cssi/SciSciGPT-SciSciNet huggingface dataset:
Recovery of striatal dopamine function after acute amphetamine- and methamphetamine-induced neurotoxicity in the vervet monkey.

In six vervet monkeys, presynaptic striatal dopamine function was assessed longitudinally by [18F]fluoro-L-DOPA (FDOPA)-positron emission tomography (PET) after administration (2 x 2 mg/kg, i.m., 4 h apart) of either amphetamine (Amp), n = 3, or methamphetamine (MeAmp), n = 3. At 1-2 weeks postdrug, both Amp and MeAmp exposure effected similar decreases (60-70%) in the FDOPA influx rate constant (FDOPA Ki), an index of striatal dopamine synthesis capacity. Subsequent studies in these subjects showed that FDOPA Ki values were decreased by 45-67% at 3-6 weeks, by 25% at 10-12 weeks and by 16% in one Amp-treated subject at 32 weeks. Biochemical analysis showed that striatal dopamine concentrations were decreased by 75% at 3-4 weeks and by 55% at 10-12 weeks. These results indicate that in vervet monkey striatum, an acute Amp or MeAmp drug dosage produces extensive striatal dopamine system neurotoxicity. However, these effects were reversible; observed time-dependent recovery in both FDOPA Ki and dopamine concentrations indicates that neurochemical plasticity remains active in the adult primate striatum. At 3-4 and 10-12 weeks postdrug, the concurrent characterization of the striatal FDOPA Ki and dopamine concentrations for individual subjects showed that Ki decreases between 24 and 67% corresponded to dopamine depletions of 55-85%. These relatively larger postdrug decrements in steady-state striatal dopamine concentrations suggest that compensatory increases in dopamine synthesis capacity develop in the partially lesioned striatum. In contrast to the dopamine depletion in striatum, substantia nigra concentrations remained unchanged from referent values at both 3-4 and 10-12 weeks postdrug. Thus, the integrity of the substantia nigra could not be inferred from decreases in the striatal FDOPA Ki parameter. This disparity between striatum and substantia nigra reactivity to systemic administration of amphetamines suggests that each has unique dopamine system regulatory mechanisms.
Identification and analysis of gene families from the duplicated genome of soybean using EST sequences

Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. However it does have the 6th largest EST collection comprised of ESTs from a variety of soybean genotypes. Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean (Glycine max L. Merr.) using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion.
An operating systems implementation project for an undergraduate course

While the adoption of an implementation project for an operating systems course is certainly beneficial, non-trivial projects are inherently demanding in terms of student efforts and computer costs. This paper reports on a project which has been designed to keep the effort for an extensive simulation of a contemporary system within acceptable limits. The project involves both a hardware simulator and an operating system, and a considerable reduction of the overall effort could be achieved by enhancing the hardware with operating systems support features. The design criteria as well as the characteristics of the resulting hardware configuration and operating system are presented, and the value of the project as a teaching tool is discussed
Review Series--Inflammation & Fibrosis. Fibrocytes and fibrosis.

Fibrocytes are a subpopulation of mesenchymal progenitor cells, which were first described in 1994 as fibroblast-like, peripheral blood cells that enter sites of tissue invasion or injury. Fibrocytes are unique in their expression of extracellular matrix proteins (collagens) together with myeloid (CD45) and hematopoietic progenitor markers (CD34). Fibrocytes contribute to the innate response to injury and tissue remodeling. They serve as antigen-presenting and immunomodulatory cells; they produce a distinct profile of cytokines, chemokines and growth factors that contributes to repair and tissue remodeling; and they mediate fibrogenesis in a number of systemic and organ-specific fibrosing disorders. Regulatory networks involving serum amyloid P (SAP), immune cytokines and chemokines and T cells emphasize the role of fibrocytes in an integrated host response to injury. The therapeutic targeting of fibrocytes now holds promise for the augmentation of wound repair and the treatment of different fibrosing disorders. Fibrocytes were first identified in a murine model of wound repair that relied on the sampling of exudate cells in wound chambers surgically implanted into subcutaneous tissues.1 A flow cytometric examination of peripheral blood cells within 2 days of wound chamber implantation revealed a unique population of CD34+ and collagen I (Col I)+ cells. The coincident expression of the hematopoietic progenitor marker, CD34, together with connective tissue collagen thus led to the naming of these circulating, spindle-shaped cells as ‘fibrocytes’. An abundance of information regarding fibrocyte biology has since been acquired from both experimental murine and human clinical investigations. Fibrocytes now are appreciated as participating in normal and aberrant wound repair, including hypertrophic scars and keloids, airway remodeling in asthma, interstitial pulmonary fibroses, the systemic disorders scleroderma and nephrogenic systemic fibrosis, atherosclerosis, the stromal response to tumor invasion and Graves ophthalmopathy.2,3 Fibrocytes express a unique cytokine and chemokine profile distinct from …
Shortened complex span tasks can reliably measure working memory capacity.

Measures of working memory capacity (WMC), such as complex span tasks (e.g., operation span), have be- come some of the most frequently used tasks in cognitive psychology. However, due to the length of time it takes to complete these tasks many researchers trying to draw conclu- sions about WMC forgo properly administering multiple tasks. But can the complex span tasks be shortened to take less administration time? We address this question by splitting the tasks into three blocks of trials, and analyzing eachblock's contribution to measuring WMC and predicting fluid intelli- gence (Gf). We found that all three blocks of trials contributed similarlytothetasks'abilitytomeasureWMCandGf,andthe tasks can therefore be substantially shortened without chang- ing what they measure. In addition, we found that cutting the number of trials by 67 % in a battery of these tasks still accounted for 90 % of the variance in their measurement of Gf. We discuss our findings in light of administering the complex span tasks in a method that can maximize their accuracy in measuring WMC, while minimizing the time taken to administer.
Label-Free Profiling of Ligands for Endogenous GPCRs Using a Cell-Based High-Throughput Screening Technology

This article reports the use of Corning Epic system— a label-free and noninvasive optical system that is centered on resonant waveguide grating biosensors—to profile endogenous G protein-coupled re...
A novel approach to design a massively parallel application specific architecture for image recognition systems

The goal of the paper is to present a novel approach for designing massively parallel architectures for image recognition systems. Massive parallel hardware produces high speed image recognition. Hardware architectures work much faster and are more effective for application specific processing than a software-based image recognition system. The concept of designing optimal image recognition systems with high speed, low complexity, good portability, and low cost has been present for a long time. The authors have considered the basic design factors, simple and regular design, concurrency and communication, and balancing computation with I/O. The technique presented provides a new method of designing an image recognition system by concentrating on modularity and massive parallelism. This is accomplished through the design of a processing element layer, local communicator layer, and network of new image layer. The processing element (PE) layer performs the basic recognition functions on individual pixels through logical operations. Both the local communicator and network of new image layers institute a mesh network topology, which has proven to be the fastest and most efficient. The local communicator layer has the most important function, it communicates with the other two layers, combines results from the PE layer, and houses the main control unit. All layers work simultaneously, or in other words, in a parallel fashion. The flow diagram of a CAD designer algorithm, based on this new design technique, is presented.
Mouse major histocompatibility complex and lung development: haplotype variation, H-2 immunolocalization, and progressive maturation.

The association of the mouse major histocompatibility complex (H-2), lung maturation, and corticosteroid responsiveness has recently been demonstrated in congenic B10 (H-2b) and B10.A (H-2a) mice (Hu et al.: American Journal of Medical Genetics 35:126-131, 1990). We have investigated additional haplotypes [B10.BR (H-2k) and B10.D2 (H-2d)] to confirm that there is a strong association between H-2 haplotype variation and the degree of pulmonary maturation. Lungs of B10.D2, B10.BR, B10, and B10.A congenic mice achieve haplotypic specific maturation: B10.D2 lungs greater than B10 lungs = B10.BR lung greater than B10.A lungs. It appears that the expression of these developmental potentials is under corticosteroid regulation. Further, to test the hypothesis that H-2 antigens would be expressed earlier in embryonic lungs with the H-2b (B10) or H-2k (B10.BR) haplotype than with the H-2a (B10.A) haplotype, we investigated the spatiotemporal patterns of H-2 antigen localization in B10, B10.BR, and B10.A congenic mouse strains with and without corticosteroid treatment. The spatial patterns of H-2 antigen localization was similar in the B10, B10.BR, and B10.A mouse lungs; however, these patterns appeared earlier in both untreated and treated B10 and B10.BR mice as compared with untreated B10.A mice, suggesting an H-2 haplotype associated rate of pulmonary maturation. Following corticosteroid treatment, all congenic strains had a temporally comparable spatial distribution of H-2 antigens. Our results provide preliminary evidence suggesting that both a lung "developmental gene(s)" and a "glucocorticoid responsiveness gene(s)" are most likely outside the K-D subregions of the H-2 complex. A model of the H-2 regulation of lung maturation and corticosteroid responsiveness is discussed.
MHD Power Generation in Scramjet Engines in Conjunction with Inlet Control

Megawatt-scale MHD power generation on board of air-breathing hypersonic vehicles is made possible by the high flow enthalpy and velocity, and by the high static temperature (2,300 - 3,500 K) in the combustor and just downstream of it. In this paper, a 1D model of MHD power generation downstream of scramjet combustor is developed, and power generation performance is predicted for a variety of generic hydrogen- fueled engine regimes. A modest amount of potassium seed is shown to yield good performance at magnetic fields on the order of 1 Tesla. One possible use of the MHD-generated power would be to add energy to the flow upstream of the inlet in order to optimize the inlet performance. In particular, MHD generated power can be used to create a virtual cowl that would increase mass capture and thrust of the engine. The paper also demonstrates that the megawatt-scale power, when added to the flow upstream of the inlet throat, can reduce the Mach number, leading to the possibility of substantially shortening or even eliminating the isolator.
Somatostatin Is an Agonist and Noncompetitive Antagonist of Gastrin in Oxyntic Cell Function

Somatostatin inhibits gastric acid secretionin vivo by effects on oxyntic cells which may be indirect. Using quantitative cytochemistry, we have investigated the actions of somatostatin on guinea pig oxyntic cell carbonic anhydrase activity, an index of acid secretion. Cyclic tetradecapeptide somatostatin, in the range of 2.9 × 10-15 to 2.9 × 10-10 M, stimulated oxyntic cell carbonic anhydrase activity in sections of guinea pig gastric fundus with a linear dose-response between 2.9 × 10-14 and 2.9 × 10-11 M. The maximal response to somatostatin was 50% of that to gastrin. Gastrin stimulated oxyntic cell carbonic anhydrase in the dose range of 2.3 × 10-15to 2.3 × 10-11 M. The addition of 2.9 × 10-13 M somatostatin caused an inhibition of 38-75% of the carbonic anhydrase activity stimulated by various concentrations of gastrin. The addition of 2.3 × 10-13 M gastrin (which caused 79% of maximal carbonic anhydrase activation), to each dose of somatostatin from 2.9 × 10-15 to 2.9 × 10-10 M did not alter the ac...
Morbidity of Bleeding After Cardiac Surgery: Is It Blood Transfusion, Reoperation for Bleeding, or Both?

Background Etiology for increased morbidity in patients (2% to 8%) undergoing reoperation for bleeding after cardiac surgery is unclear. Recent work suggests that it may be related to red-cell transfusion, but what role does reoperation itself play? We sought to determine prevalence of and risk factors for reoperation for bleeding, separate the effect of reoperation from that of transfusion on hospital mortality and major morbidity, and identify the source of bleeding. Methods From January 1, 2000 to January 1, 2010, 18,891 primary and repeat coronary artery bypass grafting, valve, or combined operations were performed. Risk factors for reoperation were identified by multivariable logistic regression. Hospital mortality and major morbidity were compared in propensity-matched patients requiring reoperation and not. Medical records from 2005 to 2010 were reviewed to determine bleeding source. Results A total of 566 patients (3.0%) underwent reoperation for bleeding, with considerable variability over time. Risk factors included older age, higher acuity, greater comorbidity, aortic valve surgery, longer myocardial ischemic and cardiopulmonary bypass durations, and surgeon. Mortality was higher for propensity-matched patients requiring reoperation; 8.5% (68% confidence interval [CI] 7.3% to 9.9%) versus 1.8% (CI 1.2% to 2.5%). Both greater transfusion and reoperation were independently associated with increased risk of mortality and major morbidity. At reoperation, technical factors (74%), coagulopathy (13%), both (10%), or other (3.3%) causes were responsible for bleeding. Conclusions Transfusion and reoperation for bleeding both contribute to postoperative mortality and morbidity. Technical reasons are at the root of most bleeding, emphasizing a major focus for process improvement to minimize need for reoperation and blood use.
Non-Monotonic Parsing of Fluent Umm I mean Disfluent Sentences

Parsing disfluent sentences is a challenging task which involves detecting disfluencies as well as identifying the syntactic structure of the sentence. While there have been several studies recently into solely detecting disfluencies at a high performance level, there has been relatively little work into joint parsing and disfluency detection that has reached that state-ofthe-art performance in disfluency detection. We improve upon recent work in this joint task through the use of novel features and learning cascades to produce a model which performs at 82.6 F-score. It outperforms the previous best in disfluency detection on two different evaluations.
Role of Lipocalin-2 in Thrombin-Induced Brain Injury.

Background and Purpose— Thrombin and lipocalin-2 (LCN2) contribute to intracerebral hemorrhage–induced brain injury. Thrombin-induced brain damage is partially through a thrombin receptor, protease-activated receptor-1. LCN2 is involved in cellular iron transport and neuroinflammation. This study investigated the role of LCN2 in thrombin-induced brain injury. Methods— There were 3 parts in this study. First, male adult C57BL/6 wild-type or LCN2 knockout (LCN2 KO) mice had an intracaudate injection of thrombin (0.4 U) or saline. Second, LCN2 KO mice had an injection of thrombin (0.4 U) with recombinant mouse LCN2 protein (1 μg) into the right caudate. Third, protease-activated receptor-1 KO or wild-type mice had an intracaudate injection of thrombin or saline. All mice had T2-weighted magnetic resonance imaging and behavioral tests. Brains were used for histology, immunohistochemistry, and Western blotting. Results— Intracerebral thrombin injection caused LCN2 upregulation and brain injury in mice. Thrombin-induced brain swelling, blood–brain barrier disruption, neuronal death, and neurological deficits were markedly less in LCN2 KO mice ( P <0.05) and were exacerbated by exogenous LCN2 coinjection. In addition, thrombin injection resulted in less LCN2 expression and brain injury in protease-activated receptor-1 KO mice. Conclusions— Thrombin upregulates LCN2 through protease-activated receptor-1 activation and causes brain damage.
Exemplary Contracts and Summary Terms Sheets for the Private Order of Innovation Networks

In the article "The Private Order of Innovation Networks", I summarize three exemplary alliance agreements involving Intel/Nanosys, Boeing/Spirit Aerosystems, and GlaxoSmithKline/Anacor respectively. Enclosed are the full, publicly available versions of those three contracts, retrieved from the Securities and Exchange Commission’s EDGAR electronic filing system. Summary term sheets are also included solely for the purpose of assisting the interested reader in digesting what are complex and lengthy contracts. This .pdf file is bookmarked to indicate the first page of each summary term sheet; a full version of each agreement follows the applicable term sheet.
Extended family ties among alcoholics: a neglected area of research

Half of the patients at an alcoholism treatment clinic who were not living with a spouse were found to be living with kin, mostly parents or siblings. It is suggested that social science research s...
ISOMETRIES OF THE PLANE

(1995). Isometries of the Plane. The American Mathematical Monthly: Vol. 102, No. 7, pp. 628-631.
Varying Substituents and Solvents To Maximize the Luminescence from [Ru(trpy)(bpy)CN]+ Derivatives

Ruthenium(II) in combination with monodentate, bidentate, and tridentate ligands has proven to be a useful design for a variety of applications, but the majority of systems are virtually nonluminescent in solution. The goal of this work has been to design luminescent forms with practicable emission quantum yields, and the focus has been on [Ru(X-T)(dmeb)CN]+ systems, where X-T denotes 2,2′:6′,2″-terpyridine bearing substituent X at the 4′-position and dmeb denotes [2,2′-bipyridine]-4,4′-dicarboxylic acid, dimethyl ester. Results show that varying the π-electron-donating ability of the 4′-X substituent is an effective way to tune the energy and lifetime of the charge-transfer (CT) emission. The lifetime achieved in a room-temperature, fluid solution is as high as 175 ns, depending on the 4′-substituent and the solvent employed because the excited state is very polar. That represents a 20-fold improvement in lifetime relative to that of the prototype, [Ru(trpy)(bpy)CN]+, one of the earliest examples found t...
The Continuing Battle Over Economically Targeted Investments: An Analysis of DOL Interpretive Bulletin 2015-01

In Interpretive Bulletin 2015-01 (IB 2015-01), the U.S. Department of Labor (DOL) renewed the now two-decades old battle over “economically targeted investments” (ETIs). As a matter of statutory interpretation, IB 2015-01, like its predecessors, is unpersuasive. The Employee Retirement Income Security Act of 1974 (ERISA) requires plan trustees to invest “solely” to provide participants’ retirement benefits. A trustee who invests in ETIs violates this statutory obligation by pursuing collateral economic benefits for persons other than plan participants. As a matter of policy, the social investing which ETIs exemplify is unsound. At best, such social investing in practice merely shuffles investment ownership without altering market-based allocations of capital.
Archival Description and Records from Historically Marginalized Cultures: A View from a Postmodern Window

In the archival field, the last decade has witnessed much discussion on archives' broad responsibilities for social memory. Considering that the social role of archives has stemmed from postmodern thinking suggests a paradigm shift from viewing archives as static recorded objects to viewing them as dynamic evidence of human memory. The modern archives and archivists are products of nineteenth-century positivism, limiting their function to archiving written documents within stable organizations. The new thoughts on the social role of archives provide a chance to realize that traditional archival practices have preserved only a sliver of organizational memory, thus ignoring fluid records of human activities and memory. Archival description is the primary method for users to access materials in archives. Thus, it can determine how archival materials will be used (or not used). The traditional archival description works as the representation of archival materials and is directly projected from the hierarchy of organizational documents. This paper argues that archivists will need to redefine archival description to be more sensitive to atypical types of archival materials from various cultural contexts. This paper surveys the postmodern approaches to archival concepts in relation to descriptive practices. It also examines some issues related to representing historically marginalized groups in archival description who were previously neglected in traditional archival practices.
Adélie penguin (Pygoscelis adeliae) survival rates and their relationship to environmental indices in the South Shetland Islands, Antarctica

Seabird life history is typified by low fecundity, high adult survival rates, and relatively long lives. Such traits act as buffers, enabling persistence of populations under variable environmental conditions. Numerous studies, however, have suggested strong sensitivity of seabirds to environmental variability. In the Antarctic Peninsula region, for example, Adelie penguin (Pygoscelis adeliae) populations have declined during the last three decades, attributed largely to rapid changes in environmental conditions and food availability. We use 30 years of mark-recapture data from known-age individuals in the South Shetland Islands and capture-mark-recapture models to estimate survival rates with respect to such environmental variation. We investigated specifically whether negative trends in survival rates were evident and whether indices of global, regional, and local environmental conditions considered important for Adelie penguin survival explained the variability in survival rates. Overall, negative trends in juvenile survival were evident, but adult survival rates exhibited high interannual variability. Indices of sea ice extent had the strongest correlations with survival rates, particularly Weddell Sea ice extent during spring among adults (r = 0.62) and during winter for juveniles (r = 0.46). An analysis of deviance, however, suggested that single environmental covariates explained <30 % of the observed variation in the full mark-recapture models. Despite positive effects of sea ice extent on survival rates of Adelie penguins, limited explanatory power of several environmental conditions previously identified as important for Adelie penguin survival underscores the difficulty of predicting future population responses in this region of rapid environmental change.
Diet in dermatology: Part I. Atopic dermatitis, acne, and nonmelanoma skin cancer

Patients commonly inquire about dietary modifications as a means to prevent or manage skin disease. Answering these questions is often challenging, given the vast and conflicting evidence that exists on this topic. This 2-part continuing medical education article summarizes the evidence to date to enable physicians to answer patients' questions in an evidence-based manner. Part I includes atopic dermatitis, acne, and nonmelanoma skin cancer. The role of dietary supplementation, dietary exclusion, food allergy, maternal diet, and breastfeeding in the development and/or prevention of atopic dermatitis is summarized. The dermatoendocrinologic mechanism for the effects of glycemic index/glycemic load and milk on acne is described, as well as related clinical evidence for dietary modifications. Finally, evidence and recommendations for restriction or supplementation of dietary factors in the prevention of nonmelanoma skin cancer, including fat, vitamins A, C, D, and E, and selenium, are reported.
Allogeneic Rat T-Suppressor Inducer Cells with In Vivo and In Vitro Activity

The presence of allogeneic Ag-specific T-suppressor inducer cells with in vivo activity has been demonstrated by Hutchinson (1), using a rat renal allograft model. We now demonstrate the presence of in vivo and in vitro T-suppressor inducer activity in the W3/25+ (CD4+) subset of lymphocytes from WF strain rats rejecting LEW strain heterotopic cardiac allografts transplanted 5 days previously. Adoptive transfer of 2 to 4 × 107 of these immune day 5 W3/25+ [d5 W3/25+] splenocytes, or their sonicates 7 days prior to transplantation, prolongs allograft survival two- to threefold in unmodified or irradiated hosts (200 to 300 rads). This prolongation is specific for the donor strain (Table 1).
New opportunities for fusion in the 21st century : Advanced fuels

It is shown that the long-range goal of the world fusion program can be to generate energy without long-lived radioactive waste and the associated safety problems that accompany today's nuclear power sources. This can ultimately be accomplished through the 3 He-based fusion fuel cycles. This paper compares 3 He-based fusion fuels with first-generation, D-based fusion fuels and fission. Potential applications of 3 He fusion to radioisotope generation, proliferation-resistant electrical power plants, and space propulsion are also discussed.
The Potential Economic Impact of Increasing the Minimum Wage in Massachusetts

What are the potential costs and benefits to Massachusetts in raising its minimum wage? The Commonwealth's legislature is currently considering a proposal that would increase the state minimum wage in two steps over the next two years to $8.25 per hour by 2007. Since the introduction of House Bill No. 3872 at the end of 2004, there has been considerable debate over its potential benefits and costs. Advocates on both sides of the issue have each released a report on the bill's likely economic impacts. Proponents assert that the purchasing power of the minimum wage has declined over time and that the negative impact on employment from raising the minimum would probably be small. Opponents argue that an increase would boost costs for employers, potentially resulting in higher prices for consumers, significant job loss among low-wage workers, or making Massachusetts less competitive with neighboring states. Given these competing arguments, what is the overall economic impact of this proposal likely to be? In this report I review the arguments on both sides of the issue. In doing so, I discuss and critique, where applicable, the evidence presented in the two reports that have been issued on either side of the debate. I also produce my own projection of the likely impact of raising the minimum wage on aggregate employment and wages. These calculations use the two reports as a baseline, modifying some of the assumptions to better reflect evidence supported by the economic literature. According to my estimates, the current proposal to increase the minimum wage could have a negative impact on employment ranging from 2,100 to 10,500 jobs, or 1 to 4 percent of workers whose wages would be affected by the bill. On net, the combined impact of the two wage increases would raise aggregate wages by approximately $255 million.
148. AptaMetrics: A Web-Based Aptamer Bioinformatics Platform

RNA and DNA aptamer development as a therapeutic moiety and as a diagnostic tool is a rapidly growing field. The discovery process for aptamers involves iterative rounds of selection in a process termed SELEX, Systematic Evolution of Ligands by EXponentional enrichment. The modern SELEX process was revolutionized with the adoption of high-throughput sequencing (HTS), which is able to identify millions of aptamer sequences across multiple rounds of aptamer selection. The scale of aptamer HTS datasets has necessitated bioinformatics algorithms, such as clustering algorithms, to identify candidate aptamers for experimental validation. Herein we describe a web-based aptamer bioinformatics platform, AptaMetrics, which utilizes a collection of programs and algorithms to facilitate the analysis of aptamer HTS datasets.The AptaMetrics platform builds upon our previously described aptamer bioinformatics work (Thiel et. al. PLoSOne, 2012). Central to AptaMetrics is our clustering algorithm, ProcessSeqs, which we engineered to include several novel and distinct features: 1) clustering may be performed using either an “all-versus-all” or a “seed” sequence strategy; 2) clustering may be accomplished through either sequence similarity (edit distance) or structural similarity (tree distance); 3) the output of ProcessSeqs provides a visual and interactive representation of related aptamer networks; and 4) these networks of related aptamers may be analyzed using conventional network analysis tools. We also developed an aptamer structure prediction program, ProcessFold, that provides the predicted structure of millions of aptamer sequences utilizing a variety of proven oligonucleotide structure prediction algorithms (e.g., RNAfold, Mfold, RNAstructure). Integration of these two programs thereby allows users to create networks of structurally related aptamers based on the different structure prediction algorithms. We also created and incorporated an aptamer truncation algorithm, AptmR, into the AptaMetrics platform. The purpose of AptmR is to determine a predicted truncated aptamer sequence based on aptamer sequence and structure information provided by ProcessFold. AptmR can be applied to either a single aptamer sequence or to millions of aptamer sequences. The predicted truncations may then be clustered into networks of related aptamers using the ProcessSeqs clustering algorithm. Importantly, to allow the greatest versatility, each program and algorithm within AptaMetrics may be used independently or as a pipeline. The collection of programs and algorithms within AptaMetrics provide a significant degree of flexibility in analyzing aptamer HTS data while maintaining the ease of accessibility of a web-based environment.
Optimisation and adaptation of synchronisation controllers for networked second-order infinite-dimensional systems

ABSTRACTThe adaptation and optimisation of synchronisation control for networked second-order distributed parameter systems are considered. The objective is to design output feedback controllers guaranteeing agreement between the states of the N systems that individually track a reference model. The controller structure involves feedback terms consisting of the pairwise difference of the measurements of the second-order systems as well as coupling terms that enforce consensus. Placing the closed-loop networked systems in aggregate form allows for further optimisation of the synchronisation gains. Using the aggregate systems ‘closed-loop energy’ as a suitable optimisation measure, the search for the synchronisation gains reduces to the minimisation of the optimisation index, which eventually is described by the trace of the solution to a parameterised Lyapunov operator equation. Considering the adaptation of the synchronisation gains offers an alternative to optimisation. The adaptation is based on Lyapuno...
Sex disparities in substance abuse research: Evaluating 23 years of structural neuroimaging studies

Abstract Background Sex differences in brain structure and clinical course of substance use disorders underscores the need to include women in structural brain imaging studies. The NIH has supported the need for research to address sex differences. We evaluated female enrollment in substance abuse structural brain imaging research and the methods used to study sex differences in substance effects. Methods Structural brain imaging studies published through 2016 (n = 230) were evaluated for number of participants by sex and substance use status and methods used to evaluate sex differences. Temporal trends in the numbers of participants by sex and substance use status were analyzed. We evaluated how often sex effects were appropriately analyzed and the proportion of studies that found sex by substance interactions on volumetric measures. Results Female enrollment increased over time, but remained significantly lower than male enrollment ( p = 0.01), with the greatest bias for alcohol and opiate studies. 79% of studies included both sexes; however, 74% did not evaluate sex effects or used an analytic approach that precluded detection of sex by substance use interactions. 85% of studies that stratified by sex reported different substance effects on brain volumes. Only 33% of studies examining two-way interactions found significant interactions, highlighting that many studies were underpowered to detect interactions. Conclusions Although female participation in substance use studies of brain morphometry has increased, sex disparity persists. Studying adequate numbers of both sexes and employing correct analytic approaches is critical for understanding sex differences in brain morphometric changes in substance abuse.
Anxiety in Intellectual Disabilities: Challenges and Next Steps

Abstract Anxiety symptoms and disorders are common in individuals with intellectual disability (ID). Beyond this general vulnerability, certain syndromes and disorders associated with ID confer increased risk for anxiety. Autism spectrum disorders and Williams syndrome are two such disorders. This review summarizes studies assessing the prevalence and phenomenology of anxiety in autism spectrum disorders and Williams syndrome, and discusses the current state of measurement and treatment in regards to anxiety in ID. Overall, studies suggest that individuals with autism spectrum disorders and those with Williams syndrome experience greater levels of anxiety relative to both typically developing controls and to individuals with ID of varying etiology, although this anxiety may manifest in different ways. Recent years have seen an influx of measures tailored to assessing anxiety in ID. Although treatment options remain limited, they are growing in number. Next steps for research investigating anxiety in ID are discussed, as are the advantages of phenotypic work in ID for understanding psychopathology in the general population.
Plant community composition influences fine root production and biomass allocation in perennial bioenergy cropping systems of the upper Midwest, USA

Abstract Fine roots play a key role in the global carbon (C) cycle because much of the C accumulating in soil is the result of fine root production and turnover. Here we explore the effect of plant community composition and diversity on fine root production in surface soils and plant biomass allocation to fine roots in six perennial cropping systems differing in composition and diversity planted as biofuel feedstocks. The six systems were established in 2008 at both a high and a moderate fertility site located in the upper Midwest, USA and included: switchgrass ( Panicum virgatum) , miscanthus ( Miscanthus × giganteus ), hybrid poplar ( Populus nigra × P . maximowiczii ‘NM6), native grasses (a five-species assemblage of Andropogon gerardii, Elymus canadensis, P. virgatum, Schizachrium scoparium, and Sorghastrum nutans) , an early successional system, and a restored prairie with 25 sown grass, legume, and forb species. For three years (2011–2013) at both sites ingrowth cores were deployed each spring; half were extracted at mid-season and the rest in late fall. Native grasses and restored prairie systems produced 31–77% more fine roots by mid-season compared to the other cropping systems at both sites. Miscanthus and hybrid poplars tended to have the lowest fine root production. The polyculture cropping systems allocated 39–94% more energy to the production of fine roots, with the exception of switchgrass at the low fertility site. Findings demonstrate a greater potential for diverse biofuel cropping systems to allocate C belowground to fine roots as compared to monocultures, with potential implications for soil C sequestration.
A Study of RMBS Litigation Cases of Six Major U.S. Banks

Prior to the financial crisis of 2008–2009, banks engaged in activities related to mortgages and mortgage-backed securities that caused financial losses to investors. This resulted in a wave of residential mortgage-backed securities (RMBS) litigation. Investors and U.S. government entities filed hundreds of lawsuits in federal court in the years during and after the credit crisis. In this research, the authors consider 43 settlements of RMBS litigation pertaining to major U.S. banks. First, they provide a chronology of major events in the history of RMBS litigation. Second, using a unique dataset, they quantify the impact and involvement of such litigation on major U.S. banks, U.S. government agencies, and other entities. There are two important findings: U.S. banks were not equally impacted, and RMBS settlements were not equally distributed among the various plaintiffs. Third, the authors provide a breakdown of the litigation by year of settlement. They show that litigation settlement activity increased in 2013 and 2014 but declined during the period 2014–2016.
Is optical coherence tomography a coherent strategy for carotid artery stenting

Optical coherence tomography (OCT) is rarely necessary to guide clinical decisions about the appropriateness of carotid revascularization. For carotid artery stenting (CAS), computed tomography angiography is the best imaging tool to assess arch, carotid, and lesion-specific anatomy, including vessel dimensions and calcification. OCT is a coherent strategy after CAS to assess ambiguous angiographic findings and to guide appropriate therapy for dissection, thrombosis, and plaque prolapse.
Short communication: Thermal performance of a cryogenic helium pulsating heat pipe with three evaporator sections

Abstract This short communication reports surprising results from on-going measurements of a helium pulsating heat pipe (PHP) in which the adiabatic length has been increased from 0.3 m to 1 m. In addition, the PHP has been constructed with a total of three evaporator sections. The PHP contains 42 parallel stainless steel tubes with an outer and inner diameter of 0.8 mm and 0.5 mm, respectively. PHPs with this configuration can serve as thermal spreaders for cryocoolers and can be used to cool multiple hot spots. Results and configuration details of the PHP with a 300 mm long adiabatic section have been previously published (Fonseca et al., 2017, 2018). The same PHP, now modified with a 1-meter long adiabatic section has been tested at the same heat load and fill ratio values as the 0.3 m PHP. The PHP operates between 3 K and 5.2 K using a Sumitomo cryocooler model RDK-408A2 with a cooling capacity of 1 W at 4.2 K. Interestingly, the results show that the temperature difference (T) between the evaporator and condenser sections of the PHP with the 1-m adiabatic section length is almost identical to that measured with the 0.3 m adiabatic section length PHP when the two different configurations are each operated at their respective optimum fill ratio. Temperature differences below 1 K are achieved when the heat load is less than 0.26 W per evaporator section (0.78 W total). Very similar optimal thermal conductance ( Q / Δ T ) values are obtained for both configurations, where a maximum thermal conductance of 0.383 W/K at a fill ratio of 58% and 0.387 W/K at a fill ratio of 70% are achieved for the 1 m and 0.3 m PHP, respectively. In addition, the optimal thermal performance can be expressed as an effective thermal conductivity that is proportional to the adiabatic length, resulting in a higher value for the 1-m PHP of 150 kW/m-K; while the 0.3 m PHP achieved a maximum thermal conductivity of almost 53 kW/m-K. This paper will present results based on equal heat load distribution throughout the evaporator sections.
National trends in adoption of ACRL information literacy guidelines and impact on business instruction practices: 2003–2015

This study compares business librarians' information literacy practices and perceptions in response to the publication of the Information Literacy Competency Standards for Higher Education and Fram...
Fluxes of Major Biochemicals in the Equatorial Pacific Ocean

A coordinated study of the geochemistry of major biochemical classes has been carried out in the equatorial Pacific Ocean (EqPac) as part of the U.S. Global Ocean Flux Study (JGOFS). Amino acids, carbohydrates, pigments, and lipids were measured at the molecular level in plankton, sediment trap material, and sediments along a transect from 12°N to 12°S along 140°W to address questions related to the efficiency and dynamics of the carbon pump in the equatorial Pacific and how processes in the water column affect the burial of biogenic components. Here we present an overview of our findings, discussing fluxes and relative reactivities of the biochemical classes. We conclude with an inventory of the major particulate biochemicals in the equatorial Pacific, in which the proportion of organic carbon amenable to conventional molecular-level analyses decreases from ~82% in plankton to ~20% in sediments, demonstrating the need for new analytical approaches to characterize residual macromolecular material.
Variation-Tolerant Microprocessor Architecture at Low Power

This chapter focuses on the different techniques at the microarchitectural level to handle variations and to provide a variation-tolerant low-power design. An overview of the different sources of parameter variations is presented, and a discussion of the different models used at the architectural level to understand their effect on processor power and performance is provided. All sources of variations lead to timing overhead and uncertainty, but each kind of variation has different characteristics. Designers typically account for parameter variations by inserting conservative margins that guard against worst-case variation characteristics to guarantee functional correctness of the system under all operating conditions. However, such a conservative approach leads to significant performance degradation in the current technology and will worsen with technology scaling. This chapter presents alternative error-tolerant schemes to deal with these different sources of parameter variations. Error-tolerant schemes aim to run with nominal timing margins but without comprising robustness and correctness.
Molecular Dynamics Simulation of Melting

By a rapid quenching technique, the equilibrium atomic configurations during the melting of a Lennard-Jones fcc crystal are examined at femtosecond intervals. The various processes during the “nucleation” stage are observed. A point of no return is found before which the system can be quenched into a perfect fcc crystal and after which it can be quenched only into a defective or amorphous structure. The melting process is further illuminated by the cavity distribution which can detect order even in an amorphous structure.
The Effects of AHS on the Environment

As a key culmination of ITS technology, an Automated Highway System (AHS) will substantially improve the safety and efficiency of highway travel. The general AHS concept consists of instrumented vehicles operating on instrumented roadways without operator intervention.(1) Various sensors and communication devices will link the vehicles and roadway, virtually eliminating driver error and maximizing traffic performance. Drivers equipped with a vehicle instrumented for AHS operation will be able to enter an AHS through a check-in area and proceed onto a transition lane, where control of the vehicle will be assumed by the AHS. The system will then move the vehicle onto one of the automated lanes where it then merges with other traffic. When the driver’s destination is reached, the system will move the vehicle back to the transition lane where the driver will be able to resume control of the vehicle.(1)
Double-Tuned Cable Traps For Multinuclear MRI And MRS

Using the method of pole-insertion, double-tuned cable traps were constructed and studied. The effectiveness of the method was examined for four different magnetic field strengths. The double-tuned cable trap design was able to effectively block shield currents at two frequencies simultaneously for all field strengths attempted. The effectiveness of the design seemed to increase at higher field strengths, eventually outperforming even the single-tuned cable traps at the highest frequencies examined. The double-tuning method demonstrated here could be a useful cable trap design for multinuclear studies and is considerably more spaceefficient than using two single-tuned cable traps mounted in series. This design should be particularly useful in cases where space is limited, such as when using high channel-count array coils.