cssi/SciSciGPT-SciSciNet huggingface dataset:
MUP - The UIC Standoff Markup Tool

Recently developed markup tools for dialogue work are quite sophisticated and require considerable knowledge and overhead, but older tools do not support XML standoff markup, the current annotation style of choice. For the DIAG-NLP project we have created a "lightweight" but modern markup tool that can be configured and used by the working NLP researcher.
Place-Based Environmentalism and Global Warming: Conceptual Contradictions of American Environmentalism

Until recently, the history of environmentalism was primarily a history of attention to place. In the United States, environmentalists have gotten rather good at protecting and managing particular places such as mountains, forests, and watersheds and specific resources such as trees, soil, wildlife, air, and water. Environmentalism has become an enormously popular social movement, with, by some measures, more than 80 percent of Americans considering themselves environmentalists. Thousands of organizations, ranging from local volunteer groups to national nonprofits, address issues as diverse as open space, air and water pollution, biological diversity, environmental justice, and environmental effects on human health. The successes of this movement have been striking. Our National Parks, National Forests, and wilderness areas are touted as models for the world and are well complemented by state, municipal, and private protected areas. The Endangered Species Act successfully resolves many conflicts between rare creatures and development. Rivers have been cleaned up, and once-spurned urban waterfronts now draw real estate and tourism development. Americans drink cleaner water and breathe cleaner air than much of the rest of the world, and attempts to weaken regulatory frameworks are consistently met with public disapproval.
Case Article---Vermillion OVA1 Test

Tying classroom material to current business events helps motivate and engage students. It also exposes them to examples of how to apply what they learn in practice. We present an example of how, in a course on modeling with spreadsheets, we used or article in The Wall Street Journal WSJ about approval of a medical test as the basis for an exercise on conditional probabilities, conflicting objectives, and the value of information. We present the plan of the discussion followed in class and the exercises assigned to students to help them understand the concepts. We use spreadsheet functions and tools new to many of our students, in particular, lookup functions and tools for sensitivity analysis. We also demonstrate how to create and interpret a tornado chart. We believe that examining the WSJ article in detail has value because it allows students to solidify their understanding of conditional probabilities and spreadsheet modeling and also gives them an appreciation of the complexities and the balancing of multiple perspectives in medical decision making. Case Teaching Note: Interested Instructors please see the Instructor Materials page for access to the restricted materials. To maintain the integrity and usefulness of cases published in ITE, unapproved distribution of the case teaching notes and other restricted materials to any other party is prohibited.
Eukaryotic Translation Initiation Factor 3 (eIF3) and eIF2 Can Promote mRNA Binding to 40S Subunits Independently of eIF4G in Yeast

Recruitment of the eukaryotic translation initiation factor 2 (eIF2)-GTP-Met-tRNAiMet ternary complex to the 40S ribosome is stimulated by multiple initiation factors in vitro, including eIF3, eIF1, eIF5, and eIF1A. Recruitment of mRNA is thought to require the functions of eIF4F and eIF3, with the latter serving as an adaptor between the ribosome and the 4G subunit of eIF4F. To define the factor requirements for these reactions in vivo, we examined the effects of depleting eIF2, eIF3, eIF5, or eIF4G in Saccharomyces cerevisiae cells on binding of the ternary complex, other initiation factors, and RPL41A mRNA to native 43S and 48S preinitiation complexes. Depleting eIF2, eIF3, or eIF5 reduced 40S binding of all constituents of the multifactor complex (MFC), comprised of these three factors and eIF1, supporting a mechanism of coupled 40S binding by MFC components. 40S-bound mRNA strongly accumulated in eIF5-depleted cells, even though MFC binding to 40S subunits was reduced by eIF5 depletion. Hence, stimulation of the GTPase activity of the ternary complex, a prerequisite for 60S subunit joining in vitro, is likely the rate-limiting function of eIF5 in vivo. Depleting eIF2 or eIF3 impaired mRNA binding to free 40S subunits, but depleting eIF4G led unexpectedly to accumulation of mRNA on 40S subunits. Thus, it appears that eIF3 and eIF2 are more critically required than eIF4G for stable binding of at least some mRNAs to native preinitiation complexes and that eIF4G has a rate-limiting function at a step downstream of 48S complex assembly in vivo.
Study of the RF Capture Process in the Argonne Rapid Cycling Synchrotron

The 500-MeV Rapid Cycling Synchrotron (RCS) guide field is energized by a dc-biased, 30 Hz sinusoidal ac power supply, and the field strength varies between 2.81-9.81 kG. During the acceleration period, the ? varies in a half-sine function from zero to a maximum of 670 kG/s and back to zero. Although the average ? during injection is not equal to zero, efficient capture has been obtained experimentally by adjustment of the RF voltage program and the injection timing. In this paper, we describe a simulation study of the capture process in order to understand the experimental results.
The role of the lissencephaly protein Pac1 during nuclear migration in budding yeast.

During mitosis in Saccharomyces cerevisiae, the mitotic spindle moves into the mother–bud neck via dynein-dependent sliding of cytoplasmic microtubules along the cortex of the bud. Here we show that Pac1, the yeast homologue of the human lissencephaly protein LIS1, plays a key role in this process. First, genetic interactions placed Pac1 in the dynein/dynactin pathway. Second, cells lacking Pac1 failed to display microtubule sliding in the bud, resulting in defective mitotic spindle movement and nuclear segregation. Third, Pac1 localized to the plus ends (distal tips) of cytoplasmic microtubules in the bud. This localization did not depend on the dynein heavy chain Dyn1. Moreover, the Pac1 fluorescence intensity at the microtubule end was enhanced in cells lacking dynactin or the cortical attachment molecule Num1. Fourth, dynein heavy chain Dyn1 also localized to the tips of cytoplasmic microtubules in wild-type cells. Dynein localization required Pac1 and, like Pac1, was enhanced in cells lacking the dynactin component Arp1 or the cortical attachment molecule Num1. Our results suggest that Pac1 targets dynein to microtubule tips, which is necessary for sliding of microtubules along the bud cortex. Dynein must remain inactive until microtubule ends interact with the bud cortex, at which time dynein and Pac1 appear to be offloaded from the microtubule to the cortex.
Neuromorphic architectures for nanoelectronic circuits

SUMMARY This paper reviews recent important results in the development of neuromorphic network architectures ('CrossNets') for future hybrid semiconductor=nanodevice-integrated circuits. In particular, we have shown that despite the hardware-imposed limitations, a simple weight import procedure allows the CrossNets using simple two-terminal nanodevices to perform functions (such as image recognition and pattern classication) that had been earlier demonstrated in neural networks with continuous, determin- istic synaptic weights. Moreover, CrossNets can also be trained to work as classiers by the faster error-backpropagation method, despite the absence of a layered structure typical for the usual neural networks. Finally, one more method, 'global reinforcement', may be suitable for training CrossNets to perform not only the pattern classication, but also more intellectual tasks. A demonstration of such training would open a way towards articial cerebral-cortex-scale networks capable of advanced infor- mation processing (and possibly self-development) at a speed several orders of magnitude higher than that of their biological prototypes. Copyright ? 2004 John Wiley & Sons, Ltd.
Lipid Oxidation in Poultry Döner Kebab: Pro‐oxidative and Anti‐oxidative Factors

: The effect of mechanically separated turkey (MST), ascorbate, and vacuum packaging on rates of lipid oxidation in chicken doner kebab during storage at 4 °C or -20 °C was investigated. MST and MST/ascor-bate accelerated lipid oxidation compared to control kebab. Ascorbate application and vacuum packaging inhibited lipid oxidation. The antioxidative effect of ascorbate in the absence of MST was converted to a pro-oxidative effect in the presence of MST. This suggests that the excess lipid hydroperoxides and iron complexes in MST were activated as lipid oxidation catalysts by ascorbate to overwhelm the ability of ascorbate to inhibit lipid oxidation at lower concentrations of hemoglobin, iron, and peroxides.
A Kantian argument against comparatively advantageous genetic modification

The genetic modification of children is becoming a more likely possibility given our rapid progress in medical technologies. I argue, from a broadly Kantian point of view, that at least one kind of such modification—modification by a parent for the sake of a child9s comparative advantage—is not rationally justified. To argue this, I first characterize a necessary condition on reasons and rational justification: what is a reason for an agent to do an action in one set of circumstances must be a reason for any in those circumstances to do the action. I then show that comparatively advantageous genetic modification violates this principle since a child9s “getting ahead” through genetic modification cannot be rationally justified unless other children also could receive the modification, thus rendering the advantage useless. Finally, I consider the major objection to this conclusion: it seems to disallow all cases of a parent9s helping a child get ahead, something that parents normally engage in with their children. I argue that typical practices of developing a comparative advantage in a child, as well as practices of societal competition in general, do not conflict because they involve circumstances that mitigate the universal character of reasons. Many ordinary cases of competitive advantage that we think of as unjust, in fact, can be explained by my argument.
Catastrophe Models for Cognitive Workload and Fatigue Memory Functions, Multitasking, Vigilance, Financial Decisions and Risk

The cusp catastrophe models for cognitive workload and fatigue and their supporting research program evolved in response to numerous difficulties encountered in previous research. The two cusp mode...
Influence of procainamide on sodium and potassium exchange and permeabilities in cultured human cells

The effect of procainamide on membrane cation exchange was investigated using monolayer cultures of Girardi heart cells. The initial effect of procainamide (10(-6) to 10(-3) mol/litre) was to produce a prompt reduction of the passive Na influx, dose-dependent along a sigmoid log dose-response curve. This effect was complete within 3 min and thereafter showed no further time-dependent increase. Mean passive Na influx (pmol-cm-2/s) decreased from 19.1 to 17.7 (P less than 0.05) and 10.4 (P less than 0.001) in 10(-5) and 10(-3) mol/litre procainamide, respectively. No effect on active Na extrusion was noted before 3 min following exposure to the drug, after which time it progressively declined reaching a minimum value for each concentration by 6 min and remaining at this level throughout a further 60 min exposure. For each concetnration this minimum value was similar to the Na influx measured under identical conditions. Na-coupled active K influx showed a parallel pattern of inhibition. K efflux was not decreased until approximately 20 min following exposure to the drug, but once present the reduction was similar in magnitude to that in the correspondingly measured K influx. Kinetic flux analysis revealed a decrease in both PNa and PK but indicated a greater effect on PNa. The results suggest that all of the above effects could be explained on the basis of one direct action of the drug, namely, the prompt initial decrease in PNa and Na influx. All other effects noted, both active and passive, could then be secondary to this phenomenon.
Habitat structure determines resource use by zooplankton in temperate lakes

AbstractWhile the importance of terrestrial linkages to aquatic ecosystems is well appreciated, the degree of terrestrialsupport of aquatic consumers remains debated. Estimates of terrestrial contributions to lake zooplankton haveomitted a key food source, phytoplankton produced below the mixed layer. We used carbon and nitrogen stableisotope data from 25 Paciﬁc Northwest lakes to assess the relative importance of particulate organic matter(POM) from the mixed layer, below the mixed layer and terrestrial detritus to zooplankton. Zooplankton anddeep POM were depleted in 13 C relative to mixed layer POM in lakes that can support deep primaryproduction. A Bayesian stable isotope mixing model estimated that terrestrial detritus contributed <5% tozooplankton production, and conﬁrms the role of lake optical and thermal properties; deep POM accountedfor up to 80% of zooplankton production in the clearest lakes. These results suggest terrestrial support of lakezooplankton production is trivial.KeywordsAllochthony, aquatic-terrestrial coupling, carbon isotopes, deep chlorophyll maxima, habitat heterogeneity,phytoplankton, stable isotopes, zooplankton.Ecology Letters (2011) 14: 364–372
Hospitalizations in patients with heart failure: who and why.

In this issue of the Journal , Dunlay et al. ([1][1]) assessed the frequency, reasons, and risk factors for hospitalizations in patients with heart failure (HF). The work is unique because they assessed the lifetime burden of hospitalizations in a population-based cohort of incident HF identified by
H. R. Anna Company

This brief case can be used to cover the concepts discussed in "Process Performance Measures" (OM-0833). Calculations required include capacity, bottlenecks, utilization, the effects of setup reduction, and batch size.
Are breast and pelvic exams necessary when prescribing hormonal contraception

Only a medical history and blood pressure measurement are needed before prescribing estrogen contraceptives.
The Desert of Anatopism: War in the Age of Globalization

This essay argues that forces of globalization have changed how American combatants define their identities within and against a foreign environment. Building on notions that soldiers construct identity by rendering foreign landscapes as Other, this piece considers how familiarity within the combat zone traumatically destabilizes the attempts to delineate self and enemy. This essay examines textual and film representations of the first and second Gulf Wars, highlighting the increasing presence of anatopisms—items jarringly dislocated from their proper “expected” spaces. Focusing particularly on Evan Wright’s Generation Kill, this piece investigates the consequences of American soldiers’ encounters with the global familiar—goods and spaces within the war zone that unsettle distinctions due to the homogenizing forces of the global market. Encounters with the global familiar, the essay argues, may lead to new acts of solidarity between combatants, but they also hold the potential to compound the traumas of combat and produce new acts of violence.
On the Study of Consumer Typologies

This article presents a new method of empirical classification, shows how it is used to develop a consumer typology, and tests the sensitivity of the typology to various changes in assumptions, ope...
Some North and South American Bees.

There are signs that interest in wild bees is spreading in this country, particularly in the west. I hear of activities in Utah, Wyoming and Montana, all promising important results. The works of P. H. Timberlake and C. L. Fox, of California, will, when published, throw a flood of light on the genera Perdita and Nomada respectively. Dr. Kennedy writes me of collections in Ohio, and Messrs. Crawford and Mitchell are busy in North Carolina. Miss Sandhouse, at the National Museum, has begun to revise the whole series of Halictinae. Frison will give us an entirely new treatment of our Bombidae. The bees have been too much neglected. They share with the birds and butterflies the advantage of being readily seen, so that it is not difficult to make a fairly exhaustive collection in a locality. They are interesting and attractive, and their habits, parasites, etc., afford abundant materials for biological studies. The genera are not very numerous, and are easily learned. The species, however, are very many, and often extremely “critical.” No one can name bees (unless perhaps Bombus ) by just looking at them. The labor of sorting out the great masses of specimens accumulating in museums is too great for the workers now available, and hastily made determinations are often unreliable.
Abstract 2910: Mono- or double-site phosphorylation distinctly regulates the proapoptotic function of Bax

Bax is the major multidomain proapoptotic molecule that is required for apoptosis. It has been reported that phosphorylation of Bax at serine(S) 163 or S184 activates or inactivates its proapoptotic function, respectively. To uncover the mechanisms by which phosphorylation at these two sites regulate the proapoptotic function of Bax, a series of serine (S)→ alanine/glutamate (A/E) mutants, including S163A, S184A, S163E, S184E, S163E/S184A (EA), S163A/S184E (AE), S163A/S184A (AA) and S163E/S184E (EE), were created to mimic or abrogate, respectively, either single or double-site phosphorylation. The compound Bax mutants (i.e. EA and AE) can flesh out the functional contribution of individual phosphorylation site(s). WT and each of these Bax mutants were overexpressed in Bax −/− MEF or human lung cancer H157 cells and the proapoptotic activities were compared. Intriguingly, expression of any of Bax mutants containing the mutation S→A at S184 (i.e. S184A, EA or AA) represents more potent proapoptotic activity as compared to WT Bax in association with conformational change, mitochondrial localization/insertion and prolonged half-life. In contrast, all Bax mutants containing the mutation S→E at S184 (i.e. S184E, AE or EE) have decreased protein stability and less apoptotic activity without conformational change and mitochondrial localization/insertion. Unexpectedly, mutation either S→A or S→E at S163 site does not significantly affect the proapoptotic activity of Bax. These findings indicate that S184 but not S163 is the major phosphorylation site for functional regulation of Bax9s activity. Thus, manipulation of the phosphorylation status at S184 may represent a novel strategy for treatment of cancers that express Bax. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2910.
Megakaryocytes Exchange Significant Levels of Their Alpha-Granular PF4 with Their Environment

Abstract Platelet factor 4 (PF4, CXCL4) is a major chemokine in megakaryocytes (megs). It is synthesized almost exclusively by megs during their development and may have important roles in regulating both hematopoietic stem cell and megakaryocyte proliferation. We now show that megs both release significant amounts of PF4 into their environment as well as take up PF4 into alpha granules. This PF4 is then available for release by thrombin activation. We examined PF4 recycling during megakaryopoiesis based on the observation that in vitro-cultured human meg hematopoietic precursors release significant amounts of PF4 into the media beginning after approximately 7 days of culture, when definitive megs begin to emerge. Using immunohistochemistry, we find that in vivo in murine bone marrow, human PF4 (hPF4) is released by hPF4 transgenic (hPF4+) megs during the steady-state, and this release is markedly accentuated 48 hours after sub-lethal 660 cGy whole body irradiation from an X-ray source to induce bone marrow injury. By comparison, animals without endogenous PF4 expression (Pf4-/-) showed only background staining. After irradiation, the levels of PF4 staining within the hPF4+ megs decreased with a concomitant increase in background staining suggesting that the stored PF4 was released into the bone marrow milieu. The increase in the PF4 staining in the intramedullary space was not due to released PF4 from entrapped platelets as similar changes were seen in untreated hPF4+ mice and in mice made thrombocytopenic by injection of antiCD41 antibody. We then asked whether the released PF4 could be taken back up by the megs and whether internalized PF4 could reach significant levels compared to endogenously synthesized PF4. We show that murine megs can take up significant levels of hPF4 so that peak hPF4 uptake at 24 hours (19±2 ng/10e6 cells) is equivalent to the amount of mouse (m) PF4 (30±1 ng/106 cells) natively present within the megs. Blocking antibodies to either PF4 itself or to lipoprotein receptor related protein 1 (LRP1) prevented PF4 uptake (53±17 IU/10e6 cells and 32±9 IU/10e6, respectively, vs 95±9 IU/10e6 cells, p Disclosures Xiao: ECRI Institute: Employment.
Relationships between Prospective Middle Grades Mathematics Teachers' Beliefs and TPACK.

ABSTRACTAs technology become more ubiquitous in the classroom, teachers need to overcome two types of barriers to use it effectively: access to resources (including the development of knowledge) and the development of appropriate beliefs. To assist teachers in overcoming these barriers, we must understand the relationships that exist among them. We examined relationships between middle grade prospective teachers' beliefs and their technology, pedagogy, and content knowledge framework (TPACK). We found possible relationships between their beliefs about the nature of mathematics, learning and teaching mathematics, and the use of technology and their content knowledge, pedagogical content knowledge, and technological pedagogical content knowledge, respectively.
Italian sexualities uncovered, 1789–1914

This volume is a welcome collection showcasing the state of the field in nineteenth-century Italian history of sexuality and gender. The editors have gathered thirteen contributions, originally fro...
Quaternionic Artin representations of ℚ

Isomorphism classes of dihedral Artin representations of ℚ can be counted asymptotically using Siegel's asymptotic averages of class numbers of binary quadratic forms. Here we consider the analogous problem for quaternionic representations. While an asymptotic formula is out of our reach in this case, we show that the asymptotic behaviour in the two cases is quite different.
Posterior Distributions and Bayes Solutions

In the first three chapters of this work, prior distributions with finite support and the corresponding Bayes procedures were used to establish some of the main theorems relating to comparison of experiments. Bayes procedures with respect to more general prior distributions have played a very important role in the development of statistics, including its asymptotic theory.
An Automated Solution of the Low-Thrust Interplanetary Trajectory Problem

Preliminary design of low-thrust interplanetary missions is a highly complex process. The mission designer must choose discrete parameters such as the number of flybys, the bodies at which those flybys are performed, and in some cases the final destination. In addition, a time-history of control variables must be chosen that defines the trajectory. There are often many thousands, if not millions, of possible trajectories to be evaluated, which can be a very expensive process in terms of the number of human analyst hours required. An automated approach is therefore very desirable. This work presents such an approach by posing the mission design problem as a hybrid optimal control problem. The method is demonstrated on hypothetical missions to Mercury, the main asteroid belt, and Pluto.
Parametric Inversion of 3-D Anisotropic Permittivities From Scattered Electromagnetic Fields

A model-based inversion algorithm combined with the curl-conforming volume integral equation (VIE) method is presented for sensitivity analysis of electromagnetic measurement for anisotropic objects. The forward algorithm utilizes the curl-conforming VIE method. The inversion algorithm is based on the Gauss–Newton method. The approach is applied to the reconstruction of the permittivities of 3-D anisotropic objects. Moreover, sensitivity analysis of the data from different polarizations of transmitters and receivers to the anisotropic properties is performed. Numerical examples show the effectiveness of the inversion algorithm and demonstrate the sensitivities of data from different transmitter and receiver pairs to the anisotropy.
Setbacks and Successes: How Young Adults on the Autism Spectrum Seek Friendship

Abstract Objective: To describe the perspectives of young adults on the autism spectrum about how they seek and make friends and explore the diverse ways that some develop satisfying friendships despite social difficulties. Methods: We conducted semistructured interviews with 20 young adults on the autism spectrum about their lives after high school. Although interviews covered a broad range of topics related to transition, the subject of friendship came up frequently throughout the interviews. We extracted data specifically related to friendship for this article and used an inductive approach derived from grounded theory to identify and examine concepts. Results: Participants had the most success in relationships in which their atypical behavior was normalized. Specifically, this occurred among friends who accepted and appreciated their social differences and through common interests where these differences were not a concern. In other relationships, participants felt that they were expected to adhere to...
On the Convergence of the Interpenetrating Bipolar Expansion for the Coulomb Potential

Abstract In the interpenetrating region where | r 1 - r 2 | R r 1 + r 2 , individual terms in the bipolar expansion for the Coulomb potential are shown to decay like (l1 + l2)-1, rendering convergence of the expansion at best conditional. Moreover, Laplace’s equation, which is satisfied term-by-term in the separated R > r1 + r2 region, is shown to be satisfied neither term-by-term nor pointwise.
Preparation of YBa2Cu3Ox Thin Films by Multisource Deposition

Multisource evaporation and sputtering techniques for the preparation of YBa2Cu3Ox thin films are reviewed. The relative merits of different source materials, processes for oxygen incorporation, and procedures for forming the superconducting phase are discussed and the properties of films prepared by various techniques are summarized. Methods for the monitoring of deposition rates, which is necessary for achieving the desired film composition in a reproducible manner, are also described.
Dynamics of Nuclear Energy Policies in India: A Case Study on the Emergence of Nuclear Safety Regulatory Authority:

This study analyses the dynamics of nuclear energy policies in India by using Punctuated Equilibrium Theory (PET) and examines the emergence of India’s Nuclear Safety Regulatory Authority (NSRA) bi...
Multi-Sensor Integration Onboard a UAV-Based Mobile Mapping System for Agricultural Management

Due to the advances in technological and industrial fields, remote sensing has been adopted to a considerable extent in precision agricultural applications. Over the past few years, remote sensing utilized Mobile Mapping Systems (MMS) as the platforms for agricultural data collection. For accurate generation of georeferenced products using such MMSs, there should be a robust calibration approach that can accurately estimate the mounting parameters of the involved sensors, i.e., LiDAR unit, camera, and hyperspectral push-broom scanner. In this paper, we propose novel calibration approaches for various sensors onboard a UAV platform – 1) simultaneous estimation of lever arm and boresight angles relating LiDAR unit and camera to the GNSS/INS unit, and 2) estimation of boresight angles relating hyperspectral push-broom scanner and the GNSS/TNS unit.
A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.

In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association. Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels. Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant’s gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status. In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.
Bioinformatic Approaches to Validation and Functional Analysis of 3D Lung Cancer Models

3D models of cancer have the potential to improve basic, translational, and clinical studies. Patient-derived xenografts, spheroids, and organoids are broad categories of 3D models of cancer, and to date, these 3D models of cancer have been established for a variety of cancer types. In lung cancer, for example, 3D models offer a promising new avenue to gain novel insights into lung tumor biology and improve outcomes for patients afflicted with the number one cancer killer worldwide. However, the adoption and utility of these 3D models of cancer vary, and demonstrating the fidelity of these models is a critical first step before seeking meaningful applications. Here, we review use cases of current 3D lung cancer models and bioinformatic approaches to assessing model fidelity. Bioinformatics approaches play a key role in both validating 3D lung cancer models and high dimensional functional analyses to support downstream applications.
Could Obesity Be Contagious

This paper contributes to explaining the obesity epidemic and finding a potential remedy. We build a theoretical model of food consumption decisions that accounts for social influence. In our model, individuals’ rationality is affected by an endogenous social weight norm, which influences their calorie consciousness and perceived survival chances. Individuals are positional, and the degree of positionality describes the extent to which individuals’ discounted utility is influenced by the social weight norm. With an endogenous social weight norm reflecting a heavier and heavier average body weight, we show that a high degree of positionality could explain the obesity epidemic. In this environment, a government intervention decreasing energy density is ineffective at reducing steady state body weight. This result could explain why this type of government dietary intervention seem to have had no effect on obesity and suggests that the same type of intervention through the Food Stamps Program would be ineffective on its own. We also find that in the steady state, individuals can be overweight or underweight depending on their degree of positionality relative to the education they receive about the healthy weight. While education programs focusing on either diet or exercise have had moderate success, we show that focusing on healthy weight education could combat social influence and reduce obesity.
Ornithine Transcarbamylase Deficiency Presenting with Symptoms of Mania in a Young Adult Male

Study Objective The purpose of this case study is to review the clinical presentation and medical workup of a young adult male presenting with acute behavior changes in the setting of undiagnosed ornithine transcarbamylase deficiency (OTCD) Method This case study involves a 19-year-old male with a psychiatric history of depression and one previous suicide attempt, who presented to a large midwestern university hospital emergency department after being found by police naked in a neighbor’s yard. He displayed manic signs and symptoms, including euphoria, lack of sleep for five days, and attempting to purchase a new car and three large screen TVs. Family reported the patient uncharacteristically announced three weeks earlier that he was vegetarian and stopped eating his frequent customary cheeseburgers. Due to increased anxiety and inability to sleep, the patient received lorazepam 2 mg in the emergency department. Upon transfer to the psychiatric unit, therapy was initiated with aripiprazole 5 mg daily and valproate 1000 mg nightly on Day 1 of treatment. The patient refused medications on hospital Day 2, then received this combination again on Day 3. The next morning, the patient complained of lethargy, headache, nausea, and vomiting. Results The patient’s ammonia level was found to be 204 micromol/L with ALT and AST of 714 and 647 IU/L respectively. Tests for infectious hepatitis were negative. Medical consultation recommended discontinuation of current medications, vigorous hydration, and further work up. On further investigation, the patient was found to have low plasma citrulline level of 8 micromol/L, undetectable plasma arginine, and high urinary orotic acid. The laboratory data showed a biochemical phenotype consistent with a diagnosis of partial OTCD, an X-linked urea cycle disorder resulting in toxic hyperammonemia. The patient was treated with a low protein diet modification as well as a combination of sodium benzoate and sodium phenylbutyrate to reduce serum ammonia concentration. With treatment the patient’s laboratory values normalized, and mental status improved. Conclusions In conclusion, partial ornithine transcarbamylase deficiency may manifest with psychiatric symptoms in early adulthood. In young patients with elevated ammonia and mental status change, OTCD is an important diagnosis to consider, as it is the most common inherited cause of hyperammonemia.
Identification and Prediction of Disruptions in Airline Networks

Disruptions in the air transportation system oftentimes lead to demand-capacity imbalances, resulting in flight delays and cancellations as byproducts of traffic management and system recovery actions. In order to better predict the impact of disruptions, as well as provide more targeted and proactive system recovery actions, it is critical to unambiguously identify key characteristics such as: (1) When did the disruption occur, (2) what was the duration of the disruption and subsequent recovery, and (3) how will an ongoing disruption evolve. In particular, providing performance measures regarding the duration, intensity, and type of disruption is straightforward for individual airports; for a large, geographically disparate, and interconnected network of airports, these characteristics are less clear. To address this, we first formalize the notion of \textit{disruption-recovery trajectories} (DRTs) for the air transportation system through representing key network delay and cancellation performance measures as evolving between discrete states. These DRTs capture information regarding both the magnitude and spatial impact of air transportation system disruptions. Using this DRT framework, we report on past disruption and recovery characteristics for four major US airlines, as well as demonstrate the ability to predict short-term evolution of disruptions and recoveries without detailed schedule information, potentially enabling near-real time decision support for prescriptive management actions.
Functional Status Examination Yields Higher Measurement Precision than the Glasgow Outcome Scale-Extended after Moderate-to-Severe Traumatic Brain Injury

A limited evidence base supports the Functional Status Examination (FSE) as superior to the more commonly used Glasgow Outcome Scale-Extended (GOSE) for precisely characterizing injury-related functional limitations. The aim of this study was to use modern psychometric tools to test the hypothesis that the FSE is more precise than the GOSE in characterizing individual differences in functional limitations after moderate-to-severe traumatic brain injury (TBI). Secondarily, we sought to confirm that the type of interviewee (patient, significant other) does not affect the test performance of the FSE. Using data from 357 individuals with TBI who participated in the Magnesium Sulfate clinical trial and had six-month outcome data, we performed item response theory (IRT) analyses comparing the FSE and GOSE at six months post-injury. Results showed that the FSE yielded higher measurement precision (IRT test information) than the GOSE across most of the disability severity spectrum. The GOSE yielded more information than the FSE at a very high level of disability, because of the GOSE's assignment of a unique score for individuals who are in a vegetative state. Finally, the FSE showed no evidence of differential item functioning by interviewee, indicating it is appropriate to interview either persons with TBI or significant others and combine data across respondents as is typically done. The findings support the FSE as a viable and oftentimes advantageous substitute for the GOSE in clinical trials and translational studies of TBI.
Aquinas's Acount of Human Embryogenesis and Recent Interpretations

In addressing bioethical issues at the beginning of human life, such as abortion, in vitro fertilization, and embryonic stem cell research, one primary concern regards establishing when a developing human embryo or fetus can be considered a person. Thomas Aquinas argues that an embryo or fetus is not a human person until its body is informed by a rational soul. Aquinas’s explicit account of human embryogenesis has been generally rejected by contemporary scholars due to its dependence upon medieval biological data, which has been far surpassed by current scientific research. A number of scholars, however, have attempted to combine Aquinas’s basic metaphysical account of human nature with current embryological data to develop a contemporary Thomistic account of a human person’s beginning. In this paper, I discuss two recent interpretations in which it is argued that a human person does not begin to exist until a fetus has developed a functioning cerebral cortex.
Cardiovascular Toxicities of Proteasome Inhibitors

A dramatic number of new therapies have developed over the past decade for the treatment of multiple myeloma (MM) and those treatments have resulted in substantial improvement in patient outcomes. Proteasome inhibitors (PI) are one such class of therapy and are now included in first-line regimens for MM. However, PIs are associated with important cardiotoxicities including heart failure, arrhythmias, and thromboembolism. These adverse effects are particularly deleterious to patients with MM who have a high incidence of underlying cardiovascular comorbidities. This chapter will review the cardiovascular toxicities associated with PIs and illustrate the utility of imaging in diagnosing and managing these complications.
Physician dominance in the 21st century: Examining the rise of non-physician autonomy through prevailing theoretical lenses

Theories of physician dominance are a foundational contribution of medical sociology to the study of health care, but must be revisited in the light of ongoing changes in medicine. As non-physician specialists like nurse practitioners grow in number and acquire more autonomy, increasing medical profession differentiation presents a challenge for traditional physician dominance theories. After evaluating potential theoretical explanations for subordinate occupations' autonomy gains, we conduct a state-level quantitative analysis of variation in nursing policies across U.S. states. We construct our dependent variable, nursing autonomy, using seven state-level advanced practice nursing policies adopted from 2001-2017. Using an ordered scale, we code nurse practitioner, nurse anaesthetist, nurse midwife and clinical-nurse-specialist practice and prescription polices according to each policy's autonomy level. We then use time-series regression to examine theory-driven propositions regarding nursing autonomy change. Nursing autonomy has increased over time, signalling a general erosion of physician dominance. However, we find differential patterns of policy adoption, indicating that erosion is not uniform. Physicians have maintained dominance in relatively prestigious specialties (e.g. anaesthesiology) while dominance declined in others (e.g. obstetrician). Factors external to the profession, such as consumer power, continue to influence within-profession dynamics. Examining ongoing professional differentiation in medicine illustrates how physician dominance depends on shifting social and professional contexts.
Specialization, Diversity, and Indian Manufacturing Growth

This paper examines the specialization and diversity of manufacturing industries within Indian districts. Prior to India's recent economic growth and liberalization, specialization levels in 1989 were substantially higher than similar metrics calculated for the United States. From 1989 to 2010, average specialization levels for Indian districts declined to a level that is now quite comparable to the United States. Diversity levels similarly increased. Specialization and diversity levels in India are becoming more persistent with time. Manufacturing plants display higher productivity in districts that display both properties. From 1989 to 2010, manufacturing employment growth was higher in districts that were more specialized at the start of the period.
Resting state functional connectivity subtypes predict discrete patterns of cognitive-affective functioning across levels of analysis among patients with treatment-resistant depression.

Abstract Resting state functional connectivity (RSFC) in ventral affective (VAN), default mode (DMN) and cognitive control (CCN) networks may partially underlie heterogeneity in depression. The current study used data-driven parsing of RSFC to identify subgroups of patients with treatment-resistant depression (TRD; n = 70) and determine if subgroups generalized to transdiagnostic measures of cognitive-affective functioning relevant to depression (indexed across self-report, behavioral, and molecular levels of analysis). RSFC paths within key networks were characterized using Subgroup-Group Iterative Multiple Model Estimation. Three connectivity-based subgroups emerged: Subgroup A, the largest subset and containing the fewest pathways; Subgroup B, containing unique bidirectional VAN/DMN negative feedback; and Subgroup C, containing the most pathways. Compared to other subgroups, subgroup B was characterized by lower self-reported positive affect and subgroup C by higher self-reported positive affect, greater variability in induced positive affect, worse response inhibition, and reduced striatal tissue iron concentration. RSFC-based categorization revealed three TRD subtypes associated with discrete aberrations in transdiagnostic cognitive-affective functioning that were largely unified across levels of analysis and were maintained after accounting for the variability captured by a disorder-specific measure of depressive symptoms. Findings advance understanding of transdiagnostic brain-behavior heterogeneity in TRD and may inform novel treatment targets for this population.
Production of 3-hydroxypropionate from biomass

Biorenewable technology is a developing field of science that researches alternative sources for petroleum products like fuels, plastics, paints, etc. The DoE biomass program has identified the 12 top chemicals that can be produced from biomass and further processed to replace many petroleum products; 3-hydroxypropionate (3HP) is a top 12 chemical that can be used to produce plastics, paints, tires, and other consumer products. This thesis describes the attempts to produce 3HP from glucose in E. coli and from syngas in R. rubrum. Malonyl CoA reductase from C. aurantiacus and R. castenholzii was cloned and expressed in E. coli and R. rubrum respectively. This enzyme converts malonyl-CoA (a central metabolic intermediate) to 3-HP. Gas chromatography-mass spectrometry showed recombinant E. coli and R. rubrum produced 3HP in low levels. The quantity of 3-HP produced is not economical for commercial production so further studies were conducted to increase 3HP production.
5 – SCAVENGING AND TRANSPORTATION OF AEROSOL PARTICLES BY ICE CRYSTALS IN CLOUDS

This chapter discusses the impact of ice crystals on aerosol particles in clouds, focusing on aerosol collection by ice particles. The chapter compares the calculated collection efficiencies of cloud droplets, ice plates, and ice columns, and draws several conclusions from the experimental data. The three collectors are about equally efficient in collecting very small aerosol particles. Ice plates are most efficient in removing aerosol particles in the size range between 0.01 and 1.0 μm. For aerosol particles of radius greater than 1 μm, both droplets and columnar ice crystals are fairly efficient in removing them. Because snow crystals have complicated shapes, it is impossible to describe both the size and the shape simultaneously by a single parameter. Therefore, in experimental results, the chapter presents collection efficiencies as a function of crystal size only. The data points show a fair amount of scatter, which may be due to many factors, such as non-uniformity of ice crystals and exposure to environmental air. The effect of aerosol charge on the collection efficiency is also investigated in the chapter. Because of the many experimental difficulties and non-ideal conditions, an exact comparison is not possible. Thus, the only parameter that can be used as the basis of comparison is the crystal length.