cssi/SciSciGPT-SciSciNet huggingface dataset:
A rat β-interferon-induced mRNA: sequence characterization

Abstract Polymerase chain reaction amplification of a cDNA derived from rat aortic smooth muscle cells, using sequences from conserved regions of the intramembrane domains of adrenergic receptors as primers, yielded the clone, rat8. This clone possesses a high degree of sequence similarity to a series of human interferon (IFN)-inducible genes. The rat8 sequence is 70% similar to that derived from the human α-IFN-induced gene, 9–27; there is 66% similarity between the deduced amino acid sequences encoded by the rat and the human genes. The rat homologue hybridizes with many bands in Southern analysis of rat DNA, suggesting that it is a member of a large multigene family.
Predicting secondary organic aerosol formation rates in southeast Texas

[1] Rates of secondary organic aerosol (SOA) formation, due to the reactions of aromatics and monoterpenes, were estimated for southeast Texas by incorporating a modified version of the Statewide Air Pollution Research Center's chemical mechanism (SAPRC99) into the Comprehensive Air Quality Model with extensions (CAMx version 3.10). The model included explicit representation of the reactions of five SOA precursors (α-pinene, β-pinene, sabinene, d-limonene, and Δ3-carene). Reactions of each SOA precursor with O3, OH radical, and NO3 radical were included. The model also included separate reactions for low- and high-SOA-yield aromatic groups with the OH radical. SOA yields in the mechanisms were estimated using compound-specific yield information (ΔSOA/ΔHC) derived from smog chamber experiments conducted by J. R. Odum and colleagues and R. J. Griffin and colleagues. The form of the SOA yield model was based on the work of J. R. Odum and colleagues and is a function of existing organic aerosol concentrations. Existing organic aerosol concentrations were estimated on the basis of ambient measurements of total organic carbon in southeast Texas. The reactions of monoterpenes (predominantly α-pinene and β-pinene) with ozone led to the most regional SOA formation, followed by monoterpenes with the nitrate radical. Aromatic-OH reactions led to less regional SOA formation compared to monoterpenes; however, this formation occurs close to the urban and industrial areas of Houston. In contrast, SOA formation due to the reactions of monoterpenes occurred in the forested areas north of the urban area. The results of this study are in qualitative agreement with estimates of SOA formation based on ambient data from the same time period.
Use of the Rasch IRT Model in Standard Setting: An Item‐Mapping Method

This article provides both logical and empirical evidence to justify the use of an item-mapping method for establishing passing scores for multiple-choice licensure and certification examinations. After describing the item-mapping standard-setting process, the rationale and theoretical basis for this method are discussed, and the similarities and differences between the item-mapping and the Bookmark methods are also provided. Empirical evidence supporting use of the item-mapping method is provided by comparing results from four standard-setting studies for diverse licensure and certification examinations. The four cut score studies were conducted using both the item-mapping and the Angoff methods. Rating data from the four standard-setting studies, using each of the two methods, were analyzed using item-by-rater random effects generalizability and dependability studies to examine which method yielded higher inter-judge consistency. Results indicated that the item-mapping method produced higher inter-judge consistency and achieved greater rater agreement than the Angoff method.
Unsupervised clustering with the Octave Fuzzy Logic Toolkit

The Octave Fuzzy Logic Toolkit, a free, open-source toolkit for Octave that provides a large subset of the functionality of the MATLAB Fuzzy Logic Toolbox as well as many extensions, has recently been updated to support fuzzy clustering. This paper introduces the fuzzy clustering capabilities of the toolkit and illustrates their use through two examples. Future work will focus on implementing GUI tools and additional advanced fuzzy inference techniques. The Octave Fuzzy Logic Toolkit is shared on Octave-Forge and SourceForge under the GNU GPL.
Reconstruction using photographed serial sections.

A method is described whereby serial sections are photographed through a microscope and printed on a clear acetate film. The pictures are mounted on Plexiglas rectangles and placed back to back. A solid stack of plates with the reconstructed structure visible inside, or a slide-box arrangement of every other section may be produced. Variations of the technique are presented so that one can print high-contrast or low-contrast pictures, reconstruct simple or complex structures, and work more rapidly with less equipment. This is a simple, accurate, and rapid method.
SIGNAL TRANSDUCTION IN AXON GUIDANCE

Neurons establish specific connections by extending projections to contact their targets. Projections, such as axons, navigate to the target by sensing guidance cues in their environment and responding with directed movement and shape change. The recent identification of the molecular identities of many guidance cues and guidance receptors has demonstrated that axons are guided to their targets by combinations of cues that attract and repel them. The current challenge is to elucidate how these guidance cue/receptor interactions control navigation. This review focuses on recent progress in identifying the signaling pathways downstream of these receptors and in determining why an axon is attracted or repelled by a particular guidance cue.
A method for calculating codon frequencies in DNA.

Abstract Since the biological code is degenerate, the frequencies of occurrence of codons are not uniquely determined by the amino acid frequencies in proteins. A method of calculating these codon frequencies is presented here. It is assumed that the anti-sense strand of DNA consists of a sequence of codons randomly juxtapositioned, as is indicated by the statistically random sequence of amino acids in proteins. Using experimental data on average frequencies of amino acids in proteins, and on nearestneighbor frequencies and frequencies of pyrimidine runs flanked by purines in DNA, it is possible to write equations expressing constraints on the codon frequencies. Using the existing data, the frequencies of 20 codons and 24 linear combinations of codons can be calculated. This is done using a newly developed optimization procedure. The type of data that would be needed to calculate frequencies of all 64 codons is described. The method has been tested on hypothetical DNA molecules. The solutions are rather insensitive to errors in the estimates of amino acid frequencies but are very sensitive to errors in the estimate of doublet frequencies and pyrimidine runs. Since the equations are of degree up to five, the solutions are not unique. It is found, however, that “acceptable” solutions (those not containing negative values for the codon frequencies) do not seem to be numerous. Since most of the degeneracy of the genetic code is at the third place, for a given set of amino acid frequencies certain percentages of A, C, G and T are required for the first two places. The initial guess used for the iterative procedure is obtained by assuming that the percentage of nucleotides left for the third place is distributed randomly. A random perturbation of the initial guess of up to 10% yields the same solution. The method has been used to calculate codon frequencies in the DNA of three vertebrates, one plant (yeast) and seven bacteria. It is found that, in general, all the codons for a given amino acid are not used equally, and the relative frequencies vary with the species.
Talking with children about death.

A group of 75 children between the ages of six and fifteen were asked four questions about their perceptions of the meaning of death and. about their expectations in regard to their own death. None of the children appeared to experience severe anxiety in response to the subject matter. As was expected, children's ideas about death, as given in response to the questions, were quite different at different age levels. Suggestions are offered for discussing death with a child who has suffered a loss.
Developing Generalized Behavior-Modification Skills in High-School Students Working with Retarded Children.

Seven high-school trainees each conducted training sessions with two profoundly retarded children. Each trainee was asked to teach one child to follow the instruction "Bring ball" and the other child to follow the instructions "Sit down" and "Come here". During baseline sessions, before the trainees had been instructed in behavior-modification techniques, no trainee successfully taught either child to follow the instructions. After differing numbers of baseline sessions, trainees were exposed to training procedures designed to teach them to teach one child to follow the instruction "Bring ball". The training procedures consisted of videotaped modelling, rehearsal, and corrective feedback and praise. Following the training procedures, four of the seven trainees successfully taught their child the instruction "Bring ball". Further, all trainees were able to teach their other children to follow the instructions "Sit down" and "Come here", even though they had received no modelling, rehearsal, or feedback on how to teach the children to follow these instructions. The ability of the trainees to teach new behaviors to different children indicates the development of generalized skills in behavior modification.
Understanding Release Kinetics of Calcium Alginate Microcapsules Using Drop on Demand Inkjet Printing

This paper investigates the use of calcium alginate microcapsules to transport biomaterials for drug delivery. Rhodamine 6G dye was encapsulated in microcapsules for different formulations of the hydrogels using drop-on-demand printing. An experimental design was constructed to compare the effect of different concentrations of calcium chloride (M) and sodium alginate (% w/v) solutions in addition to the microcapsule diameter on the release kinetics profiles of the microcapsules. The results of these findings provide a basis to identify favorable sizes of microcapsules and concentrations of sodium alginate and calcium chloride solutions for controlled release behavior of microcapsules.© 2009 ASME
Role of tissue factor in mycobacterium tuberculosis-induced inflammation and disease pathogenesis

Tuberculosis (TB) is a chronic lung infectious disease characterized by severe inflammation and lung granulomatous lesion formation. Clinical manifestations of TB include hypercoagulable states and thrombotic complications. We previously showed that Mycobacterium tuberculosis (M.tb) infection induces tissue factor (TF) expression in macrophages in vitro. TF plays a key role in coagulation and inflammation. In the present study, we investigated the role of TF in M.tb-induced inflammatory responses, mycobacterial growth in the lung and dissemination to other organs. Wild-type C57BL/6 and transgenic mice expressing human TF, either very low levels (low TF) or near to the level of wild-type (HTF), in place of murine TF were infected with M.tb via aerosol exposure. Levels of TF expression, proinflammatory cytokines and thrombin-antithrombin complexes were measured post M.tb infection and mycobacterial burden in the tissue homogenates were evaluated. Our results showed that M.tb infection did not increase the overall TF expression in lungs. However, macrophages in the granulomatous lung lesions in all M.tb-infected mice, including low TF mice, showed increased levels of TF expression. Conspicuous fibrin deposition in the granuloma was detected in wild-type and HTF mice but not in low TF mice. M.tb infection significantly increased expression levels of cytokines IFN-γ, TNF-α, IL-6 and IL-1s in lung tissues. However, no significant differences were found in proinflammatory cytokines among the three experimental groups. Mycobacterial burden in lungs and dissemination into spleen and liver were essentially similar in all three genotypes. Our data indicate, in contrast to that observed in acute bacterial infections, that TF-mediated coagulation and/or signaling does not appear to contribute to the host-defense in experimental tuberculosis.
“Foot-stomping” in the Gerbil: Rewarding Brain Stimulation, Sexual Behaviour, and Foot Shock

IN our programme of research directed toward understanding brain mechanisms of motivation, we have considered that other animals, as well as the white rat, should be used to investigate the phenomenon of reward elicited by direct stimulation of the brain. While widespread use of the white rat has the advantages of reducing variability within subjects, between experiments, and among experimenters, such standardization tends to limit generality of findings. Even within the order Rodentia clear differences in the open field and visual cliff may be obtained from mammals of different families. Thus the gerbil, Meriones, from the family Cricitidae, and the white rat, Rattus, from the family Muridae, demonstrate different responses in an activity situation and in a depth perception apparatus1–3. It seemed worthwhile, therefore, to determine whether any differences existed between these two mammals in the brain reward situation. Our brain-stimulation experiments on the gerbil have led to the observation of a unique pattern of behaviour not seen in the albino rat. Such a result has suggested new directions in the investigation of the brain reward phenomenon.
Effect of hydrogen peroxide on hydrofluoric acid etching of high-k materials: ESR investigations

Abstract Oxides and silicates of zirconium and hafnium are being actively considered for use as gate dielectrics in MOS devices. Because of their higher dielectric constant (k ∼ 16–22), they permit the use of thicker layers without sacrificing the capacitance value. Wet chemical etching is the method of choice for patterning these oxides. The etching process has to be selective to zirconium/hafnium oxides over silicon dioxide, which may be present in other areas. In this paper, work done on HF etching of ZrO2 and HfO2 in presence of hydrogen peroxide is presented and discussed. It was found that addition of hydrogen peroxide to HF solutions lower the etch rate of ZrO2 and HfO2 films. Electron spin resonance (ESR) spectroscopy was used to probe the reasons for the decrease in etch rates in this solution.
Influence of dietary fat on self-reported menstrual symptoms

The Moos Menstrual Distress Questionnaire (MMDQ) was completed by thirty healthy premenopausal women randomized into one of two sets of weight-maintaining diets, those with a ratio of polyunsaturated to saturated fatty acids (P/S ratio) of 1.0 and those with a P/S ratio of 0.3. After a baseline interval of one menstrual cycle, both groups were fed a high fat diet (40% energy from fat) for four menstrual cycles per subject, followed by a similar interval on a low fat diet (20% energy from fat). There were no significant differences in self-reported menstrual symptoms between the two P/S groups. During both menses and the premenstrual week of the low fat dietary period there were significant decreases in self-reported symptoms associated with water retention. A decrease in symptoms in the group labelled "arousal" during the rest of the menstrual cycle was also reported.
Thyroid storm presenting as coma

Presented is the case of a 32-year-old man admitted with coma, hyperthermia, and tachycardia. The patient had a progressive downhill course and died in the medical ICU ten hours after admission. Autopsy and further investigation revealed thyroid storm as the most likely cause of death.
Anomalous nitrate concentrations in polar ice cores—Do they result from solar particle injections into the polar atmosphere?

Nitrate concentrations and electrical conductivity in an ice core from central Greenland have been measured simultaneously on 1.5 cm sections along the entire length of the 122 m core. This method of micro-resolution (time resolution is 1 week-1 month) provides for statistically significant determinations of rapid variations in nitrate fallout from the polar stratosphere superimposed on a background from all other sources. The seasonal NO3− background variations and the volcanic signal contained in the electrical conductivity data provide accurate dating of the ice core. This type of micro-resolution nitrate measurement appears to be useful as a tool to investigate the possible sources of polar nitrate anomalies such as solar proton events.
Endocytic adaptors: recruiters, coordinators and regulators

Clathrin-dependent endocytosis allows cells to bring plasma membrane and extracellular molecules into the cell. Forming a clathrin-coated vesicle requires the sequential action of numerous factors, beginning with endocytic adaptors. Adaptors are thought to initiate the process in two ways: by selecting cargo for packaging into the vesicle and assembling the clathrin coat and other components necessary to shape the vesicle. Here, we review recent work focusing on the sequential and cooperative interactions of adaptors with their binding partners, and how adaptors contribute to initial stages of endocytic internalization. The regulation of adaptors might be a key step for controlling endocytosis, and thus aid in homeostasis and cell physiology.
Toward a Radical and Ecological Constructivist Approach to Family Communication

(1989). Toward a radical and ecological constructivist approach to family communication. Journal of Applied Communication Research: Vol. 17, Applying Communication Theory to Family Process, pp. 1-26.
Don't Forget to Protect Abundant Resources

We examine an entry-deterrence model with multiple incumbents who strategically increase their individual appropriation in order to prevent entry. We show that entry deterrence yields a welfare improvement, relative to contexts of unthreatened entry, if firms exploit a relatively scarce resource. When incumbents compete for an abundant commons, however, their exploitation becomes large, and welfare losses can arise. Hence, our paper suggests that policies that protect the commons from further entry are actually more necessary when the resource is abundant than when it is scarce.
Automatic evaluation of breast density for full-field digital mammography

Women who have large breast area that is mammographically dense are greater risk of breast cancer than women with less mammographically dense breasts. It is a labor-intensive task to generate such a breast cancer risk information with the conventional screen film mammography. We have developed an automatic method to segment dense breast tissue areas using images acquired from full-field digital mammography systems. To evaluate its performance, a study was conducted to compare the segmentation results between the automatic method and a manually contouring method. A quantitative measurement, (delta) , is defined as the proportion of the segmented areas within a breast. The evaluation results indicate that there are 12 images whose (delta) difference between the automatic method and the manual method is less than 5%. Forty-nine images are between 5% and 10% and twenty images are within 15% in difference. On average, the process time required for the automatic method is approximately 18 seconds per image and 33 seconds per image for the manual method. The performance of our automatic method is comparable with the manual method. Yet, the automatic method does not require human intervention with the computer. We believe the automatic dense breast tissue segmentation method can be an effective tool to conduct studies of risk for breast cancer using FFDM images.
Abstract 5569: N-glycosylation in cultured cells and hepatocellular carcinoma

Purpose: Incidence of hepatocellular cancer (HCC) continues to increase primarily due to hepatitis C viral (HCV) infection. Prognosis and survival of patients is highly affected by the disease stage at the time of diagnosis. Our mass spectrometric study evaluated N-glycans during the progression of HCV infection to cancer. Glycosylation of immunoglobulins and other serum proteins was examined in cultured cells and in serum of patients with hepatocellular carcinoma. Methods and Results: Protein associated N-glycans were released with PNGaseF and analyzed by MALDI-TOF/TOF analysis following solid phase permethylation. Analysis of less than 0.04 ml of serum led to relative quantification of 70 N-glycan structures. Immunoaffinity isolation of immunoglobulins and other serum proteins allowed us to study protein-specific glycosylation. Progression of HCV infection to HCC was strongly associated with changes in the glycosylation of immunoglobulins. In a pilot case-control study (25 HCC cases and 35 controls), N-glycosylation of eight glycans was significantly different in HCC compared to chronic liver disease controls. The glycosylation of serum proteins was further compared to the proteins secreted by the Huh-7.5 cell line. Conclusion: This study demonstrates mass spectrometric analysis of 70 N-glycans in serum, cultured cells, and isolated proteins. Our results show that the analysis of permethylated N-glycans helps to define changes associated with the progression of HCV infection to HCC. Evaluation of glycan abundance suggests the potential to use glycans for the detection of liver disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5569.
Concomitant giant coronary artery and coronary sinus aneurysms.

consecutive reoperations were needed because of recurrent prosthetic dehiscence and mitral valve dysfunction. It was considered that a mitral homograft could be a valid alternative, but functional results were disappointing because of limited mobility and deficient coaptation of the anterior leaflet. Implantation of an annuloplasty ring and repair of the valve commissure were unsuccessful, and instead of explanting the homograft it was decided to remove the annuloplasty ring and insert a bioprosthesis in a transvalvular position, with the homograft acting as a native valve. At 14 months of follow-up, the patient is free of symptoms, and functional results are satisfactory. Hypersensitivity to the suture ring of the valve prosthesis is an appealing explanation for our findings. In this respect, the interposed homograft avoided the potential risk of intolerance to the suture ring and also prevented direct contact between the infected tissue and the prosthesis.
Novel Micropatterned Cardiac Cell Cultures with Realistic Ventricular Microstructure

Systematic studies of cardiac structure-function relationships to date have been hindered by the intrinsic complexity and variability of in vivo and ex vivo model systems. Thus, we set out to develop a reproducible cell culture system that can accurately replicate the realistic microstructure of native cardiac tissues. Using cell micropatterning techniques, we aligned cultured cardiomyocytes at micro- and macroscopic spatial scales to follow local directions of cardiac fibers in murine ventricular cross sections, as measured by high-resolution diffusion tensor magnetic resonance imaging. To elucidate the roles of ventricular tissue microstructure in macroscopic impulse conduction, we optically mapped membrane potentials in micropatterned cardiac cultures with realistic tissue boundaries and natural cell orientation, cardiac cultures with realistic tissue boundaries but random cell orientation, and standard isotropic monolayers. At 2 Hz pacing, both microscopic changes in cell orientation and ventricular tissue boundaries independently and synergistically increased the spatial dispersion of conduction velocity, but not the action potential duration. The realistic variations in intramural microstructure created unique spatial signatures in micro- and macroscopic impulse propagation within ventricular cross-section cultures. This novel in vitro model system is expected to help bridge the existing gap between experimental structure-function studies in standard cardiac monolayers and intact heart tissues.
Divalent cation-dependent structure in the platelet membrane glycoprotein Ia–IIa (VLA-2) complex

Recent studies have shown that the platelet membrane glycoprotein Ia–IIa (VLA-2) complex mediates the Mg++-dependent adhesion of platelets to collagen and that this adhesion is inhibited by Ca++ in a simple, linear, noncompetitive manner. These findings suggested that separate binding sites for Mg++ and Ca++ stabilize different divalent cation-dependent structures within the receptor complex. To provide evidence for the existence of such structures purified platelet Ia–IIa complex was subjected to limited proteolytic digestion in the presence of Mg++, Ca++, Mg++ and Ca++, or EDTA and the resulting peptides mapped by SDS-PAGE using both one- and two-dimensional techniques. Unique patterns of tryptic peptides were produced under each of the conditions. The results indicate that Mg++ and Ca++ stabilize different structures within the Ia–IIa (VLA-2) complex and that these structures influence both the collagen binding activity and proteolytic susceptibility of the complex.
1-Acetamido-17-carbomethoxydihydrothebainone

Treatment of 1-(5′-benzyloxy-4′-methoxy-2′-nitrobenzyl)-3,4-dihydroisoquinoline 2 with lithium/ammonia followed by the addition of ethanol gave a mixture of the dibenz[b,g]indolizines 3 and 4. Omission of ethanol resulted in the formation of 3 only. The dihydroisoquinoline from 3,4-dimethoxyphenylethyl amine behaved similarly. Reduction of 2a with sodium/ammonia resulted in cleavage to give the nitro-guaiacol 8. Oxidation of 2a in the presence of potassium t-butoxide gave a complex mixture from which the benzoyldihydroisoquinoline 5 and 2-benzyloxy-5-nitroanisole were isolated in low yield. Treatment of the hexahydrobenzylisoquinoline 10 with diazotized sulfanilic acid, followed by reduction and then acetylation gave a diacetyl compound 12 which was hydrolyzed to 13. Ring closure with boron trifluoride gave the dihydrothebainone 14.
Planning and incorporating public health preparedness into the medical curriculum

Abstract As part of a 2010 conference entitled “Patients and Populations: Public Health in Medical Education,” faculty from four U.S. medical schools (Case Western Reserve University, Harvard Medical School, the University of Colorado School of Medicine, and the University of Vermont College of Medicine), collaborated on a workshop to help other medical educators develop scenario-based learning experiences as practical, engaging, and effective mechanisms for teaching public health principles to medical school students. This paper describes and compares four different medical schools' experiences using a similar pandemic exercise scenario, discusses lessons learned, and suggests a curricular framework for medical schools adding such exercises to their population health curriculum. Different strategies to create realistic scenarios and engage students, including use of professionals and stakeholders from the community, are described.
Collagen metabolism in granulating wounds.

Abstract A technique for studying small granulating wounds in man and laboratory animals is described. The wounds are produced and later excised using standard skin punches. Using this tissue we have determined the profile of a number of biochemical steps in collagen biosynthesis occurring in the early stages of wound healing. The most useful indicator of collagen synthesis was measurement of protocollagen proline hydroxylase (PPH) activity the enzyme which hydroxylates peptide-bound proline. In rat skin PPH-activity reaches a maximum 5 days after wounding. During starvation, the level of PPH-activity falls within a few days as does the soluble collagen content indicating decreased collagen synthesis. Systemic cortisone administration decreases the PPH level in wounds, and the effect can be reversed by adding systemic vitamin A (which has no effect by itself). Preliminary studies in humans indicate that similar elevations in PPH-activity occur in 5-day-old wounds. Patients with scleroderma have higher baseline levels of PPH-activity in their skin but show a normal response of PPH-activity to wounding.
Whole-Transcriptome profiling of formalin-fixed, paraffin-embedded renal cell carcinoma by RNA-seq

Formalin-fixed paraffin-embedded (FFPE) tissue samples are routinely archived in the course of patient care and can be linked to clinical outcomes with long-term follow-up. However, FFPE tissues have degraded RNA which poses challenges for analyzing gene expression. Next-generation sequencing (NGS) is rapidly becoming accepted as an effective tool for measuring gene expressions for research and clinical use. However, the feasibility of NGS has not been firmly established when using FFPE tissue. We optimized strategies for whole transcriptome sequencing (RNA-seq) using FFPE tissue. Ribosomal RNA (rRNA) was successfully depleted by competitive hybridization using the Ribo-zero™ Kit (Epicentre Biotechnologies), and rRNA sequence content was less than one percent for each library. Gene expression measured by FFPE RNA-seq was compared to two different standards: RNA-seq from fresh frozen (FF) tissue and quantitative PCR (qPCR). Both FF and FFPE tumors were sequenced on an Illumina Genome Analyzer IIX with an average of 10 million reads. The distribution of FPKMs (fragments per kilobase of exon per million fragments mapped) and number of detected genes were similar between FFPE and FF. RNA-seq expressions from FF and FFPE samples from the same renal cell carcinoma (RCC) correlated highly (r = 0.919 for tumor 1 and r = 0.954 for tumor 2). On hierarchical cluster analysis, samples clustered by patient identity rather than method of preservation. TaqMan qPCR of 424 RCC-related genes correlated highly with FFPE RNA-seq expressions (r = 0.775 for FFPE tumor 1, r = 0.803 for FFPE tumor 2). Expression fold changes were considered, to assess biologic relevance of gene expressions. Expression fold changes between FFPE tumors (tumor 1/tumor 2) correlated well when comparing qPCR and RNA-seq (r = 0.890). Expression fold changes between tumors from different risk groups (our high risk RCC/The Cancer Genome Atlas, TCGA, low risk RCC) also correlated well when comparing RNA-seq from FF and FFPE tumors (r = 0.887). FFPE RNA-seq provides reliable genes expression data, comparable to that obtained from fresh frozen tissue. It represents a useful tool for discovery and validation of biomarkers.
Selection of a validated scale for measuring medication adherence

Objective To evaluate literature describing medication adherence surveys/scales to gauge patient behaviors at the point of care. Data sources Literature was identified via PubMed and Ovid (1950 to June 2009) using the search terms medication adherence, medication compliance, and medication persistence and combined with the terms questionnaire, survey, scale, or self-report. Study selection All articles in English with adherence scales validated in two or more diseases and containing 30 or fewer questions were selected. Data synthesis Five adherence scales were identified and reviewed by evaluating positive characteristics (short length, internal consistency, reliability, barriers to adherence, literacy appropriate, and self-efficacy), sensitivity, specificity, and diseases in which they have been validated. The Medication Adherence Questionnaire (MAQ) is the shortest scale and easiest to score. MAQ identifies barriers to nonadherence but not self-efficacy. The Self-efficacy for Appropriate Medication Use Scale (SEAMS) is a 13-question scale, and the Brief Medication Questionnaire (BMQ) has three main question headings and multiple subquestions. Both assess barriers and self-efficacy; however, scoring is difficult. The Hill-Bone Compliance Scale and Medication Adherence Rating Scale (MARS) address barriers and self-efficacy but are limited in their generalizability. The Hill-Bone Compliance Scale focuses on hypertensive patients, while MARS is specific to psychiatric populations. Conclusion No gold-standard medication adherence scale exists. MAQ is most adaptable at the point of care and across populations. MAQ is the quickest to administer and score and has been validated in the broadest range of diseases. SEAMS, BMQ, and the Hill-Bone Compliance Scale allow self-efficacy to be assessed and therefore may be useful in medication management clinics. MARS is specific to psychiatric populations.
Biomarker Selection for Predicting Alzheimer Disease Using High-Resolution MALDI-TOF Data

High-resolution MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry has shown promise as a screening tool for detecting discriminatory peptide/protein patterns. The major computational obstacle in analyzing MALDI-TOF data is the large number of mass/charge peaks (a.k.a. features, data points). With such a huge number of data points for a single sample, efficient feature selection is critical for unequivocal protein pattern discovery. In this paper, we propose a feature selection method and a new biclassification algorithm based on error-correcting output coding (ECOC) in multiclass problems. Our scheme is applied to the analysis of alzheimer's disease (AD) data. To validate the performance of the proposed algorithm, experiments are performed in comparison with other methods. We show that our proposed framework outperforms not only the standard ECOC framework but also other algorithms.
Linkage of the leuS, emtB, and chr genes on chromosome 5 in humans and expression of human genes encoding protein synthetic components in human--Chinese hamster hybrids.

We isolated interspecific hybrids between normal human leukocytes and a Chinese hamster ovary cell line that has mutations in three genes, leuS, emtB,and chr,all of which are linked to chromosome 2. The conditionally lethal mutation in the leuSgene in this cell line affects leucyl-tRNA synthetase and renders the cell line nonviable at 39°C. The mutation in the emtBlocus alters ribosomal protein S14 and results in the cell line being resistant to the protein synthesis inhibitor, emetine, while the mutation in the chrlocus renders the cells resistant to sodium chromate. The interspecific hybrids were selected at 39°C so that they were required to retain and express the human leuSgene. Ten out of ten such heat-resistant hybrids also expressed the human emtBand chrgenes. Segregants selected as having lost the human emtBgene simultaneously lost the human chrand leuSgenes as well. The linkage relationship between these three genes has thus been conserved during the evolution of the human and Chinese hamster genomes. All three genes were localized to human chromosome 5. Furthermore, our results indicate that the ribosomal protein product of the human emtBgene is incorporated into functional ribosomes in place of the corresponding Chinese hamster protein, raising several interesting questions concerning the coordinate regulation of genes encoding ribosomal proteins in mammalian cells.
Aggregated Impact of Plug-in Hybrid Electric Vehicles on Electricity Demand Profile

Greenhouse gas emissions, air pollution in urban areas, and dependence on fossil fuels are among the challenges threatening the sustainable development of the transportation sector. Plug-in hybrid electric vehicle (PHEV) technology is one of the most promising solutions to tackle the situation. While PHEVs partially rely on electricity from the power grid, they raise concerns about their negative impacts on power generation, transmission, and distribution installations. On the other hand, they have the potential to be used as a distributed energy storage system for the grid. Therefore, they can pave the way for a more sustainable power grid in which renewable resources are widely employed. Positive and negative impacts of PHEVs on the power grid cannot be thoroughly examined unless extensive data on the utilization of each individual PHEV are available. For instance, in order to estimate the aggregated impact of PHEVs on the electricity demand profile, one needs to know 1) when each PHEV would begin its charging process, 2) how much electrical energy it would require, and 3) how much power would be needed. This paper extracts and analyzes the data that are available through national household travel surveys (NHTS). Three charging scenarios are considered in order to obtain various PHEV charging load profiles (PCLPs). Further, the characteristics of each developed PCLP are studied. Finally, the effects of three suggested policies on the derived PCLPs are examined.
Epigenome-modifying tools in asthma

Asthma is a chronic disease which causes recurrent breathlessness affecting 300 million people worldwide of whom 250,000 die annually. The epigenome is a set of heritable modifications and tags that affect the genome without changing the intrinsic DNA sequence. These marks include DNA methylation, modifications to histone proteins around which DNA is wrapped and expression of noncoding RNA. Alterations in all of these processes have been reported in patients with asthma. In some cases these differences are linked to disease severity and susceptibility and may account for the limited value of genetic studies in asthma. Animal models of asthma suggest that epigenetic modifications and processes are linked to asthma and may be tractable targets for therapeutic intervention.
Local Reasoning for Global Convergence of Parameterized Rings

This paper presents a method that can generate Self-Stabilizing (SS) {\it parameterized} protocols that are generalizable, i.e., correct for arbitrary number of finite-state processes. Specifically, we present {\em necessary and sufficient} conditions specified in the local state space of the representative process of parameterized rings for deadlock-freedom in their global state space. Moreover, we introduce sufficient conditions that guarantee live lock-freedom in arbitrary-sized unidirectional rings. We illustrate the proposed approach in the context of several classic examples including a maximal matching protocol and an agreement protocol. More importantly, the proposed method lays the foundation of an approach for automated design of global convergence in the local state space of the representative process.
Decrease of cholesterol turnover in old rats

Abstract Serum cholesterol is significantly higher in 13-month old male Sprague-Dawley rats than in 2-months old animals. 1 day after i.v. injections of cholesterol-7- 3 H, (the same dose according to body wt.) serum level of the isotope is much higher in the older group and the decrease of serum radioactivity from 24 to 72 hr is faster in the younger animals. Incorporation of 3 H-cholesterol into the aorta is much lower in older animals if the incorporation into the aorta is corrected according to the blood isotope level. After the ligation of the common bile duct for 3 days the differences in serum isotope level in young and old animals is smaller but remains significant. It is concluded that both slower incorporation into the tissues and slower cholesterol excretion are responsible for higher 3 H-cholesterol level in the blood of older animals. Slower incorporation of cholesterol in the aorta of old animals in vivo corresponds to the previously described experiments in vitro .
Senescence and functional failure in hematopoietic stem cells

Maintaining normal function of hematopoietic stem cells (HSCs) is critical to blood coagulation, oxygen transportation, and host defense against infection. A potential cause of HSC dysfunction is senescence, in which HSCs and progenitor cells suffer from proliferative arrest. Studies on humans and various animal models have indicated that HSCs can become senescent, showing a significant decline in functional ability with increasing age. There are genetic elements mapped to specific chromosomal sites that regulate HSC senescence. These elements may differ among species, strains, and even individuals. HSC senescence and related pathological effects may not be obvious during normal lifetime under most circumstances since individual primitive HSC clones can function long-term to produce progeny that sustain life-long mature blood cell production. Shortening of telomeres at the chromosomal ends could contribute to HSC senescence, especially when HSCs are stressed under certain pathological conditions. Future studies should define the molecular elements that are important in the regulation of HSC senescence.
Stability of matrix second-order systems: new conditions and perspectives

Modeling of many dynamic systems results in matrix second-order differential equations. In the paper, the stability issues of matrix second-order dynamical systems are discussed. In the literature, only sufficient conditions of stability and/or instability for a system in matrix second-order form are available. In this paper, necessary and sufficient conditions of asymptotic stability for time-invariant systems in matrix second-order form under different types of dynamic loadings (conservative/nonconservative) are derived and a physical interpretation is carried out. The stability conditions in the sense of Lyapunov (the jw-axis behavior of eigenvalues) are also analyzed. As the conditions are gained directly in terms of physical parameters of the system, the effect of different loadings on the system stability is made transparent by dealing with the stability issues directly in matrix second-order form.
Effects of chronic treatment with diazepam, phenobarbital, or amphetamine on naloxone-precipitated morphine withdrawal

The present study examines the severity of naloxone-precipitated opiate withdrawal in morphine-pelleted rats and mice. Animals were chronically pretreated with either saline, diazepam, phenobarbital or amphetamine for 8 days prior to withdrawal precipitation. Indicators of withdrawal were changes in plasma corticosterone in rats and jumping behavior in mice. The use of chronic intravenous catheters in rats and one-way vision boxes allowed for serial blood sampling and sequential hormone determinations. Opiate dependence was established by the subcutaneous implantation of a 75-mg morphine pellet 72 h prior to withdrawal precipitation. All pretreated groups of rats with morphine pellets showed a substantial elevation of plasma corticosterone following the injection of naloxone (0.4 mg/kg, i.v.). Those with lactose pellets showed little change. The group pretreated with phenobarbital showed a lower, more attenuated withdrawal response as compared to saline or the other pretreated groups. The responsiveness of the hypothalamo-pituitary-adrenal axis to ether stress was evaluated. This was found to be unaffected by chronic phenobarbital suggesting that the drug may have a more specific effect on opiate dependence/withdrawal mechanisms. Similar studies in mice showed no differences in ED50 for naloxone-induced jumping behavior in any of the pretreatment groups.
The prevalence of platelet activating factor acetylhydrolase single nucleotide polymorphisms in relationship to necrotizing enterocolitis in Northwest Louisiana infants

Studies documented that platelet activating factor (PAF) and the enzyme platelet activating factor acetylhydrolase (PAFAH) play a very important role in the pathogenesis of neonatal necrotizing enterocolitis (NEC). In this retrospective, case-controlled pilot study, the authors investigated the prevalence of single nucleotide polymorphisms (Ile198Thr and Ala379Val) of the PAFAH gene. We screened 570 blood samples from both Caucasian and African-American preterm infants in the Northwest Louisiana population for the above mentioned PAFAH gene polymorphisms. Out of 570 infants, 36 had stage I or II NEC based on diagnostic coding, the International Classification of Diseases, 9th revision, Clinical Modification, 2009 (ICD-9-CM). The remaining infants without an ICD-9-CM diagnosis of NEC were recruited as control population. The DNA was isolated and restriction fragment length polymorphism microplate polymerase chain reaction assay was performed. Variants of the PAFAH gene polymorphism (Ile198Thr and Ala379Val) frequencies were not significantly different between the infants with NEC and the control group (P value of 0.26 by either multiple logistic regression analysis or the Cochran-Mantel-Haenszel test). This is the first study of its kind in exploring the relationship between NEC and single nucleotide polymorphisms in the coding genes of the enzyme PAFAH. Our preliminary data demonstrated that adjusted for the effect of race, PAFAH polymorphisms (Ile198Thr and Ala379Val) have no significant effect on NEC.
Utility of human-computer interactions: toward a science of preference measurement

The success of a computer system depends upon a user choosing it, but the field of Human-Computer Interaction has little ability to predict this user choice. We present a new method that measures user choice, and quantifies it as a measure of utility. Our method has two core features. First, it introduces an economic definition of utility, one that we can operationalize through economic experiments. Second, we employ a novel method of crowdsourcing that enables the collection of thousands of economic judgments from real users.
The SH4-Unique-SH3-SH2 domains dictate specificity in signaling that differentiate c-Yes from c-Src.

c-Src and c-Yes are highly homologous members of the Src family of non-receptor tyrosine kinases. The overall sequence similarity between c-Src and c-Yes allows them to perform many overlapping functions. However, the phenotypes of the c-src and c-yes knockout mice, and cells derived from them, are quite different, indicating functional specificity between the two proteins. Specifically, c-src ‐/‐ cells are deficient in several processes that require dynamic regulation of the actin cytoskeleton. In order to begin to understand why c-Yes is unable to compensate for c-Src signaling, we used a series of Src/Yes chimeras in which the non-catalytic functional domains of Src 527F were replaced by those of c-Yes. Using chicken embryo fibroblasts as a model system, our results indicate that the c-Yes N-terminal SH4-Unique domains are sufficient to inhibit the ability of Src 527F to alter cell morphology, induce actin filament rearrangements or stimulate motility or invasive potential. The data also indicate that the SH4Unique-SH3-SH2 domains of c-Yes work cooperatively and prevent activation of signaling proteins associated with Src 527F transformation, including activation of phosphatidylinositol 3-kinase, phosphorylation of c-Raf and Akt and downregulation of RhoA-GTP. These data indicate that c-Yes may not modulate signals associated with c-Src-induced changes in actin filament integrity and may explain why c-Yes fails to compensate for c-Src signaling in src ‐/‐ cells. Summary
Boundary control, quiet boundaries, super-stability and super-instability

This paper deals with the boundary feedback control of a bar undergoing axial vibrations. The feedback force is applied to one end of the bar and it is proportional to its velocity. The problem is of fundamental interest in control theory, structural dynamics, and the development of 'quiet boundaries' in fields like earthquake engineering and computational mechanics. The system is not self-adjoint and exhibits a variety of interesting behaviors which are explained through a combination of several inter-twined strands of thought using mathematics, physical interpretations, and numerical simulations. Besides providing a rigorous mathematical solution to the problem, the paper explains the physical origin of super-stable behavior, introduces the new concept of super-unstable behavior, and points out that these regimes of behavior are intricately connected with the continuum model that is used. It is shown that any finite-dimensional approximation of the system, no matter how finely discretized, can not qualitatively depict superstable behavior.