cssi/SciSciGPT-SciSciNet huggingface dataset:
DNA microarray technology: The anticipated impact on the study of human disease

One can imagine that, one day, there will be a general requirement that relevant array data be deposited, at the time of publication of manuscripts in which they are described, into a single site made available for the storage and analysis of array data (modeled after the GenBank submission requirements for DNA sequence information). With this system in place, one can anticipate a time when data from thousands of gene expression experiments will be available for meta-analysis, which has the potential to balance out artifacts from many individual studies, thus leading to more robust results and subtle conclusions. This will require that data adhere to some type of uniform structure and format that would ideally be independent of the particular expression technology used to generate it. The pros and cons of various publication modalities for these large electronic data sets have been discussed elsewhere [12], but, practical difficulties aside, general depositing must occur for this technology to reach the broadest range of investigators. Finally, as mentioned at the beginning of this review, it is unfortunate that this important research tool remains largely restricted to a few laboratories that have developed expertise in this area and to a growing number of commercial interests. Ultimately the real value of microarray technology will only be realized when this approach is generally available. It is hoped that issues including platforms, instrumentation, clone availability, and patents [20] will be resolved shortly, making this technology accessible to the broadest range of scientists at the earliest possible moment.
Multi-wavelength impacts on coastal radar performance during a sea breeze

Sea breeze circulations dramatically impact the detection performance of coastal radar and are forecast to increase in strength and frequency into the 21st century. Dry and warm air from the land flows offshore between 100 and 200 meters above sea level out to 100km offshore. This redistribution of water vapor and temperature creates strong vertical humidity and temperature gradients resulting in significant radar ducting. These thermodynamic gradients and resulting non-standard propagation structures vary in time and space as the sea breeze develops. Spatio-temporal radar skip zones develop within the ducts and reduced target detection ranges develop above the ducts. Notional S, C and X band radars are modeled with the Advanced Refractive Effects Prediction System and are located at the shoreline during a sea breeze. The azimuth and range dependent refractivity field is modeled by the Regional Atmospheric Mesoscale Prediction System.
Indications for spirometry in outpatients with respiratory disease.

It has been suggested that spirometry should be incorporated into the routine examination of every patient, analogous to obtaining vital signs. To determine the impact of spirometry on the management of outpatients with respiratory disease, spirometry was performed on 150 consecutive patients (123 men and 27 women, mean age 57 ± 12 years) seen in our pulmonary disease outpatient clinics. Patients with obstructive (n = 75), restrictive (n = 31), mixed (n = 26) or other respiratory diseases (n = 18) were initially assessed by history and physical examination and classified as improved, stable, or worse compared to previous visits. A clinical management plan (CMP) was formulated based on this initial evaluation. Spirometric results were then made available to the examiner who could then make changes in the proposed CMP. The addition of spirometric results caused alteration of the CMP in only eight (5 percent) patients; in the remaining 142 patients, results did not affect the CMP. Two clinical findings identified those patients whose CMP was most likely to be altered by spirometry: severity of lung dysfunction (determined from previous spirometry) and deterioration of clinical status (judged by history and physical examination). Of the eight patients whose CMP was changed after review of spirometry, six (75 percent) had previous severe ventilatory dysfunction (FEV 1 or FVC ≤40 percent of predicted or FEV 1 /FVC ratio ≤0.40). In 6 of 38 patients (16 percent) with severe ventilatory dysfunction, CMP was altered after spirometry while only 2 of 112 patients (1.8 percent) with mild or moderate dysfunction had changes in their CMP. Patients who were clinically assessed as worse compared to their previous visit were more likely to have their CMP altered after review of spirometry when compared to those considered improved or stable by a ratio of 6:1. These results suggest that spirometry is most likely to supplement the physician's history and physical examination in the management of outpatients with pulmonary disease when the initial evaluation suggests that the patient has clinically deteriorated since the previous clinic visit, or when he or she has previous severe ventilatory dysfunction. (Chest 1991; 99:730–34)
Preservice Physical Education Teacher Attitudes Toward Fitness Tests and the Factors Influencing Their Attitudes

This study examined preservice teacher (PT) attitudes toward fitness tests in schools. A total of 613 PTs at 10 state universities took part in the study. Participants completed a previously validated instrument designed to measure the affective and cognitive components of attitude toward fitness tests. Results suggested that PTs had only slightly positive attitudes toward fitness tests. They did not believe strongly that fitness tests were important or useful. Similar attitude responses were found as students’ professional preparation increased. Thus, physical education teacher education (PETE) programs did not appear to significantly change PT attitudes. Age, gender, associations with professional organizations, or the type of fitness test PTs had performed in their K-12 education also did not impact their attitudes. PT previous experience with fitness tests, however, did influence their attitudes. As might be expected, those who had positive experiences had more positive attitudes.
Alternative splicing of neurofibromatosis type 1 gene transcript in malignant brain tumors: PCR analysis of frozen-section mRNA.

The neurofibromatosis type 1 (NF1) gene encodes a 360-residue region showing significant homology to the catalytic domains of both mammalian GTPase-activating protein (GAP) and yeast IRA protein. The product of the GAP-related domain of the NF1 gene (NF1-GRD) has been shown to stimulate ras GTPase and consequently to inactivate ras protein. We previously reported that the NF1-GRD has two types of transcripts, type I and type II, which are generated by an alternative splicing mechanism, and that the differential splicing of the NF1-GRD may be related to differentiation of neuroectodermal cells. Here we examined the differential expression of type I and type II transcripts of NF1-GRD in clinical samples of supratentorial malignant brain tumors by the RNA-polymerase chain reaction (PCR) method using frozen tissue sections. Our observations revealed that normal cerebrum predominantly expressed the type II NF1-GRD transcript, whereas primitive neuroectodermal tumors predominantly expressed the type I transcript. Additionally, although the type I/type II ratio in astrocytomas varied widely among tissue samples, all glioblastomas showed higher type I/type II ratios than adjacent brain samples. The RNA-PCR analysis using frozen tissue sections is a useful and sensitive method for detecting genetic markers in clinical tissue samples. © 1992 Wiley-Liss, Inc.
IDSA Ebola Summary-August 2014.

During 2014, a complex and expanding outbreak of EVD has been recognized in West Africa. Isolation of cases and follow-up of contacts are the main components of the strategy to halt the outbreak, but it will likely take months to achieve the goal. IDSA members will play key roles in preparedness and response for imported cases and should become knowledgeable of the available clinical and public health guidance. They can guide facility preparations toward plans that are clinically responsive and use resources effectively and responsibly. The IDSA is working with colleagues at the CDC, public health agencies, and professional organizations and will update members on additional developments and new guidance including anticipated provider and facility checklists, laboratory aspects, travel, and other topics. A web version of this communication can be found at http://www.idsociety.org/2014_ebola/.
LOX-1, an Oxidized LDL Endothelial Receptor, Induces CD40/CD40L Signaling in Human Coronary Artery Endothelial Cells

Background— Despite increasing appreciation that atherogenesis involves participation of inflammatory cells, information on mediators of communication between different constituents of atherosclerotic plaque remain incomplete. We examined the role of LOX-1, a receptor for oxidized (ox) LDL, in the expression of CD40/CD40L in cultured human coronary artery endothelial cells (HCAECs). Methods and Results— We observed that ox-LDL increased the expression of CD40 and CD40L in a concentration (10 to 80 μg/mL)- and time (1 to 24 hours)- dependent manner. These effects of ox-LDL were mediated by activation of LOX-1, because pretreatment of HCAECs with a blocking antibody to LOX-1 (JTX92) prevented the expression of CD40 and CD40L in response to ox-LDL ( P <0.01). In parallel experiments, HCAECs were incubated with the protein kinase C (PKC) inhibitor bisindolylmaleimide I, and the cells were then exposed to ox-LDL. Both LOX-1 antibody and the PKC inhibitor inhibited PKC activation in response to ox-LDL ( P <0.01). The PKC inhibitor also blocked the effects of ox-LDL on the expression of CD40 and CD40L ( P <0.01). In additional experiments, we found that it is the PKCα, but not PKCβ and PKCγ, isoform that mediated ox-LDL–induced CD40 and CD40L upregulation. Further experiments showed that upregulation of CD40 mediated induction of proinflammatory genes, because CD40 antibody markedly reduced ox-LDL–induced TNF-α generation and P-selectin expression, whereas nonspecific mouse IgG had no effect. Conclusions— These findings indicate that ox-LDL through its receptor LOX-1 triggers the CD40/CD40L signaling pathway that activates the inflammatory reaction in HCAECs. These observations provide novel insight into ox-LDL–mediated inflammation in atherosclerosis.
The Development of Anticipatory Smiling

When do infants begin to communicate positive affect about physical objects to their social partners? We examined developmental changes in the timing of smiles during episodes of initiating joint attention that involved an infant gazing between an object and a social partner. Twenty-six typically developing infants were observed at 8, 10, and 12 months during the Early Social-Communication Scales, a semistructured assessment for eliciting initiating joint attention and related behaviors. The proportion of infant smiling during initiating joint attention episodes did not change with age, but there was a change in the timing of the smiles. The likelihood of infants smiling at an object and then gazing at the experimenter while smiling (anticipatory smiling) increased between 8 and 10 months and remained stable between 10 and 12 months. The increase in the number of infants who smiled at an object and then made eye contact suggests a developing ability to communicate positive affect about an object.
On the Boundaries of Linguistic Competence: Matched-Guise Experiments as Evidence of Knowledge of Grammar

Abstract This paper illustrates a methodology for discovering whether speakers have knowledge of the non-categorical grammatical constraints which are evident in the distribution of sociolinguistic variables, through a case study of copula absence in AAVE. It is hypothesized that social and grammatical constraints on variation can interact. The matched-guise methodology of Lambert and others is adapted to determine whether the grammatical environment can affect listeners’ social evaluation of a linguistic variable. The evidence, though preliminary, suggests that it can, and this in turn suggests that listeners do have knowledge of the relevant non-categorical constraints.
Micro-Analysis of Textile Fibres : Part V. Observations on the Structure of Kemp

The recent work on the actual structure of kemp has proven the following: First, that there is a definite scale formation on the surface of the ftbre completely encasing it. In all respects this is similar to wool. In themselves, however, the scales are smootlaer in surface and less jagged in edge; they are less prominent, in their projection from the fibre, both in length and angle; nor do they overlap to the extent common in wool. Second, in cross-section the fibre is strikingly different. Scale and outer casing are the same; the interior of the fibre, however, is just the reverse of normal wool. In kemp the cortical layer is extremely small, whereas in wool it forms the major portion of the fibre. In both, this layer appears as a hontogeneovs mass, though in reality it is formed by myriads of tightly-packed and closely-cemented spindle- cells. In some wools a fine medulla forms a core through the centre of the cortex, Third, it is this medulla that comprises the major part of, and is the distinguishing aspect of a kemp fabre. It is cellular in composition, the cells being spaced without break throughout the fibre. They are irregular in size and outline and are arranged in similar order to the cells in a honey-comb. This medulla in true kemp is the prod-net of a special group of cells in the root (is annular in growth) and therefore can scarcely be considered an abnormality. The murch greater reflection from kemp (due to the air filled ineditlla) is the cause of the difference observed after dyeing. In reality, however, it has been shown by removing the air that kemp and wool are almost eqacally dyed; penetration and affinity being very similar.
Michigan microwave canopy scattering model

Abstract The Michigan Microwave Canopy Scattering model (MIMICS) is based on a first-order solution of the radiative-transfer equation for a tree canopy comprising a crown layer, a trunk layer and a rough-surface ground boundary. The crown layer is modelled in terms of distributions of dielectric cylinders (representing needles and/or branches) and discs (representing leaves), and the trunks are treated as dielectric cylinders of uniform diameter. This report describes MIMICS I, which pertains to tree canopies with horizontally continuous (closed) crowns. The model, which is intended for use in the 0·5-10GHz region at angles greater than 10° from normal incidence, is formulated in terms of a 4 × 4 Stokes-like transformation matrix from which the backscattering coefficient can be computed for any transmit/receive polarization configuration.
Religious and secular giving, by race and ethnicity

New data help to determine whether differences in philanthropic practices are due to race and ethnicity themselves or to a variety of factors that are correlated with these labels.
SURFACE CHARGE CHARACTERIZATION OF LAYER SILICATES BY COMPETITIVE ADSORPTION OF TWO ORGANIC DIVALENT CATIONS

Diquat2+ (1, 1’-ethylene-2, 2’-dipyridinium ion) and paraquat2+ (1, 1’-dimethyl-4, 4’-di-pyridinium ion) were competitively adsorbed by Na-saturated kaolinites, smectites and expanded and collapsed vermiculites. The relative preference for one or the other cation varied with the surface charge densities of the adsorbents and the location of the adsorption site, i.e. internal or external. Minerals with high surface charge exhibited preference for diquat whereas minerals with low surface charge preferred paraquat. Expanded vermiculites preferentially adsorbed diquat on internal surfaces. Collapsed vermiculites generally showed a preference for paraquat. Smectites and kaolinites preferentially adsorbed paraquat.
Constrained Texture Synthesis via Energy Minimization

This paper describes CMS (constrained minimization synthesis), a fast, robust texture synthesis algorithm that creates output textures while satisfying constraints. We show that constrained texture synthesis can be posed in a principled way as an energy minimization problem that requires balancing two measures of quality: constraint satisfaction and texture seamlessness. We then present an efficient algorithm for finding good solutions to this problem using an adaptation of graphcut energy minimization. CMS is particularly well suited to detail synthesis, the process of adding high-resolution detail to low-resolution images. It also supports the full image analogies framework, while providing superior image quality and performance. CMS is easily extended to handle multiple constraints on a single output, thus enabling novel applications that combine both user-specified and image-based control
The synthesis of (3H)-xylamine, an irreversible inhibitor of norepinephrine uptake

Xylamine [N-(2-chloroethyl)-N-ethyl-2-methylbenzylamine], an irreversible inhibitor of neuronal norepinephrine uptake, has been synthesized with tritium incorporated in the aromatic nucleus. Initially, 2-methylbenzyl bromide was nonselectively mono-brominated on the ring and the resulting isomeric products were condensed with 2-(ethylamino)ethanol. Unequivocal identification of the products of each reaction was provided by mass spectral analysis. A mixture of mono-bromobenzylamine isomers was isolated for catalytic reduction with 3H2 at a commercial facility. Carrier N-(2-hydroxyethyl)-N-ethyl-2-methylbenzylamine was added to the crude tritiated product prior to refluxing in the presence of excess thionyl chloride. (3H)-Xylamine was obtained as the hydrochloride salt and repeated recrystallizations yielded a radiochemically pure product with a specific activity of 3.09 Ci/mmol. Several analytical procedures established that the radiolabel was associated with xylamine.
Analysis of dipeptidyl peptidase IV gene regulation in transgenic mice: DNA elements sufficient for promoter activity in the kidney, but not the intestine, reside on the proximal portion of the gene 5'-flanking region.

Abstract The dipeptidyl peptidase IV (DPPIV) gene encodes a brush border membrane exopeptidase that is expressed in a tissue-restricted fashion. To examine the regulation of DPPIV transcription in various tissues in vivo, we examined the expression of DPPIV 5′-flanking region (promoter)–human growth hormone reporter constructs in transgenic mice. These mice exhibited cell-type specific reporter expression in kidney. Surprisingly, however, only very low to non-detectable levels of reporter were found in small intestine. These results indicate that DNA elements sufficient for DPPIV expression in kidney, but not intestine, reside in the 5′-flanking region of the gene.
Laser-induced gas breakdown as a light source for schlieren and shadowgraph particle image velocimetry

The "schlieren PIV" technique combines schlieren or shadowgraph optics with particle image veloci- metry PIV equipment to measure the velocities of turbulent eddies in flows with sufficiently strong changes of the refrac- tive index without actual particle seeding. Prior work on this technique used direct laser illumination that produced inad- equate schlieren image quality due to coherent artifact noise and other problems. By way of a simple equipment modifi- cation, we show the white-light emission of a laser-induced air or argon breakdown to be an improved light source for schlieren and shadowgraph PIV. The Nd:YAG illumination used in standard PIV is converted to a white-light pulse by this means. High-quality schlieren images are obtained and measurements in a helium jet using this new approach com- pare well with previous data. The method is especially appli- cable to high-speed flows requiring time delays of 5 so r less between the images of a PIV pair. © 2006 Society of Photo-
Reshaping technique for MOEM system fabrication

Today, the fabrication of microactuators and micromechanical parts is merely based on IC fabrication technologies. However, the 2D world of microelectronics sets a limit to the 3D micromechanical world. With a new micromachining technology, reshaping, which combines advantages of 2D IC fabrication with the third dimension of the mechanical world, a surface micromachined polycrystalline structure can be deformed to any desired 3D shape. In this work, this technique is employed for the first time to realize 3D actuators, and micro-opto-electro-mechanical systems. In this work, the design, fabrication and characterization of a micromirror are discussed. The structure is reshaped in such a way that the mirror platform, which is placed between two bimorph actuators, is tilted at a desired angle. The experimental results of electro-thermally actuated structure are in good agreement with the numerical results carried out by using IntelliCAD, an FEA tool to design and simulate MEMS. The reshaped micromirror demonstrates how reshaping technology eliminates complicated, silicon area consuming actuators. The fabrication steps of the micromirror are much simpler than those of previously reported device. A barcode scanner system employing reshaped micromirrors and optical filters is proposed as one example of many possible reshaped 3D MOEM Systems.© (1998) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Particle Accelerators in Cancer Therapy Current Status and Overview of the Planned Program for Heavy Particle Therapy

The goal of radiation therapy is uncomplicated local control of cancer. Practical approaches to this goal currently utilize a variety of electron accelerators which produce electron and photon beams at a range of energies for the treatment of cancer. To capitalize on the physical advantages of the available beams and the mechanical sophistication of isocentric mounting, treatment planning (tumor and organ localization, beam shaping, accuracy and reproducibility of setup, and computerized dosimetry) must be individualized and optimized so far as possible. An exciting potential for improvement in results of cancer treatment is the use of heavy particles for therapy (neutrons, protons, heavy ions, and negative pi mesons). These offer the potential for either or both an increased biological effect and improved dose distribution over standard photon or electron beam therapy. A program for heavy particle therapy has been proposed by the Committee for Radiation Oncology Studies and reviewed by the National Cancer Institute. The proposal and current status of the program are described briefly.
Metabolic Bone Disease in Low Birth Weight Neonates

The marked advances in neonatal care over the last decade have allowed survival of the small premature infant less than 1500 gms. Unfortunately, the advances in survivorship have been accompanied by a multitude of new problems, including the presence of bone disease which may result in short term morbidity and also affect future growth potential.
Anxiety in Youth: Assessment, Treatment, and School-Based Service Delivery

Anxiety is a natural, protective, and normal part of childhood. Temporary fears are developmentally typical; however, fears and worries that persist and impair functioning may be indicative of an anxiety disorder (Muris, Merckelbach, Mayer, & Prins, 2000). Anxiety disorders are the most common mental health problem in children and youth and are a significant source of distress for those afflicted (Costello, Mustillo, Erkanli, Keeler, & Angold, 2003; Merikangas et al., 2011).
Quality of life and late toxicities in head and neck cancer.

While the past fifteen years have shown many advances in the field of HNC QOL research, there are still a number of continued challenges that command attention. Little QOL research has been included in randomized trials. As survival rates continue to improve and methods of treatment become potentially more toxic, the inclusion of QOL data in randomized trials can be invaluable in interpreting the results of those studies. On the other hand, while mean QOL scores, (i.e., group averages) are necessary for these types of comparisons, how that same data might be useful clinically for an individual patient is a relatively uncharted area of investigation. The end result of QOL research should be to make treatment decisions easier and better for individual patients. How that can be done remains to be seen. Additionally, a review of all the HNC QOL literature published in 1999 and 2000 included only one study devoted to interventional research with HNC patients. While difficult to evaluate with traditional methods of statistical analysis, continued and expanded application of QOL data to the design of psychosocial or other interventions is now necessary and warranted.
On the application of the method of finite spheres to problems in tribology

In this paper we introduce the method of finite spheres, a truly meshfree numerical technique, as a promising scheme for the solution of problems arising in tribology. Some of the attractive features of this technique, contrasted to the traditional finite element methods, include the use of smooth approximation spaces which can be enriched using known asymptotic solutions of the governing partial differential equations as well as the freedom from generation of a complex computational mesh and the need for remeshing for problems involving very large deformations or changes in topology. An elastostatic punch indentation problem is used to showcase the various positive attributes of this method.
Automatic Design of Machine Tool Components

Techniques of computer-aided design for the automatic design of machine tool components are discussed. Two particular components are highlighted: (1) the automatic design of compact spur gear sets (2) the automatic design of hydrodynamic oil journal bearings
Heightened cleavage of Axl receptor tyrosine kinase by ADAM metalloproteases may contribute to disease pathogenesis in SLE

Systemic lupus erythematosus (SLE) is characterized by antibody-mediated chronic inflammation in the kidney, lung, skin, and other organs to cause inflammation and damage. Several inflammatory pathways are dysregulated in SLE, and understanding these pathways may improve diagnosis and treatment. In one such pathway, Axl tyrosine kinase receptor responds to Gas6 ligand to block inflammation in leukocytes. A soluble form of the Axl receptor ectodomain (sAxl) is elevated in serum from patients with SLE and lupus-prone mice. We hypothesized that sAxl in SLE serum originates from the surface of leukocytes and that the loss of leukocyte Axl contributes to the disease. We determined that macrophages and B cells are a source of sAxl in SLE and in lupus-prone mice. Shedding of the Axl ectodomain from the leukocytes of lupus-prone mice is mediated by the matrix metalloproteases ADAM10 and TACE (ADAM17). Loss of Axl from lupus-prone macrophages renders them unresponsive to Gas6-induced anti-inflammatory signaling in vitro. This phenotype is rescued by combined ADAM10/TACE inhibition. Mice with Axl-deficient macrophages develop worse disease than controls when challenged with anti-glomerular basement membrane (anti-GBM) sera in an induced model of nephritis. ADAM10 and TACE also mediate human SLE PBMC Axl cleavage. Collectively, these studies indicate that increased metalloprotease-mediated cleavage of leukocyte Axl may contribute to end organ disease in lupus. They further suggest dual ADAM10/TACE inhibition as a potential therapeutic modality in SLE.
Oil, Autocratic Survival, and the Gendered Resource Curse: When Inefficient Policy Is Politically Expedient

Economic development generally promotes women’s autonomy. Yet women in resource-rich autocracies fare more poorly than women in similarly wealthy industrial and postindustrial states. Some attribute this puzzling outcome to cultural causes, describing the apparent link between restrictions on women’s autonomy in resource-rich countries (especially in the Middle East) as spurious. Others argue that oil and gas rents cause a gendered resource curse through macroeconomic mechanisms. By contrast, we explain the association as a consequence of a political mechanism. We propose a theory of autocratic survival via antisocial policies chosen for the harms they inflict on targeted groups. Autocrats need to placate ideologically motivated members of their winning coalition. Antisocial policies serve as a costly and visible measure of rulers’ fidelity to these winning coalition members. Resource rents enable rulers to afford such policies, which would be infeasible in tax-reliant regimes. Restricting women’s autonomy thus forms part of a strategy of autocratic rule in resource-rich autocracies. Using quantitative evidence, we demonstrate that variations in women’s autonomy correlate with variations in oil income per capita in cross-country regressions. To trace variations within cases, we present case studies of Saudi Arabia and Iran to demonstrate processes consonant with our theory.
Quantitative Analysis of Keratin 18 in the Urine of Patients with Bladder Cancer

The level of urinary keratin was compared in patients with and without bladder cancer using the newly developed IRMAK-18. Patients with bladder cancer had higher levels of keratin (74.6 +/- 146.9) than normals (2.5 +/- 4.7). When the upper limit of normal was set at keratin less than 20 ng./ml., the test was highly specific (98%) for bladder cancer but had a sensitivity of only 46%. Adjusting to keratin less than 10 ng./ml. increased the sensitivity to 57% but decreased the specificity to 91%. Elevated keratins were associated with stage and grade, aneuploidy and disease history. The IRMAK-18 assay for keratin may be useful for monitoring the clinical progress of some patients.
Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants

Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead to missing information. There is thus a clear expectation for how missing data should be distributed, with fewer loci recovered between more distantly related samples. This observation has led to a related expectation: that RAD-seq data are insufficiently informative for resolving deeper scale phylogenetic relationships. Here we investigate the relationship between missing information among samples at the tips of a tree and information at edges within it. We re-analyze and review the distribution of missing data across ten RAD-seq data sets and carry out simulations to determine expected patterns of missing information. We also present new empirical results for the angiosperm clade Viburnum (Adoxaceae, with a crown age >50 Ma) for which we examine phylogenetic information at different depths in the tree and with varied sequencing effort. The total number of loci, the proportion that are shared, and phylogenetic informativeness varied dramatically across the examined RAD-seq data sets. Insufficient or uneven sequencing coverage accounted for similar proportions of missing data as dropout from mutation-disruption. Simulations reveal that mutation-disruption, which results in phylogenetically distributed missing data, can be distinguished from the more stochastic patterns of missing data caused by low sequencing coverage. In Viburnum, doubling sequencing coverage nearly doubled the number of parsimony informative sites, and increased by >10X the number of loci with data shared across >40 taxa. Our analysis leads to a set of practical recommendations for maximizing phylogenetic information in RAD-seq studies. [hierarchical redundancy; phylogenetic informativeness; quartet informativeness; Restriction-site associated DNA (RAD) sequencing; sequencing coverage; Viburnum.].
Treatment Using Aerobic Bioreactors

Aerobic biological processes have a long history of use for treatment of wastewaters in cities and urban areas of the United States and abroad. Application of aerobic treatment in decentralized systems evolved in an attempt to produce a higher quality effluent than that typically produced by a septic tank or other anaerobic unit operation. Aerobic treatment of wastewater is capable of producing an advanced secondary effluent that can enable surface discharge and reuse options. Chapter 7 describes the principles and processes involved in aerobic biological treatment and the design and implementation of aerobic treatment units using bioreactors to achieve organic matter removal and nitrification. Biological treatment for enhanced nutrient removal is covered in Chap. 13.
Abundance and patchiness of Chrysaora quinquecirrha medusae from a high-frequency time series in the Choptank River, Chesapeake Bay, USA

Despite strong control over marine plankton dynamics and negative impacts on human activities, jellyfish are not well quantified due primarily to sampling difficulties with nets. Therefore, some of the longest records of jellyfish are visual shore-based surveys. As surface counting is inexpensive and simple, it is of interest to determine what can be learned from such records as well as the usefulness of the method. We analyzed a 4-year high-frequency time series of Chrysaora quinquecirrha medusa counts collected using three sampling methods in the Choptank River, Chesapeake Bay. Medusa abundance was modeled by change points and was highly correlated between the sampling methods. The remaining signal was random, and indices of aggregation [fit to the Poisson distribution, Taylor’s Power Law (TPL), and Morisita’s Index] indicated that medusae were aggregated. TPL suggested that patches grew in the number of individuals as abundance increased. Additionally, a simple conceptualization of where the time series sampled in space revealed that the upper bound of patch size was on the order of kilometers. Our results enhance the knowledge of local C. quinquecirrha abundance and patchiness, alluding to processes that generate these patterns. This study also provides direction for improving population monitoring from visual shore-based surveys.
The emergency medicine management of severe alcohol withdrawal.

Abstract Introduction Alcohol use is widespread, and withdrawal symptoms are common after decreased alcohol intake. Severe alcohol withdrawal may manifest with delirium tremens, and new therapies may assist in management of this life-threatening condition. Objective To provide an evidence-based review of the emergency medicine management of alcohol withdrawal and delirium tremens. Discussion The underlying pathophysiology of alcohol withdrawal syndrome (AWS) is central nervous system hyperexcitation. Stages of withdrawal include initial withdrawal symptoms, hallucinations, seizures, and delirium tremens. Management focuses on early diagnosis, resuscitation, and providing medications with gamma-aminobutyric acid (GABA) receptor activity. Benzodiazepines with symptom-triggered therapy have been the predominant medication class utilized and should remain the first treatment option with rapid escalation of dosing. Treatment resistant withdrawal warrants the use of phenobarbital or propofol, both demonstrating efficacy in management. Propofol can be used as an induction agent to decrease the effects of withdrawal. Dexmedetomidine does not address the underlying pathophysiology but may reduce the need for intubation. Ketamine requires further study. Overall, benzodiazepines remain the cornerstone of treatment. Outpatient management of patients with minimal symptoms is possible. Conclusions Alcohol withdrawal syndrome can result in significant morbidity and mortality. Physicians must rapidly diagnose these conditions while evaluating for other diseases. Benzodiazepines are the predominant medication class utilized, with adjunctive treatments including propofol or phenobarbital in patients with withdrawal resistant to benzodiazepines. Dexmedetomidine and ketamine require further study.
Plasmodium falciparum in vitro: diminished growth in hemoglobin H disease erythrocytes.

Studies of the ability of Plasmodium falciparum to grow in vitro in the red blood cells of subjects with certain beta-thalassemia syndromes are often difficult to interpret because of the known inhibitory effect of an elevated cellular content of human fetal hemoglobin (HbF). P falciparum therefore was cultured in vitro in the erythrocytes of subjects with hemoglobin H (HbH) disease and various other alpha- thalassemia genotypes that are unaccompanied by increased levels of HbF. Growth of the malaria parasite was markedly retarded in HbH red blood cells, when compared with growth in blood from normal control subjects. No consistent impairment of growth was seen in the erythrocytes of subjects having deletion of only one or two alpha- globin genes. These results indicate that erythrocytes with a severe thalassemia phenotype provide a less hospitable growth environment for P falciparum than normally hemoglobinized red blood cells, even in the absence of increased levels of HbF.
Characterization of a low-cost, commercially available, vanadium oxide microbolometer array for spectroscopic imaging

Many long-wave infrared spectroscopic imaging applications are limited by the portability and cost of detector arrays. We present a characterization of a newly available, low-cost, uncooled vanadium oxide microbolometer array, the Seek Compact, in accordance with common infrared detector specifications: noise-equivalent differential temperature (NEDT), optical responsivity spectra, and Allan variance. The Compact’s imaging array consists of 156×206 pixels with a 12-μm pixel pitch, 93% of the pixels yield useful temperature readings. Characterization results show optical response between λ=7.4 and 12 μm with an NEDT of 148 mK (at ≈7 fps). Comparing these results to a research-grade camera, the Seek Compact exhibits a 4× and 48× reduction in weight (2.0/0.5 lbs) and cost ($12,000/$250) but takes 93× longer to achieve the same NEDT (1.55 s/16.6 ms for 45 mK). Additionally, a proof-of-concept spectral imaging experiment of SiN thin films is conducted. Leveraging this price reduction and spectroscopic imaging capability, the Seek Compact has potential in enabling field-deployable and distributed active midinfrared spectroscopic imaging, where cost and portability are the dominate inhibitors and high frame rates are not required.
A Targeted Mass Spectrometry Assay for Detection of HIV Gag Protein Following Induction of Latent Viral Reservoirs

During early infection, HIV-1 establishes a reservoir of latently infected cells that persist during antiretroviral therapy. These reservoirs are considered the primary obstacle to eradicating HIV-1 from patients, and multiple strategies are being investigated to eliminate latently infected cells. Measuring the reservoir size using an affordable and scalable assay is critical as these approaches move into clinical trials: the current “gold-standard” viral outgrowth assay is costly, labor-intensive, and requires large numbers of cells. Here, we assessed whether selective reaction monitoring-mass spectrometry (SRM-MS) is sufficiently sensitive to detect latent HIV reservoirs following reactivation of virus. The Gag structural proteins were the most abundant viral proteins in purified virus and infected cells, and tractable peptides for monitoring Gag levels were identified. We then optimized a Gag immunoprecipitation procedure that permitted sampling of more than 107 CD4+ T cells, a requirement for detectin...
The animacy advantage for free-recall performance is not attributable to greater mental arousal

People often demonstrate better memory for animate concepts (e.g., lion and sailor) than for inanimate concepts (e.g., hammer and mountain). Researchers have attributed this effect to an adaptive memory mechanism that favours information relevant for survival, including information about living things. In the present experiment, we examined the hypothesis that people demonstrate better free-recall performance for animate than inanimate words because animate words tend to be associated with greater mental arousal than inanimate words, a factor that was not controlled for in previous experiments on this topic. To this end, we matched animate and inanimate word lists on mental arousal (and several other factors), and compared participants' free-recall performance for the two word types. We were able to replicate past findings that participants' free-recall of animate words exceeds their free-recall of inanimate words, but we found no support for the possibility that the effect stems from differences in mental arousal between animate and inanimate concepts, as this effect maintained even when the word lists were matched on mental arousal. The present results therefore indicate that mental arousal cannot explain the effects of animacy on free-recall performance.
NUCLEAR POLYHEDROSIS VIRUS TRANSMISSION BY INFECTED HELIOTHIS ZEA (BODDIE) (LEPIDOPTERA: NOCTUIDAE) PRIOR TO DEATH

The potential of Heliothis zea (Boddie) larvae infected with nuclear polyhedrosis virus (NPV) to transmit the virus prior to their death was examined in the laboratory. In two separate tests fourth instar larvae were infected with NPV by either artificial diet surface treatment or virus treated soybean leaf disks. Each day NPV washed from the body surface of larvae, in larval feces and on the diet surface was bioassayed utilizing neonate H. zea. External contamination of the larvae with NPV resulted using the diet surface treatment technique but not with the leaf disk technique. Tests of surface contaminated larvae subsequently showed NPV contamination on the diet and in the feces. Bioassays revealed that progeny virus from infected larvae was not present on the body surface or in feces until late stages in the disease.
Development and evaluation of two interventricular sulcus extraction methods for cardiac PET

The goal is to develop and evaluate two methods to extract interventricular sulcus (IS) from 4D cardiac gated (CG) myocardial perfusion (MP) PET images for use in quantitative cardiac motion estimation. In Method 1, the entire myocardium was first segmented from the 3D MP PET image of each CG frame by 3D region growing. The left ventricle (LV) was then extracted by 3D image erosion and dilation, and the right ventricle (RV) by subtracting the LV from the segmented myocardium. Finally, the IS was identified from the overlap of the extracted LV and RV. In Method 2, the inner boundary (InB) of the RV was first extracted by segmenting the blood pool (BP) within the RV using 3D region growing. The septal side of the BP boundary, or the LV outer boundary (OutB) within the RV, was separated out. We then identified segments of the LV OutB on the anterior (Ant) and posterior (Post) sides of the RV. The three extracted line segments were fitted with a B-spline curve while the lateral side of the RV InB was extrapolated using B-spline. The intersection points of the fitted curves were identified as the Ant and Post IS which, when assembled from all short-axis images, formed entire IS. The two IS extraction methods were applied to realistic CG MP PET images simulated from the 4D XCAT phantom at PET system resolution from 0.6mm to 4.5mm for 4 CG frames. The accuracy of the extracted IS were compared with the true IS from the XCAT. For both methods, the errors of the extracted IS locations increased with poorer PET system resolution with the Ant IS showing lower accuracy than the Post IS. Method 1 achieved lower accuracy than Method 2 and failed to provide reliable estimates at 4.5mm system resolution. We conclude the B-spline based interpolation and extrapolation curve fitting method was capable of extracting the IS with high reliability and accuracy from the 4D CG MP PET images obtained from state-of-the-art and PET systems and will be useful in the cardiac motion estimation.
Health IT Usability Focus Section: Adapting EHR-Based Medication Instructions to Comply with Plain Language Guidance—A Randomized Experiment

Objective Patient instructions are generally written by clinicians. However, clinician-centered language is challenging for patients to understand; in the case of pediatric medication instructions, consequences can be serious. Using examples of clinician-written medication instructions from an electronic health record, we conducted an experiment to determine whether parental misinterpretations would be reduced by instructions that followed best practices for plain language. Methods We selected examples of dosing instructions from after-visit summaries in a commercial electronic health record. A demographically diverse sample of parents and adult caregivers was recruited from an online panel to participate in an English-language experiment, in which they received a comprehension questionnaire with either original after-visit summary instructions or instructions revised to comply with federal and other sources of plain-language guidance. Results Nine-hundred and fifty-one respondents completed the experiment; 50% were women, the mean age was 36 years, and 38% had less than a 4-year college education. The revisions were associated with an 8 percentage point increase in correct answers overall (from 55% to 63%, p Conclusion In this experimental study, a relatively simple intervention of revising text was associated with a modest reduction in frequency of misinterpretations of medication instructions. As a supplement to more intensive high-touch interventions, revising electronic health record output to replace complex language with patient-centered language in an automated fashion is a potentially scalable solution that could reduce medication administration errors by parents.
Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

Non-coding RNAs contain dozens of chemically distinct modifications, of which only a few have been identified in mRNAs. The recent discovery that certain tRNA modifying enzymes also target mRNAs suggests the potential for many additional mRNA modifications. Here, we show that conserved tRNA 2′-O-methyltransferases Trm3, 7,13 and 44, and rRNA 2′-O-methyltransferase Spb1, interact with specific mRNA sites in yeast by crosslinking immunoprecipitation and sequencing (CLIP-seq). We developed sequencing of methylation at two prime hydroxyls (MeTH-seq) for transcriptome-wide mapping of 2′-O-methyl ribose (Nm) with single-nucleotide resolution, and discover thousands of potential Nm sites in mRNAs. Genetic analysis identified hundreds of mRNA targets for the Spb1 methyltransferase, which can target both mRNA and non-coding RNA for environmentally regulated modification. Our work identifies Nm as a prevalent mRNA modification that is likely to be conserved and provides methods to investigate its distribution and regulation.
Abstract 15967: Electrical Surrogates for Severely Reduced Left Ventricular Ejection Fraction

Introduction: Severely depressed LV systolic function is currently the most common clinical criterion for identifying patients that may benefit from the primary prevention ICD. We have previously d...
Factors controlling the rate of incubation water loss in bird eggs

The relative water content of freshly laid eggs is essentially the same as that of eggs at the end of incubation (Ar and Rahn, 1980). To achieve this state of hydration at the end of incubation, presumably needed for optimal hatching success, an egg must lose a total amount of H2O equal to 18% of its initial mass, given an overall O2 uptake of 102 ml · g−1 (Hoyt and Rahn, 1980). Field observations show that on average 15% of initial egg mass is lost as water vapor by diffusion across the eggshell (Ar and Rahn, 1980), while additional water is lost by other routes after pipping.