cssi/SciSciGPT-SciSciNet huggingface dataset:
The Rose and the Thorn: Some Ethical Dilemmas in a Qualitative Study of Older Adults∗

ABSTRACT Researchers engaged in exploring the social worlds of older adults have a keen awareness of a range of ethical issues associated with qualitative methodology. As is the case with quantitative work, qualitative social gerontologists can forecast the likelihood of encountering certain ethical issues in a study. However, there are some thorns, perhaps intrinsically connected to the small sample size, or the rose, of qualitative work. This paper discusses some of the unforeseen and thorny ethical issues that emerged during initial field work for a recent study. The issues involved making an assessment of the potential for harm that might come to participants from an inability to assure their confidentiality and privacy. The study's purpose—to understand the experience of older adults from non-western religious traditions—was and remains worthwhile; but, at least for the present, the small sample size in a small state precluded its completion.
American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis of hearing loss.

American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis of hearing loss
A new temperature- and pH-responsive copolymer for possible use in protein conjugation

The temperature- and pH-sensitive copolymers of N-isopropylacrylamide (NIPAAm) with 4-pentenoic acid (PAc) were synthesized and the monomer reactivity ratios were estimated. The effects of polymer composition, pH and ionic strength of the aqueous solution on the lower critical solution temperature (LCST) of the copolymers were investigated. It was found that the LCSTs of these unusual copolymers can be either lowered or raised compared to the LCST of poly(N-isopropylacrylamide) by changing the pH.
Anchor effects on the discrimination of pitch

Two experiments considered the effects of introducing an extreme stimulus (anchor) upon the differential perception of tonal stimuli. In the first experiment, in which Ss rated series stimuli from 1,000 to 2,000 Hz or from 2,000 to 3,000 Hz, the presence of a 750-Hz anchor apparently disrupted discrimination. A second experiment involved testing for a difference threshold (method of limits) in which the standard was a tone of 1,500 Hz. The uncertainty interval (Iu) was larger when the interval between paired stimulus presentations was filled with a 750-Hz tone, again suggesting that discrimination is impaired by the introduction of a low-frequency anchor. Results are discussed in terms of theories relating range extent and discriminability. Anchor effects (AE), for this study, are measured in terms of the modification of judgments made about a series of stimuli as the result of the presence of a stimulus value which falls outside the series. One conjecture about such effects is that they are limited by the distance of the anchor from the series stimuli. A further conjecture is that such limits may define relevance between an anchor value and a particular set of stimuli, possibly leading to description of stimulus dimensions in terms of a minimal number of relevant subsets (e.g., Adamson, 1967; Bevan & Pritchard, 1963; Sarris, 1969). This study began with an attempt to define AE limits for a portion of the auditory frequency dimension, itself chosen as possibly anomalous when compared to other quantitative dimensions (see Attneave & Olsen, 1 9 71 ). The singular findings of Experiment 1, however, prompted a change in direction and necessitated running a second experiment, in an attempt to ascertain whether the findings were related to basic properties of the perception of pitch. EXPERIMENT1
An analysis of conformational changes upon RNA-protein binding

RNA-binding proteins (RBPs) have myriad functions in transcription, translation, and post-transcriptional gene regulation, with central roles in normal development as well as in both genetic and infectious diseases. When a protein binds RNA, a conformational change often occurs. For RNA-protein complexes that have been characterized, conformational changes have been observed in the protein, the RNA, or both. These conformational changes have not been sufficiently characterized, however, in part due to the small number of structures of bound and unbound complexes of RNA-binding proteins available until recently. Here we systematically analyze a new dataset of 90 pairs of bound and unbound proteins to evaluate the conformational changes that occur upon RNA binding. Most of the conformational changes were observed in non-interfacial regions of the RNA-binding proteins. Detailed analyses of the modes of RNA binding and any associated conformational changes in proteins are critical for fully understanding the mechanisms of RNA-protein recognition, for developing better RNA-protein docking methods and methods for predicting interfacial residues, and for RNA-based drug design.
Going beyond Comprehension: Solutions for the Concrete Reader

One of the greatest challenges in my teaching is helping students do something with ideas they have read and comprehended. They compre hend most texts fairly well, but they have more difficulty when we begin such matters as evaluating a text they have comprehended or applying the ideas. In this paper I will analyze some of the reasons for those difficulties, first by highlighting a system of strategies which all readers must use to process ideas beyond comprehension, then?drawing from Piaget's distinction between con crete and formal operational thinking? by discussing these strategies as potential obstacles for readers who are basically concrete operational thinkers. My final purpose is to suggest some guidelines which have helped me help students go beyond "just" comprehending the ideas of a text.
Computational history: applying computing, simulation, and game design to explore historic events

This research project is an experiment of multiple dimensions, based on interdisciplinary concepts from both the computer science and history disciplines: 1) to determine if an interdisciplinary historical simulation model can be constructed using a game design engine and game programming techniques and technologies. This question is investigated and answered through the actual construction. 2) Can a historical military model be created that is based on records and analysis, and then validated by comparing results generated by the model against historical outcomes? This research both creates and validates a simulation model. 3) Can a validated historical model be used to reveal new knowledge about the battle and answer questions that research has previously been unable to answer? The use of a validated computational simulation model to investigate past historic events is a novel application of computing in a new interdisciplinary research area.This paper presents a computational historic experimental simulation model, explains how the simulation has been validated against historical evidence, and then uses that simulation to investigate unanswered questions from history.
An effective therapeutic method for the LSD user.

Observations obtained during the first 6 mo. of a psychoanalytically oriented psychotherapeutic procedure, capable of shortening and easing the initial phase of psychotherapy of LSD users, are reported. This procedure consisted of combined individual and group therapy, adding the LSD users to open mixed groups of abstinent patients. This procedure enabled the LSD users to participate in psychoanalysis, using the classical procedure, within less than 6 mo. Specific character trends and the underlying psychodynamic processes are also suggested. These processes appear to be specific for the LSD user and differ from those of the heroin addict and the chronic alcoholic.
The use of mass spectrometry in deducing the sequence of somatostatin — A hypothalamic polypeptide that inhibits the secretion of growth hormone

Abstract A peptide has been isolated from the extracts of ovine hypothalamic tissues that inhibits the secretion of somatotropin (growth hormone). The primary structure of this peptide, named somatostatin, has been determined to be H-Ala-Gly- Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys -OH. The sequence -Asn-Phe-Phe-Trp-Lys- was confirmed by direct mass spectrometry, using an acetylated and permethylated tryptic digest of somatostatin.
Deuterium Fractionation in Protoplanetary Disks

We investigate the chemistry of deuterium-bearing molecules in outer regions of protoplanetary disks, where comets may form. We find that molecules formed in the disk have higher D/H ratios (by which we mean abundance ratios between the singly deuterated species and the normal species) than the elemental D/H ratio in protosolar abundance, which is consistent with observations of recent comets. Despite the higher densities in protoplanetary disks, deuterium fractionation occurs in a similar way as in molecular clouds; because of the differences in zero-point energies and the existence of rapid ion-molecule isotopic exchange reactions, species such as H have high D/H ratios, which propagate to other molecules via gas-phase chemical reactions. Our results depend on a variety of factors such as the ionization rate and the temperature of the disk, which is somewhat uncertain because of possible variations in stellar luminosity and the existence of accretion shocks. In order to reproduce the observed cometary values of DCN/HCN and HDO/H2O, a lower ionization rate (~10-18 s-1) than is "standard" in molecular clouds is more favorable. The calculated DCN/HCN ratio also depends on whether the products assumed for the grain surface recombination reaction between HCO+ and electrons are dissociative or not.
A model for substrate concentrations in tissue surrounding single capillaries

The mathematical analysis of a model for substrate concentration in tissue is presented. The model consists of a single capillary from which substrate diffuses into a surrounding cylinder of tissue. The substrate is consumed at a rate proportional to the amount present. The results correlate well with those obtained from a similar model with a constant consumption rate.
Calcium influx is not required for thyrotropin-releasing hormone stimulation of prolactin release from GH3 cells.

Abstract TRH stimulation of prolactin release from GH 3 cells is dependent on Ca 2+ ; however, whether TRH-induced influx of extracellular Ca 2+ is required for stimulated secretion remains controversial. We studied prolactin release from cells incubated in medium containing 110 mM K + and 2 mM EGTA which abolished the electrical and Ca 2+ concentration gradients that usually promote Ca 2+ influx. TRH caused prolactin release and 45 Ca 2+ efflux from cells incubated under these conditions. In static incubations, TRH stimulated prolactin secretion from 11.4±1.2 to 19±1.8 ng/ml in control incubations and from 3.2±0.6 to 6.2±0.8 ng/ml from cells incubated in medium with 120 mM K + and 2 mM EGTA. We conclude that Ca 2+ influx is not required for TRH stimulation of prolactin release from GH 3 cells.
Formalin-Induced Short- and Long-Term Modulation of Cav Currents Expressed in Xenopus Oocytes: An In Vitro Cellular Model for Formalin-Induced Pain

Abstract Xenopus oocytes expressing high voltage-gated calcium channels (Ca(v)) were exposed to formalin (0.5%, v/v, 5 min.) and the oocyte death and Ca(v) currents were studied for up to 10 days. Ca(v) channels were expressed with alpha(1)beta(1)b and alpha(2)delta sub-units and the currents (I(Ba)) were studied by voltage clamp. None of the oocytes was dead during the exposure to formalin. Oocyte death was significant between day 1 and day 5 after the exposure to formalin and was uniform among the oocytes expressing various Ca(v) channels. Peak I(Ba) of all Ca(v) and A(1), the inactivating current component was decreased whereas the non-inactivated R current was not affected by 5 min. exposure to formalin. On day 1 after the exposure to formalin, Ca(v)1.2c currents were increased, 2.1 and 2.2 currents were decreased and 2.3 currents were unaltered. On day 5, both peak I(Ba) and A(1) currents were increased. Ca(v)1.2c, 2.2 and 2.3 currents were increased and Ca(v)2.1 was unaltered on day 10 after the exposure to formalin. Protein kinase C (PKC) may be involved in formalin-induced increase in Ca(v) currents due to the (i) requirement for Ca(v)beta(1)b sub-units; (ii) decreased phorbol-12-myristate,13-acetate potentiation of Ca(v)2.3 currents; (iii) absence of potentiation of Ca(v)2.3 currents following down-regulation of PKC; and (iv) absence of potentiation of Ca(v)2.2 or 2.3 currents with Ser-->Ala mutation of Ca(v)alpha(1)2.2 or 2.3 sub-units. Increased Ca(v) currents and PKC activation may coincide with changes observed in in vivo pain investigations, and oocytes incubated with formalin may serve as an in vitro model for some cellular mechanisms of pain.
Modulation of equine tracheal smooth muscle contractility by epithelial-derived and cyclooxygenase metabolites.

Abstract The role of epithelium in the modulation of contractile responses to electrical field stimulation (EFS), acetylcholine (ACh), and KCl were studied in vitro in strips of equine tracheal smooth muscle (TSM). EFS with 0.5 ms pulses of voltage (70 V) resulted in frequency dependent contractions of equine TSM that were sensitive to tetrodotoxin (TTX) and atropine. In TSM without epithelium, preincubation with indomethacin significantly potentiated contractile responses to EFS. The potentiating effect of indomethacin on EFS contractions was abolished by the addition of 3 nM prostaglandin E 2 (PGE 2 ). ACh and KCl cumulative concentration-response curves were shifted to the left by removal of epithelium from equine TSM strips with a significant decrease in the 50% effective concentration (EC 50 ) for both ACh and KCl. The mean EC 50 (± SE) for ACh in TSM without epithelium was 0.51 ± 0.09 μ M vs 4.30 ± 1.03 μ M in TSM with epithelium. Similarly, the mean EC 50 (± SE) for KCl in TSM without epithelium was 22.20 ± 2.61 mM vs 32.35 ± 2.66 mM in TSM with epithelium. The addition of indomethacin (3 μM) had no effect on the ACh concentration-response curves in TSM strips with or without epithelium. Our results suggest that in the equine airway there is (1) an epithelial-derived relaxant factor that modulates tracheal smooth muscle contractility postsynaptically, and (2) a nonepithelial-derived inhibitory factor, possibly PGE 2 , that modulates ACh release from nerves presynaptically.
Thermomechanical postbuckling analysis of laminated composite shells

The nonlinear response of laminated composite structures subjected to thermal loads is investigated. Analysis is performed using a refined theory and an associated finite element model for geometrically nonlinear analysis of laminated composite shell structures. The model is based on a third-order displacement field which accounts for both transverse shear and transverse normal deformations. Numerical studies of simply-supported plates and cylindrical panels indicate that when the panels are free to expand or contract in the transverse direction, the predicted critical buckling temperatures do not depend significantly upon whether or not transverse normal deformations are explicitly accounted for in the analysis model. However, the critical buckling temperatures are strongly dependent upon whether or not the transverse normal deformations are restrained along the boundaries of the panels.
A Case Study of a Minority Language Maintenance Program in Italy: Students’ and Teachers’ Perspectives on the Slovene-medium School Network

Abstract A K-13 Slovene-medium school network devoted to the protection and promotion of the cultural and linguistic heritage of the Slovene national minority has been in existence in the Italian north-eastern borderlands since the end of WWII and as part of the national public school system since 1961. This study unveils Slovene teacher's and student's language ideologies and attitudes toward the role of mother-tongue education for (a) academic achievement in the minority and dominant language; and (b) minority language maintenance. These questions were explored in a Slovene-medium high school in Gorizia, Italy, in an attempt to contribute to the understanding of secondary language minority education.
Effects of Age and Interstimulus Interval on the Brainstem Auditory Evoked Potential

Brainstem auditory evoked potentials (BAEPs) were studied in young (mean age 25 years; n = 8) and very healthy elderly women (mean age 71.2 years; n = 8) in order to evaluate the effects of age on transmission time over the brainstem auditory afferent pathway. Peak latencies, interwave latencies (ILs) and response amplitudes were determined at interstimulus intervals (ISIs) of 100, 50, 20 and 10 msec. Four repeated measures were obtained at each ISI in order to assess response variability as a function of age. While the elderly group had delayed peak latencies for all BAEP components, ILs were equivalent in the two age groups. Response amplitude tended to be reduced in the elderly compared to the young group and this effect was dependent upon ISI. Latency values (both peak and ILs) increased with decreasing ISI but there was no age-ISI interaction. Response variability did not change with age. The peak latency increases observed in the elderly were shown to be due to peripheral processes (mild presbycusis). The lack of an age effect for ILs and the lack of an ISI-age interaction indicate no age related slowing of central transmission time in the afferent auditory system at least to the region of the superior olivary complex and inferior colliculi.
Sticky Patches on Lipid Nanoparticles Generate Binding Geometries that Enable Effective Targeting of Otherwise Untargetable Cancers

The majority of breast cancer patients (70%) have tumors designated as ‘HER2-negative’ (<1+ HER2-expression evaluated by immunohistochemistry or < 200,000 HER2-copies per cell). For these patients there are no targeted therapeutic options utilizing the HER2 receptor. The ability of conventionally targeted nanoparticles for specific targeting stops to hold on cancer cells expressing less than 200,000 copies of HER2 per cell or less than two receptors per nanoparticle's projected area (for particles of 100 nm in-diameter). This geometry corresponds to the limit of multivalent interactions (avidity) loosely defined as multiple contacts between neighboring same-cell receptors with ligands from a single nanoparticle. An alternative therapeutic approach is needed, therefore, to enable selective targeting and effective killing of cancer cells with low or too low HER2 expression.Towards this goal we designed targeted lipid nanoparticles (vesicles) that contain HER2-targeting short peptides densely conjugated (for high local multivalency) within sticky patches. Sticky patches are phase-separated raft-like lipid-domains of high local multivalency which is induced by preferential partitioning of peptide-functionalized lipids. To enable selectivity in binding, sticky patches are exclusively triggered to form in mildly acidic environments matching the tumor interstitium. Lipid phase-separation with lowering pH is a result of the interplay of decreasing (pH-tunable) electrostatic repulsion and attractive hydrogen bonding among the domain-forming lipids.We show that lipid nanoparticles with sticky patches selectively associate with and kill HER2-negative and triple negative breast cancer cells (MCF-7 and MDA-MB-231, respectively, with 60,000 and 90,000 HER2-copies per cell) while do not affect cardiomyocytes and breast normal cells. Systematic studies of association, dissociation and internalization rates of nanoparticles by cells will be presented, and a mechanistic mathematical model will be discussed with the aim to explain the observed high avidity.
The Implementation of the 65nm Dual-Core 64b Merom Processor

Merom is a dual-core 64b processor implementing the Coretrade architecture. The 143mm2 die has 291M transistors in a 65nm 8M process. The shared 4MB 16-way L2 cache uses PMOS power gating to minimize leakage. The processor operates in a wide core frequency range of 1 to 3GHz, a bus frequency range of 666 to 1333MHz and voltage range of 0.85 to 1.325V, while providing 40% better power performance.
cDNA sequences and organization of IgM heavy chain genes in two holostean fish

Abstract Immunoglobulin M heavy chain (μ) sequences of two holostean fish, the bowfin, Amia calva, and the longnose gar, Lepisosteus osseus, were amplified from spleen mRNA by RACE-PCR, cloned, and sequenced. Each μ chain showed the conserved four constant domain structure typical of a secreted μ chain. Southern blot analyses with specific heavy chain variable (VH) and constant (CH) region probes suggest that both fish possess an IgH locus that resembles that of the teleosts, amphibians, and mammals in its organization. The overall sequence similarity of gar and bowfin μ chains was 60% and 48% at the nucleotide and amino acid levels, respectively, while similarity to the μ chains of teleosts and elasmobranchs was lower. The bowfin μ chain possesses a distinctive proline-rich sequence at the Cμ1/Cμ2 boundary; a shorter proline-rich sequence is present at this position in the gar μ chain. Both gar and bowfin show, in their Cμ4 sequences, motifs that could serve as cryptic splice donor sites for the production of mRNA encoding the membrane-bound form of the μ chains, and the bowfin also shows a potential cryptic splice donor site in the Cμ3 exon.
Stability and benefits of suboptimal utility maximization

Network utility maximization has been widely used to model resource allocation and network architectures. However, in practice, often it cannot be solved optimally due to complexity reasons. Thus motivated, we address the following two questions in this paper: 1) Can suboptimal utility maximization maintain queue stability? 2) Can underoptimization of utility objective function in fact benefit other network design objectives? We quantify the following intuition: A resource allocation that is suboptimal with respect to a utility maximization formulation maintains maximum flow-level stability when the utility gap is sufficiently small and information delay is bounded, and it can still provide a guaranteed size of stability region otherwise. Utility-suboptimal rate allocation can also enhance other network performance metrics, e.g., it may reduce link saturation. These results provide a theoretical support for turning attention from optimal but complex solutions of network optimization to those that are simple even though suboptimal.
Abundance and Diversity of Viruses in Six Delaware Soils

The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 × 109 to 4.17 × 109 g−1 dry weight) than in agricultural soils (8.7 × 108 to 1.1 × 109 g−1 dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.
Information-theoretic bounds on model selection for Gaussian Markov random fields

The problem of graphical model selection is to estimate the graph structure of an unknown Markov random field based on observed samples from the graphical model. For Gaussian Markov random fields, this problem is closely related to the problem of estimating the inverse covariance matrix of the underlying Gaussian distribution. This paper focuses on the information-theoretic limitations of Gaussian graphical model selection and inverse covariance estimation in the high-dimensional setting, in which the graph size p and maximum node degree d are allowed to grow as a function of the sample size n. Our first result establishes a set of necessary conditions on n(p, d) for any recovery method to consistently estimate the underlying graph. Our second result provides necessary conditions for any decoder to produce an estimate Θ Θ of the true inverse covariance matrix T satisfying ‖ Θ-Θ ‖ ∞ -norm (which implies analogous results in the Frobenius norm as well). Combined with previously known sufficient conditions for polynomial-time algorithms, these results yield sharp characterizations in several regimes of interest.
Recent climatic trends in nearshore water temperatures in the St. Lawrence Great Lakes

In the Great Lakes region, the observational evidence for climatic change has been primarily limited to changes in lake-ice conditions, with no long-term trends identified in water temperatures. Seven nearshore water intake sites (Bay City, Michigan; Green Bay, Wisconsin; Sault Ste. Marie, Michigan; St. Joseph, Michigan; Sandusky Bay, Ohio; Put-In-Bay, Ohio; and Erie, Pennsylvania) in the Great Lakes were chosen, and their data were examined for any climatic trends. Regression results on the annual mean temperatures showed varying support in favor of a warming trend at five of the seven sites. A new approach facilitated determination of the interannual variability in the timing of the 48C temperature of maximum density. Two of the three sites with data records extending back to the early part of this century (Sault Ste. Marie and Put-In-Bay, respectively) showed a 4- and a 6-h yr 21 rate of increase in the maximum potential duration of summer stratification (DSS). Over the time span of these two data sets, this equates to a 14- and 18-d increase in the potential DSS, respectively. The rate of increase in the duration data was skewed, with most of the increase due to an earlier transition to springlike conditions. Finally, the data do not extend far enough back in time to know if these climatic trends are part of an unresolvable natural cycle or forced by anthropogenic activity. General circulation models (GCM) representing physical processes from both the atmosphere and ocean have seen widespread application in attempting to forecast the longterm implications of increasing atmospheric CO2. Observational evidence for global warming centers on long-term temperature records (Hansen and Lebedeff 1988; Wigley et al. 1989) and proxy climate variables, which infer historical global temperatures based on ice core analyses (Barnola et al. 1987), tree ring data (Feng and Epstein 1996), bore hole temperatures, and the retreat of mountain glaciers (Ott 1997). At the same time, new insights suggest that much of the observed warming may be partially explained by a reduction in the diurnal temperature range for most parts of the world (Easterling et al. 1997). Both modeling and data approaches toward understanding global processes are hampered by uncertainty. Grotch (1988) documents a 2‐3 8C departure from global median temperatures with four different GCMs when they were used to simulate current conditions. Observational data also suffer from possible bias due to changes in land use patterns and inadequate spatial coverage. The limitations of GCMs on global
Regulation of activation-induced cytidine deaminase DNA deamination activity in B-cells by Ser38 phosphorylation.

Human and mouse Ig genes are diversified in mature B-cells by distinct processes known as Ig heavychain CSR (class switch recombination) and Ig variable-region exon SHM (somatic hypermutation). These DNA-modification processes are initiated by AID (activation-induced cytidine deaminase), a DNA cytidine deaminase predominantly expressed in activated B-cells. AID is post-transcriptionally regulated via multiple mechanisms, including microRNA regulation, nucleocytoplasmic shuttling, ubiquitination and phosphorylation. Among these regulatory processes, AID phosphorylation at Ser 38 has been a focus of particularly intense study and debate. In the present paper, we discuss recent biochemical and mouse genetic studies that begin to elucidate the functional significance of AID Ser 38 phosphorylation in the context of the evolution of this mode of AID regulation and the potential roles that it may play in activated B-cells during a normal immune response.
Classroom Demonstrations in Introductory Mechanics

This is a continuing series of quarterly articles on lessons learned and best practices in civil engineering education. The intent of the series is to reinforce good practices, describe new or developing practices, and provide a forum for what works well and what does not. It is hoped that this series will be an important quarterly read for all civil engineering educators and all those interested in what’s going on in civil engineering education today. Writers and topics will vary from issue to issue. Contact the column editor, Steve Ressler, if you wish to contribute to an upcoming issue. This is the fifth in a series of articles that expand on ideas and techniques that are included in the ASCE ExCEEd ~Excellence in Civil Engineering Education! Teaching Workshops.
Chemotaxis to the Quorum-Sensing Signal AI-2 Requires the Tsr Chemoreceptor and the Periplasmic LsrB AI-2-Binding Protein

AI-2 is an autoinducer made by many bacteria. LsrB binds AI-2 in the periplasm, and Tsr is the l-serine chemoreceptor. We show that AI-2 strongly attracts Escherichia coli. Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.
Inferring gene networks from discrete expression data

The modeling of gene networks from transcriptional expression data is an important tool in biomedical research to reveal signaling pathways and to identify treatment targets. Current gene network modeling is primarily based on the use of Gaussian graphical models applied to continuous data, which give a closed-form marginal likelihood. In this paper, we extend network modeling to discrete data, specifically data from serial analysis of gene expression, and RNA-sequencing experiments, both of which generate counts of mRNA transcripts in cell samples. We propose a generalized linear model to fit the discrete gene expression data and assume that the log ratios of the mean expression levels follow a Gaussian distribution. We restrict the gene network structures to decomposable graphs and derive the graphs by selecting the covariance matrix of the Gaussian distribution with the hyper-inverse Wishart priors. Furthermore, we incorporate prior network models based on gene ontology information, which avails existing biological information on the genes of interest. We conduct simulation studies to examine the performance of our discrete graphical model and apply the method to two real datasets for gene network inference.
Lymphocytes Lacking IκB-α Develop Normally, But Have Selective Defects in Proliferation and Function

NF-κB has been implicated in the development, activation, and function of B and T lymphocytes. We have evaluated the in vivo effects of deletion of IκB-α, a major inhibitor of NF-κB, on lymphocyte development, proliferation, and function. To elucidate the long term role of IκB-α in lymphocytes, fetal liver cells of 14.5-day-old IκB-α−/− or wild-type embryos were transplanted into irradiated recombinase-activating gene-2-deficient mice. Within 4 wk, the IκB-α−/− fetal liver cells reconstitute mature B and T cell populations in the recipients comparable to those produced by wild-type fetal liver cells. However, the proliferative responses of IκB-α−/− B cells are enhanced, whereas those of IκB-α−/− T cells are reduced. The levels of IgG1, IgG2a, IgA, and IgE produced by IκB-α−/− B cells are elevated relative to those produced by IκB-α+/+ or IκB-α+/−. Moreover, the specific immune responses to OVA and the generation of germinal centers are impaired in recipients of IκB-α−/− fetal liver cells. These results indicate that IκB-α plays a vital role in signal transduction pathways regulating lymphocyte proliferation and also in the production of specific Ig isotypes.
A Hands-on Approach to Teaching Protein Translation & Translocation into the ER

The process of protein translation and translocation into the endoplasmic reticulum (ER) can often be challenging for introductory college biology students to visualize. To help them understand how proteins become oriented in the ER membrane, I developed a hands-on activity in which students use Play-Doh to simulate the process of protein insertion into the ER membrane. After completing the hands-on activity, students are better able to solve problems in which they have to predict the membrane orientation of a protein.
J/Psi --> e+e- and J/Psi --> mu+mu- measurements in AuAu and pp collisions at root s(NN)=200 GeV.

Abstract First results are presented from J Φ→ ee and J /Φ→ μμ measurements by the PHENIX experiments at RHIC. These results are from a preliminary analysis of dielectrons from AuAu and pp data and dimuons from pp data measured in the RHIC run 2. A total cross section for J /Φ production in √s = 200 GeV pp collisions of 3.8 ± 0.6 (stat) ±1.3 (sys) μb is found. The J /Φ→ ee yield is presented versus number of binary collisions.
Study of strawberry flavored milk under pulsed electric field processing

Abstract Few studies exist on flavored milk processed by pulsed electric fields (PEF). The main concern is product stability. This study aimed to analyze the degradation of coloring agent Allura Red in strawberry milk under PEF. Four systems were tested containing Allura Red: two commercial milks and two model systems. PEF conditions were 40 kV/cm, 48 pulses (2.5 μs), and 55 °C; coloring agent was quantified via RP-HPLC. After processing, only minor changes were observed in color, Allura Red concentration, and pH. During storage (32 d) at refrigerated conditions (4 °C) commercial samples maintained pH above 6. Model systems dropped below pH 6 after 10 days of storage. Color of samples showed important decrease in a⁎; hue angle and chroma changed during storage. HPLC analysis reported a bi-phasic effect in Allura Red concentrations versus time. Concentration changed, reaching a maximum value during the middle of storage, possibly attributed to microbial growth, pH reduction, or interaction of proteins. However, PEF affected the stability of Allura Red in milk when additional ingredients were not added to the product.
Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

Significance: The colonization of wounds by specific microbes or communities of microbes may delay healing and/or lead to infection-related complication. Studies of wound-associated microbial communities (microbiomes) to date have primarily relied upon culture-based methods, which are known to have extreme biases and are not reliable for the characterization of microbiomes. Biofilms are very resistant to culture and are therefore especially difficult to study with techniques that remain standard in clinical settings. Recent Advances: Culture-independent approaches employing next-generation DNA sequencing have provided researchers and clinicians a window into wound-associated microbiomes that could not be achieved before and has begun to transform our view of wound-associated biodiversity. Within the past decade, many platforms have arisen for performing this type of sequencing, with various types of applications for microbiome research being possible on each. Critical Issues: Wound care incorporating knowledge of microbiomes gained from next-generation sequencing could guide clinical management and treatments. The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing. Future Directions: As DNA sequencing technology progresses, platforms will continue to produce longer reads and more reads per run at lower costs. A major future challenge is to implement these technologies in clinical settings for more precise and rapid identification of wound bioburden.
Establishment of A New Stink Bug Pest, Oebalus insularis (Hemiptera: Pentatomidae), in Florida Rice

ABSTRACT The stink bug, Oebalus insularis (Stal), was first observed in Florida rice fields in 2007. An extensive survey was conducted during 2008 and 2009 to determine the relative abundance and population biology of O. insularis in Florida rice fields. It occurred in 100% of all fields sampled and constituted 20% of all stink bugs collected. Data from this study show that O. insularis, a well known rice pest in Caribbean islands, Central America, and South America, is now widespread in Florida rice fields. This is the first report of this species being found in commercial rice fields in the United States.
Annotating protein function through lexical analysis

We now know the full genomes of more than 60 organisms. The experimental characterization of the newly sequenced proteins is deemed to lack behind this explosion of naked sequences (sequencefunction gap). The rate at which expert annotators add the experimental information into more or less controlled vocabularies of databases snails along at an even slower pace. Most methods that annotate protein function exploit sequence similarity by transferring experimental information for homologues. A crucial development aiding such transfer is large-scale, work- and management-intensive projects aimed at developing a comprehensive ontology for gene-protein function, such as the Gene Ontology project. In parallel, fully automatic or semiautomatic methods have successfully begun to mine the existing data through lexical analysis. Some of these tools target parsing controlled vocabulary from databases; others venture at mining free texts from MEDLINE abstracts or full scientific papers. Automated text analysis has become a rapidly expanding discipline in bioinformatics. A few of these tools have already been embedded in research projects.
Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

The transcriptional regulatory networks that specify and maintain human tissue diversity are largely uncharted. To gain insight into this circuitry, we used chromatin immunoprecipitation combined with promoter microarrays to identify systematically the genes occupied by the transcriptional regulators HNF1α, HNF4α, and HNF6, together with RNA polymerase II, in human liver and pancreatic islets. We identified tissue-specific regulatory circuits formed by HNF1α, HNF4α, and HNF6 with other transcription factors, revealing how these factors function as master regulators of hepatocyte and islet transcription. Our results suggest how misregulation of HNF4α can contribute to type 2 diabetes.
The Desert Fax: A Research Note on Calling Home from Somalia

Survey data from near 500 civilian wives of soldiers from who deployed to Somalia for Operation Restore Hope were analyzed to determine how the mechanics of soldier-family communications affected s...
Men tend to be neoplasia prone and women neoplasia resistant

Background: Patients with a colorectal neoplasm are at risk for metachronous neoplasia. This risk usually is stratified according to the number, size, and histology of the index lesion(s). This study was performed to search for factors contributing not only to a very high risk of metachronous lesions but also to a very low risk.
Appropriate Expression of Filamentous Phage f1 DNA Replication Genes II and X Requires RNase E-Dependent Processing and Separate mRNAs

The products of in-frame overlapping genes II and X carried by the filamentous phage f1 genome are proteins with required but opposing functions in phage DNA replication. Their normal relative levels are important for continuous production of phage DNA without killing infected Escherichia coli hosts. Here we identify several factors responsible for determining the relative levels of pII and pX and that, if perturbed, alter the normal distribution of phage DNA species in infected hosts. Translation of the two proteins is essentially relegated to separate mRNAs. The mRNAs encoding genes II and X are also differentially sensitive to cleavage dependent on rne, the gene encoding the only E. coli endo-RNase known to have a global role in mRNA stability. Whereas pII levels are limited at the level of mRNA stability, normal pX levels require transcription in sufficient amounts from the promoter for the smaller mRNA encoding only pX.
An Air Force organization process model using formal software engineering techniques

This paper presents a methodology for developing an organizational process model based on the principles of object-oriented design and formal software engineering methods. The methodology begins with the development of an object-oriented domain model which consists of an informal Rumbaugh model formally specified in the Z (Zed) formal specification language. The Z specifications are then translated into an executable model in the Software Refinery Environment. The Refine environment provides an executable language that allows behavior to be expressed declaratively, giving the developer an executable specification. This results in an observable domain model with attributes to describe organizational level metrics. While the model described in this paper is based on the Air Force wing C3I domain, both the methodology and the resulting model are shown to be very general and tailorable for other domain applications. The use of formal methods and an object-oriented approach leads to a more mathematically verifiable and more easily maintained executable process model.
FlashRelate: extracting relational data from semi-structured spreadsheets using examples

With hundreds of millions of users, spreadsheets are one of the most important end-user applications. Spreadsheets are easy to use and allow users great flexibility in storing data. This flexibility comes at a price: users often treat spreadsheets as a poor man's database, leading to creative solutions for storing high-dimensional data. The trouble arises when users need to answer queries with their data. Data manipulation tools make strong assumptions about data layouts and cannot read these ad-hoc databases. Converting data into the appropriate layout requires programming skills or a major investment in manual reformatting. The effect is that a vast amount of real-world data is "locked-in" to a proliferation of one-off formats. We introduce FlashRelate, a synthesis engine that lets ordinary users extract structured relational data from spreadsheets without programming. Instead, users extract data by supplying examples of output relational tuples. FlashRelate uses these examples to synthesize a program in Flare. Flare is a novel extraction language that extends regular expressions with geometric constructs. An interactive user interface on top of FlashRelate lets end users extract data by point-and-click. We demonstrate that correct Flare programs can be synthesized in seconds from a small set of examples for 43 real-world scenarios. Finally, our case study demonstrates FlashRelate's usefulness addressing the widespread problem of data trapped in corporate and government formats.
Some Aviation Growth Events

The growth of aviation since the first flight of a heavier-than-air powered manned vehicle in 1903 has been somewhat remarkable. Some of the events that have influenced this growth are reviewed in this paper. This review will include some events prior to World War I; the influence of the war itself; the events during the post-war years including the establishment of aeronautical research laboratories; and the influence of World War II which, among other things, introduced new technologies that included rocket and jet propulsion and supersonic aerodynamics. The subsequent era of aeronautical research and the attendant growth in aviation over the past half century will be reviewed from the view point of the author who, since 1944, has been involved in the NACA/NASA aeronautical research effort at what is now the Langley Research Center in Hampton, Virginia. The review will discuss some of the research programs related to the development of some experimental aircraft, the Century series of fighter aircraft, multi-mission aircraft, advanced military aircraft and missiles, advanced civil aircraft, supersonic transports, spacecraft and others.
Communication media use in the grandparent-grandchild relationship

This study surveyed college-aged grandchildren as to the frequency of their communication with a grandparent using various media. Face-to-face (FtF) and telephone communication were used more frequently than written media, but all were used fairly frequently. Communication using all media was more frequent when the grandparent or grandchild initiated interaction as opposed to the parent. Relationships in which the grandparent initiated contact featured more use of written media (letters, e-mail, cards). Frequency of communication using all media was positively associated with relational quality. Telephone communication best predicted relational quality when use of other media was controlled. In this paper, I discuss implications for media richness theory, the communication predicament of aging model, and future research on grandparent-grandchild relationships. This paper examines the grandparent-grandchild (GP-GC) relationship in the context of a growing literature concerning communication between older and younger adults that has enlightened us as to the processes and problems of such communication. The work of Hummert and her colleagues has provided new insights on the nature of intergenerational stereotypes and their role in influencing communication in intergenerational settings featuring elderly people (Hummert, 1994; Hummert, Shaner, Garstka, & Henry, 1998; see also Harwood, McKee, & Lin, 2000). Ryan, Giles, and their colleagues have provided important information concerning the determinants and consequences of patronizing speech in such settings (Harwood & Giles, 1996; Ryan, Giles, Bartolucci, & Henwood, 1986). Giles and collaborators have provided information on cross-cultural dimensions to the intergenerational communication process (Williams et al., 1997). Finally, N. Coupland, J. Coupland, and their coworkers have provided insights into the discoursal management of intergenerational relations (Coupland, Coupland, &
Factors Influencing Home-Range Sizes of Eastern Indigo Snakes in Central Florida

Abstract Wide-ranging snake species are particularly sensitive to landscape fragmentation, and understanding area requirements is important for their conservation. We used radiotelemetry to quantify how Eastern Indigo Snake home-range sizes were influenced by sex, land cover, and the length of time (weeks) individuals were radio tracked. We found that Eastern Indigo Snakes had the largest home ranges among other snake species studied. Female home ranges averaged 44 and 76 ha, respectively, for kernel and minimum convex polygon estimators. Male home ranges averaged 156 and 202 ha, respectively, for kernel and minimum convex polygon estimators. Many animal species respond to habitat fragmentation by using larger areas than in unfragmented landscapes, but we found that Indigo Snakes in fragmented landscapes used much smaller areas. The length of time that snakes were tracked had almost no influence on home-range size compared to sex and land cover type. Our results suggest that maintaining populations of thi...