cssi/SciSciGPT-SciSciNet huggingface dataset:
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions

Motivation: Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills. Results: Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO. Availability and implementation: GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/. Contact: ude.mssm@nayaam.iva
CO/sub 2/ lidar technique for observing characteristic drop size in water clouds

An analytical evaluation which demonstrates that a calibrated 10.6- mu m-wavelength lidar can measure the mean radius and the effective radius of the drop size distribution in a water cloud is discussed. The radius parameter observed is a weighted average over the penetration depth of the pulse, with weighting factor decreasing with optical depth. In this method the lidar signal is integrated and boundary conditions on optical depth are applied to obtain the average extinction-to-backscatter ratio. The radius parameter is determined by comparing the measured ratio with that found from Mie scatter calculations for a variety of typical drop size distributions. This extinction-to-backscatter method was originally proposed in the literature for measuring mode radius, but at 10.6- mu m wavelength the current results show better accuracy for mean or effective radius. Sources of error are discussed. A lidar probed the sides of fair-weather cumulus clouds in the first application of this method. The resulting values of effective radius were reasonable, and the expected increase of effective radius with height was observed. >
A SIP-based architecture model for contextual coalition access control for ubiquitous computing

A significant deterrent to the ability to connect in a spontaneous manner in cross-enterprise collaborative applications is the difficulty in users from different domains being able to access resources or services located and owned by other entities. Coalition access control encompasses control mechanisms dealing with access between users of two or more different security domains. In this paper we present an approach to add contextual information to the distributed role based access control (dRBAC) model to support spontaneous coalition. The dRBAC model is a relatively new approach for coalition access control based on a delegation model but has been targeted towards pre-arranged delegations among distributed enterprises. A delegation architecture is presented that leverages SIP communication sessions to discover delegation security managers that can automatically exchange roles and delegations based on location and communication session contexts.
Bright Mutants of Vibrio fischeri ES114 Reveal Conditions and Regulators That Control Bioluminescence and Expression of the lux Operon

Vibrio fischeri ES114, an isolate from the Euprymna scolopes light organ, produces little bioluminescence in culture but is 1,000-fold brighter when colonizing the host. Cell-density-dependent regulation alone cannot explain this phenomenon, because cells within colonies on solid medium are much dimmer than symbiotic cells despite their similar cell densities. To better understand this low luminescence in culture, we screened 20,000 mini-Tn5 mutants of ES114 for increased luminescence and identified 28 independent “luminescence-up” mutants with insertions in 14 loci. Mutations affecting the Pst phosphate uptake system led to the discovery that luminescence is upregulated under low-phosphate conditions by PhoB, and we also found that ainS, which encodes an autoinducer synthase, mediates repression of luminescence during growth on plates. Other novel luminescence-up mutants had insertions in acnB, topA, tfoY, phoQ, guaB, and two specific tRNA genes. Two loci, hns and lonA, were previously described as repressors of bioluminescence in transgenic Escherichia coli carrying the light-generating lux genes, and mutations in arcA and arcB were consistent with our report that Arc represses lux. Our results reveal a complex regulatory web governing luminescence and show how certain environmental conditions are integrated into regulation of the pheromone-dependent lux system. Vibrio fischeri is a valuable model for examining bioluminescence, pheromone signaling, and symbiotic bacteria-animal interactions. Studies of V. fischeri’s mutualistic interactions have gained momentum since the discovery that this bacterium’s light organ symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, can be reconstituted in the laboratory (54, 70, 83). Moreover, the bioluminescence induced by V. fischeri in the host light organ is a pheromone-mediated behavior, making this an attractive system for examining environmental influences on bacterial pheromone signaling in a natural infec
Gender and Agricultural Development: Surveying the Field

Gender and Agricultural Development: Surveying the Field. Helen Kreider Henderson. ed. Tucson: University of Arizona Press, 1995.
Retroviruses and the Placenta

Retroviruses are often expressed in the placenta. Placental expression probably evolved to facilitate retroviral transmission from mother to offspring and from offspring to mother. In the process, the placenta became a site where retroviral genes were 'domesticated' to serve adaptive functions in the host, including the manipulation of maternal physiology for the benefit of the fetus. The evolutionary interplay between retroviruses and host defenses may have contributed to the remarkable diversity of form among mammalian placentas and to mechanisms of genomic imprinting.
Pre-Bond and Post-Bond Test and Signal Recovery Structure to Characterize and Repair TSV Defect Induced Signal Degradation in 3-D System

In this paper, we present a methodology for characterization and repair of signal degradation in through-silicon-vias (TSVs) in 3-D integrated circuits (ICs). The proposed structure can detect the signal degradation through TSVs due to resistive shorts in liner oxide and variations in resistance of TSV due to weak open and/or bonding resistance. For TSVs with moderate signal degradations, the proposed structure reconfigures itself as signal recovery circuit to maintain signal fidelity. This allows electrical repair of TSVs with moderate defects leading to better design yield and system functionality. This paper presents the design of the test and recovery structure and demonstrates their effectiveness through stand alone simulations as well as in a full-chip physical design of a 3-D IC.
An Image Encryption Scheme Based on Lorenz Chaos System

This paper proposes a 3-D Lorenz system based image encryption scheme, which improves the security and performance of the encryption system over conventional simple chaos system based ones. The balance and correlation properties of the analog sequences generated by Lorenz system are analyzed and a pre-process method is proposed, which makes the key stream have good statistical properties. Three initial parameters of Lorenz system are combined together as one key, which greatly enlarges the key space under precision restricted condition. The encryption speed is also improved since the position permutation and grayscale substitution of a pixel can be done by one iteration operation. Besides, the encryption system is strong against adaptive parameter synchronous attack since it has more complicated structure than simple chaos system based ones. The experimental results indicate that the algorithm is more secure and efficient than conventional algorithms.
Role of SNAREs in Membrane Fusion

Fusion between opposing cellular membranes is essential for numerous cellular activities such as protein maturation, neurotransmission, hormone secretion, and enzyme release. The universal molecular mechanism of membrane fusion involves Ca2+, and the assembly of a specialized set of proteins present in the opposing membrane bilayers. For example in cell secretion, target membrane proteins at the cell plasma membrane SNAP-25 and syntaxin termed t-SNAREs, and secretory vesicle-associated protein VAMP or v-SNARE, are part of the conserved protein complex involved in fusion of opposing membranes. In the presence of Ca2+, t-SNAREs and v-SNARE in opposing bilayers interact and self-assemble in a ring conformation, to form conducting channels. Such self-assembly of t-/v-SNARE ring occurs only when the respective SNAREs are in association with membrane. The size of the SNARE ring complex is dependent on the curvature of the opposing bilayers. Electron density map and 3-D topography of the SNARE ring complex, suggests the formation of a leak-proof channel measuring 25 A in ring thickness, and 42 A in height. The mechanism of membrane-directed SNARE ring complex assembly, and the mathematical prediction of SNARE ring size, has been determined. X-ray diffraction measurements and simulation studies have further advanced that membrane-associated t-SNAREs and v-SNARE overcome repulsive forces to bring the opposing membranes close to within a distance of approximately 2.8 A. Calcium is then able to bridge the closely apposed bilayers, leading to the release of water from hydrated Ca2+ ions as well as the loosely coordinated water at phospholipid head groups, leading to membrane destabilization and fusion.
There's more than one way to analyze feedback on design

Most studies on feedback and design use thematic analysis. In this paper, we apply three text analysis methods that are not commonly used in feedback and design studies to encourage researchers to think outside of the box and try different methods. We show how word cloud representation, word frequency, and reading ease and grade level tests can be applied to a feedback on design dataset in order to highlight the strengths and limitations of each approach. In general, findings of these three methods are aligned with those from our previous thematic analysis and provide new insights about the feedback. We recommend that these methods be used in addition to thematic analysis in analyzing feedback on design research.
Closing the Gap Between Neurobiology and Human Presbycusis: Behavioral and Evoked Potential Studies of Age-Related Hearing Loss in Animal Models and in Humans

Any reader who has grown up with a pet dog cannot have failed to notice that the effects of advancing age in dogs are not very different from those apparent in aging grandparents, except that in calendar time they appear more rapidly. Although domesticated animals may present a special case compared with wild animals that hardly survive to the age of sexual maturity, a few wild animals do survive and they also exhibit these common effects of human aging. Very close to human sympathies are the observations of elderly chimpanzees by naturalists who, having followed their stable groups for many years, write that the rare creature that has successfully survived the challenges of the wild exhibits the same thinning hair, slow movements, and sagging and wrinkled facial skin as the elderly human (Hill et al. 2001). And given the laboratory studies of hearing in old monkeys (Bennett et al. 1983) and examinations of cochlear pathology in postmortem studies of aged pet dogs (Shimada et al. 1998), this wrinkled and slowly moving chimpanzee and the graying and arthritic dear old pet must both suffer from poor hearing as do elderly humans.
Muscles: Testing and Function With Posture and Pain, ed 5 (with Primal Anatomy CD-ROM)

Kendall FP, McCreary EK, Provance PG, et al. Baltimore, MD 21201, Lippincott Williams & Wilkins, 2005, hardcover (with CD-ROM), 512 pp, illus. ISBN: 0-7817-4780-5, $74.95. The fifth edition of this classic text has had a makeover. Colorful headers top every page. Blocks of text are enhanced by colored titles and subtitles. Terms are bolded. Even the tables look brighter with colored grid lines. This fresh appearance has been aided by the extensive reorganizing of material started in the third edition, and continued in the fourth and, now, the fifth edition. Except for the first 2 chapters, “Fundamental Concepts” and “Posture,” the remaining 5 chapters are organized by body region: head and face; neck; trunk and respiratory muscles; upper extremity and shoulder girdle; and lower extremity. The material within the body region chapters now has the general order of innervations, joints, range of motion, muscle length tests, muscle strength tests, painful conditions, case studies, corrective exercises, and references. Many of the line drawings, photographs, and even blocks of text will be familiar to experienced Kendall users. With the consolidation of chapters and the reordering of contents in …
Time Consistent and Currency Invariant Risk Adjusted Valuations

In order to study time-consistent monetary risk measures in a continuous time, finite horizon setting, there arises a need to define risk-adjusted valuations at all dates in the time continuum. One approach of tackling this issue is to define risk-adjusted valuations at all dates and call this sequence of risk valuations as the risk valuation process. However, monetary risk measures enjoy the translation invariance property which enables us to define monetary risk-adjusted valuations at intermediate stopping times in terms of the date-0 risk measure.We characterize these intermediate risk-adjusted valuations in terms of the date-0 risk measure for strongly relevant time-consistent monetary risk measures. We develop a representation for strongly relevant monetary risk measures which are time consistent at certain specified dates. We develop two methods for constructing time-consistent monetary convex risk measures in a discrete time setting.We seek to characterize monetary convex risk measures which are both time consistent and currency invariant. We define currency invariance for monetary convex risk measures. We show that only trivial monetary convex risk measures satisfy both time consistency and currency invariance for all currency exchange rate processes.We define weak time consistency and currency invariance for concave risk-adjusted valuation processes. We show that all time-consistent concave risk-adjusted valuation processes are trivially currency invariant. We propose a class of concave risk-adjusted valuation processes, which we call Psuedo-Monetary Concave Risk Adjusted Valuation Processes(PCRVPs), which are not necessarily monetary but possess some of the appeal of monetary concave risk-adjusted valuations. We develop a representation for PCRVPs which are weakly time consistent at certain specified dates. This representation is similar to the one we develop for monetary convex risk measures. We show that the only a very specific class of Psuedo-Monetary Coherent Risk Adjusted Valuation Processes are currency invariant for all exchange rate processes.
Ribosome biogenesis may augment resistance training-induced myofiber hypertrophy and is required for myotube growth in vitro

Resistance exercise training (RT) is the most effective method for increasing skeletal muscle mass in older adults; however, the amount of RT-induced muscle growth is highly variable between indivi...
Spiritually Oriented Disaster Psychology

According to Ronan and Johnston (2005) the number of people who will experience a disaster will double by 2050 from one billion people to two billion people. Since 1985 there has been an almost 400% increase in global natural disasters (Center for Research on the Epidemiology of Disasters, 2007). Researchers managing the global terrorism database report a similar increase in terrorist events over the last decade, with almost 5,000 events annually. Some of the worst disasters, such as Hurricane Katrina, Haiti Earthquake, Japan Tsunami, and Philippines Typhoon occurred in the past decade alone. Disasters are becoming more complex, with primary disasters (e.g., earthquake) often triggering secondary disasters (e.g., nuclear meltdown). Research shows that disasters often leave a significant psychological and spiritual “footprint” on affected communities. Thus, the purpose of this article is to introduce readers to empirical research on the psychology of religion/ spirituality and disasters as well as to introduce a framework for spiritually oriented disaster psychology.
Coccidioides immitis spherule antigen in a complement fixation test for experimental coccidioidomycosis.

Summary1. A method is described for the preparation of a serologically active antigen from egg yolk material containing spherules. 2. “Spherule antigen” used in a complement fixation test reacted with sera from animals infected with Coccidioides and animals hyperimmunized with the antigen. 3. The antigen was found to stimulate low titers to coccidioidin in hyperimmunized animals. 4. The “Spherule antigen” completely absorbed anti- bodies to the homologous antigen and coccidioidin from the serum of a hypenmmunized rabbit, but failed to absorb antibodies from the serum of a rabbit infected with Coccidioides immitits.
Epizootiology of eastern equine encephalomyelitis virus in upstate New York, USA. III. Population dynamics and vector potential of adult Culiseta morsitans (Diptera: Culicidae).

Collections of Culiseta morsitans adults were made from 3 sites in and near a breeding swamp between 1977 and 1979. Data indicated that Cs. morsitans was univoltine, commonly survived 8–12 weeks and was strongly ornithophilic. Populations were moderate in size and present from mid-May to early September and had parous rates above 75% during the last ½ of each season. Its vector potential parallels that of Culiseta melanura.
Large Wind Turbine in Variable Speed Transition Operation: Adaptive Disturbance Tracking Control

The transition region control problem for wind turbines occurs while the wind speed varies from Region II to Region III and vice versa. This is the phase when both speed and torque must change separately to get the rated rotor speed and rated rotor torque when the wind speed reaches its rated value. Adaptive Disturbance Tracking Control (ADTC) theory was developed previously to track a desired Tip Speed Ratio (TSR) and hence optimize the power production in Region II of the wind turbine. In this paper we further extended this theory for transition region control, and present numerical results on a NREL’s 5 MW offshore turbine model.
Pseudospectral Optimal Control: A Clear Road for Autonomous Intelligent Path Planning

This paper captures the essence of intelligent path planning by posing the problem in a framework based on optimal control theory. Design requirements for autonomous vehicles call for on-board intelligence capable of making timely decisions, performing tasks in a "smarter" fashion, and ultimately accomplishing missions with extreme accuracy. This is the definition of an optimal control problem! Indeed, most, if not all, motion planning problems can be formulated and solved using optimal control techniques. Motivated by the significant advancements in optimal control techniques over the last decade, we demonstrate the broad range of unmanned systems that can operate both optimally and autonomously by solving path-planning problems using pseudospectral methods.
EPID-31ATRX AND TERT ASSAYS PROVIDE NON-REDUNDANT INFORMATION IN ADULT GLIOMA PATIENTS: INCORPORATING TELOMERE MARKERS INTO NEUROPATHOLOGY PRACTICE

BACKGROUND: Recent work indicates that molecularly-defined glioma subgroups have similar clinical presentation and patient prognoses. These molecularly-defined subgroups often incorporate a measure of the tumor's telomere maintenance strategy, defined by mutations in either TERT or ATRX. Somatic mutations in these genes are typically mutually exclusive and there is ongoing debate over which telomere marker should be adopted into neuropathology practice. METHODS: We assessed both TERT promoter mutation status and ATRX mutation status in 1174 infiltrative adult gliomas (Grades II-IV) from the UCSF Adult Glioma Study, The Mayo Clinic, and TCGA using a combination of sequencing and immunohistochemistry. RESULTS: 653 gliomas were TERTmt only (56%), 337 were ATRXmt only (29%), 164 were TERTwt/ATRXwt (14%), and 20 were TERTmt/ATRXmt (2%). Among IDHwt patients, those with TERTwt/ATRXwt tumors had similar overall survival to patients with TERTmt tumors (HR = 0.91, 95%CI = 0.70-1.18, P = 0.47) but significantly worse survival than patients with ATRXmt tumors (HR = 1.88, 95%CI = 1.01-3.51, P = 0.047) after adjusting for age and grade. Among IDHmt patients, those with TERTwt/ATRXwt tumors had significantly worse overall survival than patients with TERTmt tumors (HR = 2.97; 95%CI = 1.43-6.17, P = 0.0035) and moderately worse survival than patients with ATRXmt tumors (HR = 1.61, 95%CI = 0.98-2.67, P = 0.063) after adjusting for age, grade and 1p/19q status. CONCLUSIONS: These data suggest that among patients with IDHwt glioma, ATRX status may be adequate for prognostication, as both TERTmt and TERTwt/ATRXwt patients differed from ATRXmt patients but did not differ from each other. Among IDHmt patients, those with TERTmt tumors, ATRXmt tumors, and TERTwt/ATRXwt tumors all had different survival experiences. This suggests that knowing both ATRX status and TERT status may be important for patients with IDHmt glioma in order to identify the TERTwt/ATRXwt patients.
Coronary Occlusion and Coronary Insufficiency

Acute coronary attacks may be divided clinically, electrocardiographically, pathologically and therapeutically into (i) classical angina pectoris, (2) acute coronary insufficiency and (3) acute coronary occlusion. In 1000 consecutive cardiac consultations, 450 of 618 cases with organic heart disease had coronary artery disease. Of these 450 cases, 38 per cent had chronic coronary insufficiency (angina pectoris or congestive failure), 26 per cent had acute coronary insufficiency, and 36 per cent had acute coronary occlusion. The differentiation between coronary occlusion and insufficiency which can be made electrocardiographically in 95 per cent of cases is discussed in this paper.
Solvent desorption-gas chromatography for detection of methyl isoamyl alcohol in workplace air

Objective:To establish a method for determination of methyl isoamyl alcohol in the workplace air by solvent desorption-gas chromatography.Methods:Methyl isoamyl alcohol was collected from workplace air using activated carbon tube,desorbed with 5% isopropyl alcohol and CS2 solution,separated on FFAP capillary column,and finally detected by FID detector.Results:The linear range of methyl isoamyl alcohol in workplace air was 0 μg/ml~200 μg/ ml,the detection limit was 2.5 μg/ ml(1 μl liquid for injection),the minimum detection concentration was 0.2029 mg/ m3(with acquisition of 1.5 l),and the relative standard deviation was 4.7%~6.4%.Conclusion:This method is rapid,accurate,high sensitive,easy to operate,with low-level instrument,thus it is applicable to the daily monitoring of methyl isoamyl alcohol in workplace air.
URANIUM DIOXIDE-CLADDING INTERACTIONS. AXIAL EXPANSION OF UO$sub 2$ COLUMN IN FUEL ELEMENTS

Irradiation experiments were conducted to determine the axial expansion of UO/sub 2/ in fuel elements. The experiments included fuel segments with 304 stainless and Zircaloy-2 sheaths in self-supporting tubular geometries under boiling water conditions, as well as fuel elements with 304 stainless UO/sub 2/- supported geometries under superheated steam conditions. The relative UO/sub 2/ expansion during irradiation was measured by mechanical devices included in the fuel segments andd by visual and other observations. (auth)
A muted voice in academe: the Korean version of entrepreneurial scholarship

The imperatives of social democratization and global economic competition have opened a new phase of development for the Korean university and its scholarship. The increased social demands for knowledge creation and dissemination gradually extend the scope of professional practice beyond the conventional areas of academic work. This paper explores, based upon the findings of a case study, how Korean universities and their professors have been responding to these demands and what consequences are observable. It also explains how the new demands and responses are contributing to local development. Finally, it highlights several controversial issues in the discourse on entrepreneurial scholarship and discusses these in the Korean context as points for further investigation.
Differential Refinement Logic

We introduce differential refinement logic (dRL), a logic with first-class support for refinement relations on hybrid systems, and a proof calculus for verifying such relations. dRL simultaneously solves several seemingly different challenges common in theorem proving for hybrid systems: 1. When hybrid systems are complicated, it is useful to prove properties about simpler and related subsystems before tackling the system as a whole. 2. Some models of hybrid systems can be implementation-specific. Verification can be aided by abstracting the system down to the core components necessary for safety, but only if the relations between the abstraction and the original system can be guaranteed. 3. One approach to taming the complexities of hybrid systems is to start with a simplified version of the system and iteratively expand it. However, this approach can be costly, since every iteration has to be proved safe from scratch, unless refinement relations can be leveraged in the proof. 4. When proofs become large, it is difficult to maintain a modular or comprehensible proof structure. By using a refinement relation to arrange proofs hierarchically according to the structure of natural subsystems, we can increase the readability and modularity of the resulting proof. dRL extends an existing specification and verification language for hybrid systems (differential dynamic logic, dL) by adding a refinement relation to directly compare hybrid systems. This paper gives a syntax, semantics, and proof calculus for dRL. We demonstrate its usefulness with examples where using refinement results in easier and better-structured proofs.
Untangling Neurons With Endothelial Nitric Oxide

Alzheimer’s disease (AD) is the most prevalent cause of age-related dementia, which, because of demographic shifts and increasing life expectancy, afflicts a growing segment of the world population and is anticipated to reach epidemic proportions in the decades to come.1 Central to the pathogenesis of AD is the cerebral accumulation of amyloid-β peptides (Aβ) and the microtubule-associated protein tau leading to the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles, respectively.2 Much of the attention in this field has focused on neurons and on neuronal mechanisms responsible for Aβ cleavage from the amyloid precursor protein (APP) and for tau phosphorylation, misfolding, and aggregation.2 In this issue of the journal, however, Austin et al3 shift the focus from neurons to cerebral blood vessels and provide evidence that the endothelial isoform of nitric oxide (NO) synthase (eNOS) protects neurons from tau phosphorylation, thought to be a key step in tau pathogenicity.4 Although the findings implicate for the first time the endothelium in the molecular pathology of tau, they also provide further evidence of the importance of vascular factors in the expression of AD pathology. Article, see p 1128 Tau is involved in the assembly and stabilization of microtubular networks, interconnected track-like structures that shuttle mitochondria and other cargo between the neuronal soma and its most distant processes.4 Tau also participates in glutamate receptor signaling and is released extracellularly from presynaptic terminals during neural activity.4 In AD and other tau-related diseases, several post-translational modifications have been implicated in tau pathogenicity, including phosphorylation.4 Aberrant phosphorylation disrupts the assembly of tau with molecular partners resulting either in loss of its physiological functions or in a toxic gain of function because of mislocalization from axonal to somatodendritic compartments.4 Hyperphosphorylated tau becomes misfolded and tends to aggregate …
The Regionalization of Total Ankle Arthroplasties and Ankle Fusions in New York State: A 10-Year Comparative Analysis

Background. Total ankle arthroplasty (TAA) provides an alternative to ankle fusion (AF). The purpose of this study is to (1) determine the extent of TAA regionalization, as well as examine the grow...
Older Adults' Views and Communication Preferences About Cancer Screening Cessation.

Importance Older adults with limited life expectancy are frequently screened for cancer even though it exposes them to risks of screening with minimal benefit. Patient preferences may be an important contributor to continued screening. Objective To examine older adults’ views on the decision to stop cancer screening when life expectancy is limited and to identify older adults’ preferences for how clinicians should communicate recommendations to cease cancer screening. Design, Setting, and Participants In this semistructured interview study, we interviewed 40 community-dwelling older adults (≥ 65 years) recruited at 4 clinical programs affiliated with an urban academic medical center. Main Outcomes and Measure We transcribed the audio recorded discussions and analyzed the transcripts using standard techniques of qualitative content analysis to identify major themes and subthemes. Results The participants’ average age was 75.7 years. Twenty-three participants (57.5%) were female; 25 (62.5%) were white. Estimated life expectancy was less than 10 years for 19 participants (47.5%). We identified 3 key themes. First, participants were amenable to stopping cancer screening, especially in the context of a trusting relationship with their clinician. Second, although many participants supported using age and health status to individualize the screening decision, they did not often understand the role of life expectancy. All except 2 participants objected to a Choosing Wisely statement about not recommending cancer screening in those with limited life expectancy, often believing that clinicians cannot accurately predict life expectancy. Third, participants preferred that clinicians explain a recommendation to stop screening by incorporating individual health status but were divided on whether life expectancy should be mentioned. Specific wording of life expectancy was important; many felt the language of “you may not live long enough to benefit from this test” was unnecessarily harsh compared with the more positive messaging of “this test would not help you live longer.” Conclusions and Relevance Although research and clinical practice guidelines recommend using life expectancy to inform cancer screening, older adults may not consider life expectancy important in screening and may not prefer to hear about life expectancy when discussing screening. The described communication preferences can help inform future screening discussions. Better delineating patient-centered approaches to discuss screening cessation is an important step toward optimizing cancer screening in older adults.
Preceptor Expectations and Experiences in a Longitudinal Integrated Clerkship.

Introduction The Longitudinal Integrated Clerkship (LIC) as a pedagogical model in medical education is a burgeoning area of interest as an alternative to a traditional, rotation- (block) based curriculum and presents a distinct set of considerations. A large number of studies examine the impact on students participating in LIC programs, but fewer assessments exist for the preceptors involved. This study sought to understand changes in expectations and experiences following LIC program participation. Methods We conducted a survey-based prospective cohort study of preceptors before and after first-time LIC program participation. Five-point Likert-type questions were grouped into four subscales determined by areas of practice and preceptor role: clinical, administrative, professional, and educational. For statistical analyses of the nonmatched responses we used Pearson Chi-Square measures of association and independent t-tests. Results Forty-seven of 84 (56%) preceptors responded to the presurvey and 42% responded to the postsurvey (35/84), totaling 82 unique responses. Thirty-nine (48%) were female, 64 (79%) had over 5 years teaching experience, and 61 (74%) had prior rotation-based clerkship experience. Only the clinical subscale (evaluating aspects of physical exam, history taking, and patient relationship with physician and student) was significantly different pre- (M1= 3.09[SD=0.40]) to post-LIC (M2= 3.47[SD=0.29]) showing a positive change at post-LIC participation (P=0.03). Conclusion For first-time LIC preceptors in a new LIC program, participation led to improvements in clinical practice without detriment to administrative, professional, or educational roles. Future research should examine changes among individual preceptors over time as well as assessments of students, including knowledge, skills, and attitude outcomes.
Characteristics and Outcomes of Psychology Referrals in a Palliative Care Department.

Abstract Context Psychologists can provide unique contributions to interdisciplinary palliative care. Despite research indicating high distress in palliative care cancer patients, little has been reported regarding the feasibility and practice of psychology in this setting. Objectives To review the integration of clinical psychology practice in a palliative care department at a major comprehensive cancer center. Methods Retrospective chart review of 1940 unique cancer patients (6451 total patient contacts) referred for psychology services provided by clinical psychologists in palliative care from September 1, 2013 to February 29, 2016. Results Psychologists provided services to 1644 inpatients (24% of palliative care inpatients) and 296 outpatients (19% of palliative care outpatients). Most of them (85%) received services in the inpatient setting. Most patients were females (57%) and white (68%) with a variety of cancer diagnoses. Adjustment disorders were the most prevalent in both settings with significant differences in other Diagnostic and Statistical Manual of Mental Disorders (5th Edition) diagnoses by service location (P Conclusion Palliative care psychology services successfully integrated into an interdisciplinary palliative care department and rapidly grew in both inpatient and outpatient settings.
A DIFFERENT FORM OF THE Ca2+-DEPENDENT PROTEINASE ACTIVATED BY MICROMOLAR LEVELS OF Ca2+

ABSTRACT A new form of the calcium-activated proteinase has been isolated from beef heart muscle. This new form contains two subunits, 80,000 and 30,000 daltons, respectively, and is inhibited completely by iodoacetamide and 1mM EDTA. In these respects, it is identical to the originally isolated calcium-activated proteinase but, while the original enzyme required 2 to 5mM Ca2+ for maximal activity and was inactive below 0.2mM Ca2+, the new form is completely activated at a Ca2+ concentration of 50μM. The new form is less negatively charged than the original form.
Antibodies to Ehrlichia equi in dogs from the northeastern United States.

OBJECTIVE: To determine whether dogs living in tickinfested areas of the northeastern United States had been exposed to Ehrlichia equi, an etiologic agent of granulocytic ehrlichiosis. DESIGN: Analyses of dog sera. ANIMALS: 106 ill dogs and 12 clinically normal dogs. PROCEDURE: Antibodies to E equi were detected by indirect fluorescent antibody staining methods and western blot analyses. RESULTS: 10 of 106 (9.4%) sera tested from ill, privately owned dogs living in tick-infested areas of Connecticut and New York state had antibodies to E equi, a member of the E phagocytophila genogroup. Titration end points ranged from 1:80 to 1:1,280. Immunoblots revealed antibodies to proteins of E equi having molecular masses of predominantly 29, 40, 44, 105, 120, and 160 kd. There was good agreement between results of serologic testing methods, but use of the human isolate (NCH-1 strain) in western blot analyses detected 2 additional seropositive dogs found to be negative by indirect fluorescent antibody staining methods with the MRK strain. CLINICAL IMPLICATIONS: Dogs living in areas where ixodes scapularis is abundant may be exposed to multiple pathogens, such as E equi or Borrelia burgdorferi. Although mild or subclinical infections with E equi may develop, dogs with marked leukopenia, thrombocytopenia, or anemia should be viewed as possibly having ehrlichiosis. Laboratory diagnosis should include examinations for morulae in granulocytes or monocytes in addition to serologic analyses.
Runoff Phosphorus Loss as Affected by Tillage, Fertilizer, and Swine Manure Phosphorus Management in Corn-Soybean Production Systems

Introduction Information on phosphorus (P) loss from surface runoff in fields managed with different cropping and P management systems is scarce. Swine manure can supply nitrogen (N), P, and K (potassium) for crops. Continued use of N-based manure rates can result in P buildup in the soil, mainly in continuous corn or when manure is applied for both corn and soybean production. Excessive soil P and P applications increase the risk of P loss from fields and of water quality impairment.
On the Physics of the Warm Water Volume and El Niño/La Niña Predictability

AbstractPrevious work has shown that warm water volume (WWV), usually defined as the volume of equatorial Pacific warm water above the 20°C isotherm between 5°S and 5°N, leads El Nino. In contrast ...
Response to PD-1 inhibition in early- and late-relapsing cutaneous melanoma.

e21038Background: Up to 45% of stage I-II melanomas will relapse within 5 years, and some relapses occur more than 10 years after surgical resection. Little is known about the differences in tumor ...
Abstract 2482: A portable bioinformatics pipeline for the FDA authorized IMPACT DNAseq assay

On November 2017, the US Food and Drug Administration (FDA) authorized Memorial Sloan Kettering Cancer Center9s (MSKCC) IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) tumor profiling assay and bioinformatics pipeline for clinical decisions in treating all solid tumors. The IMPACT test uses next-generation sequencing (NGS) to identify the presence of mutations in 468 unique genes, fusions at known sites, copy-number alterations, and microsatellite instability (MSI). A version freeze of the bioinformatics pipeline was made public in May 2017 in Zehir et al. "Mutational Landscape of Metastatic Cancer Revealed from Prospective Clinical Sequencing of 10,000 Patients", Nat Med. 23(6): 703-713. Active development of the pipeline has continued in its CLIA-compliant computing environment, and the resulting improvements have been incorporated into an open-source portable research-grade bioinformatics pipeline. Here, we present results from Roslin , our research bioinformatics pipeline built to be functionally equivalent to the IMPACT clinical reporting workflow that includes manual filtering/annotation and signout by molecular oncologists. Roslin can be installed and executed on laptops, workstations, local compute clusters, or cloud compute servers. As a research-grade pipeline it is flexible enough to handle new assays including exomes/genomes, and extensible enough to add or replace components like reference genomes, sequence aligners, variant callers, false-positive filters, and functional/clinical annotation. Tracking all components and parameters used in each pipeline run allows researchers to easily generate method sections for manuscripts that are sufficiently detailed for peer-review and reproducibility of published results. Roslin has been deployed and tested on multiple high-performance clusters and cloud computing resources. It offers end users GUI driven workflow logging, run reporting, and real-time tracking (https://github.com/mskcc/roslin). Evaluated on NGS data from 128 tumors with signed out IMPACT clinical reports, Roslin achieves a recall rate of 98% for both somatic substitutions and indels, and 60% for fusions. Precision was 96% for substitutions, and 86% for indels. We present our work in maximizing precision and recall rates while retaining the portability, modularity, and reproducibility of Roslin . Citation Format: Zuojian Tang, Nikhil Kumar, Allan Bolipata, Timothy Song, Cyriac Kandoth, Feng Liu, David Mcmanamon, Oliver Hampton, Nicholas Socci, David Solit. A portable bioinformatics pipeline for the FDA authorized IMPACT DNAseq assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2482.
Why Does Therapy Work? An Idiographic Approach to Explore Mechanisms of Change Over the Course of Psychotherapy Using Digital Assessments.

Author(s): Altman, Allison Diamond; Shapiro, Lauren A; Fisher, Aaron J | Abstract: Background and Objective(s): While psychotherapy treatments are largely effective, the processes and mechanisms underlying such positive changes remain somewhat unknown. Focusing on a single participant from a treatment outcome study that used a modular-based cognitive behavior therapy protocol, this article aims to answer this question by identifying changes in specific symptomatology over the course of the treatment. Using quantitative data derived from digital health methodology, we analyzed whether a given therapeutic intervention was related to downstream effects in predicted symptom domains, to assess the accuracy of our interventions.Methods: This case study employed an observational N-of-1 study design. The participant (n = 1) was a female in the age range of 25–35 years. Using digital health data from ambulatory assessment surveys completed prior to and during therapy, separate linear regression analyses were conducted to assess if hypothesized treatment targets reduced after a given module, or intervention.Results: Support was found for some of the hypothesized quantitative changes (e.g., decreases in avoidance after exposures module), yet not for others (e.g., decreases in rumination following the mindfulness module).Conclusion: We present data and results from our analyses to offer an example of a novel design that may allow for a greater understanding of the nature of symptom changes with increased granularity throughout the course of a psychological treatment from the use of digital health tools.
Teaching With Televised Stories: A Story-Focused Narrative Preview Supports Learning in Young Children

Researchers examined the effects of previewing on preschoolers' comprehension of narrative and educational content in a television program. Children (3-5 years, N = 107) watched an educational math episode in one of three conditions: no-preview control, education-focused expository preview, or story-focused narrative preview. A main effect of previewing was found, controlling for age, character familiarity, prior knowledge, and visual attention. Specifically, the narrative preview enhanced both narrative comprehension (including central, incidental, and inferential content) and educational comprehension (including direct learning and transfer), compared to a no-preview control. Conversely, the expository preview had no effect on comprehension. Findings are interpreted with respect to story schema and relevant cognitive theories of learning from media. Implications for educational media production are discussed.
Inverse analysis of strain distributions sensed by distributed fiber optic sensors subject to strain transfer

Abstract Strains measured by distributed fiber optic sensors with protective coatings can be different from the real strains in host matrix due to strain transfer effect. This study presents a novel inverse method to determine the real strain distributions in host matrix using strain distributions measured from distributed fiber optic sensors. Two different scenarios of strain distributions in host matrix are investigated, which have known and unknown types of strain fields, respectively. Three representative metaheuristic algorithms are respectively utilized in the inverse analysis, which are colliding bodies optimization algorithm, particle swarm optimization algorithm, and genetic algorithm. The performance of the proposed method was evaluated by analytical case studies and experimental testing of a prestressed concrete beam subjected to four-point bending. The results demonstrated high accuracy and efficiency of the proposed method. This study is expected to greatly advance distributed fiber optic sensing capabilities in measuring strain distributions for structural health monitoring.
Modeling the behavior of reinforced concrete slabs subjected to impact

Abstract In recent years, safety of nuclear power plants against external missile impacts such as those due to tornadoes has gained significant attention. In many cases, advanced simulation tools based on finite element method (FEM) or smooth particle hydrodynamics (SPH) are being employed to simulate missile impact behavior and to evaluate vulnerability of nuclear facilities. Due to the complex nature of impact behavior, it requires appropriate calibration of parameters in the advanced simulation models that are used to represent them. In this manuscript, we propose a novel approach for modeling the behavior of reinforced concrete slabs subjected to missile impact. First, we use data from one experimental study to develop and calibrate various models needed to conduct the finite element analysis. Then, the calibrated models are used to conduct a predictive analysis for a different experimental setup. A comparison of the experiment and the analytical results for the new test provides confidence in the predictive capability of the simulation approach with calibrated parameters.
Large Scale Network Analytics with SNAP: Tutorial at the World Wide Web 2015 Conference

Many techniques for the modeling, analysis and optimization of Web related datasets are based on studies of large scale networks, where a network can contain hundreds of millions of nodes and billions of edges. Network analysis tools must provide not only extensive functionality, but also high performance in processing these large networks. The tutorial will present Stanford Network Analysis Platform (SNAP), a general purpose, high performance system for analysis and manipulation of large networks. SNAP is being used widely in studies of the Web datasets. SNAP consists of open source software, which provides a rich set of functions for performing network analytics, and a popular repository of publicly available real world network datasets. SNAP software APIs are available in Python and C++. The tutorial will cover all aspects of SNAP, including APIs and datasets. The tutorial will include a hands-on component, where the participants will have the opportunity to use SNAP on their computers.