cssi/SciSciGPT-SciSciNet huggingface dataset:
From molecular clusters to nanoparticles: second-generation ion-mediated nucleation model

Ions, which are generated in the atmosphere by galactic cosmic rays and other ionization sources, may play an important role in the formation of atmospheric aerosols. In the paper, a new second-generation ion-mediated nucleation (IMN) model is presented. The new model explicitly treats the evaporation of neutral and charged clusters and it describes the evolution of the size spectra and composition of both charged and neutral clusters/particles ranging from small clusters of few molecules to large particles of several micrometers in diameter. Schemes used to calculate the evaporation coefficients for small neutral and charged clusters are consistent with the experimental data within the uncertainty range. The present IMN model, which is size-, composition-, and type-resolved, is a powerful tool for investigating the dominant mechanisms and key parameters controlling the formation and subsequent growth of nanoparticles in the atmosphere. This model can be used to analyze simultaneous measurements of the ion-mobility spectra and particle size distributions, which became available only recently. General features of the spectra for ions smaller than the critical size, size-dependent fractions of charged nanoparticles, and asymmetrical charging of freshly nucleated particles predicted by the new IMN model are consistent with recent measurements. Results obtained using the second generation IMN model, in which the most recent thermodynamic data for neutral and charged H 2 SO 4 -H 2 O clusters were used, suggest that ion-mediated nucleation of H 2 SO 4 -H 2 O can lead to a significant production of new particles in the lower atmosphere (including the boundary layer) under favorable conditions. It has been shown that freshly nucleated particles of few nanometers in size can grow by the condensation of low volatile organic compounds to the size of cloud condensation nuclei. In such cases, the chemical composition of nucleated particles larger than ~10 nm is dominated by organics.
Spreading the Risk: Native Trout Management in a Warmer and Less-Certain Future

Abstract Management strategies that increase biological diversity and promote varied approaches to population protection are more likely to succeed during a future in which global warming drives rapid environmental change and increases uncertainty of future conditions. We describe how the concept of a diverse management portfolio can be applied to native trout conservation by increasing representation (protecting and restoring diversity), resilience (having sufficiently large populations and intact habitats to facilitate recovery from rapid environmental change), and redundancy (saving a sufficient number of populations so that some can be lost without jeopardizing the species). Saving diversity for native trout requires the conservation of genetically pure populations, the protection and restoration of life history diversity, and the protection of populations across the historical range. Protecting larger stronghold populations is important because such populations will have a better chance of surviving ...
Computer Implementation of Flexible Multibody Equations

A nonlinear finite element formulation for flexible multibody dynamics is summarized. In this formulation, it is required that the element shape functions can describe large rigid body translations. Of particular interest in the dynamics and control of flexible multibody systems is the concept of equivalent systems of forces. The formulation of the generalized forces and the nonlinear dynamic equations of substructures in flexible multibody dynamics is discussed and the validity of using the linear theory of elastodynamics in mechanical system applications such as tracked vehicles is reexamined.
Maintaining Tidal Inlet Channel by Fluidization

Along the barrier islands off the east coast of the U.S. and at other areas of the world, there exist many tidal inlet channels which connect the ocean to back bay areas. An innovative technique is tested to maintain a stable, navigable channel. Water is pumped into a perforated pipe buried beneath the sand, and the water flowing through the perforations fluidizes the overlying sand. The fluidized sand along the pipe is then removed either by gravity flow, slurry pump, or entrainment in the overlying ebb tidal current. Laboratory experiments provided information necessary for the design of such a fluidization system, specifically, data on hole orientation, hole size, hole spacing, flow rate necessary for fluidization, and the effect of slurry removal on the channel shape. A small-scale field test, designed from the laboratory data and performed on a beach face, shows that the technique is technically feasible and that the design data is sound. In the field test, full fluidization along fluidization pipe was achieved and the fluidized sand was removed by pumping the slurry or, when the pipe was sloped, by gravity flow.
Psychosocial Rehabilitation of Civilians in Conflict-Affected Settings

Civilians worldwide are exposed to traumatic events as a result of mass violence, often in the context of conflict-affected settings. These individuals are often forcibly displaced and suffer extreme loss and violence. In most cases, they are likely to remain in conflict-affected and/or developing country settings that are characterized by limited resources and various competing priorities. The mental-health consequences of conflict have a far-reaching impact on multiple domains of life and community. In the past, mental health assistance to conflict-affected populations focused primarily on providing specialized mental health services to individuals with psychiatric disorders. Recently, however, there is growing acknowledgement that such interventions alone cannot promote full recovery and rehabilitation of traumatized populations and the war-torn societies in which they live. Current understanding of needs in the aftermath of trauma can provide a framework for promoting the psychosocial recovery and rehabilitation of conflict-affected populations.
A haptic-inspired approach of ultrasonic nondestructive damage classification

This paper adopts the idea of involving human subjects in making structural damage detection and classification decisions. Inspired by human haptics, ultrasonic guided wave scattering information is transformed into audible signals rather than tactile excitations. Ultrasonic waveforms are encoded chordally or melodically into audio signals. Human subjects are trained on these encodings and subject to blind tests. Damage conditions, manifested as scattering changes, are enabled through the scattering matrix to and also audio-encoded for comparison to chordal and melodic encodings. The performance is better than the cases encoded with raw data, as there is more straightforward physics contained in the feature domain.
Neurologic evaluation of violent juveniles

Any juvenile who has acted violently requires a systematic, meticulous neurologic evaluation. There is no substitute for an adequate medical, family, and social history, the latter focusing on abuse and neglect. Evaluation should include a full physical and a conventional neurologic examination. If the neurologic or neuropsychologic examinations demonstrate brain dysfunction, the patient has brain dysfunction, even if MR imaging is normal.
A Recombinant System to Model Proteoglycan Aggregate Interactions and Aggrecan Degradation

The proteoglycan aggregate is a major component of the articular cartilage extracellular matrix comprising hyaluronan (HA), aggrecan, and link protein. Aggrecan, heavily substituted with chondroitin sulfate (CS) and keratan sulfate (KS) glycosaminoglycans, contributes to cartilage hydration by binding water, thus lending articular cartilage its resistance to compressive deformation. A loss of aggrecan is observed in the early stages of osteoarthritis, which may relate to age-dependent changes in biochemical properties of proteoglycan aggregates. The research reported in this thesis was focused on producing recombinant molecules for modeling proteoglycan aggregate assembly and aggrecan proteolytic degradation. First, the proteoglycan tandem repeat (PTR) domains of link protein, which are responsible for HA binding, were expressed in E. coli to develop a tool for studying the PTR-HA interaction. Soluble monomeric PTR domains were obtained by a novel refolding procedure. Second, full-length recombinant link protein and aggrecan were expressed in a mammalian expression system as functional molecules capable of forming a ternary complex with HA. Furthermore, the expression of recombinant aggrecan in various mammalian cell lines allows the production of differently glycosylated aggrecans for comparison of glycosylation-specific functional differences. Last, both cartilage-derived and recombinant wild-type and mutagenized aggrecans were used to study proteinase-dependent aggrecan degradation observed in the cartilage extracellular matrix. The present work demonstrated that sulfated glycosaminoglycans covalently attached to both cartilage-derived and recombinant aggrecans regulate the susceptibility of aggrecan to ADAMTS4. A study using mutagenized recombinant aggrecan suggested that potentially glycosylated threonine and serine residues N-terminal and C-terminal to the ADAMTS4 cleavage site within the interglobular domain of aggrecan influence the rate of cleavage by ADAMTS4. The degree of hydrophobicity N-terminal to the ADAMTS4 cleavage site also affects aggrecan s susceptibility to ADAMTS4. Recombinant aggrecan was substituted with KS by co-transfecting aggrecan with KS-sulfotransferases. KS-substituted aggrecan, which also had altered CS components, was found to be differentially susceptible to different isoforms of ADAMTS4. This work demonstrates the usefulness of the recombinant system for studies of molecular interactions with HA, aggrecan, and link protein, as well as for in vitro analyses of matrix proteinase-mediated degradation of aggrecan.
Analysis Of E2A Point Mutations In B Cell Leukemia

Introduction TCF3 encodes for E2A protein, which belongs to the helix loop helix transcription factor family. E2A activates transcription of downstream genes by binding to E-box motifs as a homo or hetero dimer. E2A plays an important role in B lymphocyte development. Therefore deletion or mutations in TCF3 or even lowered activity of E2A are causes of B cell leukemia and lymphomas. Recently, three mutations V557E, D561E and N551K in E2A were isolated in Burkitt’s lymphoma (Schmitz, Young et al. 2012). The first two mutations are present in the homo dimerization region of E2A while N551K is present in the DNA binding region. Though the paper enumerated role of TCF3 in Burkitt’s lymphoma but the significance of these TCF3 mutations or mechanism needed further characterization. We hypothesized that these TCF3 mutations have an alternate mechanism as compared to wild type TCF3 and therefore may affect B cell development. Methods We characterized three TCF3 mutants by cloning them into in MIGR1 backbone using TOPO cloning. E2A activity was measured using an E2A-specific luciferase reporter assay in 293T cells. DNA binding activity was measured using a DNA protein binding colorimetric assay. Results V557E and D561E mutants have lower activity as compared to wild type E2A as studied using E2A-specific luciferase reporter assay; while N551K showed no activity in the same assay as compared to wild type E2A activity. Similarly V557E and D561 form weaker bonds with the E box motifs while N551K showed no DNA binding activity as studied using colorimetric DNA-protein binding assay. The plasmid expressions were verified using western blot analysis. Conclusion Our findings suggest mutations V557E and D561E may follow a similar pathway as wild-type E2A but have lower activity. The N551K mutation has an alternate pathway to wild type TCF3 that may impact B cell proliferation, survival and development. Disclosures: No relevant conflicts of interest to declare.
Groundwater and Stream E. coli concentrations in coastal plain watersheds served by onsite wastewater and a municipal sewer treatment system

The goal of this study was to determine if onsite wastewater treatment systems (OWS) were influencing groundwater and surface water Escherichia coli concentrations in a coastal plain watershed. Piezometers for groundwater monitoring were installed at four residences served by OWS and five residences served by a municipal wastewater treatment system (MWS). The residences were located in two different, but nearby (<3 km), watersheds. Effluent from the four septic tanks, groundwater from piezometers, and the streams draining the OWS and MWS watersheds were sampled on five dates between September 2011 and May 2012. Groundwater E. coli concentrations and specific conductivity were elevated within the flow path of the OWS and near the stream, relative to other groundwater sampling locations in the two watersheds. Groundwater discharge in the OWS watershed could be a contributor of E. coli to the stream because E. coli concentrations in groundwater at the stream bank and in the stream were similar. Stream E. coli concentrations were higher for the OWS in relation to MWS watersheds on each sampling date. Water quality could be improved by ensuring OWS are installed and operated to maintain adequate separation distances to water resources.
A Control Theoretic Framework for Optimally Locating Passive Vibration Isolators to Minimize Residual Vibration

This paper investigates the problem of optimally locating passive vibration isolators to minimize residual vibration caused by exogenous disturbance forces. The stiffness and damping properties of the isolators are assumed to be known and the task is to determine the isolator locations, which are nonlinearly related to system states. This paper proposes an approach for reformulating the nonlinear isolator placement problem as a LTI control problem by linking the control forces to measured outputs using a feedforward term. Accordingly, the isolator locations show up as a static output feedback gain matrix which is optimized for residual vibration reduction using standard H∞ optimal control methods. Simulations and experiments on SISO and MIMO case studies are used to demonstrate the merits of the proposed approach. Even though presented in the specific context of ultra-precision manufacturing machines, the proposed method is applicable to the optimal design of other passive systems with nonlinear relationships between design variables and system states.Copyright © 2015 by ASME
Using Small-Area Estimation to Calculate the Prevalence of Smoking by Subcounty Geographic Areas in King County, Washington, Behavioral Risk Factor Surveillance System, 2009–2013

Introduction King County, Washington, fares well overall in many health indicators. However, county-level data mask disparities among subcounty areas. For disparity-focused assessment, a demand exists for examining health data at subcounty levels such as census tracts and King County health reporting areas (HRAs).
X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CLpro) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 A X-ray structure of 3CLpro from PEDV. Analysis of the PEDV 3CLpro structure and comparison to other coronaviral 3CLpro’s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CLpro’s are conserved, with the exception of a loop that comprises the protease S2 pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro, (R)-16, to have inhibitor activity against PEDV 3CLpro, despite that SARS-3CLpro and PEDV 3CLpro share only 45.4% sequence identity. Structural comparison reveals that the majority of residues involved in (R)-16 binding to SARS-3CLpro are conserved in PEDV-3CLpro; however, the sequence variation and positional difference in the loop forming the S2 pocket may account for large observed difference in IC50 values. This work advances our understanding of the subtle, but important, differences in coronaviral 3CLpro architecture and contributes to the broader structural knowledge of coronaviral 3CLpro’s.
How much testing is needed after myocardial infarction

PreviewAre expensive, complicated, and sometimes risky techniques always necessary to assess a patient's condition after myocardial infarction? Not according to the author, who discusses variations in the management of three typical patients and also endorses a cost-saving algorithmic guide to testing and treatment of infarction survivors.
THE PROPORTION OF TERRAMYCIN-RESISTANT MUTANTS IN B. MEGATHERIUM CULTURES

The number of terramycin-resistant mutants in Bacillus megatherium cultures, their mutation rate, and the growth rate of the wild and mutant cells have been determined under various conditions. These values are in agreement with the following equations (Northrop and Kunitz, 1957):— See PDF for Equation λ = mutation rate, A = growth rate constant of wild cells, B = growth rate constant of mutants, See PDF for Equation equilibrium. The value of the mutation rate as determined from equation (6) agrees with that found by the null fraction method.
Long-Term Mortality in Patients With Radiation-Associated Coronary Artery Disease Treated With Percutaneous Coronary Intervention

Background— The incidence and predictors of long-term mortality after percutaneous coronary intervention (PCI) for radiation-associated coronary artery disease are unknown. Methods and Results— In this observational study of 314 patients (age, 65.2±11.4 years; 233 [74%] women) treated with PCI, 157 patients with previous external beam radiation therapy (XRT) were matched 1:1 with 157 comparison patients with atherosclerotic coronary artery disease without previous XRT, based on age, sex, lesion artery, and PCI type. The primary end point was all-cause mortality, and the secondary end point was cardiovascular mortality. After follow-up of 6.6±5.5 years, there were 101 deaths; 59 in the XRT group and 42 in the comparison group ( P =0.04). On Cox proportional hazards multivariable survival analysis, previous XRT remained an independent predictor of all-cause mortality (hazard ratio [HR] 1.85; 95% confidence interval [CI], 1.21–2.85; P =0.004) and cardiovascular mortality (HR, 1.70; 95% CI, 1.06–2.89; P =0.03). Additional independent predictors of increased all-cause mortality included balloon angioplasty or bare-metal stent placement compared with drug-eluting stent placement (HR, 2.50; 95% CI, 1.61–3.97; P <0.0001), SYNTAX (Synergy Between PCI With Taxus and Cardiac Surgery) score of ≥11 (the sample median; HR, 1.99; 95% CI, 1.32–3.04; P <0.001), New York Heart Association functional class ≥3 (HR, 1.83; 95% CI, 1.15–2.91; P =0.012), history of smoking (HR, 1.88; 95% CI, 1.10–3.09; P =0.022), and age ≥65 years (HR, 1.70; 95% CI, 1.07–2.07; P =0.024). Conclusions— Compared with patients with typical atherosclerotic coronary artery disease, patients with radiation-associated coronary artery disease are at higher risk for mortality after PCI. Previous XRT exposure is independently associated with increased all-cause and cardiovascular mortality in patients treated with PCI.
Primary cytoreductive surgery and adjuvant hormonal monotherapy in women with advanced low-grade serous ovarian carcinoma: Reducing overtreatment without compromising survival?

Abstract Objectives Women with advanced-stage, low-grade serous ovarian carcinoma (LGSC) have low chemotherapy response rates and poor overall survival. Most LGSC tumors overexpress hormone receptors, which represent a potential treatment target. Our study objective was to determine the outcomes of patients with advanced-stage LGSC treated with primary cytoreductive surgery (CRS) and hormone therapy (HT). Methods A retrospective study was performed at two academic cancer centers. Patients with Stage II–IV LGSC underwent either primary or interval CRS followed by adjuvant HT between 2004 and 2016. Gynecologic pathologists reviewed all cases. Two-year progression-free (PFS) and overall survival (OS) were calculated. Results Twenty-seven patients were studied; primary CRS followed by HT were administered in 26, while 1 patient had neoadjuvant chemotherapy followed by CRS and HT. The median patient age was 47.5, and patients had Stage II (n=2), Stage IIIA (n=6), Stage IIIC (n=18), and Stage IV (n=1) disease. Optimal cytoreduction to no gross residual was achieved in 85.2%. Ninety six percent of tumors expressed estrogen receptors, while only 32% expressed progesterone receptors. Letrozole was administered post operatively in 55.5% cases, anastrozole in 37.1% and tamoxifen in 7.4%. After a median follow up of 41months, only 6 patients (22.2%) have developed a tumor recurrence and two patients have died of disease. Median PFS and OS have not yet been reached, but 2-year PFS and OS were 82.8% and 96.3%, respectively, and 3-year PFS and OS were 79.0% and 92.6%, respectively. Conclusions Our series describes the initial experience with cytoreductive surgery and hormonal monotherapy for women with Stage II–IV primary ovarian LGSC. While surgery remains the mainstay of treatment, chemotherapy may not be necessary in patients with advanced-stage disease who receive adjuvant hormonal therapy. A cooperative group, Phase III trial is planned to define the optimal therapy for women with this ovarian carcinoma subtype.
Hardwood-Pine Mixedwoods Stand Dynamics following Thinning and Prescribed Burning

Restoration of hardwood-pine (Pinus L.) mixedwoods is an important management goal in many pine plantations in the southern Cumberland Plateau in north-central Alabama, USA. Pine plantations have been relatively unmanaged since initiation, and thus include a diversity of hardwoods developing in the understory. These unmanaged pine plantations have become increasingly vulnerable to insects, and management activities were initiated to facilitate transition towards hardwood-pine mixedwoods. We evaluated a combination of thinning and prescribed fire prescriptions in a randomized complete block design with a 3 × 3 factorial treatment arrangement and four replications of each treatment. Treatments were combinations of thinning to three residual basal areas (no thin, light thin to 17.2 m2 ha−1, heavy thin to 11.5 m2 ha−1) and three prescribed burn applications (no burn, one burn to be repeated every 9 years, three burns repeated every 3 years). Burning without thinning altered stand structure by reducing overstory stem density by 15%, whereas thinning without burning reduced density by 70% and burning coupled with thinning resulted in reduced overstory trees by 72%. Frequent fire had the greatest impact on midstory structure and regeneration. Midstory stem density was reduced by 90% following thinning and burning. Oaks (Quercus L.) and red maple (Acer rubrum L.) were the most common understory species after thinning only, burning only, and thinning combined with burning. There were more oak and red maple seedling sprouts following frequent burning. Currently, >75% of red maple sprouts dominate the regeneration, compared to only 40% of the oaks. Although the treatments have accelerated the transition toward hardwood-pine mixedwoods, the fate of oak and which hardwood species will be dominant in the future remains uncertain.
Multiagent-Based Optimal Microgrid Control Using Fully Distributed Diffusion Strategy

This paper proposes a multiagent-based optimal microgrid control scheme using a fully distributed diffusion strategy. A two-level cooperative optimization multiagent system is adapted for distributed energy resources economic dispatch. The lower level implements an adaptive droop scheme based on online no-load frequency adjustments. The upper level implements distributed communication using diffusion between neighboring agents for optimal microgrid management. The proposed control scheme enables peer-to-peer communication among the agents without the necessity of a centralized controller, and simultaneously performs resource optimization while regulating the system frequency. The results are compared with centralized and consensus-based optimization algorithms. We have concluded that the proposed algorithm is superior over consensus algorithms in terms of convergence speed and utilizes reduced communication infrastructure compared to centralized controllers. Simulation demonstrations were conducted along with experimental results from a hardware-based microgrid using an industrial multiagent framework. The simulation and experimental results show that the proposed method and the agent framework can be deployed in real-world microgrids and offer superior decision making on optimal microgrid control.
Physician Burnout and the Calling to Care for the Dying: A National Survey.

Background:Physician burnout raises concerns over what sustains physicians’ career motivations. We assess whether physicians in end-of-life specialties had higher rates of burnout and/or calling to...
Measuring extended red sensitivity in a 1.7μm-cutoff HgCdTe detector array

Infrared detectors with cutoff wavelengths of ~ 1.7 μm have much lower sensitivity to thermal background contamination than those with longer cutoff wavelengths. This low sensitivity offers the attractive possibility of reducing the need for fully cryogenic systems for YJH-band work, offering the potential for “warm-pupil" instrumentation that nonetheless reduces detected thermal background to the level of dark current. However, residual sensitivity beyond the cutoff wavelength is not well characterized, and may preclude the implementation of such warm-pupil instruments. We describe an experiment to evaluate the long-wavelength sensitivity tail of a 1.7 µm-cutoff HAWAII-2RG array using a thermal blocking filter. Our results suggest the possibility of measurable red sensitivity beyond ~ 2 μm. Ongoing improvements will confirm and refine this measurement. The thermal blocking filter offers the prospect of warm-pupil NIR instrument operation, which is particularly valuable for cost-effective and efficient testing systems: it has facilitated NIR detector characterization and will enable crucial laboratory tests of laser frequency comb calibration systems and other NIR calibration sources.
Modeling contact detonations with ALE3D and PARADYN

Publisher Summary This chapter presents modeling contact detonations with ALE3D and Paradyn. Several severe responses are possible including cracking, crater formation, and breaching. Previously used models resulted in mesh distortions and inadequate representations of the blast loading that lowered the accuracy of the simulation results. Arbitrary Lagrangian-Eulerian (ALE) methods combine the best of Lagrangian and Eulerian methods to provide a more accurate solution by allowing a controlled amount of mesh movement, alleviating mesh distortions, while following the flow of the detonation. ALE methods allow movement of a structure to better track the pressures on the concrete as it deforms. PARADYN is used to calculate the concrete damage because the material model computes the local nonlinear material behavior, providing more accurate results. Blast simulations are performed with ALE3D that generated pressure time histories for the surface of the concrete. The structural response of the concrete is calculated with PARADYN, and the ALE3D time histories are applied as pressure-boundary conditions. Test data are compared to the simulation results to validate the process of using ALE3D and PARADYN to analyze the contact detonation problem. A validated ALE3D-PARADYN process is used for predicting other contact detonation scenarios.
A 16-channel FPGA-based time-to-digital converter for pulse width modulation circuitry for silicon photomultiplier readout

This work presents a 16-channel time-to-digital converter (TDC) implemented in a field programmable gate array (FPGA) that can be used for a positron emission tomography (PET) detector with pulse width modulation (PWM) circuit readout. Simple tapped delay line methods using dedicated carry chain structures are used to measure short time intervals in conventional TDCs. We propose a TDC with more sophisticated algorithms implemented in a Spartan-6 FPGA, that consists of a fine time measurement block, a coarse counter, a ring oscillator and a buffer. The ring oscillator generates frequency signal related delay chain in order to compensate the process, voltage, and temperature effect in real-time without causing dead-time in the TDC. The performance of our proposed TDC was measured with two input pulses that were generated from a pulse generator. The average timing resolution of the TDC channel is 75.5 ± 13.6 ps FWHM for all 16 channels. The proposed TDC was also used to acquire the flood histogram of the PET detector with a 2 × 2 array of 5 mm × 5 mm position sensitive solid state photo multiplier (PS-SSPM) coupled to an 18 × 18 array of 0.5 mm × 0.5 mm × 1.0 mm LYSO scintillation crystal at room temperature. The proposed TDC with PWM readout circuit clearly identified 0.5 mm × 0.5 mm crystals. In selected rows of crystals, the average ratio of distance between crystal peaks to peak standard deviation was 4.7 and the minimum ratio was 3.2. These results verify the feasibility of our TDC for PET detectors with sub-millimeter width crystals.
SparkBench: a spark benchmarking suite characterizing large-scale in-memory data analytics

Spark has been increasingly employed by industries for big data analytics recently, due to its resilience, scalability and efficient in-memory distributed programming model. Meanwhile, the rapid growing community is also actively incubating a rich ecosystem around Spark to tackle various big data challenges. The current benchmarks fall short in providing guidance of development, optimization, configuration and deployment of Spark. To this end, we introduce SparkBench, a Spark specific benchmarking suite. It selectively embraces a set of representative applications to identify various performance bottlenecks and reveals the resource consumption behaviors across execution phases. Overall, SparkBench covers four critical usage patterns of Spark, including machine learning, graph processing, stream computations and SQL query processing. We present comprehensive characterization of resource consumptions, data flows and timing information under different execution patterns and demonstrate that SparkBench can effectively guide the optimization of data analytic platforms to better suit for various workloads.
Maximum likelihood identification of an information matrix under constraints in a corresponding graphical model

This paper is addressed to the problem of identifying the neighborhood structure of an undirected graph, whose nodes are labeled with the elements of a multivariate normal (MVN) random vector. A semi-definite program is given for estimating the information matrix under arbitrary constraints on its elements. More importantly, closed-form expressions are given for the maximum likelihood (ML) estimator of the information matrix, under the constraint that the inverse of the covariance matrix, called here the information matrix, has pre-specified elements in a given pattern (e.g., in a principal submatrix). The results apply to the identification of conditional dependencies in a graphical model with neighborhood constraints.
Conformations and Chemistry of Oxocarbenium Ion

While the conformational analysis of stable compounds has been studied in detail, determining the conformational preferences of reactive intermediates is much more difficult. For example, knowledge of the three-dimensional structures of cyclic oxocarbenium ions is very important for understanding both uncatalyzed and enzymatic reactions of carbohydrates involving the anomeric carbon, since these reactions often involve oxocarbenium ion intermediates [1–5]. Since the charged intermediates are generally much too reactive, it is impossible to directly observe oxocarbenium ions, particularly in aqueous environments [6, 7].
The benefits of grid-scale storage on Oahu

Abstract The Hawaiian Electric Company intends to procure grid-scale Battery Energy Storage System (“BESS”) capacity. The purpose of this study is to determine whether providing contingency reserve or time-of-day shifting is of more benefit to the Oahu grid, and to better understand the relationship between BESS size and level of benefit. This is an independent study by Sandia, and is not being used to support the regulatory case for BESS capacity by Hawaiian Electric. The study team created a production cost model of the Oahu grid using data primarily from the Hawaiian Electric Company. The proposed BESS supplied contingency reserve in one set of runs and time-of-day shifting in another. Supplying contingency reserve led to larger savings than time-of-day energy shifting. Assuming a renewable reserve and a quick-start reserve, and $15/MMBtu for Low-Sulphur Fuel Oil, the 50-MW/25-MWh, 100-MW/50-MWh, and 150-MW/75-MWh systems supplying contingency reserve provided, respectively, savings of 9.6, 15.6, and 18.3 million USD over system year 2018. Over the range of fuel prices tested, these cost savings were found to be directly proportional to the cost of fuel. As the focus is the operational benefit of BESS capacity, the capacity value of the BESS was not included in benefit calculations.
On-chip ultraviolet holography for high-throughput nanoparticle and biomolecule detection

Nanoparticle and biomolecule imaging has become an important need for various applications. In an effort to find a higher throughput alternative to existing devices, we have designed a lensfree on-chip holographic imaging platform operating at an ultraviolet (UV) wavelength of 266 nm. With a custom-designed free-space light delivery system to illuminate the sample that is placed very close ( 16 mm 2 ) was utilized as the imaging field-of-view (FOV) capturing holographic signatures of target objects on a chip. These holograms were then digitally back propagated to extract both the amplitude and phase information of the sample. The increased forward scattering from nanoparticles due to this shorter illumination wavelength has enabled us to image individual particles that are smaller than 30 nm over an FOV of >16 mm 2 . Our platform was further utilized in high-contrast imaging of nanoscopic biomolecule aggregates since 266 nm illumination light is strongly absorbed by biomolecules including proteins and nucleic acids. Aggregates of Cu/Zn-superoxide dismutase (SOD1), which has been linked to a fatal neurodegenerative disease, ALS (amyotrophic lateral sclerosis), have been imaged with significantly improved contrast compared to imaging at visible wavelengths. This unique UV imaging modality could be valuable for biomedical applications (e.g., viral load measurements) and environmental monitoring including air and water quality monitoring.
Chromatin Architectural Changes during Cellular Senescence and Aging

Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics of genome architecture, their associated proteins, and the underlying mechanisms involved in regulating chromatin spatial organization and gene expression. Cellular senescence and aging, which involve multiple cellular and molecular functional declines, also undergo significant chromatin structural changes, including alternations of heterochromatin and disruption of higher-order chromatin structure. In this review, we summarize recent findings related to genome architecture, factors regulating chromatin spatial organization, and how they change during cellular senescence and aging.
Association between comorbid cancer and outcomes among admissions for acute ischemic stroke receiving systemic thrombolysis

BackgroundThe impact of cancer on outcomes was not assessed in major trials of systemic thrombolysis in acute ischemic stroke.AimsTo evaluate the association between comorbid cancer and hospital ou...
Promoting Spatial Inclusion: How Everyday Places Signal Who Is Welcome

Regardless of whether we live in urban, suburban, or rural areas, we all “read” landscapes for indications of whether we fit in and are welcome. Identities relating to race, ethnicity, class, gender and sexuality all contribute to the lenses through which we interpret these signs. This chapter considers how we make sense of public and private places and what elements of the built and social environment we can change to make a wider range of people feel welcome. Specific examples focus on how people navigate food stores and neighborhood parks based on their intersecting identities.
Evaluation of RapidEye data for mapping algal blooms in inland waters

The high spatial resolution multispectral imaging sensor onboard RapidEye (RE) has a red-edge band centred at 710 nm, which can be used to produce a product equivalent to the Maximum Chlorophyll In...
Analysis of Interdependent Kinetic Controls of Fatty Acid Synthases

Biocatalytic systems (e.g., multienzyme pathways or complexes) enable the conversion of simple sugars into complex products under ambient conditions and, thus, represent promising platforms for the synthesis of renewable fuels and chemicals. Unfortunately, to date, many of these systems have proven difficult to engineer without a detailed understanding of the kinetic relationships that regulate the concerted action of their constituent enzymes. This study develops a mechanistic kinetic model of the fatty acid synthase (FAS) of Escherichia coli and uses that model to determine how different FAS components work together to control the production of free fatty acids—precursors to a wide range of oleochemicals. Perturbational analyses indicate that the modification or overexpression of a single FAS component can depress fatty acid production (a commonly observed phenomenon) by sequestering the proteins with which it interacts and/or by depleting common substrate pools. Compositional studies, in turn, suggest ...
Abstract B72: Secretory autophagy in tumor-associated fibroblasts alter effector function of natural killer cells against HNSCC

Tumor-associated fibroblasts (TAFs) are the most abundant cell type in the microenvironment of head and neck squamous cell carcinoma (HNSCC). We and others previously reported that secreted factors from TAFs increase the proliferation, migration, and invasion of HNSCC. Further studies revealed that HNSCC-secreted factors induce secretory autophagy in TAFs. However, the contribution of TAF autophagy to immune-evasion in the HNSCC microenvironment is unknown. Natural killer (NK) cells are an essential arm of anti-tumor immunity; thus, our study set out to determine the role of TAF autophagy in suppressing NK cell effector functions against HNSCC. To address this, we treated the NK cell line NK-92MI with conditioned media from primary HNSCC TAFs or normal fibroblasts derived from cancer-free subjects and assessed changes in IFN-γ production and cytotoxicity, measures of NK cell activation. We then assessed the role of TAF autophagy in mediating this effect by repeating the studies using conditioned media from TAFs whose autophagy had either been inhibited by chloroquine treatment or knocked down by siRNA. Finally, we assessed the mechanisms by which autophagy in the TAF affects NK cell function. Our data demonstrate HNSCC tumor cells orchestrate a complex mechanism of NK cell inhibition through the modulation of TAFs in the microenvironment. Treatment with TAF-conditioned media induced IFN-γ mRNA expression in NK-92MI cells. Interestingly, TAF-conditioned media also reduced NK cell-mediated cytotoxicity as compared to conditioned media from normal fibroblasts. Knockdown of key regulators in the secretory autophagy pathway by siRNA abrogated release of TAF-secreted factors, including hepatocyte growth factor (HGF). HGF induced NK-92MI expression of IFN-γ mRNA, which could be abrogated by an inhibitor of the HGF receptor, c-MET. In conclusion, these data describe a previously undefined effect of TAFs on NK cell function in the HNSCC microenvironment. Citation Format: Jonathan David Enders, Jacob New, Rana Aliani, Sufi Mary Thomas. Secretory autophagy in tumor-associated fibroblasts alter effector function of natural killer cells against HNSCC [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B72.
A Simpler and More Sensitive Single-Copy HIV-1 RNA Assay for Quantification of Persistent HIV-1 Viremia in Individuals on Suppressive Antiretroviral Therapy

A real-time quantitative reverse transcriptase PCR assay with single-copy sensitivity targeting the integrase region of HIV-1 (integrase single-copy assay [iSCA] v1.0) has been widely used to quantify plasma viremia in individuals on antiretroviral therapy (ART). iSCA v1.0 requires the use of an ultracentrifuge, and only about half of the nucleic acid extracted from plasma is assayed for HIV-1 RNA. We sought to simplify sample processing using microcentrifugation and improve assay sensitivity by testing more than 75% of the total extracted nucleic acid for HIV-1 RNA (iSCA v2.0). We evaluated the limit of detection (LoD) of iSCA v2.0 by testing replicates of low-copy plasma HIV-1 RNA standards. By probit analysis, the 95% LoD was 1 copy of HIV-1 RNA per milliliter for a 5-ml plasma sample. To compare the sensitivity of iSCA v1.0 and v2.0, we tested plasma samples with both assays from 60 participants on ART with HIV-1 RNA below 20 cps/ml. Of the 31 samples that had no detectable HIV-1 RNA by iSCA v1.0, 17 (55%) were detectable by v2.0 with an HIV-1 RNA mean value of 3.5 cps/ml. Twenty-nine samples were detectable with both assay versions, but average values of HIV-1 RNA cps/ml were 2.7-fold higher for v2.0 than v1.0. These results support the adoption of a new, more sensitive and simpler single-copy HIV-1 RNA assay (iSCA v2.0) to quantify residual viremia on ART and to assess the impact of experimental interventions designed to decrease HIV-1 reservoirs.
Prognostic features for testicular cancers (TCs): Can this be gleaned from pathology reports?

e15550 Background: TCs are very curable cancers.Patients with stage I disease are offered surveillance, based on risk criteria, the low probability of relapse and the high curability with chemother...
Identification and Characterization of Neofabraea kienholzii and Phlyctema vagabunda Causing Leaf and Shoot Lesions of Olive in California

California produces over 95% of the olives grown in the United States. In 2017, California's total bearing acreage for olives was 14,570 hectares producing 192,000 tons of olives valued at $186.6 million. During the early spring of 2016, unusual leaf and shoot lesions were detected in olive trees from superhigh-density orchards in the Northern San Joaquin and Sacramento valleys of California. Affected trees displayed numerous leaf and shoot lesions developing at wounds created by mechanical harvesters. The 'Arbosana' cultivar was highly affected by the disease, whereas the disease was sporadic in 'Arbequina' and not found in 'Koroneiki' cultivar. Two fungal species, Neofabraea kienholzii and Phlyctema vagabunda, were found to be consistently associated with the disease, and Koch's postulates were completed. Species identity was confirmed by morphology and molecular data of the partial large subunit rDNA, the internal transcribed spacer region, and partial beta-tubulin region. The disease signs and symptoms are described and illustrated.
Chance-Constrained Energy Management System for Power Grids With High Proliferation of Renewables and Electric Vehicles

This paper proposes a two-stage energy management system (EMS) for power grids with massive integration of electric vehicles (EVs) and renewable energy resources. The first stage economic dispatch determines the optimal operating points of charging stations and battery swapping stations (BSS) for EVs under plug-in and battery swapping modes, respectively. The proposed stochastic model predictive control (SMPC) problem in this stage is characterized through a chance-constrained optimization formulation that can effectively capture the system and the forecast uncertainties. A distributed algorithm, the alternating direction method of multipliers (ADMM), is applied to accelerate the optimization computation through parallel computing. The second stage is aimed in coordinating the EV charging mechanisms to continuously follow the first-stage solutions, i.e., the target operating points, and meeting the EV customers’ charging demands captured via the Advanced Metering Infrastructure (AMI). The proposed solution offers a holistic control strategy for large-scale centralized power grids in which the aggregated individual parameters are predictable and the system dynamics do not vary sharply within a short time-interval.
Complete Intrasubstance Long Head Biceps Brachii Rupture with Successful Repair: A Case Report.

Introduction Intrasubstance biceps brachii rupture is a rare injury. Non-operative management of this injury has demonstrated worse outcomes than early operative intervention. Case Report We report a case of a traumatic long head of the biceps brachii muscle belly rupture repaired primarily throughthe Kragh technique augmented with human dermal collagen matrix. The patient demonstrated full strength, an intact repair throughclinical exam and magnetic resonance imaging at 6-year follow-up. Dash scoring demonstrated 0 (no disability) out of 100 at this time. Conclusion Repair of acute traumatic closed transection of the biceps brachii can be successfully repaired utilizing this technique with excellent post-operative function.
How Bargaining Power Affects Non-Price Terms in Contracts

While practitioners and commentators in industry invoke bargaining power to explain patterns in non-price contract terms, conventional law and economics scholarship contends that bargaining power should affect only the price and not other contract terms. This paper looks at the impact of bargaining power on non-price terms, such as warranties, termination rights and dispute resolution provisions, when the value and cost of these terms varies across contracting parties, and when such values are private information. We conceptualize bargaining power as having three primary components: (1) lack of competition; (2) power to dictate the contract terms; and (3) power to commit not to renegotiate. In the extreme cases in which one or the other party enjoys overwhelming bargaining power, the efforts of that party to capture a larger share of the surplus by screening or signaling will compromise the efficiency of the non-price terms. We demonstrate that this incentive is mitigated or disappears when bargaining power is more evenly shared between the parties. This analysis provides a basis for understanding the intuition among market participants that the impact of bargaining power extends beyond price terms. We also suggest implications for legal policy, particularly the contract law doctrine of unconscionability.