cssi/SciSciGPT-SciSciNet huggingface dataset:
Viral load decay in antiretroviral-naïve patients receiving once-daily tenofovir and emtricitabine plus twice-daily nevirapine.

AbstractPurpose: The once-daily nucleoside reverse transcriptase inhibitor backbone of tenofovir and emtricitabine has been proven effective in combination with efavirenz and protease inhibitors in large clinical trials. This study evaluated tenofovir and emtricitabine in combination with nevirapine. Methods: Viral load was assessed at baseline, Day 3, and Day 7 in addition to Weeks 2, 4, 8, 12, 16, 24, 32, 40, 48, 60, 72, and 84 in 10 antiretroviral-naive patients participating in an open-label clinical trial of tenofovir and emtricitabine once daily in combination with nevirapine twice daily. Results: All patients achieved viral decay with this combination. Two patients discontinued prior to virologic suppression, one with a viral load of 55 copies/mL. Virologic suppression (<50 copies/mL) was achieved by Week 24 in the remaining 8 patients. An undetectable viral load was maintained during ≥60 weeks follow-up. Conclusion: In this study of treatmentnaive patients, the combination of tenofovir and emtrici...
DNA modeling reveals an extended Lac repressor conformation in classic in vitro binding assays

Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, remain. Recent single-molecule observations suggest that the two DNA-binding domains of LacI are capable of splaying open about the tetramerization domain into an extended conformation. We hypothesized that if recent experiments were able to reveal the extended conformation, it is possible that such structures occurred in previous studies as well. In this study, we tested our hypothesis by reevaluating two classic in vitro binding assays using a computational rod model of DNA. The experiments and computations evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA interoperator lengths. The computed energetic minima align well with the experimentally observed interoperator length for optimal loop stability. Of equal importance, the model reveals that the most stable loops for linear DNA occur when LacI adopts the extended conformation. In contrast, for DNA minicircles, optimal stability may arise from either the closed or the extended protein conformation depending on the degree of supercoiling and the interoperator length.
Torsion of an accessory spleen: Case report and review of the literature

Torsion of an accessory spleen is an uncommon cause of abdominal pain. Only a few cases have been reported in the literature. Most cases occur in children, and in most cases the diagnosis is made at surgery. We report a case of torsion of an accessory spleen in an adult female who presented with acute left-flank pain. The diagnosis was made on contrast-enhanced computed tomography (CT) and was confirmed at surgery. Without treatment, torsion of an accessory spleen can lead to hemorrhagic shock, peritonitis, and bowel obstruction. It is useful for the radiologist to make this diagnosis on imaging so that biopsy can be avoided and surgery performed to avoid complications.
Decentralized operation strategies for an integrated building energy system using a memetic algorithm

Abstract The emerging technology in net-zero building and smart grids drives research moving from centralized operation decisions on a single building to decentralized decisions on a group of buildings, termed a building cluster which shares energy resources locally and globally. However, current research has focused on developing an accurate simulation of single building energy usage which limits its application to building clusters as scenarios such as energy sharing and competition cannot be modeled and studied. We hypothesize that the study of energy usage for a group of buildings instead of one single building will result in a cost effective building system which in turn will be resilient to power disruption. To this end, this paper develops a decision model based on a building cluster simulator with each building modeled by energy consumption, storage and generation sub modules. Assuming each building is interested in minimizing its energy cost, a bi-level operation decision framework based on a memetic algorithm is proposed to study the tradeoff in energy usage among the group of buildings. Two additional metrics, measuring the comfort level and the degree of dependencies on the power grid are introduced for the analysis. The experimental result demonstrates that the proposed framework is capable of deriving the Pareto solutions for the building cluster in a decentralized manner. The Pareto solutions not only enable multiple dimensional tradeoff analysis, but also provide valuable insight for determining pricing mechanisms and power grid capacity.
Ranked set sampling with concomitant variables

Ranked set sampling is a procedure which may be used to improve the precision of the estimator of the mean. It is useful in cases where the variable of interest is much more difficult to measure than to order. However, even if ordering is difficult, but there is an easily ranked concomitant variable available, then it may be used to “judgment order” the original variable. The amount of increase in the precision of the estimator is dependent upon the correlation between the 2 variables.
Protein turnover and cell-cycle initiation in yeast.

Abstract The effects of short pulses of cycloheximide on the traversal of the G1 phase of the cell cycle of the yeast Saccharomyces cerevisiae were examined. Cells were released from a block at the regulatory stage of G1, termed ‘start’, and pulsed with cycloheximide. Delays in budding which were considerably longer than the length of the pulse were observed. During the delay the cells remained blocked at ‘start’. No delay in budding was observed after cycloheximide pulses, when cells were released from a cdc 24 block which arrests the budding process but not ‘start’. Overall protein synthesis did not show an additional delay after the pulse. The extra lag following cycloheximide pulses appears to reflect a unique feature of ‘start’. It may be accounted for by a requirement at ‘start’ for a labile protein with a half-life time of about 6 min.
Quasi-static intergranular brittle fracture at 0.5 tm: A non-equilibrium segregation mechanism of sulphur embrittlement in stress-relief cracking of low-alloy steels

Abstract A theory of elastic-plastic-diffusive crack growth along grain boundaries is developed and compared with experimental observations of stress-relief cracking of low-alloy steels. Intergranular decohesion advances atomistically by coupled surface and grain-boundary diffusion, while the macroscopic plain-strain crack grows quasi-statistically by maintaining a deformation field in small-scale yielding. Near an advancing crack tip, a surface diffusion distance is found within which steady-state diffusion is driven by a sharp curvature, while a corresponding boundary diffusion distance is found within which diffusion plating overtakes elastic-plastic stretching to smooth out the stress concentration. Diffusional and elastic-plastic processes at an extending crack tip are thus coupled to each other and to the loading parameter at distance. Fast diffusants are predicted to accumulate near the crack tip on both surfaces and grain boundary, confirming a recent scanning Auger observation of sulphur segregation by Hippsley et al. Considerations of non-equilibrium interfacial energies and fracture work reveal the embrittling role of sulphur, both as a fast diffusant and as a strong surface segregant. Predictions of growth rates are in excellent agreement with the data of Shin and McMahon, over the entire range of stress intensity factor and temperature studied. Metallurgical factors promoting brittle stress-relief cracking in the heat-affected zones of welding of low-alloy steels, including sulfide distribution, hot yield strength, and notch sensitivity, are explained.
Probing the Local Dynamics of Nucleotide-Binding Pocket Coupled to the Global Dynamics: Myosin versus Kinesin

Based on the elastic network model, we develop a new analysis for protein complexes, which probes the local dynamics of a subsystem that is elastically coupled to a fluctuating environment. This method is applied to a comparative dynamical analysis of the nucleotide-binding pocket of two motor proteins—myosins and kinesins. In myosins, the observed structural changes in the nucleotide-pocket from the transition state to the rigorlike state are dominated by the lowest normal mode that involves significant movements in both switch I and switch II; in kinesins, the measured conformational changes in the nucleotide-pocket are also dominated by the lowest mode, which, however, only involves large movement in switch I. We then compute the global structural changes induced by the nucleotide-pocket deformations as described by the dominant pocket-mode, which yield encouraging results: in myosins, multiple hinge motions involving the opening/closing of the cleft between the upper and lower 50 -kDa subdomains and the swinging movement of the converter are induced, which are dominated by precisely the same global mode that has been recently identified by us as important to the dynamical correlations among the nucleotide-pocket, the actin-binding site, and the converter; in kinesins, the induced global conformational changes are well described by a highly collective global mode which hints for a dynamical pathway spanning from the nucleotide-pocket to the neck-linker via the H6 helix.
A novel communication method for semi-passive RFID based sensors

This paper presents a novel communication method for semi-passive RFID based sensors. The new method uses a digitally reconfigurable UHF RFID tag antenna to modulate sensed information at an RFID tag on to the received signal strength indicator (RSSI) response perceived at an RFID reader. This technique is completely compatible with the existing class 1 generation 2 UHF air interface protocol thereby enabling the use of existing RFID reader infrastructure to decode the additional sensed information. The effect of read distance, environment and bit duration on the performance of the communication method is examined through measurements obtained from a prototype. Through experimental verification, it is demonstrated that error free transmission of sensor information can be achieved up to 3.5 meters in different environments with a bit duration of 500 ms. Prospective future research directions are also discussed.
Integrating sphere charge coupled device-based measurement method for organic light-emitting devices

An integrating sphere charge coupled device (CCD)-based measurement system has been developed to accurately characterize the optoelectronic performance of organic polymer light-emitting devices (PLEDs). By theoretically analyzing a previously developed lens-coupled method and comparing it with the integrating sphere CCD-based method, we have found that the integrating sphere-based measurement method provides more stable reliable optical data in comparison with the lens-coupled measurement method. In addition, we demonstrate that inappropriate calibration of the PLED measurement system can greatly exaggerate device performance.
Asymmetric electrode kinetics induced by concurrent metal-ligand bond dissociation

Abstract The electrochemistry of the Cu(II)/Cu(I) couple under nitrogen and carbon monoxide has been investigated in the ambient-temperature molten salt AlCl 3 :MEICl (MEICl = 1-methyl-3-ethyl-imidazolium chloride) at a 250 μm tungsten disk electrode. Under nitrogen, the couple exhibits reversible electrode kinetics; however, under carbon monoxide, a Cu(I)CO complex is formed and the Cu(II)/Cu(I) couple displays asymmetric, quasi-reversible electrode kinetics. Pulse voltammetric data were fit with a nonlinear least-squares fitting program to give an apparent standard rate constant ( k 0 a ) of 1.5 × 10 −3 cm s −1 and an anodic transfer coefficient (β) of 0.12–0.17 for the oxidation of the Cu(I)CO complex. The change from reversible to quasi-reversible electrode kinetics is attributed to the concurrent dissociation of the Cu(I)CO bond during the electron transfer process.
The PhoB regulatory system modulates biofilm formation and stress response in El Tor biotype Vibrio cholerae.

The PhoBR regulatory system is required for the induction of multiple genes under conditions of phosphate limitation. Here, we examine the role of PhoB in biofilm formation and environmental stress response in Vibrio cholerae of the El Tor biotype. Deletion of phoB or hapR enhanced biofilm formation in a phosphate-limited medium. Planktonic and redispersed biofilm cells of the Δ phoB mutant did not differ from wild type for the expression of HapR, suggesting that PhoB negatively affects biofilm formation through an HapR-independent pathway. The Δ phoB mutant exhibited elevated expression of exopolysaccharide genes vpsA and vpsL compared with the wild type. Deletion of hapR enhanced the expression of the positive regulator vpsT , but had no effect on the expression of vpsR . In contrast, deletion of phoB enhanced the expression of the positive regulator vpsR , but had no effect on the expression of hapR and vpsT . The Δ phoB mutant was more sensitive to hydrogen peroxide compared with the wild type and with an isogenic Δ rpoS mutant. Conversely, the Δ phoB mutant was more resistant to acidic conditions and high osmolarity compared with the wild type and with an isogenic Δ rpoS mutant. Taken together, our data suggest that phosphate limitation induces V. cholerae to adopt a free-swimming life style in which PhoB modulates environmental stress response in a manner that differs from the general stress response regulator RpoS.
Induction of tyrosine aminotransferase by phentolamine

Abstract The characteristics of tyrosine aminotransferase induction by phentolamine in rat liver are described. After an initial lag period of about 60 min, phentolamine produced a marked increase in enzyme activity which reached a maximum in about 3 hr. This effect was eliminated by either actinomycin D or cycloheximide. The relation of the induction by phentolamine to adrenal steroids was studied. Phentolamine was found to increase plasma corticosterone levels in normal intact animals. The induction by phentolamine was almost completely abolished by either adrenalectomy or hypophysectomy. However, if a small dose of hydrocortisone was given to adrenalectomized rats, phentolamine then produced a significant increase in enzyme activity. The administration of amino-glutethimide completely eliminated any increase in plasma corticosterone but did not completely eliminate the enzyme induction produced by phentolamine. It is concluded that at least two factors are operative in the induction of tyrosine aminotransferase by phentolamine—(1) a response to an increased plasma corticosterone concentration, and (2) an additional effect which may be a direct substrate type of induction.
Pulmonary hypertensive effects of bretylium tosylate in the dog

Abstract A sympathetic-blocking agent, bretylium tosylate, was given intravenously in large dosage to 15 anesthetized mongrel dogs with closed chests. This drug caused a significant increase in mean pulmonary arterial pressure, total pulmonary vascular resistance, and pulmonary arteriolar resistance. Pulmonary blood volume did not change significantly. These changes are compatible with constriction of a small segment of the pulmonary vascular bed, such as the arterioles.
When a loss is due to suicide: Unique aspects of bereavement

Abstract Although bereavement from suicide shares a common core of experience with other bereavement, there are unique features as well. These include stigma, feelings of blame and personal responsibility, other unusually strong emotional reactions, an exacerbated search for meaning, and deception about the cause of death. Bereaved persons also are misunderstood, and they face inappropriate comforting, which includes being asked intrusive questions, receiving sympathy from those who feel uncomfortable, and being offered diminished social support. Research on suicidal bereavement is often limited by its retrospective nature, biased respondents, noncomparable control groups, idiosyncratic dependent measures, and failure to examine family factors. These shortcomings are only now beginning to be addressed. Therapists for suicidally bereaved individuals should assess for suicide and refrain from overly ambitious goals and should consider referral to self-help groups that comprise individuals who have had simil...
B Lymphocytes Exit Lymph Nodes through Cortical Lymphatic Sinusoids by a Mechanism Independent of Sphingosine-1-Phosphate-Mediated Chemotaxis

Sphingosine-1-phosphate (S1P) helps mediate lymphocyte egress from lymph nodes, yet many mechanistic questions remain. Here, we show the presence of B lymphocyte egress sites located in the lymph node cortex close to lymph node follicles. B cells exited lymph nodes by squeezing through apparent portals in the lymphatic endothelium of these sinusoids. Treatment with the S1P receptor agonist FTY720 emptied the cortical sinusoids of lymphocytes, blocked lymphatic endothelial penetration, and displaced B lymphocytes into the T cell zone. S1pr3(-/-) B cells, which lack chemoattractant responses to S1P, transited lymph nodes normally, whereas Gnai2(-/-) B cells, which have impaired responses to chemokines and S1P, transited more rapidly than did wild-type cells. This study identifies a major site of B lymphocyte lymph node egress, shows that FTY720 treatment blocks passage through the cortical lymphatic endothelium, and argues against a functional role for S1P chemotaxis in B lymphocyte egress.
A preliminary comparison of CIE color differences to textile color acceptability using average observers

Ninety-six nylon pairs were prepared, including red, yellow, green, and blue standards, each at two lightness levels with CIE94 ΔE units ranging from 0.15 to 4.01. Visual assessments of acceptability were carried out by 21 females. Logistic regression compared visual results to four color-difference equations, CIELAB, CMC, CIE94, and CIEDE2000. It was found that CMC most closely represented judgments of average observers. © 2005 Wiley Periodicals, Inc. Col Res Appl, 30, 288–294, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.20124
Varietal Resistance to Onion Thrips (Thysanoptera: Thripidae) in Processing Cabbage

Resistance to Thrips tabaci Lindeman injury in processing cabbage was observed among the 16 varieties tested. Although all varieties had some injury, ‘Titanic 90’ and ‘Blue Boy’ were the least susceptible, with only a few, slight feeding patches on 2 to 3 of the outer 10 leaves of the head. ‘Hinova’ and ‘NKX 9035’ were the most severly damaged varieties and had >90% of their outer leaves severely injured by thrips. Differences in susceptibility could not be attributed to high dry-matter quality or date of maturity.
A set of validity criteria for modeling job-based compensation systems

In their classic text, Cook and Campbell (1979) presented a set of principles for evaluating the validity of field research in social science that is designed to test hypotheses about cause-effect relations. In the present article, we develop a parallel set of criteria for the evaluation of the validity of predictive models. Our four criteria are: statistical conclusion validity, latent variable validity, structural validity, and external validity. After drawing a distinction between the measurement and structural level of models, we present a framework for assessing model validity and apply it to job-based compensation systems as an illustrative case. The article includes a summary of the advantages of structural equations modeling over traditional regression approaches for assessing wage structure within organizations.
5HT1A receptors inhibit glutamate inputs to cardiac vagal neurons post-hypoxia/hypercapnia

Synaptic inputs to cardiac vagal neurons (CVNs) regulate parasympathetic activity to the heart. Previous work has shown insults such as hypoxia and hypercapnia (H/H) alter CVN activity by activating post-synaptic serotonergic, purinergic, and glutamatergic receptors in CVNs. This study examines the role of serotonergic 5HT1A receptors in modulating these excitatory neurotransmissions to CVNs during control conditions, H/H and recovery from H/H. Excitatory post-synaptic currents (EPSCs) were recorded from identified CVNs in vitro before, during and post H/H. The 5HT1A receptor antagonist WAY 100635 had no effect on EPSCs in CVNs before, and during H/H. However, during recovery from H/H inspiratory-related excitatory serotonergic and purinergic pathways were recruited to excite CVNs. However, when these serotonergic and purinergic pathways are blocked, the 5HT1A receptor antagonist WAY 100635 restores an excitatory glutamatergic neurotransmission to CVNs. This study indicates endogenous activation of serotonergic 5HT1A receptors diminishes glutamatergic neurotransmission to CVNs following H/H, likely via a presynaptic site of action.
Friars on the Edge: Socio-Economic Networking and the Dominicans of Conquered Mallorca

Abstract Though often disappointing as sources for religious history, urban convent archives have the potential to shed valuable light on otherwise invisible social networks of the medieval bourgeoisie. Analysis of merchant and other names appearing in a wide variety of mundane contracts reveals the realia of economic relationships that, in the frontier context of Mallorca, occasionally crossed confessional lines. The case studies included in this article hint at the diverse array of characters whose entrepreneurial careers led to associations with and around the thirteenth-century Dominican convent of Sant Domingo de Mallorca. From social-climbing archers and tailors to converso shipping magnates and landowners, speculators of all sorts crossed paths within the cloistered halls of a mendicant sanctuary whose function was never exclusively spiritual. Dominican archives appear primarily to have served as repositories for such clients’ transaction records, especially in unstable colonial situations—an aspect of the order’s pastoral mission which has hitherto received little attention.
Nominalism, Trivialism, Logicism

This paper is an effort to extract some of the main theses in the philosophy of mathematics from my book, The Construction of Logical Space. I show that there are important limits to the availability of nominalistic paraphrase-functions for mathematical languages, and suggest a way around the problem by developing a method for specifying nominalistic contents without corresponding nominalistic paraphrases. Although much of the material in this paper is drawn from the book—and from an earlier paper (Rayo 2008)—I hope the present discussion will earn its keep by motivating the ideas in a new way, and by suggesting further applications.
Relational Uncertainty and Message Production Within Courtship: Features of Date Request Messages

This paper theorizes about how relational uncertainty may predict features of date request messages within courtship. It reports a study in which 248 individuals role-played leaving a date request voice mail message for their partner. Relational uncertainty was negatively associated with the fluency (H1), affiliativeness (H2), relationship focus (H3), explicitness (H4), and perceived effectiveness (H5) of messages. Also as expected, relational uncertainty was negatively associated with people’s perceptions of the effectiveness of their messages after covarying the judgments of independent observers (H6). Relational uncertainty continued to predict features of messages when length of romantic interest was covaried (RQ1). The paper concludes by discussing the implications of the results for understanding the link between relational uncertainty and message production.
Chemical composition of blood and bile of the shovelnose sturgeon

Abstract Samples of gallbladder bile and blood from shovelnose sturgeons (Scaphirhynchus platorynchus) collected from the Chippewa River, Wisconsin, contained concentrations of Na+, K+, Ca+ +, Mg+ +, Cl-, inorganic phosphate, and total cholesterol closely comparable with those reported for similar samples from other species of freshwater sturgeons.
Multinational enterprise: The old and the new in history and theory

Abstract This historical paper reveals that international economic integration is neither new or necessarily driven by technological change, and examines the traditional, pre-1940, “vertical” multinational, which invested up- and downstream of their innovation, in light of this fact. An analysis is given of how this older multinational relates to current, “horizontal” firms, which produce a number of products in several places. Using the language of industrial organization theory, this paper shows that technological discoveries of the late nineteenth century explain the shift in multinational organization and the emergence of global oligopolies.
Plant Pathogens in Irrigation Water: Challenges and Opportunities

Plant pathogens in irrigation water were recognized early in the last century as a significant crop health issue. This issue has increased greatly in scope and degree of impact since that time and it will continue to be a problem as agriculture increasingly depends on the use of recycled water. Plant pathogens detected from water resources include 17 species of Phytophthora, 26 of Pythium, 27 genera of fungi, 8 species of bacteria, 10 viruses, and 13 species of plant parasitic nematodes. There is substantial evidence demonstrating that contaminated irrigation water is a primary, if not the sole, source of inoculum for Phytophthora diseases of numerous nursery, fruit, and vegetable crops. These findings pose great challenges and opportunities to the plant pathology community. A variety of water treatment methods are available but few have been assessed for agricultural purposes under commercial conditions. Investigations into their technical feasibility and economics are urgently needed. Aquatic ecology of...
Survival disparities by Medicaid status: an analysis of 8 cancers.

BACKGROUND: A study was undertaken to compare survival and 5-year mortality by Medicaid status in adults diagnosed with 8 select cancers. METHODS: Linking records from the Ohio Cancer Incidence Surveillance System (OCISS) with Ohio Medicaid enrollment data, the authors identified Medicaid and non-Medicaid patients aged 15 to 54 years and diagnosed with the following incident cancers in the years 1996-2002: cancer of the testis; Hodgkin and non-Hodgkin lymphoma; early stage melanoma, colon, lung, and bladder cancer; and pediatric malignancies (n = 12,703). Medicaid beneficiaries were placed in the pre-diagnosis group if they were enrolled in Medicaid at least 3 months before cancer diagnosis, and in the peri/post-diagnosis group if they enrolled in Medicaid upon or after being diagnosed with cancer. The authors also linked the OCISS with death certificates and data from the US Census. By using Cox and logistic regression analysis, they examined the association between Medicaid status and survival and 5-year mortality, respectively, after adjusting for patient covariates. RESULTS: Nearly 11% of the study population were Medicaid beneficiaries. Of those, 45% were classified in the peri/post-diagnosis group. Consistent with higher mortality, findings from the Cox regression model indicated that compared with non-Medicaid, patients in the Medicaid pre-diagnosis and peri/post-diagnosis groups experienced unfavorable survival outcomes (adjusted hazard ratio [AHR], 1.52; 95% confidence interval [CI], 1.27-1.82 and AHR, 2.01; 95% CI, 1.70-2.38, respectively). CONCLUSIONS: Medicaid status was associated with unfavorable survival, even after adjusting for confounders. The findings reflect the vulnerability of Medicaid beneficiaries and possible inadequacies in the process of care. Cancer 2012. © 2011 American Cancer Society.
Molecular dynamics studies of U1A-RNA complexes

The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity.
Current perspective on produced water management challenges during hydraulic fracturing for oil and gas recovery

Environmental context There is growing worldwide interest in the production of oil and gas from deep, shale formations following advances in the technical expertise to exploit these resources such as hydraulic fracturing (fracking). The potential widespread application of hydraulic fracturing has raised concerns over deleterious environmental impacts on fragile water resources. We discuss the environmental management challenges faced by the oil and gas industry, and the opportunities for innovation in the industry. Abstract The need for cheap and readily available energy and chemical feedstock, and the desire for energy independence have spurred worldwide interest in the development of unconventional oil and gas resources; in particular, the production of oil and gas from shale formations. Although these resources have been known for a long time, the technical expertise and market forces that enable economical development has coincided over the last 15 years. The amalgamation of horizontal drilling and hydraulic fracturing have enabled favourable economics for development of fossil energy from these unconventional reservoirs, but their potential widespread application has raised concerns over deleterious environmental impacts on fragile water resources. The environmental management challenges faced by the oil and gas industry arise from local water availability and infrastructure for treating and disposing of the high-strength wastewater that is produced. Although there are significant challenges, these create opportunities for innovation in the industry.
Quasi-cyclic LDPC codes: an algebraic construction

This paper presents two new large classes of QC-LDPC codes, one binary and one non-binary. Codes in these two classes are constructed by array dispersions of row-distance constrained matrices formed based on additive subgroups of finite fields. Experimental results show that codes constructed perform very well over the AWGN channel with iterative decoding based on belief propagation. Codes of a subclass of the class of binary codes have large minimum distances comparable to finite geometry LDPC codes and they offer effective tradeoff between error performance and decoding complexity when decoded with low-complexity reliability-based iterative decoding algorithms such as binary message passing decoding algorithms. Non-binary codes decoded with a Fast-Fourier Transform based sum-product algorithm achieve significantly large coding gains over Reed-Solomon codes of the same lengths and rates decoded with either the hard-decision Berlekamp-Massey algorithm or the algebraic soft-decision Kotter-Vardy algorithm. They have potential to replace Reed-Solomon codes in some communication or storage systems where combinations of random and bursts of errors (or erasures) occur.
The West Haven-Yale Multidimensional Pain Inventory (WHYMPI)

The complexity of chronic pain has represented a major dilemma for clinical researchers interested in the reliable and valid assessment of the problem and the evaluation of treatment approaches. The West Haven-Yale Multidimensional Pain Inventory (WHYMPI) was developed in order to fill a widely recognized void in the assessment of clinical pain. Assets of the inventory are its brevity and clarity, its foundation in contemporary psychological theory, its multidimensional focus, and its strong psychometric properties. Three parts of the inventory, comprised of 12 scales, examine the impact of pain on the patients' lives, the responses of others to the patients' communications of pain, and the extent to which patients participate in common daily activities. The instrument is recommended for use in conjunction with behavioral and psychophysiological assessment strategies in the evaluation of chronic pain patients in clinical settings. The utility of the WHYMPI in empirical investigations of chronic pain is also discussed.
Density-dependent distribution of demersal juvenile Atlantic cod ( Gadus morhua ) in Placentia Bay, Newfoundland

Age 0 cod (Gadus morhua) were surveyed with beach-seines monthly from September to December, 1997-1999, at sites located throughout Placentia Bay, Newfoundland. Catch rates (densities) varied annually, being highest in 1998 (7 fish per sample) and lowest in 1997 (<1). Each year, fish size and density increased from September to November, as expected from a stock that tends to produce a single cohort spawned in April/May. However, in December the expected larger fish were absent, and the presence of smaller cod suggested a later cohort (July spawning). Large-scale spatial patterns also persisted among years, with densities consistently higher in the inner bay and on the western side, and lower on the eastern side. The rank of the sites from greatest to lowest density of age 0 cod remained fairly consistent among years. In a comparison of all 12 sampling events, the proportion of sites occupied by cod was strongly and positively correlated with the total number caught (r 2 = 0.95). These observations suggested a density-dependent range expansion not previously reported for age 0 cod.
Limits to Mechanical Positioning and Displacement Measurements

An essential requirement for any type of machine designed to shape or structure matter is the ability to move a forming tool or probe in an accurate, prescribed path throughout a workspace. Since the advent of the scanning tunneling microscope, we have been evolving rapidly in our capabilities to perform this function from machine-controlled cutting edges, to cutting with lasers and ions, to e-beam lithography, to recent demonstrations of controllably positioning individual atoms on a suitable substrate with STM tips. Any of these approaches requires that the probe or probes be moved and located in the workspace with a positional accuracy significantly smaller than the dimensions of the smallest feature being fabricated, and that the positioning be accomplished within a time scale to make the fabrication process practical.
Shallow P- and S-Wave Velocities and Site Resonances in the St. Louis Region, Missouri-Illinois

Abstract As part of the seismic hazard–mapping efforts in the St. Louis metropolitan area we determined the compressional and shear-wave velocities (Vp and Vs) to about a 40-m depth at 17 locations in this area. The Vs measurements were made using high-resolution seismic refraction and reflection methods. We find a clear difference in the Vs profiles between sites located on the river floodplains and those located in the upland urban areas of St. Louis. Vs30 (average Vs to 30-m depth) values in floodplain areas range from 200 to 290 m∕s (NEHRP category D) and contrast with sites on the upland areas of St. Louis, which have Vs30 values ranging from 410 to 785 m∕s (NEHRP categories C and B). The lower Vs30 values and earthquake recordings in the floodplains suggest a greater potential for stronger and more prolonged ground shaking in an earthquake. Spectral analysis of a M3.6 earthquake recorded on the St. Louis–area ANSS seismograph network indicates stronger shaking and potentially damaging S-wave resonan...
Expression of gene‐gun injected plasmid DNA in the ovine mammary gland and in lymph nodes draining the injection site

Abstract A jet‐injection based gene‐gun delivery system has been evaluated as a means to transiently transfect the lactating mammary gland in vivo. The model expression plasmid contained the human growth hormone (hGH) structural gene driven by the human cytomegalovirus immediate early gene 1 promoter/enhancer region (CMV). Expression from plasmid DNA jet‐injected into lactating mammary glands of sheep was at a level sufficient to allow detection by Northern blot analysis when tissue was obtained 48 hours post‐transfection. In contrast, mRNA expression following DNA transfer by needle and syringe was detectable by RT‐PCR, but not by Northern blot analysis. Furthermore, specific mRNA was detected by RT‐PCR in lymph nodes draining the mammary gland injection sites. Jet‐injection of CMV‐hGH into either muscle or mammary gland resulted in the development of serum antibodies to hGH. The ability to transiently transfect lactating mammary tissue in vivo may circumvent the difficulties encountered with in vitro cu...
Wildfire and Aspect Effects on Hydrologic States after the 2010 Fourmile Canyon Fire

Wildfire is one of the most significant disturbances in mountainous landscapes, affecting water supply and ecologic function and setting the stage for natural hazards such as flash floods. The impacts of wildfire can affect the entire hydrologic cycle. Measurements of soil-water content and matric potential in the near surface (top 30 cm) captured the hydrologic state in both burned and unburned hillslopes during the first spring through fall period (1 June–1 Oct. 2011) after the 2010 Fourmile Canyon Fire near Boulder, CO. This time span included different hydrologic periods characterized by cyclonic frontal storms (low-intensity, long duration), convective storms (high-intensity, short duration), and dry periods. In mountainous environments, aspect can also control hydrologic states, so north- vs. south-facing slopes were compared. Wildfire tended to homogenize soil-water contents across aspects and with depth in the soil, yet it also may have introduced an aspect control on matric potential that was not observed in unburned soils. Post-wildfire changes in hydrologic state were observed in south-facing soils, probably reflecting decreased soil-water retention after wildfire. North-facing soils were impacted the most, in terms of hydrologic state, by the loss of water storage in the combusted litter–duff layer and forest canopy, which had provided a large “hydrologic buffering” capacity when unburned. Unsaturated zone measurements showed increased variability in hydrologic states and more rapid state transitions in wildfire-impacted soils. A simple, qualitative analysis suggested that the range of unsaturated-zone processes along the gravity–capillarity–adsorption continuum was expanded by wildfire for a given soil. The small number of experimental plots in this study suggests that further work is needed before these conclusions can be generalized to other geographic areas.
HLA Class II genes associated with REM sleep behavior disorder

Twenty-five white men with rapid eye movement (REM) sleep behavior disorder, but without narcolepsy, underwent HLA class II antigen typing ; 84% (N = 21) were DQw1 (DQB1*05,06) positive (28% [N = 7] were DR2 positive) ; DQB1*0501 (N = 9) and DQB1*0602 (N = 7) were the most common phenotypes. The 84% DQw1 rate in men with REM sleep behavior disorder was significantly greater (p = 0.015) than the 56% DQw1 rate found in a local white comparison group (N = 66), and was greater than the 39 to 66% DQw1 rates published for 12 white groups (N = 40-418/group). Thus, another disorder of REM sleep dysregulation (besides narcolepsy) appears to be strongly associated with specific HLA class II genes.
Weed community characteristics and crop performance: a neighbourhood approach.

Summary The presence of weeds in crop fields often causes yield reductions. However, the effects of weed diversity have not been fully examined. This study tested the hypothesis that, holding density constant, increased weed species richness would decrease the effects of competition on spring wheat target plant performance. Measurements were taken from circular neighbourhoods (16.5 cm radius) with a single spring wheat plant surrounded by combinations of Setaria viridis, Avena fatua, Kochia scoparia, Thlaspi arvense and spring wheat plants, representing all combinations of neighbour species at four density levels. Using regression models, we found that species richness had no significant direct effect on spring wheat biomass, yield, or relative growth rate and that there were no significant neighbour species interaction terms. For weedy target plants, the presence of negative interaction terms suggested that increasing species richness had negative effects on growth of individual weed species. Additional analysis suggested that increased species richness may limit competitive ability of dominant weeds. Although we found no evidence of a direct effect of weed species richness on crop performance, increased weed species richness had no negative effect on spring wheat performance. Further, species richness of the weed community appears to influence weedy plant performance, which may offer a future opportunity to influence crop performance.
Electrical Properties of Fine Grain Composite Carbon Films

We have studied the electrical properties of boron doped composite films that consist of diamond and amorphous carbon. These films were deposited by hot filament chemical vapor deposition at a relatively high carbon/hydrogen ratio. The mixture of trimethyl borate vapor, and methane served as a source gas. The composite films had much smoother surfaces than polycrystalline diamond films. p]The surface morphology and average roughness were determined by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Raman spectroscopy and x-ray diffraction were used to analyze the structure of the films. p]A composite film grown with 4% methane in hydrogen had a higher resistivity than a well faceted diamond film grown at 0.5% methane. In contrast to hydrogenated amorphous carbon films which have a lower resistivity after thermal annealing, the resistivities of composite films increased by a factor of two to ten after 3 hours annealing at 600°C.
Effect of ionizing radiation on the electrical characteristics of polyvinylidene fluoride (PVF/sub 2/)

The influence of high-energy electron irradiation on the electrical properties of biaxially oriented polyvinylidene fluoride (PVF/sub 2/) film was investigated. The film was irradiated in air with a 1-MeV electron beam at a dose rate of 10/sup 6/ rad/min to different dose levels of up to 10/sup 8/ rad. Electrical properties measured included dielectric permittivity and dielectric loss, AC and DC breakdown voltages, and DC volume resistivity, X-ray diffraction and IR spectroscopy measurements were also made. The most pronounced of the radiation-induced changes were a decrease in like AC breakdown voltage and an increase in dielectric loss, both corresponding to increasing total absorbed dose. DC breakdown voltage and volume resistivity also showed noticeable changes. These changes are believed to be associated initially with a radiation-induced crystal phase transformation. This was confirmed by the X-ray diffraction curve and the IR spectra, which showed an increase in the beta -phase and a decrease in the alpha -phase peaks at higher dose levels. >
Walleye dermal sarcoma virus Orf C is targeted to the mitochondria

Walleye dermal sarcomas are associated with the presence of a complex retrovirus, walleye dermal sarcoma virus (WDSV). These sarcomas develop and regress seasonally in naturally infected fish. In addition to gag, pol and env, WDSV contains three open reading frames (ORFs), designated orf a, orf b and orf c. orf c is located between the 5′ long terminal repeat and gag. Developing tumours contain low levels of orf a and orf b transcripts, whereas regressing tumours contain high levels of genomic transcripts and virus particles. Orf C protein is encoded by the full-length, genomic transcript and can be detected in tumour extracts with anti-Orf C-specific antisera. To determine the subcellular location of WDSV Orf C, cultured cells were transfected with an expression vector encoding haemagglutinin-tagged Orf C and examined by immunofluorescence. Orf C was observed throughout the cytoplasm and accumulated in cytoplasmic organelles. Dual-antibody staining for Orf C and mitochondrial cytochrome c demonstrated colocalization of Orf C with mitochondria and loss of the normal distribution of mitochondria in the cytoplasm. Cells transiently expressing Orf C exhibited apoptotic morphology and increased levels of surface phosphatidylserine and were unable to retain MitoTracker Orange, a dye that accumulates in active mitochondria. These results imply a functional role for WDSV Orf C in an alteration of mitochondrial function that results in apoptosis contributing to tumour regression.
Randomized Exercise Trial of Aromatase Inhibitor–Induced Arthralgia in Breast Cancer Survivors

Purpose Arthralgia occurs in up to 50% of breast cancer survivors treated with aromatase inhibitors (AIs) and is the most common reason for poor AI adherence. We conducted, in 121 breast cancer survivors receiving an AI and reporting arthralgia, a yearlong randomized trial of the impact of exercise versus usual care on arthralgia severity.
Performance analysis of Shufflenet with deflection routing

Multi-hop communication networks are drawing increasing interest. Shufflenet is a multi-hop communication network which achieves high performance while overcoming the current shortcomings in device technology. The authors present a new and comprehensive analysis for Shufflenet. By making use of the connectivity properties of any (p, k) Shufflenet, they characterize the probabilistic behavior of a typical packet in the network in terms of a simple discrete-time Markov chain with only 2k states, one of which is an absorbing state. They then derive analytic expressions for several important network performance parameters such as hops distribution, average delay for a packet to travel to its destination and the probability of don't care in each hop that the packet takes. The expressions derived can be applied to any (p, k) Shufflenet. The calculation of throughput of the Shufflenet can then be obtained by finding the relationship between network packet generation probability. >
Computing Inter-Rater Reliability for Observational Data: An Overview and Tutorial

Many research designs require the assessment of inter-rater reliability (IRR) to demonstrate consistency among observational ratings provided by multiple coders. However, many studies use incorrect statistical procedures, fail to fully report the information necessary to interpret their results, or do not address how IRR affects the power of their subsequent analyses for hypothesis testing. This paper provides an overview of methodological issues related to the assessment of IRR with a focus on study design, selection of appropriate statistics, and the computation, interpretation, and reporting of some commonly-used IRR statistics. Computational examples include SPSS and R syntax for computing Cohen’s kappa and intra-class correlations to assess IRR.
Chronic myeloid leukemia in the imatinib era

Abstract The results of imatinib (Gleevec) (formerly STI571) therapy for chronic myeloid leukemia (CML) have continued to improve and have surpassed almost everyone's predictions. However, the long-term results with imatinib and its ability to cure CML as a single agent are unknown. These issues will be discussed along with potential strategies to improve the cure rate, using imatinib as a building block to achieve this goal. Semin Hematol 40(suppl 2):1-3. © 2003 Elsevier Inc. All rights reserved.