cssi/SciSciGPT-SciSciNet huggingface dataset:
Cyber Attack Exposure Evaluation Framework for the Smart Grid

The smart grid's heavy reliance on cyber resources introduces numerous security concerns. The substantial attack surface presented by the advanced metering infrastructure (AMI) along with the dissemination of sensitive data including privacy, billing, and control information will provide attackers with significant economic incentive. In addition, the scale and complexity of the architecture will stress the capabilities of many security controls such as public key encryption (PKI), authentication, and access control. The aforementioned concerns produce a requirement for increased risk management including security models that have the capability to scale to such a complex environment. A security model is introduced to represent various privilege states in a large architecture and evaluates viable paths that an attacker could exploit. The resulting model is used to produce a quantitative information-based exposure metric to evaluate the completeness of implemented security mechanisms. Various applications are proposed to show how the metric can enhance current risk management processes by identifying information dependencies of the deployed security mechanisms. Finally, the applicability of the proposed methodologies has been evaluated through a simulation study using realistic AMI infrastructure to demonstrate the utility of the proposed metric.
Measuring Light Reflectance of BGO Crystal Surfaces

A scintillating crystal's surface reflectance has to be well understood in order to accurately predict and optimize the crystal's light collection through Monte Carlo simulations. In this paper, we measure the inner surface reflectance properties for BGO. The measurements include BGO crystals with a mechanically polished surface, rough-cut surface, and chemically etched surface, and with various reflectors attached, both air-coupled and with coupling compound. The measurements are performed with a laser aimed at the center of a hemispherical shaped BGO crystal. The hemispherical shape eliminates any non-perpendicular angles for light entering and exiting the crystal. The reflected light is collected with an array of photodiodes. The laser can be set at an arbitrary angle, and the photodiode array is rotated to fully cover 2pi of solid angle. The current produced in the photodiodes is readout with a digital multimeter connected through a multiplexer. The two rows of photodiodes achieve 5-degree by 4-degree resolution, and the current measurement has a dynamic range of 105:1. The acquired data was not described by the commonly assumed linear combination of specular and diffuse (Lambertian) distributions, except for a very few surfaces. Surface roughness proved to be the most important parameter when choosing crystal setup. The reflector choice was of less importance and of almost no consequence for rough-cut surfaces. Pure specular reflection distribution for all incidence angles was measured for polished surfaces with VM2000 film, while the most Lambertian distribution for any surface finish was measured for titanium dioxide paint. The distributions acquired in this paper will be used to create more accurate Monte Carlo models for light reflection distribution within BGO crystals.
5-GHz optical arbitrary waveform generation using > 100 independently controlled spectral lines from a compressed phase-modulated CW laser comb

We demonstrate high-fidelity optical arbitrary waveform generation via spectral line-by-line shaping on more than 100 spectral comb lines selected from a compressed phase-modulated CW laser frequency comb with 5 GHz line spacing.
From informing to remembering: ubiquitous systems in interactive museums

Museums are excellent locations for testing ubiquitous systems; the Exploratorium in San Francisco offers a unique and challenging environment for just such a system. An important design consideration is how users switch between virtual and physical interactions.
Section Reviews Biologicals & Lmmunologicals: The interferons in haematologic malignancies

(1995). Section Reviews Biologicals & Lmmunologicals: The interferons in haematologic malignancies. Expert Opinion on Investigational Drugs: Vol. 4, No. 1, pp. 9-21.
Efficiently Scheduling Multi-Core Guest Virtual Machines on Multi-Core Hosts in Network Simulation

Virtual machine (VM)-based simulation is a method used by network simulators to incorporate realistic application behaviors by executing actual VMs as high-fidelity surrogates for simulated end-hosts. A critical requirement in such a method is the simulation time-ordered scheduling and execution of the VMs. Prior approaches such as time dilation are less efficient due to the high degree of multiplexing possible when multiple multi-core VMs are simulated on multi-core host systems. We present a new simulation time-ordered scheduler to efficiently schedule multi-core VMs on multi-core real hosts, with a virtual clock realized on each virtual core. The distinguishing features of our approach are: (1) customizable granularity of the VM scheduling time unit on the simulation time axis, (2) ability to take arbitrary leaps in virtual time by VMs to maximize the utilization of host (real) cores when guest virtual cores idle, and (3) empirically determinable optimality in the tradeoff between total execution (real) time and time-ordering accuracy levels. Experiments show that it is possible to get nearly perfect time-ordered execution, with a slight cost in total run time, relative to optimized non-simulation VM schedulers. Interestingly, with our time-ordered scheduler, it is also possible to reduce the time-ordering error from over 50% of non-simulation scheduler to less than 1% realized by our scheduler, with almost the same run time efficiency as that of the highly efficient non-simulation VM schedulers.
Grammar Pedagogy in Second and Foreign Language Teaching.

To provide some perspective on current issues and challenges concerning the role of grammar in language teaching, the article reviews some methodological trends of the past 25 years. When, and to what extent, one should teach grammar to language learners is a controversial issue. The paper proposes a decision-making strategy for resolving this controversy, based on learner and instructional variables. Then taking Canale and Swain's (1980) model of communicative competence, which views grammatical competence as one component of communicative competence, the paper argues that grammar instruction is part of language teaching. In this new role, grammar interacts with meaning, social function, or discourse—or a combination of these—rather than standing alone as an autonomous system to be learned for its own sake. After addressing feedback and correction in terms of research and pedagogical techniques, the article concludes with a survey of options for integrating grammar instruction into a communicative curriculum and with a reformulation of the role of grammar in language teaching.
The extended on/off process for modeling traffic in high-speed communication networks

High-speed network traffic is impulsive and exhibits long-range dependence. While the latter characteristic has been studied extensively, the former has received much less attention. The on/off model is a well-known model for capturing the long-range dependence of traffic. We propose an extension to the on/off model, which allows the model to also capture the traffic impulsiveness. We provide queuing analysis of the proposed model, which along with numerical results suggests that the traffic marginal distribution may have significant impact on network engineering.
Summertime Incursions of Midlatitude Air into Subtropical and Tropical South America

Abstract Transient incursions of midlatitude air to the east of the Andes Mountains into subtropical and tropical latitudes are a distinctive feature of the synoptic climatology over South America. The mean synoptic-scale structure of these incursions is documented in this paper on the basis of a compositing analysis of NCEP–NCAR reanalyzed meteorological fields and satellite-based outgoing longwave radiation measurements. Although these incursions are a year-round phenomenon, with relatively modest seasonal changes in their structure, this analysis is focused on the austral summer, when they have their largest impact in the precipitation field. The summertime incursions move equatorward at a mean speed of 10 m s−1 and retain their identities over intervals of about 5 days. The upper-level circulation is characterized by a midlatitude trough–ridge couplet that provides the quasigeostrophic forcing of the system. Before the onset of the incursions of midlatitude air, the approaching upper-level trough tend...
Practical Tips for Developing Leadership Skills Early in a Career

Leadership is often the furthest thing from one’s mind early in their surgical career. After finishing residency and finding your first position, your early priorities focus on learning the policies of the institution, navigating the electronic medical record, as well as your new role as an attending surgeon and resident/student educator. However, it is in this time period that your leadership skills are most critical as they will help you achieve your goals and ultimately help you accomplish something larger for yourself. Good leaders inspire others to want to help a program be successful. The people that you work with on a daily basis will go out of their way to help you reach your goals and see that the daily pressures of building a new practice are eased. The difficulty arises in recognizing the face of leadership at this point in your career. In this chapter, we elucidate the leadership skills it takes to be effective in these first few years and how attaining these skills early on will translate into a successful leadership style that will enable you to lead on a larger scale.
Deporting Our Souls and Defending Our Immigrants

What does crime in Asian American mean to you? To me, it's been about immigrants who have faced deportation because of their criminal convictions. Like anyone who has represented or worked with those who have been or are in the criminal justice system, the experience has made me wonder and want to know more about how and why different individuals wind up behind bars or regarded as criminals by the system.
The SCRAPESIM Computer Simulation

One of the newest techniques for estimating earth-moving operations in the construction industry today is the use of computer simulation. The computer simulation is designed to incorporate probability distributions as a data base and to have the capability of simulating any type of scraper project. The most effective use of the model is for estimating purposes where it is proven to be a much better method than those currently used. It is validated by simulating the earth-moving operations on three scraper projects, a highway construction project, and the site excavation of two nuclear power plants. The simulated results in all three cases are found to be very close to the actual project results. The versatility of the program is cited in such areas as balancing scraper and pusher fleet sizes, determining which type of scraper to use under a given set of project conditions, and the production to expect from a specific fleet size.
The next step in verification testing of complex Systems is Automation

Automation has been proven to increase productivity, improve quality, and reduce cost in many industries. Applied heavily in manufacturing, automation has also been used extensively to validate software. This study explores the benefits and considerations of automating the execution and analysis of verification tests of complex radar systems. This testing is performed on a complete integrated system evaluating compliance against specified requirements.
Interactive Collaboration Development System for Biomedical Research in a University

We describe a web-based interactive collaboration development system for biomedical research in a university for use by researchers, clinicians, and administrators. It can be used to (a) identify and seek collaborators, and (b) analyze the networks of collaborators in the university. At its core is a comprehensive biographic, publications, and grants database of all biomedical researchers in the university. The database has been created from public and institutional sources. Users can correct and complete the data. It is kept current by (a) semi-automatically updating from the original sources, and (b) users updating manually. In the future, users will be able to network within the system and manage collaborations using it. As of December 2008 the database had 4,800 researchers with 8,200 funded NIH and NSF grants, and 25,200 distinct Medline sourced publications. There are approximately 4,200 distinct grant-related keywords and 45,000 distinct MeSH terms.
Regulation of insulin-like growth factor-I (IGF-I) and IGF-binding proteins by tumor necrosis factor

The purpose of the present study was to determine 1) whether exogenous administration of tumor necrosis factor-alpha (TNF-alpha) alters insulin-like growth factor-I (IGF-I) and IGF-binding proteins (BPs) and 2) whether the enhanced endogenous production of TNF mediates the lipopolysaccharide (LPS)-induced changes in the IGF system. The overnight infusion of murine TNF-alpha reduced circulating concentrations of both growth hormone (GH) and IGF-I in fasted rats. Furthermore, TNF-alpha decreased IGF-I content in liver, gastrocnemius muscle, and pituitary. In contrast, TNF-alpha increased IGF-I content in kidney and brain. IGFBP-1 was increased in plasma, liver, and muscle in response to TNF-alpha. In a second study, rats were injected with LPS after treatment with a neutralizing anti-TNF antibody (Ab), and blood and tissues were collected 4 h later. In LPS-treated rats, plasma concentrations of GH and IGF-I were reduced. LPS also decreased the IGF-I content in liver and skeletal muscle and increased plasma, liver, and muscle concentrations of IGFBP-1. Pretreatment with anti-TNF Ab attenuated the LPS-induced reduction in IGF-I and the increased IGFBP-1 in plasma and liver and completely prevented the decrease in IGF-I observed in muscle. In contrast, the LPS-induced decrease in plasma GH and the increased IGFBP-1 observed in muscle were unaltered by the anti-TNF Ab.(ABSTRACT TRUNCATED AT 250 WORDS)
RTRB-06TIME BETWEEN DIAGNOSTIC MRI AND FRAME-FIXED STEREOTACTIC RADIOSURGERY PLANNING MRI IS ASSOCIATED WITH BRAIN METASTASIS GROWTH BUT NOT WORSE LOCAL CONTROL

RTRB-06. TIME BETWEEN DIAGNOSTIC MRI AND FRAME-FIXED STEREOTACTIC RADIOSURGERY PLANNING MRI IS ASSOCIATED WITH BRAIN METASTASIS GROWTH BUT NOT WORSE LOCAL CONTROL Michael Garcia, Sai Duriseti, Shannon Fogh, Jean Nakamura, David Larson, Philip Theodosopoulos, Michael McDermott, Penny Sneed, and Steve Braunstein; University of California, San Francisco, San Francisco, CA, USA BACKGROUND: Frame-fixed stereotactic radiosurgery (FFSRS) and frameless SRS precisely target brain metastases (BM). Seymour et al. recently showed patients treated with frameless SRS planned on MRI completed ≥ 14 days before treatment delivery have worse local control. An advantage of FFSRS is acquisition of planning MRI on day of SRS. We sought to describe BM growth (BMG) before SRS by comparing the preceding diagnostic MRI (dMRI) and FFSRS MRI scans. METHODS: Patients treated with FFSRS for BM at our institution from 2010 through 2013 were retrospectively reviewed. We identified 256 patients (1302 BM) without upfront surgical resection who had a dMRI for comparison of BM size on FFSRS MRI. Post-FFSRS local failure free progression (LFFP) and overall survival (OS) were compared by log-rank tests. RESULTS: Median imaging follow up was 10 months. Mean size [95%CI] of largest BM was 1.4cm [1.2-1.5]. BMG was observed on FFSRS MRI compared to dMRI for 30% patients. Mean time interval between dMRI and FFSRS was 25 days, and time interval was associated with BMG (Pearson’s r 1⁄4 0.14, p 1⁄4 0.02). The frequencies of BMG for time intervals between dMRI and FFSRS of ,7, 7-13, 14-20, 21-27, and ≥ 28 days were 11%, 12%, 32%, 36% and 38% respectively (p 1⁄4 0.02, chi square). Melanoma patients more commonly had BMG (p 1⁄4 0.03), but chemotherapy, neurologic symptoms, and dMRI slice thickness were not associated with BMG. Patients with BMG at FFSRS had similar LFFP compared to patients without growth (82% versus 88% at 6 months, p 1⁄4 0.71), and OS did notdiffer (p 1⁄4 0.47). CONCLUSION: Timebetween diagnosticMRI and SRS is associated with BMG, but LFFP is not compromised when patients receive FFSRS. Over a third of patients have clear BMG at SRS delivered 14 days afterdMRI.For framelessSRS, BMGafterplanningMRI may lead tomarginal miss. Neuro-Oncology 17:v195–v200, 2015. doi:10.1093/neuonc/nov231.6 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.
Absorbed Coping and Practical Wisdom

Hubert Dreyfus has recently taken the position that practical wisdom is not primarily an excellence of the intellect, or even of the mind. According to Dreyfus, contra the Aristotelian tradition from which the notion derives, true practical wisdom supersedes rationality, rather than perfecting it. Practical wisdom on his view is an absorbed or engaged way of ‘coping’ with the world; something that humans are capable of doing ‘‘without thinking at all.’’ It is therefore best understood on the perceptual model of response to affordances. In what follows I will be concerned with two, related questions. First, can practical wisdom be understood in terms of response to affordances, as the latter idea is developed in the work of Dreyfus and of Sean Kelly? I will argue that the answer is no, because as it stands the model of response to affordances cannot account for the practical role of the agent in her own absorbed coping, including her absorbed acts of practical wisdom. Response to affordances is, as it were, too purely
Abort, retry, litigate: dependable systems and contract law

The law will play an increasingly important role in the design of dependable systems, and designers of such systems will need to familiarize themselves with fundamental legal concepts. This note focus on Contract Law in the context of distributed systems.1 Nodes in distributed systems are constantly making promises to one another. While promises are generally kept, they may also be broken, either intentionally (e.g. for malicious or economic reasons), or unintentionally (e.g. hardware or software failure). An example is one node promising to store a file for another node, and to provide future access to it when requested. Traditional distributed systems were deployed within a single administrative domain (e.g. a bank) and thus the motivations to break promises were limited. The emergence of the Internet brought multi-party systems, usually organized as a server servicing multiple clients. Many of these services, such as IRC servers and web-mail sites, were provided at no cost. These free services were provided on a best effort basis, and broken promises were not a serious design constraint on such systems; clients simply retried. A recent trend is Peer-to-Peer and Multiple Administrative Domain (MAD) systems, such as cooperativebackup and file sharing networks. Nodes in such systems are no longer simply clients, but also play a role in the provision of the service. The idea is that every node plays its part in serving the other nodes, in return for the benefits it receives from the service as a whole. There is often no centralized authority that owns or controls the system. One of the problems that can occur in such systems is that a node can become a free rider, where it enjoys the benefits of the service while refusing to contribute its own resources to the service. This problem has been the focus of recent research. For example, the BARmodel2 treats nodes as rational actors, and provides them with incentives to behave properly. The assumption is that ”without appropriate punishment, nodes may find it in their interest to misbehave”. Thus, rational nodes are forced to keep their promises to avoid the severe sanctions that would befall them. We approach the same problem from a different angle. We observe that the environment is not anarchic, and that enforcement mechanisms exist for certain promises. This approach is not incompatible with other approaches (e.g. BAR), but simply takes into account the legal con-
Common nonarticular syndromes in the elbow, wrist, and hand

Nonarticular elbow, wrist, and hand discomfort commonly results from periarticular or tendon disorders or nerve entrapment. Physicians with a practical knowledge of upper extremity anatomy and mechanics and an awareness of the typical features of disease are best equipped to treat these often-encountered conditions. Therapy is based on an accurate diagnosis and should be tailored to each disorder.
Paul Ricoeur on Language, Ethics and Philosophical Anthropology

This essay relates to three major themes in Ricoeur’s oeuvre, themes that recur throughout but with considerable development. These are: philosophy of language, ethics and politics, and philosophical anthropology. Although Ricoeur is not a system-builder as such, these themes and their interrelations help us to see the systematic character of his thought, how each area has a distinct treatment, yet interconnects with the others.
WE‐AB‐209‐05: Development of an Ultra‐Fast High Quality Whole Breast Radiotherapy Treatment Planning System

Purpose: To enable near-real-time (<20sec) and interactive planning without compromising quality for whole breast RT treatment planning using tangential fields. Methods: Whole breast RT plans from 20 patients treated with single energy (SE, 6MV, 10 patients) or mixed energy (ME, 6/15MV, 10 patients) were randomly selected for model training. Additional 20 cases were used as validation cohort. The planning process for a new case consists of three fully automated steps:1. Energy Selection. A classification model automatically selects energy level. To build the energy selection model, principle component analysis (PCA) was applied to the digital reconstructed radiographs (DRRs) of training cases to extract anatomy-energy relationship.2. Fluence Estimation. Once energy is selected, a random forest (RF) model generates the initial fluence. This model summarizes the relationship between patient anatomy's shape based features and the output fluence. 3. Fluence Fine-tuning. This step balances the overall dose contribution throughout the whole breast tissue by automatically selecting reference points and applying centrality correction. Fine-tuning works at beamlet-level until the dose distribution meets clinical objectives. Prior to finalization, physicians can also make patient-specific trade-offs between target coverage and high-dose volumes.The proposed method was validated by comparing auto-plans with manually generated clinical-plans using Wilcoxon Signed-Rank test. Results: In 19/20 cases the model suggested the same energy combination as clinical-plans. The target volume coverage V100% was 78.1±4.7% for auto-plans, and 79.3±4.8% for clinical-plans (p=0.12). Volumes receiving 105% Rx were 69.2±78.0cc for auto-plans compared to 83.9±87.2cc for clinical-plans (p=0.13). The mean V10Gy, V20Gy of the ipsilateral lung was 24.4±6.7%, 18.6±6.0% for auto plans and 24.6±6.7%, 18.9±6.1% for clinical-plans (p=0.04, <0.001). Total computational time for auto-plans was < 20s. Conclusion: We developed an automated method that generates breast radiotherapy plans with accurate energy selection, similar target volume coverage, reduced hotspot volumes, and significant reduction in planning time, allowing for near-real-time planning.
Kinetics of a Rigid Body

We start by discussing Euler’s laws for a rigid body. These laws are known as the balances of linear and angular momenta. An alternative form of these laws is also presented that is useful for solving many classes of problems. We then discuss the kinetic energy of a rigid body and establish the Koenig decomposition. This decomposition, combined with the balance laws, can be used to prove a work-energy theorem for a rigid body. As illustrations of the theory we consider four classes of problems: purely translational motion of a rigid body, rigid bodies that are free to rotate about one of their fixed material points, rolling and sliding bodies, and an imbalanced rotor problem. These applications are far from exhaustive, but we feel they are the chief representatives of problems for an undergraduate engineering dynamics course.
Quantitative community ecology

Among the more startling assertions in the contemporary ecological literature are “Community ecology is in its infancy” (Pianka 1980) and “Recently ecologists have expanded their scope from studies of single species populations to include analysis of broader assemblages of several co-occurring species loosely defined as communities” (Peterson 1975). In fact, the study of communities or assemblages of co-occurring species is one of the oldest of concerns that may be reasonably identified as ecological. The clearest way to distinguish self-conscious ecology from the other elements of natural history, genetics, physiology, or evolution with which it overlaps is its concern with organisms as members of multispecies aggregates, under a variety of pseudonyms: census, formations, coenoses, associations, societies, guilds, or more generally, communities. The long tradition of natural history, the ordinary experience of farmers, seamen, woodsmen, hunters, anglers, and herbalists, indeed, of the earliest of food gatherers, and the plethora of words in many languages describing particular kinds of aggregates of organisms, and often their associated habitats, testifies that the earth is covered with a complex pattern of “more or less” recognizable plant and animal communities. Biogeographical origins Although references to communities studded the classic literature of natural history, it is usual to attribute to Humboldt the earliest formal recognition of “association” based on the growth forms of the plants which gave the association the distinctive appearance or physiognomy by which it was recognized (Humboldt and Bonpland 1807).
Precision engagement: the PMI’s success will depend on more than genomes and big data

Genet Med advance online publication 27 October 2016Genetics in Medicine (2016); doi:10.1038/gim.2016.165.
Outcome of First Salvage Therapy in Core Binding Factor Associated Acute Myelogenous Leukemia Is Less Than Optimal

Background: Core binding factor (CBF) associated acute myelogenous leukemia (AML) is considered to have a better prognosis compared to that of other patients with AML. Reinduction with cytarabine based therapy followed by allogeneic stem cell transplant is a standard salvage approach. Method: We performed a retrospective analysis of outcome in patients with CBF AML. Results: Between the years 1992 and 2005, 107 patients with CBF AML were treated at M.D. Anderson Cancer Center. Sixty-six (62%) patients had inv 16 abnormality and 41 (38%) had t(8;21) abnormality. Induction chemotherapy regimens included fludarabine and cytarabine with or without granulocyte colony stimulating factor (G-CSF) (66 patients) or idarubicin and cytarabine with/without G-CSF (41 patients). One hundred and one (94%) patients achieved complete remission (CR). After a median CR duration of 159 weeks, 37 (37%) patients relapsed. Relapse rate was 26/66 (39%) among patients with inv 16 abnormality and 11/41 (27%) among those with t (8;21) abnormality. Higher WBC count predicted for relapse (p=.001) and relapse rate did not differ among induction regimens (p=0.1). Salvage chemotherapy included cytarabine based regimen in 22 (59%) patients, clofarabine and idarubicin (2 patients), topoisomerase inhibitor (5 patients), histone deacetylase inhibitor (2 patients) and miscellaneous regimens (6 patients). Sixteen (43%) of the patients with relapsed CBF AML achieved CR after first salvage therapy. Eleven of 26 (42%) patients with inv 16 and 7/11 (64%) of patients with t (8;21) were resistant to first salvage therapy. Thirteen patients (10 in CR) underwent allogeneic stem cell transplant and 12 of them remained in CR post-transplant. Overall survival was significantly worse among patients who relapsed compared to the ones who did not (p=.001). Conclusion: A significant proportion of patients with CBF AML relapse and second remissions can be achieved in less than half the patients. This highlights the need for better induction/consolidation regimens in this group of patients with ‘good-risk’ AML.
Optical Studies of Product State Distributions in Thermal Energy Ion-Molecule Reactions

Product state distributions of thermal energy ion-molecule reactions are determined by the sensitive optical methods of infrared chemiluminescence and laser-induced fluorescence detection. Experiments to obtain detailed vibrational state populations are carried out in a flowing afterglow reaction vessel, and measurements to extract rotational state distributions are performed in a single-collision, crossed-beam apparatus that uses a flowing afterglow ion source. Product state information is obtained for a series of proton transfer reactions and charge transfer reactions, which reveals many aspects of the dynamical behaviors of these processes. Measurements are also presented for polyatomic ion-molecule reactions, for optically-determined rates of ion collisional excitation and deactivation, and on visible chemiluminescence yields and branching fractions for reactions important in the aurora.
APC acts as a transcription factor and down-regulates the β-catenin gene, CTNNB1, and tumor suppressor gene SIAH1

5076 Truncation of the tumor suppressor protein adenomatous polyposis coli (APC) constitutively activates the Wnt/β-catenin signalling pathway. Apc has a role in development: mouse embryos with truncated Apc do not complete gastrulation, and Apc mutation in zebrafish results in heart malformations. Recently, APC was found to shuttle in and out of the nucleus; however, the functional significance of this trafficking remains unclear. We examined the hypothesis that nuclear APC acts as a direct regulator of gene expression. Using a CTNNB1 promoter-luciferase reporter construct we showed that APC strongly inhibited the CTNNB1 promoter activity in HT29 cells. We also found that in HT29 cells transfected with APC there was a marked decrease in β-catenin mRNA levels. One possible explanation for this finding was that APC interacted directly with the promoter region of CTNNB1 and this was confirmed in mobility-shift and chromatin immunoprecipitation (ChIP) assays. To assess the role of other transcription factors, a 2.4 Kb promoter fragment of CTNNB1 was used to ‘pull down’ proteins from nuclear extracts of HT29 cells treated with APC, and the proteins were identified using TranSignal Protein/DNA arrays. Several transcription factors were identified through their interaction with the CTNNB1 promoter, and the profiles were qualitatively similar in the presence and absence of APC. However, APC increased in the expression of several bound transcription factors, most notably AP2, which was augmented more than four-fold. Reporter assays showed that over-expression of AP2 markedly decreased CTNNB1 promoter activity, but no increase in AP2 mRNA or protein was observed, suggesting that APC recruits AP2 to the CTNNB1 promoter. ChIP assays also showed that APC binds to the promoter of SIAH1, a p53-inducible tumor suppres sor involved in β-catenin degradation. Surprisingly, truncated APC was shown to bind the SIAH1 promoter and down-regulate SIAH1 mRNA and protein. Taken together, these results suggest that APC can act as a transcription factor and down-regulate CTNNB1 transcription by recruiting AP2 to CTNNB1 promoter. Truncated APC contributes to β-catenin accumulation by down-regulating SIAH1. These findings define an important new nuclear role for APC, namely as a transcriptional regulator of genes involved in differentiation, development, and cancer. Supported by NIH grants CA6552, CA80176, CA90890.
Three-dimensional evaluation of postural stability in Parkinson's disease with mobile technology.

BACKGROUND Postural instability is a hallmark of Parkinson's disease. Objective metrics to characterize postural stability are necessary for the development of treatment algorithms to aid in the clinical setting. OBJECTIVE The aim of this project was to validate a mobile device platform and resultant three-dimensional balance metric that characterizes postural stability. METHODS A mobile Application was developed, in which biomechanical data from inertial sensors within a mobile device were processed to characterize movement of center of mass in the medial-lateral, anterior-posterior and trunk rotation directions. Twenty-seven individuals with Parkinson's disease and 27 age-matched controls completed various balance tasks. A postural stability metric quantifying the amplitude (peak-to-peak) of sway acceleration in each movement direction was compared between groups. The peak-to-peak value in each direction for each individual with Parkinson's disease across all trials was expressed as a normalized value of the control data to identify individuals with severe postural instability, termed Cleveland Clinic-Postural Stability Index. RESULTS In all conditions, the balance metric for peak-to-peak was significantly greater in Parkinson's disease compared to controls (p < 0.01 for all tests). CONCLUSIONS The balance metric, in conjunction with mobile device sensors, provides a rapid and systematic metric for quantifying postural stability in Parkinson's disease.
Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies

B-1 cells are a unique subset of B cells that are positively selected for expressing autoreactive BCRs. We isolated RNA from peritoneal (B-1a, B-1b, B-2) and splenic (B-1a, marginal zone, follicular) B cells from C57BL/6 mice and used 5'-RACE to amplify the IgH V region using massively parallel sequencing. By analyzing 379,000 functional transcripts, we demonstrate that B-1a cells use a distinct and restricted repertoire. All B-1 cell subsets, especially peritoneal B-1a cells, had a high proportion of sequences without N additions, suggesting predominantly prenatal development. Their transcripts differed markedly and uniquely contained VH11 and VH12 genes, which were rearranged only with a restricted selection of D and J genes, unlike other V genes. Compared to peritoneal B-1a, the peritoneal B-1b repertoire was larger, had little overlap with B-1a, and most sequences contained N additions. Similarly, the splenic B-1a repertoire differed from peritoneal B-1a sequences, having more unique sequences and more frequent N additions, suggesting influx of B-1a cells into the spleen from nonperitoneal sites. Two CDR3s, previously described as Abs to bromelain-treated RBCs, comprised 43% of peritoneal B-1a sequences. We show that a single-chain variable fragment designed after the most prevalent B-1a sequence bound oxidation-specific epitopes such as the phosphocholine of oxidized phospholipids. In summary, we provide the IgH V region library of six murine B cell subsets, including, to our knowledge for the first time, a comparison between B-1a and B-1b cells, and we highlight qualities of B-1 cell Abs that indicate unique selection processes.
Development of wide temperature electrolyte for graphite/ LiNiMnCoO2 Li-ion cells: High throughput screening

Abstract In this report, we demonstrate that the low temperature power capability of a Li-ion battery can be substantially improved not by adding commercially unavailable additives into the electrolyte, but by rational design of the composition of the most commonly used solvents. Through the detail analysis with electrochemical impedance spectroscopy, the formation of a homogenous solid electrolyte interface (SEI) layer on the carbon anode surface is found to be critical to ensure the performance of a Li-ion battery in a wide temperature range. The post mortem analysis of the negative electrode by XPS revealed that all the electrolyte compositions form similar compounds in the solid electrolyte interphase. However, the electrolytes which give higher capacities at low temperature showed higher percentage of LiF and lower percentage of carbon containing species such as lithium carbonate and lithium ethylene di-carbonate. The electrolyte compositions where cyclic carbonates make up less than 25% of the total solvent showed increased low temperature performance. The solvent composition with higher percentage of linear short chain carbonates showed an improved low temperature performance. The high temperature performances were similar in almost all the combinations.
Protecting China from Secondhand Tobacco Smoke

The 1980s saw the burgeoning of local and national smoke-free laws to protect nonsmokers from the harms of tobacco smoke in China. Most of these early laws had loopholes in them in particular allowing designated smoking areas and enforcement was generally poor. More localities passed smoke-free laws in the 2000s following the guidelines of the FCTC and high compliance was achieved in several cities especially in Beijing and Shenzhen. Valuable lessons were learned in pushing for smoke-free initiatives with collective partnership and in ensuring effective implementation through mobilizing political leadership. The momentum generated from these successes failed to expand to the entire country when the first national comprehensive smoke-free law proposal was blocked by the tobacco monopoly. Interference from the tobacco monopoly in smoke-free policy making intensified after the successes in implementation in Beijing and Shenzhen. The power wrangling between tobacco control advocates and the tobacco monopoly in the smoke-free arena and beyond will likely continue both at national and at local level. The engagement of the tobacco monopoly in tobacco control policy making continues to be a major impediment in tobacco control in China. This serious conflict of interest needs to be addressed before any major development in tobacco control policy can be achieved.
Clinical Study Data Management Systems

Clinical Study Data Management Systems (CSDMSs) support the process of managing data gathered during clinical research. Clinical research involves much more than clinical data management – for example, research-grant tracking and reporting to the sponsor and to institutional review boards (IRBs, also called Human Investigations Committees) as well as financial management. I’ll focus on the data-capture, reporting and query aspects, as these are the components that benefit from metadata.
Fermentation Theory: Empirical Difficulties and Guiding Assumptions

How do scientists react when their guiding assumptions run into empirical difficulties? This project leads us to consider six answers: (GA2.1-GA2.6). To evaluate the adequacy of these answers to the question of how scientists deal with empirical difficulties that confront their guiding assumptions, I will examine two empirical difficulties that confronted the guiding assumptions of early 20th-century biochemists working on fermentation and discuss the way the biochemical community responded to these difficulties.
Electron Beam-Specimen Interactions in the Analytical Electron Microscope

Energetic electrons interact with the atoms and electrons of a specimen in a wide variety of ways, many of which can be used to obtain information when using the analytical electron microscope (AEM). It is the purpose of this chapter to describe the properties of these interactions so as to provide a basis for discussions of imaging and microanalysis in subsequent chapters. Only a cursory examination of the complex subject of electron interactions can be presented. A catalog of equations that describe the various forms of electron scattering will be provided, together with examples of the application of these equations to specific calculations. This “user’s guide” to electron interactions will be accompanied by references to more complete treatments, which enable the interested reader to find additional detail, e. g., Bethe and Ashkin (1953). The separate topic of diffraction contrast will be treated at length in Chapter 9.
Component-wise AdaBoost algorithms for high-dimensional binary classification and class probability prediction

Abstract Freund and Schapire (1997) introduced “Discrete AdaBoost” (DAB) which has been mysteriously effective for the high-dimensional binary classification or binary prediction. In an effort to understand the myth, Friedman, Hastie, and Tibshirani (FHT, 2000) show that DAB can be understood as statistical learning which builds an additive logistic regression model via Newton-like updating minimization of the “exponential loss.” From this statistical point of view, FHT proposed three modifications of DAB, namely, Real AdaBoost (RAB), LogitBoost (LB), and Gentle AdaBoost (GAB). All of DAB, RAB, LB, GAB solve for the logistic regression via different algorithmic designs and different objective functions. The RAB algorithm uses class probability estimates to construct real-valued contributions of the weak learner, LB is an adaptive Newton algorithm by stagewise optimization of the Bernoulli likelihood, and GAB is an adaptive Newton algorithm via stagewise optimization of the exponential loss. The same authors of FHT published an influential textbook, The Elements of Statistical Learning (ESL, 2001 and 2008). A companion book An Introduction to Statistical Learning (ISL) by James et al. (2013) was published with applications in R. However, both ESL and ISL (e.g., sections 4.5 and 4.6) do not cover these four AdaBoost algorithms while FHT provided some simulation and empirical studies to compare these methods. Given numerous potential applications, we believe it would be useful to collect the R libraries of these AdaBoost algorithms, as well as more recently developed extensions to AdaBoost for probability prediction with examples and illustrations. Therefore, the goal of this chapter is to do just that, i.e., (i) to provide a user guide of these alternative AdaBoost algorithms with step-by-step tutorial of using R (in a way similar to ISL, e.g., section 4.6), (ii) to compare AdaBoost with alternative machine learning classification tools such as the Deep Neural Network (DNN), logistic regression with LASSO and SIM-RODEO, and (iii) to demonstrate the empirical applications in economics, such as prediction of business cycle turning points and directional prediction of stock price indexes. We revisit Ng (2014) who used DAB for prediction of the business cycle turning points by comparing the results from RAB, LB, GAB, DNN, logistic regression, and SIM-RODEO.
Is the Power Threshold of 0.8 Applicable to Surgical Science?—Empowering the Underpowered Study

Abstract Background Many articles in the surgical literature were faulted for committing type 2 error, or concluding no difference when the study was “underpowered”. However, it is unknown if the current power standard of 0.8 is reasonable in surgical science. Methods PubMed was searched for abstracts published in Surgery, JAMA Surgery, and Annals of Surgery and from January 1, 2012 to December 31, 2016, with Medical Subject Heading terms of randomized controlled trial (RCT) or observational study (OBS) and limited to humans were included (n = 403). Articles were excluded if all reported findings were statistically significant (n = 193), or if presented data were insufficient to calculate power (n = 141). Results A total of 69 manuscripts (59 RCTs and 10 OBSs) were assessed. Overall, the median power was 0.16 (interquartile range [IQR] 0.08-0.32). The median power was 0.16 for RCTs (IQR 0.08-0.32) and 0.14 for OBSs (IQR 0.09-0.22). Only 4 studies (5.8%) reached or exceeded the current 0.8 standard. Two-thirds of our study sample had an a priori power calculation (n = 41). Conclusions High-impact surgical science was routinely unable to reach the arbitrary power standard of 0.8. The academic surgical community should reconsider the power threshold as it applies to surgical investigations. We contend that the blueprint for the redesign should include benchmarking the power of articles on a gradient scale, instead of aiming for an unreasonable threshold.
Mapping Mars's Eastern Valles Marineris

Abstract. The purpose of this mapping project was to create a cartographically accurate representation of an Exploration Zone at the Eastern Valles Marineris outflow region within equatorial Mars. There are numerous problems associated with mapping planetary surfaces. Data and imagery for Exploration Zones at a spatial and spectral resolution sufficient for human landing site evaluation and traverse planning have not been acquired yet. Additionally, as technology evolves, it is very difficult to extrapolate which mapping technologies will be used in the near and far future. In order to create this map, assumptions about the future of mapping had to be made, publicly released data for the area of interest had to be sourced, and data analysis had to be performed. One of the key elements of a successful mission is how to communicate the geospatial aspects of the mission planning process to the general public. The results show that using existing data and traditional static cartographic methods, even extra-terrestrial geographic discoveries can be made and disseminated to the public in an attractive and easily understood format.
Predicting Congestion Level in Wireless Networks Using an Integrated Approach of Supervised and Unsupervised Learning

The usage data from user devices can be analyzed to answer a number of possible questions in regards to congestion, access point (AP) load balancing, user mobility trends and efficient channel allocation. In this paper, we attempt to identify Wi-Fi usage trends in a dynamic environment and use it to further predict the congestion in various locations. To accomplish this, we use various supervised learning algorithms to find the existing patterns in spectrum usage inside University of Nevada, Reno. Using these patterns, we predict the values for certain key attributes that directly correlate to the congestion status of any location. Finally, we apply unsupervised learning algorithms to these predicted data instances to cluster them into different groups. Each group will determine the level of congestion for any building at any time of any day. This way, we will be able to ascertain whether or not any place at any time in the future might require additional resources, which can be utilized from places with low congestion rate, to be able to deliver wireless services efficiently.
Matching Methods for Clustered Observational Studies in Education

Many interventions in education occur in settings where treatments are applied to groups. For example, a reading intervention may be implemented for all students in some schools and withheld from s...
Single-molecule long-read sequencing reveals a conserved selection mechanism determining intact long RNA and miRNA profiles in sperm

Abstract Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to be shaped by paternal environments and impact offspring phenotypes, we know little about long RNAs in sperm, including mRNAs and long non-coding RNAs. Here, by integrating PacBio single-molecule long reads with Illumina short reads, we found 2,778 sperm intact long transcript (SpILT) species in mouse. The SpILTs profile is evolutionarily conserved between rodents and primates. mRNAs encoding ribosomal proteins are enriched in SpILTs, and in mice they are sensitive to early trauma. Mouse and human SpILT profiles are determined by a post-transcriptional selection process during spermiogenesis, and are co-retained in sperm with base pair-complementary miRNAs. In sum, we have developed a bioinformatics pipeline to define intact transcripts, added SplLTs into the “sperm RNA code” for use in future research and potential diagnosis, and uncovered selection mechanism(s) controlling sperm RNA profiles.