cssi/SciSciGPT-SciSciNet huggingface dataset:
Insect Population Dynamics, Pesticide Use, and Farmworker Health

We address the impacts of regulations designed to reduce pesticide poisoning of farmers and farm laborers. Attention is concentratedon pre-harvest interval regulations that impose a time interval between pesticide application and harvest. The incidence of poisoning is determined by aggregate pesticide use, worker exposure, and toxicity. A dynamic, stochastic model of insect population growth is developedandusedto measure the incentives for pesticide use. Increasing the pre-harvest interval has an ambiguous effect on the number of harvest worker poisonings. Pesticide taxation unambiguously reduces the number of worker poisonings. Theoretical results are quantified in a case study of mevinphos application on leaf lettuce in California’s Salinas Valley.
Radiation Damage Effects on the Magnetic Properties of Pu(1-x)Am(x) (x=0.224)

Pu(Am) is stable in the fcc {delta}-phase from a few atomic percent to nearly 80 atomic percent Am, expanding the average interatomic separation as the alloy concentration of Am increases. Both Pu and Am spontaneously decay by {alpha}-emission creating self-damage in the lattice in the form of vacancy-interstitial pairs and their aggregates. At sufficiently low temperatures, the damage is frozen in place, but can be removed by thermal annealing at sufficiently high temperatures, effectively resetting the system to an undamaged condition. The magnetic susceptibility and magnetization are observed to increase systematically as a function of accumulated damage in the fcc {delta}-Pu{sub 1-x}Am{sub x} (x=0.224). Some results of these observations are reported here.
Model-Based Predictive Control of Weld Penetration in Gas Tungsten Arc Welding

Skilled welders can estimate and control the weld joint penetration, which is primarily measured by the backside bead width, based on weld pool observation. This suggests that an advanced control system could be developed to control the weld joint penetration by emulating the estimation and decisionmaking process of the human welder. In this paper an innovative 3-D vision sensing system is used to measure the characteristic parameters of the weld pool in real-time in gas tungsten arc welding. The measured characteristic parameters are used to estimate the backside bead width, using an adaptive neuro-fuzzy inference system (ANFIS) as an emulation of skilled welder. Dynamic experiments are conducted to establish the model that relates the backside bead width to the welding current and speed. The dynamic linear model is first constructed and the modeling result is analyzed. The linear model is then improved by incorporating a nonlinear operating point modeled by an ANFIS. Because the weld pool needs to gradually change, being controlled by a skilled welder, a model predictive control is used to follow a trajectory to reach the desired backside bead width and the control increment is penalized. Because the weld pool is not supposed to change in an extremely large range, the resultant model predictive control is actually linear and an analytical solution is derived. Welding experiments confirm that the developed control system is effective in achieving the desired weld joint penetration under various disturbances and initial conditions.
The Sensor Histidine Kinase RgfC Affects Group B Streptococcal Virulence Factor Expression Independent of Its Response Regulator RgfA

Group B streptococci (GBS; Streptococcus agalactiae) are beta-hemolytic, Gram-positive bacteria that are common asymptomatic colonizers of healthy adults. However, these opportunistic bacteria also cause invasive infections in human newborns and in certain adult populations. To adapt to the various environments encountered during its disease cycle, GBS encodes a number of two-component signaling systems. Previous studies have indicated that the TCS comprising the sensor histidine kinase RgfC and the response regulator RgfA mediate GBS binding to extracellular matrix components, such as fibrinogen. However, in certain GBS clinical isolates, a point mutation in rgfA results in premature truncation of the response regulator. The truncated RgfA protein lacks the C-terminal DNA binding domain necessary for promoter binding and gene regulation. Here, we show that deletion of rgfC in GBS strains lacking a functional RgfA increased systemic infection. Furthermore, infection with the rgfC mutant increased induction of proinflammatory signaling pathways in vivo. Phosphoproteomic analysis revealed that 19 phosphopeptides corresponding to 12 proteins were differentially phosphorylated at aspartate, cysteine, serine, threonine, or tyrosine residues in the rgfC mutant. This included aspartate phosphorylation of a tyrosine kinase, CpsD, and a transcriptional regulator. Consistent with this observation, microarray analysis of the rgfC mutant indicated that >200 genes showed altered expression compared to the isogenic wild-type strain and included transcriptional regulators, transporters, and genes previously associated with GBS pathogenesis. Our observations suggest that in the absence of RgfA, nonspecific RgfC signaling affects the expression of virulence factors and GBS pathogenesis.
When does human life begin?: an evolutionary perspective

The question – »when does human life begin?« – is without doubt an important one, and the answer to it has different yet equally profound consequences in diverse fields such as medicine, theology, ethics, and anthropology. But before one can begin to tackle the topic and its ramifications, one must first be certain that that one is not conflating a conception about »the beginning of human life« with the biology relating to »the beginning of life«. Here I shall discuss these issues from the perspectives of the history and philosophy of science and evolutionary biology with the hope that this might shed light on the multifaceted and hierarchical nature of this typically highly charged subject.
The All or Nothing Doctrine in Criminal Cases: Independent Trial Strategy or Gamesmanship Gone Awry?

The All-or-Nothing Doctrine. A simple catchy phrase, it speaks in shorthand of a strategy that permits parties in a criminal trial to forego instructions on provable lesser-included offenses, thereby forcing the jury to choose between conviction and acquittal on the greater charge. The doctrine is a starkly contrasting study in the relative worth of trial party freedom at the expense of full jury deliberations. Where sanctioned, the All-or-Nothing Doctrine flourishes because trial parties, rather than the court, are able to determine which of the provable charges will be sent to the jury. Upon closer review, however, what appears to be uniformly held is in actuality a series of splintered views regarding the Lesser-Included Offense Doctrine and the role of the court in its administration. This article suggests that the tremendous disparity in approaches to the All-or-Nothing Doctrine is fueled by two diametrically opposed and irreconcilable policies. On the one hand, the premium attached to uncompromising and truthful jury deliberations necessitates giving lesser-included instructions where the evidence warrants it. On the other, the doctrine is promoted by historical deference given to parties to develop their own trial strategy unimpeded by outside interference. Designated in this article as the “trial integrity” model of analysis (for its commitment to the fact finding process) and the “party autonomy” model of analysis (for its deference to the parties’ freedom to determine trial strategy), these underlying policies have shaped the parameters of the doctrine. Where competing values of trial integrity and party autonomy meet head to head, the All-or-Nothing Doctrine poses a serious dilemma and question: Does the lesser-included offense instruction exist primarily as a permissive tool for the pleasure of one or both trial parties, or is its inclusion impelled by external judicial and societal considerations? This article attempts to shed light on the varied and multi-layered responses to this question.
Sports as a CSR Initiative: Empowering the Youth

Corporate Social Responsibility (CSR) requires organizations to consider the inherent interests of all stakeholders - inclusive of investors, consumers, employees, the community and last but not the least the environment in order to discharge their commercial activities. The implicit idea being the assumption that both sports and corporate influence the social trends from a series of multiple angles. This novel viewpoint inadvertently leads to an examination of the overlaps between the social responsibilities of the sport and corporate worlds. The present conceptual paper explores the role that sport can play as a vehicle for deploying CSR. It is an attempt to explain and explore the social responsibilities existent in sport as well as those found in the corporate world. An overarching opportunity is present at the intersection of these mutual responsibilities in the combination of the financial leverage available to corporations and the distributive/symbolism displayed in sport. The authors point that sport offers a bridge across social and economic gaps, a stimulus to encourage corporate to share a little of their prosperity by providing the youth with a viable but little explored theme of sport as a means to develop their personal skills and simultaneously improve the future prospects in terms of employability.
Addressing Stroke Risk Factors in Black and White Americans: Findings from the National Health and Nutrition Examination Survey, 2009-2010.

Objectives: Recurrent stroke affects 5%-15% of stroke survivors, is higher among Blacks, and preventable with secondary stroke prevention medications. Our study aimed to examine racial differences in risk factors being addressed (defined as either on active treatment or within guideline levels) among stroke survivors and those at risk for stroke. Methods: A cross-sectional study using NHANES 2009-2010 standardized interviews of Whites and Blacks aged ≥18 years. Risk factors were defined as being addressed if: 1) for hypertension, SBP <140, DBP <90 (SBP<130, DBP<80 for diabetics) or using BP-lowering medications; 2) for current smoking, using cessation medications; and 3) for hyperlipidemia, LDL<100 (LDL<70 for stroke survivors) or using lipid-lowering medications. Participants were stratified by stroke history. Prevalence of addressed risk factors was compared by race. Results: Among 4005 participants (mean age 48, 52% women, 15% Black), 4% reported a history of stroke. Among stroke survivors, there were no statistically significant differences in Blacks and Whites having their hypertension or hyperlipidemia addressed. Among stroke naive participants, the prevalence of addressed hypertension (P<.01) and hyperlipidemia (P<.01) was lower in Blacks compared with Whites. Conclusions: We found that addressed hypertension and hyperlipidemia in stroke naive participants were significantly lower in Blacks than Whites. Our observations call attention to areas that require further investigation, such as why black Americans may not be receiving evidence-based pharmacologic therapy for hypertension and hyperlipidemia or why Black Americans are not at goal blood pressure or goal LDL. A better understanding of this information is critical to preventing stroke and other vascular diseases. Ethn Dis . 2016;26(1):9-16; doi:10.18865/ed.26.1.9
Ion Exchange Membranes for Water Softening and High-Recovery Desalination

Water softening is typically performed by contacting hard water with cation exchange beads that are originally in the sodium ion form. When the ion exchange capacity of the beads is exhausted, they are regenerated by soaking them with a concentrated solution of NaCl, a cyclic and rather inefficient process that contributes considerable salt to the environment. The same cation exchange material can be made into a membrane and used to achieve water softening in a continuous process called Donnan dialysis. The regenerant NaCl solution (called the stripper) flows across one surface of the cation exchange membrane, and the hard water flows across the other. Diffusion of Na + ions from the concentrated stripper causes counter-diffusion of Ca 2+ ions out of the hard water into the stripper solution where their concentration reaches much higher levels than in the feed.
Antithrombotic Therapy in Percutaneous Coronary Intervention

Numerous agents are available for anticoagulation during percutaneous coronary intervention (PCI). These agents have been evaluated in a variety of clinical settings, including elective, urgent, and emergent PCI. Although unfractionated heparin remains a frequent choice, accumulating data support the use of newer agents to mitigate bleeding risk, especially in the setting of femoral access and concomitant use of glycoprotein IIb/IIa receptor inhibition. With several antithrombotic agents available, an assessment must be made regarding the ischemic and bleeding risks. This article summarizes existing data examining the benefits and limitations of the various anticoagulants and guidelines for their use.
Sexual commerce and the global flow of bodies, desires, and social policies

In anticipation of the 2006 World Cup games in Munich, a broad international coalition of feminist and faith-based activists joined together to protest Germany’s world-renowned system of legalized prostitution. Although Germany’s system of licensed, regulated, and taxed prostitution has been regarded by some commentators as a progressive exemplar of sex workers’ rights, a diverse spectrum of antiprostitution activists were able to ignite a fervor regarding an anticipated epidemic of sex trafficking on the occasion of the World Cup, recasting the German state’s embrace of prostitution as a human rights catastrophe and rallying cause. In the antiprostitution activists’ analysis, human trafficking had little to do with the vast economic inequalities that propel individuals of all genders to migrate west and north under hazardous conditions, but was instead a manifestation of unchecked male desires run rampant—desires that, like Germany’s prostitution system itself, were badly in need of reform (see, for example, Coalition Against Trafficking in Women, 2006; Lopez, 2006; “Sex Isn’t a Spectator Sport,” 2006). Though much was initially made by activists, international officials, and the press of the estimated 40,000 women who would be trafficked into Germany to service the sexual needs of the sports fans attending the World Cup games,1 after the event was held, the International Organization on Migration (IOM) concluded that there was no evidence whatsoever that any influx of trafficking in women had occurred.2 The 48-page IOM report on prostitution during the games identified only five women who had been trafficked into Germany and concluded that the dire predictions of concerned activists had been, in fact, “unfounded and unrealistic” (International Organization on Migration, 2007, p. 5). In response to the report, many prominent antiprostitution activists claimed that it was their very efforts that had prevented worse atrocities from occurring, vowing to keep up a concerted fight against male sexual demand and sex trafficking, both in Germany and the world beyond (see, for example, Crouse, 2007; Westen, 2006).3 As the articles compiled for this special issue demonstrate, the World Cup games in Munich constitute but one example of how the globalization of sexual commerce entails a rapid circulation of bodies and desires—not merely those of potential sex workers and their customers but also, and perhaps most especially, those of other interested parties, including feminist and religious activists, members of a burgeoning transnational nongovernmental organization (NGO) sector, and local and state-level policymakers. Describing contexts ranging from Europe to South Korea, from India and the Caribbean to the
Peripheral nerve regeneration monitoring using multilayer microchannel scaffolds.

Over 200,000 Americans have peripheral nerve injuries annually that result in a loss of function and a compromised quality of life. Of these, a significant percent involves unsuccessful repair of peripheral nerve gaps that occur due to traumatic limb injury or collateral damage to peripheral nerves during tumor resection. The clinical gold standard to repair a nerve gap is to use sural nerve autografts. However, autografts are not ideal because of the need for secondary surgery to source the nerve, loss of function at the donor site, lack of source nerve in the event of diabetic neuropathies, neuroma formation, and the need for multiple grafts to bridge nerves. An alternative to autografting that has proved to have significantly less risks and sacrifices is a nerve conduit. While there are some nerve conduits approved for clinical applications (Pabari et al., 2010; Giusti et al., 2012), commercial nerve conduits for nerve repair are usually composed of type I collagen or biodegradable polymers, such that the conduit will degrade once the nerve has healed. Although possible complication from foreign materials is not negligible, nerve conduits have had success in bridging nerve gaps and restoring functionality to limbs. Unlike autografting, it does not require the sacrifice of the donor sural nerve.
Multi-view coded aperture coherent scatter tomography

We use coded apertures and multiple views to create a compressive coherent scatter computed tomography (CSCT) system. Compared with other CSCT systems, we reduce object dose and scan time. Previous work on coded aperture tomography resulted in a resolution anisotropy that caused poor or unusable momentum transfer resolution in certain cases. Complimentary and multiple views resolve the resolution issues, while still providing the ability to perform snapshot tomography by adding sources and detectors.
Development of the Miniaturized Pressuremeter Test to Evaluate Unbound Pavement Layers

The development of a reliable field test that can be utilized to determine in situ pavement characteristics is discussed in this work. The developed device, which is a modified version of the PENCEL pressuremeter has a 6-in. inflatable probe capable of measuring field stress–strain response of the soils without worrying about edge effects of thin unbound granular layers. A roadway project was selected to conduct some preliminary field measurements in its subgrade layer. The PENCEL pressuremeter (PPMT) along with the miniaturized pressuremeter (MPMT) were used during the testing program to check the performance of the new device, and to validate its results. The results indicated that strength and stiffness properties of poorly graded sand subgrade, measured from running the miniaturized pressuremeter, compare well with those measured from the PENCEL pressuremeter. The MPMT data can be employed as essential inputs to evaluate existing pavement structures as part of a pavement-management system, and as critical inputs in empirical design methods of new flexible pavements and/or pavement overlays.
Importance of doping, dopant distribution, and defects on electronic band structure alteration of metal oxide nanoparticles: Implications for reactive oxygen species

Metal oxide nanoparticles (MONPs) are considered to have the potency to generate reactive oxygen species (ROS), one of the key mechanisms underlying nanotoxicity. However, the nanotoxicology literature demonstrates a lack of consensus on the dominant toxicity mechanism(s) for a particular MONP. Moreover, recent literature has studied the correlation between band structure of pristine MONPs to their ability to introduce ROS and thus has downplayed the ROS-mediated toxicological relevance of a number of such materials. On the other hand, material science can control the band structure of these materials to engineer their electronic and optical properties and thereby is constantly modulating the pristine electronic structure. Since band structure is the fundamental material property that controls ROS-producing ability, band tuning via introduction of dopants and defects needs careful consideration in toxicity assessments. This commentary critically evaluates the existing material science and nanotoxicity literature and identifies the gap in our understanding of the role of important crystal structure features (i.e., dopants and defects) on MONPs' electronic structure alteration as well as their ROS-generation capability. Furthermore, this commentary provides suggestions on characterization techniques to evaluate dopants and defects on the crystal structure and identifies research needs for advanced theoretical predictions of their electronic band structures and ROS-generation abilities. Correlation of electronic band structure and ROS will not only aid in better mechanistic assessment of nanotoxicity but will be impactful in designing and developing ROS-based applications ranging from water disinfection to next-generation antibiotics and even cancer therapeutics.
Update on clinical attire requirements in dental hygiene programs.

PURPOSE Many changes have occurred in the clinical appearance of dental hygienists in the past few years because of increased emphasis on infection control and disease prevention. The purpose of this study was to assess dental hygiene program clinical attire requirements in 1993 and to compare them with requirements as described by a 1988 survey. METHODS Checklist questionnaires were mailed to the directors of all 211 dental hygiene programs in the United States and Puerto Rico in October 1993. Questions were asked regarding clinical attire requirements for students and faculty, including uniforms, gowns, lab coats, masks, protective eyewear, shoes, hair coverings, laundry management, and changes under consideration. Percentages were calculated by region and for all responding programs. RESULTS Of 211 questionnaires mailed, 178 were returned, for a response rate of 84%. Results indicated that students and faculty are currently wearing more colorful uniforms and scrubs than in 1988. Long-sleeved lab coats, disposable gowns, and washable surgical gowns are increasing in use. Glasses and face masks were required for all students and faculty in both surveys, but chin-length face shields are increasing in use as optional face protection. In most instances, face shields are worn with face masks. Laundry services are being provided for faculty (employees); however, most students continue to be responsible for their own laundry after being instructed to follow stringent guidelines taught by the faculty. CONCLUSIONS Increasing emphasis on personal and patient protection is moving clinical attire requirements toward a more surgical appearance. Dental hygiene educators continue to monitor and to stay current with federal infection control recommendations, regulations, and guidelines.
“Race doesn’t matter” A dialogic analysis of interracial romantic partners’ stories about racial differences

This study examines constructions of racial differences within online stories narrated by individuals involved in interracial romantic relationships. A dialogic analysis of the stories (n = 76) revealed that interracial romantic partners challenged difference by positioning racial dissimilarity as problematic, contrasting differences with partner similarities, devaluing difference in the evaluation of relational success, and erasing difference or refuting an interracial relational identity altogether. The marginalization of difference in contrast to the dominance of similarity in individuals’ talk suggests that interracial partners participate in a great deal of discursive work to legitimize their relationships.
Effects of Medial Displacement Calcaneal Osteotomy and Calcaneal Z Osteotomy on Subtalar Joint Pressures: A Cadaveric Flatfoot Model

Medial displacement calcaneal osteotomies have been shown to be successful in the surgical management of adult acquired flatfoot, in particular, stage 2 deformity. Classically, the medial displacement calcaneal osteotomy technique has been performed. However, a calcaneal Z osteotomy has been more recently described and applied in the surgical management of flatfoot deformity. Although the potential advantages of the calcaneal Z technique have been reported, data on its effect on the subtalar joint are lacking. A validated flatfoot model was induced in 8 cadaveric feet that had been randomly assigned to either medial displacement calcaneal osteotomy (n = 4) or calcaneal Z osteotomy (n = 4). The feet were loaded through the tibia with a constant ground reaction force of 400 N, with a simultaneous increase in the Achilles tendon force to 300 or 500 N. The subtalar joint pressures were recorded before and after osteotomy. We did not detect any statistically significant differences between the 2 techniques in terms of their effects on subtalar joint pressure.
Orbital inflammatory disease management

ABSTRACTIntroduction: Orbital inflammatory disease (OID) represents a spectrum of conditions that can be placed into two groups, specific orbital inflammatory disease (SOIS) and nonspecific orbital inflammatory disease (NSOIS). This manuscript aims to systematically review the therapies for the different types of OID.Areas covered: The therapy for OID has evolved significantly with the advent of biologic medications, although certain mainstays are still widely used. The authors conducted a review of literature published in the last 20 years with the use of PubMed. This article is organized according to disease syndrome. Specific diseases and their associated treatments are addressed.Expert commentary: Although corticosteroids are still the mainstay of treatment in most OID, a focus on disease specificity combined with increasing understanding of inflammatory pathways has allowed utilization of inflammatory modulatory medications. Investigating these therapeutics in prospective trials will likely be the vi...
The Anoikis Effector Bit1 Inhibits EMT through Attenuation of TLE1-Mediated Repression of E-Cadherin in Lung Cancer Cells

The mitochondrial Bcl-2 inhibitor of transcription 1 (Bit1) protein is part of an anoikis-regulating pathway that is selectively dependent on integrins. We previously demonstrated that the caspase-independent apoptotic effector Bit1 exerts tumor suppressive function in lung cancer in part by inhibiting anoikis resistance and anchorage-independent growth in vitro and tumorigenicity in vivo. Herein we show a novel function of Bit1 as an inhibitor cell migration and epithelial–mesenchymal transition (EMT) in the human lung adenocarcinoma A549 cell line. Suppression of endogenous Bit1 expression via siRNA and shRNA strategies promoted mesenchymal phenotypes, including enhanced fibroblastoid morphology and cell migratory potential with concomitant downregulation of the epithelial marker E-cadherin expression. Conversely, ectopic Bit1 expression in A549 cells promoted epithelial transition characterized by cuboidal-like epithelial cell phenotype, reduced cell motility, and upregulated E-cadherin expression. Specific downregulation of E-cadherin in Bit1-transfected cells was sufficient to block Bit1-mediated inhibition of cell motility while forced expression of E-cadherin alone attenuated the enhanced migration of Bit1 knockdown cells, indicating that E-cadherin is a downstream target of Bit1 in regulating cell motility. Furthermore, quantitative real-time PCR and reporter analyses revealed that Bit1 upregulates E-cadherin expression at the transcriptional level through the transcriptional regulator Amino-terminal Enhancer of Split (AES) protein. Importantly, the Bit1/AES pathway induction of E-cadherin expression involves inhibition of the TLE1-mediated repression of E-cadherin, by decreasing TLE1 corepressor occupancy at the E-cadherin promoter as revealed by chromatin immunoprecipitation assays. Consistent with its EMT inhibitory function, exogenous Bit1 expression significantly suppressed the formation of lung metastases of A549 cells in an in vivo experimental metastasis model. Taken together, our studies indicate Bit1 is an inhibitor of EMT and metastasis in lung cancer and hence can serve as a molecular target in curbing lung cancer aggressiveness.
Journalists’ Normative Constructions of Political Viewpoint Diversity

This in-depth interview-based study with US political journalists explores how they conceptualize the portrayal of political viewpoint diversity as a journalistic norm, particularly in light of changes to news and the news media ecology. The political journalists still discursively embrace the normative role of providing audiences with a range of political viewpoints, but express assumptions about democracy that seem to thwart their intentions. The implications for the journalistic field and field theory are considered.
IMPROVING THE BACTERIOLOGICAL QUALITY OF CHICKEN FRYERS1,2

Two commercial fryer processing operations were investigated to determine the bacteriological quality of the fryers during and after evisceration. Alterations of washing, rinsing, and chilling methods were made to reduce bacterial numbers on skin surfaces of fryers. Swab samples were collected from fryer skin surfaces at various points in the processes and from table surfaces. Total plate counts, psychrophile counts, and coliform counts were determined. Total plate counts provided the greatest amount of useful information. Coliform counts were not suitable indicators of bacteriological conditions in the evisceration process. The major sources of bacteria on the skin surface of chilled fryers were the skin of freshly picked fryers and contamination added during the transfer of carcasses from the picker to the evisceration line. Evisceration of the fryers did not add significant numbers of bacteria to the skin surface. Bacteria on the skin of freshly picked fryers were firmly affixed to the surface. They co...
Molecular Signature for Parthenolide-Induced Apoptosis in AML CD34+ Cells Reveals Targets for Improving Induction of Leukemia-Specific Cell Death.

Previous studies have demonstrated that the plant-derived compound parthenolide (PTL) induces AML stem cell specific apoptosis while sparing normal counterparts. We have observed that PTL strongly inhibits NF-kappaB activity. Moreover, anti-oxidants such as N-acetylcysteine block the apoptotic process. However, the molecular events involved in the process are not completely understood. Given the demonstrated efficacy of PTL at targeting AML stem cells (AML-SCs), we hypothesized that a molecular signature that captures events invoked during PTL-induced apoptosis will provide a powerful tool for improving AML-SC targeting. To this end, we have conducted pharmacogenomic studies using primary CD34-enriched cells obtained from 12 randomly selected AML specimens. To capture dynamics of the PTL response, primary CD34+ AML were cultured in vitro and exposed to 5 micromolar PTL for either 1 hour or 6 hours. Labeled mRNA was hybridized to Affymetrix HG-U133plus2 chips. Differential expression of individual genes was assessed using moderated and permutation-based paired tests with false discovery rate control. Additionally, to capture pathway-level events possibly representing drugable targets, we employed functional, network, and robust geneset-based approaches to mine the data for coordinated changes in the expression of groups of biologically related genes, e.g., those controlled by a common transcription factor. By 1 hour post-treatment, we were able to detect the beginning stages of a cascade of responses leading to activation of antioxidant enzymes, cytoskeletal reorganization and downregulation of adhesion molecules, modulation of protein synthesis, proteasome remodeling, and modulation of cell cycle progression genes (q
Evaluation of Anemia in Adults: Going after the Common Causes.

Abstract Unexplained anemia is a common problem in adult medicine. Traditional approaches to etiologic diagnosis have included testing for “nutritional” deficiencies such as serum vitamin B12, folic acid, iron and iron binding capacity (IBC)(often a house staff approach); performing upper and lower endoscopy (often the Gastroenterologist or the Surgeon); or review of peripheral blood and bone marrow smears and biopsy (the Hematologist). Decision trees starting from MCVs and reticulocyte counts are commonly suggested in Hematology teaching manuals. However none of these approaches are based on knowledge of the most likely causes of anemia in the population to be tested. We hoped to improve on these largely unfounded and unevaluated empiric strategies by determining the actual frequencies of different causes of anemia among non-pregnant adults (20 and older) with initially unexplained anemias (Hb
Genome-wide regulatory model from MPRA data predicts functional regions, eQTLs, and GWAS hits

Massively-parallel reporter assays (MPRA) enable unprecedented opportunities to test for regulatory activity of thousands of regulatory sequences. However, MPRA only assay a subset of the genome thus limiting their applicability for genome-wide functional annotations. To overcome this limitation, we have used existing MPRA datasets to train a machine learning model that uses DNA sequence information, regulatory motif annotations, evolutionary conservation, and epigenomic information to predict genomic regions that show enhancer activity when tested in MPRA assays. We used the resulting model to generate global predictions of regulatory activity at single-nucleotide resolution across 14 million common variants. We find that genetic variants with stronger predicted regulatory activity show significantly lower minor allele frequency, indicative of evolutionary selection within the human population. They also show higher overlap with eQTL annotations across multiple tissues relative to the background SNPs, indicating that their perturbations in vivo more frequently result in changes in gene expression. In addition, they are more frequently associated with trait-associated SNPs from genome-wide association studies (GWAS), enabling us to prioritize genetic variants that are more likely to be causal based on their predicted regulatory activity. Lastly, we use our model to compare MPRA inferences across cell types and platforms and to prioritize the assays most predictive of MPRA assay results, including cell-dependent DNase hypersensitivity sites and transcription factors known to be active in the tested cell types. Our results indicate that high-throughput testing of thousands of putative regions, coupled with regulatory predictions across millions of sites, presents a powerful strategy for systematic annotation of genomic regions and genetic variants.
Cellular and Molecular Mechanisms of Amine Modulation in Crustacea

It is now well accepted that neuromodulators play a critical role in the control of behavior (for review, see Katz 1999). These versatile compounds adjust neuronal function at every level of the nervous system, from sensory reception through central neural networks to the neuromuscular junction, to make movements adaptive to the situation of the moment. The monoamines serotonin (5HT), octopamine (Oct), and dopamine (DA) have been the focus of many studies of neuromodulation in the Crustacea. These amines have been studied at many levels of analysis, from the behavioral (summarized in the chapter by Kravitz and Beltz, this Vol.) to the molecular. In this chapter, we will review the cellular mechanisms used by amines to shape neural activity in crustacean nervous systems. In addition, we will summarize recent progress in molecular biological approaches to crustacean neurobiology, which offer great promise in deepening our understanding of the substrates for neuromodulation.
Combinatorial Set Theory and Inner Models

Core model theory has lead to a new hierarchy of square principles. In the other direction, various combinatorial principles have been used to construct core models with Woodin cardinals.
Distributed optimization for evolving networks of growing connectivity

We focus on the problem of distributed optimization for multi-agent networks via distributed dual averaging (DDA) over an evolving network of growing connectivity. It is known that the convergence rate of DDA is influenced by the algebraic connectivity of the underlying network, where better connectivity leads to faster convergence. However, the effect of the growth of network connectivity on the convergence rate has not been fully understood. This paper provides a tractable approach to analyze the improvement in the convergence rate of DDA induced by the growth of network connectivity. This analysis is applicable, for example, to successive refinement strategies in massive multi-core optimizers where an increasing number of local data passage edges are successively added between cores in order to accelerate total run time. Compared to the existing convergence results, our analysis gives tighter bounds on the convergence of DDA over networks of growing connectivity. Numerical experiments show that our analysis leads to orders of improvement for evaluating convergence rate, which is not captured by existing analysis.
Korean Ethnic Orientation and Regional Linguistic Variability in the Multiethnic Context of Houston

Few studies in variationist sociolinguistics have investigated the Englishes of speakers of Asian heritage in the United States, and even fewer have looked at the correlation between ethnicity and linguistic variability among them. To address these limitations in the literature, this study offers an investigation of ethnic Koreans in the multiethnic context of Houston, Texas. The data come from sociolinguistic interviews with 15 Koreans of first- and second-generation immigrant backgrounds. Of particular interest to the chapter is the phonetic variation and sound changes of these Korean interviewees. Specifically, the chapter examines the fronted production of the back vowel GOAT (i.e., the pronunciation of the vowel in the word goat further forward in the mouth)—a dialect feature known as GOAT-fronting. The findings reveal how these speakers’ orientations to the Korean ethnic group and generational differences influence their linguistic behavior.
The Distribution of Absorbed Light Energy for Algal Photosynthesis

Photosynthesis is the process through which light energy is transformed into the chemical energy useful to biological organisms. This conversion is accomplished primarily through the enzymatic reduction of carbon from the highly oxidized CO2 to the more reduced level equivalent to formaldehyde, (CH2O)n. The reactions of carbon reduction occur in the soluble phase of the cell or chloroplast and require both reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP) [1,2]. In the simple case where only the reactions of the Calvin-Benson-Bassham Cycle [2] occur, the reduction of one molecule of CO2 requires three molecules of ATP and two of NADPH. However, in many photosynthetic organisms, other biochemical pathways, such as photorespiration of “C4” metabolism [3,4,5], change the above mentioned requirements. In addition, rapid growth or “luxury accumulation” [1] may require supplemental energy inputs. Thus, the commonly quoted ratio for ATP:NADPH: CO2 of 3:2:1 must be considered a minimum for promotion of growth.
Analysis of Factors Limiting Bacterial Growth in PDMS Mother Machine Devices.

The microfluidic mother machine platform has attracted much interest for its potential in studies of bacterial physiology, cellular organization, and cell mechanics. Despite numerous experiments and development of dedicated analysis software, differences in bacterial growth and morphology in narrow mother machine channels compared to typical liquid media conditions have not been systematically characterized. Here we determine changes in E. coli growth rates and cell dimensions in different sized dead-end microfluidic channels using high resolution optical microscopy. We find that E. coli adapt to the confined channel environment by becoming narrower and longer compared to the same strain grown in liquid culture. Cell dimensions decrease as the channel length increases and width decreases. These changes are accompanied by increases in doubling times in agreement with the universal growth law. In channels 100 micrometers and longer, cell doublings can completely stop as a result of frictional forces that oppose cell elongation. Before complete cessation of elongation, mechanical stresses lead to substantial deformation of cells and changes in their morphology. Our work shows that mechanical forces rather than nutrient limitation are the main growth limiting factor for bacterial growth in long and narrow channels.
A comparative study of non-native N-acyl l-homoserine lactone analogs in two Pseudomonas aeruginosa quorum sensing receptors that share a common native ligand yet inversely regulate virulence.

Abstract Certain bacteria can coordinate group behaviors via a chemical communication system known as quorum sensing (QS). Gram-negative bacteria typically use N-acyl l -homoserine lactone (AHL) signals and their cognate intracellular LuxR-type receptors for QS. The opportunistic pathogen Pseudomonas aeruginosa has a relatively complex QS circuit in which two of its LuxR-type receptors, LasR and QscR, are activated by the same natural signal, N-(3-oxo)-dodecanoyl l -homoserine lactone. Intriguingly, once active, LasR activates virulence pathways in P. aeruginosa, while activated QscR can inactivate LasR and thus repress virulence. We have a limited understanding of the structural features of AHLs that engender either agonistic activity in both receptors or receptor-selective activity. Compounds with the latter activity profile could prove especially useful tools to tease out the roles of these two receptors in virulence regulation. A small collection of AHL analogs was assembled and screened in cell-based reporter assays for activity in both LasR and QscR. We identified several structural motifs that bias ligand activation towards each of the two receptors. These findings will inform the development of new synthetic ligands for LasR and QscR with improved potencies and selectivities.
Adaptive Immunity to Listeria monocytogenes

Serious complications resulting from human infection with Listeria monocytogenes are usually limited to pregnant women, the very young or very old, or otherwise immunocompromised individuals (Schlech 2000). However, infection of experimental animals with L. monocytogenes serves as an extremely useful immunological tool because the bacteria are well characterized, easily manipulated, and infect virtually all mammals (Sixl et al. 1978). In particular, murine listeriosis has been used for many decades to dissect the fundamental components of innate and adaptive immunity to intracellular pathogens (Mackaness 1962; North et al. 1997; Unanue 1997a,b,c; Finelli et al. 1999; Harty et al. 2000). In a naturally occurring infection, L. monocytogenes is introduced into the gastrointestinal tract after consumption of contaminated food products where it binds to, and is taken up by, epithelial cells via interaction of bacterial internalin A and E-cadherin on the host cells (Gaillard et al. 1991). In comparison to humans, mice exhibit markedly reduced susceptibility to intestinal infection with L. monocytogenes due to a single amino-acid difference in mouse E-cadherin (Lecuit et al. 2001); therefore, intravenous (i.v.) or intraperitoneal (i.p.) infection of mice is used in most experimental systems. Regardless of the route of infection (i.p or i.v.), administration of one of the many laboratory L. monocytogenes strains available results in a highly reproducible infection that can be easily quantitated by assaying bacterial load (colony forming units; CFUs) in the spleen and liver at various days postinfection (White et al. 1999; Messingham et al. 2003). Mortality is dependent on the strain of bacteria used, with LD50 ranging from ∼1× 104 virulent bacteria to 1× 109 for some attenuated strains (Bouwer et al. 1999; Messingham et al. 2003; Badovinac et al. 2005). Upon infection, the bacteria are taken up by splenic and hepatic (primarily) phagocytes where the majority are killed within the phagosomes; however, a small percentage of bacteria are able to escape destruction and invade the cytosol where the race between bacterial replication and priming of the immune response begins.
US Regulators May Not Prevent Private Space Activity on the Basis of Article VI of the Outer Space Treaty

Article VI of the Outer Space Treaty states that “the activities of non-governmental entities shall require authorization and continuing supervision.” This has caused confusion for the US government and for private entities that plan to operate in outer space engaging in nontraditional businesses such as satellite servicing or asteroid mining. Many interested parties believe Article VI means that private entities may not operate without governmental authorization and continuing supervision. The Federal Aviation Administration (FAA) suggests that Article VI gives it authority to deny access to space to the unauthorized and unsupervised. A clearer understanding of the law should put these concerns to rest. Article VI is not self-executing. This means that it is not enforceable federal law unless Congress enacts domestic implementing legislation. Therefore, private actors may operate in outer space, even without authorization or supervision, and the FAA and other regulatory agencies may not rely on Article VI to attempt to deny these actors access to space.
Performance-Aware Energy Saving for Data Center Networks

Today’s data center networks (DCNs) tend to have tens to hundreds of thousands of servers that provide massive and sophisticated services. The architectural design of DCNs are usually over-provisioned for peak workloads and fault tolerance. Statistically, DCNs remain highly under-utilized, with typical utilization of around 30%. Network over-provisioning and under-utilization can be exploited for energy-saving. Most research efforts on DCN energy saving focus on how to save maximum energy but have little or no consideration to the performance of the residual network. Thus, the DCN performance can become degraded and the network left vulnerable to sudden traffic surges. In this paper, we have studied the energy-saving problem in DCNs while preserving network performance. The problem was formulated as mixed integer linear problem (MILP) solvable by CPLEX in order to minimize the energy consumed by DCN; meanwhile, safety threshold constraints for links utilization are met. To overcome CPLEX high computational time, a heuristic algorithm to provide practical and efficient solution for the MILP is introduced. The heuristic algorithm uses switches grouping and links consolidation to switch the traffic to a small number of network devices and turn off unused switches and links. Valiant load balancing is used to distribute the loads over active links. Simulation experiments using synthetic and real packet traces were conducted to validate the heuristic in terms of energy consumption and network performance. The results show that the heuristic can save up to 45% of the network energy and improve the average imbalance scores for links and switches by more than 50% with minimal effect on network performance.