Functional, fractal nonlinear response with application to rate processes with memory, allometry, and population genetics.
We give a functional generalization of fractal scaling laws applied to response problems as well as to probability distributions. We consider excitations and responses, which are functions of a given state vector. Based on scaling arguments, we derive a general nonlinear response functional scaling law, which expresses the logarithm of a response at a given state as a superposition of the values of the logarithms of the excitations at different states. Such a functional response law may result from the balance of different growth processes, characterized by variable growth rates, and it is the first order approximation of a perturbation expansion similar to the phase expansion. Our response law is a generalization of the static fractal scaling law and can be applied to the study of various problems from physics, chemistry, and biology. We consider some applications to heterogeneous and disordered kinetics, organ growth (allometry), and population genetics. Kinetics on inhomogeneous reconstructing surfaces leads to rate equations described by our nonlinear scaling law. For systems with dynamic disorder with random energy barriers, the probability density functional of the rate coefficient is also given by our scaling law. The relative growth rates of different biological organs (allometry) can be described by a similar approach. Our scaling law also emerges by studying the variation of macroscopic phenotypic variables in terms of genotypic growth rates. We study the implications of the causality principle for our theory and derive a set of generalized Kramers-Kronig relationships for the fractal scaling exponents.


Sustained therapeutic reversal of Huntington's disease by transient repression of huntingtin synthesis.
The primary cause of Huntington's disease (HD) is expression of huntingtin with a polyglutamine expansion. Despite an absence of consensus on the mechanism(s) of toxicity, diminishing the synthesis of mutant huntingtin will abate toxicity if delivered to the key affected cells. With antisense oligonucleotides (ASOs) that catalyze RNase H-mediated degradation of huntingtin mRNA, we demonstrate that transient infusion into the cerebrospinal fluid of symptomatic HD mouse models not only delays disease progression but mediates a sustained reversal of disease phenotype that persists longer than the huntingtin knockdown. Reduction of wild-type huntingtin, along with mutant huntingtin, produces the same sustained disease reversal. Similar ASO infusion into nonhuman primates is shown to effectively lower huntingtin in many brain regions targeted by HD pathology. Rather than requiring continuous treatment, our findings establish a therapeutic strategy for sustained HD disease reversal produced by transient ASO-mediated diminution of huntingtin synthesis.


Inefficient immune response is associated with microbial permissiveness in juvenile oysters affected by mass mortalities on field.
Since 2008, juvenile Crassostrea gigas oysters have suffered from massive mortalities in European farming areas. This disease of complex etiology is still incompletely understood. Triggered by an elevated seawater temperature, it has been associated to infections by a herpes virus named OsHV-1 as well as pathogenic vibrios of the Splendidus clade. Ruling out the complexity of the disease, most of our current knowledge has been acquired in controlled experiments. Among the many unsolved questions, it is still ignored what role immunity plays in the capacity oysters have to survive an infectious episode. Here we show that juvenile oysters susceptible to the disease mount an inefficient immune response associated with microbial permissiveness and death. We found that, in contrast to resistant adult oysters having survived an earlier episode of mortality, susceptible juvenile oysters never exposed to infectious episodes died by more than 90% in a field experiment. Susceptible oysters were heavily colonized by OsHV-1 herpes virus as well as bacteria including vibrios potentially pathogenic for oysters, which proliferated in oyster flesh and body fluids during the mortality event. Nonetheless, susceptible oysters were found to sense microbes as indicated by an overexpression of immune receptors and immune signaling pathways. However, they did not express important immune effectors involved in antimicrobial immunity and apoptosis and showed repressed expression of genes involved in ROS and metal homeostasis. This contrasted with resistant oysters, which expressed those important effectors, controlled bacterial and viral colonization and showed 100% survival to the mortality event. Altogether, our results demonstrate that the immune response mounted by susceptible oysters lacks some important immune functions and fails in controlling microbial proliferation. This study opens the way to more holistic studies on the "mass mortality syndrome", which are now required to decipher the sequence of events leading to oyster mortalities and determine the relative weight of pathogens, oyster genetics and oyster-associated microbiota in the disease.


Endothelial dysfunction in systemic lupus erythematosus - a case-control study and an updated meta-analysis and meta-regression.
Endothelium-dependent flow-mediated dilation (ED-FMD), a biophysical marker of endothelial dysfunction, is apparently impaired in patients with systemic lupus erythematosus (SLE) but such observation is inconsistent. Here, we assessed and compared the brachial artery ED-FMD (baED-FMD) using ultrasonography between SLE patients without cardiovascular disease and healthy controls (HC) matched for age, gender and body mass index. We then performed a comprehensive meta-analysis of case-control studies which compared baED-FMD between SLE patients and HC by determining the effect size of baED-FMD as standardized mean difference (SMD). Factors associated with the effect size were explored by mixed-model meta-regression. Seventy one SLE patients and 71 HC were studied. SLE patients had lower baED-FMD than HC (3.72 ± 2.8% vs 4.63 ± 3.1%, p = 0.032). Meta-analysis of 25 case-control studies involving 1,313 SLE patients and 1,012 HC with the random effects model revealed lower baED-FMD in SLE patients compared to HC (SMD -1.077, p < 0.001). The presence of diabetes mellitus (p = 0.04747), higher diastolic blood pressure (p = 0.044), renal involvement (p = 0.027) and aspirin use (p = 0.001) were associated with more discrepant baED-FMD between both groups. In conclusion, SLE patients naïve of cardiovascular disease have impaired endothelial function. Diabetes mellitus, renal disease and diastolic hypertension are major contributors of endothelial dysfunction in SLE patients.


'Super Rehab': can we achieve coronary artery disease regression? A feasibility study protocol.
Patients diagnosed with coronary artery disease (CAD) are currently treated with medications and lifestyle advice to reduce the likelihood of disease progression and risk of future major adverse cardiovascular events (MACE). Where obstructive disease is diagnosed, revascularisation may be considered to treat refractory symptoms. However, many patients with coexistent cardiovascular risk factors, particularly those with metabolic syndrome (MetS), remain at heightened risk of future MACE despite current management.Cardiac rehabilitation is offered to patients post-revascularisation, however, there is no definitive evidence demonstrating its benefit in a primary prevention setting. We propose that an intensive lifestyle intervention (Super Rehab, SR) incorporating high-intensity exercise, diet and behavioural change techniques may improve symptoms, outcomes, and enable CAD regression.This study aims to examine the feasibility of delivering a multicentre randomised controlled trial (RCT) testing SR for patients with CAD, in a primary prevention setting. This is a multicentre randomised controlled feasibility study of SR versus usual care in patients with CAD. The study aims to recruit 50 participants aged 18-75 across two centres. Feasibility will be assessed against rates of recruitment, retention and, in the intervention arm, attendance and adherence to SR. Qualitative interviews will explore trial experiences of study participants and practitioners. Variance of change in CAD across both arms of the study (assessed with serial CT coronary angiography) will inform the design and power of a future, multi-centre RCT. Ethics approval was granted by South West-Frenchay Research Ethics Committee (reference: 21/SW/0153, 18 January 2022). Study findings will be disseminated via presentations to relevant stakeholders, national and international conferences and open-access peer-reviewed research publications. ISRCTN14603929.


Risk-Reducing Options for Women with a Hereditary Breast Cancer Predisposition.
Genetic testing is now widely utilized to identify women with a hereditary predisposition for breast cancer. Women who carry mutations that increase breast cancer risk may consider three options to reduce risk: screening, chemoprevention, and prophylactic surgery. Yet, no randomized trials have specifically assessed the efficacy of these options in mutation carriers. In many developed countries, mammography is regarded as the optimal means of screening for breast cancer in the general population. However, breast MRI is a more sensitive screening tool, and for mutation carriers, any breast cancer screening strategy should incorporate screening with MRI. In randomized trials of women at high risk for developing breast cancer, chemoprevention reduces that risk, but it has not been shown to reduce mortality. Finally, observational studies suggest that, in mutation carriers, prophylactic surgery may reduce the risk of developing breast cancer by 90-95%. There are several prophylactic mastectomy procedures to choose from, and these are generally done in conjunction with breast reconstruction. In this article, we discuss management of women who carry mutations that have been associated with an increased breast cancer risk. Mutation carriers should be informed of the potential risks and benefits of the three available options to reduce breast cancer risk.


Transitions in spousal caregiving.
This study describes transitions over 5 years among community-dwelling elderly spouses into and within caregiving roles and associated health outcomes. Participants in the Caregiver Health Effects Study (n = 818) were interviewed four times over 5 years with changes in their caregiving status described. Analyses of the effect on health outcomes of transitions were performed on those for whom four observations were available (n = 428). Only half (49.5%) of noncaregivers at baseline remained noncaregivers at 5-year follow-up. The remainder experienced one or more transitions, including moving into the caregiving role, their own or their spouse's death, or placement of their spouse in a long-term care facility. The trajectory of health outcomes associated with caregiving was generally downward. Those who transitioned to heavy caregiving had more symptoms of depression, and poorer self-reported health and health behaviors. Transitions into and within the caregiving role should be monitored for adverse health effects on the caregiver, with interventions tailored to the individual's location in the caregiving trajectory.


Effect of Exercise Training on Cardiac Biomarkers in At-Risk Populations: A Systematic Review.
Studies have demonstrated beneficial effects of exercise on cardiovascular disease biomarkers for healthy individuals; however, a comprehensive review regarding the effect of exercise on cardiovascular disease biomarkers in at-risk populations is lacking. A literature search was performed to identify studies meeting the following criteria: randomized controlled study, participants with pathology/activity limitations, biomarker outcome (total cholesterol, high-density lipoprotein, low-density lipoprotein, C-reactive protein, insulin, triglycerides, or glucose), and exercise intervention. Means and standard deviations from each biomarker were used to calculate standardized Cohen's d effect sizes with 95% confidence intervals. In total, 37 articles were included. The majority (44/57; 77%) of data points demonstrated moderate to strong effects for the reduction in total cholesterol, triglycerides, and low-density lipoprotein, and elevation in high-density lipoprotein following exercise. The majority of data points demonstrated strong effects for reductions in blood glucose (24/30; 80%) and insulin (23/24; 96%) levels following exercise intervention. Evidence is heterogeneous regarding the influence of exercise on cardiovascular disease biomarkers in at-risk patients, which does not allow a definitive conclusion. Favorable effects include reductions in triglycerides, total cholesterol, low-density lipoprotein, glucose, and insulin, and elevation in high-density lipoprotein following exercise intervention. The strongest evidence indicates that exercise is favorable for the reduction in glucose and cholesterol levels among obese patients, and reduction of insulin regardless of population.


Elevated plasma triglycerides and growth rate are early indicators of reproductive status in post-spawning female steelhead trout (Oncorhynchus mykiss).
Many iteroparous fishes spawn after skipping one or more yearly cycles, which impacts recruitment estimates used for fisheries management and conservation. The physiological mechanisms underlying the development of consecutive and skip spawning life histories in fishes are not well understood. In salmonids, lipid energy reserves and/or growth are thought to regulate the initiation of reproductive maturation during a critical period ~1 year prior to spawning. The fasting spawning migration of summer-run steelhead trout (Oncorhynchus mykiss) results in significant depletion of energy reserves during the proposed critical period for repeat spawning. To determine whether and when lipid energy reserves and growth influence repeat spawning, measures of lipid energy reserves, growth rate and reproductive development were tracked in female steelhead trout from first to second spawning as a consecutive or skip spawner in captivity. Plasma triglyceride (TG) levels and growth rate were elevated by 10 weeks after spawning in reproductive (i.e. consecutive spawning) versus non-reproductive (i.e. skip spawning) individuals. Muscle lipid (ML) levels, condition factor and plasma estradiol levels increased at later time points. The early differences in plasma TG levels and increases in growth rate are attributable to differential rates of feeding and assimilation between the groups following spawning. A year after spawning, plasma TG levels, MLs and growth rate decreased in consecutive spawners, attributable to transfer of lipid reserves into the ovary. During the year prior to second spawning, energy reserves and plasma estradiol levels were higher in reproductive skip spawners versus consecutive spawners, reflecting the energy deficit after first spawning. These results suggest that the decision to initiate ovarian recrudescence occurs by 10 weeks after first spawning and are consistent with the differences in energy reserves acquired following spawning being a consequence of that decision. This information will increase the success of conservation projects reconditioning post-spawning summer-run steelhead trout.


Fine mapping of polymorphic alcohol-related quantitative trait loci candidate genes using interval-specific congenic recombinant mice.
The inbred long-sleep (ILS) and inbred short-sleep (ISS) strains of mice are widely studied as a model of initial sensitivity to alcohol. Recently, a large comparative DNA sequencing study of candidate genes located within the four Lore quantitative trait loci (QTLs) associated with the ethanol-induced loss of righting reflex in ILS and ISS mice has identified eight genes that contain coding region differences corresponding to amino acid changes. Here, recently developed interval-specific congenic recombinant mice (ISCRs) have been used to map these genes in relationship to newly narrowed QTL regions. Regions of candidate genes containing DNA differences corresponding to previously identified amino acid changes between ISS and ILS mice were amplified from either genomic DNA or complementary DNA from ISCR mice using polymerase chain reaction. The products were purified and directly sequenced to determine the genotypes for each polymorphism. On the basis of these genotypic data, each candidate gene was determined to be located either within or outside of recently narrowed Lore QTL intervals. Of these eight candidates with protein-coding differences, five are now excluded from their respective Lore intervals. The other three (Znf142, Ptprn, and Znf133) have been localized to the narrowed QTL intervals. These three central nervous system genes (Znf142, Ptprn, and Znf133) represent promising candidates for involvement in the differential sensitivity to alcohol exhibited between ILS and ISS mice. This study also demonstrates how the combination of high-throughput comparative gene sequencing and concomitant genetic fine mapping of QTL regions with ISCRs can be an effective tool for accelerating the process of moving from QTL to gene.


Thermodynamic metrics and optimal paths.
A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.


Reconciliation between operational taxonomic units and species boundaries.
The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.


Prevalence of celiac disease in at-risk and not-at-risk groups in the United States: a large multicenter study.
Celiac disease (CD) is an immune-mediated enteropathic condition triggered in genetically susceptible individuals by the ingestion of gluten. Although common in Europe, CD is thought to be rare in the United States, where there are no large epidemiologic studies of its prevalence. The aim of this study was to determine the prevalence of CD in at-risk and not-at-risk groups in the United States. Serum antigliadin antibodies and anti-endomysial antibodies (EMA) were measured. In EMA-positive subjects, human tissue transglutaminase IgA antibodies and CD-associated human leukocyte antigen DQ2/DQ8 haplotypes were determined. Intestinal biopsy was recommended and performed whenever possible for all EMA-positive subjects. A total of 13 145 subjects were screened: 4508 first-degree and 1275 second-degree relatives of patients with biopsy-proven CD, 3236 symptomatic patients (with either gastrointestinal symptoms or a disorder associated with CD), and 4126 not-at-risk individuals. In at-risk groups, the prevalence of CD was 1:22 in first-degree relatives, 1:39 in second-degree relatives, and 1:56 in symptomatic patients. The overall prevalence of CD in not-at-risk groups was 1:133. All the EMA-positive subjects who underwent intestinal biopsy had lesions consistent with CD. Our results suggest that CD occurs frequently not only in patients with gastrointestinal symptoms, but also in first- and second-degree relatives and patients with numerous common disorders even in the absence of gastrointestinal symptoms. The prevalence of CD in symptomatic patients and not-at-risk subjects was similar to that reported in Europe. Celiac disease appears to be a more common but neglected disorder than has generally been recognized in the United States.


The Wisconsin wrestling minimum weight project: a model for weight control among high school wrestlers.
In 1989, the Wisconsin Interscholastic Athletic Association implemented a project including new rules and an educational program, consistent with ACSM and AMA guidelines, to curtail "weight cutting" among high-school wrestlers. The project included skinfold estimates of body fatness to determine a minimum competitive weight, a limit on weekly weight loss, and presentation of nutrition education information to help wrestlers diet effectively. Implementation of the project has overcome a variety of obstacles and has received widespread endorsement from parents, teachers, wrestlers, and coaches. The success of this project offers a model for other states to emulate and should encourage clinicians in other sports to initiate interventions addressing these unhealthy weight loss behaviors.


Multicriteria optimization enables less experienced planners to efficiently produce high quality treatment plans in head and neck cancer radiotherapy.
To demonstrate that novice dosimetry planners efficiently create clinically acceptable IMRT plans for head and neck cancer (HNC) patients using a commercially available multicriteria optimization (MCO) system. Twenty HNC patients were enrolled in this in-silico comparative planning study. Per patient, novice planners with less experience in dosimetry planning created an IMRT plan using an MCO system (RayStation). Furthermore, a conventionally planned clinical IMRT plan was available (Pinnacle(3)). All conventional IMRT and MCO-plans were blind-rated by two expert radiation-oncologists in HNC, using a 5-point scale (1-5 with 5 the highest score) assessment form comprising 10 questions. Additionally, plan quality was reported in terms of planning time, dosimetric and normal tissue complication probability (NTCP) comparisons. Inter-rater reliability was derived using the intra-class correlation coefficient (ICC). In total, the radiation-oncologists rated 800 items on plan quality. The overall plan score indicated no differences between both planning techniques (conventional IMRT: 3.8 ± 1.2 vs. MCO: 3.6 ± 1.1, p = 0.29). The inter-rater reliability of all ratings was 0.65 (95% CI: 0.57-0.71), indicating substantial agreement between the radiation-oncologists. In 93% of cases, the scoring difference of the conventional IMRT and MCO-plans was one point or less. Furthermore, MCO-plans led to slightly higher dose uniformity in the therapeutic planning target volume, to a lower integral body dose (13.9 ± 4.5 Gy vs. 12.9 ± 4.0 Gy, p < 0.001), and to reduced dose to the contra-lateral parotid gland (28.1 ± 11.8 Gy vs. 23.0 ± 11.2 Gy, p < 0.002). Consequently, NTCP estimates for xerostomia reduced by 8.4 ± 7.4% (p < 0.003). The hands-on time of the conventional IMRT planning was approximately 205 min. The time to create an MCO-plan was on average 43 ± 12 min. MCO planning enables novice treatment planners to create high quality IMRT plans for HNC patients. Plans were created with vastly reduced planning times, requiring less resources and a short learning curve.


Association Between Leukocyte Telomere Length and Plasma Homocysteine in a Singapore Chinese Population.
Leukocyte telomere length (LTL) and plasma homocysteine (HCY) have been independently associated with cardiovascular disease (CVD) morbidity and mortality. However, few studies have investigated the association between LTL and HCY levels. This study investigated the association of LTL with CVD risk factors, including HCY, in an overt CVD-free Singapore Chinese population comprised of middle aged and elderly, the age group at risk of developing CVD. The association of plasma HCY and other CVD biomarkers with LTL were assessed in 100 samples drawn from the Singapore Chinese Health Study (SCHS). SCHS, a population-based cohort, recruited Chinese individuals, aged 45-74 years, between 1993 and 1998. Questionnaire data were collected via face-to-face interviews. Known CVD biomarkers were measured from the blood collected at the time of recruitment, and LTL was measured using the conventional Southern blot method. After adjustment for age, gender, smoking status, education, and dialect, LTL was found to be inversely associated with plasma HCY levels (p for trend=0.014). Serum urate showed a weak association (p for trend=0.056). Other CVD risk factors and nutrients, namely total cholesterol, low-density lipoprotein (LDL), triglycerides and creatinine, high-density lipoprotein (HDL), folate, and vitamin B6 showed the expected trend with LTL, but did not reach statistical significance. LTL displayed an inverse association with plasma HCY. This LTL-HCY inverse association in subjects lacking obvious cardiovascular events suggests that telomere length may be an intermediary in the biological mechanism by which elevated HCY leads to CVD.


Seeing behind the surface: communicative demonstration boosts category disambiguation in 12-month-olds.
In their first years, infants acquire an incredible amount of information regarding the objects present in their environment. While often it is not clear what specific information should be prioritized in encoding from the many characteristics of an object, different types of object representations facilitate different types of generalizations. We tested the hypotheses that 1-year-old infants distinctively represent familiar objects as exemplars of their kind, and that ostensive communication plays a role in determining kind membership for ambiguous objects. In the training phase of our experiment, infants were exposed to movies displaying an agent sorting objects from two categories (cups and plates) into two locations (left or right). Afterwards, different groups of infants saw either an ostensive or a non-ostensive demonstration performed by the agent, revealing that a new object that looked like a plate can be transformed into a cup. A third group of infants experienced no demonstration regarding the new object. During test, infants were presented with the ambiguous object in the plate format, and we measured generalization by coding anticipatory looks to the plate or the cup side. While infants looked equally often towards the two sides when the demonstration was non-ostensive, and more often to the plate side when there was no demonstration, they performed more anticipatory eye movements to the cup side when the demonstration was ostensive. Thus, ostensive demonstration likely highlighted the hidden dispositional properties of the target object as kind-relevant, guiding infants' categorization of the foldable cup as a cup, despite it looking like a plate. These results suggest that infants likely encode familiar objects as exemplars of their kind and that ostensive communication can play a crucial role in disambiguating what kind an object belongs to, even when this requires disregarding salient surface features.


High-fat diet suppresses the positive effect of creatine supplementation on skeletal muscle function by reducing protein expression of IGF-PI3K-AKT-mTOR pathway.
High-fat (HF) diets in combination with sedentary lifestyle represent one of the major public health concerns predisposing to obesity and diabetes leading to skeletal muscle atrophy, decreased fiber diameter and muscle mass with accumulation of fat tissue resulting in loss of muscle strength. One strategy to overcome the maleficent effects of HF diet is resistance training, a strategy used to improve muscle mass, reverting the negative effects on obesity-related changes in skeletal muscle. Together with resistance training, supplementation with creatine monohydrate (CrM) in the diet has been used to improve muscle mass and strength. Creatine is a non-essential amino acid that is directly involved in the cross-bridge cycle providing a phosphate group to ADP during the initiation of muscle contraction. Besides its antioxidant and anti-inflammatory effects CrM also upregulates IGF-1 resulting in hyperthophy with an increase in muscle function. However, it is unknown whether CrM supplementation during resistance training would revert the negative effects of high-fat diet on the muscle performance. During 8 weeks we measured muscle performance to climb a 1.1m and 80° ladder with increasing load on trained rats that had received standard diet or high-fat diet, supplemented or not with CrM. We observed that the CrM supplementation up-regulated IGF-1 and phospho-AKT protein levels, suggesting an activation of the IGF1-PI3K-Akt/PKB-mTOR pathway. Moreover, despite the CrM supplementation, HF diet down-regulated several proteins of the IGF1-PI3K-Akt/PKB-mTOR pathway, suggesting that diet lipid content is crucial to maintain or improve muscle function during resistance training.


Optimizing amino acid substitution matrices with a local alignment kernel.
Detecting remote homologies by direct comparison of protein sequences remains a challenging task. We had previously developed a similarity score between sequences, called a local alignment kernel, that exhibits good performance for this task in combination with a support vector machine. The local alignment kernel depends on an amino acid substitution matrix. Since commonly used BLOSUM or PAM matrices for scoring amino acid matches have been optimized to be used in combination with the Smith-Waterman algorithm, the matrices optimal for the local alignment kernel can be different. Contrary to the local alignment score computed by the Smith-Waterman algorithm, the local alignment kernel is differentiable with respect to the amino acid substitution and its derivative can be computed efficiently by dynamic programming. We optimized the substitution matrix by classical gradient descent by setting an objective function that measures how well the local alignment kernel discriminates homologs from non-homologs in the COG database. The local alignment kernel exhibits better performance when it uses the matrices and gap parameters optimized by this procedure than when it uses the matrices optimized for the Smith-Waterman algorithm. Furthermore, the matrices and gap parameters optimized for the local alignment kernel can also be used successfully by the Smith-Waterman algorithm. This optimization procedure leads to useful substitution matrices, both for the local alignment kernel and the Smith-Waterman algorithm. The best performance for homology detection is obtained by the local alignment kernel.


Phenotypic characteristics associated with insulin resistance in metabolically obese but normal-weight young women.
Metabolically obese, normal-weight (MONW) individuals are a hypothesized subgroup of the general population. These normal-weight individuals potentially display a cluster of obesity-related features, although this has not been systematically tested in young women. We hypothesized that MONW young women would display higher levels of total and visceral fat and lower levels of physical activity than normal women. In a cohort of 71 healthy nonobese women (21-35 years old), we identified MONW women based on cut points for insulin sensitivity (normal = glucose disposal >8 mg x min(-1) x kg(-1) of fat-free mass [FFM], n = 58; impaired = glucose disposal <8 ml x min(-1) x kg(-1) of FFM, n = 13). Thereafter, we measured body composition (dual energy X-ray absorptiometry) and body fat distribution (computed tomography), cardiorespiratory fitness (VO2max on a treadmill), physical activity energy expenditure (doubly labeled water and indirect calorimetry), glucose tolerance (oral glucose tolerance test), serum lipid profile, and dietary intake. We found a higher body fat percentage (32 +/- 6 vs. 27 +/- 6%, P = 0.01) and higher subcutaneous (213 +/- 61 vs. 160 +/- 78 cm2, P = 0.03) and visceral (44 +/- 16 vs. 35 +/- 14 cm2, P < 0.05) abdominal adiposity in the MONW group versus the normal group. The MONW group showed a lower physical activity energy expenditure (2.66 +/- 0.92 vs. 4.39 +/- 1.50 MJ/day, P = 0.01), but no difference in cardiorespiratory fitness was noted between groups. In conclusion, despite a normal body weight, a subset of young, apparently healthy women displayed a cluster of risky phenotypic characteristics that, if left untreated, may eventually predispose them to type 2 diabetes and cardiovascular disease.


Risk behaviors and HIV care continuum outcomes among criminal justice-involved HIV-infected transgender women and cisgender men: Data from the Seek, Test, Treat, and Retain Harmonization Initiative.
Transgender persons are highly victimized, marginalized, disproportionately experience incarceration, and have alarmingly increased rates of HIV infection compared to cis-gender persons. Few studies have examined the HIV care continuum outcomes among transgender women (TW), particularly TW who are involved with the criminal justice (CJ) system. To improve our understanding of HIV care continuum outcomes and risk behaviors among HIV-infected TW who are involved with the CJ system, we analyzed data from the National Institute on Drug Abuse-supported Seek, Test, Treat, Retain (STTR) Data Harmonization Initiative. Baseline data were pooled and analyzed from three U.S. STTR studies to examine HIV risk and care continuum indicators among CJ-involved HIV-infected TW compared to cisgender men (CM), matched on age (within 5 years) and study at a ratio of 1:5. Eighty-eight TW and 440 CM were included in the study. Among matched participants, TW were more likely to report crack and cocaine use compared to CM (40%,16% respectively, p<0.001); both TW and CM reported high rates of condomless sex (58%, 64%, respectively); TW were more likely than CM to have more than one sexual partner (OR = 2.9, 95% CI: 1.6, 5.2; p<0.001) and have engaged in exchange sex (OR = 3.9, 95% CI: 2.3, 6.6; p<0.001). There were no significant differences between TW and CM in the percentage currently taking ART (52%, 49%, respectively), the mean percent adherence to ART (77% for both groups), and the proportion who achieved viral suppression (61%, 58%, respectively). HIV-infected CJ-involved TW and CM had similar use of ART and viral suppression but TW were more likely than matched CM to engage in exchange sex, have multiple sexual partners, and use crack/cocaine. TW and CM had similarly high rates of condomless sex and use of other drugs. TW require tailored risk reduction interventions, however both CJ-involved TW and CM require focused attention to reduce HIV risk and improve HIV continuum of care outcomes.


Association of measles and mumps with cardiovascular disease: The Japan Collaborative Cohort (JACC) study.
Although it has been suggested that exposure to infections during childhood could decrease risk of atherosclerotic cardiovascular disease (CVD), the evidence is scarce. We investigated the association of measles and mumps with CVD. 43,689 men and 60,147 women aged 40-79 years at baseline (1988-1990) completed a lifestyle questionnaire, including their history of measles and mumps, and were followed until 2009. Histories of infections were categorized as having no infection (reference), measles only, mumps only, or both infections. Hazard ratios (HR) for mortality from CVD across histories of infections were calculated. Men with measles only had multivariable HR (95% confidence interval) of 0.92 (0.85-0.99) for total CVD, those with mumps only had 0.52 (0.28-0.94) for total stroke and 0.21 (0.05-0.86) for hemorrhagic stroke, and those with both infections had 0.80 (0.71-0.90) for total CVD, 0.71 (0.53-0.93) for myocardial infarction, and 0.83 (0.69-0.98) for total stroke. Women with both infections had 0.83 (0.74-0.92) for total CVD and 0.84 (0.71-0.99) for total stroke. We also compared subjects with measles only or mumps only (reference) and those with both infections. Men with both infections had 0.88 (0.78-0.99) for total CVD. Women with both infections had 0.85 (0.76-0.94) for total CVD, 0.79 (0.67-0.93) for total stroke, 0.78 (0.62-0.98) for ischemic stroke and 0.78 (0.62-0.98) for hemorrhagic stroke. Measles and mumps, especially in case of both infections, were associated with lower risks of mortality from atherosclerotic CVD.


Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.
The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 "ML4Microbiome" that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.


Network elasticity of a model hydrogel as a function of swelling ratio: from shrinking to extreme swelling states.
In this work, we intended to investigate the relationship between the swelling ratio Q and Young's modulus E of hydrogels from their contracted state to extreme swelling state and elucidate the underlining molecular mechanism. For this purpose, we used tetra-poly(ethylene glycol) (tetra-PEG) gel, whose network parameters are well known, as the polymer backbone, and we succeeded in tuning the swelling of the gel by a factor of 1500 times while maintaining the topological structure of the network unchanged, using an approach combining a molecular stent method and a PEG dehydration method. A master curve of Q-E, independent of the method of obtaining Q, was obtained. Using the worm-like chain model, the experimentally determined master curve can be well reproduced. We also observed that the uniaxial stress-strain curve of the hydrogel can be well predicted by the worm-like chain model using the structure parameters determined from the fitting of the Q-E experimental curve.


Post-translational folding of the influenza C virus glycoprotein HEF: defective processing in cells expressing the cloned gene.
The post-translational processing of the influenza C virus glycoprotein HEF was analysed. In cells infected with influenza C virus, HEF protein is synthesized as a glycosylated 80K polypeptide. A post-translational conformational rearrangement involving the formation of intramolecular disulphide bonds results in a decrease in its electrophoretic mobility. Therefore, SDS-PAGE under non-reducing conditions suggests an Mr of about 100K, whereas under reducing conditions an 80K protein is observed which is in accordance with the sequence data. The 100K form was detected 10 min after synthesis of HEF, and transport to the cell surface took about 60 min. This result indicates that the conformational change presumably occurs in the endoplasmic reticulum. A difference in post-translational processing was observed when the HEF gene was expressed in the absence of other influenza C virus genes. In cells infected with recombinant simian virus 40, the 80K precursor was synthesized, but this protein was neither converted to the 100K form nor transported to the cell surface. Deletion of the short cytoplasmic tail of HEF (Arg-Thr-Lys) or replacement of the two basic amino acids by hydrophobic (Ile) or acidic residues (Glu) resulted in HEF protein which was partially converted to the 100K form. Influenza C virus glycoprotein obtained after transient expression of the HEF gene using the vaccinia virus system was completely converted to the 100K form. However, in neither expression system was HEF transported to the cell surface. The possibility is discussed that the interaction of HEF with another viral protein is required for the post-translational folding and transport of this glycoprotein. The M protein of influenza C virus is suggested as a candidate for the chaperone which might interact with the cytoplasmic tail of HEF.


Impact of low intensity summer rainfall on E. coli-discharge event dynamics with reference to sample acquisition and storage.
Understanding the role of different rainfall scenarios on faecal indicator organism (FIO) dynamics under variable field conditions is important to strengthen the evidence base on which regulators and land managers can base informed decisions regarding diffuse microbial pollution risks. We sought to investigate the impact of low intensity summer rainfall on Escherichia coli-discharge (Q) patterns at the headwater catchment scale in order to provide new empirical data on FIO concentrations observed during baseflow conditions. In addition, we evaluated the potential impact of using automatic samplers to collect and store freshwater samples for subsequent microbial analysis during summer storm sampling campaigns. The temporal variation of E. coli concentrations with Q was captured during six events throughout a relatively dry summer in central Scotland. The relationship between E. coli concentration and Q was complex with no discernible patterns of cell emergence with Q that were repeated across all events. On several occasions, an order of magnitude increase in E. coli concentrations occurred even with slight increases in Q, but responses were not consistent and highlighted the challenges of attempting to characterise temporal responses of E. coli concentrations relative to Q during low intensity rainfall. Cross-comparison of E. coli concentrations determined in water samples using simultaneous manual grab and automated sample collection was undertaken with no difference in concentrations observed between methods. However, the duration of sample storage within the autosampler unit was found to be more problematic in terms of impacting on the representativeness of microbial water quality, with unrefrigerated autosamplers exhibiting significantly different concentrations of E. coli relative to initial samples after 12-h storage. The findings from this study provide important empirical contributions to the growing evidence base in the field of catchment microbial dynamics.


Statistical design and the analysis of gene expression microarray data.
Gene expression microarrays are an innovative technology with enormous promise to help geneticists explore and understand the genome. Although the potential of this technology has been clearly demonstrated, many important and interesting statistical questions persist. We relate certain features of microarrays to other kinds of experimental data and argue that classical statistical techniques are appropriate and useful. We advocate greater attention to experimental design issues and a more prominent role for the ideas of statistical inference in microarray studies.


Enhancement by yohimbine of nicotine- and dimethylphenylpiperadinium-induced release of norepinephrine from cardiac sympathetic nerves of the dog: interaction of presynaptic alpha and nicotinic receptors.
The effect of yohimbine on nicotine- and dimethylphenylpiperadinium (DMPP)-induced release of norepinephrine (NE) from sympathetic cardiac nerves of the dog was examined in order to elucidate the interaction of presynaptic alpha and nicotinic receptors. Intracoronary infusion of nicotine (300 or 500 micrograms/min) or DMPP (100 or 300 micrograms/min) into the left circumflex artery increased coronary sinus output of NE (NE output), left ventricular dp/dt maximum (LV dp/dt max) and coronary sinus blood flow. The nicotine-induced increases in NE output, LV dp/dt max and coronary sinus blood flow were enhanced by simultaneous yohimbine infusion in doses of 10 and 30 micrograms/min into the same artery, and were attenuated by the drug in a dose of 100 micrograms/min. The DMPP-induced increases were enhanced by 10 micrograms/min of yohimbine infusion, but the enhancement was decreased by 30 and 100 micrograms/min. Yohimbine did not modify increases in NE output, LV dp/dt max and coronary sinus blood flow induced by intracoronary infusion of tyramine (100 micrograms/min). We have reported previously that yohimbine in the dose range used enhanced cardiac sympathetic nerve stimulation-induced increases in these parameters in a dose-dependent manner in the same preparation. The enhancement by yohimbine of nicotinic receptor-mediated NE release would be due to the blockade of presynaptic alpha-2 adrenoceptors. Therefore, it is suggested that presynaptic alpha-2 adrenoceptor-mediated feedback control operates on the process of NE release induced by nicotinic receptor activation as well as nerve stimulation. Although the mechanism of loss of the enhancement of the nicotinic effect by the large dose of yohimbine is not known, the possible mechanisms are discussed.


Neuronavigation in cranioorbital neurosurgery - do we really need it?
The value of neuronavigation in cranioorbital neurosurgery is controversial and relatively unstudied. The aim of this study was to evaluate the application, the usefulness and the reliability of neuronavigation in the neurosurgical treatment of orbital tumours. A frameless armless infrared-based neuronavigation system was applied in the microsurgical removal of 7 orbital tumors. Image guidance was CT-based in 3 cases, MRI-based in another 3 cases and based on image fusion between CT and MRI image sets in one patient. The extradural fronto-orbital approach was performed in 3 cases, lateral orbitotomy in 2 cases, trans-supraciliar approach in 1 case and inferomedial orbitotomy in 1 case. The surgical procedures were successful in all cases. The procedure-related morbidity and mortality rate in the series was zero. The registration accuracy of the neuronavigation ranged between 1.0 and 1.7 mm, with an average of 1.3 mm. Neuronavigated image guidance was evaluated as useful in all patients. Total tumour removal was achieved in 5 patients and partial tumour excision in 1 case. One patient was only biopsied. Neuronavigation is not a substitute for surgical knowledge and experience, but it is a valuable complement with significant intraoperative potential in cranioorbital surgery.


The effect of artifacts on dependence measurement in fMRI.
The study of effective connectivity by means of neuroimaging depends on the measurement of similarity between activity patterns at different locations in the brain, without necessarily presupposing a particular model for this dependence. When these interactions are measured using functional magnetic resonance imaging (fMRI) techniques, however, imaging and physiological artifacts create patterns of dependence that may be unrelated to cortical activity. We demonstrate some of these effects through the measurement of short-range dependencies present in fMRI scans of the primary visual cortex (V1) in the anaesthetized macaque monkey. High-field (4.7 T) fMRI scans were conducted to measure responses based on the blood oxygen level-dependent contrast mechanism, during periods of no sensory stimulation and of visual stimulation with rotating polar-transformed checkerboard gratings. Dependence between the haemodynamic activity at different spatial locations (i.e., different voxels) was measured using correlation, mutual information and functional covariance. Particular attention was paid to understanding the sources of spurious dependence that may be observed during such investigations. Two main effects were detected: (a) short-range correlations introduced by the process of image reconstruction and (b) perturbations in the haemodynamic response caused by breathing. The image reconstruction artifacts were shown to create an artificially high short-range dependence in the readout direction of the scan, and the breathing artifacts caused enhanced short-range dependence in both the readout and phase-encode directions. Additional dependence in the phase-encode direction due to image-ghosting is also possible but will not be discussed in this report, as it can be alleviated by fine adjustment of preemphasis (elimination of eddy currents). A technique is described for removing breathing artifacts, and the effect of breathing on the apparent dependence between voxels is illustrated. The correlation of haemodynamic activity with the stimulus was found to be affected by breathing, although this effect can be neutralised by averaging the haemodynamic responses over many repetitions of the stimulus. Nonetheless, patterns of dependent activity between voxels may be lost in this averaging process, which makes the removal of breathing artifacts necessary if statistical dependence and the study of effective connectivity is the primary aim of an investigation.


Soliton trapping of dispersive waves in photonic crystal fiber with two zero dispersive wavelengths.
Based on the generalized nonlinear Schrödinger equation, we present a numerical study of trapping of dispersive waves by solitons during supercontinuum generation in photonic crystal fibers pumped with femtosecond pulses in the anomalous dispersion region. Numerical simulation results show that the generated supercontinuum is bounded by two branches of dispersive waves, namely blue-shifted dispersive waves (B-DWs) and red-shifted dispersive waves (R-DWs). We find a novel phenomenon that not only B-DWs but also R-DWs can be trapped by solitons across the zero-dispersion wavelength when the group-velocity matching between the soliton and the dispersive wave is satisfied, which may led to the generation of new spectral components via mixing of solitons and dispersive waves. Mixing of solitons with dispersive waves has been shown to play an important role in shaping not only the edge of the supercontinuum, but also its central part around the higher zero-dispersion wavelength. Further, we show that the phenomenon of soliton trapping of dispersive waves in photonic crystal fibers with two zero-dispersion wavelengths has a very close relationship with pumping power and the interval between two zero-dispersion wavelengths. In order to clearly display the evolution of soliton trapping of dispersive waves, the spectrogram of output pulses is observed using cross-correlation frequency-resolved optical gating technique (XFROG).


Safety and efficacy of clindamycin phosphate 1.2%-benzoyl peroxide 3% fixed-dose combination gel for the treatment of acne vulgaris: a phase 3, multicenter, randomized, double-blind, active- and vehicle-controlled study.
Topical fixed-combination therapy containing 1% clindamycin as 1.2% clindamycin phosphate (CLNP) and 3% benzoyl peroxide (BPO) is an effective treatment for acne vulgaris (acne). To demonstrate that the combination of 1.2% CLNP with lower strength BPO (CLNP 1.2%-BPO 3%) in a gel formulation is superior to each individual ingredient, CLNP 1.2% and BPO 3%, and vehicle gel. A total of 1,319 patients with acne, aged 12 years or older, were enrolled and randomized (1:1:1:1) to receive CLNP 1.2%-BPO 3%, CLNP 1.2% gel, BPO 3% gel, or vehicle gel once-daily in a 12-week, multicenter, double-blind, parallel-group, vehicle-controlled study. Subjects were evaluated at baseline, weeks 2, 4, 8, and 12 or early termination. Assessment of efficacy was evaluated using a six-point Investigator's Static Global Assessment (ISGA) and Subject's Global Assessment (SGA) of acne severity and lesion counts (inflammatory, non-inflammatory, and total). Safety assessments included skin tolerability and adverse events (AEs). A greater proportion of subjects who used CLNP 1.2%-BPO 3% gel (39%) had a two grade improvement in ISGA from baseline to week 12 compared with CLNP 1.2% (25%; P<0.001), BPO 3% (30%; P=0.016), and vehicle (18%; P<0.001). CLNP 1.2%- BPO 3% was superior to CLNP 1.2% and vehicle alone in the absolute reduction from baseline to week 12 in all three lesion types (P<0.001 all pair-wise comparisons). CLNP 1.2%-BPO 3% was superior to BPO 3% alone in the absolute reduction from baseline to week 12 in inflammatory (P=0.015) and total (P=0.032) lesion counts. The incidence of product-related AEs was low and similar in all study groups (1% with CLNP 1.2%-BPO 3%, 2% with CLNP 1.2%, 2% with BPO 3%, and 2% with vehicle). Local tolerability assessments showed similar minimal changes from baseline to week 12 in all study groups. CLNP 1.2%-BPO 3% gel provides superior efficacy to improve ISGA score and reduce inflammatory and total lesion counts compared with the individual active ingredients (CLNP 1.2% and BPO 3%) and vehicle, while maintaining a highly favorable safety and tolerability profile similar to BPO 3% alone.


Kidney expression of glutathione peroxidase-1 is not protective against streptozotocin-induced diabetic nephropathy.
In many diseases, including progressive renal disorders, tissue injury and pathological intracellular signaling events are dependent on oxidative stress. Glutathione peroxidase-1 (Gpx1) is an antioxidant enzyme that is highly expressed in the kidney and removes peroxides and peroxynitrite that can cause renal damage. Therefore, we examined whether this abundant renal antioxidant enzyme limits renal damage during the development of type 1 diabetic nephropathy. Wild-type (Gpx1+/+) and deficient (Gpx1-/-) mice were made diabetic by intraperitoneal injection of streptozotocin (100 mg/kg) on 2 consecutive days. Diabetic Gpx1+/+ and -/- mice with equivalent blood glucose levels (23 +/- 4 mM) were selected and examined after 4 mo of diabetes. Compared with normal mice, diabetic Gpx1+/+ and -/- mice had a two- to threefold increase in urine albumin excretion at 2 and 4 mo of diabetes. At 4 mo, diabetic Gpx1+/+ and -/- mice had equivalent levels of oxidative renal injury (increased kidney reactive oxygen species, kidney lipid peroxidation, urine isoprostanes, kidney deposition of advanced glycoxidation, and nitrosylation end products) and a similar degree of glomerular damage (hypertrophy, hypercellularity, sclerosis), tubular injury (apoptosis and vimentin expression), and renal fibrosis (myofibroblasts, collagen, TGF-beta excretion). A lack of Gpx1 was not compensated for by increased levels of catalase or other Gpx isoforms in diabetic kidneys. Contrary to expectations, this study showed that the high level of Gpx1 expressed in the kidney is not protective against the development of renal oxidative stress and nephropathy in a model of type 1 diabetes.


Restoration by corticosteroids of the hyperaldosteronism in hyponatraemic rats with panhypopituitarism.
1. In the syndrome of inappropriate secretion of antidiuretic hormone, hyponatraemia is associated with a normal bicarbonate concentration despite dilution. This normal bicarbonate concentration is related to the development of a hyperaldosteronism, which is attributed to a direct stimulation of the zona glomerulosa by the hyponatraemic state. Some workers have suggested that, to develop this hyperaldosteronism requires the presence of a pituitary factor. To determine whether the pituitary gland plays a role in this hyponatraemia-induced hyperaldosteronism, water intoxication was performed for 24 h in normal and in panhypopituitaric rats. 2. In normal rats, hyponatraemia (108 mmol/l), induced by the administration of 1-desamino-8-D-arginine vasopressin and 2.5% D-glucose-0.45% NaCl by gavage (15% body weight) was associated with a mild increase in bicarbonate concentration, and blood acid-base equilibrium showed a mixed metabolic and respiratory alkalosis (pH 7.57, partial pressure of CO2 29 mmHg, base excess +5.5 mmol/l), and aldosterone concentration was increased 3-fold as compared with the control value. When hyponatraemia (110 mmol/l) was induced in a similar manner in panhypopituitaric rats, we observed a very low aldosterone concentration (< 50 pg/ml) and a compensated respiratory alkalosis (pH 7.45, partial pressure of CO2 30 mmHg, base excess -2.6 mmol/l). The restoration of a hyperaldosteronaemic state in this group of rats was related essentially to corticosteroid intake. 3. These data suggest that corticosteroids play a critical role in the development of hyponatraemia-related hyperaldosteronism, a phenomenon not necessarily dependent on a pituitary factor.


Minimally-invasive, direct coronary artery bypass grafting.
Minimally-invasive, direct vision coronary artery bypass grafting (MIDCAB) is a new surgical technique performed via limited thoracotomy in a beating heart without cardiopulmonary bypass. From June 1996 to December 1996, MIDCAB was performed in 12 patients (all male, average age, 65.9 years). In 11 patients with left anterior descending coronary artery lesions, thoracotomy was performed via the left, fourth intercostal space and the pericardium was incised to identify the target site. About 8 cm of the left internal mammary artery was harvested. Bilateral anterolateral thoractomy was performed in one patient with left anterior descending and right coronary artery lesions. Anastomosis was performed under direct vision in the beating heart without cardiopulmonary bypass. MIDCAB was performed successfully without morbidity. The patients' average stay in the intensive care unit was 1.8 days. No patient had any early cardiac event requiring additional surgery or percutaneous transluminal coronary angioplasty. Postoperatively, all patients were asymptomatic and their recovery was uneventful. Our initial experience indicates that MIDCAB offers good results and is a treatment option for selected patients with left anterior descending and/or right coronary artery lesions.


Analysis of cagA in Helicobacter pylori strains from Colombian populations with contrasting gastric cancer risk reveals a biomarker for disease severity.
Helicobacter pylori infection is a risk factor for the development of gastric cancer, and the bacterial oncoprotein CagA contributes to gastric carcinogenesis. We analyzed H. pylori isolates from persons in Colombia and observed that there was marked variation among strains in levels of CagA expression. To elucidate the basis for this variation, we analyzed sequences upstream from the CagA translational initiation site in each strain. A DNA motif (AATAAGATA) upstream of the translational initiation site of CagA was associated with high levels of CagA expression. Experimental studies showed that this motif was necessary but not sufficient for high-level CagA expression. H. pylori strains from a region of Colombia with high gastric cancer rates expressed higher levels of CagA than did strains from a region with lower gastric cancer rates, and Colombian strains of European phylogeographic origin expressed higher levels of CagA than did strains of African origin. Histopathologic analysis of gastric biopsy specimens revealed that strains expressing high levels of CagA or containing the AATAAGATA motif were associated with more advanced precancerous lesions than those found in persons infected with strains expressing low levels of CagA or lacking the AATAAGATA motif. CagA expression varies greatly among H. pylori strains. The DNA motif identified in this study is associated with high levels of CagA expression, and may be a useful biomarker to predict gastric cancer risk. These findings help to explain why some persons infected with cagA-positive H. pylori develop gastric cancer and others do not.


Are older adults more risky readers? Evidence from meta-analysis.
According to an influential account of aging effects on reading, older adults (65+ years) employ a more "risky" reading strategy compared to young adults (18-30 years), in which they attempt to compensate for slower processing by using lexical and contextual knowledge to guess upcoming (i.e., parafoveal) words more often. Consequently, while older adults may read more slowly, they might also skip words more often (by moving their gaze past words without fixating them), especially when these are of higher lexical frequency or more predictable from context. However, this characterization of aging effects on reading has been challenged recently following several failures to replicate key aspects of the risky reading hypothesis, as well as evidence that key effects predicted by the hypothesis are not observed in Chinese reading. To resolve this controversy, we conducted a meta-analysis of 102 eye movement experiments comparing the reading performance of young and older adults. We focused on the reading of sentences displayed normally (i.e., without unusual formatting or structures, or use of gaze-contingent display-change techniques), conducted using an alphabetic script or Chinese, and including experiments manipulating the frequency or predictability of a specific target word. Meta-analysis confirmed that slower reading by older compared to younger adults is accompanied by increased word-skipping, although only for alphabetic scripts. Meta-analysis additionally showed that word-skipping probabilities are unaffected by age differences in word frequency or predictability effects, casting doubt on a central component of the risky reading hypothesis. We consider implications for future research on aging effects on reading. (PsycInfo Database Record (c) 2022 APA, all rights reserved).


Cost-effectiveness of recombinant human hyaluronidase-facilitated subcutaneous versus intravenous rehydration in children with mild to moderate dehydration.
To evaluate the cost-effectiveness of recombinant human hyaluronidase-facilitated subcutaneous (rHFSC) fluid administration compared to intravenous (IV) fluid administration in children with mild to moderate dehydration in the emergency department (ED). A decision analytic model was created based on the results of a controlled clinical trial that compared the administration of isotonic fluids via rHFSC or IV for rehydration. The costs were determined from the hospital's perspective. The effectiveness unit was successful rehydration in the ED without the need for hospitalization for continued hydration. Mean estimates were determined for both the cost and effectiveness of each treatment. The incremental differences in costs and effectiveness were determined between treatments. Sensitivity analysis testing was also conducted. The treatment success rate was 93% with rHFSC fluids and 76% for IV fluids. Across all ages, the mean cost of rHFSC fluids was $722, compared to $889 for IV fluids. The difference in effectiveness was due to the larger number of patients for whom IV access could not be established, necessitating a rescue route of administration to deliver parenteral fluids. The difference in the overall cost was primarily due to the shorter time in the ED for patients receiving rHFSC fluids versus those treated with IV fluids. The cost-effectiveness of rHFSC compared to IV was most apparent in younger patients (<3 years of age), where IV access was more difficult to obtain. Analysis of this clinical trial data revealed that rHFSC fluid administration demonstrated greater treatment effectiveness and cost-effectiveness than traditional IV fluid administration in the ED. The primary reasons for this were the ease of obtaining parenteral access via rHFSC in young patients (especially those under 3) where IV access is difficult, and a shorter ED stay with rHFSC fluid administration.


Appropriateness of no-fault compensation for research-related injuries from an African perspective: an appeal for action by African countries.
Compensation for research-related injuries (RRIs) remains a challenge in the current environment of global collaborative biomedical research as exemplified by the continued reluctance of the US government, a major player in international biomedical research, to enact regulation for mandatory compensation for RRIs. This stance is in stark contrast to the mandatory compensation policies adopted by other democracies like the European Union (EU) countries. These positions taken by the USA and the EU create a nexus of confusion when research is exported to low-income and middle-income countries which have no laws guiding compensation for RRIs. In this paper, we begin by exploring the background to policies concerning RRIs, how they reflect on the traditional dispute resolution mechanisms in African societies, and how this compares with the no-fault compensation model. We then explore the underlying African ethical framework of Ubuntu in the sub-Saharan region, guiding traditional practices of dispute resolution and compensation, and how this framework can help to form the moral justification for no-fault compensation as the preferred compensation model for RRIs for African countries. Finally, we call upon countries in the African Union (AU), to adopt a no-fault policy for compensation of RRIs, and enact it into a regulatory requirement for insurance-based no-fault compensation for biomedical research, which will then be enforced by member states of the AU.


E1A promotes association between p300 and pRB in multimeric complexes required for normal biological activity.
The oncogenes of the small DNA tumor viruses encode transforming proteins with multiple domains that influence the cell cycle and aspects of the transformed phenotype. Like other gene products of this type, the adenovirus E1A proteins influence the cell by binding to specific cell growth control proteins. These include members of the retinoblastoma gene product (pRB) family, which are bound by the E1A region 2-specific site, and p300, which is bound at the E1A amino terminus. Binding at these two sites is largely independent, and discrete transcription-regulating functions remain intact in E1A products when only one or the other binding site is functional. In this report, immunoprecipitation with p300 antibodies reveals the presence of the pRB family proteins in p300 complexes when E1A is expressed in host cells, indicating that E1A can mediate physical contact between p300 and the pRB-related proteins. The ability of E1A to induce proliferation efficiently in quiescent primary cells correlates closely with the ability to bind p300 and individual members of the pRB family simultaneously in multimeric complexes, even though the E1A active sites can bind their target proteins efficiently when separated on different molecules. Conservation of a spacer region between the two binding sites that is required for simultaneous binding and efficient induction of proliferation supports the concept that the E1A protein structure has evolved to facilitate simultaneous binding. These results indicate that the E1A proteins are designed not merely to sequester these cellular products, but also to bring them into proximal association with each other in biologically significant complexes.


Mutations affecting the tRNA-splicing endonuclease activity of Saccharomyces cerevisiae.
Two unlinked mutations that alter the enzyme activity of tRNA-splicing endonuclease have been identified in yeast. The sen1-1 mutation, which maps on chromosome 12, causes temperature-sensitive growth, reduced in vitro endonuclease activity, and in vivo accumulation of unspliced pre-tRNAs. The sen2-1 mutation does not confer a detectable growth defect, but causes a temperature-dependent reduction of in vitro endonuclease activity. Pre-tRNAs do not accumulate in sen2-1 strains. The in vitro enzyme activities of sen1-1 and sen2-1 complement in extracts from a heterozygous diploid, but fail to complement in mixed extracts from separate sen1-1 and sen2-1 haploid strains. These results suggest a direct role for SEN gene products in the enzymatic removal of introns from tRNA that is distinct from the role of other products known to affect tRNA splicing.


Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis.
Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria. Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning. A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.


Analysis of patient claims data to determine the prevalence of hidradenitis suppurativa in the United States.
Recent prevalence estimates for hidradenitis suppurativa (HS), a chronic inflammatory skin condition, are limited by timeliness, population size, and generalizability. We sought to develop prevalence estimates for HS in the United States using large health care claims databases. A retrospective analysis used PharMetrics Integrated Database to gather health care claims information for HS among patients with 12 or more months of continuous enrollment in a commercial health care plan throughout 2007. Included patients had: 1 or more diagnoses with International Classification of Diseases, Ninth Revision, Clinical Modification code 705.83 for HS during 2007 without a Current Procedural Terminology code for HS; 1 or more Current Procedural Terminology codes of 11450, 11451, 11462, 11463, 11470, or 11471 during 2007 without International Classification of Diseases, Ninth Revision, Clinical Modification code 705.83; or both. Age- and gender-specific prevalence projections were calculated. Among included patients (n = 7927), mean age (SD) was 38.2 (14.73) years, and 5834 (74%) were women. Most patients (n = 5205; 66%) were aged 30 to 64 years. The overall prevalence estimate was 0.053% (95% confidence interval 0.051-0.054). When adjusted for gender and age, prevalence rates were 0.052% and 0.051%, respectively. The most common procedures for HS were excision of skin and subcutaneous tissue axillary/inguinal simple or intermediate repair. Limitations were a health insured-only population; 12-month enrollment period for 2007; HS-specific procedural codes; and possible HS misclassifications. We found a low rate of clinically detected HS (0.053%; approximately 146,000-162,000 patients in the United States in 2007), with affected persons almost 3 times as likely to be female and the highest prevalence in those aged 18 to 44 years.


Cancer excess after arsenic exposure from contaminated milk powder.
Long-term exposure to inorganic arsenic is related to increased risk of cancer in the lung, skin, bladder, and, possibly, other sites. However, little is known about the consequences of developmental exposures in regard to cancer risk. During early summer in 1955, mass arsenic poisoning of infants occurred in the western part of Japan because of contaminated milk powder. Okayama Prefecture was most severely affected. We examined whether the affected birth cohorts in this prefecture experienced increased cancer mortality. We targeted subjects who were born from September 1950 to August 1960 and died in Okayama Prefecture between January 1969 and March 2008 due to malignant neoplasm (N = 3,141). We then compared cancer mortality (total, liver, pancreatic, lung, bladder/kidney, and hematopoietic cancers) between cohorts born before the milk poisoning (exposed group) and cohorts born after the poisoning (nonexposed group). We estimated mortality ratios and 95% confidence intervals. Total and liver cancers were elevated in the cohort up to 1 year of age at time of the poisoning. In addition, pancreatic and hematopoietic cancers were elevated in the cohorts up to 5 years of age, and mortality ratios were approximately twice those of the nonexposed group. Increased risk of lung and bladder/kidney cancers was not apparent. Although dilution is present in these cohort-based data, our study highlights the notion that developmental arsenic exposure may lead to a different pattern of cancer, including increases in pancreatic and hematopoietic cancer, as compared with adult or lifetime exposures to inorganic arsenic.


A position-sensitive Stroop effect: further evidence for a left-to-right component in print-to-speech conversion.
In the classical Stroop effect, response times for naming the color in which a word is printed are affected by the presence of semantic, phonological, or orthographic relationships between the stimulus word and the response word. We show that color naming responses are faster when the printed word shares a phoneme with the color name to be produced than when it does not, in conditions where there is no semantic relationship between the printed word and the color name. This result is compatible with a variety of computational models of reading. However, we also found that these effects are much larger when it is the first phoneme that the stimulus and response share than when it is the last. Our data are incompatible with computational models of reading in which the computation of phonology from print is purely parallel. The dual route cascaded model computational model of reading, which has a lexical route that operates in parallel and a nonlexical route that operates serially letter by letter, successfully simulates this position-sensitive Stroop effect. The model also successfully simulates the "onset effect" in masked priming (Forster & Davis, 1991) and the interaction between the regularity effect and the position in a word of a grapheme-phoneme irregularity (Rastle & Coltheart, 1999b)--effects which, we argue, arise for the same reason as the position-sensitive Stroop effect we report.


Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar.


Fluidization of a vertically vibrated two-dimensional hard sphere packing: a granular meltdown.
We report measurements of the fluidization process in vertically vibrated two-dimensional granular packings. An initially close packed granular bed is exposed to sinusoidal container oscillations with gradually increasing amplitude. At first the particles close to the free surface become mobile. When a critical value of the forcing strength is reached the remaining crystal suddenly breaks up and the bed fluidizes completely. This transition leads to discontinuous changes in the density distribution and in the root mean square displacement of the individual particles. Likewise the vertical center of mass coordinate increases by leaps and bounds at the transition. It turns out that the maximum container velocity v0 is the crucial driving parameter determining the state of a fully fluidized system. For particles of various sizes the transition to full fluidization occurs at the same value of v 2 0/gd, where d is the particle diameter and g is the gravitational acceleration. A discontinuous fluidization transition is only observed when the particles are highly elastic.


Profiling circulating miRNAs in serum from pigs infected with the porcine whipworm, Trichuris suis.
microRNAs (miRNAs) are recently discovered as key regulators of gene translation and are becoming increasingly recognized for their involvement in various diseases. This study investigates the miRNA profile in pig serum during the course of an infection with the gastrointestinal parasite, Trichuris suis. Of this panel, the expression of selected miRNAs in serum from T. suis infected and uninfected pigs were determined by quantitative real time PCR using Exiqon Human Panel assays at 0, 2, 4, 6, 8 and 10 weeks post first infection (wpi). One miRNA, ssc-let-7d-3p, was significantly up-regulated in infected pigs 8 wpi. Interestingly, ssc-let-7d-3p shows high complementary to tsu-let-7a, which is the most highly transcribed miRNA in T. suis. The let-7 family miRNAs have been shown to post-transcriptionally regulate the translation of the helminth-controlling cytokine, IL-13, in a murine model for asthma and we hypothesize possible interactions between these host- and parasite-derived miRNAs and their immunomodulating roles.


Detection of mutations in the gyrA gene in fluoroquinolone resistance Salmonella enterica serotypes typhi and paratyphi A isolated from the Infectious Diseases Hospital, Kuwait.
Enteric fever due to Salmonella enterica is a major health problem, and fluoroquinolones such as ciprofloxacin are mostly the antibiotic of choice for treatment. Resistance to ciprofloxacin has been noticed to increase due to the emergence of new mutations in the bacterial DNA. To explore the fluoroquinolone resistance and molecular characterisation of reduced quinolone susceptibility in S typhi and S paratyphi A in Kuwait. 136 clinical isolates of S typhi and 40 of S paratyphi A were collected over five years. The antimicrobial susceptibility was studied by various methods. DNA sequencing of gyrA, gyrB, parC and parE genes was performed in 31 isolates. There was a substantial difference in MIC range between the two serotypes, with the most common MIC for S typhi being 0.25 mg/l and for S paratyphi A being 1 mg/l. The proportion of nalidixic acid resistant strains increased gradually over the years. These strains had a significantly higher range of MIC of ciprofloxacin (0.023 mg/l to 1.0 mg/l) compared to the nalidixic acid sensitive strains (0.0016 mg/l to 0.125 mg/l). DNA sequencing of gyrA gene showed the presence of three different point mutations: Ser83-->Phe in 17 strains, Ser83-->Leu in 3 strains and Asp87-->Asn in 6 strains. No mutations in the other genes were found. It is very important to keep searching for new mutations and continuously monitor drug resistance in different parts of the world in order to efficiently manage cases with enteric fever.


Medium-term culture of normal human oral mucosa: a novel three-dimensional model to study the effectiveness of drugs administration.
Tissue-engineered oral mucosal equivalents have been developed for in vitro studies for a few years now. However, the usefulness of currently available models is still limited by many factors, mainly the lack of a physiological extracellular matrix (ECM) and the use of cell populations that do not reflect the properly differentiated cytotypes of the mucosa of the oral cavity. For this reason, we have developed a novel three-dimensional culture model reflecting the normal architecture of the human oral mucosa, with the main aim of creating a better in vitro model where to test cellular responses to drugs administration. This novel 3D cell culture model (3D outgrowth) was set up using an artificial extracellular matrix (Matrigel™ ), allowing the interactions required for proper differentiation of the various citotypes which form the mucosal layer. Biopsies of human oral mucosa, in fragments of about 0.5 mm3, were placed onto 6.5mm Transwells, covered with Matrigel™ and grown in a specific culture medium. A gradual formation of an architectural structure similar to that of the in vivo oral mucosa was observed. Transmission electron and confocal microscopy were employed to characterize the newly developed model: the cell components (keratinocytes and fibroblasts) differentiated properly within the outgrowth and reconstituted, in vitro, the physiological structure of the human oral mucosa, including a stratified non-keratinized squamous layer composed of four different layers, a proper basal membrane and a lamina propria where fibroblasts produce ECM. Moreover, keratinocytes expressed CK5, CK13, CK19 and E-cadherin, whereas fibroblasts expressed collagen type I and IV, laminin and fibronectin. 3D outgrowths could be considered a valid alternative to animal models, and provide useful information for researchers interested in studying the responses of the human oral mucosa to locally delivered drugs or other exogenous treatments.


Association of Urinary and Dietary Selenium and of Serum Selenium Species with Serum Alanine Aminotransferase in a Healthy Italian Population.
The trace element selenium is of considerable interest due to its toxic and nutritional properties, which markedly differ according to the dose and the chemical form. It has been shown that excess selenium intake increases the risk of type 2 diabetes and, possibly, other metabolic diseases like hyperlipidemia and non-alcoholic fatty liver disease (NAFLD). For the latter, however, epidemiologic evidence is still limited. We carried out a cross-sectional study recruiting 137 healthy blood donors living in Northern Italy and assessed their exposure to selenium through different methods and measuring serum selenium species. We performed linear and spline regression analyses to assess the relation of selenium and its forms with serum alanine aminotransferase (ALT) levels, a marker of NAFLD. Urinary selenium levels were positively and somewhat linearly correlated with ALT (beta regression coefficient (β) 0.11). Conversely, the association of dietary selenium intake with ALT was positive up to 100 µg/day and null above that amount (β 0.03). Total serum selenium was inversely associated with ALT up to 120 µg/L, and slightly positive above that amount. Concerning the different serum selenium species, ALT positively correlated with two organic forms, selenocysteine (β 0.27) and glutathione peroxidase-bound selenium (β 0.09), showed a U-shaped relation with the inorganic tetravalent form, selenite, and an inverse association with human serum albumin-bound selenium (β -0.56). Our results suggest that overall exposure to selenium, and more specifically to some of its chemical forms, is positively associated with ALT, even at levels so far generally considered to be safe. Our findings add to the evidence suggesting that low-dose selenium overexposure is associated with NAFLD.


89Zr-Immuno-Positron Emission Tomography in Oncology: State-of-the-Art 89Zr Radiochemistry.
Immuno-positron emission tomography (immunoPET) with 89Zr-labeled antibodies has shown great potential in cancer imaging. It can provide important information about the pharmacokinetics and tumor-targeting properties of monoclonal antibodies and may help in anticipating on toxicity. Furthermore, it allows accurate dose planning for individualized radioimmunotherapy and may aid in patient selection and early-response monitoring for targeted therapies. The most commonly used chelator for 89Zr is desferrioxamine (DFO). Preclinical studies have shown that DFO is not an ideal chelator because the 89Zr-DFO complex is partly unstable in vivo, which results in the release of 89Zr from the chelator and the subsequent accumulation of 89Zr in bone. This bone accumulation interferes with accurate interpretation and quantification of bone uptake on PET images. Therefore, there is a need for novel chelators that allow more stable complexation of 89Zr. In this Review, we will describe the most recent developments in 89Zr radiochemistry, including novel chelators and site-specific conjugation methods.


Facing up to paternalism in research ethics.
Bioethicists have failed to understand the pervasively paternalistic character of research ethics. Not only is the overall structure of research review and regulation paternalistic in some sense; even the way informed consent is sought may imply paternalism. Paternalism has limits, however. Getting clear on the paternalism of research ethics may mean some kinds of prohibited research should be reassessed.


Decreased BMD and limb deformities in mice carrying mutations in both Lrp5 and Lrp6.
Humans and mice lacking Lrp5 have low BMD. To evaluate whether Lrp5 and Lrp6 interact genetically to control bone or skeletal development, we created mice carrying mutations in both Lrp5 and the related gene Lrp6. We found that compound mutants had dose-dependent deficits in BMD and limb formation, suggesting functional redundancy between these two genes in bone and limb development. Lrp5 and Lrp6 are closely related members of the low density lipoprotein receptor family and are co-receptors for Wnt ligands. While Lrp5 mutations are associated with low BMD in humans and mice, the role of Lrp6 in bone formation has not been analyzed. To address whether Lrp5 and Lrp6 play complimentary roles in bone and skeletal development, we created mice with mutations in both genes. We inspected limbs of mice from the different genotypic classes of compound mutants to identify abnormalities. DXA and muCT were used to evaluate the effect of mutations in Lrp5 and Lrp6 on BMD and microarchitecture. Mice heterozygous for mutations in Lrp6 and either heterozygous or homozygous for a mutation in Lrp5 (Lrp6(+/-);Lrp5(+/-) or Lrp6(+/-);Lrp5(-/-)) display limb defects with incomplete penetrance and variable expression. DXA analysis showed that BMD decreased as mice progressively were more deficient in Lrp5 and Lrp6. Lrp6(+/-);Lrp5(-/-) mice were more severely affected than Lrp6(+/+);Lrp5(-/-) mice, whereas Lrp6(+/-);Lrp5(+/-) mice had statistically higher BMD than Lrp6(+/+);Lrp5(-/-) mice and lower BMD compared with wildtype mice and mice heterozygous for either mutation alone. Lrp6 and Lrp5 genetically interact in limb development in mice. Furthermore, heterozygosity for an inactivating mutation in Lrp6 further reduces BMD in both male and female mice lacking Lrp5.


Rocket launcher mechanism of collaborative actin assembly defined by single-molecule imaging.
Interacting sets of actin assembly factors work together in cells, but the underlying mechanisms have remained obscure. We used triple-color single-molecule fluorescence microscopy to image the tumor suppressor adenomatous polyposis coli (APC) and the formin mDia1 during filament assembly. Complexes consisting of APC, mDia1, and actin monomers initiated actin filament formation, overcoming inhibition by capping protein and profilin. Upon filament polymerization, the complexes separated, with mDia1 moving processively on growing barbed ends while APC remained at the site of nucleation. Thus, the two assembly factors directly interact to initiate filament assembly and then separate but retain independent associations with either end of the growing filament.


Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.
The structure of three consecutive laminin-type EGF-like (LE) modules of mouse laminin gammma1 chain, gamma1III3-5 (positions 738 to 899), has been determined by multiple isomorphous replacement in a crystal of space group p6(4)22 (a=b=74.57 angstroms, c = 185.11 angstroms and gamma = 120 degrees). The crystal structure was refined using restrained crystallographic refinement to an R-factor of 19.72% for 14,983 independent reflections with intensities F(obs)> 0 at 2.1 angstroms resolution, with root mean square deviation of 0.012 angstroms and 1.690 degrees from ideal bond lengths and bond angles, respectively. The final model consisted of 1179 (non-hydrogen) protein atoms within 162 residues and 119 water molecules. The molecule showed a rod-like structure of about 76 angstroms length with individual modules twisted relative to each other by about 70 degrees. Each module has the same disulfide bond connections Cys1-Cys3 (loop a), Cys2-Cys4 (loop b), Cys5-Cys6 (loop c) and Cys7-Cys8 (loop d), the first three being identical to epidermal growth factor (EGF). All three LE modules showed little secondary structure which was mainly restricted to loop d, but they differed in several other details of their structure. The interface contacts between the LE modules are based on hydrogen bonds and hydrophobic interactions between the hydrophobic core of loop d of the preceding module and the first cysteine and an exposed residue in loop b of the following module. Module 4 was previously shown to contribute the major nidogen binding site of laminis and site-directed mutagenesis demonstrated a specific binding role for Asp800, Asn802, Val804 and Tyr819 in loops a and c. The side-chain of these four residues are all located on the surface in a linear array and separated by a distance of 17 angstroms between Tyr819 and Val804. The entire nidogen binding site is stabilized via main-chain hydrogen bonds which are in part derived from the link between loops b and c (residues Leu815 and Lys816). The data demonstrate the unique nature of the LE modules and only a remote similarity to EGF. They also indicate that the crucial residues in the binding loops provide direct contacts with nidogen and explain the synergism between loops a and c which is essential for binding.


Improving local health through community health workers in Cambodia: challenges and solutions.
Volunteer community health workers (CHWs) are an important link between the public health system and the community. The 'Community Participation Policy for Health' in Cambodia identifies CHWs as key to local health promotion and as a critical link between district health centres and the community. However, research on the challenges CHWs face and identifying what is required to optimise their performance is limited in the Cambodian context. This research explores the views of CHWs in rural Cambodia, on the challenges they face when implementing health initiatives. Qualitative methodology was used to capture the experiences of CHWs in Kratie and Mondulkiri provinces. Two participatory focus groups with CHWs in Mondulkiri and ten semi-structured interviews in Kratie were conducted. Results from both studies were used to identify common themes. Participants were CHWs, male and female, from rural Khmer and Muslim communities and linked with seven different district health centres. Findings identify that CHWs regularly deliver health promotion to communities. However, systemic, personal and community engagement challenges hinder their ability to function effectively. These include minimal leadership and support from local government, irregular training which focuses on verticalised health programmes, inadequate resources, a lack of professional identity and challenges to achieving behaviour change of community members. In addition, the CHW programme is delivered in a fragmented way that is largely influenced by external aid objectives. When consulted, however, CHWs demonstrate their ability to develop realistic practical solutions to challenges and barriers. The fragmented delivery of the CHW programme in Cambodia means that government ownership is minimal. This, coupled with the lack of defined core training programme or adequate resources, prevents CHWs from reaching their potential. CHWs have positive and realistic ideas on how to improve their role and, subsequently, the health of community members. CHWs presented with the opportunity to share learning and develop ideas in a supportive environment would benefit health initiatives.


Chronic herbivory: impacts on architecture and sex expression of pinyon pine.
Pinyon pine, Pinus edulis (Engelm.), in Northern Arizona is exposed to recurring high levels of herbivory by the moth Dioryctria albovitella (Hust.). During a 3-year period, infested trees experienced on average a 30 percent reduction in annual shoot production. This herbivory affects tree architecture, growth rate, reproductive output, and sexual expression. Less infested trees produce 47 percent more trunk wood, 43 percent more branch wood, and are monoecious. Architectural changes in infested trees can result infunctionally male plants due to a complete loss of normal female cone-bearing ability. When herbivores are experimentally removed, normal growth and reproduction patterns resume. These strong herbivore impacts should represent a potent selection pressure in the evolution of host traits.


The emerging role of HDL in glucose metabolism.
A low plasma level of HDL cholesterol is an atherosclerotic risk factor; however, emerging evidence suggests that low HDL levels might also contribute to the pathophysiology of type 2 diabetes mellitus (T2DM) through direct effects on plasma glucose. In the past decade, animal and clinical studies have uncovered a previously undescribed spectrum of HDL actions, indicating that HDL may control glucose homeostasis through mechanisms including insulin secretion, direct glucose uptake by muscle via the AMP-activated protein kinase, and possibly enhanced insulin sensitivity. These effects are mediated by multiple cell types via mechanisms including preservation of cell function through cellular lipid removal and also via direct signaling events. We suggest a paradigm shift from HDL being a bystander to being an active player in diabetic pathophysiology, which raises the possibility that HDL elevation could be a novel therapeutic avenue for T2DM. The entry of HDL-raising agents of the cholesteryl ester transfer protein (CETP) inhibitor class into late-phase clinical trials creates potential for rapid clinical translation. This Review will discuss the emerging evidence for a role of HDL-mediated glucose regulation in the pathophysiology of T2DM, and will also outline the therapeutic potential for HDL elevation for the prevention and management of T2DM.


DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia.
Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed "epitypes") using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.