rater and test-retest reliability: methods and results for the neighborhood observational checklist.
The popularity of direct or systematic social observation as a method to evaluate the mechanisms by which neighborhood environments impact health and contribute to health disparities is growing. The development of measures with adequate inter-rater and test-retest reliability is essential for this research. In this paper, based on our experiences conducting direct observation of neighborhoods in Detroit, MI, we describe strategies to promote high inter-rater and test-retest reliability and methods to evaluate reliability. We then present the results and discuss implications for future research efforts using direct observation in four areas: methods to evaluate reliability, instrument content and design, observer training, and data collection.


Fibrillar organization of fibronectin is expressed coordinately with cell surface gangliosides in a variant murine fibroblast.
NCTC 2071A cells, a line of transformed murine fibroblasts, grow in serum-free medium, are deficient in gangliosides, synthesize fibronectin, but do not retain and organize it on the cell surface. When the cells are exposed to exogenous gangliosides, fibrillar strands of fibronectin become attached to the cell surface. A morphologically distinct variant of NCTC 2071A cells was observed to both retain cell surface fibronectin and organize it into a fibrillar network when the cells were stained with anti-fibronectin antibodies and a fluorescent second antibody. A revertant cell type appeared to resemble the parental NCTC 2071A cells in terms of morphology and fibronectin organization. All three cell types were subjected to mild NaIO4 oxidation and reduction with KB3H4 of very high specific radioactivity in order to label the sialic acid residues of surface gangliosides. The variant had much more surface gangliosides than the parental, particularly more complex gangliosides corresponding to GM1 and GD1a. The surface gangliosides of the revertant were intermediate between the parental and the variant. By using sialidase, which hydrolyzes GD1a to GM1, and 125I-labeled cholera toxin, which binds specifically to GM1, the identity and levels of these gangliosides were confirmed in the three cell types. When variant cells were exposed to sialidase for 2 d, there appeared to be little change in fibronectin organization. Concomitant treatment of the cells with the B subunit of cholera toxin, which bound to all the surface GM1 including that generated by the sialidase, however, eliminated the fibrillar network of fibronectin. In addition, exposure of the variant cells to a 70,000-mol-wt fragment of fibronectin, which lacks the cell attachment domain but contains a matrix assembly domain, inhibited the formation of fibers. Finally, all three cell types were assayed for their ability to attach to and spread on fibronectin-coated surfaces; no significant differences were found. Our results further establish that the ability of a cell to organize fibronectin into an extracellular matrix is dependent on certain gangliosides, but they also indicate that cell adhesion to fibronectin is independent of these gangliosides. We suggest that matrix organization and cell attachment and spreading are based on separate mechanisms and that these functions are associated with different cell surface "receptors."


Two positively charged residues of phi29 DNA polymerase, conserved in protein-primed DNA polymerases, are involved in stabilisation of the incoming nucleotide.
In DNA polymerases from families A and B in the closed conformation, several positively charged residues, located in pre-motif B and motif B, have been shown to interact with the phosphate groups of the incoming nucleotide at the polymerisation active site: the invariant Lys of motif B and the nearly invariant Lys of pre-motif B (family B) correspond to a His in family A DNA polymerases. In phi29 DNA polymerase, belonging to the family B DNA polymerases able to start replication by protein-priming, the corresponding residues, Lys383 and Lys371, have been shown to be dNTP-ligands. Since in several DNA polymerases a third residue has been involved in dNTP binding, we have addressed here the question if in the DNA polymerases of the protein-primed subfamily, and especially in phi29 DNA polymerase, there are more than these two residues involved in nucleotide binding. By site-directed mutagenesis in phi29 DNA polymerase the functional role of the remaining two conserved positively charged amino acid residues of pre-motif B and motif B (besides Lys371 and Lys383) has been studied. The results indicate that residue Lys379 of motif B is also involved in dNTP binding, possibly through interaction with the triphosphate moiety of the incoming nucleotide, since the affinity for nucleotides of mutant DNA polymerase K379T was reduced in DNA and TP-primed reactions. On the other hand, we propose that, when the terminal protein (TP) is present at the polymerisation active site, residue Lys366 of pre-motif B is involved in stabilising the incoming nucleotide in an appropriate position for efficient TP-deoxynucleotidylation. Although mutant DNA polymerase K366T showed a wild-type like phenotype in DNA-primed polymerisation in the presence of DNA as template, in TP-primed reactions as initiation and transition it was impaired, especially in the presence of the phi29 DBP, protein p6.


Breakup of a homeobox cluster after genome duplication in teleosts.
Several families of homeobox genes are arranged in genomic clusters in metazoan genomes, including the Hox, ParaHox, NK, Rhox, and Iroquois gene clusters. The selective pressures responsible for maintenance of these gene clusters are poorly understood. The ParaHox gene cluster is evolutionarily conserved between amphioxus and human but is fragmented in teleost fishes. We show that two basal ray-finned fish, Polypterus and Amia, each possess an intact ParaHox cluster; this implies that the selective pressure maintaining clustering was lost after whole-genome duplication in teleosts. Cluster breakup is because of gene loss, not transposition or inversion, and the total number of ParaHox genes is the same in teleosts, human, mouse, and frog. We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish.


A comparative study on the CO2 hydrogenation catalyzed by Ru dihydride complexes: (PMe3)4RuH2 and (Me2PCH2CH2PMe2)2RuH2.
The phosphine complexes of Ru dihydride are model catalysts for CO2 hydrogenation. Despite many theoretical studies, important questions remain unresolved regarding the underlying catalytic mechanisms. We report a comparative study by using density functional theory on two catalysts, (PMe3)4RuH2 and (dmpe)2RuH2, with dmpe = Me2PCH2CH2PMe2, for which very different mechanisms have been suggested in previous studies. By comparing their energy profiles along all possible reaction paths side by side, we are able to clarify the similarity and difference between them, and provide a consistent account for all the experimental observations reported, including the kinetic models, the cis to trans transformation of (dmpe)2RuH2, and the significant enhancement of the catalytic rate in supercritical CO2 for (PMe3)4RuH2 and its lack thereof for (dmpe)2RuH2. The crucial difference between the two mechanisms involves the formation of an intermediate, in which a formate ion binds to Ru as a bidentate ligand. When this step results in the dissociation of a ligand, the reaction rate is enhanced under supercritical conditions, due to the increase in entropy, which should be a valid consideration for other catalytic reactions as well.


Tract-based morphometry for white matter group analysis.
We introduce an automatic method that we call tract-based morphometry, or TBM, for measurement and analysis of diffusion MRI data along white matter fiber tracts. Using subject-specific tractography bundle segmentations, we generate an arc length parameterization of the bundle with point correspondences across all fibers and all subjects, allowing tract-based measurement and analysis. In this paper we present a quantitative comparison of fiber coordinate systems from the literature and we introduce an improved optimal match method that reduces spatial distortion and improves intra- and inter-subject variability of FA measurements. We propose a method for generating arc length correspondences across hemispheres, enabling a TBM study of interhemispheric diffusion asymmetries in the arcuate fasciculus (AF) and cingulum bundle (CB). The results of this study demonstrate that TBM can detect differences that may not be found by measuring means of scalar invariants in entire tracts, such as the mean diffusivity (MD) differences found in AF. We report TBM results of higher fractional anisotropy (FA) in the left hemisphere in AF (caused primarily by lower lambda(3), the smallest eigenvalue of the diffusion tensor, in the left AF), and higher left hemisphere FA in CB (related to higher lambda(1), the largest eigenvalue of the diffusion tensor, in the left CB). By mapping the significance levels onto the tractography trajectories for each structure, we demonstrate the anatomical locations of the interhemispheric differences. The TBM approach brings analysis of DTI data into the clinically and neuroanatomically relevant framework of the tract anatomy.


A dominant-negative isoform of hypoxia-inducible factor-1 alpha specifically expressed in human testis.
Spermatogenesis in the seminiferous tubuli of the testis occurs under a high proliferation rate, suggesting considerable oxygen consumption. Because of the lack of blood vessels, the oxygen partial pressure in the lumen of these tubuli is very low. We previously identified a testis isoform of the hypoxia-inducible factor (HIF)-1alpha in the mouse, termed mHIF-1alphaI.1. Here, we demonstrate that expression of mHIF-1alphaI.1 increases during puberty, further demonstrating its gene induction in postmeiotic germ cells. Using 5'-rapid amplification of cDNA ends, we identified a novel HIF-1alpha isoform in the human testis, called hHIF-1alphaTe. Like mHIF-1alphaI.1, hHIF-1alphaTe mRNA is derived from an alternative promoter-first exon combination, but with a different genomic organization and a different nucleotide sequence. Reverse transcription-polymerase chain reaction analysis confirmed that hHIF-1alphaTe is exclusively expressed in the testis. As determined by immunofluorescence of ejaculated sperm cells, HIF-1alpha protein is mainly localized in the postacrosomal head and in the midpiece of spermatozoa. Though overlapping with mitochondrial localization in human and mouse spermatozoa, neither hHIF-1alphaTe nor hHIF-1alpha associated with mitochondria. In contrast with the ubiquitously expressed HIF-1alpha protein and the mouse testis-specific mHIF-1alphaI.1 isoform, the hHIF-1alphaTe mRNA sequence predicts a protein with an N-terminal truncation of the DNA-binding domain. As shown by yeast two-hybrid assays, hHIF-1alphaTe still formed heterodimeric complexes with HIF-1beta. However, hHIF-1alphaTe was incapable of forming a DNA-binding HIF-1 complex. Overexpression of exogenous hHIF-1alphaTe resulted in the inhibition of the endogenous HIF-1 transcriptional activity, demonstrating that the testis-specific hHIF-1alphaTe isoform is a dominant-negative regulator of normal HIF-1 activity.


Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die?
The human genome contains nearly 1.1 million Alu elements comprising roughly 11% of its total DNA content. Alu elements use a copy and paste retrotransposition mechanism that can result in de novo disease insertion alleles. There are nearly 900,000 old Alu elements from subfamilies S and J that appear to be almost completely inactive, and about 200,000 from subfamily Y or younger, which include a few thousand copies of the Ya5 subfamily which makes up the majority of current activity. Given the much higher copy number of the older Alu subfamilies, it is not known why all of the active Alu elements belong to the younger subfamilies. We present a systematic analysis evaluating the observed sequence variation in the different sections of an Alu element on retrotransposition. The length of the longest number of uninterrupted adenines in the A-tail, the degree of A-tail heterogeneity, the length of the 3' unique end after the A-tail and before the RNA polymerase III terminator, and random mutations found in the right monomer all modulate the retrotransposition efficiency. These changes occur over different evolutionary time frames. The combined impact of sequence changes in all of these regions explains why young Alus are currently causing disease through retrotransposition, and the old Alus have lost their ability to retrotranspose. We present a predictive model to evaluate the retrotransposition capability of individual Alu elements and successfully applied it to identify the first putative source element for a disease-causing Alu insertion in a patient with cystic fibrosis.