cssi/SciSciGPT-SciSciNet huggingface dataset:
Evidence That Base-pairing Interaction between Intron and mRNA Leader Sequences Inhibits Initiation of HAC1 mRNA Translation in Yeast

The Hac1 transcription factor in yeast up-regulates a collection of genes that control protein homeostasis. Base-pairing interactions between sequences in the intron and the 5′-untranslated region (5′ UTR) of the HAC1 mRNA represses Hac1 protein production under basal conditions, whereas cytoplasmic splicing of the intron by the Ire1 kinase-endonuclease, activated under endoplasmic reticulum stress conditions, relieves the inhibition and enables Hac1 synthesis. Using a random mutational screen as well as site-directed mutagenesis, we identify point mutations within the 5′ UTR-intron interaction site that derepress translation of the unspliced HAC1 mRNA. We also show that insertion of an in-frame AUG start codon upstream of the interaction site releases the translational block, demonstrating that an elongating ribosome can disrupt the interaction. Moreover, overexpression of translation initiation factor eIF4A, a helicase, enhances production of Hac1 from an mRNA containing an upstream AUG start codon at the beginning of the base-paired region. These results suggest that the major block of translation occurs at the initiation stage. Supporting this interpretation, the point mutations that enhanced Hac1 production resulted in an increased percentage of the HAC1 mRNA associating with polysomes versus free ribosomal subunits. Thus, our results provide evidence that the 5′ UTR-intron interaction represses translation initiation on the unspliced HAC1 mRNA.
MATING TYPE AND SPORULATION IN YEAST I. MUTATIONS WHICH ALTER MATING-TYPE CONTROL OVER SPORULATION

In Saccharomyces cerevisiae, meiosis and spore formation as well as mating are controlled by mating-type genes. Diploids heterozygous for mating type (aalpha) can sporulate but cannot mate; homozygous aa and alpha-alpha diploids can mate, but cannot sporulate. From an alpha-alpha diploid parental strain, we have isolated mutants which have gained the ability to sporulate. Those mutants which continue to mate as alpha-alpha cells have been designated CSP (control of sporulation). Upon sporulation, CSP mutants yield asci containing 4alpha spores. The mutant gene which allows alpha-alpha cells to sporulate is unlinked to the mating-type locus and also acts to permit sporulation in aa diploid cells. Segregation data from crosses between mutant alpha-alpha and wild-type aa diploids and vice versa indicate (for all but one mutant) that the mutation which allows constitutive sporulation (CSP) is dominant over the wild-type allele. Some of the CSP mutants are temperature-sensitive, sporulating at 32 degrees, but not at 23 degrees. In addition to CSP mutants, our mutagenesis and screening procedure led to the isolation of mutants which sporulate by virtue of a change in the mating-type locus itself, resulting in loss of ability to mate.
Blood Perfusion Measurements in the Canine Prostate During Transurethral Hyperthermia

Using a thermal pulse decay technique, blood perfusion rates were measured within different regions in the canine prostate under normal and hyperthermic conditions induced either by the microwave or the radio frequency heating. Results indicate that, under the normal condition, the periurethral region is most highly perfused with an average rate of 0.60 +/- 0.25 ml/min/gm (n = 4) while the perfusion rate is 0.34 +/- 0.22 ml/min/gm (n = 10) in parenchyma. An approximately 3.5 fold increase in perfusion from the respective baselines was observed in both regions when the local tissue temperature was raised to 41.5 degrees C by the microwave heating. Another 0.5 fold increase was found in parenchyma after the tissue was further heated to 43.1 degrees C at which oscillatory behaviors in tissue temperature have been observed. To further study the cause of these oscillatory behaviors, the instantaneous blood perfusion response to changes in local tissue temperature was investigated using the radio frequency heating. It has been revealed that blood flow acts as a feedback of local tissue temperature in a closed control system. The thermally stimulated blood perfusion increase appeared to be a function of tissue temperature and its temporal gradient. Results from this study have shown experimental evidences of local thermoregulation in the prostate during hyperthermia.
The relocation experience analysis of factors thought to influence adjustment to transition

This paper provides an overview of the literature on the psychological, sociological, and environmental factors associated with relocation. From this review of the literature several hypotheses have been abstracted and are suggested for further study. A new model is also presented which examines these factors in relation to their influence on adjustment to transition.
Mechanistic explanation at the limit

Resurgent interest in both mechanistic and counterfactual theories of explanation has led to a fair amount of discussion regarding the relative merits of these two approaches. James Woodward is currently the pre-eminent counterfactual theorist, and he criticizes the mechanists on the following grounds: Unless mechanists about explanation invoke counterfactuals, they cannot make sense of claims about causal interactions between mechanism parts or of causal explanations put forward absent knowledge of productive mechanisms. He claims that these shortfalls can be offset if mechanists will just borrow key tenets of his counterfactual theory of causal claims. What mechanists must bear in mind, however, is that by pursuing this course they risk both the assimilation of the mechanistic theories of explanation into Woodward’s own favored counterfactual theory, and they risk the marginalization of mechanistic explanations to a proper subset of all explanations. An outcome more favorable to mechanists might be had by pursuing an actualist-mechanist theory of the contents of causal claims. While it may not seem obvious at first blush that such an approach is workable, even in principle, recent empirical research into causal perception, causal belief, and mechanical reasoning provides some grounds for optimism.
A pioneering spirit: using administrative metadata to manage electronic resources

This article describes administrative metadata and their use in managing electronic resources. The focus of the article is an interview with Tim Jewell, Head of Collection Management Services at the University of Washington, and Adam Chandler, Information Technology Librarian at Cornell University.
Efficacies of Measures of Association for Ordinal Contingency Tables

Abstract The concept of statistical efficacy is applied to measures of association appropriate for contingency tables in which both classifications are ordinal. Measures considered are those based on pairs (such as Kendall's tau and Somers's D), those interpretable as product-moment correlations, Spearman's rho, and those related to Cohen's kappa. Formulas are given, and techniques for estimating efficacies from data are discussed.
Failures on a therapeutic milieu

“An intolerance of increasing regressive behavior seems to oblige the patient to control herself. This seems similar to the young child who gets hurt outside the house but is able to control himself until home with his mother, at which time he is able to relinquish controls. In other words, the readiness to regress appears to be related in part to its acceptance by those in the environment.”
Engineering Design in Industry: Teaching Students and Faculty to Apply Engineering Science in Design

In a typical engineering curriculum students and faculty rarely have the opportunity to take a real problem, extract its essence, apply an analysis, and then make design decisions based on this analysis. This extractive link between fundamentals and design is particularly critical to a smooth transition from engineering study at the university to engineering practice in industry. Historically, universities have taken the responsibility for rigorous theoretical and technical training in subjects that include the basic sciences and fundamentals of engineering, while industry has been responsible for making engineering graduates contributors to specific tasks important to the company and its core competency. In this division of training, however, no one teaches students how to apply fundamental engineering principles to practical problems. To make matters worse, faculty often ignore engineering relevance of basic theory and the students then reject these fundamentals; in both cases engineering performance suffers. One solution to this missing bridge is being developed in the Mechanical and Aerospace Engineering Department at the University of California, Irvine (UCI) in the form of the “Engineering Design in Industry” program.
Fabricating Microlens Arrays by Surface Wrinkling

The ability to generate microlens arrays in a rapid and costeffective manner allows for the fabrication of a variety of inexpensive functional devices, such as optical refractive elements or smart surfaces that mimic the patterned surfaces in biological systems used to control solid and liquid adhesion. A variety of strategies have been adopted for fabricating microlens structures. In general, they can be broadly classified into three categories: 1) surface-tension-driven techniques consisting of melt-reflow and ink-jet printing; 2) imprinting methods; and 3) lithographic approaches such as grayscale photolithography or interference lithography. While these approaches demonstrate the ability to produce microlens arrays with uniform surface profiles, the techniques are either high-cost or require long fabrication times. In this paper, we introduce an alternative and novel approach for fabricating microlens arrays that is based on the confinement of surface wrinkles. We demonstrate the ability to control the size and the arrangement of the microlenses through clever control of the geometric shape and material properties of the wrinkled regions. Our approach offers several advantages over previous methodologies of microlens fabrication, including: 1) the ability to create microlens arrays rapidly; 2) ease of tuning the dimensions of the microlenses; and 3) versatility in the process that allows the formation of microlens arrays on nonplanar substrates. We demonstrate the flexibility of our approach in patterning nonplanar surfaces by patterning a hemispherical surface with an array of microlenses, thereby forming a compound lens (Fig. 1). To fabricate the microlens arrays, we modified our previously developed methodology for generating wrinkle-pattern surfaces (Fig. 2a). We began by selective ultraviolet/ ozone (UVO) oxidation of a crosslinked polydimethylsiloxane (PDMS) film to convert specific regions of the PDMS surface into a silicate thin film. The chemical modification created the necessary elastic-moduli differences on the PDMS surface to allow us to control and define the wrinkle formation. Following the silicate formation, the surface was coated with photopolymerizable n-butyl acrylate (nBA) and then covered with a glass superstrate. The acrylate monomer swelled the PDMS surface globally, but the surface wrinkles occurred only in regions where the moduli mismatch existed—that is, in the oxidized PDMS regions. This selective UVO allowed for the control of the spatial distribution of the wrinkle patterns (Fig. 2b and c). The wrinkle patterns disappeared upon evaporation of the acrylate swelling agent; however, we stabilized these wrinkle structures through photopolymerization of the nBA. Finally, we lifted away the glass superstrate, which caused cohesive fracture of the polymerized poly(n-butyl acrylate) (PnBA) film. Due to the extreme interfacial moduli mismatch between the PnBA and silicate layers, the fracture path proceeded along the contours of the wrinkle surface. Hence, the microlens arrays were revealed upon removal of the glass superstrate (Fig. 2b). C O M M U N IC A TI O N
The enhanced pedestal H-mode in the National Spherical Torus experiment

Abstract Typical H-mode pedestal electron and ion temperatures in NSTX range from 100–300 eV. A new operating regime termed the ‘enhanced pedestal’ (EP) H-mode has been observed in which the pedestal ion temperature increases to ∼600 eV in about 50 ms, or one energy confinement time, resulting in a global confinement improvement. Ion temperature gradients as high as 30 keV/m are observed. The regime is correlated with a localized braking of the edge toroidal rotation near the q = 3 surface, in which case the pressure gradient term in the radial force balance becomes dominant over the toroidal and poloidal rotation terms. Coupled with increased rotation just inside the barrier, the radial electric field shear is also increased. An MHD trigger event (large edge localized mode) is common to the formation of the EP H-mode phase, which can occur either during the Ip ramp-up or flat-top phases of discharges. The observed characteristics of this scenario are presented.
Carbonitridation of Fly Ash. 3. Effect of Indecomposable Additives

A series of indecomposable additives was tested for its effect on the nitridation of fly ash. The carbonitridation reaction was carried out in a tubular high-temperature furnace. SiAlON (silicon aluminum oxynitride)-based powders were prepared from fly ash/carbon mixture in a nitrogen atmosphere. Fly ash from the Huntley and Hatfield power plant was examined in this paper. The additives, in the amount of 4 wt %, are represented by several inorganic salts. Systematic analysis made it possible to select proper elements or groups having a strong effect on the nitridation reaction. The results revealed the possibility of manufacturing of expensive SiAlON whiskers at a low cost. This group of additives was never tested in the literature. A nitrogen/oxygen analyzer measured nitrogen content in the final product. Weight losses were also measured to indicate the extent of the evaporation of the solid materials. Scanning electron microscopy and an energy-dispersive X-ray spectrometer were used to characterize the ...
URF13, a ligand-gated, pore-forming receptor for T-toxin in the inner membrane of cms-T mitochondria

URF13 is the product of a mitochondrial-encoded gene (T-urf13) found only in maize plants containing the Texas male-sterile cytoplasm (cms-T), and it is thought to be responsible for both cytoplasmic male sterility and the susceptibility of cms-T maize to the fungal pathogens Bipolaris maydis race T and Phyllosticata maydis. Mitochondria isolated from cms-T maize are uniquely sensitive to pathotoxins (T-toxin) produced by these fungi and to methomyl (a commercial insecticide). URF13 acts as a receptor that specifically binds T-toxin to produce hydrophilic pores in the inner mitochondrial membrane. When expressed in Escherichia coli cells, URF13 also forms hydrophilic pores in the plasma membrane if exposed to T-toxin or methomyl. Topological studies established that URF13 contains three membrane-spanning alpha-helices, two of which are amphipathic and can contribute to pore formation. Chemical cross-linking of URF13 was used to demonstrate the existence of URF13 oligomers in cms-T mitochondria and E. coli cells. The ability of the carboxylate-specific reagent, N,N'-dicyclohexycarbodiimide, to cross-link URF13 was used in conjunction with site-directed mutagenesis to establish that the URF13 tetramer has a central core consisting of a four-alpha-helical bundle which undergoes a conformational change after interaction with T-toxin or methomyl. Overall, the experimental evidence indicates that URF13 functions as a ligand-gated, pore-forming T-toxin receptor in cms-T mitochondria.
Fine dissection of a nine amino acid glycoprotein epitope, a major determinant recognized by lymphocytic choriomeningitis virus-specific class I-restricted H-2Db cytotoxic T lymphocytes.

We define a nine-amino acid (aa) sequence of VAL-GLU-ASN-PRO-GLY-GLY-TYR-CYS-LEU as a major epitope for immunologic recognition of lymphocytic choriomeningitis virus (LCMV) by H-2b-restricted CTL. The epitope was characterized using molecular genetics to bracket broadly and chemistry to precisely identify aa residues 278-286 of the viral glycoprotein. The epitope's composition is characteristic of a reverse (beta turn) but not an amphipathic alpha helix. A series of peptides with a single aa substitution in position 278 of VAL with other nonpolar (hydrophobic) amino acids (LEU, ILE, ALA, or GLY) coat targets that are recognized and lysed by CTL clones recognizing this epitope. In contrast, substitution of VAL with either large aromatic amino acids (that add bulk: PHE, TYR) or polar side chains (SER, THR) segregates CTL clones normally recognizing aa 278-286 into two groups, one that remains lytic (permissive) despite these changes and another that fails to lyse, indicating CTL can discriminate at a single aa. A change in charge at this position (VAL\---|-ASP or GLU), in general, reduces CTL lysis while a change of VAL to LYS or ASN has minimal affect for four of the five CTL clones analyzed. CTL reactivity with the viral epitope is restricted by the Db but not the Kb of the murine MHC haplotype. A 16-aa peptide of Db that spans alpha 1 residues 37-52 blocks CTL lysis, whereas the corresponding Kb peptide that differs from Db in a single aa in position 50 does not.
The role of cortisone acetate in liver RNA synthesis of gamma-irradiated rats.

SummaryThe possible role of induced endogenous glucocorticoid levels stimulated by ionizing radiation and their subsequent effect on rat-liver RNA was investigated in adrenalectomized rats using an intraperitoneal injection of cortisone acetate immediately prior to exposure to gamma-radiation (1800 rad). Adrenalectomized rats were divided into four groups: (1) control rats, (2) irradiated rats, (3) non-irradiated rats treated with cortisone acetate (10 mg/rat), and (4) irradiated rats which received cortisone acetate immediately before irradiation. Newly synthesized RNA was measured by an intraperitoneal injection of 8 µCi (6-14C) orotic acid either immediately after irradiation or 40 min prior to killing. All the rats were killed 6 hours post-irradiation. The results of these investigations indicate that (1) newly synthesized (40 min labelling) RNA increased in irradiated adrenal-intact rats, but not in adrenalectomized animals; (2) cortisone acetate by itself stimulated RNA synthesis whether the radioac...
A skeptic assesses the Net as a resource for teaching

The purpose of the talk (and this paper) is to explore the advantages and disadvantages of providing courses, programs and degrees using On-Line Learning (OLL). It is the author's thesis that, yes, OLL does provide new opportunities for the delivery of education. However, we need to be very careful as to how we use this medium in order not to "reshape" courses which are more effectively taught in other (possibly more traditional) ways nor to embrace this mode of delivery simply for perceived economic gains.The rush of higher education institutions to place courses and programs on the Internet for distance education students raises some very interesting questions concerning their quality and value. The initial development of courses for online learning has been based on text based delivery --- for the most part using traditional lecture notes. The rapid sophistication brought about by html programming, advanced browsers, and template authorware on the one hand, and more sophisticated and powerful hardware and multimedia devices on the other, have permitted great strides in resource integration. Yet, for all of these technological advances, a number of problems still exist. The rest of this paper will explore some of these problems and offer some suggestions for solving them..
One-dimensional transport from a highly concentrated, transfer type source

Abstract In both heat and mass transfer, situations arise in which an entity considered as a source/sink has strength which can only be expressed in terms of an unknown rate of source—flow field transfer. This occurs when transfer between the source and medium is driven by a dependent variable difference which is unknown, because the responding medium value is unknown. Manifold mathematical complexities arise when in addition the source is highly concentrated spatially, relative to the size of the overall domain. A 1-dim. convective-diffusive transport equation suitable for this case may be solved by simultaneous use of the Fourier transform and its inverse in the same equation, together with other transformation and manipulation. From the solution obtained for the case of constant source intensity, one may construct a general expression for the solution when source intensity varies arbitrarily in time. Explicit expressions are obtained for solution of the fundamental case of temporally sinusoidal source intensity.
Renal cell carcinoma presenting with paraneoplastic hypercalcemic coma : A case report and review of the literature

We report a case of a 62-year-old woman with renal cell carcinoma (RCC) presenting with a hypercalcemia-induced coma. A laboratory evaluation indicated nonparathyroid-mediated hypercalcemia with an initial serum calcium level of 18.6 mg/dL. Our patient's parathyroid hormone (PTH)-related peptide level was undetectable. Initial imaging was negative, but PET scan identified a mass in the upper pole of the left kidney. Our patient underwent partial nephrectomy, and the mass was identified as RCC on final pathology. After surgery, her hypercalcemia resolved and PTH returned to normal limits. This case report describes a patient with RCC with the unusual presentation of hypercalcemic coma. We review the differential diagnosis of malignant hypercalcemia and the evaluation of hypercalcemia occurring with RCC. This case illustrates the need to carefully review and interpret all available data, especially when conventional testing in the work-up of hypercalcemia is unrevealing.
Effect of hypothalamic lesions on canine neurogenic arterial hypertension.

SummaryChronic neurogenic hypertension in dogs induced by moderator nerve section producing an increase in the central excitatory state of the medullary cardiovascular centers, is not permanently influenced to a significant degree by lesions of the hypothalamus or its descending pathways compatible with survival of the animals. It is suggested that the most important neurogenic homeostatic influence upon the arterial tension is exerted by the moderator nerves at the medullary level and that higher levels of the central nervous system act as temporary modulating influences in response to momentary needs rather than as chronic adjusters of the arterial tension.
EndNote Web: Web-Based Bibliographic Management

Web-based bibliographic management tools provide researchers with the ability to manage their resources at the point of discovery, whether at home, in the office, or abroad. EndNote Web from Thomson Reuters is one such tool that allows the user to access, manage, and use saved citations from an entirely web-based system. As research and researchers, professionals, and students alike become more and more mobile, tools such as EndNote Web cater to the changing nature of resource collection and management. This article provides an overview of the features and functions EndNote Web has to offer.
Fragmentation and choreography: caring for a patient and a chart during childbirth

CSCW has long been concerned with how work is coordinated. A rich body of literature examines the mechanisms underlying cooperative work and the articulation of discrete tasks into meaningful sequences of action. However, there is less treatment of how workers balance multiple streams of work at once. In hospitals, the introduction of Health Information Technologies coupled with increased requirements for documentation means that workers must simultaneously care for and integrate two work trajectories: that related to the patient and that related to the medical record. Using data from an ethnographic study of labor & delivery nurses in a mid-size hospital, I describe the situated, embodied, and effortful work of coordinating multiple streams of action into a single coherent performance of work, a process I refer to as choreography, and present a number of choreography practices. I then describe implications of this perspective for CSCW.
Bilateral anterior inferior iliac spine avulsion fractures

A case of bilateral groin pain of sudden onset in a 14-yr-old boy is presented. The patient reported sudden onset of pain in both inguinal regions during a 100-m dash. He presented a week later to the clinic where physical examination revealed a shuffling gait, bilateral hip flexion contractures, limited active and passive hip extension, and bilateral weakness of hip flexion and knee extension. Plain radiographs of the pelvis revealed avulsion fragments minimally displaced from both anterior inferior iliac spines (AIIS). Pain relief in the acute phase was achieved by limiting ambulation until weight bearing was painless. The patient was treated conservatively and returned to full speed running in 10 wk. Only one case of bilateral AIIS avulsion fractures has previously been reported. AIIS avulsion fractures that are not widely displaced may be treated conservatively. Following a careful program of rehabilitation, full functional recovery following AIIS avulsion fractures may be achieved in 4-6 wk.
Association of RNA Polymerase Complexes of the Parasitic Protozoan Cryptosporidium parvum with Virus-Like Particles: Heterogeneous System

RNA polymerase complexes were purified from Cryptosporidium parvum, a parasitic protozoan known to infect many species of mammals including humans. Western blot analysis revealed the association of the complexes with two different proteins, encoded by large and small segments of viral double-stranded RNAs. Each complex was found to contain only double-stranded RNA, both double- and single-stranded RNA, or only single-stranded RNA. Maximum RNA-dependent RNA polymerase activity was observed within the complexes containing both double- and single-stranded RNAs. These complexes possessed both transcriptase and replicase polymerase activities. Virus-like particles with a diameter of 31 nm were copurified with RNA polymerase complexes, and buoyant density and polymerase studies suggest that C. parvum harbors a putative double-stranded RNA virus which separately encapsidates the large and small RNA segments. The mechanism of replication and other characteristics of this virus are similar to those of the viruses of the family Partitiviridae, previously identified only in fungi and plants.
Dynamics, Brandom-style

This paper discusses the semantic theory presented in Robert Brandom’s Making It Explicit. I argue that it is best understood as a special version of dynamic semantics, so that these semantics by themselves offer an interesting theoretical alternative to more standard truth-conditional theories. This reorientation also has implications for more foundational issues. I argue that it gives us the resources for a renewed argument for the normativity of meaning. The paper ends by critically assessing the view in both its development and motivations.
A low-pass notch filter for bioelectric signals

Many bioelectric signals have relatively low-frequency content, but measurement devices are susceptible to power-line interference. The Type II Chebyshev low-pass filter can simultaneously perform the required low-pass filtering and removal of the narrowband interference. This filter has transfer-function zeros which result in zero gain (- infinity dB) at specific 'null' frequencies. A procedure for the low-pass filter design makes the first null frequency a design parameter so that the notch can occur at the interference frequency. >
Gamma-gamma directional correlation study in 92 Zr

The gamma-gamma directional correlation of the 2+′-2+-0+, 913(Iγ=1.69)-934(Iγ =100)keV cascade in92Nb decay has been investigated with a NaI-Ge(Li) system. Our results yieldδ=−0.013 −0.024 +0.041 . This is one of a very few cases where the second 2+ to first 2+ transition is not predominatelyE2. This may be related to the closed neutron shell, as earlier suggested. [Radioactivity92Zr; measuredγ-γ(θ), deducedδ]
Volume Warrant for Free Right-Turn Lanes at Unsignalized Intersections on Rural Two-Lane Highways

The objective of the research presented in this paper was to develop a volume warrant for free right-turn (FRT) lanes at unsignalized intersections on rural two-lane highways. The warrant was based on a cost-benefit analysis that determined the right-turn volumes required to justify the construction and maintenance of FRT lanes at such locations. The research involved the evaluation of the safety and operational effects of FRT lanes. The safety effects of FRT lanes were determined from a comparison of the accident experience at intersections with and without FRT lanes. The operational effects of FRT lanes were analyzed using kinematic and traffic flow models. FRT lanes were not found to affect the frequency, severity, or types of accidents that occur at unsignalized intersections on rural two-lane highways. Thus, the benefits of FRT lanes are limited to improving the efficiency of right-turn movements. The results of the research indicate that design-year right-turn annual average daily traffic ranging from 440 to 825 vehicles per day, depending on the percentage of trucks, is required to warrant an FRT lane. A design speed of 64 km/h (40 mph) was found to be the most cost-effective design speed for FRT lanes. However, design speeds up to 89 km/h (55 mph) do not significantly reduce the cost effectiveness of an FRT lane.
Risk factors associated with the presence of viable Listeria monocytogenes in bulk tank milk from US dairies.

Summary The objective of the study was to screen a large number of herd management practices and herd characteristics from US dairies to identify herd-level risk factors associated with the presence of Listeria monocytogenes in bulk tank milk (BTM). A total of 71 variables was univariately evaluated for their association with the presence of L. monocytogenes in BTM. Results from the univariate analysis indicated that using automatic take offs and having an open herd management increased the risk of BTM contamination with L. monocytogenes, while storing manure in outside pens not accessible to cattle decreased the risk. These variables, however, were not sustained in the multivariable model, which indicated that the presence of L. monocytogenes in BTM was significantly associated with region of the country (farms in the southeast and northeast were six and four times more likely respectively, to have BTM contamination than farms in the west) and number of milking cows (herds with >500 milking cows were five times more likely to have BTM contamination than herds with <100 milking cows). In conclusion, our results suggest that risk factors associated with BTM contamination are different depending on the geographical region and herd size of the operation.
Ambiguity, pessimism, and rational religious choice

Using a subclass of the α-maximin expected-utility preference model, in which the decision maker’s degree of ambiguity and degree of pessimism are each parameterized, we present a theory of religious choice in the Pascalian decision theory tradition, one that can resolve dilemmas, address the “many Gods objection,” and address the ambiguity inherent in religious choice. Parameterizing both the degree of ambiguity and the degree of pessimism allows one to examine how the two interact to impact choice, which is useful regardless of the application. Applying this model to religious choice is a move beyond subjective expected-utility theory, allowing us to show that a change in either the degree of ambiguity or the degree of pessimism can lead a decision maker to “convert” from one religion to another.
The many paths to p38 mitogen-activated protein kinase activation in the immune system

Signals emanating from many cell-surface receptors and environmental cues converge on mitogen-activated protein kinases (MAPKs), which in turn phosphorylate and activate various transcription factors and other molecular effectors. Members of the p38 MAPK family, which respond to pro-inflammatory cytokines and cellular stresses, are typically activated by serial phosphorylation and activation of upstream kinases (the MAPK cascade). In this Review, I highlight the recent studies that indicate that p38-subfamily members can also be activated by non-canonical mechanisms, at least one of which seems to have an important role in antigen-receptor-activated T cells. These alternative pathways might have particular relevance for cells that participate in immune and inflammatory responses.
The Suburbanization of New York: Is the World's Greatest City Becoming Just Another Town?

The article reviews the book "The Suburbanization of New York: Is the World's Greatest City Becoming Just Another Town?" edited by Jerilou Hammett and Kingsley Hammett.
Electrostatics at the nanoscale

Electrostatic forces are amongst the most versatile interactions to mediate the assembly of nanostructured materials. Depending on experimental conditions, these forces can be long- or short-ranged, can be either attractive or repulsive, and their directionality can be controlled by the shapes of the charged nano-objects. This Review is intended to serve as a primer for experimentalists curious about the fundamentals of nanoscale electrostatics and for theorists wishing to learn about recent experimental advances in the field. Accordingly, the first portion introduces the theoretical models of electrostatic double layers and derives electrostatic interaction potentials applicable to particles of different sizes and/or shapes and under different experimental conditions. This discussion is followed by the review of the key experimental systems in which electrostatic interactions are operative. Examples include electroactive and “switchable” nanoparticles, mixtures of charged nanoparticles, nanoparticle chains, sheets, coatings, crystals, and crystals-within-crystals. Applications of these and other structures in chemical sensing and amplification are also illustrated.
Expert and novice intuitive judgments about animal behavior

Although research in comparative psychology often relies on direct behavioral observation for data gathering, the influence of the observer is often overlooked. To study the effect of expertise on making judgments about behavior, novices and experts observed videotapes of rats from enriched and impoverished environments and attempted to determine each rat’s history. The judgment accuracy of all groups exceeded chance. Although experts used a broader vocabulary for describing the foundations of their judgments concerning animal behavior, novices were as accurate as experts at making the discrimination. Subjects were not able to correctly assess their own accuracy. The results of this study suggest that observer expertise does influence the data-gathering process in comparative psychology, but in indirect and often subtle ways.
Scanning Tunneling Microscopy Study of the Anatase (100) Surface

Abstract Scanning tunneling microscopy (STM) has been used to investigate the structure of the TiO2 anatase (1 0 0) surface. Natural single crystals of anatase were employed; and after several cycles of sputtering and annealing at T=450 °C, the TiO2(1 0 0) surface was free of impurities, and reconstructed to a (1×n) termination. No evidence for point defects was found in the atomic resolution STM images. The STM results were accounted for on the basis of a surface structure model in which (1 0 1)-oriented microfacets run along the anatase [0 1 0] direction.
Engineering of Human Pluripotent Stem Cells by AAV-mediated Gene Targeting

Precise genetic manipulation of human pluripotent stem cells will be required to realize their scientific and therapeutic potential. Here, we show that adeno-associated virus (AAV) gene targeting vectors can be used to genetically engineer human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Different types of sequence-specific changes, including the creation and correction of mutations, were introduced into the human HPRT1 and HMGA1 genes (HPRT1 mutations being responsible for Lesch–Nyhan syndrome). Gene targeting occurred at high frequencies in both ESCs and iPSCs, with over 1% of all colony-forming units (CFUs) undergoing targeting in some experiments. AAV vectors could also be used to target genes in human fibroblasts that were subsequently used to derive iPSCs. Accurate and efficient targeting took place with minimal or no cytotoxicity, and most of the gene-targeted stem cells produced were euploid and pluripotent.
Connectotyping: Model Based Fingerprinting of the Functional Connectome

A better characterization of how an individual’s brain is functionally organized will likely bring dramatic advances to many fields of study. Here we show a model-based approach toward characterizing resting state functional connectivity MRI (rs-fcMRI) that is capable of identifying a so-called “connectotype”, or functional fingerprint in individual participants. The approach rests on a simple linear model that proposes the activity of a given brain region can be described by the weighted sum of its functional neighboring regions. The resulting coefficients correspond to a personalized model-based connectivity matrix that is capable of predicting the timeseries of each subject. Importantly, the model itself is subject specific and has the ability to predict an individual at a later date using a limited number of non-sequential frames. While we show that there is a significant amount of shared variance between models across subjects, the model’s ability to discriminate an individual is driven by unique connections in higher order control regions in frontal and parietal cortices. Furthermore, we show that the connectotype is present in non-human primates as well, highlighting the translational potential of the approach.
Computational Insights into Retinal Dynamics in Rhodopsin

Rhodopsin is one of the primary systems for computational studies of G-protein coupled receptor (GPCR) activation pathways [1,2]. Activation occurs through isomerization of its covalently bound ligand, retinal, from an 11-cis to an all-trans conformation. FTIR spectroscopy studies indicated the importance of retinal methyl groups, clearly demonstrating that retinal desmethyl analogs caused a backshift in the activation pathway [3]. Additionally, recent 2H nuclear magnetic resonance (NMR) studies on retinal bound to rhodopsin hint towards a much lower methyl rotation activation barrier than observed in previous MD simulations [4]. Here we report quantum chemical calculations of torsional surfaces of model compounds and molecular dynamics (MD) simulations of the proteolipid complex in full atomic detail, to aid in the interpretation of the body of experimental data. Specifically, by using larger retinal fragments and a higher level of theory (MP2/cc-pVDZ), we are able to accurately reproduce the rotational behavior observed from 2H NMR relaxation data [4]. For example, the relaxation data indicate an unusually low activation energy (Ea) for C9-methyl rotation, due to intraretinal interactions with H7 and H11 of the retinal polyene chain. These results in turn should lead to the ability to begin to simulate the coupling of small- to large-scale motions in rhodopsin activation. Ultimately, these efforts are aimed towards modeling more accurate comparisons to other GPCR proteins. [1] P.-W. Lau et al. (2007) J. Mol. Biol. 372(4) 906-917. [2] K. Martinez-Mayorga et al. (2006) J. Amer. Chem. Soc. 128(51) 16502-16503. [3] R. Vogel et al. (2006) Biochemistry 45(6), 1640-1652. [4] M.F. Brown et al. (2009) Biochim. Biophys. Acta, in press.
Local Influence Diagnostics for Quasi‐Likelihood and Lognormal Estimates of a Biological Reference Point from Some Fish Stock and Recruitment Models

We present local influence diagnostics to measure the sensitivity of a biological limit reference point (LRP) estimated from fitting a model to stock and recruitment data. LRPs are low levels of stock size that the management of commercial fisheries should avoid with high probability. The LRP we examine is the stock size at which recruitment is 50% of the maximum (S(50%)). We derive analytic equations to describe the effects on S(50%) of changing the weight that observations are given in estimation. We derive equations for the Ricker, Beverton-Holt, and hockey-stick stock-recruit models, and four estimation methods including the error sums of squares method on log responses and three quasi-likelihood methods. We conclude from case studies that the hockey-stick model produces the most robust estimates.
Cold-shock regulation of the arabidopsis TCH genes and the effects of modulating intracellular calcium levels

The Arabidopsis TCH genes, which encode calmodulin-related proteins and a xyloglucan endotransglycosylase, are shown to be up-regulated in expression following cold shock. We investigated a possible role of fluctuations in intracellular calcium ion concentra- tions ([Ca2+]) in the cold-shock-induced TCH gene expression. Transgenic plants harboring the apoaequorin gene were generated to monitor [Ca2+] and to test the necessity of cold-induced [Ca2+] increases for TCH expression. Cold-shock-induced [Ca2+] increases can be blocked by La3+ and Gd3+, putative plasma membrane Ca2+ channel blockers, and 1,2-bis(o-aminophenoxy)ethane-N,N,N[prime],N[prime]- tetraacetic acid, an extracellular Ca2+ chelator. Cold-shock-induced expression of the TCH genes is inhibited by levels of La3+, Gd3+, and 1,2-bis(o-aminophenoxy)ethane-N,N,N[prime],N[prime]-tetraacetic acid, that have been shown to block [Ca2+] increases. These data support the hypotheses that (a) intracellular [Ca2+] increases following cold shock require extracellular Ca2+ and may derive from a Ca2+ influx mediated by plasmalemma Ca2+ channels, and (b) cold up-regulation of expression of at least a subset of the TCH genes requires an intracellular [Ca2+] increase. The inhibitors are also shown to have stimulus-independent effects on gene expression, providing strong evidence that these commonly used chemicals have more complex effects than generally reported.
Eosinophilia Myalgia Syndrome Secondary to Contaminated Tryptophan—Clinical Experience

This article describes the history of an outbreak of eosinophilia myalgia syndrome (EMS) in 1989, which was rapidly linked by researchers to the amino acid L-tryptophan (tryptophan), which is widely taken as a supplement. An alternative hypothesis was proposed for the cause of EMS, based on the safety associated with the use of tryptophan over decades and the possibility of contamination of the tryptophan during manufacture. The process by which this hypothesis has been substantiated and the contaminant identified is described here.
Replication data sets and favored-hypothesis bias: Comment on Jeremy Freese (2007) and Gary King (2007)

Jeremy Freese makes the case for data sharing as a condition of publication for quantitative research in sociology, and Gary King tells us of a Dataverse Network under construction that is designed...
NOSH-Aspirin: A Novel Nitric Oxide–Hydrogen Sulfide-Releasing Hybrid: A New Class of Anti-inflammatory Pharmaceuticals

A series of new hybrids of aspirin (ASA), bearing both nitric oxide (NO) and hydrogen sulfide (H2S)-releasing moieties were synthesized and designated as NOSH compounds (1–4). NOSH-1 (4-(3-thioxo-3H-1,2-dithiol-5-yl) phenyl 2-((4-(nitrooxy)butanoyl)oxy) benzoate); NOSH-2 (4-(nitrooxy)butyl (2-((4-(3-thioxo-3H-1,2-dithiol-5-yl)phenoxy)carbonyl)phenyl)); NOSH-3 (4-carbamothioylphenyl 2-((4-(nitrooxy)butanoyl)oxy)benzoate); and NOSH-4 (4-(nitrooxy)butyl 2-(5-((R )-1,2-dithiolan-3-yl)pentanoyloxy)benzoate). The cell growth inhibitory properties of compounds 1–4 were evaluated in eleven different human cancer cell lines of six different tissue origins. These cell lines are of adenomatous (colon, pancreatic, lung, prostate), epithelial (breast), and lymphocytic (leukemia) origin. All NOSH compounds were extremely effective in inhibiting the growth of these cell lines. NOSH-1 was the most potent, with an IC50 of 48 ± 3 nM in HT-29 colon cancer cells. This is the first NSAID-based compound with such potency. This...
A Study of the Cell and Colony Variations of Blastomyces Dermatitidis

Fungi like bacteria show striking variations of their cell and colony forms under different growth conditions. In 1932 Emmons1 reviewed the accumulated literature on cell pleomorphism and colony variation in the fungi in his report of new colony forms of Achorion and Trichophyton. More recently Fabian and McCullough2 have shown that the yeasts undergo true dissociation into phases analogous to those of bacterial mutation. Whether or not other fungi exhibit a similar uniformity of cell and colony variation has not as yet been ascertained. This paper is the report of a study of the cell and colony variations of Blastomyces dermatitidis and a description of a new colony form of that organism. The observations were made on a stock strain of the fungus originally isolated from a case of blastomycosis. The cultures were grown at 37.5 C. upon beef extract agar in the preparation of which the constituents and the hydrogen ion concentrations were varied as will be described. All cultures were incubated in a humidor to prevent fluid loss through evaporation from the medium. In as much as the materials and methods were those
Estimates of the demand for ethical pharmaceutical drugs across countries and time

The aggregate demand for ethical pharmaceutical drugs using country-level data for seven countries pooled across an eight-year period is estimated. The regression analysis reveals that the net price paid by consumers has a negative effect on the average number of prescriptions per capita while income has a positive effect. Moreover, the parameter estimates suggest thst the demand is relatively elastic in most countries, and that the income elasticity is greater than one.
Cultural revitalization movements in organization change management

Abstract The 1992 study of Kotter and Heskett on successful corporate culture change reveals one of the most empirically convincing models for organization change management. The procedure demonstrated by Kotter and Heskett's research fits the pattern and dynamics of a universal social phenomenon of culture change defined in 1956 by Wallace as revitalization. Applying the psychodynamics of revitalization explains how this procedure of corporate culture change in distressed organizational cultures creates an adaptable culture of new behavioral norms. The driving force of this procedure is the transference of dependency wishes among anxious organization members onto their perceived powerful organization leader. An understanding of how and why organizational cultures change according to this model can guide the values and behavior of organizational leaders in successfully managing organizational change.
CHARACTERISATION OF THE ISOMETRIC COMPOSITION OPERATORS ON THE BLOCH SPACE

In this paper, we characterise the analytic functions ’ mapping the open unit disk into itself whose induced composition operator C’ : f 7! f ’ is an isometry on the Bloch space. We show that such functions are either rotations of the identity function or have a factorisation ’ = gB where g is a non-vanishing analytic function from into the closure of , and B is an infinite Blaschke product whose zeros form a sequence {zn} containing 0 and a subsequence {znj } satisfying the conditions g(znj ) ! 1, and lim j!1 Y k6nj znj zk 1 znj zk = 1.