Protein-prime/modified vaccinia virus Ankara vector-boost vaccination overcomes tolerance in high-antigenemic HBV-transgenic mice.
Therapeutic vaccination is a novel treatment approach for chronic hepatitis B, but only had limited success so far. We hypothesized that optimized vaccination schemes have increased immunogenicity, and aimed at increasing therapeutic hepatitis B vaccine efficacy. Modified Vaccinia virus Ankara (MVA) expressing hepatitis B virus (HBV) antigens was used to boost protein-prime vaccinations in wildtype and HBV-transgenic (HBVtg) mice. Protein-prime/MVA-boost vaccination was able to overcome HBV-specific tolerance in HBVtg mice with low and medium but not with high antigenemia. HBV-specific antibody titers, CD8+ T-cell frequencies and polyfunctionality inversely correlated with HBV antigen levels. However, optimization of the adjuvant formulation, increasing the level of antigen expression and utilization of HBsAg of heterologous subtype induced HBV-specific CD8+ and CD4+ T-cells and neutralizing antibodies even in high-antigenemic HBVtg mice. Our results indicate that high HBV antigen levels limit the immunological responsiveness to therapeutic vaccination but optimization of the vaccine formulation can overcome tolerance even in the presence of high antigenemia. These findings have important implications for the development of future therapeutic hepatitis B vaccination strategies and potentially also for the stratification of chronic hepatitis B patients for therapeutic vaccination.


DNA released from neutrophil extracellular traps (NETs) activates pancreatic stellate cells and enhances pancreatic tumor growth.
Neutrophil extracellular trap (NET) formation results in the expulsion of granulocyte proteins and DNA into the extracellular space. This process is mediated by the enzyme peptidyl arginine deiminase 4 (PADI4) and translocation of elastase to the nucleus. NET formation, marked by increased levels of extracellular DNA, promotes pancreatic cancer proliferation and metastasis. Mice deficient in Padi4 demonstrate decreased pancreatic tumor growth, associated with a reduction in circulating extracellular DNA levels, diminished pancreatic stromal activation and improved survival in murine orthotopic pancreatic adenocarcinoma. Transplantation of Padi4-/- bone marrow into genetically engineered mice with Kras driven pancreatic adenocarcinoma (Pdx1-Cre:KrasG12D/+, KC mice) limits the frequency of invasive cancers when compared with syngeneic controls. DNA from neutrophils activates pancreatic stellate cells that form dense, fibrous stroma which can promote and enable tumor proliferation. DNase treatment diminishes murine tumor growth and stromal activation to reverse the effect of NETs within the tumor microenvironment. Furthermore, deletion of the receptor for advanced glycation end products (RAGE) in pancreatic stellate cells abrogates the effects of DNA in promoting stellate cell proliferation and decreases tumor growth. Circulating neutrophil-derived DNA correlates with the stage in patients with pancreatic ductal adenocarcinoma, confirming the role of NETs in human pancreatic cancer. These findings support further investigation into targeting of NETs, PADI4 and extracellular DNA as a potential treatment strategy in patients with pancreatic cancer. Trial Registration: This study reports correlative data from a clinical trial registered with clinicaltrials.gov, NCT01978184 (November 7, 2013).


Analysis validation has been neglected in the Age of Reproducibility.
Increasingly complex statistical models are being used for the analysis of biological data. Recent commentary has focused on the ability to compute the same outcome for a given dataset (reproducibility). We argue that a reproducible statistical analysis is not necessarily valid because of unique patterns of nonindependence in every biological dataset. We advocate that analyses should be evaluated with known-truth simulations that capture biological reality, a process we call "analysis validation." We review the process of validation and suggest criteria that a validation project should meet. We find that different fields of science have historically failed to meet all criteria, and we suggest ways to implement meaningful validation in training and practice.


Changes in nutritional metabolites of young ginger (Zingiber officinale Roscoe) in response to elevated carbon dioxide.
The increase of atmospheric CO2 due to global climate change or horticultural practices has direct and indirect effects on food crop quality. One question that needs to be asked, is whether CO2 enrichment affects the nutritional quality of Malaysian young ginger plants. Responses of total carbohydrate, fructose, glucose, sucrose, protein, soluble amino acids and antinutrients to either ambient (400 μmol/mol) and elevated (800 μmol/mol) CO2 treatments were determined in the leaf and rhizome of two ginger varieties namely Halia Bentong and Halia Bara. Increasing of CO2 level from ambient to elevated resulted in increased content of total carbohydrate, sucrose, glucose, and fructose in the leaf and rhizome of ginger varieties. Sucrose was the major sugar followed by glucose and fructose in the leaf and rhizome extract of both varieties. Elevated CO2 resulted in a reduction of total protein content in the leaf (H. Bentong: 38.0%; H. Bara: 35.4%) and rhizome (H. Bentong: 29.0%; H. Bara: 46.2%). In addition, under CO2 enrichment, the concentration of amino acids increased by approximately 14.5% and 98.9% in H. Bentong and 12.0% and 110.3% in H. Bara leaf and rhizome, respectively. The antinutrient contents (cyanide and tannin) except phytic acid were influenced significantly (P ≤ 0.05) by CO2 concentration. Leaf extract of H. Bara exposed to elevated CO2 exhibited highest content of cyanide (336.1 mg HCN/kg DW), while, highest content of tannin (27.5 g/kg DW) and phytic acid (54.1 g/kg DW) were recorded from H.Bara rhizome grown under elevated CO2. These results demonstrate that the CO2 enrichment technique could improve content of some amino acids and antinutrients of ginger as a food crop by enhancing its nutritional and health-promoting properties.


Topographical projection from the superior colliculus to the nucleus of the brachium of the inferior colliculus in the ferret: convergence of visual and auditory information.
The normal maturation of the auditory space map in the deeper layers of the ferret superior colliculus (SC) depends on signals provided by the superficial visual layers, but it is unknown where or how these signals influence the developing auditory responses. Here we report that tracer injections in the superficial layers label axons with en passant and terminal boutons, both in the deeper layers of the SC and in their primary source of auditory input, the nucleus of the brachium of the inferior colliculus (nBIC). Electron microscopy confirmed that biocytin-labelled SC axons form axodendritic synapses on nBIC neurons. Injections of biotinylated dextran amine in the nBIC resulted in anterograde labelling in the deeper layers of the SC, as well as retrogradely labelled superficial and deep SC neurons, whose distribution varied systematically with the rostrocaudal placement of the injection sites in the nBIC. Topographical order in the projection from the SC to the ipsilateral nBIC was confirmed using fluorescent microspheres. We demonstrated the existence of functional SC-nBIC connections by making whole-cell current-clamp recordings from young ferret slices. Both monosynaptic and polysynaptic EPSPs were generated by electrical stimulation of either the superficial or deep SC layers. In addition to unimodal auditory units, both visual and bimodal visual-auditory units were recorded in the nBIC in vivo and their incidence was higher in juvenile ferrets than in adults. The SC-nBIC circuit provides a potential means by which visual and other sensory or premotor signals may be delivered to the nBIC to calibrate the representation of auditory space.


Violent deaths in small children in northern Sweden.
To identify causes and trends of violent deaths among children younger than 4 years in a northern region. Retrospective analysis of medico-legal autopsy and police data. Data from all 72 deaths from "external causes" 1977-2004, in children < 4 years from the northern half of Sweden were analysed. The death rate was 7.1 per 100,000 children and year during the first half of the study period, and 5.2 during the second half. Vehicle- and drowning-related deaths were halved. Fifteen were struck by motor vehicles (in 8 cases by heavy vehicles), 14 car occupants were killed in car crashes, 12 were killed by intentional violence inflicted by an adult, and 9 each were killed by (i) carbon monoxide/smoke inhalation, (ii) asphyxiation, or (iii) drowning. The boy:girl ratio was 1:1 in all groups, except in the groups "drowning" and "run over by motor vehicle", where boys dominated. Medical professionals have a difficult but important task in identifying and taking action against child abuse and in promoting child safety especially in the traffic and home environments.


Pest categorisation of Diabrotica undecimpunctata undecimpunctata.
The EFSA Panel on Plant Health performed a pest categorisation of the beetle Diabrotica undecimpunctata undecimpunctata (Coleoptera: Chrysomelidae) for the EU. This species occurs in western USA and Mexico. Adults oviposit on annual plants in the families Chenopodiaceae, Cucurbitaceae, Fabaceae, Poaceae, Polygonaceae and Solanaceae. Adults feed on tender plant parts in hosts in 30 additional botanical families. Preimaginal development takes place on the roots of the host plant, where larvae feed and pupate. The insect completes one to three generations per year depending on temperature. Overwintering adults (no diapause) may abandon crops to seek shelter in wild vegetation and reinvade crops in spring. D. undecimpunctata undecimpunctata is not known to occur in the EU and is regulated in Annex IIA of Commission Implementing Regulation 2019/2072. This species is a competent vector of squash mosaic virus, a pathogen already present and not regulated in the EU. Within Commission Implementing Regulation 2019/2072, potential entry pathways for D. undecimpunctata undecimpunctata, such as Poaceae and Solanaceae plants for planting with foliage and soil/growing medium, and soil/growing media by themselves can be considered as closed. However, plants for planting of the families Chenopodiaceae, Cucurbitaceae, Fabaceae and Polygonaceae are not specifically regulated. Should D. undecimpunctata undecimpunctata arrive in the EU, climatic conditions and availability of susceptible hosts provide conditions suitable for establishment and further spread. Economic impact is anticipated. D. undecimpunctata undecimpunctata satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest. This species does not meet the criteria of being present in the EU nor plants for planting being the main pathway for spread for it to be regarded as a potential regulated non-quarantine pest.


Non-Ambulant Duchenne Patients Theoretically Treatable by Exon 53 Skipping have Severe Phenotype.
Exon skipping therapy is an emerging approach in Duchenne Muscular Dystrophy (DMD). Antisense oligonucleotides that induce skipping of exon 51, 44, 45, or 53 are currently being evaluated in clinical trials. These trials were designed on the basis of data available in general DMD population. Our objective was to compare the clinical and functional statuses of non-ambulant DMD patients theoretically treatable by exon 53 skipping and of DMD patients with other mutations. We first compared fifteen non-ambulant DMD patients carrying deletions theoretically treatable by exon 53 skipping (DMD-53) with fifteen closely age-matched DMD patients with mutations not treatable by exon 53 skipping (DMD-all-non-53) then with fifteen DMD patients carrying deletions not treatable by exon 53 skipping (DMD-del-non-53). We found that DMD-53 patients had a lower left ventricular ejection fraction, more contractures and they tend to have weaker grips and pinch strengths than other DMD patients. DMD-53 patients lost ambulation significantly younger than other DMD patients. This result was confirmed by comparing ages at loss of ambulation in all non-ambulant DMD patients of the DMD cohort identified in a molecular diagnostic lab. These prospective and retrospective data demonstrate that DMD-53 patients have clinically more severe phenotypes than other DMD patients.


The incidence of pulmonary embolism in open versus laparoscopic gastric bypass.
Obesity independently increases the risk of pulmonary embolism (PE). We compare a superobese population (body mass index [BMI] > 55 kg/m(2)) undergoing open gastric bypasses (OGBs) with a similarly matched group of laparoscopic gastric bypasses (LGB) to see if the incidence of PE differs. We included all patients undergoing OGB (n = 193, average BMI = 51 kg/m(2)) at our institution by a single surgeon between July 1999 and April 2001. Thirty-one patients were superobese (BMI > 55 kg/m(2)). LGB was started at our institution in April 2001. Since that time 213 patients (average BMI = 52 kg/m(2)) have undergone the procedure. One hundred and nine patients were superobese. Pre- and postoperative prophylaxis included sequential compression stockings and subcutaneous heparin. Postoperatively, patients who developed signs of hypoxia, tachypnea, or tachycardia underwent a chest X-ray and spiral computed tomography. In addition, all patients who expired in the 30-day postoperative period underwent postmortem examination. Data were analyzed using the chi-squared test. In the OGB group, four patients (2.1%) developed PE. All occurred in superobese patients with a BMI > 55 kg/m(2). Three were fatal PEs and one was nonfatal. None of these patients had a prior history of deep vein thrombosis, PE, venous stasis disease, or pulmonary hypertension. In the LGB group, one patient (0.9%) had a nonfatal PE. This patient had a history of deep vein thrombosis. The incidence of PE was statistically higher in the superobese OGB group (P < 0.01). Despite the theoretical hindrance to venous return and vena caval compression observed with pneumoperitoneum, fewer PEs occurred in the laparoscopic group. Our data, however, suggest that patients with a BMI > 55 kg/m(2) might be at an increased risk for PE independent of operative approach.


Inhaled drug therapy for treatment of tuberculosis.
The lungs have received attention as a portal for drug delivery in tuberculosis (TB) from researchers addressing diverse objectives. These include: (a) targeting alveolar macrophages that harbour TB bacilli; (b) maintaining high drug concentrations in lung tissue; (c) systemic delivery of potent or second-line anti-TB agents; and (d) delivering agents that may change the host-pathogen dialectic. Formulation design considerations for each of the above objectives differ in slight, but important ways. As distinct from vaccine delivery formulations, inhalations intended for drug delivery are presumed to require chronic and repeated administration of larger amounts of material. This review seeks to summarize the consensus on the ways and means available or under development, to deliver different anti-TB agents as aerosols for inhalation. These agents include drugs in current clinical use, singly or in combination, experimental chemical entities, siRNA against host molecules, and finally, drugs in clinical use for unrelated pharmacological action, as modifiers of the host-pathogen dialectic. The pharmacokinetics of drug bioavailability in the lung, the blood and other tissues following lung deposition of inhaled therapies are also addressed. Finally, considerations on efficacy studies of drugs administered through aerosol delivery are discussed.


Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.
A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.


Patient knowledge of HIV and its treatment in South Africa.
Patients on antiretroviral therapy (ART) need to achieve a 90% adherence rate to ART in order to prevent disease progression and drug resistance. The patients' knowledge of ART and HIV is thus crucial to ensuring good adherence, decreased risk for drug resistance and cost-effective treatment for these patients. To determine the knowledge of infected patients with regard to HIV and the ART they were receiving. The study was conducted at a comprehensive community health centre in a developing low socio-economic community near Cape Town, South Africa. A quantitative descriptive correlative research design was applied. A sample consisting of 200 (8.5%) respondents was selected from a population of 2349. A multiple-choice questionnaire, comprising 29 questions, including 14 critical knowledge testing questions, was used in individual interviews conducted by either the researcher or fieldworker who assessed the respondents' knowledge regarding various key aspects of HIV and ART. Misconceptions regarding HIV and ART were revealed and scores for the 14 critical knowledge testing questions in the questionnaire revealed that 0% of the respondents had good knowledge, 20% had average knowledge and 80% had poor knowledge. The respondents on ART in this particular community health centre had poor knowledge of HIV and ART. This may contribute to poor adherence rates, increased drug resistance, disease progression and increased costs for the government with regard to treating such patients. Increased attention needs to be given to patient education.


Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model.
Characterizing atomic details of membrane binding of peripheral membrane proteins by molecular dynamics (MD) has been significantly hindered by the slow dynamics of membrane reorganization associated with the phenomena. To expedite lateral diffusion of lipid molecules without sacrificing the atomic details of such interactions, we have developed a novel membrane representation, to our knowledge, termed the highly mobile membrane-mimetic (HMMM) model to study binding and insertion of various molecular species into the membrane. The HMMM model takes advantage of an organic solvent layer to represent the hydrophobic core of the membrane and short-tailed phospholipids for the headgroup region. We demonstrate that using these components, bilayer structures are formed spontaneously and rapidly, regardless of the initial position and orientation of the lipids. In the HMMM membrane, lipid molecules exhibit one to two orders of magnitude enhancement in lateral diffusion. At the same time, the membrane atomic density profile of the headgroup region produced by the HMMM model is essentially identical to those obtained for full-membrane models, indicating the faithful representation of the membrane surface by the model. We demonstrate the efficiency of the model in capturing spontaneous binding and insertion of peripheral proteins by using the membrane anchor (γ-carboxyglutamic-acid-rich domain; GLA domain) of human coagulation factor VII as a test model. Achieving full insertion of the GLA domain consistently in 10 independent unbiased simulations within short simulation times clearly indicates the robustness of the HMMM model in capturing membrane association of peripheral proteins very efficiently and reproducibly. The HMMM model will provide significant improvements to the current all-atom models by accelerating lipid dynamics to examine protein-membrane interactions more efficiently.


Existence, functional impairment, and lung repair potential of endothelial colony-forming cells in oxygen-induced arrested alveolar growth.
Bronchopulmonary dysplasia and emphysema are life-threatening diseases resulting from impaired alveolar development or alveolar destruction. Both conditions lack effective therapies. Angiogenic growth factors promote alveolar growth and contribute to alveolar maintenance. Endothelial colony-forming cells (ECFCs) represent a subset of circulating and resident endothelial cells capable of self-renewal and de novo vessel formation. We hypothesized that resident ECFCs exist in the developing lung, that they are impaired during arrested alveolar growth in experimental bronchopulmonary dysplasia, and that exogenous ECFCs restore disrupted alveolar growth. Human fetal and neonatal rat lungs contain ECFCs with robust proliferative potential, secondary colony formation on replating, and de novo blood vessel formation in vivo when transplanted into immunodeficient mice. In contrast, human fetal lung ECFCs exposed to hyperoxia in vitro and neonatal rat ECFCs isolated from hyperoxic alveolar growth-arrested rat lungs mimicking bronchopulmonary dysplasia proliferated less, showed decreased clonogenic capacity, and formed fewer capillary-like networks. Intrajugular administration of human cord blood-derived ECFCs after established arrested alveolar growth restored lung function, alveolar and lung vascular growth, and attenuated pulmonary hypertension. Lung ECFC colony- and capillary-like network-forming capabilities were also restored. Low ECFC engraftment and the protective effect of cell-free ECFC-derived conditioned media suggest a paracrine effect. Long-term (10 months) assessment of ECFC therapy showed no adverse effects with persistent improvement in lung structure, exercise capacity, and pulmonary hypertension. Impaired ECFC function may contribute to arrested alveolar growth. Cord blood-derived ECFC therapy may offer new therapeutic options for lung diseases characterized by alveolar damage.


The use of heated fuwa tubes.
This paper describes the use, for atomic absorption, of long, heated absorption tubes first described by Fuwa and Vallee. Heating the absorption tube provides advantages in increased sensitivity for certain elements and reduced interferences. The remaining effects of interferences are discussed, and methods for their control are given.


Rafting on floating fruit is effective for oceanic dispersal of flightless weevils.
Terrestrial species, especially non-vagile ones (those unable to fly or swim), cannot cross oceans without exploiting other animals or floating objects. However, the colonisation history of flightless Pachyrhynchus weevils, inferred from genetic data, reveals their ability to travel long distances to colonise remote islands. Here, we used captive-bred Pachyrhynchus jitanasaius to analyse (i) the physiological tolerance of weevils (egg, larva and adult stages) to different levels of salinity; (ii) the survival rate of larvae in a simulated ocean environment in the laboratory; and (iii) the survival rate of larvae in a field experiment in the ocean using fruit of the fish poison tree floating on the Kuroshio current in the Pacific Ocean. We found that the survival rate of larvae in seawater was lower than in fresh water, although if the larvae survived 7 days of immersion in seawater, some emerged as adults in the subsequent rearing process. No adults survived for more than 2 days, regardless of salinity level. After floating separately for 6 days in salt water in the laboratory and in the Kuroshio current, two of 18 larvae survived in the fruit. This study provides the first empirical evidence that P. jitanasaius larvae can survive 'rafting' on ocean currents and that the eggs and larvae of these weevils have the highest probability of crossing the oceanic barrier. This ability may facilitate over-the-sea dispersal of these flightless insects and further shape their distribution and speciation pattern in the Western Pacific islands.


Tissue concentrations as the dose metric to assess potential toxic effects of metals in field-collected fish: Copper and cadmium.
The present study examined the available literature linking whole-body tissue concentrations with toxic effects in fish species for copper and cadmium. The variability in effect concentration for both copper and cadmium among species occurred within an order of magnitude for all responses, whereas the range for lethal toxicity based on water exposure spanned approximately 4 to 5 orders of magnitude. Fish tissue concentrations causing adverse effects were just above background concentrations, occurring between 1 μg/g and 10 μg/g for copper and 0.1 μg/g to 4 μg/g for cadmium. The results also show that salmonids are especially sensitive to cadmium, which appears to be a function of chemical potency. No studies were found that indicated adverse effects without increases in whole-body concentration of these metals. This narrow range for dose-response implies that a toxicological spillover point occurs when the detoxification capacity of various tissues within the animal are exceeded, and this likely occurs at a similar whole-body concentration for all naïvely exposed fish species. Elevated whole-body concentrations in fish from the field may be indicative of possible acclimation to metals that may or may not result in effects for target species. Acclimation concentrations may be useful in that they signal excessive metal concentrations in water, sediment, or prey species for a given site and indicate likely toxic effects for species unable to acclimate to excess metal exposure. Using tissue residues as the dose metric for these metals provides another line of evidence for assessing impaired ecosystems and greater confidence that hazard concentrations are protective for all fish species.


The Contribution of Missed Clinic Visits to Disparities in HIV Viral Load Outcomes.
We explored the contribution of missed primary HIV care visits ("no-show") to observed disparities in virological failure (VF) among Black persons and persons with injection drug use (IDU) history. We used patient-level data from 6 academic clinics, before the Centers for Disease Control and Prevention and Health Resources and Services Administration Retention in Care intervention. We employed staged multivariable logistic regression and multivariable models stratified by no-show visit frequency to evaluate the association of sociodemographic factors with VF. We used multiple imputations to assign missing viral load values. Among 10 053 patients (mean age = 46 years; 35% female; 64% Black; 15% with IDU history), 31% experienced VF. Although Black patients and patients with IDU history were significantly more likely to experience VF in initial analyses, race and IDU parameter estimates were attenuated after sequential addition of no-show frequency. In stratified models, race and IDU were not statistically significantly associated with VF at any no-show level. Because missed clinic visits contributed to observed differences in viral load outcomes among Black and IDU patients, achieving an improved understanding of differential visit attendance is imperative to reducing disparities in HIV.


Modified posterior exenteration for ovarian cancer.
The operative description of a modified posterior exenteration along with operative findings, other operative procedures, postoperative course, and follow-up information are presented for 47 patients (37 primary cytoreduction, ten secondary cytoreduction). All had stage IIIC or IV epithelial ovarian cancer with pelvic disease encasing the reproductive organs, pelvic peritoneum, cul-de-sac, and sigmoid colon. In addition to modified posterior exenteration, all patients had multiple other procedures performed as part of the cytoreductive efforts. Forty-five (95.7%) had optimal (less than 2 cm) cytoreduction and 18 (38.3%) had complete cytoreductive surgery. Thirty-four patients were ultimately rendered continent of feces (25 primarily and nine after colostomy reversal). Nine patients (19.1%) had serious morbidity and one (2.1%) died postoperatively. The median follow-up for those undergoing primary cytoreduction was 13.3 months (6-84). Nineteen (51.4%) were alive at the time of writing, 16 (43.2%) were dead, and two (5.4%) were lost to follow-up. Modified posterior exenteration effectively removes all visible pelvic disease with acceptable mortality. Hence, even patients with the most advanced cases of ovarian cancer may attain optimal cytoreduction and become ideal candidates for adjunctive therapy, with improved survival or a chance for cure.


Sex-specific expression of alternative transcripts in Drosophila.
Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster. We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes. Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists.


Cryoglobulins: Identification, classification, and novel biomarkers of mysterious proteins.
Cryoglobulins consist of serum immunoglobulins that precipitate below 37°C and resolubilize upon warming. The clinical triad of cryoglobulinemia usually includes purpura, weakness, and arthralgia. Cryoglobulinemic syndrome, clinically defined as a systemic vasculitis, is associated with chronic infection with hepatitis C virus (HCV) and autoimmune disorders and can evolve into B-cell malignancies. While the current literature about HCV-associated cryoglobulinemia is not very limited, little is known about the immunologic and serologic profiles of affected patients. Therefore, comprehension of the pathogenetic mechanisms underlying cryoprecipitation could be very helpful. Due to the persistence of viral antigenic stimulation, biomarkers to use after the worsening progression of HCV infection to lymphoproliferative and/or autoimmune diseases are widely needed. Laboratory methods used to detect and characterize low concentrations of cryoprecipitates and immunotyping patterns could improve patient management. The most critical factor affecting cryoglobulin testing is that the pre-analytical phase is not fully completed at 37°C.


Shrub establishment favoured and grass dominance reduced in acid heath grassland systems cleared of invasive Rhododendron ponticum.
Rhododendron ponticum L. is a damaging invasive alien species in Britain, favouring the moist, temperate climate, and the acidic soils of upland areas. It outshades other species and is thought to create a soil environment of low pH that may be higher in phytotoxic phenolic compounds. We investigated native vegetation restoration and R. ponticum regeneration post-clearance using heathland sites within Snowdonia National Park, Wales; one site had existing R. ponticum stands and three were restoring post-clearance. Each site also had an adjacent, uninvaded control for comparison. We assessed whether native vegetation restoration was influenced post-invasion by soil chemical properties, including pH and phytotoxic compounds, using Lactuca sativa L. (lettuce) bioassays supported by liquid chromatography-mass spectroscopy (LC-MSn). Cleared sites had higher shrub and bare ground cover, and lower grass and herbaceous species cover relative to adjacent uninvaded control sites; regenerating R. ponticum was also observed on all cleared sites. No phenolic compounds associated with R. ponticum were identified in any soil water leachates, and soil leachates from cleared sites had no inhibitory effect in L. sativa germination assays. We therefore conclude that reportedly phytotoxic compounds do not influence restoration post R. ponticum clearance. Soil pH however was lower beneath R. ponticum and on cleared sites, relative to adjacent uninvaded sites. The lower soil pH post-clearance may have favoured shrub species, which are typically tolerant of acidic soils. The higher shrub cover on cleared sites may have greater ecological value than unaffected grass dominated sites, particularly given the recent decline in such valuable heathland habitats. The presence of regenerating R. ponticum on all cleared sites however highlights the critical importance of monitoring and re-treating sites post initial clearance.


US weight guidelines: is it also important to consider cardiorespiratory fitness?
The health consequences of weight ranges across low to moderate and high levels of cardiorespiratory fitness are unknown. To evaluate the validity of the 1995 US weight guidelines, while considering cardiorespiratory fitness. We followed 21,856 men, aged 30-83 y, who had a complete preventive medical examination, including a maximal treadmill exercise test and body composition assessment. There were 427 deaths (144 cardiovascular disease (CVD); 143 cancer; 140 others) during an average of 8.1 y of follow-up. We used Cox proportional hazards regression to examine the relations among cardiorespiratory fitness, body mass index (BMI, kg/m2), and all-cause and CVD mortality. After adjustment for age, examination year, cigarette smoking and alcohol intake, we observed that men with a BMI of 19.0 to < 25.0 and who were unfit had 2.3 times the risk of all-cause mortality (95% confidence interval (95% CI), 1.59-3.17, P < 0.001) compared with fit men in this BMI group (reference category). Unfit men with a BMI of 25.0 to < 27.8 also had a greater risk of all-cause mortality than fit men in the same BMI category. Fit but overweight men (BMI > or = 27.8) had a similar rate of all-cause mortality as physically fit men of normal weight (BMI 19.0 to < 25.0) and had a lower risk of all-cause mortality than unfit and normal weight men. Fit men of normal weight had the lowest CVD mortality, while unfit and overweight men experienced the highest CVD mortality. Unfit men had substantially higher CVD mortality than fit men in each BMI group. Unfit men had higher all-cause and CVD mortality than fit men. The health benefits of normal weights appear to be limited to men who have moderate or high levels of cardiorespiratory fitness. These data suggest that the 1995 US weight guidelines may be misleading unless cardiorespiratory fitness is taken into account.


Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi.
Cleavage factor I (CFI) proteins are core components of the polyadenylation machinery that can regulate several steps of mRNA life cycle, including alternative polyadenylation, splicing, export and decay. Here, we describe the regulatory mechanisms that control two fungal CFI protein classes in Magnaporthe oryzae: Rbp35/CfI25 complex and Hrp1. Using mutational, genetic and biochemical studies we demonstrate that cellular concentration of CFI mRNAs is a limited indicator of their protein abundance. Our results suggest that several post-transcriptional mechanisms regulate Rbp35/CfI25 complex and Hrp1 in the rice blast fungus, some of which are also conserved in other ascomycetes. With respect to Rbp35, these include C-terminal processing, RGG-dependent localization and cleavage, C-terminal autoregulatory domain and regulation by an upstream open reading frame of Rbp35-dependent TOR signalling pathway. Our proteomic analyses suggest that Rbp35 regulates the levels of proteins involved in melanin and phenylpropanoids synthesis, among others. The drastic reduction of fungal CFI proteins in carbon-starved cells suggests that the pre-mRNA processing pathway is altered. Our findings uncover broad and multilayer regulatory mechanisms controlling fungal polyadenylation factors, which have profound implications in pre-mRNA maturation. This area of research offers new avenues for fungicide design by targeting fungal-specific proteins that globally affect thousands of mRNAs.


Randomised comparison of procedures for obtaining informed consent in clinical trials of treatment for cancer.
Methods of obtaining informed consent have evolved differently in Western countries without substantive information on the impact of these different practices on the patients. A randomised study was performed to compare two commonly adopted methods of seeking consent to randomised treatment: an individual approach at the discretion of each doctor and a uniform policy of total disclosure of all relevant information. The impact of both consent procedures on the patient's understanding and anxiety levels and on the doctor-patient relationship was assessed by means of a questionnaire given soon after the consent interview. Fifty seven patients were assigned at random to two groups: to 29 patients an individual approach to seeking consent was adopted and to 28 patients all relevant information was given. Seven patients refused consent to randomised treatment, with slightly more refusals by patients in the total disclosure group (5 v 2, p = 0.25). The main effects of total disclosure of all information compared with an individual approach to seeking consent were: a better understanding of treatment and side effects and of research aspects of the treatments; less willingness to agree to randomised treatment; and increased anxiety. No significant differences were found in patients' perceptions of the doctor-patient relationship. A repeat questionnaire given three to four weeks later no longer showed significant differences between the two groups.


Association between added sugar intake and micronutrient dilution: a cross-sectional study in two adult Swedish populations.
The evidence on the impact of high sugar consumption on micronutrient dilution does not yet allow for the establishment of clear thresholds of consumption. To establish upper and lower limit intake thresholds for added sugar, more studies from different countries and multiple populations are needed. The aim of this study was to examine the association between the intakes of added sugar and various micronutrients among the adult Swedish population across almost two decades. The data were obtained from the samples from two populations: 1) Riksmaten Adults, a national dietary survey (n = 1797, 44% male, aged 18-80 years, data collection from 2010 to 11) that assessed dietary intake using a 4-day web-based food diary; and 2) the Malmö Diet and Cancer Study, a population-based cohort study (n = 12,238, 45% male, aged 45-68 years, data collection from 1991 to 1994) that assessed dietary intake via a combination of a 7-day food diary, a food frequency questionnaire and an interview. The mean daily intake of nine micronutrients (calcium, folate, iron, magnesium, potassium, selenium, vitamin C, vitamin D, and zinc), adjusted for age, sex, BMI and energy intake, were examined across six added-sugar-intake groups (< 5%E, 5-7.5%E, 7.5-10%E, 10-15%E, 15-20%E, and > 20%E). We observed significant inverse associations between the intake of added sugar and the intake of all micronutrients in both populations. The associations were linear; however, we could not determine the threshold of added sugar intake beyond which the micronutrient intake was clearly compromised. These findings suggest that in two Swedish populations the higher the intake of added sugar in the diet, the more likely it is that the intake of micronutrients will be compromised, in two Swedish populations. However, although the trends are significant and consistent with those obtained in other studies on the subject, future studies are needed in order to build the necessary scientific knowledge to establish a threshold of added sugar intake based on micronutrient dilution.


Assessment of the In Vivo Toxicity of Gold Nanoparticles.
The environmental impact of nanoparticles is evident; however, their toxicity due to their nanosize is rarely discussed. Gold nanoparticles (GNPs) may serve as a promising model to address the size-dependent biological response to nanoparticles because they show good biocompatibility and their size can be controlled with great precision during their chemical synthesis. Naked GNPs ranging from 3 to 100 nm were injected intraperitoneally into BALB/C mice at a dose of 8 mg/kg/week. GNPs of 3, 5, 50, and 100 nm did not show harmful effects; however, GNPs ranging from 8 to 37 nm induced severe sickness in mice. Mice injected with GNPs in this range showed fatigue, loss of appetite, change of fur color, and weight loss. Starting from day 14, mice in this group exhibited a camel-like back and crooked spine. The majority of mice in these groups died within 21 days. Injection of 5 and 3 nm GNPs, however, did not induce sickness or lethality in mice. Pathological examination of the major organs of the mice in the diseased groups indicated an increase of Kupffer cells in the liver, loss of structural integrity in the lungs, and diffusion of white pulp in the spleen. The pathological abnormality was associated with the presence of gold particles at the diseased sites, which were verified by ex vivo Coherent anti-Stoke Raman scattering microscopy. Modifying the surface of the GNPs by incorporating immunogenic peptides ameliorated their toxicity. This reduction in the toxicity is associated with an increase in the ability to induce antibody response. The toxicity of GNPs may be a fundamental determinant of the environmental toxicity of nanoparticles.


F-DIO obesity-prone rat is insulin resistant before obesity onset.
We previously created a novel F-DIO rat strain derived by crossing rats selectively bred for the diet-induced obesity (DIO) phenotype with obesity-resistant Fischer F344 rats. The offspring retained the DIO phenotype through 3 backcrosses with F344 rats but also had exaggerated insulin responses to oral glucose before they became obese on a 31% fat high-energy (HE) diet. Here, we demonstrate that chow-fed rats from the subsequent randomly bred progeny required 57% lower glucose infusions to maintain euglycemia during a hyperinsulinemic clamp in association with 45% less insulin-induced hepatic glucose output inhibition and 80% lower insulin-induced glucose uptake than F344 rats. The DIO phenotype and exaggerated insulin response to oral glucose in the nonobese, chow-fed state persisted in the F6 generation. Also, compared with F344 rats, chow-fed F-DIO rats had 68% higher arcuate nucleus proopiomelanocortin mRNA expression which, unlike the increase in F344 rats, was decreased by 26% on HE diet. Further, F-DIO lateral hypothalamic orexin expression was 18% lower than in F344 rats and was increased rather than decreased by HE diet intake. Finally, both maternal obesity and 30% caloric restriction during the third week of gestation produced F-DIO offspring which were heavier and had higher leptin and insulin levels than lean F-DIO dam offspring. Third-gestational week dexamethasone also produced offspring with higher leptin and insulin levels but with lower body weight. Thus F-DIO rats represent a novel and potentially useful model for the study of DIO, insulin resistance, and perinatal factors that influence the development and persistence of obesity.


Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.
A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.


Response assessment in paediatric high-grade glioma: recommendations from the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group.
Response criteria for paediatric high-grade glioma vary historically and across different cooperative groups. The Response Assessment in Neuro-Oncology working group developed response criteria for adult high-grade glioma, but these were not created to meet the unique challenges in children with the disease. The Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group, consisting of an international panel of paediatric and adult neuro-oncologists, clinicians, radiologists, radiation oncologists, and neurosurgeons, was established to address issues and unique challenges in assessing response in children with CNS tumours. We established a subcommittee to develop response assessment criteria for paediatric high-grade glioma. Current practice and literature were reviewed to identify major challenges in assessing the response of paediatric high-grade gliomas to various treatments. For areas in which scientific investigation was scarce, consensus was reached through an iterative process. RAPNO response assessment recommendations include the use of MRI of the brain and the spine, assessment of clinical status, and the use of corticosteroids or antiangiogenics. Imaging standards for brain and spine are defined. Compared with the recommendations for the management of adult high-grade glioma, for paediatrics there is inclusion of diffusion-weighted imaging and a higher reliance on T2-weighted fluid-attenuated inversion recovery. Consensus recommendations and response definitions have been established and, similar to other RAPNO recommendations, prospective validation in clinical trials is warranted.


Bordetella pertussis evolution in the (functional) genomics era.
The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps.


A case-control study of mesothelioma in Minnesota iron ore (taconite) miners.
An excess of mesothelioma has been observed in iron ore miners in Northeastern Minnesota. Mining and processing of taconite iron ore generate exposures that include elongate mineral particles (EMPs) of amphibole and non-amphibole origin. We conducted a nested case-control study of mesothelioma in a cohort of 68,737 iron ore miners (haematite and taconite ore miners) to evaluate the association between mesothelioma, employment and EMP exposures from taconite mining. Mesothelioma cases (N=80) were identified through the Minnesota Cancer Surveillance System (MCSS) and death certificates. Four controls of similar age were selected for each case with 315 controls ultimately eligible for inclusion. Mesothelioma risk was evaluated by estimating rate ratios and 95% CIs with conditional logistic regression in relation to duration of taconite industry employment and cumulative EMP exposure [(EMP/cc)×years], defined by the National Institute for Occupational Safety and Health (NIOSH) 7400 method. Models were adjusted for employment in haematite mining and potential exposure to commercial asbestos products used in the industry. All mesothelioma cases were male and 57 of the cases had work experience in the taconite industry. Mesothelioma was associated with the number of years employed in the taconite industry (RR=1.03, 95% CI 1.00 to 1.06) and cumulative EMP exposure (RR=1.10, 95% CI 0.97 to -1.24). No association was observed with employment in haematite mining. These results support an association between mesothelioma and employment duration and possibly EMP exposure in taconite mining and processing. The type of EMP was not determined. The potential role of commercial asbestos cannot be entirely ruled out.


Male fetal sex affects uteroplacental angiogenesis in growth restriction mouse model†.
Abnormally increased angiotensin II activity related to maternal angiotensinogen (AGT) genetic variants, or aberrant receptor activation, is associated with small-for-gestational-age babies and abnormal uterine spiral artery remodeling in humans. Our group studies a murine AGT gene titration transgenic (TG; 3-copies of the AGT gene) model, which has a 20% increase in AGT expression mimicking a common human AGT genetic variant (A[-6]G) associated with intrauterine growth restriction (IUGR) and spiral artery pathology. We hypothesized that aberrant maternal AGT expression impacts pregnancy-induced uterine spiral artery angiogenesis in this mouse model leading to IUGR. We controlled for fetal sex and fetal genotype (e.g., only 2-copy wild-type [WT] progeny from WT and TG dams were included). Uteroplacental samples from WT and TG dams from early (days 6.5 and 8.5), mid (d12.5), and late (d16.5) gestation were studied to assess uterine natural killer (uNK) cell phenotypes, decidual metrial triangle angiogenic factors, placental growth and capillary density, placental transcriptomics, and placental nutrient transport. Spiral artery architecture was evaluated at day 16.5 by contrast-perfused three-dimensional microcomputed tomography (3D microCT). Our results suggest that uteroplacental angiogenesis is significantly reduced in TG dams at day 16.5. Males from TG dams are associated with significantly reduced uteroplacental angiogenesis from early to late gestation compared with their female littermates and WT controls. Angiogenesis was not different between fetal sexes from WT dams. We conclude that male fetal sex compounds the pathologic impact of maternal genotype in this mouse model of growth restriction.


Cosmesis and body image after single-port laparoscopic or conventional laparoscopic cholecystectomy: a multicenter double blinded randomised controlled trial (SPOCC-trial).
Emerging attempts have been made to reduce operative trauma and improve cosmetic results of laparoscopic cholecystectomy. There is a trend towards minimizing the number of incisions such as natural transluminal endoscopic surgery (NOTES) and single-port laparoscopic cholecystectomy (SPLC). Many retrospective case series propose excellent cosmesis and reduced pain in SPLC. As the latter has been confirmed in a randomized controlled trial, patient's satisfaction on cosmesis is still controversially debated. The SPOCC trial is a prospective, multi-center, double blinded, randomized controlled study comparing SPLC with 4-port conventional laparoscopic cholecystectomy (4PLC) in elective surgery. The hypothesis and primary objective is that patients undergoing SPLC will have a better outcome in cosmesis and body image 12 weeks after surgery. This primary endpoint is assessed using a validated 8-item multiple choice type questionnaire on cosmesis and body image. The secondary endpoint has three entities: the quality of life 12 weeks after surgery assessed by the validated Short-Form-36 Health Survey questionnaire, postoperative pain assessed by a visual analogue scale and the use of analgesics. Operative time, surgeon's experience with SPLC and 4PLC, use of additional ports, conversion to 4PLC or open cholecystectomy, length of stay, costs, time of work as well as intra- and postoperative complications are further aspects of the secondary endpoint. Patients are randomly assigned either to SPLC or to 4PLC. Patients as well as treating physicians, nurses and assessors are blinded until the 7th postoperative day. Sample size calculation performed by estimating a difference of cosmesis of 20% (alpha = 0.05 and beta = 0.90, drop out rate of 10%) resulted in a number of 55 randomized patients per arm. The SPOCC-trial is a prospective, multi-center, double-blind, randomized controlled study to assess cosmesis and body image after SPLC. (clinicaltrial.gov): NCT 01278472.


Pnictogens in medicinal chemistry: evolution from erstwhile drugs to emerging layered photonic nanomedicine.
Pnictogens (the non-metal phosphorus, metalloids arsenic and antimony, and metal bismuth) possess diverse chemical characteristics that support the formation of extended molecular structures. As witnessed by the centuries-old (and ongoing) clinical utilities, pnictogen-based compounds have secured their places in history as "magic bullet" therapeutic drugs in medicinal contexts. Moreover, with the development of recent metalloproteomics and bio-coordination chemistry, the pnictogen-based drugs functionally binding to proteins/enzymes in biological systems have been underlaid for "drug repurposing" with promising opportunities. Furthermore, advances in the modern materials science and nonotechnology have stimulated a revolution in other newly discovered forms of pnictogens-phosphorene, arsenene, antimonene, and bismuthine (layered pnictogens). Based on their favorable optoelectronic properties, layered pnictogens have shown dramatic superiority as emerging photonic nanomedicines for the treatment of various diseases. This tutorial review outlines the history and mechanism of action of ancient pnictogen-based drugs (e.g., arsenical compounds in traditional Chinese medicine) and their repurposing into modern therapeutics. Then, the revolutionary use of emerging layered pnictogens as photonic nanomedicines, alongside assessments of their in vivo biosafety, is discussed. Finally, the challenges to further development of pnictogens are set forth and insights for further exploration of their appealing properties are offered. This tutorial review may also provide some deep insights into the fields of integrated traditional Chinese and Western medicines from the perspective of materials science and nanotechnology.


Traumatic brain injury and vestibulo-ocular function: current challenges and future prospects.
Normal function of the vestibulo-ocular reflex (VOR) coordinates eye movement with head movement, in order to provide clear vision during motion and maintain balance. VOR is generated within the semicircular canals of the inner ear to elicit compensatory eye movements, which maintain stability of images on the fovea during brief, rapid head motion, otherwise known as gaze stability. Normal VOR function is necessary in carrying out activities of daily living (eg, walking and riding in a car) and is of particular importance in higher demand activities (eg, sports-related activities). Disruption or damage in the VOR can result in symptoms such as movement-related dizziness, blurry vision, difficulty maintaining balance with head movements, and even nausea. Dizziness is one of the most common symptoms following traumatic brain injury (TBI) and is considered a risk factor for a prolonged recovery. Assessment of the vestibular system is of particular importance following TBI, in conjunction with oculomotor control, due to the intrinsic neural circuitry that exists between the ocular and vestibular systems. The purpose of this article is to review the physiology of the VOR and the visual-vestibular symptoms associated with TBI and to discuss assessment and treatment guidelines for TBI. Current challenges and future prospects will also be addressed.


Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.
As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework.


Estimating the genetic architecture of quantitative traits.
Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architecture parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance. With multiple traits and multiple environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment interactions can also be estimated. We review the method and discuss issues associated with multiple interval mapping, such as likelihood analysis, model selection, stopping rules and parameter estimation. The potential power and advantages of the method for mapping multiple QTL and estimating the genetic architecture are discussed. We also point out potential problems and difficulties in resolving the details of the genetic architecture as well as other areas that require further investigation. One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.


Intake and macronutrient content of human milk given to extremely preterm infants.
Human milk (HM) is the preferred basis of nutrition for infants, including those born prematurely. Information on HM macronutrient content is necessary to optimize nutritional support of preterm infants. This study aimed to describe the types and amounts of enteral feeds given to Swedish extremely preterm infants during hospitalization and to investigate the energy and macronutrient contents in HM given to these infants. A population-based study of Swedish extremely preterm infants (n = 586) born before 27 gestational weeks was conducted. Data on ingested volumes of different milk during hospitalization and analyses of macronutrient content in HM samples were obtained from hospital records. Nutritional content of HM was determined by mid-infrared spectrophotometry analysis. During the first 4 weeks of life, 99% of the infants were exclusively fed HM, and at 4 weeks of life, 70% of the infants received only mother's own milk (MOM). Nutritional content in 821 MOM samples was analyzed. Protein content in MOM decreased significantly from 2.2 to 1.2 g/100 mL during the first 112 postpartum days, whereas fat and energy content were highly variable within and between MOM samples. In addition, 354 samples of donor milk were analyzed. Content of protein, fat, and energy in pooled donor milk (n = 129) was lower compared to single donor milk. Swedish extremely preterm infants receive MOM to a large extent during hospitalization. Protein, carbohydrates, and energy in MOM changed significantly with time. Weekly analyses of MOM during the first month of lactation would allow more individualized nutritional support for these vulnerable infants.


A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.


Complicated rheumatic mitral stenosis presenting in an elderly patient and the challenges in its management.
A 76 -year-old lady with a recent diagnosis of rheumatic heart disease (RHD), and a history of repeated lower respiratory tract infections, came with symptoms of gastritis unrelated to the primary disease but further diagnostic study in the hospital revealed poorly controlled atrial fibrillation, grossly dilated left atrium with two large left atrial thrombi and mitral valve area<1 cm(2). It was decided that the best approach in our patient would be mitral valve replacement with mechanical prosthesis. Despite the usual trend of using bioprosthesis in the elderly, our decision was influenced by the fact that the patient would need chronic anticoagulation for atrial fibrillation in any case. The purpose of our case presentation is to illustrate a late-presenting case of RHD with unusual associations and the challenges to choose the best possible management.


The most common spoligotype of Mycobacterium bovis isolated in the world and the recommended loci for VNTR typing; A systematic review.
Mycobacterium bovis is a neglected zoonotic organism that epidemiological studies are of crucial importance in identifying its source, control it and prevent it from spreading. The aim of this study was to investigate the most common spoligotypes of Mycobacterium bovis circulating around the world and introduce the most and least strong determine powers of loci for VNTR. We have used different databases such as ISC, science direct, Embase (Elsevier), Web of Science, Scopus and Medline via PubMed. Searches were performed by key words including: Mycobacterium bovis, MIRU -VNTR, spoligotyping and discrimination power. Finally, thirty-one articles were selected after filtering out some titles, abstracts and full texts. Spoligotype SB0120 was the most common circulating type on several continents while SB0121 existed in Europe, Africa and America. SB0140 was also detected in Asia, Europe and America. QUB3232 and QUB11b were more appropriate loci among the loci with high discriminatory power. MIRU 10 and MIRU4 were among the loci with poor discriminatory power. Taking the published data into consideration, SB0120 and SB0121 are predominant spoligotypes of M. bovis circulating among animals around the world. Determining the most common spoligotype of M. bovis is the key to find source of infection, control and prevent the disease.


Diagnostic miscues in congenital long-QT syndrome.
Long-QT syndrome (LQTS) is a potentially lethal cardiac channelopathy that can be mistaken for palpitations, neurocardiogenic syncope, and epilepsy. Because of increased physician and public awareness of warning signs suggestive of LQTS, there is the potential for LQTS to be overdiagnosed. We sought to determine the agreement between the dismissal diagnosis from an LQTS subspecialty clinic and the original referral diagnosis. Data from the medical record were compared with data from the outside evaluation for 176 consecutive patients (121 females, median age 16 years, average referral corrected QT interval [QTc] of 481 ms) referred with a diagnosis of LQTS. After evaluation at Mayo Clinic's LQTS Clinic, patients were categorized as having definite LQTS (D-LQTS), possible LQTS (P-LQTS), or no LQTS (No-LQTS). Seventy-three patients (41%) were categorized as No-LQTS, 56 (32%) as P-LQTS, and only 47 (27%) as D-LQTS. The yield of genetic testing among D-LQTS patients was 78% compared with 34% for P-LQTS and 0% among No-LQTS patients (P<0.0001). The average QTc was greater in either D-LQTS or P-LQTS than in No-LQTS (461 versus 424 ms, P<0.0001). Vasovagal syncope was more common among the No-LQTS subset (28%) than the P-LQTS/D-LQTS group (8%; P=0.04). Determinants for discordance (ie, positive outside diagnosis versus No-LQTS) included overestimation of QTc, diagnosing LQTS on the basis of "borderline" QTc values, and interpretation of a vasovagal fainting episode as an LQTS-precipitated cardiac event. Diagnostic concordance was present for less than one third of the patients who sought a second opinion. Two of every 5 patients referred with the diagnosis of LQTS departed without such a diagnosis. Miscalculation of the QTc, misinterpretation of the normal distribution of QTc values, and misinterpretation of symptoms appear to be responsible for most of the diagnostic miscues.


Scaled Coupled Norms and Coupled Higher-Order Tensor Completion.
Recently, a set of tensor norms known as coupled norms has been proposed as a convex solution to coupled tensor completion. Coupled norms have been designed by combining low-rank inducing tensor norms with the matrix trace norm. Though coupled norms have shown good performances, they have two major limitations: they do not have a method to control the regularization of coupled modes and uncoupled modes, and they are not optimal for couplings among higher-order tensors. In this letter, we propose a method that scales the regularization of coupled components against uncoupled components to properly induce the low-rankness on the coupled mode. We also propose coupled norms for higher-order tensors by combining the square norm to coupled norms. Using the excess risk-bound analysis, we demonstrate that our proposed methods lead to lower risk bounds compared to existing coupled norms. We demonstrate the robustness of our methods through simulation and real-data experiments.


Elevated levels of fractalkine expression and accumulation of CD16+ monocytes in glomeruli of active lupus nephritis.
Fractalkine (Fkn) is a chemokine that affects cells expressing its receptor, CX3CR1, including CD16-positive (CD16+) monocytes/macrophages (CD16+ Mos). The relationship of levels of glomerular Fkn expression and infiltration by CD16+ Mos with the severity and diversity of glomerular lesions in human lupus nephritis is not known. Retrospective cross-sectional analysis of variables observed in biopsy specimens. 88 patients with systemic lupus erythematosus. Histological class and severity of lupus nephritis according to the International Society of Nephrology/Renal Pathology Society and clinicopathologic factors. Outcome variables are assays related to the degree of glomerular Fkn expression and CD16+ Mo infiltration. Immunohistological grading of Fkn staining, number of CD16+ Mos, and messenger RNA levels of Fkn and CD16 in glomeruli. Patients with proliferative lupus nephritis (class III and IV glomeruli) showed significantly greater glomerular Fkn expression and CD16+ Mo counts than those with other classes. Infiltrating CD16+ Mos within glomeruli expressed CX3CR1. Moreover, glomerular Fkn expression significantly correlated with the histopathologic activity index and CD16+ Mo counts, and CD16+ Mo counts significantly correlated with serum levels of blood urea nitrogen, complement (CH50), and anti-DNA antibody; estimated glomerular filtration rate; and urinary protein excretion. Glucocorticoid therapy had a tendency to decrease both glomerular Fkn expression and CD16+ Mo counts. Only frozen biopsy specimens (from 49 patients) were analyzed for the evaluation of glomerular Fkn expression. Disease activity and proliferative glomerular lupus nephritis lesions are associated with the glomerular Fkn expression and CD16+ Mo accumulation.


Interaction between reference frames during subjective vertical estimates in a tilted immersive virtual environment.
Numerous studies highlighted the influence of a tilted visual frame on the perception of the visual vertical ('rod-and-frame effect' or RFE). Here, we investigated whether this influence can be modified in a virtual immersive environment (CAVE-like) by the structure of the visual scene and by the adjustment mode allowing visual or visuo-kinaesthetic control (V and VK mode, respectively). The way this influence might dynamically evolve throughout the adjustment was also investigated in two groups of subjects with the head unrestrained or restrained upright. RFE observed in the immersive environment was qualitatively comparable to that obtained in a real display (portable rod-and-frame test; Oltman 1968, Perceptual and Motor Skills 26 503-506). Moreover, RFE in the immersive environment appeared significantly influenced by the structure of the visual scene and by the adjustment mode: the more geometrical and meaningful 3-D features the visual scene contained, the greater the RFE. The RFE was also greater when the subjective vertical was assessed under visual control only, as compared to visuo-kinaesthetic control. Furthermore, the results showed a significant RFE increase throughout the adjustment, indicating that the influence of the visual scene upon subjective vertical might dynamically evolve over time. The latter effect was more pronounced for structured visual scenes and under visuo-kinaesthetic control. On the other hand, no difference was observed between the two groups of subjects having the head restrained or unrestrained. These results are discussed in terms of dynamic combination between coexisting reference frames for spatial orientation.


Treatment Effect of Balloon Pulmonary Angioplasty in Chronic Thromboembolic Pulmonary Hypertension Quantified by Automatic Comparative Imaging in Computed Tomography Pulmonary Angiography.
Balloon pulmonary angioplasty (BPA) in patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH) can have variable outcomes. To gain more insight into this variation, we designed a method for visualizing and quantifying changes in pulmonary perfusion by automatically comparing computed tomography (CT) pulmonary angiography before and after BPA treatment. We validated these quantifications of perfusion changes against hemodynamic changes measured with right-sided heart catheterization. We studied 14 consecutive CTEPH patients (12 women; age, 70.5 ± 24), who underwent CT pulmonary angiography and right-sided heart catheterization, before and after BPA. Posttreatment images were registered to pretreatment CT scans (using the Elastix toolbox) to obtain corresponding locations. Pulmonary vascular trees and their centerlines were detected using a graph cuts method and a distance transform method, respectively. Areas distal from vessels were defined as pulmonary parenchyma. Subsequently, the density changes within the vascular centerlines and parenchymal areas were calculated and corrected for inspiration level differences. For visualization, the densitometric changes were displayed in color-coded overlays. For quantification, the median and interquartile range of the density changes in the vascular and parenchymal areas (ΔVD and ΔPD) were calculated. The recorded changes in hemodynamic parameters, including changes in systolic, diastolic, and mean pulmonary artery pressure (ΔsPAP, ΔdPAP, and ΔmPAP, respectively) and vascular resistance (ΔPVR), were used as reference assessments of the treatment effect. Spearman correlation coefficients were employed to investigate the correlations between changes in perfusion and hemodynamic changes. Comparative imaging maps showed distinct patterns in perfusion changes among patients. Within pulmonary vessels, the interquartile range of ΔVD correlated significantly with ΔsPAP (R = -0.58, P = 0.03), ΔdPAP (R = -0.71, P = 0.005), ΔmPAP (R = -0.71, P = 0.005), and ΔPVR (R = -0.77, P = 0.001). In the parenchyma, the median of ΔPD had significant correlations with ΔdPAP (R = -0.58, P = 0.030) and ΔmPAP (R = -0.59, P = 0.025). Comparative imaging analysis in CTEPH patients offers insight into differences in BPA treatment effect. Quantification of perfusion changes provides noninvasive measures that reflect hemodynamic changes.


Attention modulates maintenance of representations in visual short-term memory.
Recent studies have shown that selective attention is of considerable importance for encoding task-relevant items into visual short-term memory (VSTM) according to our behavioral goals. However, it is not known whether top-down attentional biases can continue to operate during the maintenance period of VSTM. We used ERPs to investigate this question across two experiments. Specifically, we tested whether orienting attention to a given spatial location within a VSTM representation resulted in modulation of the contralateral delay activity (CDA), a lateralized ERP marker of VSTM maintenance generated when participants selectively encode memory items from one hemifield. In both experiments, retrospective cues during the maintenance period could predict a specific item (spatial retrocue) or multiple items (neutral retrocue) that would be probed at the end of the memory delay. Our results revealed that VSTM performance is significantly improved by orienting attention to the location of a task-relevant item. The behavioral benefit was accompanied by modulation of neural activity involved in VSTM maintenance. Spatial retrocues reduced the magnitude of the CDA, consistent with a reduction in memory load. Our results provide direct evidence that top-down control modulates neural activity associated with maintenance in VSTM, biasing competition in favor of the task-relevant information.


Spatial Pyramid Pooling in Deep Convolutional Networks for Visual Recognition.
Existing deep convolutional neural networks (CNNs) require a fixed-size (e.g., 224 × 224) input image. This requirement is "artificial" and may reduce the recognition accuracy for the images or sub-images of an arbitrary size/scale. In this work, we equip the networks with another pooling strategy, "spatial pyramid pooling", to eliminate the above requirement. The new network structure, called SPP-net, can generate a fixed-length representation regardless of image size/scale. Pyramid pooling is also robust to object deformations. With these advantages, SPP-net should in general improve all CNN-based image classification methods. On the ImageNet 2012 dataset, we demonstrate that SPP-net boosts the accuracy of a variety of CNN architectures despite their different designs. On the Pascal VOC 2007 and Caltech101 datasets, SPP-net achieves state-of-the-art classification results using a single full-image representation and no fine-tuning. The power of SPP-net is also significant in object detection. Using SPP-net, we compute the feature maps from the entire image only once, and then pool features in arbitrary regions (sub-images) to generate fixed-length representations for training the detectors. This method avoids repeatedly computing the convolutional features. In processing test images, our method is 24-102 × faster than the R-CNN method, while achieving better or comparable accuracy on Pascal VOC 2007. In ImageNet Large Scale Visual Recognition Challenge (ILSVRC) 2014, our methods rank #2 in object detection and #3 in image classification among all 38 teams. This manuscript also introduces the improvement made for this competition.


Changes in cortical thickness and volume after cranial radiation treatment: A systematic review.
Cognitive decline has a clear impact on quality of life in patients who have received cranial radiation treatment. The pathophysiological process is most likely multifactorial, with a possible role for decreased cortical thickness and volume. As radiotherapy treatment systems are becoming more sophisticated, precise sparing of vulnerable regions and tissue is possible. This allows radiation oncologists to make treatment more patient-tailored. A systematic search was performed to collect and review all available evidence regarding the effect of cranial radiation treatment on cortical thickness and volume. We searched the Pubmed, Embase and Cochrane databases, with an additional reference check in the Scopus database. Studies that examined cortical changes on MRI within patients as well as between treated and non-treated patients were included. The quality of the studies was assessed with a checklist specially designed for this review. No meta-analysis was performed due to the lack of randomised trials. Out of 1915 publications twenty-one papers were selected, of which fifteen observed cortical changes after radiation therapy. Two papers reported radiation-dependent decrease in cortical thickness within patients one year after radiation treatment, suggesting a clear relation between the two. However, study quality was considered mostly suboptimal, and there was great inhomogeneity between the included studies. This means that, although there has been increasing interest in the effects of radiation treatment on cortex morphology, no reliable conclusion can be drawn based on the currently available evidence. This calls for more research, preferably with a sufficiently large patient population, and adequate methodology.


Psychological therapies for the management of chronic and recurrent pain in children and adolescents.
Chronic pain affects many children, who report severe pain, distressed mood, and disability. Psychological therapies are emerging as effective interventions to treat children with chronic or recurrent pain. This update adds recently published randomised controlled trials (RCTs) to the review published in 2009. To assess the effectiveness of psychological therapies, principally cognitive behavioural therapy and behavioural therapy, for reducing pain, disability, and improving mood in children and adolescents with recurrent, episodic, or persistent pain. We also assessed the risk of bias and methodological quality of the included studies. Searches were undertaken of MEDLINE, EMBASE, and PsycLIT. We searched for RCTs in references of all identified studies, meta-analyses and reviews. Date of most recent search: March 2012. RCTs with at least 10 participants in each arm post-treatment comparing psychological therapies with active treatment were eligible for inclusion (waiting list or standard medical care) for children or adolescents with episodic, recurrent or persistent pain. All included studies were analysed and the quality of the studies recorded. All treatments were combined into one class: psychological treatments; headache and non-headache outcomes were separately analysed on three outcomes: pain, disability, and mood. Data were extracted at two time points; post-treatment (immediately or the earliest data available following end of treatment) and at follow-up (at least three months after the post-treatment assessment point, but not more than 12 months). Eight studies were added in this update of the review, giving a total of 37 studies. The total number of participants completing treatments was 1938. Twenty-one studies addressed treatments for headache (including migraine); seven for abdominal pain; four included mixed pain conditions including headache pain, two for fibromyalgia, two for pain associated with sickle cell disease, and one for juvenile idiopathic arthritis. Analyses revealed five significant effects. Pain was found to improve for headache and non-headache groups at post-treatment, and for the headache group at follow-up. Mood significantly improved for the headache group at follow-up, although, this should be interpreted with caution as there were only two small studies entered into the analysis. Finally, disability significantly improved in the non-headache group at post-treatment. There were no other significant effects. Psychological treatments are effective in reducing pain intensity for children and adolescents (<18 years) with headache and benefits from therapy appear to be maintained. Psychological treatments also improve pain and disability for children with non-headache pain. There is limited evidence available to estimate the effects of psychological therapies on mood for children and adolescents with headache and non-headache pain. There is also limited evidence to estimate the effects on disability in children with headache. These conclusions replicate and add to those of the previous review which found psychological therapies were effective in reducing pain intensity for children with headache and non-headache pain conditions, and these effects were maintained at follow-up.


Era of faster FDA drug approval has also seen increased black-box warnings and market withdrawals.
After approval, many prescription medications that patients rely on subsequently receive new black-box warnings or are withdrawn from the market because of safety concerns. We examined whether the frequency of these safety problems has increased since 1992, when the Prescription Drug User Fee Act, legislation designed to accelerate the drug approval process at the Food and Drug Administration, was passed. We found that drugs approved after the act's passage were more likely to receive a new black-box warning or be withdrawn than drugs approved before its passage (26.7 per 100.0 drugs versus 21.2 per 100.0 drugs at up to sixteen years of follow-up). We could not establish causality, however. Our findings suggest the need for reforms to reduce patients' exposure to unsafe drugs, such as a statement or symbol in the labeling, medication guides for patients, and marketing materials indicating that a drug was approved only recently.


Micro-ureteroscopy for treatment of pelvic ureteral stone in pediatric patient.
During the last years there has been an effort in miniaturizing the endoscopic devices. The video presents an alternative for the management of distal ureteral stone, using a ureteral access of 4.85 Fr and 27 cm of length, previously described as micro-ureteroscopy. This procedure was performed through a 3-part all-seeing needle, consisting of micro-optics 0.9 mm in diameter with a 120-degree angle of view, an irrigation channel and an integrated light. Seven year-old boy, with history of preterm birth (29 weeks) was referred to our consultation complaining of left back pain and an elevation of serum creatinine. The renal ultrasound revealed a left ureterohydronephrosis, caused by a 10 mm stone located 13 mm from the ureterovesical junction. The patient underwent a micro-ureteroscopy with laser lithotripsy. The stone was fragmented with an average energy of 0.5 J with 12 Hz of frequency. The total energy spent was 12514 J. At the end of the procedure, a double J stent was placed. The procedure lasted 45 minutes and was uneventful. The patient was discharged 24h after the procedure without complaints and remained stone free. Micro-ureteroscopy is a safe and effective technique in distal ureteral lithiasis treatment in children. The small dimensions of the equipment increase the safety of the procedure making this a good option for the treatment of ureteral stones in children.


Length of the antibody heavy chain complementarity determining region 3 as a specificity-determining factor.
The antigen binding site of an antibody is made up of residues residing in six hypervariable loops of the heavy and light chains. In most cases several or all of these loops are required for the establishment of the antigen-binding surface. Five of these loops display a limited diversity in length and sequence while the third complementarity determining region (CDR) of the heavy chain is highly different between antibodies not only with respect to sequence but also with respect to length. Its extensive diversity is a key component in the establishment of binding sites allowing for the recognition of essentially any antigen by humoral immunity. The relative importance of its sequence vs its length diversity in this context is however, not very well established. To investigate this matter further we have used an approach employing combinatorial antibody libraries and antigen-specific selection in the search for CDRH3 length and sequence diversity compatible with a given antigen specificity, the major antigenic determinant on the tumour-associated antigen mucin-1. In this way we have now defined heavy chain CDR3 length as a critical parameter in the creation of an antigen-specific binding site. We also propose that this may reflect a dependence of a particular structure of this hypervariable loop, the major carrier of diversity in the binding site, for establishment of a given specificity.


Out of the frying pan, into the fire: mixed affective reactions to social proximity in borderline and avoidant personality disorders in daily life.
Social proximity typically helps individuals meet their belongingness needs, but several forms of psychopathology, including borderline and avoidant personality disorders (BPD and APD, respectively) are characterized by social difficulties. This experience-sampling study is one of the first to directly investigate the affective reactions of individuals with BPD and APD (compared with healthy controls [HC]) to social proximity in daily life. We examined both person-level and day-level reactions. At the person level, the rate of social proximity across the diary period was associated with diminished feelings of rejection, isolation, shame, and dissociation in the HC group. In contrast, it was not associated with any affective reaction in the BPD group, and was associated with decreased rejection and isolation on the one hand, but also with increased anxiety in the APD group. At the day level, we used multilevel regression to examine affective reactions when in social proximity. The HC group showed a consistent benefit when in social proximity. In contrast, both PD groups exhibited mixed affective reactions to social proximity; specifically, benefits (increased positive affect, decreased rejection, isolation, and dissociation) were interspersed with costs (increased shame for both PD groups; increased anger for BPD; increased anxiety for APD). The mixed reactions found in both PDs may contribute to the disturbed relationships of individuals with these disorders.


N-carboxymethyllysine as a biomarker for coronary artery disease and age-related macular degeneration.
An association between coronary artery disease (CAD) and age-related macular degeneration (ARMD) has long been postulated, but exact mechanisms remain unclear. The global prevalence of CAD and ARMD increases and early biomarkers for early diagnosis of these diseases are necessary. The aim of this study was to investigate the plasma level of oxidative stress biomarker CML in patients with and without angiographic findings of atherosclerosis in the coronary arteries (CADath+ and CADath-, respectively) and to assess if there was an association of CAD with ARMD. The study enrolled 233 subjects. Based on cardiologic and ophthalmologic examinations, the patients were divided into four subgroups: CADath+ARMD+, CADath+ARMD-, CADath-ARMD+, and CADath-ARMD-. The enzyme-linked immunosorbent assay was used for the measurement of plasma CML levels. Serum lipid levels were determined by an automatic analyzer using conventional enzymatic methods. CADath+ patients had higher CML concentration compared to CADath- subjects (1.04±0.6 vs. 0.83±0.4ng/mL, P<0.001). The highest mean CML level (1.12±0.7ng/mL) was found in CADath+ARMD+ patients. The mean plasma CML concentration was higher in subjects with any of the analyzed diseases compared to CADath-ARMD- subjects. A significant positive association of CADath+ (OR=2.50, 95% CI 1.60-3.90, P=0.0001), ARMD (OR=2.08, 95% CI 1.40-3.11, P=0.0001) and both analyzed diseases (OR=4.67, 95% CI 2.29-9.53, P=0.0001) with an increased level of plasma CML in a logistic regression model adjusting by age was identified. The level of CML, an oxidative stress biomarker, reflects the presence of atherosclerosis in coronary arteries and shows a possible link between ARMD and CADath+ via oxidative status.


Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma.
It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals, and thus high-resolution technologies are likely required. We used cytometry by time-of-flight and next-generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related precancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 precancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T-cell, B-cell, and natural killer-cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0% ± 0.7% (mean ± SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27(+)) and naïve (CD24(lo)CD38(+)) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells.


Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta.
DNA polymerase catalysis and fidelity studies typically compare incorporation of "right" versus "wrong" nucleotide bases where the leaving group is pyrophosphate. Here we use dGTP analogues replacing the beta,gamma-bridging O with CH2, CHF, CF2, or CCl2 to explore leaving-group effects on the nucleotidyl transfer mechanism and fidelity of DNA polymerase (pol) beta. T.G mismatches occur with fidelities similar to dGTP with the exception of the CH2 analogue, which is incorporated with 5-fold higher fidelity. All analogues are observed to bind opposite template C with Kds between 1 and 4 microM, and structural evidence suggests that the analogues bind in essentially the native conformation, making them suitable substrates for probing linear free energy relationships (LFERs) in transient-kinetics experiments. Importantly, Brnsted correlations of log(kpol) versus leaving-group pKa for both right and wrong base incorporation reveal similar sensitivities (betalg approximately -0.8) followed by departures from linearity, suggesting that a chemical step rather than enzyme conformational change is rate-limiting for either process. The location of the breaks relative to pKas of CF2, O, and the sterically bulky CCl2-bridging compounds suggests a modification-induced change in the mechanism by stabilization of leaving-group elimination. The results are addressed theoretically in terms of the energetics of successive primer 3'-O addition (bond forming) and pyrophosphate analogue elimination (bond breaking) reaction energy barriers.


Can glasgow score at discharge represent final outcome in severe head injury?
Patients with head injury continue to improve over time and a minimum follow-up of six months is considered necessary to evaluate outcome. However, this may be difficult to assess due to lack of follow-up. It is also well known that operated patients who return for cranioplasty usually have the best outcome. To assess the outcome following severe head injury using cranioplasty as a surrogate marker for good outcome. This was a retrospective study carried out from January 2009 to December 2010. All patients with severe head injury who underwent decompressive craniectomy (DC) in the study period were included. Patients who came back for cranioplasty in the same period were also included. Case records, imaging and follow up visit data from all patients were reviewed. Glasgow Coma Score (GCS) on admission and Glasgow Outcome Score (GOS) at discharge were assessed. Of the 273 patients, 84.25% (n=230) were males and 15.75% (n= 43) were females. The mean age was 34.3 years (range 2-81 years, SD 16.817). The mean GCS on admission was 5.615 (range 3-8, SD 1.438). The in-hospital mortality was 54% (n=149). Good outcome (GOS of 4 or 5) at discharge was attained in 22% (n=60) patients. Sixty five patients returned for cranioplasty (with a GOS of 4 or 5) during the study period. There was no statistical difference in the number of patients discharged with good outcome and those coming back for cranioplasty in the study period (P>0.5). Patients who came back for cranioplasty were younger in age (mean age 28.815 years SD 13.396) with better admission GCS prior to DC (mean GCS 6.32 SD1.39). In operated severe head injury patients significant number of patients (24% in our study) have excellent outcome. However, insignificant number of patients had further improvement to GOS 4 or 5 (good outcome) from the time of initial discharge. This suggests that due to lack of intensive rehabilitative facilities, GOS at discharge may be representative of final outcome in the vast majority of cases of severe head injury in developing countries like India.


Keeping your head on target.
The mechanisms by which the human brain controls eye movements are reasonably well understood, but those for the head less so. Here, we show that the mechanisms for keeping the head aimed at a stationary target follow strategies similar to those for holding the eyes steady on stationary targets. Specifically, we applied the neural integrator hypothesis that originally was developed for holding the eyes still in eccentric gaze positions to describe how the head is held still when turned toward an eccentric target. We found that normal humans make head movements consistent with the neural integrator hypothesis, except that additional sensory feedback is needed, from proprioceptors in the neck, to keep the head on target. We also show that the complicated patterns of head movements in patients with cervical dystonia can be predicted by deficits in a neural integrator for head motor control. These results support ideas originally developed from animal studies that suggest fundamental similarities between oculomotor and cephalomotor control, as well as a conceptual framework for cervical dystonia that departs considerably from current clinical views.