cssi/SciSciGPT-SciSciNet huggingface dataset:
Development of a toxR-based loop-mediated isothermal amplification assay for detecting Vibrio parahaemolyticus

Background: Vibrio parahaemolyticus is a leading cause of seafood-related bacterial gastroenteritis and outbreaks worldwide. Sensitive and specific detection methods are needed to better control V. parahaemolyticus infections. This study aimed at developing a highly specific and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting V. parahaemolyticus in oysters. A set of five LAMP primers, two outer, two inner, and one loop were designed based on the published V. parahaemolyticus toxR sequence. Specificity of the assay was evaluated using a panel of 36 V. parahaemolyticus and 39 other strains. The assay sensitivity was determined using serial dilutions of V. parahaemolyticus ATCC 27969 culture ranging from 10 8 CFU/ml to extinction. The assay was also tested in experimentally inoculated oyster samples. Results: The toxR-based LAMP assay was able to specifically detect all of the 36 V. parahaemolyticus strains without amplification from 39 other strains. The detection limit was 47-470 cells per reaction in pure culture, up to 100-fold more sensitive than that of toxR-PCR. When applied in spiked oysters, the assay was able to detect 1.1 × 10 5 V. parahaemolyticus cells per gram of oyster without enrichment, up to 100-fold more sensitive than that of toxR-PCR. Standard curves generated for detecting V. parahaemolyticus in both pure culture and spiked oyster samples showed good linear relationship between cell numbers and the fluorescence or turbidity signals. Conclusions: The toxR-based LAMP assay developed in this study was sensitive, specific, and quantitative, holding great potential for future field detection of V. parahaemolyticus in raw oysters.
Micro-computed tomographic evaluation of fetal skeletal changes induced by all-trans-retinoic acid in rats and rabbits.

BACKGROUND: Our laboratory has been conducting positive control studies to evaluate the utility of micro-computed tomography (micro-CT) for qualitative evaluation of fetal skeletal morphology. All-trans-retinoic acid (atRA) was used to produce a different spectrum of defects compared to our previous studies with boric acid and hydroxyurea. METHODS: Groups of five mated Crl:CD(SD) female rats each were administered vehicle or atRA (2.5–50mg/kg) on GD 10, and groups of four mated Dutch Belted rabbits each were dosed with vehicle or atRA (6.25–25mg/kg) on GD 9. Cesarean sections were performed on GD 21 and 28, respectively. Following external examination the viscera were removed and fetuses scanned in a micro-CT imaging system. Fetuses were subsequently stained with alizarin red. Skeletal morphology was evaluated by each method without the knowledge of treatment group. Total bone mineral content (BMC) of each fetus was quantitated using the micro-CT images. RESULTS: In rats there were dose-related increases in the incidence of extra lumbar vertebra and non-dose-related increases in supernumerary ribs at all dose levels. There were decreases in mean number of ossified sacrocaudal vertebra at Z5mg/kg, and increases in skull bone malformations at Z10mg/kg. Rabbits were less sensitive on a mg/kg basis since skeletal malformations and a decrease in mean number of ossified sacrocaudal vertebra were observed only in the 25-mg/kg group. Micro-CT evaluation detected essentially the same incidence of skeletal abnormalities as seen in alizarin red-stained rat and rabbit fetuses. BMC analysis showed a trend toward slight decreases in atRA-treated rats, but no notable changes in rabbits. CONCLUSIONS: These results add support to our previous work that demonstrates that micro-CT imaging can effectively assess rat and rabbit fetal skeletal morphology. Birth Defects Res (Part B) 89:408–417, 2010. r 2010 Wiley-Liss, Inc.
Performance analysis of Rayleigh fading ad hoc networks with regular topology

For wireless ad hoc networks with stationary and deterministically placed nodes, finding the optimal placement of the nodes is an interesting and challenging problem, especially under energy and QoS constraints. We study and compare the performance of several networks with regular topologies utilizing a Rayleigh fading link model. For nearest neighbor and shortest path routing, analytical expressions of the path efficiency, delay, and energy consumption for a given end-to-end reception probability are derived. For the interference analysis, the maximum throughput and optimum transmit probability are determined, and a simple MAC scheme is compared with an optimum scheduler, yielding lower and upper performance bounds
Dugdale model for circumferential through-cracks in pipes loaded by bending

The paper contains an analytical solution to the title problem by means of the semi-membrane theory of cylindrical shells. Results include the crack opening displacements as a function of circumferential angle, the fracture parameter J, and the effects of the crack on the compliance of the pipe.
Climatological features of regional surface air quality from the Atmospheric Integrated Research Monitoring Network (AIRMoN) in the USA

Abstract The Atmospheric Integrated Research and Monitoring Network (AIRMoN) of NOAA is a research program aimed at developing and implementing improved dry and wet deposition monitoring methodologies. For dry deposition, the array is built on the basis of air-surface exchange research stations, originally set up as the “CORE/Satellite Dry Deposition Inferential Method” array under the National Acid Precipitation Assessment Program (NAPAP). For wet deposition, the program is founded on the Multistate Atmospheric Power Production Pollution Study (MAP3S), previously operated by the Department of Energy but now continuing under NOAA sponsorship. AIRMoN-wet is a research subnetwork of the National Atmospheric Deposition Program. In general, AIRMoN sites are located (a) in locations where changes should be most easily detected, (b) at sites where experienced and interested operators are already on hand, and (c) so that research opportunities (such as may result from collocation with other activities) can be maximized. The present analysis concerns the air chemistry data collected as part of the AIRMoN-dry activity. Sulfur data indicate a slow downward trend in air concentrations, at the rate of 3–4% yr −1 over the last 15 yr, doubtlessly partially attributable to the emissions reductions mandated by the Clean Air Act Amendments of 1990. For the same period, nitric acid vapor concentrations in air indicate a slight increase rather than the decrease seen for sulfur.
Spreading of the Indonesian Throughflow in the Indian Ocean

The Indonesian Throughflow (ITF) spreading pathways and time scales in the Indian Ocean are investigated using both observational data and two numerical tracer experiments, one being a three-dimensional Lagrangian trajectory experiment and the other a transit-time probability density function (PDF) tracer experiment, in an ocean general circulation model. The model climatology is in agreement with observations and other model results except that speeds of boundary currents are lower. Upon reaching the western boundary within the South Equatorial Current (SEC), the trajectories of the ITF tracers within the thermocline exhibit bifurcation. The Lagrangian trajectory experiment shows that at the western boundary about 38%±5% thermocline ITF water flows southward to join the Agulhas Current, consequently exiting the Indian Ocean, and the rest, about 62%±5%, flows northward to the north of SEC. In boreal summer, ITF water penetrates into the Northern Hemisphere within the Somali Current. The primary spreading pathway of the thermocline ITF water north of SEC is upwelling to the surface layer with subsequent advection southward within the surface Ekman layer toward the southern Indian Ocean subtropics. There it is subducted and advected northward in the upper thermocline to rejoin the SEC. Both the observations and the trajectory experiment suggest that the upwelling occurs mainly along the coast of Somalia during boreal summer and in the open ocean within a cyclonic gyre in the Tropics south of the equator throughout the year. All the ITF water eventually exits the Indian Ocean along the western boundary within the Mozambique Channel and the east coast of Madagascar and, farther south, the Agulhas Current region. The advective spreading time scales, represented by the elapsed time corresponding to the maximum of transit- time PDF, show that in the upper thermocline the ITF crosses the Indian Ocean, from the Makassar Strait to the east coast of the African continent, on a time scale of about 10 yr and reaches the Arabian Sea on a time scale of over 20 yr.
Variation in the duration of survival of patients with the chronic leukemias.

few studies the omission of cases of unusually short duration. An attempt was made to overcome some of the above difficulties in the present study by using data from a community-wide survey of patients with leukemia. We have attempted to answer the following questions: ( 1 ) What are the parameters of duration of survival from date of diagnosis for patients with chronic lymphocytic and chronic myelocytic leukemia? (2) Are there any statistically significant differences between the median survival times of groups of these patients classified according to sex, age, religion, blood type or duration of symptoms prior to diagnosis? The results of a similar study for patients with the acute leukemias have been reported previously.2
Partial orbit irradiation achieves excellent outcomes for primary orbital lymphoma.

Abstract Purpose Primary radiation therapy (RT) achieves excellent local control and overall survival when treating localized orbital lymphoma. However, evidence supporting irradiation of partial orbit volumes to spare nearby critical structures is lacking. We sought to investigate outcomes for patients with localized orbital lymphoma treated with partial orbit irradiation. Methods and materials We retrospectively reviewed patients with orbital lymphoma treated with RT at our institution who met our inclusion criteria: biopsy-confirmed, low-grade lymphoma, localized disease, partial orbit treatment volumes, and follow-up >3months. The Kaplan-Meier method was used to measure overall survival (OS), and the cumulative incidence function adjusted for the competing risk of death was used to measure local failure (LF), contralateral orbit recurrence (COR), and progression. Patient characteristics were compared with outcomes using Fisher exact test for dichotomous variables and Wilcoxon rank-sum test for continuous variables. Results Thirty-two patients meeting inclusion criteria were identified with median follow-up of 45.8months (range, 3.6-171.9). The majority had stage IEA disease; their sites included conjunctiva (n=20) and retrobulbar or lacrimal gland (n=12). Median partial orbit RT dose was 30.6Gy (range, 22.5-36). Five-year OS was 100%. Five-year cumulative incidence of LF, COR, and overall disease progression was 5.3%, 5.9%, and 21.4%, respectively. Five-year cumulative incidence of LF was 8.3% for conjunctival disease versus 0.0% for retrobulbar or lacrimal gland involvement ( P =.15). No significant association was observed between the outcomes of LF, COR, or progression and pretreatment characteristics. Acute and late toxicity included grade 2 periorbital edema (n=3, 9.4%), dry eye (n=3, 9.4%), retinal vascular disorder (n=1, 3.1%), conjunctivitis (n=2, 6.3%), and grade 3 cataract (n=1, 3.1%). Conclusions Use of partial orbit irradiation in treating low-grade, localized orbital lymphoma achieves excellent survival with low rates of LF, COR, or progression.
Theorems on L 2 -transform and its applications

In the present paper the author proves Parseval-Goldstein-type theorems involving a Laplace-type integral tranform, the Widder transform and the K-transform. The theorem is then shown to yield a number of new identities involving several well-known integral transforms. Using the theorems and its corollaries, a number of interesting infinite integrals of elementary and special functions are presented. Some illustrative examples are also given.
Long-Term Stress and DSM III

With the advent of the recognition of Psychosomatic Disorders, now called Psychophysiological Reactions, it has become apparent that various measurable effects of psychological stress can manifest themselves in human organisms. A particular aspect of this phenomenon namely, psychic trauma, was recognized as such, in the early 1940’s. Following the notion of “shell-shock” in World War I, where it was believed that the noise of explosives contributed to a noticeable condition manifesting itself in military personnel, it was discovered that this disorder had a psychological basis and was later termed “War Neurosis”1. It has long been recognized that such disturbances could have both acute or long termed effects. The range of stressors which could evoke such disorders has come in to focus only within the last couple of decades and was officially recognized for the first time in the third edition of the Diagnostic and Statistical Manual (DSM III) of the American Psychiatric Association (1980)2.The author can personally validate this phenomenon in both the research and treatment spheres covering a wide variety of situations, such as the following: hostage taking, airplane crashes and auto accidents, natural and human-induced disastrous events, rape, physical battering, military combat, prisoners of war, and political siege and holocaust.3,4
Association of Levee Vegetation to Rice Water Weevil (Coleoptera: Curculionidae) Infestation in California Rice

The association between levee vegetation and rice infestation level by the rice water weevil, Lissorhoptrus oryzophilus Kuschel, was evaluated in California’s Sacramento Valley. Fields with vegetated versus bare levees were compared for adult weevil infestation during the spring flight period. Lower infestations were associated with bare levees at 13 of 15 locations from 1990 to 1992. Weevil infestation remained below the recommended treatment level at 8 of 15 bare levee sites, but only 1 of 15 weedy levee sites.
Executive Dysfunction Following Critical Illness: Exploring Risk Factors and Management Options in Geriatric Populations

Cognitive impairment is a common occurrence that has been shown to occur in over 50 % of patients following critical illness. This impairment occurs across a range of domains including attention, memory, processing speed, and executive dysfunction. In this article, we will discuss the pathophysiology behind cognitive impairment including hypoxemia and cytokines. Secondly, we will describe the risk factors for cognitive impairment including age, length of stay, and delirium. Lastly, we will review emerging data related to the use of cognitive rehabilitation, formation of postintensive care clinics in qualifying patients, and potential neuropharmacologic therapy. While our chapter focuses on cognitive impairment generally, it places a particular emphasis on executive dysfunction, not because impairment occurs solely in this domain but because impairments of an executive nature may be uniquely debilitating.
Successful importation of cytarabine into the United States during a critical national drug shortage.

Purpose The importation of cytarabine into the United States during a critical national drug shortage is described. Summary In March 2011, the hospital pharmacy team at an acute care hospital was struggling to supply cytarabine for four specific patients, all of whom needed critical maintenance therapy after induction. Cytarabine was not available from any source in the United States, and the team had no realistic projected release dates for back orders. Idis UK, a pharmaceutical distributor, was asked to identify available drug and eventually found an unrestricted source of cytarabine in Switzerland. Once available drug was identified, a price quote for the supply amount was written for our consideration. This was inspected carefully to ensure that the drug, strength, dosage form, and any other ingredients listed were indeed what were expected. The pharmacy department worked with the hospital’s department of finance and accounting to submit the necessary financial paperwork. Payment was electronically sent to the distributor before the drug was shipped. Before the order for cytarabine was placed, the associated risks and benefits were assessed. The patients provided consent to treatment with the unapproved product. Acceptance of the price quote and instructions to order the drug were e-mailed to the distributor. The necessary documentation was completed and included with the shipment. The importation process, from initial inquiries to delivery, took 21 days. Conclusion The importation of cytarabine amid a drug shortage required a complex process that involved the efforts of an overseas distributor, the cooperation of multiple health professionals, and meticulous attention to detail.
Measurement of dc dielectric conductance (reciprocal resistance) at elevated temperature

The general principles given in ASTM D 257(1) apply to measurements of dielectric conductance at elevated temperatures. However, special precautions must be taken in the design of the cell or holder and the measuring circuit to insure that the supporting insulator conductances are Iow enough so that they do not appreciably affect the instrument indication when the conductance of a specimen is being measured. This includes conductance between the measuring electrode and the guard ring when volume conductance is being measured. This generally requires that the supporting insulators for the measuring electrode be Iocated outside the heated area. lt is possible to have the supporting insulators in the heated area if special insulating materials are used and special care is taken to have long lengths of insulators with relatively small cross section. Surface conductance usually has little meaning at elevated temperatures.
High-Throughput Approaches

The discovery and development of polymeric materials is fundamental to numerous industrial, commercial, and medicinal applications. A major challenge in polymer research is evaluating the large number of parameters involved in developing new materials for these applications. High-throughput combinatorial methods are rising to the challenges posed by polymer research and are well-suited to query the parameters in polymer synthesis, characterization, and evaluation. Laboratory automation previously feasible for only large companies has now become accessible to academic research groups, greatly enhancing efforts to apply combinatorial methods. Here we provide an overview of the area as it applies to medicinal, commercial, and industrial applications.
Hidden-Markov Factor Analysis as a spatiotemporal model for electrocorticography

We present a new approach to extracting low-dimensional neural trajectories that summarize the electrocorticographic (ECoG) signals recorded with high-channel-count electrode arrays implanted subdurally. In our approach, Hidden-Markov Factor Analysis (HMFA), a finite set of factor analyzers are used to model the relationship between the high-dimensional ECoG neural space and a low-dimensional latent neural space; the factor analyzers at different time points are in turn linked together with a hidden Markov model. The recorded ECoG signals were band-pass filtered such that our analysis was focused on a sub-band (76–100Hz) of high gamma. HMFA affords the quantization of the ECoG neural space and dimensionality reduction in a common probabilistic space. We applied this method to the ECoG recordings of 2 subjects who responded with button presses to audiovisual stimuli in an experimental task. Using a goodness-of-fit metric that measures how well the ECoG activity of each electrode can be predicted by all the other electrodes, we found that HMFA performed best when compared with Gaussian-Process Factor Analysis (GPFA) and other related spatiotemporal modeling techniques. In contradistinction to HMFA, GPFA and the other techniques integrate temporal smoothing with dimensionality reduction. We believe that this method will provide a powerful tool for relating high-channel-count ECoG signals to the perception and behavior of subjects.
Dual-polarized directivity enhanced active metamaterial antenna for polarimetric radar applications

An active substrate integrated waveguide based dual-polarized directivity enhanced full-space scanning composite right/left handed leaky-wave antenna for polarimetric radar applications is proposed. The proposed antenna is realized by using reflection type amplifiers to compensate both radiation and material losses, thereby increasing the effective aperture dimension and directivity of the antenna without compromising all unique features of metamaterial leaky-wave antenna including full frequency-scanning (backfire-to-endfire) capability and bilateral operation. Bilateral operation is essential in radar applications to allow both transmitting and receiving operations. The proposed dual-polarized full frequency-scanning polarimetric radar antenna may be operated in either: 1) linear slant (+45° and −45°) polarization mode, 2) linear horizontal/vertical polarization mode, or 3) right/left-handed circular polarization mode. This paper demonstrates the operation of the proposed active antenna in horizontal/vertical polarization mode. The realized active antenna shows directivity enhancement compared to its all passive counterpart.
On Line Monitoring and Diagnosis of the Operation of a Hybrid CSTR by Using PCA Models

Abstract Testing strategies for process monitoring, diagnosis and control is expensive, and usually requires either complex pilot plant facilities or to deal with the hard constraints posed by experimentation in real plants. The experience developing hybrid systems, combining pilot plants and models is presented. A model is used to simulate the reaction, given measured and virtual variables. Feed temperature and flow rate and reactor temperature are measured on line, while feed component concentrations are given as a stochastic disturbance. The temperature in the reactor can be controlled by regulating the cold water flow rate in the coil. The potential of developing this class of hybrid systems is illustrated by the use of principal component analysis (PCA) methodology to build a model from experimental data. Hotelling T 2 and Q residual tests were running on line every time a steady state is reached. Both tests are used to identify the main causes of two kinds of problems: when the process target (product concentration) is not met and when a measuring device failed. Examples of these applications are discussed.
HIF1A up-regulates the ADORA2B receptor on alternatively activated macrophages and contributes to pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a deadly chronic lung disease. Extracellular accumulation of adenosine and subsequent activation of the ADORA2B receptor play important roles in regulating inflammation and fibrosis in IPF. Additionally, alternatively activated macrophages (AAMs) expressing ADORA2B have been implicated in mediating adenosine's effects in IPF. Although hypoxic conditions are present in IPF, hypoxia's role as a direct modulator of macrophage phenotype and identification of factors that regulate ADORA2B expression on AAMs in IPF is not well understood. In this study, an experimental mouse model of pulmonary fibrosis and lung samples from patients with IPF were used to examine the effects and interactions of macrophage differentiation and hypoxia on fibrosis. We demonstrate that hypoxia-inducible factor 1-α (HIF1A) inhibition in late stages of bleomycin-induced injury attenuates pulmonary fibrosis in association, with reductions in ADORA2B expression in AAMs. Additionally, ADORA2B deletion or pharmacological antagonism along with HIF1A inhibition disrupts AAM differentiation and subsequent IL-6 production in cultured macrophages. These findings suggest that hypoxia, through HIF1A, contributes to the development and progression of pulmonary fibrosis through its regulation of ADORA2B expression on AAMs, cell differentiation, and production of profibrotic mediators. These studies support a potential role for HIF1A or ADORA2B antagonists in the treatment of IPF.-Philip, K., Mills, T. W., Davies, J., Chen, N.-Y., Karmouty-Quintana, H., Luo, F., Molina, J. G., Amione-Guerra, J., Sinha, N., Guha, A., Eltzschig, H. K., Blackburn, M. R. HIF1A up-regulates the ADORA2B receptor on alternatively activated macrophages and contributes to pulmonary fibrosis.
A holistic view of nucleation and self-assembly

Nucleation is the seminal process in the formation of ordered structures ranging from simple inorganic crystals to macromolecular matrices. Observations over the past 15 years have revealed a rich set of hierarchical nucleation pathways involving higher-order species ranging from multi-ion clusters to dense liquid droplets, as well as transient crystalline or amorphous phases. Despite this complexity, the pathways that lead to nucleation can be described by a holistic framework that is rooted in classical concepts, but which takes into account the coupled effects of perturbations in free-energy landscapes and the impact of dynamical factors. This article describes that framework using a series ofin situ transmission electron microscopy and atomic force microscopy studies on inorganic, organic, and macromolecular systems to illustrate the evolution in nucleation processes as these perturbations and dynamical factors come into play. The results provide a common basis for understanding development of order in systems as diverse as simple salt crystals, branched semiconductor nanowires, and microbial membranes.
Resveratrol for Alzheimer's disease

The amyloid hypothesis suggests that the progressive accumulation and deposition of central nervous system (CNS) amyloid with aging is the proximate cause of Alzheimer's disease (AD). Thus, targeting molecular mechanisms of aging may be a viable treatment approach. Caloric restriction prevents diseases of aging, including AD, in animal models, perhaps by activation of sirtuins. The sirtuins (e.g., mammalian SIRT1) are deacetylases that link energy balance (NAD+ /NADH) to regulation of gene transcription. Resveratrol is a potent activator of SIRT1, and thus may mimic caloric restriction to prevent diseases of aging. We conducted a randomized, double-blind, placebo-controlled, phase II trial of resveratrol for individuals with mild-to-moderate AD. Resveratrol (1) is detectable in cerebrospinal fluid (at low nanomolar levels), (2) is safe and well tolerated, (3) alters AD biomarker trajectories, (4) preserves blood-brain barrier integrity, and (5) modulates the CNS immune response. Further studies are needed to determine the safety and efficacy of resveratrol and the validity of this approach in the treatment and prevention of AD and other diseases of aging.
The association of insomnia and depressive symptoms with all‐cause mortality among middle‐aged and old adults

Objectives Insomnia and depressive symptoms are commonly reported by adults and have independently been found to be associated with mortality, though contrasting findings are reported. Given the high comorbidity and interrelatedness between these symptoms, we tested whether insomnia symptoms explain risk of death independent of depressive symptoms. We examined insomnia symptoms and depressive symptoms, in addition to other health and demographic covariates, as predictors of all-cause mortality. Methods The sample included 15 418 adults aged 51 and older drawn from a nationally representative, population-based study of adults in the United States, the Health and Retirement Study. Cox survival models were used to analyze time to death between the 2002 and 2014 study waves (5 waves). Controlling for health and demographic covariates, in 3 separate models, depressive symptoms and insomnia symptoms were independently and then together considered as risk factors for all-cause mortality (drawn from the National Death Index). Results After adjustment for covariates, insomnia symptoms (HR = 1.10, CI:1.07-1.13) and depressive symptoms (HR = 1.14, CI:1.12-1.16) each were associated with a greater hazard of death. When considered together, however, depressive symptoms fully accounted for the association between insomnia symptoms and mortality. Conclusion Though their effects are small relative to health and demographic characteristics, both insomnia symptoms and depressive symptoms were associated with a greater hazard of death. Yet depressive symptoms accounted for the insomnia association when both were considered in the model. Screening for depression and providing validated treatments may reduce mortality risk in old adults with depressive symptoms.
What’s Going on? Multi-sense Attention for Virtual Agents

When designing virtual humans, it is imperative that the virtual agent behave in a human-like fashion. In certain circumstances, this requires agents to be bounded in their ability to sense and understand the environment. To this end, we create a methodology that provides perceptual attention based on a linear combination of senses. We use different heuristics on the object and events that can be sensed by a virtual agent, and combine these scores to create an overall score for a given object or event. This allows the virtual agent to perceive interesting or unexpected items. To demonstrate our technique, we give an example showing the ability of using a linear combination of senses.
Analytical and Empirical Study of the Tails of Probability Distributions

For the distribution function F(x) of a random variable X we define the end points $$\alpha (F) = \inf \{ x:F(x) > 0\} {\text{and }}\omega {\text{(F) = sup\{ x:F(x) < 1\} }}$$ (1) .
Network Dynamics Analysis and Benchmarking on an Outdoor Heterogeneous Wireless Sensor Network

We present an empirical study on network dynamics in an outdoor heterogeneous multi-hop WSN deployment for long-term environmental monitoring. We analyze the network dynamics in three aspects, the link level characteristics, the routing level characteristics, and the overall temporal characteristics. Our analysis provides insights including: (1) asymmetric links are the majority in heterogeneous networks which are mainly caused by the hardware heterogeneity; and (2) routing protocol plays an essential role in generating routing dynamics in addition to wireless link dynamics. We also create/compose benchmark profiles based on the observations of network testbed dynamics obtained during a long-term operation. The benchmark profiles include the link information between heterogeneous hardware platforms and the complete routing topological information.
U.S. acute care hospital shootings, 2012-2016: A content analysis study.

BACKGROUND Healthcare workers experience a disproportionately high frequency of workplace assaults. Incidents involving firearms are of particular concern. OBJECTIVE To provide detailed characterizations of recent hospital shootings to better inform prevention and mitigation strategies. METHODS Quantitative content analysis of reports involving hospital shootings resulting in casualties derived from web searches for each year from 2012-2016. Data were abstracted independently by two investigators, with differences resolved by consensus. Data were compared between subgroups by chi-square test, Fisher's exact test, or Kruskal-Wallis test, as appropriate. RESULTS Eighty-eight shootings occurred in 86 hospitals resulting in 121 firearms-related casualties, including 54 victims and 67 perpetrators. Case fatality rates were 55.6% (n = 30) and 70.1% (n = 47), respectively. The most frequent sites involved were the emergency department, (n = 27, 30.3%), patient room (n = 19, 21.3%), and parking lot (n = 13, 14.6%). Grudge (n = 17, 19.3%), suicide (n = 14, 15.9%), and mental instability (n = 13, 14.8%) were the most common explanations for these shootings. Four inadvertent discharges occurred and were more likely to involve a female perpetrator (p = 0.03). Shootings were most frequent during summer (p = 0.03) and winter (p = 0.04). CONCLUSIONS Out study findings on location and seasonal patterns can guide the development or improvement of prevention and mitigations strategies for hospital shootings.
Probing axial anisotropy in dinuclear alkoxide-bridged Er–COT single-molecule magnets

Abstract Developing well-coupled lanthanide-based magnetic materials via a building block approach has proven difficult since few systems exists that are able to simultaneously maintain anisotropy and promote adequate coupling. Employing the anisotropic building block consisting of Er3+ bound to the cyclooctatetraenide dianion ([Er(COT)]+), two alkoxide-bridged dinuclear single-molecule magnets displaying ferromagnetic coupling were synthesized: centrosymmetric [Er(COT)(µ-OEt)(THF)]2 (1) and non-centrosymmetric [Er(COT)]2(µ-OtBu)2(THF) (2). AC relaxation studies reveal that both systems have similar weak temperature dependence of their relaxation, despite anisotropy axes being parallel in 1 and nearly perpendicular in 2. Due to the strong crystal field provided by the alkoxide ligands, both complexes display enhanced mixing of the total angular momentum states, which provides a fast relaxation pathway even with conserved single-ion anisotropy and ferromagnetic coupling.
Inhibition of carcinogenesis by naturally-occurring and synthetic compounds

Cancer can be prevented by administration of a variety of chemical compounds. Some of these are naturally-occurring. Others are purely synthetic. Compounds belonging to over 25 different classes of chemicals have preventive capacities (30). There are two implications of the existence of a wide chemical diversity of inhibitors. One is that it enhances the likelihood that a variety of approaches can be made to cancer prevention by chemopreventive compounds. The second is that the occurrence of many naturally-occurring preventive agents in food indicates that the composition of the diet can be an important factor in determining the response of individuals to carcinogenic agents to which they are exposed.
18F-fluorodeoxyglucose positron emission tomography correlates with tumor immunometabolic phenotypes in resected lung cancer

Enhanced tumor glycolytic activity is a mechanism by which tumors induce an immunosuppressive environment to resist adoptive T cell therapy; therefore, methods of assessing intratumoral glycolytic activity are of considerable clinical interest. In this study, we characterized the relationships among tumor 18F-fluorodeoxyglucose (FDG) retention, tumor metabolic and immune phenotypes, and survival in patients with resected non-small cell lung cancer (NSCLC). We retrospectively analyzed tumor preoperative positron emission tomography (PET) 18F-FDG uptake in 59 resected NSCLCs and investigated correlations between PET parameters (SUVMax, SUVTotal, SUVMean, TLG), tumor expression of glycolysis- and immune-related genes, and tumor-associated immune cell densities that were quantified by immunohistochemistry. Tumor glycolysis-associated immune gene signatures were analyzed for associations with survival outcomes. We found that each 18F-FDG PET parameter was positively correlated with tumor expression of glycolysis-related genes. Elevated 18F-FDG SUVMax was more discriminatory of glycolysis-associated changes in tumor immune phenotypes than other 18F-FDG PET parameters. Increased SUVMax was associated with multiple immune factors characteristic of an immunosuppressive and poorly immune infiltrated tumor microenvironment, including elevated PD-L1 expression, reduced CD57+ cell density, and increased T cell exhaustion gene signature. Elevated SUVMax identified immune-related transcriptomic signatures that were associated with enhanced tumor glycolytic gene expression and poor clinical outcomes. Our results suggest that 18F-FDG SUVMax has potential value as a noninvasive, clinical indicator of tumor immunometabolic phenotypes in patients with resectable NSCLC and warrants investigation as a potential predictor of therapeutic response to immune-based treatment strategies.
Facultative brood parasitism by an American Robin (Turdus migratorius) in the nest of a Gray Catbird (Dumetella carolinensis)

Avian brood parasites can be classified as either obligate or facultative. Obligate brood parasites, such as Brown-headed Cowbirds (Molothrus ater), must lay their eggs in the nests of other species because they exhibit no parental care. Although facultative brood parasitism, when species that would normally lay eggs in their own nests dump eggs in the nest of another individual, may occur frequently among conspecifics, facultative interspecific brood parasitism is relatively rare. Here I report on observations made during the breeding season of 2018 of an example of facultative brood parasitism by an American Robin (Turdus migratorius) in the nest of a Gray Catbird (Dumetella carolinensis). Two robin eggs were laid in the nest of the catbird and were successfully raised by the catbird to fledging age. Although the young of obligate brood parasitic cowbirds are rarely raised successfully by catbirds, this is the first documented example, of which I am aware, of a Gray Catbird successfully raising the young of a facultative brood parasite.
A Neurochemical Recording Microsystem with Analog Background Current Subtraction and 400V/s FSCV Sensing Using a 1 st -Order ΔΣM

This paper reports on a new neurochemical recording microsystem that employs 400V/s fast-scan cyclic voltammetry (FSCV) at a carbon-fiber microelectrode (CFM). Featuring analog background current subtraction in situ to reduce the requisite input dynamic range of the sensing front-end, this design employs a 1st-order, continuous-time, delta-sigma modulator (ΔΣM) with 1b quantization clocked at a frequency of 1.6MHz. The analog building blocks of the microsystem are fabricated in TSMC 0.18μm 1P/6M CMOS, while the digital blocks such as memories, decimation filter, and control units are implemented on a field-programmable gate array (FPGA). Experimental results from flow injection analysis (FIA) tests show a highly linear response (r2 = 0.988) in calibration curve for dopamine with a measured sensitivity of ~35.9nA/μM for dopamine concentration levels in the range of 0–1μM.
Modeling for Hybrid and Electric Vehicles Using Simscape

Abstract Automobiles have played an important role in the shaping of the human civilization for over a century and continue to play a crucial role today. The design, construction, and performance o...
ReflectNet - A Generative Adversarial Method for Single Image Reflection Suppression.

Taking pictures through glass windows almost always produces undesired reflections that degrade the quality of the photo. The ill-posed nature of the reflection removal problem reached the attention of many researchers for more than decades. The main challenge of this problem is the lack of real training data and the necessity of generating realistic synthetic data. In this paper, we proposed a single image reflection removal method based on context understanding modules and adversarial training to efficiently restore the transmission layer without reflection. We also propose a complex data generation model in order to create a large training set with various type of reflections. Our proposed reflection removal method outperforms state-of-the-art methods in terms of PSNR and SSIM on the SIR benchmark dataset.
VIN: Voxel-based Implicit Network for Joint 3D Object Detection and Segmentation for Lidars.

A unified neural network structure is presented for joint 3D object detection and point cloud segmentation in this paper. We leverage rich supervision from both detection and segmentation labels rather than using just one of them. In addition, an extension based on single-stage object detectors is proposed based on the implicit function widely used in 3D scene and object understanding. The extension branch takes the final feature map from the object detection module as input, and produces an implicit function that generates semantic distribution for each point for its corresponding voxel center. We demonstrated the performance of our structure on nuScenes-lidarseg, a large-scale outdoor dataset. Our solution achieves competitive results against state-of-the-art methods in both 3D object detection and point cloud segmentation with little additional computation load compared with object detection solutions. The capability of efficient weakly supervision semantic segmentation of the proposed method is also validated by experiments.
Machine learning models compared to existing criteria for noninvasive prediction of endoscopic retrograde cholangiopancreatography-confirmed choledocholithiasis

Abstract Background and aims Noninvasive predictors of choledocholithiasis have generally exhibited marginal performance characteristics. We aimed to identify noninvasive independent predictors of endoscopic retrograde cholangiopancreatography (ERCP)-confirmed choledocholithiasis and accordingly developed predictive machine learning models (MLMs). Methods Clinical data of consecutive patients undergoing first-ever ERCP for suspected choledocholithiasis from 2015 to 2019 were abstracted from a prospectively-maintained database. Multiple logistic regression was used to identify predictors of ERCP-confirmed choledocholithiasis. MLMs were then trained to predict ERCP-confirmed choledocholithiasis using pre-ERCP ultrasound (US) imaging only as well as using all available noninvasive imaging (US, computed tomography, and/or magnetic resonance cholangiopancreatography). The diagnostic performance of American Society for Gastrointestinal Endoscopy (ASGE) “high-likelihood” criteria was compared to MLMs. Results We identified 270 patients (mean age 46 years, 62.2% female, 73.7% Hispanic/Latino, 59% with noninvasive imaging positive for choledocholithiasis) with native papilla who underwent ERCP for suspected choledocholithiasis, of whom 230 (85.2%) were found to have ERCP-confirmed choledocholithiasis. Logistic regression identified choledocholithiasis on noninvasive imaging (odds ratio (OR) = 3.045, P = 0.004) and common bile duct (CBD) diameter on noninvasive imaging (OR = 1.157, P = 0.011) as predictors of ERCP-confirmed choledocholithiasis. Among the various MLMs trained, the random forest-based MLM performed best; sensitivity was 61.4% and 77.3% and specificity was 100% and 75.0%, using US-only and using all available imaging, respectively. ASGE high-likelihood criteria demonstrated sensitivity of 90.9% and specificity of 25.0%; using cut-points achieving this specificity, MLMs achieved sensitivity up to 97.7%. Conclusions MLMs using age, sex, race/ethnicity, presence of diabetes, fever, body mass index (BMI), total bilirubin, maximum CBD diameter, and choledocholithiasis on pre-ERCP noninvasive imaging predict ERCP-confirmed choledocholithiasis with good sensitivity and specificity and outperform the ASGE criteria for patients with suspected choledocholithiasis.
An Empirical Algorithm for Mitigating the Sea Ice Effect in SMAP Radiometer for Sea Surface Salinity Retrieval in the Arctic Seas

The L-band radiometer onboard the Soil Moisture Active Passive (SMAP mission is used to retrieve sea surface salinity (SSS over global ocean. In the Arctic seas, one of the major challenges of SSS remote sensing is the presence of sea ice. This paper proposes a data-driven ice correction (IC algorithm which extracts emission from the water portion of measured brightness temperature (TB in scenes mixed with water and ice. Emission of the ice portion was removed based on estimation according to the ice fraction (fice in the satellite footprint and ice signature derived from surrounding pixels. The IC algorithm is applied to SMAP TB data to obtain TB with ice correction (TBIC, which are used for SSS retrieval using the standard JPL SMAP CAP processing system. We show that the algorithm is most effective near the ice edge, thereby increasing the fice threshold for possible SSS retrieval to 15% from the current 3% without IC. SMAP SSS are validated using in situ salinity collected during NASAs Ocean Melting Greenland (OMG mission from 2016 to 2020 along the Greenland coast. The number of collocations between OMG and SMAP daily gridded salinity increased by more than 30% with IC. The statistical analysis shows a similar retrieval accuracy with or without IC, with the standard deviation of the difference between OMG and SMAP of 1.41 psu (with IC and 1.42 psu (without IC . The bias adjusted SMAP SSS depicts salinity patterns and gradients around Greenland consistent with OMG measurements.
Chapter 14 formulation of oceanic general circulation models

Models of the oceanic general circulation are currently in a phase of rapid development and expanding utilization. This chapter provides an overview of the formulation of oceanic general circulation models (OGCMs). OGCMs are numerical models that include all of the major influences on the general circulation, constrained by limitations of formulation of the model and the available computing power. OGCMs have wind, heat, and water forcing; geographically correct domain geometry; and the equation of state for seawater—all with their inescapable approximations. The primary challenges are to extend and refine the modeling choices and to expand the observational system to reduce the empirical uncertainties for testing the models. The goal is to achieve a useful degree of consistency between OGCM solution behaviors and nature. OGCMs are used to explore hypothetical realities, such as the ocean circulation of ancient earth epocs, the consequences of deliberate biological fertilization of the oceans, or future climates under alternative planetary management strategies.
Design Criteria in Architecture

In Chapter 12 I contrasted criteria for successful design in architecture with that in engineering. I argued there, among other things, that with the advent of “postmodern historicism” in architecture, beginning in the 1970s with the work of Venturi, there ceased to be operative criteria to evaluate architectural design and I made a first step towards outlining what such criteria might look like in the current age.
Exploring genomic medicine using integrative biology

Instead of focusing on the cell, or the genotype, or on any single measurement modality, using integrative biology allows us to think holistically and horizontally. A disease like diabetes can lead to myocardial infarction, nephropathy, and neuropathy; to study diabetes in genomic medicine would require reasoning from a disease to all its various complications to the genome and back. I am studying the process of intersecting nearly-comprehensive data sets in molecular biology, across three representative modalities (microarrays, RNAi and quantitative trait loci) out of the more than 30 available today. This is difficult because the semantics and context of each experiment performed becomes more important, necessitating a detailed knowledge about the biological domain. I addressed this problem by using all public microarray data from NIH, unifying 50 million expression measurements with standard gene identifiers and representing the experimental context of each using the Unified Medical Language System, a vocabulary of over 1 million concepts. I created an automated system to join data sets related by experimental context. I evaluated this system by finding genes significantly involved in multiple experiments directly and indirectly related to diabetes and adipogenesis and found genes known to be involved in these diseases and processes. As a model first step into integrative biology, I then took known quantitative trait loci in the rat involved in glucose metabolism and build an expert system to explain possible biological mechanisms for these genetic data using the modeled genomic data. The system I have created can link diseases from the ICD-9 billing code level down to the genetic, genomic, and molecular level. In a sense, this is the first automated system built to study the new field of genomic medicine. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)