cssi/SciSciGPT-SciSciNet huggingface dataset:
Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus

Abstract The recent outbreak of a new coronavirus (2019-nCoV) in Wuhan, China, underscores the need for understanding the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. Here, we show that recombination in betacoronaviruses, including human-infecting viruses like SARS and MERS, frequently encompasses the Receptor Binding Domain (RBD) in the Spike gene. We find that this common process likely led to a recombination event at least 11 years ago in an ancestor of the 2019-nCoV involving the RBD. Compared with bat isolates, the recent ancestors of 2019-nCoV accumulated a high number of amino acid substitutions in the RBD and likewise in a region of polyprotein Orf1a that is critical for viral replication and transcription. Among these recent mutations, we identify amino acid substitutions common to the SARS 2003 outbreak isolates in positions 427N and 436Y, indicating potential adaptive convergent evolution. Both 427N and 436Y belong to a helix that appears to interact with the human ACE2 receptor. In sum, we propose a two-hit scenario in the emergence of the 2019-nCoV virus whereby the 2019-nCoV ancestors in bats first acquired genetic characteristics of SARS by incorporation of a SARS-like RBD through recombination before 2009, and subsequently, those recombinants underwent convergent evolution.
Psychological Effects of Natural Disaster: Traumatic Events and Losses at Different Disaster Stages

Communities across the globe face unprecedented environmental challenges such as natural disasters, influenced by factors such as climate change and an increasing global population. Given that disasters frequently result in loss and tragedy, this chapter describes the phenomenon of traumatic grief post-disaster. Traumatic grief is the bereavement profession’s way of defining grief thoughts and reactions that may be beyond the scope of normal grief reactions in intensity and duration, because, often, loss and tragedy occurred as a result of a traumatic event. Consequently, treating people suffering from traumatic grief can be challenging. A sudden bereavement, such as in the case of a disaster, is more likely to result in traumatic grief reactions than an expected bereavement. In this chapter, first, we will discuss the traumatic impact of a disaster event or events. Second, we review the evidence for traumatic grief interventions across the lifespan. Third, we highlight a series of community-based programs to support grieving children, adults, and families post-disaster. To advance our treatment of traumatic grief, and to adequately respond to the well-being needs of those affected by disaster events, it is advantageous to periodically review progress and identify current gaps of unmet needs.
Networking and Client–Server

The intent of this chapter is to provide a foundation in the concepts of networking to support the data sources of Part III. The sources of interest are accessed through the client–server model of distributed computing, and to fully understand this model and the way in which we design and construct clients, we must be familiar with the basics of networking. In particular, this involves the network protocol stack and, ultimately, the application level protocols to be used by the client.
Publishing and Presenting Clinical Research

After finishing a research project, the goal is to then share and communicate the findings to your colleagues. It is important to choose the right meeting for the project, and choose an appropriate format for presentation. The abstract should be well written and convey all the essential items concisely. Presentation skills can be learned, practiced, and improved upon. An oral presentation should conform to the time allowed, and there should not be too many words on one slide. You should also be prepared for questions and discussion. This is a great time to stimulate further direction in the project and improve it prior to publication.
Sex and gender differences in COVID testing, hospital admission, presentation, and drivers of severe outcomes in the DC/Maryland region

Structured AbstractO_ST_ABSBackgroundC_ST_ABSRates of severe illness and mortality from SARS-CoV-2 are greater for males, but the mechanisms for this difference are unclear. Understanding the differences in outcomes between males and females across the age spectrum will guide both public health and biomedical interventions. MethodsRetrospective cohort analysis of SARS-CoV-2 testing and admission data in a health system. Patient-level data were assessed with descriptive statistics and logistic regression modeling was used to identify features associated with increased male risk of severe outcomes. ResultsIn 213,175 SARS-CoV-2 tests, despite similar positivity rates (8.2%F vs 8.9%M), males were more frequently hospitalized (28%F vs 33%M). Of 2,626 hospitalized individuals, females had less severe presenting respiratory parameters and males had more fever. Comorbidity burden was similar, but with differences in specific conditions. Medications relevant for SARS-CoV-2 were used at similar frequency except tocilizumab (M>F). Males had higher inflammatory lab values. In a logistic regression model, male sex was associated with a higher risk of severe outcomes at 24 hours (odds ratio (OR) 3.01, 95%CI 1.75, 5.18) and at peak status (OR 2.58, 95%CI 1.78,3.74) among 18-49 year-olds. Block-wise addition of potential explanatory variables demonstrated that only the inflammatory labs substantially modified the OR associated with male sex across all ages. ConclusionHigher levels of clinical inflammatory labs are the only features that are associated with the heightened risk of severe outcomes and death for males in COVID-19. Trial registrationNA FundingHopkins inHealth; COVID-19 Administrative Supplement (HHS Region 3 Treatment Center), Office of the ASPR; NIH/NCI U54CA260492 (SK), NIH/NIA U54AG062333 (SK).
Deep Learning at the Edge for Channel Estimation in Beyond-5G Massive MIMO

Massive multiple-input multiple-output (mMIMO) is a critical component in upcoming 5G wireless deployment as an enabler for high data rate communications. mMIMO is effective when each corresponding antenna pair of the respective transmitter-receiver arrays experiences an independent channel. While increasing the number of antenna elements increases the achievable data rate, at the same time computing the channel state information (CSI) becomes prohibitively expensive. In this article, we propose to use deep learning via a multi-layer perceptron architecture that exceeds the performance of traditional CSI processing methods like least square (LS) and linear minimum mean square error (LMMSE) estimation, thus leading to a beyond fifth generation (B5G) networking paradigm wherein machine learning fully drives networking optimization. By computing the CSI of all pairwise channels simultaneously via our deep learning approach, our method scales with large antenna arrays as opposed to traditional estimation methods. The key insight here is to design the learning architecture such that it is implementable on massively parallel architectures, such as GPU or FPGA. We validate our approach by simulating a 32-element array base station and a user equipment with a 4-element array operating on millimeter-wave frequency band. Results reveal an improvement up to five and two orders of magnitude in BER with respect to fastest LS estimation and optimal LMMSE, respectively, substantially improving the end-to-end system performance and providing higher spatial diversity for lower SNR regions, achieving up to 4 dB gain in received power signal compared to performance obtained through LMMSE estimation.
The Impact of COVID-19 on National Clinical Trials Network Breast Cancer Trials.

The COVID-19 pandemic has had a devastating impact on virtually all aspects of the healthcare system, including oncology clinical trials. The purpose of this review is to describe the impact of the pandemic on national breast cancer clinical trials. Of the 61 breast cancer–specific cooperative group breast cancer clinical trials open to accrual during the pandemic, 32% of them received supplementary tailored guidance regarding current and foreseeable challenges for clinical sites and investigators due to COVID-19. Many clinical trial sites reported decreases in enrollment and accrual, drastic disruptions to protocol, and challenges related to research infrastructure, staff burden, and assuring social distancing. The challenges early in pandemic led to many operational changes in clinical trials, including use of electronic consent for enrollment, telemedicine visits, and mail order pharmacy. The pandemic highlighted aspects of breast cancer clinical trial that could be modernized while maintaining research integrity.
Integrating Research Writing and Research Methods: Toward a More Seamless Curriculum

Teaching capstone classes in which students develop an independent research project can prove challenging, especially with heterogenous student skillsets. Some students might need additional writing help, and some might need additional help with using research methods. How can a professor best address the needs of these very different student groups and ensure that everyone produces a high-quality research project? I develop a typology of individual approaches to teaching this class based on meeting student needs. Even if students have great writing skills and flawless research methods, focusing on individual attention gives ample opportunity for useful one-on-one coaching that improves the quality of written submissions.
Comparison of wheel load application methods in single-wheel testbeds

Abstract This work reviews wheel load application methods in single-wheel testbeds (SWTBs), used widely to study terramechanics. Normal force oscillations have been reported in SWTBs, and visible in time-series data when provided. This has usually been attributed to grousers, but is also visible for wheels without grousers suggesting other system dynamics (e.g. friction in the vertical axis) are the cause. Furthermore, accelerations related to periodic vertical displacements of the wheel (whether caused by grousers or otherwise) cannot explain more than a small fraction of the amplitude of normal force variations. In this work, a 4-bar mechanism was developed that balances the normal load and ensures that a constant (not oscillating) normal force is achieved throughout terramechanics experiments. System behaviour with and without the 4-bar mechanism was assessed, highlighting the need for a 4-bar mechanism or other method of balancing normal loads if a constant normal force is desired. No significant effects on average experimental results were observed due to normal force oscillation, but artifacts were observed in the time-series data. Comparisons of results with a system where wheel load is applied pneumatically and characterization of friction in each testbed provide further support to the conclusion that normal force oscillations are mainly caused by friction in the vertical axis.
Respiratory conditional reflex formation with CO2 and electric shock as unconditional stimuli

In 12 birds used in a CO2 conditioning experiment there was no evidence of the formation of either a respiratory or a cardiac conditional reflex. Tone and light separately or together were used as conditional stimuli. CS-US intervals ranging from 0.5 to 10 seconds were used. CO2 concentrations up to 7.4% were also employed. In the shock conditioning experiments six of seven birds showed a respiratory change to the conditional stimulus. In one pigeon perfect differentiation was obtained between the reinforced and nonreinforced tones. The marked difference in conditionability of sensory and chemical stimuli to the “respiratory center” is discussed in relation to the central nervous system connections of the respiratory control mechanism.
Direct Democracy and Turnout Revisited

After a decade of increased use of the initiative by numerous states, scholars during the mid to late 1990s began to revisit the impact of direct democracy in the American states (Bowler & Donovan, 1998; Bowler, Donovan, & Tolbert, 1998; Butler & Ranney, 1994; Gerber, 1999). At the turn of the twentieth century research found a relationship between direct democracy and voter turnout (Smith, 2001, 2002; Tolbert, Smith, & Grummel, 2001) that previous research from the 1980s had not found (Cronin, 1989; Everson, 1981; Magleby, 1984). Since that time there has been research further examining how to best measure the initiative process and direct democracy, more generally, given variation in its use from state to state (Bowler & Donovan, 2004), ballot measure salience (Grummel, 2008; Biggers, 2011), and other critiques (Seabrook & Dyck, 2010; Childers & Binder, 2012). These studies (and others) raised both methodological and theoretical questions. Methodologically, questions were raised concerning measurement of direct democracy and the initiative. Theoretically, there were concerns that not all initiatives, all ballot measures for that matter, were alike, and as such, would not all have the same impact on voter turnout. As such this research revisits and updates Tolbert, Smith, and Grummel’s (2001) initial research in order to reflect methodological and theoretical changes and finds that the impact of direct democracy on voter turnout is directly related to its measurement.
Overview of the Conceptual Design of the Future VENUS Neutron Imaging Beam Line at the Spallation Neutron Source

Abstract VENUS (Versatile Neutron Imaging Beam line at the Spallation Neutron Source) will be a world-class neutron-imaging instrument that will uniquely utilize the Spallation Neutron Source (SNS) time-of-flight (TOF) capabilities to measure and characterize objects across several length scales (mm to μm). When completed, VENUS will provide academia, industry and government laboratories with the opportunity to advance scientific research in areas such as energy, materials, additive manufacturing, geosciences, transportation, engineering, plant physiology, biology, etc. It is anticipated that a good portion of the VENUS user community will have a strong engineering/industrial research focus. Installed at Beam line 10 (BL10), VENUS will be a 25-m neutron imaging facility with the capability to fully illuminate (i.e., umbra illumination) a 20 cm x 20 cm detector area. The design allows for a 28 cm x 28 cm field of view when using the penumbra to 80% of the full illumination flux. A sample position at 20 m will be implemented for magnification measurements. The optical components are comprised of a series of selected apertures, T0 and bandwidth choppers, beam scrapers, a fast shutter to limit sample activation, and flight tubes filled with Helium. Techniques such as energy selective, Bragg edge and epithermal imaging will be available at VENUS.
Fatigue of Aluminides and Silicides

The fatigue resistance of two major classes of intermetallics, aluminides and silicides, are reviewed in this paper. High cycle fatigue (HCF) and fatigue crack growth (FCG) behavior are emphasized, as both are determined in most cases under stress control. Major experimental variables are composition, microstructure, temperature, state of order, mean stress (or R ratio) and test environment. Results of work on aluminides of titanium, nickel, iron and niobium aluminides are described. Methods to improve stress-controlled fatigue resistance of these alloy systems are reviewed.
Inhibition of cathepsin D-type proteinase of macrophages by pepstatin, a specific pepsin inhibitor, and other substances.

The macrophage is the main cell participating in chronic inflammation. It contains an acid-acting, cathepsin D-type proteinase with the specificity of pepsin, which may release mediators of the inflammatory process. To find new pharmaceutical inhibitors of this proteinase, we tested a variety of chemical compounds in vitro. For this survey, the possible inhibitor (at a concentration of 0.4 mg/ml) was assayed with partially purified cathepsin D-type proteinase from beef lung (a macrophage-rich tissue) and hemoglobin as the substrate. Diazophenylbutanone, three acetophenones, two barbiturates, a gold salt, a copper chelate of a substituted nicotinic acid, a hexapeptide containing a d-amino acid, and Pepstatin inhibited this enzyme; over 200 other potential inhibitors did not. By far the most active and specific inhibitor found to date is Pepstatin, a pentapeptide with two γ-NH linkages, two β-OH groups, and five branched aliphatic side chains. Banyu Pharmaceutical Co., Tokyo, Japan, produces this nontoxic compound for the treatment of peptic ulcers. In vitro, as little as 4 ng of Pepstatin inhibits the acid-acting cathepsin D-type proteinase purified from beef and rabbit lung as well as the similar proteinase of rabbit peritoneal and pulmonary macrophages.
Pollution monitoring of Puget Sound with honey bees

To show that honey bees are effective biological monitors of environmental contaminants over large geographic areas, beekeepers of Puget Sound, Washington, collected pollen and bees for chemical analysis. From these data, kriging maps of arsenic, cadmium, and fluoride were generated. Results, based on actual concentrations of contaminants in bee tissues, show that the greatest concentrations of contaminants occur close to Commencement Bay and that honey bees are effective as large-scale monitors.
Producing Text through Talk: Question-answering Activity in Classroom Peer Groups

Abstract This conversation-analytic study examines how students in peer groups interact and organize their own literacy learning activity to accomplish written question-answering tasks based on their reading of a story. Written question-answering tasks, especially those designed for literacy learning, require students to answer questions as an academic task—to “do answering.” A turn-by-turn analysis of the students’ talk-in-interaction shows that for the students examined in this study, “doing answering” involves two sub-activities. One sub-activity, question-answering, is to produce a substantive answer to the question as one would do in ordinary conversation. Then to fulfill the requirements of the written task, a second sub-activity, answer-framing, involves moving the answer from its conversationally-framed grammar to a written grammatical frame. The findings reveal the various methods or patterned ways in which the question-answering and answer-framing sub-activities are accomplished through the students’ peer group talk-in-interaction.
Block Copolymer Templating as a Path to Porous Nanostructured Carbons with Highly Accessible Nitrogens for Enhanced (Electro)chemical Performance

The design of carbon materials for improved electrochemical systems should combine the preferential occurrence of pyridinic functionalities and a structure that maximizes their exposure to the surface. The carbonization of nitrogen-rich polyacrylonitrile (PAN) retains a high level of nitrogen content, with a large percentage of the functionalities taking the form of pyridinic species at the graphene edges. A block copolymer precursor containing PAN and a second thermally sacrificial block can be converted to a nitrogen-rich carbon material with a mesoporous network mimicking that of the precursor. Here, we highlight the structural advantages of this templating approach and their improvement in several electrochemical systems.
Excision of C-4′-oxidized Deoxyribose Lesions from Double-stranded DNA by Human Apurinic/Apyrimidinic Endonuclease (Ape1 Protein) and DNA Polymerase β

Oxidative damage to DNA deoxyribose generates oxidized abasic sites (OAS) that may constitute one-third of ionizing radiation damage. The antitumor drug bleomycin produces exclusively OAS in the form of C-4-keto-C-1-aldehydes in unbroken DNA strands and 3′-phosphoglycolate esters terminating strand breaks. We investigated whether two human DNA repair enzymes can mediate OAS excision in vitro: Ape1 protein (the main human abasic endonuclease (also called Hap1, Apex, or Ref1)) and DNA polymerase β, which carries out both the abasic excision and the resynthesis steps. We used a duplex oligonucleotide substrate with one main target for bleomycin-induced damage. Ape1 catalyzed effective incision at the C-4-keto-C-1-aldehyde sites at a rate that may be only a few-fold lower than incision of hydrolytic abasic sites at the same location. Consistent with several previous studies, Ape1 hydrolyzed 3′-phosphoglycolates 25-fold more slowly than C-4-keto-C-1-aldehydes. DNA polymerase β excised the 5′-terminal OAS formed by Ape1 incision at a rate similar to its removal of unmodified abasic residues. Polymerase β-mediated excision of 5′-terminal OAS was stimulated by Ape1 as it is for unmodified abasic sites. Escherichia coli Fpg (MutM) protein also excised 5′-terminal OAS, but in our hands, the RecJ protein did not. These observations help define mammalian pathways of OAS repair, point to interactions that might coordinate functional steps, and suggest that still unknown factors may contribute to removal of 3′-phosphoglycolate esters.
Guided group discussion and attitude change: The roles of normative and informational influence

Abstract Kurt Lewin and others have showed that group discussion effectively changed attitudes and behaviors compared to individually targeted messages. This study examines the roles of normative and informational social influence in this effect. High school students heard a message about replacing toxic products with nontoxic alternatives; classes were randomly assigned to hear the message delivered as a lecture or via guided group discussion. For female students ( N =250 in 26 classes), HLM mediation analyses suggested normative influence predominated: Discussion was more effective than lecture and this effect was fully mediated by students’ perceptions that other students endorsed nontoxics. Content analyses of students’ comments indicated that three kinds of remarks led female students to this perception: (1) sharing knowledge about nontoxics; (2) asking questions about nontoxics; and (3) little praise for toxic products. For male students in separate HLM analyses ( N =107 in 19 of the same classes), informational influence was most apparent: Postmeeting attitudes were higher after discussion than lecture, and this effect was partially mediated by cognitive elaboration about the message (but not perceptions others endorsed the message). In addition, males’ quiz grades were higher after discussion, and students’ comments fully mediated the discussion to quiz grades relationship. Results support the importance of hearing others’ promessage comments for changing socially motivated behaviors, although the routes of influence appear to differ for these samples of male and female students.
Attention Issues in Spatial Information Systems: Directing Mobile Users' Visual Attention Using Augmented Reality

Knowledge of objects, situations, or locations in the environment can be productive, useful, or even life-critical for mobile augmented reality (AR) users. Users may need assistance with (1) dangers, obstacles, or situations requiring attention; (2) visual search; (3) task sequencing; and (4) spatial navigation. The omnidirectional attention funnel is a general purpose AR interface technique that rapidly guides attention to any tracked object, person, or place in the space. The attention funnel dynamically directs user attention with strong bottom-up spatial attention cues. In a study comparing the attention funnel to other attentional techniques such as highlighting and audio cueing, search speed increased by over 50 percent, and perceived cognitive load decreased by 18 percent. The technique is a general three-dimensional cursor in a wide array of applications requiring visual search, emergency warning, and alerts to specific objects or obstacles, or for three-dimensional navigation to objects in space.
Reply to comment on 'using cold atoms to measure neutrino mass'

We discuss questions raised concerning the proposal of kinematically reconstructing the neutrino mass using an ultracold source of tritium atoms (Otten E W 2011 New J. Phys. 13 078001). We provide further details about our two-dimensional fit and emphasize the importance of simultaneously utilizing information from both the neutrino mass squared peak and the β-spectrum. We also explain how the simulation evolved over various drafts of the paper, and we comment on future directions for additional simulation work, including more detailed simulations of spectrometers and electromagnetic field variations.
Test porosity in Neogloboquadrina pachyderma in late miocene to recent, DSDP site 284 South Pacific

Abstract In Pliocene and Quaternary deep-sea sediments of DSDP Site 284 (temperate South Pacific), a significant positive correlation exists between test porosity and the percentage of forms with reticulate surface ultrastructure in samples of the planktonic foraminifer Neogloboquadrina pachyderma (Ehrenberg). Surface ultrastructural characteristics have previously been shown to be related to paleoceanographic oscillations. No relation exists between porosity and surface ultrastructure in either the Late Miocene or earliest Pliocene samples measured.
A study on an integrable system of coupled KdV equations

Abstract In this work, we study a system of coupled KdV equations. The Hirota’s bilinear method is applied to show that this system is completely integrable. Multiple-soliton solutions and multiple singular soliton solutions are derived for this system. The resonance phenomenon is examined as well.
A power law tail in India's wealth distribution: Evidence from survey data

Abstract This study uses survey data from India to examine the top percentile of the wealth distribution in India. Using nationally representative samples from two years, 1991 and 2002, a power law tail is found with a Pareto exponent ranging between 1.8 and 2.4. The tail is examined for three specific groupings: households in the rural areas, households in the urban areas and all households. The distribution of top households also appear to be regionally concentrated with states having the highest number of households in the top 1% in 1991 also generally having the highest number in 2002 as well.
The effects of (+/-)-methylenedioxymethamphetamine and (+/-)-methylenedioxyamphetamine in monkeys trained to discriminate (+)-amphetamine from saline.

Abstract Recently, attention has been focused on (±)-methylenedioxymethamphetamine (MDMA), a psychotomimetic agent chemically closely related to the psychomotor stimulant methamphetamine, and also to the hallucinogen mescaline. In the present experiment, the effects of MDMA and (±)-3,4-methylenedioxyamphetamine (MDA) were determined in rhesus monkeys that were trained to discriminate intravenously administered (+)-amphetamine (AMPH) from saline in a two-lever, food-maintained paradigm or to discriminate intragastrically administered AMPH from saline in a signalled electric shock avoidance paradigm. MDMA produced 100% drug-appropriate responding in all six monkeys, regardless of the procedure and route of administration while MDA substituted completely for AMPH in only two of three monkeys in each paradigm. The results suggest that MDMA has subjective effects that are similar to those of AMPH while MDA is somewhat less like AMPH.
Construction of plasmids that produce phage P22 represser

Abstract In a series of plasmid constructions, the c 2 (repressor) gene of phage P22 was cloned in a multicopy plasmid and expressed at increasing levels. The final result of these constructions is a plasmid that maintains a level of approx. 200 times as much repressor as is found in a lysogen. A series of increasingly virulent phage mutants was isolated by plating sequentially on host cells with increasing levels of repressor. The methods used in the constructions should be applicable to obtaining elevated expression of cloned genes in other systems.
Mapping the elastic properties of granular Au films by contact resonance atomic force microscopy

Endowed with nanoscale spatial resolution, contact resonance atomic force microscopy (CR-AFM) provides extremely localized elastic property measurements. We advance here the applicability of CR-AFM on surfaces with nanosize features by considering the topography contribution to the CR-AFM signal. On nanosize granular Au films, the elastic modulus at the grain scale has been mapped out by considering a self-consistent deconvolution of the contact geometry effect in the CR-AFM image. Significant variation in the contact area over granular topography arises as the probe is either in single- or multiple-asperity contact with the surface. Consequently, in extracting the elastic modulus from CR-AFM measurements on granular surfaces we considered both the normal and lateral couplings established through multiple-asperity contacts between the tip and the surface. Thus, by appropriately considering the change in the contact mechanics during CR-AFM imaging, variations in the elastic modulus have been revealed in the intergrain regions as well as across individual grains.
The Impact of Youth and Family Risk Factors on Service Recommendations and Delivery in a School-Based System of Care

The present study examines the impact of child and family risk factors on service access for youth and families in a school-based system of care. Regression analyses examined the relationships between risk factors and services recommended, services received, and dosage of services received. Logistic regression analyses examined the relationship between risk factors and whether or not youth received specific types of services within the system of care. Results revealed that youth with a personal or family history of substance use had more services recommended than youth without these risk factors, while youth with a family history of substance use received more services. Youth with a history of substance use received a significantly higher dosage of services overall. Finally, history of family mental illness was associated with receiving mental health and operational services (e.g., family advocacy, emergency funds). Implications and limitations are discussed.
Paucity of deleted mitochondrial DNAs in brain regions of Huntington's disease patients.

Abstract Mitochondrial DNA deletions (Δ-mtDNAs), originally found at high levels in patients with sporadic mitochondrial encephalomyopathies, have also been found to accumulate at extremely low levels during normal human aging, especially in long-lived postmitotic tissues such as muscle and brain. We have now quantitated the amount of one such Δ-mtDNA species, the so-called ‘common deletion’, in brain regions from patients with Huntington's disease (HD). Surprisingly, we found a marked decrease in the amount of this Δ-mtDNA in the occipital cortex and putamen as compared to age-matched controls; however, no change was found in caudate. Using immunohistochemistry of brain sections, we found no differences in the staining pattern for selected respiratory chain polypeptides between the HD and control tissues. The reduction in the amount of Δ-mtDNAs in HD may be related in part to the astrocytic gliosis in the affected areas, in which the deletion-rich neurons are replaced by relatively deletion-poor astrocytes.
Time of Entry of Salmonella and Campylobacter into the Turkey Brooder House

The prevalence of Campylobacter (>90%) and Salmonella (33%) in turkeys at slaughter has been estimated. This report describes studies to estimate the time of entry of Campylobacter and Salmonella into the brooder house, which is the first stage of commercial turkey production. In trial 1, birds (∼100 per time point) were monitored by conventional culture at three intervals (0, 9, and 16 days of age). Campylobacter spp. were not detected in poults at the day of hatch; Salmonella was isolated from the ceca (3.9%) and yolk sac (0.1%). By day 9, Salmonella were frequently isolated from the ceca (55%) and small intestine (45%) while Campylobacter was not cultured. By day 16, the prevalence of Salmonella in the ceca (21%) and small intestine (5.1%) had declined; Campylobacter was infrequently isolated from either the ceca (2%) or small intestine (3%). In trial 2, poults (50 per time point at 5, 20, and 33 days of age) were monitored for Campylobacter and Salmonella by real-time polymerase chain reaction (PCR); Salmonella was also monitored by conventional culture. Whereas Campylobacter was not detected by real-time PCR in the ceca of 5-day-old birds, it was detected on days 20 (92%) and 33 (90%). In contrast, Salmonella was isolated from young birds at days 5 (98%), 20 (98%), and 33 (98%), after which time the turkeys were moved to the finisher house. At slaughter at 138 days, Salmonella prevalence in the ceca had declined (4.5%) in contrast to the prevalence of Campylobacter (92%). Antimicrobial sensitivity profiles of the Salmonella isolates indicated an increase of sulfonamide-resistant isolates throughout the brooder stage. Genotyping by pulsed-field gel electrophoresis analysis of Salmonella (45 isolates per sampling time) indicated fluctuating populations as the birds matured.
The sequence of the RNA primer and the DNA template influence the initiation of plus-strand DNA synthesis in hepatitis B virus

For hepadnaviruses, the RNA primer for plus-strand DNA synthesis is generated by the final RNase H cleavage of the pregenomic RNA at an 11 nt sequence called DR1 during the synthesis of minus-strand DNA. This RNA primer initiates synthesis at one of two distinct sites on the minus-strand DNA template, resulting in two different end products; duplex linear DNA or relaxed circular DNA. Duplex linear DNA is made when initiation of synthesis occurs at DR1. Relaxed circular DNA, the major product, is made when the RNA primer translocates to the sequence complementary to DR1, called DR2 before initiation of DNA synthesis. We studied the mechanism that determines the site of the final RNase H cleavage in hepatitis B virus (HBV). We showed that the sites of the final RNase H cleavage are always a fixed number of nucleotides from the 5' end of the pregenomic RNA. This finding is similar to what was found previously for duck hepatitis B virus (DHBV), and suggests that all hepadnaviruses use a similar mechanism. Also, we studied the role of complementarity between the RNA primer and the acceptor site at DR2 in HBV. By increasing the complementarity, we were able to increase the level of priming at DR2 over that seen in the wild-type virus. This finding suggests that the level of initiation of plus-strand DNA synthesis at DR2 is sub-maximal for wild-type HBV. Finally, we studied the role of the sequence at the 5' end of the RNA primer that is outside of the DR sequence. We found that substitutions or insertions in this region affected the level of priming at DR1 and DR2.
Principles and practice of plastic scintillator design

Abstract Plastic scintillators are used for ionizing radiation detection and measurement. A brief review is given of the standard plastic base materials, typical classes of fluorescent compounds, and some processing methods for producing plastic scintillators. The available parameters that determine the resultant scintillator performance are discussed.
An efficient, scalable and high performance cloud monitoring framework

Cloud computing has become a very popular platform to deploy data-intensive scientific applications, but this process faces its own set of challenges. Given the complexity of the application execution environment, routine tasks on the cloud such as monitoring, performance analysis, and debugging of applications become tedious and complex. These routine tasks often require close interaction and inspection of multiple layers in the cloud, which traditional performance monitoring tools fail to account for. In addition, many of these tools are designed for real-time analysis and only provide summaries of historical data. This makes it difficult for a user to trace the runtime performance of an application in the past. We present a new monitoring framework called All-Monitor Daemon (Almond). Almond keeps close tabs on cloud inventory by communicating with a cloud resource manager (such as VMware vCenter for a VMware private cloud). Almond then connects to each individual physical host in the inventory and retrieves performance metrics through the hypervisor. Examples of metrics include CPU, memory, disk and network usage. Almond is also designed to collect performance information from the Guest OS, allowing the retrieval of metrics from the application platform as well. Almond was designed from the ground up for enhanced scalability and performance. The framework uses a Time Series Database (TSD), and a decentralized monitoring architecture allows for fast performance queries while minimizing overhead on the infrastructure. Almond collects performance data from all the layers of the software stack, and collected data remains persistent for future analysis. As a result of our performance enhancements, our preliminary results indicate a 70% improvement in hypervisor query response time through these enhancements as compared to our previous monitoring solution, VOTUS. Almond is a work in progress, and will feature an intuitive web-based interface that allows system administrators and cloud users to view and analyze resources on the cloud. Once completed, Almond promises to be a highly scalable, fast performing and dynamic cloud resource monitor.
Hybrid compensation techniques for direct on line starting of high power induction motor

The direct on line (DOL) starting of a high power induction motor causes an acute voltage sag in the power supply system. Line to line and line to ground faults are some of the causes for voltage sags and voltage unbalance in the power supply system for industries and commercial buildings. This paper investigates hybrid compensation techniques to solve power quality problems arising from the DOL starting of a high power induction motor. The proposed solution utilizes the Static Compensator (STATCOM) and Static Synchronous Series Compensator (SSSC). In the proposed solution for voltage sags, STATCOM and SSSC are considered as the system components; therefore, a detailed mathematical model is developed for these components as well as a mathematical formulation of the proposed control schemes. Simulation results for STATCOM and SSSC based compensators are given.
Eliminating Administrative Churn: The “Big Deal” and Database Subscriptions

Abstract In the ongoing battle to control escalating costs for library resources, librarians often focus only on the purchase or subscription price of a resource and the annual inflation rates. Though these are important factors, the price libraries pay for a resource is not the only measure of its cost. The time acquisitions personnel spend negotiating with vendors, running and initiating trials, activating new packages, reviewing licenses, and engaging in other activities are also significant, though often overlooked, cost components. These behind-the-scenes activities constitute “administrative churn” that is just as costly, and in some cases more so, than the more visible and familiar initial acquisition costs. In 2009, collections personnel at the Texas A&M University Libraries initiated a discussion with a major database vendor aimed at achieving savings by reducing this churn. The result was an agreement now known as the “ProQuest Comprehensive” package. This article will reflect on this agreement and evaluate whether the Texas A&M University Libraries met its objectives by initiating this program.
Nephritogenic Antibody Reactions with Basement Membrane and Other Structural or Trapped Antigens in the Kidney

Nephritogenic antibody reactions involve antigens that are either soluble in the body fluids or that are fixed within the substance of the kidney (1-3). The latter group of antigens can be either structural elements of the kidney (such as its basement membranes) or foreign materials that have become trapped within the kidney for a variety of reasons. Antibody reactions with soluble antigens lead to circulating immune complex formation, with subsequent glomerular and vascular localization. The immune complex deposits then become fixed antigen (or antibody) sites for ongoing dynamic interaction with antibody (or antigen) still in the circulation. In addition, some soluble antigens can bind to glomerular structures for physicochemical reasons, thereby potentially serving in both soluble and fixed antigen capacities. The areas of overlap between the soluble and fixed antigen types of nephritogenic reactions will be included in this discussion which focuses on the fixed antigen mechanisms.
Nicotine enhances the learning and memory of aged rats.

Abstract The cognitive performance of young adult (2–3-month-old) and aged (22–24 month-old) rats was characterized in one of three different behavioral tasks, and the ability of daily nicotine treatment to alleviate age-related learning and memory deficits was evaluated. Aged rats received an IP injection of either nicotine (0.2 mg/kg) or saline vehicle 15 min prior to daily testing; young control rats received saline vehicle injections. Compared to young controls, aged control rats were severely impaired in the acquisition of one-way active avoidance pole jumping over 12 days of testing. Nicotine pretreatment of similar aged rats markedly improved overall learning and the rate of learning compared to aged controls. In Lashley III maze performance, aged control rats made substantially more alternation errors than young controls; however, aged rats pretreated with nicotine made significantly fewer errors over the entire 20-day test period compared to aged controls. During 30 days of 17-arm radial maze testing, aged control animals were severely impaired in general learning and reference (long-term) memory, but only mildly impaired in working (short-term) memory. Nicotine pretreatment of similar aged rats induced a substantial enhancement in overall learning and reference memory, but did not affect working memory. These results indicate that chronic nicotine administration can improve the impaired learning/memory abilities of aged rats in several tasks, and suggest that stimulation of central nicotinic receptors may be of considerable therapeutic value to treat age-related memory impairment.
Hydrodynamic effects on the macromorphology of electrodeposited zinc and flow visualization: The effect of neutral salts and electric field

Abstract The macromorphological features of electrodeposited zinc that result from hydrodynamic flow conditions on a rotating-disk electrode (RDE) and along a flat-plate electrode (FPE) in a channel flow cell have been investigated as to the effect of neutral salts, their complexing contributions to the growing surface morphology and in particular their influence on the electric field otherwise counterbalancing the flow field. All complex hydrodynamic characteristics of the re-attaching flow and the presence of streamwise-directed counter-rotating Taylor vortices behind the critical region of the stagnation and separation are clearly outlined and marked by the macromorphology of three-dimensional relief imprints. The macromorphological features of relief equiangular spirals (RDE) and ridged striations (FPE) in zinc electrodeposition represent mainly the competition between the flow field and the electric field strength, and depend on the average current density, the rotation speed (RDE) or linear flow velocity (FPE), the deposition time, the ionic zinc content, the electrolyte composition, the pH value and the local hydrodynamic flow pattern. The counterbalancing effect of a rather more homogenized electric field on and in the vicinity of the electrode surface, as provided and maintained by higher neutral salt concentrations, in particular at low zinc contents, has been clearly outlined and resulted in more compact flatter deposits. The flow field contribution is strongly suppressed, but is not eliminated, so that the macromorphology of electrodeposited zinc is characterized by a proportionally lower number density of corrugated striations. The ridged spirals (RDE) and corrugated striations (FPE) still persist and grow in more compact, flatter deposits alternating with depression channels and exhibit some features characteristic of a more homogeneous electric field.
Preliminary assessment of the acute toxicity of malathion in animals.

Laboratory studies were conducted to acquire information concerning the acute toxicity of malathion in animals under various conditions of exposure. The responses in rabbits and quail exposed to aerosols generated from technical grade malathion (95%) and approximating an ultra-low volume ground spray were compared with those from a 6% malathion/No. 2 fuel oil mixture simulating a high volume spray. Results indicate that technical grade malathion (95%) as an ultra-low volume spray and at effective insecticidal concentrations in particle sizes having a mass median diameter of about 12 µ is relatively nonhazardous compared to the possible toxic fuel oil effects of a 6% malathion/No. 2 fuel oil mixture with a mass median diameter of 25 µ. Based on blood plasma cholinesterase activity analyses, quail were more sensitive to equivalent malathion exposure concentrations than were rabbits. Oral administration of technical grade malathion to rabbits resulted in reduction of plasma and erythrocyte cholinesterase activity at dosages of 120, 300, and 600 mg/kg with death resulting from 1200 mg/kg.
Ultrastructure of rat ovarian interstitial cells II. Response to gonadotropin

Redifferentiation of ovarian interstitial cells in hypophysectomized rats was studied after treatment with pregnant mare serum gonadotropin (PMS). The most pronounced changes within 6 hours after treatment were dilation of intercellular spaces, nucleolar hypertrophy, and polysome formation. Nuclear response to PMS treatment was nearly maximal within 36 hours, when nuclei were enlarged, with reduced heterochromatin, and nucleoli were large and complex. All organelles showed some response within 6 hours, but their rate and duration of redifferentiation varied. The Golgi complex appeared unchanged after 48 hours; mitochondria, smooth endoplasmic reticulum, and ribosomal numbers continue to respond throughout the 72 hour period. Rapid nuclear response and polysome formation may implicate the nucleus as a mediator of slower cytoplasmic changes.
A comparison of B-mode real-time imaging and arteriography in the intraoperative assessment of carotid endarterectomy.

Abstract In this study we compare intraoperative B-mode imaging with arteriography in the same patient for intraoperative assessment after carotid endarterectomy. Since April 1983, 158 patients have been studied with both techniques. After a routine intraoperative arteriogram, the vessel was examined in multiple planes with a B-mode imager, and the impression of the operating surgeon was recorded before review of the arteriogram. Thirteen studies were unsatisfactory because the design of the probe did not allow examination of the high carotid bifurcation. Twelve patients had significant abnormalities (8.3%) in the internal carotid artery. Results were false negative in three intraoperative arteriograms (2.1%) and five B-mode imaging studies (3.4%). In each of the 12 cases the vessel was reopened and the abnormality confirmed and corrected. Fifty-seven patients had abnormalities (37%) in the external carotid artery. Results were false negative in eight arteriograms (5.3%) and in 12 B-mode imaging studies (7.9%). Fourteen of the 57 patients with abnormalities of the external carotid artery underwent repeat operation to correct the technical problem. Although not conclusive, the incidence of postoperative neurologic deficit as well as that of recurrent carotid stenosis seems decreased since both modalities for intraoperative assessment were used. The data suggest that neither intraoperative angiography nor B-mode imaging, when used alone, accurately detects all postoperative abnormalities. The results also suggest that a heightened sensitivity to technical details may improve both early and late postoperative morbidity. (J VASC SURG 1986;4:457-63.)