cssi/SciSciGPT-SciSciNet huggingface dataset:
Purification and characterization of equine herpesvirus-induced DNA polymerase

Abstract Infection of cells with equine herpesvirus type 1 (EHV-1) or type 3 (EHV-3) resulted in the induction of a DNA polymerase activity distinguishable from host cell DNA polymerases by its high salt requirement for maximal activity. By column chromatography on DEAE-cellulose, DNA-cellulose, phosphocellulose, and hydroxyapatite, the EHV-1-induced polymerase was purified 500-fold with 1–2% recovery of total activity from the nuclei of infected hamster livers. The final enzyme preparation was homogeneous as judged by electrophoresis in sodium dodecyl sulfate-polyacrylamide gels. Calculations based on Stokes radius, sedimentation coefficient, and electrophoretic mobility indicated that the native enzyme is composed of a single subunit having a molecular weight of 160,000. The purified enzyme exhibited anomalous gel filtration behavior indicating molecular asymmetry. It required Mg 2+ , dithiothreitol, alkaline pH (8–9), all four deoxyribonucleoside triphosphates, and 150 m M salt [K 2 SO 4 , (NH 4 ) 2 SO 4 , or K 2 HPO 4 ] for maximal activity, and utilized templates in the following order of preference: activated DNA (100%), poly(dA)·oligo(dT) (40%), poly(dC)·oligo(dG) (21%), native DNA (7%), denatured DNA (4%), and poly(rA)·oligo(dT) (3%). N-Ethylmaleimide, Zn 2+ , and phosphonoacetate acted as inhibitors of the EHV-1-induced DNA polymerase. Antiserum elicited against the EHV-1 DNA polymerase induced in hamsters inactivated the viral enzyme from infected mouse and equine cell cultures. However, the DNA polymerase induced by EHV-3 and DNA polymerases present in uninfected cells were not inhibited by the antiserum. These results support the hypothesis that a new, virus-coded DNA polymerase is induced after equine herpesvirus infection.
CONTRIBUTIONS OF JOURNEYS AWAY TO THE DEFINITION OF HOME: AN EMPIRICAL STUDY OF A DIALECTICAL PROCESS

Abstract Theory about home holds that dialectical or contrasting experiences contribute to the definition and meaning of home. Journeys from home are considered an important source of these contrasting experiences. This study is an empirical assessment of this relationship. Using qualitative methods, 22 subjects representing 11 households were asked to relate their experiences and feelings about being away from home for both short- and long-term trips. Findings support the theoretical importance of dialectical experiences. Contrasts to daily household routine and interaction with other people that arise from the experience of being away from home are found to be important to the definition of home. People need to get out of their homes to appreciate the taken-for-granted order to life provided by daily household routine. People also need to be away to recognize that interaction with friends and neighbors is an important part of home life. While these results support the findings of prior research, they also provide empirical evidence for the phenomenological concept ‘being at home’.
Tree invasion within a pine/grassland ecotone: an approach with historic aerial photography and GIS modeling.

Abstract In previous studies, evidence of tree invasion into grasslands has mainly been through comparison of historical terrestrial photographs and/or tree age data. The goal of this paper is to provide a quantitative description of the tree invasion process at a landscape scale using historical aerial photography, image processing and geographic information systems (GIS) approaches. Various map interpretive techniques provided evidence of shifts in the ponderosa pine-grassland ecotone along the Colorado Front Range since the late 1930s. Historical aerial photos were digitally scanned and the outlines of tree invasions into the grassland were determined based on gray tone density slicing. Image processing of digitized aerial photography identified areas of change in tree cover and quantified locations and total hectares of tree invasions into grassland areas. Overall, the results clearly show an increase in woodland areas where there formerly existed grasslands. GIS modeling was used to relate tree invasion patterns to topographic orientation and changes in settlement patterns. The importance of terrain aspect on rate of tree invasion is clearly shown by the greater rate of tree invasion on north-facing slopes (generally moister with less heat stress) versus south-facing slopes. The most dramatic change in the controls of vegetation patterns over the past one or two centuries has been the decline in fire frequency due to fire suppressing policy since ca. 1920. However, changes in grazing regimes may also have played an important role. When comparing these results to the instrumental climate record of the area, periods of favorable climatic conditions for seedling establishment generally correspond to periods of increased rate of tree invasion into grassland areas.
How powdered cocaine flows across the United States: Evidence from open-source price data

Patterns of flows of cocaine across the United States are identified using open-source price data. The data set consists of wholesale prices for powdered cocaine for 112 U.S. cities published biannually by the National Drug Intelligence Center (NDIC) between 2002 and 2011. For each of the 6,126 possible unique pairs of cities in the sample, cocaine is inferred to flow from the city with the lower price to the city with the higher price if the prices in the two cities show a correlation that exceeds a threshold value. This threshold value is calibrated using data on anecdotal city-to-city flows published by the U.S. Department of Justice. The results show a striking pattern of cocaine flows from the south and west of the United States to the north and east. A cluster analysis of cities based on inward and outward links is used to classify each city as a “source,” “destination,” “transit,” or “isolate.”
Relationships between scattering matrix and other matrix representations of linear two-port networks

The paper presents explicit inter-relationships of the elements of the all-p normalized scattering matrix representation and other matrices of the voltage-current representation of a linear two-port network.
Quark self-energy in the chiral bag

Abstract Confined quark and excluded pion surface eigenfunctions are constructed to study the chiral bag perturbatively. Due to the unconventional surface pion coupling, the second order quark self-energy is numerically found to be linearly divergent even for massless quarks.
Mating increases plasma levels of prostaglandin F2α in female garter snakes

Abstract Plasma levels of prostaglandin F 2α (PGF 2α ) in female red-sided garter snakes ( Thamnophis sirtalis parietalis ) were measured at intervals after mating or exposure to males. PGF 2α levels increased significantly within 15 minutes of mating and peaked 6–24 hr after mating. Females that did not mate, but received similar amounts of male courtship, had levels of PGF 2α significantly lower than those of females that mated. These results extend previous findings that unmated female garter snakes injected with PGF 2α exhibit sexual behavior characteristics of females that have mated. Together these data indicate that female garter snakes elaborate PGF 2α in response to stimuli associated with mating and that PGF 2α has a functional role in inducing post-mating declines in sexual behavior of this species.
Potato clone variation in blackspot and soft rot susceptibility, redox potential, ascorbic acid, dry matter and potassium

Tubers of 11 potato clones were compared for susceptibility to blackspot and soft rot, redox potential, ascorbic acid, dry matter, and potassium content. Evaluations were made before and after 6 mo storage at 3.9C. Clonal behavior was generally consistent over 2 yr. Significant differences occurred among clones for each factor except redox potential.
Use of relative reaction rates of CO and H2 as a measure of micro-mixing in combustion systems

Abstract A technique is proposed for the characterization of the intensity of micromixing in well-stirred, homogeneous chemical reactors used to carry out fast, gaseous-phase reactions. This involves allowing the competitive combustion of a lean feed mixture of carbon monoxide and hydrogen in air to take place in the reactor. The ratio of the concentrations of the two reactants, CO and H2, in the system is to be measured and its value, which will be higher than that of the feed due to the difference in reaction rates, used to infer the degree of micromixing by comparison with computational predictions. A simple population-balance model and a detailed kinetic scheme are employed to explore the range of usefulness of the suggested procedure and demonstrate its practical applicability in producing meaningful assessments of mixing in real systems.
Structure of "triplet" superconducting energy gaps

Application of group theory to the "triplet" superconducting states in metals is discussed with special attention to the explanation of experimental phenomena on "heavy-electron" superconductors. It is shown that naive extrapolation from the case of$^{3}\mathrm{He}$ is not justifiable.
Tensile modulus modeling of carbon-filled nylon 6,6 and polycarbonate-based resins

Electrically and thermally conductive resins can be produced by adding conductive fillers to insulating polymers. Mechanical properties, such as tensile modulus, are also important. This research focused on performing compounding runs followed by injection molding and tensile testing of carbon-filled nylon 6,6 and polycarbonate-based resins. The three carbon fillers investigated included an electrically conductive carbon black, synthetic graphite particles, and a milled pitch–based carbon fiber. For each polymer, resins were produced and tested that contained varying amounts of these single-carbon fillers. In addition, combinations of fillers were investigated by conducting a full 23 factorial design and a complete replicate in each polymer. These tensile modulus experimental results were then compared to results predicted by several different models. For the composites containing only one filler type, the Nielsen model with the modified Ψ term provided the best prediction of the actual experimental values. For the composites containing more than one filler type, a new parameter, which includes the vibrated bulk density (VBD) of the fillers, was incorporated into the Nielsen model with the modified Ψ term. This model with the new VBD parameter provided the best estimate of experimental tensile modulus for composites containing multiple-filler types. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 1716–1728, 2003
Stochastic Modeling of Daily Summertime Rainfall over the Southwestern United States. Part I: Interannual Variability

Abstract The interannual variability of summertime daily precipitation at 78 stations in the southwestern United States is studied using chain-dependent models and nonparametric empirical distributions of daily rainfall amounts. Modeling results suggest that a second-order chain-dependent model can optimally portray the temporal structure of the summertime daily precipitation process over the southwestern United States. The unconditioned second-order chain-dependent model, in turn, can explain approximately 75% of the interannual variance in the seasonal total wet days over the region and 83% of the interannual variance in the seasonal total precipitation. In addition, only a small fraction (generally smaller than 20%) of the observed years at any given station show statistically significant changes in the occurrence and intensity characteristics, related to either the number of seasonal total wet days or the distributions of daily rainfall amounts. Investigations of the year-to-year variations in the occ...
Metabolic abnormalities in adolescent patients with anorexia nervosa

The intake laboratory data of 46 patients seen between 1970 and 1980 who were 36 International Units/liter (IU/L), and 65% (27/41) had alkaline phosphatase levels
Pair production via crossed lasers

The intrinsically nonperturbative vacuum persistence probability P for e+ e- production in the overlap region of a pair of high-intensity lasers is estimated in the context of three models, each of which adapt and simplify the exact Fradkin representation for the logarithm of the fermion determinant in the fields of the crossed lasers. In each case, one finds for P an expression resembling Schwinger's 1951 result for the probability of pair production in a constant electric field, proportional to an exponential factor which contains an essential singularity and hence does not admit a perturbative expansion about zero coupling. Qualitative estimates of these models suggest that realistic yields for this form of e+ e- production must await lasers of intensity 10 29 W/m 2 . The possibility of producing a quark-antiquark pair in this way is noted, in particular, with temporary, but large separations of the qq.
Determining Acceptance of Domestic Forage‐ or Grain‐Finished Beef by Consumers from Three Southeastern U.S. States

Twenty-six crossbred steers were finished either on ryegrass (Lolium multiflorum Lam.) forage (FOR, n= 13) or a primarily grain diet containing 85% corn, 7.5% cotton-seed hulls, and 7.5% vitamin/mineral/urea supplement (GRAIN, n= 13) to determine the consumer acceptance of forage- and grain-finished beef in 3 southeastern states. Shear force values were not affected by finishing treatment (P= 0.62), and both total and heat-labile collagen content means of the FOR and GRAIN steaks were similar (P= 0.88 and 0.14, respectively). Ribeye steaks were cut from wholesale roasts after 14 d of aging and were evaluated by 1250 consumers in a retail study and 87 consumers in a take-home study across Alabama, Tennessee, and Kentucky. Retail consumers rated GRAIN steaks higher for flavor (P= 0.001), overall palatability (P= 0.001), and price per kg (P= 0.001) compared to FOR steaks, but consumers in the take-home study found no differences in any of the 3 traits. Consumers that preferred FOR steaks were willing to pay an average of $2.38/kg and $5.61/kg more for FOR steaks than for GRAIN steaks in the retail and take-home studies, respectively (P= 0.001). Among consumers surveyed across all 3 states, 34.1% of retail consumers and 54.0% of take-home consumers preferred FOR steaks. At least one-third of the consumers surveyed preferred the taste of forage-finished beef and were willing to pay a premium.
A reversibility analysis of encoding methods for spiking neural networks

There is much excitement surrounding the idea of using spiking neural networks (SNNs) as the next generation of function-approximating neural networks. However, with the unique mechanism of communication (neural spikes) between neurons comes the challenge of transferring real-world data into the network to process. Many different encoding methods have been developed for SNNs, most temporal and some spatial. This paper analyzes three of them (Poisson rate encoding, Gaussian receptor fields, and a dual-neuron n-bit representation) and tests to see if the information is fully transformed into the spiking patterns. An oft-neglected consideration in encoding for SNNs is whether or not the real-world data is even truly being introduced to the network. By testing the reversibility of the encoding methods in this paper, the completeness of the information's presence in the pattern of spikes to serve as an input to an SNN is determined.
Controlling the Spacing of Streamwise Vortices on Concave Walls

The wavelength of Gortler streamwise vortices changed by a factor of three by varying the amount of tunnel side wall boundary-layer removal just upstream of the concave wall test section's leading edge. Nondimensional wavelengths were achieved with the larger wavelengths resulting from increased suction. The minimum wavelength compares well with the maximum amplification curve based on past theoretical studies. Low-speed streaks appeared to merge with other low-speed streaks or were weakened to the point of disappearing as the suction level was increased. The downstream location of secondary instability onset changed with variation in suction level and/or wavelength. The Gortler number and amplification factor for secondary instability onset, however, was approximately independent of suction level and/or wavelength.
Point: Antibiotic Therapy Is Not the Answer for Patients with Persisting Symptoms Attributable to Lyme Disease

It is not well understood why some patients develop a subjective syndrome that includes considerable fatigue, musculoskeletal aches, and neurocognitive dysfunction after receiving standard antibiotic courses for the treatment of Lyme disease. Some practitioners use the term "chronic Lyme disease" and order prolonged courses of oral and parenteral antibiotics, believing that persistent infection with Borrelia burgdorferi is responsible. However, well-performed prospective studies have found neither evidence of chronic infection nor a benefit worthy of long-term antibiotic therapy for these patients. Such extended antibiotic therapy poses hazards and cannot be viewed as acceptable. The term "chronic Lyme disease" should be discarded as misleading; rather, the term "post-Lyme disease syndrome" better reflects the postinfectious nature of this condition. Further research is necessary to understand possible mechanisms of these chronic symptoms following Lyme disease as well as to find effective therapies.
Acid-citrate-dextrose Formula A versus heparin as primary catheter lock solutions for therapeutic apheresis

Background Unfractionated heparin (UFH) is a commonly used catheter lock solution, but may lead to various complications. Acid-citrate-dextrose Formula A (ACD-A), the standard anticoagulant used in therapeutic apheresis (TA), is an alternative. We compared the efficacy of these two anticoagulants as primary catheter lock solutions. Study Design and Methods The following outcomes were analyzed retrospectively for all TA procedures performed between July 2009 and March 2012: patent, partial occlusion, total occlusion, catheter-related blood stream infection, tissue plasminogen activator use, and premature catheter removal. Results Our primary data set included 5964 total catheter days, 3020 procedures, and 427 TA courses. The UFH group comprised 3444 catheter days and 1880 procedures; the ACD-A group, 2520 catheter days and 1140 procedures. Overall catheter-related outcomes differed by not more than 5.3% for the primary analysis and when stratified by short-term (≤10 days) duration or short dwell times ( 10 days) and long dwell times (>3 days), differences increased to not more than 10.4 and 22.4%, respectively. Conclusions For short-term courses and short dwell times, UFH and ACD-A appear equally effective; UFH appears superior to ACD-A in the setting of long-term courses and long dwell times. Major catheter-related complications were rare and occurred with similar frequency in both groups. For most indications, ACD-A appears to be a reasonable alternative to heparin; however, an adequately powered, randomized trial would be required to definitively address this issue.
Ability to pay for maternal health services: what will it take to meet who standards?

High maternal morbidity and mortality in many developing countries are highly associated with poor access to and quality of health care. Here we review the economic feasibility of the WHO’s mother–baby package as a means of reducing maternal and neonatal mortality and morbidity in Tanzania. This paper examines the costs of maternal health care in Tanzania, and how much can we expect households to contribute to these expenses, if the MBP were implemented. Using data from the Tanzanian 1993 Living Standard Measurement Survey (LSMS), we analyze responses from 757 women of reproductive age who have had a birth in the 12 months preceding the survey. We estimate current spending on maternal health care by different socio-economic groups and its share in relation to total household expenditures. Using logistic regression analyses, we examine the effect of the prices paid for maternal health care on the likelihood of using antenatal and safe delivery services, controlling for relevant socio-economic and demographic factors. Results show that if the MBP recovered 100% of its costs, most of the households would have to allocate more than half of their annual consumption on maternal health care. Poor socio-economic groups would experience the greatest increase in service utilization if MBP care were subsidized. In the face of scarce resources, subsidies should be targeted according to socio-economic group, in order to attain equitable and sustainable maternal health services. © 2004 Elsevier Ireland Ltd. All rights reserved.
Construction and Evaluation of Novel Rhesus Monkey Adenovirus Vaccine Vectors

Adenovirus vectors are widely used as vaccine candidates for a variety of pathogens, including HIV-1. To date, human and chimpanzee adenoviruses have been explored in detail as vaccine vectors. The phylogeny of human and chimpanzee adenoviruses is overlapping, and preexisting humoral and cellular immunity to both are exhibited in human populations worldwide. More distantly related adenoviruses may therefore offer advantages as vaccine vectors. Here we describe the primary isolation and vectorization of three novel adenoviruses from rhesus monkeys. The seroprevalence of these novel rhesus monkey adenovirus vectors was extremely low in sub-Saharan Africa human populations, and these vectors proved to have immunogenicity comparable to that of human and chimpanzee adenovirus vaccine vectors in mice. These rhesus monkey adenoviruses phylogenetically clustered with the poorly described adenovirus species G and robustly stimulated innate immune responses. These novel adenoviruses represent a new class of candidate vaccine vectors. IMPORTANCE Although there have been substantial efforts in the development of vaccine vectors from human and chimpanzee adenoviruses, far less is known about rhesus monkey adenoviruses. In this report, we describe the isolation and vectorization of three novel rhesus monkey adenoviruses. These vectors exhibit virologic and immunologic characteristics that make them attractive as potential candidate vaccine vectors for both HIV-1 and other pathogens.
Associations between depressive symptoms and inflammatory/hemostatic markers in women during the menopausal transition.

OBJECTIVE To test whether depressive symptoms are related to inflammatory and hemostatic markers in women approaching menopause. METHODS A total of 3292 women enrolled in the Study of Women's Health Across the Nation (SWAN) were followed for five years and had measures of Center for Epidemiologic Studies-Depression and high sensitivity C-reactive protein, Factor VIIc, fibrinogen, plasminogen activator inhibitor Type 1(PAI-1), and tissue-type plasminogen activator antigen (tPA-ag) up to four times during the follow-up period. Women were pre- or early perimenopausal status at study entry and were of Caucasian, African American, Hispanic, Japanese, or Chinese race/ethnicity. RESULTS Unadjusted longitudinal mixed regression models showed that over a 5-year period, higher depressive symptoms were related to higher fibrinogen, PAI-1, and tPA-ag levels, all p < .0001. Taking into account health history, medication use, ethnicity, aging, and menopausal status, the depressive symptoms were related to fibrinogen, p < .01, and PAI-1, p < .05. Depressive symptoms were related only to fibrinogen in models that also included body mass index, p < .05. CONCLUSIONS Depressive symptoms may be associated with cardiovascular risk in perimenopausal women in part through hypercoagulability. This is the first study to test the association of depressive symptoms and hemostatic and inflammatory markers across time.
Exploiting reconfigurability for low-cost in-situ test and monitoring of digital PLLs

We exploit the reconfigurability of recent all-digital PLL designs to provide novel in-situ output jitter test and diagnosis abilities under multiple parametric variations of key analog building blocks. Digital signatures are collected and processed under specifically designed loop filter configurations to facilitate low-cost high-accuracy performance prediction and diagnosis.
Intrapleural Alteplase in a Patient with Complicated Pleural Effusion

OBJECTIVE:To report the intrapleural use of alteplase in a patient diagnosed with complicated pleural effusion (CPE).CASE SUMMARY:A 62-year-old white woman admitted with respiratory distress and hypotension developed a right-sided multi-loculated pleural effusion. Thoracentesis and chest tube drainage were not successful in resolving the effusion. In an attempt to increase the drainage of the pleural effusion, alteplase 16 mg was administered into the pleural cavity via the chest tube on 6 consecutive days. As a result, the volume drained from the patient's chest tube increased, there was improvement on the chest X-ray, and she did not require surgical intervention.DISCUSSION:While streptokinase and urokinase have been shown to be useful adjuncts to chest tube drainage in the treatment of complicated pleural effusion and empyema, there have been no reports on the use of intrapleural alteplase. This report demonstrates that intrapleural administration of alteplase is a useful adjunct to tube drainage in re...
Multilocus variable-number tandem repeat analysis as a molecular tool for subtyping and phylogenetic analysis of bacterial pathogens.

Tandem repeat (TR) loci are abundant in both prokaryotic and eukaryotic genomes. TRs could be polymorphic in the number of repeats across strains. The polymorphic loci, referred to as variable-number TR (VNTR) loci, may have two to tens of alle-les across a population. Thus, combined multiple VNTRs can, theoretically, gener-ate a large number of genotypes. VNTRs mutate at a wide range of rates, ranging from 10
Intraoperative use of platelet-plasmapheresis in vascular surgery.

Abstract Study Objective: To determine, in a pilot study, whether pheresis of plasma and platelets before surgical blood loss, with reinfusion of the autologous plasma and platelets after completion of the aortic reconstruction, will result in decreased bleeding and decreased transfusion of allogenic blood components in patients undergoing elective aortic reconstruction. Design: Randomized study. Setting: University medical center. Interventions: Patients were randomized to perioperative (acute) platelet plasmapheresis (APP group) versus conventional blood component therapy (control group). In the APP group, blood was withdrawn after induction of anesthesia, to sequester approximately 300 mL of platelet rich plasma (PRP); platelet poor plasma (PPP) and red blood cells (RBC) were sequestered as well. An autotransfusion device was used to collect and re-infuse autologous RBC during the course of the operation in both groups. After completion of the aortic reconstruction, autologous PRP and PPP were re-infused in the APP group. Blood loss, volume of blood component transfusions, and preoperative and postoperative hemoglobin (Hb), hematocrit (Hct), platelet, international normalized ratio (INR), and activated partial thromboplastin time (aPTT) were recorded. Measurements and Main Results: There was no difference between groups in demographics, preoperative laboratory values, or surgical procedures, although more patients were treated for aneurysms (73% vs . 60%) and fewer for occlusive disease (20% vs . 40%) in the control versus APP group. Also, there were no differences between the control and APP groups in duration of operation, blood loss, volume of colloid infused, or volume of allogenic RBC and plasma transfused. Patients in the APP group received a greater volume of crystalloid solution (9.1 ± 3.4 L vs. 6.8 ± 3.0 L; p = 0.002), but fewer units of allogenic platelets than the control group (0.7 ± 1.0 units vs . 0.2 ± 0.4 units; p 3 / mm 3 vs. 182 ± 51 × 10 3 / mm 3 ; p = 0.004). Conclusions: Perioperative platelet plasmapheresis led to fewer allogenic platelet transfusions in patients undergoing elective aortic reconstruction. However, there was no decrease in blood loss and no reduction in transfusion of allogenic RBC or plasma. Perioperative platelet plasmapheresis is not recommended for routine use in elective aortic reconstruction.
Teaching Communication Skills in the Software Engineering Curriculum

Communication - between humans - remains at the heart of software development. This workshop will serve as a forum for those invested in this topic to articulate challenges and solutions, and to build links for further work.
Small molecule inhibitor of the bone morphogenetic protein pathway DMH1 reduces ovarian cancer cell growth

The bone morphogenetic protein (BMP) pathway belonging to the Transforming Growth Factor beta (TGFβ) family of secreted cytokines/growth factors is an important regulator of cancer. BMP ligands have been shown to play both tumor suppressive and promoting roles in human cancers. We have found that BMP ligands are amplified in human ovarian cancers and that BMP receptor expression correlates with poor progression-free-survival (PFS). Furthermore, active BMP signaling has been observed in human ovarian cancer tissue. We also determined that ovarian cancer cell lines have active BMP signaling in a cell autonomous fashion. Inhibition of BMP signaling with a small molecule receptor kinase antagonist is effective at reducing ovarian tumor sphere growth. Furthermore, BMP inhibition can enhance sensitivity to Cisplatin treatment and regulates gene expression involved in platinum resistance in ovarian cancer. Overall, these studies suggest targeting the BMP pathway as a novel source to enhance chemo-sensitivity in ovarian cancer.
Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

We review existing methods for the analysis of RNA-Seq data and place them in a common framework of a sequence of tasks that are usually part of the process. We show that many existing methods produce large numbers of false positives in cases where the null hypothesis is true by construction and where actual data from RNA-Seq studies are used, as opposed to simulations that make specific assumptions about the nature of the data. We show that some of those mathematical assumptions about the data likely are one of the causes of the false positives, and define a general structure that is not apparently subject to these problems. The best performance was shown by limma-voom and by some simple methods composed of easily understandable steps.
Role of glia in memory deficits following traumatic brain injury: biomarkers of glia dysfunction

Historically, glial cells have been recognized as a structural component of the brain. However, it has become clear that glial cells are intimately involved in the complexities of neural networks and memory formations. Astrocytes, microglia, and oligodendrocytes have dynamic responsibilities which substantially impact neuronal function and activities. Moreover, the importance of glia following brain injury has come to the forefront in discussions to improve axonal regeneration and functional recovery. The numerous activities of glia following injury can either promote recovery or underlie the pathobiology of memory deficits. This review outlines the pathological states of glial cells which evolve from their positive supporting roles to those which disrupt synaptic function and neuroplasticity following injury. Evidence suggests that glial cells interact extensively with neurons both chemically and physically, reinforcing their role as pivotal for higher brain functions such as learning and memory. Collectively, this mini review surveys investigations of how glial dysfunction following brain injury can alter mechanisms of synaptic plasticity and how this may be related to an increased risk for persistent memory deficits. We also include recent findings, that demonstrate new molecular avenues for clinical biomarker discovery.
Fluorescence-tagged monolignols: synthesis, and application to studying in vitro lignification.

Fluorescence-tagged coniferyl alcohols, coniferyl alcohol γ-coupled by ethylenediamine spacers to dimethylaminocoumarin or nitrobenzofuran fluorophores, were tested as photoprobes to study the oxidase-mediated polymerization of monolignols. The fluorescent coniferyl alcohol derivatives readily underwent peroxidase-catalyzed in vitro copolymerization with coniferyl alcohol to yield fluorescent dehydrogenation polymers, the backbone polymers of which were structurally indistinguishable from polymers formed solely from coniferyl alcohol. To illustrate the use of the photoprobes, we successfully monitored in real time the complexation of coniferyl alcohol with horseradish apoperoxidase by Forster resonance energy transfer (FRET) using the protein-tryptophan near the active site and a dimethylaminocoumarin moiety as donor and acceptor fluorophores. Furthermore, mixtures of fluorescence-tagged and normal coniferyl alcohols readily diffused into isolated maize cell walls and reacted with wall-bound peroxidases to form in muro artificial lignins that could be visualized by fluorescence microscopy. Thus we anticipate that fluorescence-tagged monolignols will be useful for in vitro and in vivo studies of cell wall lignification.
Policy Note: Toward an Institutional Legitimation of Sustainability

We present a three-fold test for sustainability on policies addressing environmental and natural resource management. The first — ecological holism — requires that management of natural systems not only ensure the long term viability of ecosystem functions and enhanced diversity of wildlife within that ecosystem, but also facilitate the provision of renewable energy and material resources. The second — community centeredness — is an assessment of the improvement (or reduction) in economic wellbeing of local populations measured by employment and income and in quality of life for the larger community resulting from that policy. The third — institutional legitimacy — evaluates the level of justice that a policy and its outcome(s) bring to the entire community (here, just policies will satisfy Rawls's "veil of ignorance" test). Three policies for National Forest management on Washington's Olympic Peninsula are examined and results are compared: the Northwest Forest Plan, the Wild Olympics Wilderness and Scen...
Abstract 5475: Cancer exosome promotes cisplatin resistance In bladder cancer and inhibition of exosome sensitizes bladder cancer cells to cisplatin chemotherapy

Exsosomes are nano-vesicles secreted by most types of cells, and substantially increased secretion in cancer cells. Their role in tumorigenesis/cancer progression have been extensively studied but their role in regulating therapy response have been suggested without in depth investigation. We are particularly interested in exosome9s roles in cisplatin resistant, since cisplatin is one of the most widely used chemodrugs for many cancer types. To investigate the role of exosomes in cisplatin resistance in bladder cancer, we examined the cisplatin sensitivity among five bladder cancer cell lines. The expression levels of exosome associated genes that are involved in exosome biogenesis and secretion/internalization were examined by quantative PCR. Interestingly, cisplatin resistant bladder cancer cells express relative high level of exosome associated genes as compared to cisplatin sensitive cells. More importantly, cisplatin treatment induces the expression of exosome associated genes’ expression in cisplatin resistant cells, but not in sensitive cell. Among all those genes, we are particularly interested in Rab gene family, and mechanistic study of targeting those Rab proteins is undergoing. The correlative exosome genes profiles with cisplatin resistance suggested exosome production might facilitate cancer cells escaping from cisplatin-induced cell death; thereby, inhibition of exosome might sensitize cancer cells response to cisplatin. To test this, we have screened several compounds that are known to inhibit exosome biogenesis and uptake, and. found that inhibition of exosomes by dynasore + NSC23766, indeed can sensitize bladder cancer cells to cisplatin. In summary, we concluded that cancer exosome play a critical role of promoting cisplatin resistance in bladder cancer, and inhibition of exosomes sensitizes bladder cancer cell response to cisplain. The exosome related profiles potentially can serve as therapy biomarkers Citation Format: Chiahao Wu, Chris Silvers, Elizabeths Guancial, Jong-Wei Hsu, Edward Messing, Yi-Fen Lee. Cancer exosome promotes cisplatin resistance In bladder cancer and inhibition of exosome sensitizes bladder cancer cells to cisplatin chemotherapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5475. doi:10.1158/1538-7445.AM2015-5475
Protein kinase A phosphorylation is involved in regulated exocytosis of aquaporin-2 in transfected LLC-PK1 cells

Vasopressin-dependent translocation of aquaporin-2 (AQP2) between intracellular vesicles and the plasma membrane has been demonstrated in vivo and in vitro. Furthermore, the vasopressin-induced increase in apical membrane water permeability of renal principal cells is dependent on a rise in intracellular adenosine 3',5'-cyclic monophosphate and activation of protein kinase A (PKA). To determine whether trafficking of AQP2 is dependent on PKA phosphorylation, we first examined the effect of the PKA-inhibitor N-(2[[3-(4-bromophenyl)-2-propenyl]-amino]-ethyl)-5-isoquinolinesulfonam ide (H-89) on AQP2 translocation in transfected LLC-PK1 cells. Vasopressin-induced membrane insertion of AQP2 was completely inhibited by pretreatment of the cells for 60 min with H-89. This reagent also caused a dense accumulation of AQP2 in the Golgi region. Next, LLC-PK1 cells were stably transfected with AQP2 cDNA in which the PKA phosphorylation site, Ser256, was replaced with alanine (S256A). S256A-AQP2 was not phosphorylated in vitro by PKA, and S256A-AQP2 was mainly localized to intracellular vesicles in the basal condition, similar to wild-type AQP2. However, after stimulation with vasopressin or forskolin, the cellular distribution of S256A-AQP2 remained unchanged. In addition, the usual vasopressin-induced increase in endocytosis seen in AQP2-transfected cells was not observed in S256A-AQP2-transfected cells. These results demonstrate that the Ser256 PKA phosphorylation site is possibly involved in the vasopressin-induced trafficking of AQP2 from intracellular vesicles to the plasma membrane and in the subsequent stimulation of endocytosis.
Reversible Acid-Activation of Inactive Renin: Evidence Favouring a Unimolecular Reaction

1. Purified inactive renin from human kidney or plasma was activated to a similar extent by incubation with trypsin or by dialysis to pH 3.3. 2. Trypsin- or acid-activated inactive renin was like active renal renin in terms of pH optimum (pH 5.5-6.0) and inhibition by mono-specific antibody. The apparent Km of homologous angiotensinogen for acid-activated inactive renin (1.11 μmol/l) was the same as for trypsin-activated inactive renin (1.12 μmol/l) or active renal renin (1.07 μmol/l). 3. In contrast with trypsin-activated renin, acid-activated renin was reversibly inactivated in a time-dependent manner during incubation at 37°C above pH 5. The maximal rate of reversal occurred in the pH 7–8 range. Reversal was prevented by prior incubation with trypsin, plasmin, glandular kallikrein or plasma kallikrein. 4. By kinetic analysis, the reversal of activation was found to be a first-order decay process with a reaction half-time (7–8 min at 37°C, pH 7.4) that was independent of the initial concentration of activated enzyme. 5. These results indicate that reversible acid-activation of inactive renin is a unimolecular reaction, consistent with the hypothesis that acid pH induces a conformational change in a single polypeptide chain.
PREPARATION OF FILTRATE REDUCER FOR CE-MENT SLURRY SULFONATE POLYSTYRENE AND ITS PROPERTY STUDY

The sulfonated polystyrene (SPS) has been prepared by sulfonation reaction of the polystyrene, which is used as a filtrate reducer for oil well cement slurry. In addition, we have studied the influence of reaction condition on sulfonate value, the relationship between the amount of API filtrate and sulfonate value and the influence of the SPS on cement sIurry's properties. Resuits have shown that the amount of API filtrate becomes less with the higher sulfonate value of SPS under the same conditions; the prepared SPS has good control over API filtrate; the cement slurry added the SPS becomes well flowable and more thermostable; the. thickening time can be adjusted to 337 min under 120℃ by the regular retarder. The SPS has been proved to have no side effects on cement slurry's other properties.
Aldosterone in vascular and metabolic dysfunction.

Purpose of review This review will highlight recent developments in mineralocorticoid receptor research which impact aldosterone-associated vascular and cardiometabolic dysfunction. Recent findings The mineralocorticoid receptor is also expressed in vascular smooth muscle and vascular endothelium, and contributes to vascular function and remodeling. Adipocyte-derived leptin stimulates aldosterone secretion, which may explain the observed link between obesity and hyperaldosteronism. Adipocyte mineralocorticoid receptor overexpression produces systemic changes consistent with metabolic syndrome. Ongoing studies with novel nonsteroidal mineralocorticoid receptor antagonists may provide a novel treatment for diabetic nephropathy and heart failure in patients with chronic kidney disease, with reduced risk of hyperkalemia. Summary Ongoing research continues to demonstrate novel roles of the vascular and adipocyte mineralocorticoid receptor function, which may explain the beneficial metabolic and vascular benefits of mineralocorticoid receptor antagonists.
Bacterial Characteristics and Follicle Surface Structure: Their Roles in Peyer’s Patch Uptake and Transport of Vibrio cholerae

Structural and functional specializations in the intestinal mucosal barrier over Peyer’s patches facilitate contact with and uptake of adherent luminal particles and soluble molecules. These specializations include local reduction in mucus-secreting goblet cells, interruption of the muscularis mucosae by lymphoid follicles(which may alter mucosal motility), and the presence of M cells. M cells are epithelial cells with irregular, widely spaced microvilli, reduced or absent lysosomes, an active transcellular transport system, and a pliable basolateral surface usually invaginated by lymphoid cells. At their luminal surfaces M cells form coated and uncoated vesicles, which are transported to intercellular spaces in the follicle epithelium where initial contact of intestinal antigen and lymphoid cells occurs. The mucus blanket which lies across the microvilli of enterocytes (intestinal absorptive cells) is broken over M cells, allowing microorganisms and particles to approach M cell luminal membranes. Studies with labeled lectins have demonstrated a thin but detectable glycocalyx coat on M cell membranes. Sugars detected by these lectins include beta-D-galactose (Ricinus communis agglutinin), sialic acid and N-acetyl-D-glucosamine (wheat germ agglutinin), but not alpha-D-mannose or alpha-D-glucose (Con A binds only sparsely). Cationized ferritin distributes evenly on M cell luminal membranes indicating that anionic sites are present.
Lineage Relationships Do Not Drive MGE/PoA-Derived Interneuron Clustering in the Brain.

Summary Neocortical excitatory and inhibitory neurons derive from distinct progenitor domains during embryonic development and migrate to their final positions, where they assemble into functional circuits. This process appears to be influenced by lineage relationships among locally born excitatory neurons, raising the intriguing possibility that this might be true for cortical interneurons. Two recent articles by the Fishell laboratory and our own used retrovirus-encoded DNA barcodes as unambiguous lineage-tracing tools to address this question, finding that clonally related inhibitory interneurons dispersed widely across the forebrain (Harwell et al., 2015; Mayer et al., 2015). This Matters Arising Response addresses the Sultan et al. (2016) Matters Arising paper, published concurrently in Neuron , where the authors reanalyze the datasets from both studies and propose a new interpretation, whereby clonally related interneurons would be considered clustered according to specific spatial constraints. After studying the report from Sultan et al. (2016) and carefully revisiting previously published studies, we find no evidence of lineage-dependent MGE/PoA-derived interneuron clustering in the forebrain.
Requirement and Irresolution: Language and Art Learning

Recent changes in art teacher certification requirements in New York, the state in which I teach, have prompted me to reconsider relationships between language, contemporary art, and art education....
Effects of fosaprepitan (Fosa) on ifosfamide (Ifex) metabolism in sarcoma patients (pts) receiving multi-day chemotherapy (CT) regimen on doxorubicin (Dox) and Ifex (AI): Randomized, cross-over study.

e20714 Background: AI is highly emetogenic regimen. Single dose Fosa with 5HT3RA and dexamethasone has improved the CINV control. However, delayed N/V is problematic. This study aimed to examine th...
Distance-Based Construction Behaviors for Dynamic Grid-Based Worlds

This paper proposes a method for the development of AI for autonomous agents in game worlds modeled by fixed regular grids. This approach uses context behaviors driven by distance maps to support multiple agents in a dynamic environment. This paper introduces the notion of hierarchical distance maps which allow for higher-level goals to be easily specified by designers. We also discuss potential applications of our approach in the design and development of agents and behaviors in the block world genre.
Fire, ice, water, and dirt: A simple climate model

A simple paleoclimate model was developed as a modeling exercise. The model is a lumped parameter system consisting of an ocean (water), land (dirt), glacier, and sea ice (ice) and driven by the sun (fire). In comparison with other such models, its uniqueness lies in its relative simplicity yet yielding good results. For nominal values of parameters, the system is very sensitive to small changes in the parameters, yielding equilibrium, steady oscillations, and catastrophes such as freezing or boiling oceans. However, stable solutions can be found, especially naturally oscillating solutions. For nominally realistic conditions, natural periods of order 100kyrs are obtained, and chaos ensues if the Milankovitch orbital forcing is applied. An analysis of a truncated system shows that the naturally oscillating solution is a limit cycle with the characteristics of a relaxation oscillation in the two major dependent variables, the ocean temperature and the glacier ice extent. The key to getting oscillations is having the effective emissivity decreasing with temperature and, at the same time, the effective ocean albedo decreases with increasing glacier extent. Results of the original model compare favorably to the proxy data for ice mass variation, but not for temperature variation. However, modifications to the effective emissivity and albedo can be made to yield much more realistic results. The primary conclusion is that the opinion of Saltzman [Clim. Dyn. 5, 67-78 (1990)] is plausible that the external Milankovitch orbital forcing is not sufficient to explain the dominant 100kyr period in the data.