Native American fire management at an ancient wildland-urban interface in the Southwest United States.
The intersection of expanding human development and wildland landscapes-the "wildland-urban interface" or WUI-is one of the most vexing contexts for fire management because it involves complex interacting systems of people and nature. Here, we document the dynamism and stability of an ancient WUI that was apparently sustainable for more than 500 y. We combine ethnography, archaeology, paleoecology, and ecological modeling to infer intensive wood and fire use by Native American ancestors of Jemez Pueblo and the consequences on fire size, fire-climate relationships, and fire intensity. Initial settlement of northern New Mexico by Jemez farmers increased fire activity within an already dynamic landscape that experienced frequent fires. Wood harvesting for domestic fuel and architectural uses and abundant, small, patchy fires created a landscape that burned often but only rarely burned extensively. Depopulation of the forested landscape due to Spanish colonial impacts resulted in a rebound of fuels accompanied by the return of widely spreading, frequent surface fires. The sequence of more than 500 y of perennial small fires and wood collecting followed by frequent "free-range" wildland surface fires made the landscape resistant to extreme fire behavior, even when climate was conducive and surface fires were large. The ancient Jemez WUI offers an alternative model for fire management in modern WUI in the western United States, and possibly other settings where local management of woody fuels through use (domestic wood collecting) coupled with small prescribed fires may make these communities both self-reliant and more resilient to wildfire hazards.


Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact.
Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp) and end (115 bp) of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer.


Assessing adherence to multiple medications and in daily life among patients with multimorbidity.
Chronic conditions often require multiple medication intake. However, past research has focused on assessing overall adherence or adherence to a single index medication only. This study explored adherence measures for multiple medication intake, and in daily life, among patients with multiple chronic conditions (i.e. multimorbidity). Eighty-four patients with multimorbidity and multiple-medication regimens completed three monthly panel questionnaires. A randomly assigned subsample additionally completed a 30-day daily diary. The Non-Adherence Report; a brief self-report measure of adherence to each prescribed medication (NAR-M), and in daily life. We further assessed the Medication Adherence Report Scale (MARS), and a subsample of participants were randomised to electronic adherence monitoring. The NAR-M indicated M = 94.7% adherence at Time 1 (SD = 9.3%). The NAR-M was significantly correlated with the MARS (rt1 = .52, rt2 = .57, and rt3 = .65; p < .001), and in tendency with electronically assessed adherence (rt2 = .45, rt3 = .46, p < .10). Variance components analysis indicated that between-person differences accounted for 10.2% of the variance in NAR-M adherence rates, whereas 22.9% were attributable to medication by person interactions. This study highlights the importance and feasibility of studying adherence to multiple medications differentially, and in daily life. Future studies may use these measures to investigate within-person and between-medication differences in adherence.


Fluoride reduces bone strength in older rats.
In response to recent concerns about the effect of water fluoridation on hip fracture rates, we studied the influence of fluoride intake on bone strength. Four groups of rats were fed a low-fluoride diet ad libitum and received 0, 5, 15, or 50 ppm of fluoride in their drinking water. Animals were euthanized after 3, 6, 12, or 18 months of treatment. Mechanical strength of the right femur was measured by three-point bending. Fluoride content for the left femur was measured, and static histomorphometric measurements were made on a lumbar vertebra. Femoral failure load was not significantly decreased in rats treated for 3 and 6 months, but was decreased as much as 23% in rats treated 12 and 18 months at 50 ppm fluoride. Extrapolation from regression equations predicted that older rats lose 36% of femoral bone strength when bone fluoride content is increased from 0 to 10,000 ppm, while younger rats will lose only 15%. Thus, the decreased strength appeared to be due to the combined effects of fluoride intake and age on bone tissue and was not associated with a decrease in bone density or mineralization defects. There were only small effects of fluoride on bone histomorphometry. Fluoride intake at high levels had no negative effects on bone mineralization. Fluoride intake was associated with slight increases in trabecular bone volume and trabecular thickness, but these effects could not be demonstrated consistently. The mechanism by which large amounts of fluoride affect bone strength more severely in older animals is unknown.


H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes.
The incorporation of histone variants into chromatin plays an important role for the establishment of particular chromatin states. Six human histone H3 variants are known to date, not counting CenH3 variants: H3.1, H3.2, H3.3 and the testis-specific H3.1t as well as the recently described variants H3.X and H3.Y. We report the discovery of H3.5, a novel non-CenH3 histone H3 variant. H3.5 is encoded on human chromosome 12p11.21 and probably evolved in a common ancestor of all recent great apes (Hominidae) as a consequence of H3F3B gene duplication by retrotransposition. H3.5 mRNA is specifically expressed in seminiferous tubules of human testis. Interestingly, H3.5 has two exact copies of ARKST motifs adjacent to lysine-9 or lysine-27, and lysine-79 is replaced by asparagine. In the Hek293 cell line, ectopically expressed H3.5 is assembled into chromatin and targeted by PTM. H3.5 preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes and can replace an essential function of RNAi-depleted H3.3 in cell growth.


Genetically distinct leukemic stem cells in human CD34- acute myeloid leukemia are arrested at a hemopoietic precursor-like stage.
Our understanding of the perturbation of normal cellular differentiation hierarchies to create tumor-propagating stem cell populations is incomplete. In human acute myeloid leukemia (AML), current models suggest transformation creates leukemic stem cell (LSC) populations arrested at a progenitor-like stage expressing cell surface CD34. We show that in ∼25% of AML, with a distinct genetic mutation pattern where >98% of cells are CD34(-), there are multiple, nonhierarchically arranged CD34(+) and CD34(-) LSC populations. Within CD34(-) and CD34(+) LSC-containing populations, LSC frequencies are similar; there are shared clonal structures and near-identical transcriptional signatures. CD34(-) LSCs have disordered global transcription profiles, but these profiles are enriched for transcriptional signatures of normal CD34(-) mature granulocyte-macrophage precursors, downstream of progenitors. But unlike mature precursors, LSCs express multiple normal stem cell transcriptional regulators previously implicated in LSC function. This suggests a new refined model of the relationship between LSCs and normal hemopoiesis in which the nature of genetic/epigenetic changes determines the disordered transcriptional program, resulting in LSC differentiation arrest at stages that are most like either progenitor or precursor stages of hemopoiesis.


Oligoclonal bands in multiple sclerosis: clinical-pathologic correlation.
Although oligoclonal banding is a characteristic feature of MS spinal fluid, some patients do not show this abnormality. Four of 18 consecutive patients with autopsy-proven MS had no oligoclonal bands (OB) in CSF during life or at postmortem. Patients with OB had numerous plasma cells in meninges and plaques (confirmed in sections stained for cytoplasmic immunoglobulin). The four patients without bands had few or no identifiable plasma cells. Therefore, lack of OB correlates with both inactivity of plaques and absence of plasma cells in plaques or meninges. This is another form of heterogeneity in MS.


Single-layer model for surface roughness.
Random roughness of an optical surface reduces its specular reflectance and transmittance by the scattering of light. The reduction in reflectance can be modeled by a homogeneous layer on the surface if the refractive index of the layer is intermediate to the indices of the media on either side of the surface. Such a layer predicts an increase in the transmittance of the surface and therefore does not provide a valid model for the effects of scatter on the transmittance. Adding a small amount of absorption to the layer provides a model that predicts a reduction in both reflectance and transmittance. The absorbing layer model agrees with the predictions of a scalar scattering theory for a layer with a thickness that is twice the rms roughness of the surface. The extinction coefficient k for the layer is proportional to the thickness of the layer.


Illness perceptions in relation to experiences of contemporary cancer care settings among colorectal cancer survivors and their partners.
Illness is constituted by subjective experiences of symptoms and their psychosocial consequences. Illness perceptions concern people's lay beliefs about understandings and interpretation of a disease and expectations as to disease outcome. Our knowledge about illness perceptions and coping in relation to the cancer care context among persons with colorectal cancer (CRC) and their partners is incomplete. The aim of the present study was to explore illness perceptions in relation to contemporary cancer care settings among CRC survivors and partners. The present research focused on illness rather than disease, implying that personal experiences are central to the methodology. The grounded theory method used is that presented by Kathy Charmaz. The present results explore illness perceptions in the early recovery phase after being diagnosed and treated for cancer in a contemporary cancer care setting. The core category outlook on the cancer diagnosis when quickly informed, treated, and discharged illustrates the illness perceptions of survivors and partners as well as the environment in which they were found. The cancer care environment is presented in the conceptual category experiencing contemporary cancer care settings. Receiving treatment quickly and without waiting was a positive experience for both partners and survivors; however partners experienced the information as massive and as causing concern. The period after discharge was being marked by uncertainty and loneliness, and partners tended to experience non-continuity in care as more problematic than the survivor did. The results showed different illness perceptions and a mismatch between illness perceptions among survivors and partners, presented in the conceptual category outlook on the cancer diagnosis. One illness perception, here presented among partners, focused on seeing the cancer diagnosis as a permanent life-changing event. The other illness perception, here presented among survivors, concentrated on leaving the cancer diagnosis behind and moving forward. The importance of illness perceptions among survivors, and the differences in illness perceptions between survivors and partners, should be recognized by healthcare professionals to achieve the goals of person-centered contemporary cancer care.


Impacts of dichroic prism coatings on radiometry of the airborne imaging spectrometer APEX.
The generation of well-calibrated radiometric measurements from imaging spectrometer data requires careful consideration of all influencing factors, as well as an instrument calibration based on a detailed sensor model. Deviations of ambient parameters (i.e., pressure, humidity, temperature) from standard laboratory conditions during airborne operations can lead to biases that should be accounted for and properly compensated by using dedicated instrument models. This study introduces a model for the airborne imaging spectrometer airborne prism experiment (APEX), describing the impact of spectral shifts as well as polarization effects on the radiometric system response due to changing ambient parameters. Key issues are related to changing properties of the dichroic coating applied to the dispersing elements within the optical path. We present a model based on discrete numerical simulations. With the improved modeling approach, we predict radiometric biases with an root mean square error (RMSE) below 1%, leading to a substantial improvement of radiometric stability and predictability of system behavior.


Hepatic response to increased exogenous supply of plasma amino acids by infusion into the mesenteric vein of Holstein-Friesian cows in late gestation.
The hepatic responses of late gestation, dry dairy cows to acute (6 h) infusions of an amino acid (AA) mixture (Synthamin; 0.0, 1.1, 2.2, 4.4, 8.8 and 17.6 mumol/min) into the mesenteric vein were determined. Neither blood flow nor O2 consumption across the portal-drained viscera (PDV) and liver was significantly altered by infusion. Similarly, there were no effects on net absorption, or hepatic removal, of acetate, propionate, butyrate or NH3. Glucose PDV appearance was unchanged but hepatic glucose production increased (P = 0.032) by 0.2 mumol/min per mumol/min of AA infused. Additional extraction of alanine, glycine (both infused) and glutamine (not infused) by the liver was sufficient to account for most of the extra C required for glucose synthesis. The N that would be liberated from these glucogenic AA would also account for a large proportion of the increase in urea-N produced in response to the AA infusion. This supports the concept of a correlation between gluconeogenesis and ureagenesis. Furthermore, the amide-N liberated from the extracted glutamine would contribute up to 0.17 of hepatic NH3 flux and assist in balancing N inputs into the carbamoyl phosphate and arginosuccinate entry points of the ornithine cycle. Rates of fractional extraction of the various AA by the liver were best fitted by linear equations, indicating that even at the highest rates of administration (approximately twice maximal physiological absorption) the transport systems were not saturated. Hepatic fractional extractions of infused essential AA were highest for methionine (0.83) and phenylalanine (0.87) with the lowest proportion removed observed for valine (0.25), leucine (0.30), lysine (0.31) and isoleucine (0.49). For the non-essential AA, the highest apparent fractional extractions were for glycine (0.73), arginine (0.79) and tyrosine (0.63) followed by alanine (0.54), proline (0.47) and serine (0.37). Hepatic removal of AA-N exceeded the increase in urea-N formation such that, at the highest rate of infusion, approximately 10 mmol/min of the extracted AA was apparently available for hepatic anabolism, more than is required to account for assumed increases in liver mass and export protein synthesis. Similarly, the amount of AA available for peripheral tissue protein gain, when assessed against phenylalanine supply as the limitation, would be the equivalent of a maximum of 0.5 g protein retained/min (6 mmol AA-N/min). This would provide sufficient AA for replenishment of peripheral (muscle) protein stores plus support of the placenta and fetus.


Myelodysplastic syndromes: Contemporary review and how we treat.
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal stem cell disorders with an inherent tendency for leukemic transformation. Diagnosis is currently based on the presence of peripheral blood cytopenias, peripheral blood and bone marrow dysplasia/blasts, and clonal cytogenetic abnormalities. With the advent of next generation sequencing, recurrent somatic mutations in genes involved in epigenetic regulation (TET2, ASXL1, EZH2, DNMT3A, IDH1/2), RNA splicing (SF3B1, SRSF2, U2AF1, ZRSR2), DNA damage response (TP53), transcriptional regulation (RUNX1, BCOR, ETV6) and signal transduction (CBL, NRAS, JAK2) have been identified in MDS. Conventional prognostication is by the revised International prognostic scoring system (IPSS-R) with additional adverse prognosis conferred by presence of ASXL1, EZH2, or TP53 mutations. Currently Food and Drug administration (FDA)-approved drugs for the treatment of MDS are not curative and their effect on survival is limited; they include the hypomethylating agents (HMA) azacitidine and decitabine and lenalidomide for MDS with isolated del(5q). To date, allogeneic stem cell transplant (ASCT) remains the only treatment option for possible cure. Given the current lack of drugs with convincing evidence of favorable effect on survival, we consider ASCT as the treatment of choice for most patients with symptomatic disease, and especially for those with high-risk disease. For nontransplant candidates, participation in clinical trials is preferred over conventional therapy. There is not one right way of treatment for patients who are not candidates for either ASCT or clinical trials and palliative drugs of choice depend on the clinical problem, such as symptomatic anemia (ESAs, danazol, HMA), thrombocytopenia (HMA), or neutropenia (myeloid growth factors). Conversely, there is no controlled evidence to support the use of iron chelating agents in MDS. Going forward, we believe it is time to incorporate mutation information in clinically derived prognostic models in MDS and encourage development of novel drugs with disease-modifying activity.


Uncleaved TFIIA is a substrate for taspase 1 and active in transcription.
In higher eukaryotes, the large subunit of the general transcription factor TFIIA is encoded by the single TFIIAalphabeta gene and posttranslationally cleaved into alpha and beta subunits. The molecular mechanisms and biological significance of this proteolytic process have remained obscure. Here, we show that TFIIA is a substrate of taspase 1 as reported for the trithorax group mixed-lineage leukemia protein. We demonstrate that recombinant taspase 1 cleaves TFIIA in vitro. Transfected taspase 1 enhances cleavage of TFIIA, and RNA interference knockdown of endogenous taspase 1 diminishes cleavage of TFIIA in vivo. In taspase 1-/- MEF cells, only uncleaved TFIIA is detected. In Xenopus laevis embryos, knockdown of TFIIA results in phenotype and expression defects. Both defects can be rescued by expression of an uncleavable TFIIA mutant. Our study shows that uncleaved TFIIA is transcriptionally active and that cleavage of TFIIA does not serve to render TFIIA competent for transcription. We propose that cleavage fine tunes the transcription regulation of a subset of genes during differentiation and development.


Dual computer monitors to increase efficiency of conducting systematic reviews.
Systematic reviews (SRs) are the cornerstone of evidence-based medicine. In this study, we evaluated the effectiveness of using two computer screens on the efficiency of conducting SRs. A cohort of reviewers before and after using dual monitors were compared with a control group that did not use dual monitors. The outcomes were time spent for abstract screening, full-text screening and data extraction, and inter-rater agreement. We adopted multivariate difference-in-differences linear regression models. A total of 60 SRs conducted by 54 reviewers were included in this analysis. We found a significant reduction of 23.81 minutes per article in data extraction in the intervention group relative to the control group (95% confidence interval: -46.03, -1.58, P = 0.04), which was a 36.85% reduction in time. There was no significant difference in time spent on abstract screening, full-text screening, or inter-rater agreement between the two groups. Using dual monitors when conducting SRs is associated with significant reduction of time spent on data extraction. No significant difference was observed on time spent on abstract screening or full-text screening. Using dual monitors is one strategy that may improve the efficiency of conducting SRs.


Implementation of a stroke alert protocol in the emergency department: a pilot study.
Although tissue plasminogen activator (tPA) is an effective treatment for stroke patients, it typically must be administered within 3 hours of symptom onset to substantially reduce morbidity and mortality. Because of this limited treatment window, it is essential for healthcare professionals to properly identify and quickly triage stroke patients. To determine if implementation of a stroke alert protocol coupled with a limited education program will reduce arrival time to computed tomography scan time and treatment time for stroke patients in the emergency department (ED). This prospective pilot study took place at Geisinger Medical Center in Danville, Pennsylvania, and included a formal stroke protocol based partly on The Joint Commission's stroke center recommendations. The major feature was integration of various hospital departments to quickly and accurately identify and triage stroke patients; included was a limited education program for residents and attending staff. Patients who presented between November 1, 2007, to October 31, 2008, comprised the study group (ie, after protocol implementation). A retrospective analysis of patient records from November 1, 2006, to October 31, 2007, for stroke morbidity, mortality, and tPA administration was employed as a control group (ie, prior to protocol implementation). Inclusion criteria consisted of patients aged 18 years or older who arrived at the ED with stroke-like symptoms. Exclusion criteria consisted of previous hemorrhagic stroke, seizure at stroke onset, internal bleeding, intracranial hemorrhage, recent surgery, platelet count of less than 100 × 10(3)/μL, untreated blood pressure greater than 185/110 mm Hg, symptoms lasting for longer than 6 hours, and vascular malformation. Patients with a history of ischemic stroke were included in the study. The study included a total of 233 stroke patients, 132 of whom presented to the ED prior to stroke protocol implementation and 101 of whom presented after stroke protocol implementation. For patients who arrived at the ED within 3 hours from symptom onset, median time to completion of a computed tomography (CT) scan was reduced from 65.5 minutes (interquartile range, 41.0-101.0) prior to the new protocol to 54.0 minutes (interquartile range, 25.0-54.0) after implementation (P<.004). Regarding patients who arrived in the ED 3 to 6 hours after symptom onset, median time from ED arrival to CT time decreased from 94.5 minutes (interquartile range, 68.0-136.0) before the new protocol to 48.5 minutes (interquartile range, 33.0-89.0) following implementation (P<.002). Of the 79 patients who arrived at the ED within 3 hours of symptom onset in the year after protocol implementation, 12 were treated with tPA, compared to 4 out of 86 treated in the year prior to protocol implementation. Mean time from ED arrival to tPA treatment was reduced from 85.5 minutes in the preprotocol group to 48.9 minutes in the postprotocol group. By coupling a formal stroke protocol with a limited education program, door-to-treatment time of stroke patients was reduced.


Micro-CT with respiratory and cardiac gating.
Cardiopulmonary imaging in rodents using micro-computed tomography (CT) is a challenging task due to both cardiac and pulmonary motion and the limited fluence rate available from micro-focus x-ray tubes of most commercial systems. Successful imaging in the mouse requires recognition of both the spatial and temporal scales and their impact on the required fluence rate. Smaller voxels require an increase in the total number of photons (integrated fluence) used in the reconstructed image for constant signal-to-noise ratio. The faster heart rates require shorter exposures to minimize cardiac motion blur imposing even higher demands on the fluence rate. We describe a system with fixed tube/detector and with a rotating specimen. A large focal spot x-ray tube capable of producing high fluence rates with short exposure times was used. The geometry is optimized to match focal spot blur with detector pitch and the resolution limits imposed by the reproducibility of gating. Thus, it is possible to achieve isotropic spatial resolution of 100 microm with a fluence rate at the detector 250 times that of a conventional cone beam micro-CT system with rotating detector and microfocal x-ray tube. Motion is minimized for any single projection with 10 ms exposures that are synchronized to both cardiac and breathing motion. System performance was validated in vivo by studies of the cardiopulmonary structures in C57BL/6 mice, demonstrating the value of motion integration with a bright x-ray source.


Review of health economic models exploring and evaluating treatment and management of hospital-acquired pneumonia and ventilator-associated pneumonia.
Hospital-acquired pneumonia (HAP) is pneumonia that occurs ≥48 h after hospital admission; it is the most common hospital-acquired infection contributing to death. Ventilator-associated pneumonia (VAP) arises ≥48-72 h after intubation. Opinions differ on whether VAP is a subset of HAP; the same pathogens predominate in both. Compared with VAP-free controls, patients developing VAP are twice as likely to die and have significantly longer stays in intensive care units. Guidelines recommend that microbiological cultures should guide antibiotic treatment, but these lack sensitivity and take 48-72 h to process, meaning that initial therapy must be empiric, generally with broad-spectrum agents. Given increasing pressure to improve both antibiotic stewardship and patient outcomes, the National Institute for Health and Care Excellence and the Infectious Diseases Society of America recommend research into rapid molecular diagnostic tests to identify causative organisms and their antibiotic resistances. Ideally, these would supersede culture, being quicker and more sensitive. In the UK, the INHALE research programme, funded by the National Institute for Health Research, is exploring rapid molecular diagnostics to inform treatment of HAP/VAP and, given resource implications, incorporates a health economic component. To identify previous economic modelling of HAP/VAP costs to inform this component. Literature review of HAP/VAP studies with economic modelling identified from three databases. Twenty studies were identified. Only one study specifically evaluated strategies to improve diagnosis; the remaining 19 studies omitted this important aspect. HAP/VAP modelling would be improved by better awareness of long-term outcomes and treatment complexity. To the authors' knowledge, no similar literature reviews of economic modelling for HAP/VAP have been published.


Shared genetic factors influence amygdala volumes and risk for alcoholism.
Alcohol abuse and dependence (alcohol use disorders, AUDs) are associated with brain shrinkage. Subcortical structures including the amygdala, hippocampus, ventral striatum, dorsal striatum, and thalamus subserve reward functioning and may be particularly vulnerable to alcohol-related damage. These structures may also show pre-existing deficits impacting the development and maintenance of AUD. It remains unclear whether there are common genetic features underlying both subcortical volumes and AUD. In this study, structural brain images were acquired from 872 Mexican-American individuals from extended pedigrees. Subcortical volumes were obtained using FreeSurfer, and quantitative genetic analyses were performed in SOLAR. We hypothesized the following: (1) reduced subcortical volumes in individuals with lifetime AUD relative to unrelated controls; (2) reduced subcortical volumes in individuals with current relative to past AUD; (3) in non-AUD individuals, reduced subcortical volumes in those with a family history of AUD compared to those without; and (4) evidence for common genetic underpinnings (pleiotropy) between AUD risk and subcortical volumes. Results showed that individuals with lifetime AUD showed larger ventricular and smaller amygdala volumes compared to non-AUD individuals. For the amygdala, there were no differences in volume between current vs past AUD, and non-AUD individuals with a family history of AUD demonstrated reductions compared to those with no such family history. Finally, amygdala volume was genetically correlated with the risk for AUD. Together, these results suggest that reduced amygdala volume reflects a pre-existing difference rather than alcohol-induced neurotoxic damage. Our genetic correlation analysis provides evidence for a common genetic factor underlying both reduced amygdala volumes and AUD risk.


Robust model for segmenting images with/without intensity inhomogeneities.
Intensity inhomogeneities and different types/levels of image noise are the two major obstacles to accurate image segmentation by region-based level set models. To provide a more general solution to these challenges, we propose a novel segmentation model that considers global and local image statistics to eliminate the influence of image noise and to compensate for intensity inhomogeneities. In our model, the global energy derived from a Gaussian model estimates the intensity distribution of the target object and background; the local energy derived from the mutual influences of neighboring pixels can eliminate the impact of image noise and intensity inhomogeneities. The robustness of our method is validated on segmenting synthetic images with/without intensity inhomogeneities, and with different types/levels of noise, including Gaussian noise, speckle noise, and salt and pepper noise, as well as images from different medical imaging modalities. Quantitative experimental comparisons demonstrate that our method is more robust and more accurate in segmenting the images with intensity inhomogeneities than the local binary fitting technique and its more recent systematic model. Our technique also outperformed the region-based Chan–Vese model when dealing with images without intensity inhomogeneities and produce better segmentation results than the graph-based algorithms including graph-cuts and random walker when segmenting noisy images.


Mismatch between Tissue Partial Oxygen Pressure and Near-Infrared Spectroscopy Neuromonitoring of Tissue Respiration in Acute Brain Trauma: The Rationale for Implementing a Multimodal Monitoring Strategy.
The brain tissue partial oxygen pressure (PbtO2) and near-infrared spectroscopy (NIRS) neuromonitoring are frequently compared in the management of acute moderate and severe traumatic brain injury patients; however, the relationship between their respective output parameters flows from the complex pathogenesis of tissue respiration after brain trauma. NIRS neuromonitoring overcomes certain limitations related to the heterogeneity of the pathology across the brain that cannot be adequately addressed by local-sample invasive neuromonitoring (e.g., PbtO2 neuromonitoring, microdialysis), and it allows clinicians to assess parameters that cannot otherwise be scanned. The anatomical co-registration of an NIRS signal with axial imaging (e.g., computerized tomography scan) enhances the optical signal, which can be changed by the anatomy of the lesions and the significance of the radiological assessment. These arguments led us to conclude that rather than aiming to substitute PbtO2 with tissue saturation, multiple types of NIRS should be included via multimodal systemic- and neuro-monitoring, whose values then are incorporated into biosignatures linked to patient status and prognosis. Discussion on the abnormalities in tissue respiration due to brain trauma and how they affect the PbtO2 and NIRS neuromonitoring is given.


Machine learning and social network analysis applied to Alzheimer's disease biomarkers.
Due to the fact that the number of deaths due Alzheimer is increasing, the scientists have a strong interest in early stage diagnostic of this disease. Alzheimer's patients show different kind of brain alterations, such as morphological, biochemical, functional, etc. Currently, using magnetic resonance imaging techniques is possible to obtain a huge amount of biomarkers; being difficult to appraise which of them can explain more properly how the pathology evolves instead of the normal ageing. Machine Learning methods facilitate an efficient analysis of complex data and can be used to discover which biomarkers are more informative. Moreover, automatic models can learn from historical data to suggest the diagnostic of new patients. Social Network Analysis (SNA) views social relationships in terms of network theory consisting of nodes and connections. The resulting graph-based structures are often very complex; there can be many kinds of connections between the nodes. SNA has emerged as a key technique in modern sociology. It has also gained a significant following in medicine, anthropology, biology, information science, etc., and has become a popular topic of speculation and study. This paper presents a review of machine learning and SNA techniques and then, a new approach to analyze the magnetic resonance imaging biomarkers with these techniques, obtaining relevant relationships that can explain the different phenotypes in dementia, in particular, different stages of Alzheimer's disease.


Thermal and Calorimetric Evaluations of Some Chemically Modified Carbohydrate-Based Substrates with Phosphorus-Containing Groups.
In the present article, we report on the chemical modifications of some carbohydrate-based substrates, such as potato starch, dextran, β-cyclodextrin, agar agar and tamarind, by reacting with diethylchlorophosphate (DECP), in dispersions in dichloromethane (DCM), in the presence of triethylamine (TEA) as the base. The modified substrates, after recovery and purification, were analyzed for their chemical constitutions, thermal stabilities and calorimetric properties using a variety of analytical techniques. These included: solid-state 31P NMR, inductively coupled plasma-optical emission spectroscopy (ICP-OES), thermogravimetric analysis (TGA) and pyrolysis combustion flow calorimetry (PCFC). The unmodified counterparts were also subjected to the same set of analyses with a view to serving as controls. Phosphorus analyses, primarily through ICP-OES on the recovered samples, showed different degrees of incorporation. Such observations were optionally verified through solid-state 31P NMR spectroscopy. The thermograms of the modified substrates were noticeably different from the unmodified counterparts, both in terms of the general profiles and the amounts of char residues produced. Such observations correlated well with the relevant parameters obtained through PCFC runs. Overall, the modified systems containing phosphorus were found to be less combustible than the parent substrates, and thus can be considered as promising matrices for environmentally benign fire-resistant coatings.


Gender differences in healthcare utilization of patients with diabetes.
To examine gender differences in healthcare utilization including outpatient and inpatient medical care for patients with type 2 diabetes mellitus (T2DM), despite participation in T2DM-specific disease management programs (DMP-DM). Baseline data from a cohort study in southwest Germany including 1146 patients with T2DM recruited between October 2008 and March 2010 were used. After bivariate analyses, multivariate Poisson and logistic regression models were used to estimate the effect of sex on the number of general practitioner (GP) and medical specialist appointments, prescribed medications, hospitalizations, and inpatient rehabilitations, with additional consideration of glycemic control levels. Poor glycemic control (PGC) was defined as glycated hemoglobin ≥7.5%. In total, 905 participants had acceptable glycemic control and 237 participants had poor glycemic control. PGC was more prevalent in men than in women (23% vs 18%). Bivariate analyses among participants with PGC showed significantly fewer GP and medical specialist appointments, a lower number of medications, and longer rehabilitation stays in men than in women. Multivariate regression analyses among participants with PGC confirmed statistically significant gender differences for GP appointments and number of prescribed medications (P <.05) for men compared with women. Gender differences regarding inpatient care were less evident. Our data disclosed major gender differences in healthcare utilization of diabetes patients in Germany despite a high DMP-DM rate. Future research should focus attention on gender-specific approaches to healthcare delivery to improve quality and access to care.


Design and methods of a population-based natural history study of cervical neoplasia in a rural province of Costa Rica: the Guanacaste Project.
This paper reports on the enrollment phase of a population-based natural history study of cervical neoplasia in Guanacaste, a rural province of Costa Rica with consistently high rates of invasive cervical cancer. The main goals of the study are to investigate the role of human papillomavirus (HPV) infection and its co-factors in the etiology of high-grade cervical neoplasia, and to evaluate new cervical cancer screening technologies. To begin, a random sample of censal segments was selected and enumeration of all resident women 18 years of age and over was conducted with the aid of outreach workers of the Costa Rican Ministry of Health. Of the 10738 women who were eligible to participate, 10049 (93.6%) were interviewed after giving written informed consent. After the interview on cervical cancer risk factors was administered, a pelvic examination was performed on those women who reported previous sexual activity. The pelvic examination included a vaginal pH determination and collection of cervical cells for cytologic diagnosis using three different techniques. Additional cervical cells were collected for determination of the presence and amount of DNA from 16 different types of HPV, and two photographic images of the cervix were taken and interpreted offsite by an expert colposcopist. Finally, blood samples were collected for immunologic and micronutrient assays. Women with any abnormal cytologic diagnosis or a positive Cervigram, as well as a sample of the whole group, were referred for colposcopy, and biopsies were taken when lesions were observed. The enrollment screening will serve as the basis for a prevalent case-control study, and the members of the cohort free from serious disease will be followed actively, at intervals of no more than a year, to study the natural history of HPV infection and the origins of high-grade squamous intraepithelial lesions (HSIL). Details of the field operation are outlined, with particular reference to the realization of this kind of study in developing countries. Descriptive data on the prevalence of disease and exposure to various risk factors are also presented.


Hepatic expression of tumour necrosis factor-alpha in chronic hepatitis B virus infection.
To determine the hepatic expression of tumour necrosis factor-alpha (TNF alpha) in patients with chronic hepatitis B virus (HBV) infection. Frozen liver biopsy sections from 19 patients with chronic HBV infection were studied, 12 of whom were HBeAg positive and 10 serum HBV DNA positive. Hepatic expression of TNF alpha was determined using immunohistochemistry. Only infiltrating mononuclear cells showed immunoreactive staining for TNF alpha (median 2, range 0-3; n = 19) which appeared as diffuse positive staining material in the cytoplasm. Patients with active liver disease, assessed histologically and biochemically, had a higher level of expression, both in the number of TNF alpha positive cells and the proportion of TNF alpha positive infiltrating mononuclear cells. There was no correlation between the expression of TNF alpha and serological parameters of viral infection (HBeAg and HBV DNA status and HBV DNA concentrations). Hepatic expression of TNF alpha is increased in chronic HBV infection and is related to the activity of liver disease and not to the level of HBV replication.


Oxidative damage and inflammation in obese diabetic Emirati subjects.
Visceral obesity is more common in the Arab population and more closely related to morbidity, including diabetes and related cardiovascular diseases (CVD). Possible mechanisms that link visceral fat/obesity to diabetes and CVD complications include inflammation and increased oxidative stress; however, few data are available from the Arab population. Our aim was to determine whether increased adiposity in obese diabetic United Arab Emirates citizens is associated with sub-clinical inflammation and/or increased oxidative stress. A hundred diabetic patients who were part of a randomized controlled trial of nutritional supplements had their baseline characteristics assessed from anthropometric and clinical data following informed written consent. We used WHO figures to classify general and central obesity. Fasting blood samples were collected for the measurement of antioxidants and markers of oxidative damage and inflammation. We found that increased adiposity measured by both body mass index and waist circumference was associated with increased C-reactive protein (CRP) and decreased vitamin C after adjusting for age, duration and treatment of diabetes (p < 0.05). Although there is a clear trend of increased inflammatory markers, notably CRP, and decreased antioxidants with increased BMI and waist circumference in both men and women, the results are statistically significant for women only. CRP were also inversely associated with HDL. Overall, we found that BMI underestimates the rates of obesity compared to waist circumference and that increased adiposity is associated with increased inflammation and decreased HDL and antioxidant status.


Metabolic clearance rate of arginine vasopressin in severe chronic renal failure.
1. The metabolic clearance rate of arginine vasopressin was determined using a constant infusion technique in normal subjects and patients with chronic renal failure immediately before commencing dialysis. Endogenous arginine vasopressin was suppressed in all subjects before the infusion with a water load. 2. Plasma arginine vasopressin concentrations were determined using a sensitive and specific radioimmunoassay after Florisil extraction. The detection limit of the assay was 0.3 pmol/l, and intra- and inter-assay coefficients of variation at 2 pmol/l were 9.7% and 15.3%, respectively. 3. In normal subjects, the metabolic clearance rate was determined at two infusion rates producing steady-state concentrations of arginine vasopressin of 1.3 and 4.4 pmol/l. In the patients with renal failure, a single infusion rate was used, producing a steady-state concentration of 1.5 pmol/l. 4. At comparable plasma arginine vasopressin concentrations, metabolic clearance rate was significantly reduced in patients with renal failure (normal 1168 +/- 235 ml/min versus renal failure 584 +/- 169 ml/min; means +/- SD; P < 0.001). 5. Free water clearance was significantly reduced in normal subjects during the arginine vasopressin infusion from 8.19 +/- 2.61 to -1.41 +/- 0.51 ml/min (P < 0.001), but was unchanged in the patients with renal failure after attaining comparable plasma arginine vasopressin concentrations. 6. In normal subjects there was a small but significant fall in metabolic clearance rate at the higher steady-state arginine vasopressin concentration (1168 +/- 235 ml/min at 1.3 pmol/l versus 1059 +/- 269 ml/min at 4.4 pmol/l; P = 0.016).(ABSTRACT TRUNCATED AT 250 WORDS)


Phylogeny of Wolbachia in filarial nematodes.
Intracellular bacteria have been observed in various species of filarial nematodes (family Onchocercidae). The intracellular bacterium of the canine filaria Dirofilaria immitis has been shown to be closely related to Wolbachia, a rickettsia-like micro-organism that is widespread among arthropods. However, the relationships between endosymbionts of different filariae, and between these and the arthropod wolbachiae, appear not to have been studied. To address these issues we have examined ten species of filarial nematodes for the presence of Wolbachia. For nine species, all samples examined were PCR positive using primers specific for the ftsZ gene of Wolbachia. For one species, the examined samples were PCR negative. Sequences of the amplified ftsZ gene fragments of filarial wolbachiae fall into two clusters (C and D), which are distinct from the A and B clusters recognized for arthropod wolbachiae. These four lineages (A-D) are related in a star-like phylogeny, with higher nucleotide divergence observed between C and D wolbachiae than that observed between A and B wolbachiae. In addition, within each of the two lineages of filarial wolbachiae, the phylogeny of the symbionts is consistent with the host phylogeny. Thus, there is no evidence for recent Wolbachia transmission between arthropods and nematodes. Endosymbiont 16S ribosomal DNA sequences from a subset of filarial species support these findings.


Processing of zero-derived words in English: an fMRI investigation.
Derivational morphological processes allow us to create new words (e.g. punish (V) to noun (N) punishment) from base forms. The number of steps from the basic units to derived words often varies (e.g., nationality<national<nation: two-steps) and there is evidence that complex derivations cause more brain activity than simple ones (Meinzer, Lahiri, Flaisch, Hannemann, & Eulitz, 2009). However, all studies to date have investigated derivational processes in which morphological complexity is related to a change in surface form. It is therefore unclear whether the effects reported are attributable to underlying morphological complexity or to the processing of multiple surface morphemes. Here we report the first study to investigate morphological processing where derivational steps are not overtly marked (e.g., bridge-N>bridge-V) i.e., zero-derivation (Aronoff, 1980). We compared the processing of one-step (soaking<soak-V) and two-step (bridging<bridge-V<bridge-N) derivations together with monomorphemic control words (grumble) in an fMRI experiment. Participants were presented with derived forms of words (soaking, bridging) in a lexical decision task. Although the surface derived -ing forms can be contextually participles, gerunds, or even nouns, they are all derived from verbs since the suffix -ing can only be attached to verb roots. Crucially, the verb root is the basic form for the one-step words, whereas for the two-step words the verb root is zero derived from a basic noun. Significantly increased brain activity was observed for complex (one-step and two-step) versus simple (zero-step) forms in regions involved in morphological processing, such as the left inferior frontal gyrus (LIFG). Critically, activation was also more pronounced for two-step compared to one-step forms. Since both types of derived words have the same surface structure, our findings suggest that morphological processing is based on underlying morphological complexity, independent of overt affixation. This study is the first to provide evidence for the processing of zero derivation, and demonstrates that morphological processing cannot be reduced to surface form-based segmentation.


Electron-Transfer Activity in a Cyanide-Bridged Fe42 Nanomagnet.
The ability to switch a molecule between different magnetic states is of considerable importance for the development of new molecular electronic devices. Desirable properties for such applications include a large-spin ground state with an electronic structure that can be controlled via external stimuli. Fe42 is a cyanide-bridged stellated cuboctahedron of mixed-valence Fe ions that exhibits an extraordinarily large S = 45 spin ground state. We have found that the spin ground state of Fe42 can be altered by controlling the humidity and temperature. Dehydration results in a 15 μB reduction of the saturation magnetization that can be partially recovered upon rehydration. The complementary use of UV-vis, IR, L2,3-edge X-ray absorption spectroscopy and X-ray magnetic circular dichroism is applied to uncover the mechanism for the observed dynamic behavior. It is identified that dehydration is concurrent with metal-to-metal electron transfer between Fe pairs via a cyanide π hybridization. Upon dehydration, electron transfer occurs from low-spin {FeII(Tp)(CN)3} sites to high-spin FeIII centers. The observed reduction in magnetization upon dehydration of Fe42 is inconsistent with a ferrimagnetic ground state and is proposed to originate from a change in zero-field splitting at electron-reduced high-spin sites.


DNA Methylation Score as a Biomarker in Newborns for Sustained Maternal Smoking during Pregnancy.
Maternal smoking during pregnancy, especially when sustained, leads to numerous adverse health outcomes in offspring. Pregnant women disproportionately underreport smoking and smokers tend to have lower follow-up rates to repeat questionnaires. Missing, incomplete, or inaccurate data on presence and duration of smoking in pregnancy impairs identification of novel health effects and limits adjustment for smoking in studies of other pregnancy exposures. An objective biomarker in newborns of maternal smoking during pregnancy would be valuable. We developed a biomarker of sustained maternal smoking in pregnancy using common DNA methylation platforms. Using a dimension reduction method, we developed and tested a numeric score in newborns to reflect sustained maternal smoking in pregnancy from data on cotinine, a short-term smoking biomarker measured mid-pregnancy, and Illumina450K cord blood DNA methylation from newborns in the Norwegian Mother and Child Cohort Study (MoBa). This score reliably predicted smoking status in the training set (n = 1,057; accuracy = 96%, sensitivity = 80%, specificity = 98%). Sensitivity (58%) was predictably lower in the much smaller test set (n = 221), but accuracy (91%) and specificity (97%) remained high. Reduced birth weight, a well-known effect of maternal smoking, was as strongly related to the score as to cotinine. A three-site score had lower, but acceptable, performance (accuracytrain = 82%, accuracytest = 83%). Our smoking methylation score represents a promising novel biomarker of sustained maternal smoking during pregnancy easily calculated with Illumina450K or IlluminaEPIC data. It may help identify novel health impacts and improve adjustment for smoking when studying other risk factors with more subtle effects.


Interaction of the Mechanosensitive Channel, MscS, with the Membrane Bilayer through Lipid Intercalation into Grooves and Pockets.
All membrane proteins have dynamic and intimate relationships with the lipids of the bilayer that may determine their activity. Mechanosensitive channels sense tension through their interaction with the lipids of the membrane. We have proposed a mechanism for the bacterial channel of small conductance, MscS, that envisages variable occupancy of pockets in the channel by lipid chains. Here, we analyze protein-lipid interactions for MscS by quenching of tryptophan fluorescence with brominated lipids. By this strategy, we define the limits of the bilayer for TM1, which is the most lipid exposed helix of this protein. In addition, we show that residues deep in the pockets, created by the oligomeric assembly, interact with lipid chains. On the cytoplasmic side, lipids penetrate as far as the pore-lining helices and lipid molecules can align along TM3b perpendicular to lipids in the bilayer. Cardiolipin, free fatty acids, and branched lipids can access the pockets where the latter have a distinct effect on function. Cholesterol is excluded from the pockets. We demonstrate that introduction of hydrophilic residues into TM3b severely impairs channel function and that even "conservative" hydrophobic substitutions can modulate the stability of the open pore. The data provide important insights into the interactions between phospholipids and MscS and are discussed in the light of recent developments in the study of Piezo1 and TrpV4.


A paired RNAi and RabGAP overexpression screen identifies Rab11 as a regulator of β-amyloid production.
Alzheimer's disease (AD) is characterized by cerebral deposition of β-amyloid (Aβ) peptides, which are generated from amyloid precursor protein (APP) by β- and γ-secretases. APP and the secretases are membrane associated, but whether membrane trafficking controls Aβ levels is unclear. Here, we performed an RNAi screen of all human Rab-GTPases, which regulate membrane trafficking, complemented with a Rab-GTPase-activating protein screen, and present a road map of the membrane-trafficking events regulating Aβ production. We identify Rab11 and Rab3 as key players. Although retromers and retromer-associated proteins control APP recycling, we show that Rab11 controlled β-secretase endosomal recycling to the plasma membrane and thus affected Aβ production. Exome sequencing revealed a significant genetic association of Rab11A with late-onset AD, and network analysis identified Rab11A and Rab11B as components of the late-onset AD risk network, suggesting a causal link between Rab11 and AD. Our results reveal trafficking pathways that regulate Aβ levels and show how systems biology approaches can unravel the molecular complexity underlying AD.


Quantifying T 2 relaxation time changes within lesions defined by apparent diffusion coefficient in grey and white matter in acute stroke patients.
The apparent diffusion coefficient (ADC) of cerebral water, as measured by diffusion MRI, rapidly decreases in ischaemia, highlighting a lesion in acute stroke patients. The MRI T 2 relaxation time changes in ischaemic brain such that T 2 in ADC lesions may be informative of the extent of tissue damage, potentially aiding in stratification for treatment. We have developed a novel user-unbiased method of determining the changes in T 2 in ADC lesions as a function of clinical symptom duration based on voxel-wise referencing to a contralateral brain volume. The spherical reference method calculates the most probable pre-ischaemic T 2 on a voxel-wise basis, making use of features of the contralateral hemisphere presumed to be largely unaffected. We studied whether T 2 changes in the two main cerebral tissue types, i.e. in grey matter (GM) and white matter (WM), would differ in stroke. Thirty-eight acute stroke patients were accrued within 9 h of symptom onset and scanned at 3 T for 3D T 1-weighted, multi b-value diffusion and multi-echo spin echo MRI for tissue type segmentation, quantitative ADC and absolute T 2 images, respectively. T 2 changes measured by the spherical reference method were 1.94 ± 0.61, 1.50 ± 0.52 and 1.40 ± 0.54 ms h-1 in the whole, GM, and WM lesions, respectively. Thus, T 2 time courses were comparable between GM and WM independent of brain tissue type involved. We demonstrate that T 2 changes in ADC-delineated lesions can be quantified in the clinical setting in a user unbiased manner and that T 2 change correlated with symptom onset time, opening the possibility of using the approach as a tool to assess severity of tissue damage in the clinical setting.


Down regulation of miR-124 in both Werner syndrome DNA helicase mutant mice and mutant Caenorhabditis elegans wrn-1 reveals the importance of this microRNA in accelerated aging.
Small non-coding microRNAs are believed to be involved in the mechanism of aging but nothing is known on the impact of microRNAs in the progeroid disorder Werner syndrome (WS). WS is a premature aging disorder caused by mutations in a RecQ-like DNA helicase. Mice lacking the helicase domain of the WRN ortholog exhibit many phenotypic features of WS, including a pro-oxidant status and a shorter mean life span.Caenorhabditis elegans (C. elegans) with a nonfunctional wrn-1 DNA helicase also exhibit a shorter life span. Thus, both models are relevant to study the expression of microRNAs involved in WS. In this study, we show that miR-124 expression is lost in the liver of Wrn helicase mutant mice. Interestingly, the expression of this conserved miR-124 in whole wrn-1 mutant worms is also significantly reduced. The loss of mir-124 in C. elegans increases reactive oxygen species formation and accumulation of the aging marker lipofuscin, reduces whole body ATP levels and results in a reduction in life span. Finally, supplementation of vitamin C normalizes the median life span of wrn-1 and mir-124 mutant worms. These results suggest that biological pathways involving WRN and miR-124 are conserved in the aging process across different species.


Economic analysis of treatment of functional dyspepsia. An assessment of the quality of published studies.
The objective of this study was to assess the quality of economic analysis studies published in the medical and economical literature assessing the clinical management of functional dyspepsia. Bibliographic search in the main biomedical databases, in articles from bibliographic references, health technology assessment reports, and in gray literature. A specific protocol with economic and clinical items was designed for the evaluation. Overall, 18 of 162 studies met the inclusion criteria for the assessment. The compared treatment options were very diverse. The main methodologic deficiencies were in perspective of analysis, inclusion of indirect costs, and sources of clinical information. Specific checklists with clinical and economical items may help to better assess the quality of economic analysis in the field of functional dyspepsia. The methodologic rigor in the application of economic analysis techniques, as well as the use of appropriate clinical outcome measures, is essential to guarantee the reproducibility of the studies.


Do Ancillary Studies Aid Detection and Classification of Barrett Esophagus?
Barrett esophagus is a preneoplastic condition defined by the presence of intestinal metaplasia (ie, goblet cells) in an endoscopically apparent columnar-lined esophagus. Dysplasia is the most important risk factor for cancer development among patients with Barrett esophagus; approximately 6% of patients with high-grade dysplasia progress to adenocarcinoma within 1 year. Surgical pathologists are generally expected to address 2 clinical concerns when evaluating mucosal biopsy samples from patients with suspected Barrett esophagus; they should note the presence, or absence, of goblet cells and comment on the grade of dysplasia when it is identified. Biopsy samples from patients with Barrett esophagus are categorized as negative for dysplasia, indefinite for dysplasia, or positive for dysplasia; in the latter situation, the severity of dysplasia is classified as low or high grade. Several histochemical stains, immunohistochemical stains, and molecular techniques can be used to facilitate detection of goblet cells and classify dysplasia in patients with Barrett esophagus, although their added value to routine morphologic assessment is not entirely clear. The purpose of this review is to discuss the state of the art regarding application of ancillary studies to esophageal samples from patients with a columnar-lined esophagus.


Newer agents in antiplatelet therapy: a review.
Antiplatelet therapy remains the mainstay in preventing aberrant platelet activation in pathophysiological conditions such as myocardial infarction, ischemia, and stroke. Although there has been significant advancement in antiplatelet therapeutic approaches, aspirin still remains the gold standard treatment in the clinical setting. Limitations in safety, efficacy, and tolerability have precluded many of the antiplatelet inhibitors from use in patients. Unforeseen incidences of increased bleeding risk and recurrent arterial thrombosis observed in patients have hampered the development of superior next generation antiplatelet therapies. The pharmacokinetic and pharmacodynamic profiles have also limited the effectiveness of a number of antiplatelet inhibitors currently in use due to variability in metabolism, time to onset, and reversibility. A focused effort in the development of newer antiplatelet therapies to address some of these shortcomings has resulted in a significant number of potential antiplatelet drugs which target enzymes (phosphodiesterase, cyclooxygenase), receptors (purinergic, prostaglandins, protease-activated receptors, thromboxane), and glycoproteins (αIIbβ3, GPVI, vWF, GPIb) in the platelet. The validation and search for newer antiplatelet therapeutic approaches proven to be superior to aspirin is still ongoing and should yield a better pharmacodynamic profile with fewer untoward side-effects to what is currently in use today.


Prehospital hypotension as a valid indicator of trauma team activation.
Criteria for trauma team activation are continually being evaluated to ensure proper utilization of resources. We examined the impact of prehospital (PH) hypotension (systolic blood pressure < or = 90) on outcome (operative intervention and mortality) and its usefulness as an indicator for trauma team activation. A database was created by using the trauma registry for all nonburned, injured patients from July of 1993 through October of 1998 at our Level I trauma center. Of 6,976 patients (83% blunt injury) in the database, 4,437 had a PH blood pressure recorded. Documented PH hypotension was present in 791 patients. Hypotension persisted in the emergency department (ED) in 299 patients, but 193 of them showed minimal or no signs of life on arrival. Four hundred ninety-two patients had PH hypotension but normal ED systolic blood pressure, and 130 patients developed ED hypotension after normal PH systolic blood pressure. Nearly half of the patients with hypotension were taken from the ED directly to the operating room primarily for hemorrhage control procedures. The early and late mortality rates of patients with PH and ED hypotension were 12% and 32%, respectively. Other PH interventions had minimal effect on mortality in the hypotensive patient. Prehospital hypotension remains a valid indicator for trauma team activation. Even though most of the non-DOA patients (492 of 598) were stable on arrival to the ED, nearly 50% required operative intervention, and an additional 25% required intensive care unit admission. The trauma team should be activated and involved with these patients early.


Oral vaccination. Identification of classes of proteins that provoke an immune response upon oral feeding.
Oral immunization of an animal is generally hard to achieve unless large quantities of antigen are administered. In this study a number of antigens were tested for their ability to elicit a systemic immune response upon oral administration. It was found that bacterial pili, LTB, lectins, and a viral hemagglutinin were all able to elicit significant antibody titers upon oral feeding. The immune response thus generated to LTB and K99 pili could be completely abolished by cofeeding a number of sugars that have close structural homology to the terminal sugars of the GM1 and GM2 gangliosides to which these molecules are known to bind. All of the proteins that were active in oral immunization are known to possess "lectin or lectin-like" binding activities. It is therefore proposed that these molecules are able to bind to glycolipids and glycoproteins on the intestinal mucosa and to stimulate these cells to transport the proteins into the systemic circulation, thereby eliciting a systemic immune response. Molecules that did not possess this binding activity were unable to elicit significant responses at the doses tested.


Hypodysfibrinogenaemia due to production of mutant fibrinogen alpha-chains lacking fibrinopeptide A and polymerisation knob 'A'.
Inherited disorders of fibrinogen are rare and affect either the quantity (hypofibrinogenaemia and afibrinogenaemia) or the quality of the circulating fibrinogen (dysfibrinogenaemia) or both (hypodysfibrinogenaemia). Extensive allelic heterogeneity has been found for all these disorders: in congenital afibrinogenaemia for example more than 40 mutations, the majority in FGA , have been identified in homozygosity or in compound heterozygosity. Numerous mutations have also been identified in patients with hypofibrinogenaemia, many of these patients are in fact heterozygous carriers of afibrinogenaemia mutations. Despite the number of genetic analyses performed, the study of additional patients still allows the identification of novel mutations. Here we describe the characterization of a novel FGA intron 2 donor splice-site mutation (Fibrinogen Montpellier II) identified in three siblings with hypodysfibrinogenaemia. Functional analysis of RNA produced by the mutant minigene in COS-7 cells revealed that the mutation led to the in-frame skipping of exon 2. Western blot analysis of COS-7 cells expressing an exon 2 deleted FGA cDNA revealed that an alpha-chain lacking exon 2, which codes in particular for fibrinopeptide A and polymerisation knob 'A', has the potential to be assembled into a hexamer and secreted. Analysis of precipitated fibrinogen from patient plasma showed that the defect leads to the presence in the circulation of alpha-chains lacking knob 'A' which is essential for the early stages of fibrin polymerisation. Fibrin made from purified patient fibrinogen clotted with thrombin displayed thinner fibers with frequent ends and large pores.


Combination therapy with brentuximab vedotin and cisplatin/cytarabine in a patient with primarily refractory anaplastic lymphoma kinase positive anaplastic large cell lymphoma.
Anaplastic large cell lymphoma (ALCL) is a common subtype of the heterogeneous group of peripheral T-cell lymphomas, which is characterized by large pleomorphic cells with strong expression of CD30. Translocations involving ALK, the anaplastic lymphoma kinase gene, are associated with a favorable clinical outcome. Such ALK-positive ALCLs are usually responsive to a multidrug chemotherapy with CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone). However, there is no general consensus on the optimal therapy for relapsed or refractory ALCL. We report the case of a 24-year-old male suffering from ALK-positive ALCL with an uncommon manifestation of only extranodal disease in the gastric cardia region that showed primary refractoriness to standard CHOP chemotherapy. A combination therapy consisting of the anti-CD30 drug conjugate, brentuximab vedotin, and classical lymphoma salvage regimen DHAP (cisplatin, high-dose cytarabine and dexamethasone) was administered. Following two treatment cycles in 21-day intervals, the lymphoma showed considerable regression based on imaging diagnostics and no evidence of vital lymphoma in a subsequent biopsy. We did not observe any increase in toxicity; in particular, polyneuropathy and febrile neutropenia were not observed. In summary, we report that the antibody-drug conjugate brentuximab vedotin and a classical regimen used for aggressive lymphoma, DHAP, could be combined as salvage therapy in a case of refractory ALK-positive ALCL. Phase I/II studies will be required for safety and efficacy analysis.


In vivo specific labeling of Chlamydomonas chloroplast DNA.
When Chlamydomonas reinhardi is supplied with (methyl-(3)H)-thymidine, radioactivity is incorporated specifically into chloroplast DNA Chromatographic analysis of the products of enzymatic hydrolysis of the DNA reveals that only thymidine monophosphate has been labeled. Use of thymidine-6-(3)H yields an identical result. If thymidine-(3)H monophosphate is supplied, a small amount of radioactivity is incorporated into both nuclear and chloroplast DNA in proportion to the abundance of these DNA components. These observations are consistent with earlier suggestions that algae lack cytoplasmic thymidine kinase, but that the enzyme is present within their chloroplasts.


The Porous-Coated Anatomic total knee experience. Special emphasis on complications and wear.
One hundred sixty knees in 141 patients with the Primary Porous-Coated Anatomic prosthesis (Howmedica, Rutherford, NJ) were evaluated after a follow-up period of 5.6 years (range, 1-10 years). One hundred six knees were in the latest follow-up evaluation, including clinical examination and a defined standing radiograph with a follow-up period of 6.3 years (range, 3-10 years). Survivorship analysis regarding the cumulative revision rate (including completion with a patellar component) was 0.88 at the 8-year and 0.84 at the 10-year follow-up examination. The clinical result was satisfying/good, with a mean Hospital for Special Surgery score of 83 (range, 39-97). Five percent had thinning greater than 30% of the tibial component. The wear was calculated to be 1.0 mm (range, 0-9 mm), including three revised tibial components with heavy wear. Excluding the revised cases, the wear was 0.7 mm.


Incidence of Connected Consciousness after Tracheal Intubation: A Prospective, International, Multicenter Cohort Study of the Isolated Forearm Technique.
The isolated forearm technique allows assessment of consciousness of the external world (connected consciousness) through a verbal command to move the hand (of a tourniquet-isolated arm) during intended general anesthesia. Previous isolated forearm technique data suggest that the incidence of connected consciousness may approach 37% after a noxious stimulus. The authors conducted an international, multicenter, pragmatic study to establish the incidence of isolated forearm technique responsiveness after intubation in routine practice. Two hundred sixty adult patients were recruited at six sites into a prospective cohort study of the isolated forearm technique after intubation. Demographic, anesthetic, and intubation data, plus postoperative questionnaires, were collected. Univariate statistics, followed by bivariate logistic regression models for age plus variable, were conducted. The incidence of isolated forearm technique responsiveness after intubation was 4.6% (12/260); 5 of 12 responders reported pain through a second hand squeeze. Responders were younger than nonresponders (39 ± 17 vs. 51 ± 16 yr old; P = 0.01) with more frequent signs of sympathetic activation (50% vs. 2.4%; P = 0.03). No participant had explicit recall of intraoperative events when questioned after surgery (n = 253). Across groups, depth of anesthesia monitoring values showed a wide range; however, values were higher for responders before (54 ± 20 vs. 42 ± 14; P = 0.02) and after (52 ± 16 vs. 43 ± 16; P = 0.02) intubation. In patients not receiving total intravenous anesthesia, exposure to volatile anesthetics before intubation reduced the odds of responding (odds ratio, 0.2 [0.1 to 0.8]; P = 0.02) after adjustment for age. Intraoperative connected consciousness occurred frequently, although the rate is up to 10-times lower than anticipated. This should be considered a conservative estimate of intraoperative connected consciousness.


Experience of an upper limb training program with a non-immersive virtual reality system in patients after stroke: a qualitative study.
The YouGrabber (YG) is a new virtual reality training system that focuses on unilateral and bimanual activities. This nested study was part of a larger multicenter randomized controlled trial and explored experiences of people with chronic stroke during a 4 weeks intensive upper limb training with YG. A qualitative design using semi-structured, face-to-face interviews. A phenomenological descriptive approach was used, with data coded, categorized and summarized using a thematic analysis. Topics investigated included: the experience of YG training, perceived impact of YG training on arm function, and the role of the treating therapist. Five people were interviewed (one female, age range 55 to 75 years, 1 to 6 years poststroke). Seven main themes were identified: (1) general experience, (2) expectations, (3) feedback, (4) arm function, (5) physiotherapist's role, (6) fatigue, (7) motivation. Key experiences reported included feelings of motivation and satisfaction, with positive factors identified as challenge, competition, fun and effort. The YG training appeared to trigger greater effort, however fatigue was experienced at the end of the training. Overall, patients described positive changes in upper limb motor function and activity level, e.g. automatic arm use. While the opportunity for self-practice was appreciated, input from the therapist at the start of the intervention was deemed important for safety and confidence. Reported experiences were mostly positive and the participants were motivated to practice intensively. They enjoyed the challenging component of the games.


Estrogens suppress RANK ligand-induced osteoclast differentiation via a stromal cell independent mechanism involving c-Jun repression.
Loss of ovarian function following menopause results in a substantial increase in bone turnover and a critical imbalance between bone formation and resorption. This imbalance leads to a progressive loss of trabecular bone mass and eventually osteoporosis, in part the result of increased osteoclastogenesis. Enhanced formation of functional osteoclasts appears to be the result of increased elaboration by support cells of osteoclastogenic cytokines such as IL-1, tumor necrosis factor, and IL-6, all of which are negatively regulated by estrogens. We show here that estrogen can suppress receptor activator of NF-kappaB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF)-induced differentiation of myelomonocytic precursors into multinucleated tartrate-resistant acid phosphatase-positive osteoclasts through an estrogen receptor-dependent mechanism that does not require mediation by stromal cells. This suppression is dose-dependent, isomer-specific, and reversed by ICI 182780. Furthermore, the bone-sparing analogues tamoxifen and raloxifene mimic estrogen's effects. Estrogen blocks RANKL/M-CSF-induced activator protein-1-dependent transcription, likely through direct regulation of c-Jun activity. This effect is the result of a classical nuclear activity by estrogen receptor to regulate both c-Jun expression and its phosphorylation by c-Jun N-terminal kinase. Our results suggest that estrogen modulates osteoclast formation both by down-regulating the expression of osteoclastogenic cytokines from supportive cells and by directly suppressing RANKL-induced osteoclast differentiation.


Expression of membrane-bound mucins in human nasal mucosa: different patterns for MUC4 and MUC16.
To acquire basic information concerning the function of the membrane-bound mucin MUC16 in nasal mucosa compared with the best-characterized membrane-bound mucin, MUC4. In vitro study using semiquantatitive reverse transcription-polymerase chain reaction analysis and immunoassay. Yeungnam University College of Medicine. We examined the nasal polyps obtained during endoscopic sinus surgery in 10 patients, the normal ethmoid sinus mucosa obtained from 10 patients, and human nasal polyp epithelial (HNPE) cells. Gene expression of MUC4 and MUC16 in nasal polyps and normal nasal mucosa. In addition, we evaluated the effect of 4 physiologically relevant agents, including retinoic acid, interleukin 1beta, phorbol 12-myristate 13-acetate (PMA), and dexamethasone, on the expression of MUC4 and MUC16 in HNPE cells at the gene and protein levels. In nasal polyps, MUC4 was upregulated compared with normal nasal mucosa (P = .009), whereas MUC16 expression did not differ between nasal polyps and normal nasal mucosa. Retinoic acid and interleukin 1beta increased MUC4 expression at the gene and protein level in HNPE cells, whereas MUC16 expression was not affected. Unlike retinoic acid and interleukin 1beta, PMA and dexamethasone increased MUC16 expression, whereas they had no significant effect on MUC4 expression. Expression of MUC4 and MUC16 are regulated differently in nasal mucosa. Dexamethasone and PMA are potent mediators for the expression of MUC16 in nasal polyps.


Increasing pressures and support for public healthcare in Europe.
We present the results from a natural survey-experiment that tests the effect of a sudden increase in health risks - a flu epidemic - on the public's support for government involvement in health care provision. The data covers 17 European countries and around 10,000 respondents. It was collected in 2008 as part of the European Social Survey. We find that the flu epidemic led to a significant decline in support. Interestingly, changes where located predominantly among those respondents that are self-described right-leaning in ideological terms. The effects of the flu epidemic lasted several weeks and in some instances persisted as long as it was possible to track with the data (i.e., a month). Given that this was a single-event stimulus such a comparably long-lasting effect is noteworthy for both public policy-makers and political scientists.


Abnormal Muscle Activity and Variability Before, During, and After the Occurrence of Freezing in Parkinson's Disease.
Freezing of gait (FOG) is often experienced in advanced stages of Parkinson's disease (PD) and can lead to an increased risk of falls. Although spatiotemporal characteristics of FOG are well-described, their underlying neuromuscular mechanisms remain poorly understood. Several studies have demonstrated an abnormal activation of distal muscles of the lower limb and coordination impairments during gait in people with PD (pwPD). However, few have investigated how various characteristics of electromyograms (EMGs) change before, during and after a freezing episode (FE). Our objective was to quantify changes in proximal and distal leg muscle activity associated with FEs. In this study, 12 pwPD, confirmed as freezers, performed a repetitive stepping-in-place task used to elicit FE. Surface EMGs were collected from proximal [rectus femoris and biceps femoris (BF)] and distal [tibialis anterior (TA) and gastrocnemius medialis (GM)] muscles. Data epochs of 500 ms were extracted from EMG time series at four different periods: baseline, 2 s before a FE, during a FE, and 2 s after a FE. For each epoch, EMG amplitude [root-mean-square (RMS)], variability [coefficient of variation (CoV)], and inter-muscle functional connectivity (mutual information) were quantified. Results from the analysis of 21 FEs show a significant main effect of Period for EMG amplitude in bilateral TA and in the least affected GM (p < 0.01), with decreased activation before freezing that remained low during and after the FE. On the other hand, a main effect of Period was also found in bilateral BF muscles (p < 0.01) but with increased activation before freezing that was generally sustained during and after FE. Main effects of Period were also found for all measures of variability, except for the least affected GM, showing reduced variability during the FE that returned to baseline in all muscles except both TA. Moreover, an increase in functional connectivity between the least affected distal muscles was seen before the FE. Our findings confirm that many characteristics of EMG patterns of both distal and proximal leg muscles change throughout periods of a FE, suggesting both impairment and adaptive strategies from proximal muscles.


Aggressiveness of intensive care use among patients with lung cancer in the Surveillance, Epidemiology, and End Results-Medicare registry.
Approximately 65% of elderly patients with lung cancer who are admitted to the ICU will die within 6 months. Efforts to improve end-of-life care for this population must first understand the patient factors that underlie admission to the ICU. We performed a retrospective cohort study examining all fee-for-service inpatient claims in the Surveillance, Epidemiology, and End Results (SEER)-Medicare registry for elderly patients (aged > 65 years) who had received a diagnosis of lung cancer between 1992 and 2005 and who were hospitalized for reasons other than resection of their lung cancer. We calculated yearly rates of ICU admission per 1,000 hospitalizations via room and board codes or International Classification of Diseases, Ninth Revision, Clinical Modification and diagnosis-related group codes for mechanical ventilation, stratified the rates by receipt of mechanical ventilation and ICU type (medical/surgical/cardiac vs intermediate), and compared these rates over time. A total of 175,756 patients with lung cancer in SEER were hospitalized for a reason other than surgical resection of their tumor during the study period, 49,373 (28%) of whom had at least one ICU stay. The rate of ICU admissions per 1,000 hospitalizations increased over the study period from 140.7 in 1992 to 201.7 in 2005 (P < .001). The majority of the increase in ICU admissions (per 1,000 hospitalizations) between 1992 and 2005 occurred among patients who were not mechanically ventilated (118.2 to 173.3, P < .001) and among those who were in intermediate ICUs (20.0 to 61.9, P < .001), but increased only moderately in medical/surgical/cardiac units (120.7 to 139.9, P < .001). ICU admission for patients with lung cancer increased over time, mostly among patients without mechanical ventilation who were largely cared for in intermediate ICUs.


Feeding dried purple laver (nori) to vitamin B12-deficient rats significantly improves vitamin B12 status.
To clarify the bioavailability of vitamin B12 in lyophylized purple laver (nori; Porphyra yezoensis), total vitamin B12 and vitamin B12 analogue contents in the laver were determined, and the effects of feeding the laver to vitamin B12-deficient rats were investigated. The amount of total vitamin B12 in the dried purple laver was estimated to be 54.5 and 58.6 (se 5.3 and 7.5 respectively) microg/100 g dry weight by Lactobacillus bioassay and chemiluminescent assay with hog intrinsic factor respectively. The purple laver contained five types of biologically active vitamin B12 compounds (cyano-, hydroxo-, sulfito-, adenosyl- and methylcobalamin), in which the vitamin B12 coezymes (adenosyl- and methylcobalamin) comprised about 60 % of the total vitamin B12. When 9-week-old vitamin B12-deficient rats, which excreted substantial amounts of methylmalonic acid (71.7(se 20.2) micromol/d) in urine, were fed the diet supplemented with dried purple laver (10 microg/kg diet) for 20 d, urinary methylmalonic acid excretion (as an index of vitamin B12 deficiency) became undetectable and hepatic vitamin B12 (especially adenosylcobalamin) levels were significantly increased. These results indicate that vitamin B12 in dried purple laver is bioavailable to rats.


Prediction of the hepatic and renal clearance of transporter substrates in rats using in vitro uptake experiments.
The clearance route and the absolute values for hepatic and renal clearance of drugs are important criteria for the selection of drug candidates. Based on pharmacokinetic theory, by assuming that uptake is the rate-determining process for the biliary excretion of drugs, organ intrinsic clearance should be simply estimated by the intrinsic uptake. In this study, to investigate whether organ clearance can be predicted from the in vitro uptake activity, we performed uptake experiments using isolated hepatocytes and kidney slices, integration plot analyses, and in vivo pharmacokinetic studies using 12 barely metabolized drugs in rats. The in vivo hepatic and renal clearance could be approximated by uptake clearance estimated from integration plot analyses, except for the renal clearance of some drugs that was relatively small. The comparison of intrinsic uptake clearance from in vitro experiments and integration plot studies revealed that in vivo hepatic uptake was well explained by uptake into isolated hepatocytes, whereas in kidney, in vivo uptake clearance was 10 to 100 times that in kidney slices and a scaling factor is required for its prediction from in vitro experiments. The organ clearance and the fraction excreted into urine could be predicted from in vitro studies except for drugs whose renal clearance was relatively small. This study suggests that the uptake process is the determining factor for organ clearance of minimally metabolized drugs, and uptake assays using isolated hepatocytes and kidney slices are useful for evaluating the uptake clearance.


Lack of clinical predictors of optimal V-V delay in patients with cardiac resynchronization devices.
Cardiac resynchronization therapy (CRT) is a well-established therapy for patients with moderate-to-severe heart failure (HF), left ventricular dysfunction with an ejection fraction <or= 35% and a QRS on the surface electrocardiogram of >or=130 msec. Device optimization is often performed, adjusting the timing of RV and LV stimulation to produce a pacing sequence that yields the best global cardiac performance. However, no standard guidelines exist for optimization and many invasive and non-invasive techniques have been employed with mixed results. The aim of the present study was to determine whether there are any clinical predictors of the optimal V-V settings in patients implanted with CRT devices. We prospectively evaluated 47 consecutive patients with HF who were referred to our device optimization clinic. The mean patient age was 64.9 +/- 12.7 years. Patients were in both sinus rhythm (83%) and atrial fibrillation. Prior to device implant, 51% of patients had left bundle branch block (LBBB), 17% had intra-ventricular conduction delay (IVCD) and 21% were RV paced. Sixty-two percent were male, the mean QRS duration was 152 +/- 29 ms, mean LVEF 26 +/- 8% and 60% had a non-ischemic cardiomyopathy. Overall, 82% of patients required sequential pacing with 69% requiring LV pre-excitation to produce the best global cardiac function as determined by aortic velocity time integrals (VTI). In our cohort, none of the clinical characteristics evaluated, including etiology of the cardiomyopathy, QRS duration, LVEF, pre-implant rhythm or AV delay were predictive of an optimal simultaneous or sequential V-V setting. None of the clinical variables tested in our analysis predicted optimal RV-LV settings. Our results suggest that individual optimization and programming of V-V settings is necessary. The inability to predict optimal settings likely reflects the unique characteristics of each patient and supports the need for individualized programming of each device.


Candidate screening of the bovine and feline spinal muscular atrophy genes reveals no evidence for involvement in human motor neuron disorders.
Spinal muscular atrophy (SMA) is a devastating neuromuscular disease characterised by progressive loss of spinal motor neurons. Mutations in the genes underlying spontaneous bovine and feline models of SMA have recently been described. The clinical and pathological features of these disorders are similar to human forms of SMA making both genes excellent candidates in patients with motor neuron loss of no known aetiology. Here we report that a screen for mutations in coding regions and splice sites of the LIX1 and FVT1 genes in a cohort of 96 non-5q SMA patients and 119 familial and sporadic Amyotrophic Lateral Sclerosis patients identified no obvious pathogenic changes. This study indicates that mutations in these genes do not contribute significantly to the cause of motor neuron diseases in the human population.


Activation of the cyclin D1 gene by the E1A-associated protein p300 through AP-1 inhibits cellular apoptosis.
The adenovirus E1A protein interferes with regulators of apoptosis and growth by physically interacting with cell cycle regulatory proteins including the retinoblastoma tumor suppressor protein and the coactivator proteins p300/CBP (where CBP is the CREB-binding protein). The p300/CBP proteins occupy a pivotal role in regulating mitogenic signaling and apoptosis. The mechanisms by which cell cycle control genes are directly regulated by p300 remain to be determined. The cyclin D1 gene, which is overexpressed in many different tumor types, encodes a regulatory subunit of a holoenzyme that phosphorylates and inactivates PRB. In the present study E1A12S inhibited the cyclin D1 promoter via the amino-terminal p300/CBP binding domain in human choriocarcinoma JEG-3 cells. p300 induced cyclin D1 protein abundance, and p300, but not CBP, induced the cyclin D1 promoter. cyclin D1 or p300 overexpression inhibited apoptosis in JEG-3 cells. The CH3 region of p300, which was required for induction of cyclin D1, was also required for the inhibition of apoptosis. p300 activated the cyclin D1 promoter through an activator protein-1 (AP-1) site at -954 and was identified within a DNA-bound complex with c-Jun at the AP-1 site. Apoptosis rates of embryonic fibroblasts derived from mice homozygously deleted of the cyclin D1 gene (cyclin D1(-/-)) were increased compared with wild type control on several distinct matrices. p300 inhibited apoptosis in cyclin D1(+/+) fibroblasts but increased apoptosis in cyclin D1(-/-) cells. The anti-apoptotic function of cyclin D1, demonstrated by sub-G(1) analysis and annexin V staining, may contribute to its cellular transforming and cooperative oncogenic properties.


A quantitative LC/MS method targeting urinary 1-methyl-4-imidazoleacetic acid for safety monitoring of the global histamine turnover in clinical studies.
Anaphylaxis is a potentially life-threatening condition triggered mainly by the release of inflammatory mediators, notably histamine. In pharmaceutical research, drug discovery, and clinical evaluation, it may be necessary to accurately assess the potential of a compound, event, or disorder to promote the release of histamine. In contrast to the measurement of plasma histamine, determination of the stable metabolite 1-methyl-4-imidazoleacetic acid (tele-MIAA) in urine provides a noninvasive and more reliable methodology to monitor histamine release. This study presents a repeatable high-performance liquid chromatography coupled to electrospray mass spectrometry (LC-ESI-MS) method where tele-MIAA is baseline separated from its structural isomer 1-methyl-5-imidazoleacetic acid (pi-MIAA) and an unknown in human urine. The ion-pairing chromatography method, in reversed-phase mode, based on 0.5 mM tridecafluoroheptanoic acid demonstrated high repeatability and was applied in a clinical development program that comprised a large number of clinical samples from different cohorts. The inter- and intra-run precision of the method for tele-MIAA were 8.4 and 4.3%, respectively, at the mean urinary concentration level, while method accuracy was between -16.2 and 8.0% across the linear concentration range of 22-1,111 ng mL(-1). Overall, method precision was greater than that reported in previously published methods and enabled the identification of gender differences that were independent of age or demography. The median concentration measured in female subjects was 3.0 μmol mmol(-1) of creatinine, and for male subjects, it was 2.1 μmol mmol(-1) of creatinine. The results demonstrate that the method provides unprecedented accuracy, precision, and practicality for the measurement of tele-MIAA in large clinical settings.


Feature-by-feature--evaluating de novo sequence assembly.
The whole-genome sequence assembly (WGSA) problem is among one of the most studied problems in computational biology. Despite the availability of a plethora of tools (i.e., assemblers), all claiming to have solved the WGSA problem, little has been done to systematically compare their accuracy and power. Traditional methods rely on standard metrics and read simulation: while on the one hand, metrics like N50 and number of contigs focus only on size without proportionately emphasizing the information about the correctness of the assembly, comparisons performed on simulated dataset, on the other hand, can be highly biased by the non-realistic assumptions in the underlying read generator. Recently the Feature Response Curve (FRC) method was proposed to assess the overall assembly quality and correctness: FRC transparently captures the trade-offs between contigs' quality against their sizes. Nevertheless, the relationship among the different features and their relative importance remains unknown. In particular, FRC cannot account for the correlation among the different features. We analyzed the correlation among different features in order to better describe their relationships and their importance in gauging assembly quality and correctness. In particular, using multivariate techniques like principal and independent component analysis we were able to estimate the "excess-dimensionality" of the feature space. Moreover, principal component analysis allowed us to show how poorly the acclaimed N50 metric describes the assembly quality. Applying independent component analysis we identified a subset of features that better describe the assemblers performances. We demonstrated that by focusing on a reduced set of highly informative features we can use the FRC curve to better describe and compare the performances of different assemblers. Moreover, as a by-product of our analysis, we discovered how often evaluation based on simulated data, obtained with state of the art simulators, lead to not-so-realistic results.


Use of 5% imiquimod cream in the treatment of facial basal cell carcinoma: a 3-year retrospective follow-up study.
There has been considerable research into the safety and efficacy of topical 5% imiquimod cream for the treatment of skin cancers in recent years, in particular superficial and nodular basal cell carcinomas. However, there are limited long-term follow-up studies. This retrospective study aims to determine the efficacy of 5% imiquimod cream in the treatment of facial basal cell carcinomas over 3 years. Medical records of 12 patients treated with 5% imiquimod cream at a private dermatology practice during 2001 and 2002 were retrospectively reviewed. Target tumours included superficial and nodular basal cell carcinomas, giving a total lesion number of 19. Patients were commenced on a once daily treatment regimen for up to 9 weeks, and given rest periods as required according to the severity of application site reactions. We found that 5% imiquimod cream is an effective treatment option for superficial and nodular basal cell carcinomas, giving a clearance rate of 89.5% at an average of 39 months of follow up.


Systems approaches to optimizing deep brain stimulation therapies in Parkinson's disease.
Over the last 30 years, deep brain stimulation (DBS) has been used to treat chronic neurological diseases like dystonia, obsessive-compulsive disorders, essential tremor, Parkinson's disease, and more recently, dementias, depression, cognitive disorders, and epilepsy. Despite its wide use, DBS presents numerous challenges for both clinicians and engineers. One challenge is the design of novel, more efficient DBS therapies, which are hampered by the lack of complete understanding about the cellular mechanisms of therapeutic DBS. Another challenge is the existence of redundancy in clinical outcomes, that is, different DBS programs can result in similar clinical benefits but very little information (e.g., predictive models, longitudinal data, metrics, etc.) is available to select one program over another. Finally, there is high variability in patients' responses to DBS, which forces clinicians to carefully adjust the stimulation settings to each patient via lengthy programming sessions. Researchers in neural engineering and systems biology have been tackling these challenges over the past few years with the specific goal of developing novel DBS therapies, design methodologies, and computational tools that optimize the therapeutic effects of DBS in each patient. Furthermore, efforts are being made to automatically adapt the DBS treatment to the fluctuations of disease symptoms. A review of the quantitative approaches currently available for the treatment of Parkinson's disease is presented here with an emphasis on the contributions that systems theoretical approaches have provided to understand the global dynamics of complex neuronal circuits in the brain under DBS. This article is categorized under: Translational, Genomic, and Systems Medicine > Therapeutic Methods Analytical and Computational Methods > Computational Methods Analytical and Computational Methods > Dynamical Methods Physiology > Mammalian Physiology in Health and Disease.