cssi/SciSciGPT-SciSciNet huggingface dataset:
Guest editorial: special issue on socially assistive robotics

Welcome to the Autonomous Robots special issue on the emerging area of Socially Assistive Robotics (SAR). What is SAR? Socially assistive robotics focuses on providing assistance through social rather than physical interaction between the robot and the human user. SAR has the potential to enhance human quality of life for large user populations, including the elderly, people with physical impairments, those involved in rehabilitation therapy (e.g., post-stroke patients), and people with cognitive disabilities and social and developmental disorders (e.g., children with autism spectrum disorder, children with attention deficit/hyperactivity disorder (AD/HD)). Socially assistive robotics has a great variety of potential uses and associated multi-faceted research and usability challenges. Numerous interesting questions and issues need to be addressed as we aim toward including robust, reliable, user-friendly, empathetic, and encouraging robots in our daily lives. Those questions include: “What are the circumstances in which people (especially those with special needs) accept an assistive robot in their environment?” “What modes of communication should the robot employ?” “What is the role of the robot’s physical embodiment?” “How to integrate the a priori knowledge about the users into the robot system?” “How can the human-robot interaction design ensure safety?” and “How are friendly, familiar, usable, and effective interaction models with a robot to be designed?”
Endoscopic cicatrectomy for corrosive esophageal strictures just below the piriform fossa

Corrosive esophageal strictures have been primarily treated using balloon dilatation or endoscopic bougienage. However, many patients experience recurrence after dilatation, and surgical interventions such as esophageal replacement have been attempted. We have performed endoscopic cicatrectomy using a laryngoscope for corrosive esophageal stricture just below the piriform fossa to minimize surgical invasiveness. In this case reported, repeated balloon dilatation therapy failed, and the combination of endoscopic cicatrectomy and intralesional triamcinolone acetonide injections proved most effective even though multiple cicatrectomies were required. If esophageal strictures are close to the piriform fossa, endoscopic cicatrectomy could be one useful surgical option.
Immunity against cancer: lessons learned from melanoma.

Abstract Most major advances in human cancer immunology and immunotherapy have come from studies in melanoma. We are beginning to understand the immune repertoire of T cells and antibodies that are active against melanoma, with recent glimpses of the CD4+ T cell repertoire. The view of what the immune system can see is extending to mutations and parts of the genome that are normally invisible.
Prospective, 10-year evaluation of the impact of Hispanic ethnicity on pain management practices in the ED

Abstract Introduction Hispanic ethnicity has been reported as an independent risk factor for oligoanalgesia in the emergency department (ED). Objectives The objectives are to compare pain management practices in White and Hispanic patients in the ED to determine whether treatment differences exist. Methods Prospective analysis of a convenience sample of patients presenting to an urban, academic, tertiary-care ED over the 10-year period from 2000 to 2010. We compared patients with pain-related complaints of any nature, who self-identified their race as White or Hispanic, and evaluated initial morphine administration/dosing, arrival/disposition pain scores, and overall ED satisfaction scores (0-10 scale). Results Fifteen thousand sixty patients were enrolled. Eighty-one point 2 percent (n, 12 232) of the patients were White and 11.2% (n, 1680), Hispanic. White and Hispanic patients reported similar pain at presentation (6.7 vs 7.3, P P = .14). Hispanic patients were not less likely to receive an analgesic during the ED visit (odds ratio, 1.06; confidence interval, 0.96-1.17; P = .62), nor less likely to receive an opioid analgesic (odds ratio, 0.97; confidence interval, 0.88-1.08; P = .70). Hispanic patients, on average, received similar initial doses of morphine (4.1 vs 4.3 mg, P = .29) and had similar wait times from arrival to initial dose of morphine (82 vs 86 minutes). Overall ED satisfaction scores were the same (8.7 vs 8.7, P = .65). Conclusion White and Hispanic patients were similar in rates of initial morphine administration for pain-related complaints. These findings contrast with previous studies reporting lower rates of initial analgesia administration among Hispanic patients in the ED.
A simple model of real-time flow aggregation

The IETF's Integrated Services (IntServ) architecture together with reservation aggregation provide a mechanism to support the quality-of-service demands of real-time flows in a scalable way, i.e., without requiring that each router be signaled with the arrival or departure of each new flow for which it will forward data. However, reserving resources in "bulk" implies that the reservation will not precisely match the true demand. Consequently, if the flows' demanded bandwidth varies rapidly and dramatically, aggregation can incur significant performance penalties of underutilization and unnecessarily rejected flows. On the other hand, if demand varies moderately and at slower time scales, aggregation can provide an accurate and scalable approximation to IntServ. In this paper, we develop a simple analytical model and perform extensive trace-driven simulations to explore the effectiveness of aggregation under a broad class of factors. Example findings include: 1) a simple single-time-scale model with random noise can capture the essential behavior of surprisingly complex scenarios; and 2) with a two-order-of-magnitude separation between the dominant time scale of demand and the time scale of signaling and moderate levels of secondary noise, aggregation achieves performance that closely approximates that of IntServ.
Latino/a Student Racial and Ethnic Identity Development

Citation only. Presentation at the National Association of Student Personnel Administrators Annual Conference, Tampa, FL.
Diazonium (perfluoroalkyl) arylsulfonylimide zwitterionic monomer analogues: Effective synthesis and thermal stability

Abstract It is very promising to introduce diazonium moiety into Nafion monomer based Diazonium (Perfluoroalkyl) Arylsufonylimide (PFSI) monomers for further polymerization and chemical grafting onto carbon electrodes as innovative electrolyte materials in the Proton Exchange Membrane (PEM) fuel cells. The PFSI polymers, more proton conductive and stable at high temperatures, can dramatically increase the stability and lifetime of the PEM fuel cells, compared to widely used perfluorosulfuric acid (PFSA) polymers. This paper presents such a straightforward methodology to optimally construct a new nafion based diazonium PFSI monomer analogue, 2-diazonium 4-(trifluoromethyl) perfluoro-3, 6-dioxa-4-methyl-7-octene benzenesulfonylimide II . New approaches have been investigated to dramatically increase the percent yield for another monomer I , 4-diazonium perfluoro-3, 6-dioxa-4-methyl-7-octene benzenesulfonylimide. The thermal stability of the two monomer analogues then have been measured and compared. Another monomer analogue, 4-diazonium-3-fluoro perfluoro-3, 6-dioxa-4-methyl-7-octene benzenesulfonylimide III , has been attempted and discussed.
Stochastic Control of the Activated Sludge Process

A stochastic optimal control method is introduced and applied to the real-time management of an activated sludge process. The method includes a detailed dynamic process model and accounts for input uncertainty. The objective is to minimize the expected variations of effluent organic concentrations and is met by manipulating process flowrates. The method is applied to a hypothetical case study.
Factors that bring meaning to mementos created by elders.

ABSTRACTObjectives: Reminiscing activity groups are commonly seen in various elder care settings This study addresses the impact of reminiscence activity groups, specifically a program where group members create their own mementos, on healthy Jewish elders’ sense of satisfaction and meaning. In particular, this research focused on the specific factors involved in creating the mementos themselves.Method: In this mixed methods study, occupational therapy graduate students synthesized relevant aspects of commonly used activity analysis forms into a matrix to analyze the activities. From a pool of 30 activities, students chose seven representing many factors and levels of complexity. With a matrix composed of a Likert scale and open-ended questions, students and Jewish elders explored the elders’ perceptions of factors significantly related to their experiences when creating the seven mementos.Results: Memento-making was most satisfying when elders were replicated in some way, such as with hand casting. Least...
Adult human metapneumonovirus (hMPV) pneumonia mimicking Legionnaire's disease

In adults hospitalized with viral pneumonias the main differential diagnostic consideration is influenza pneumonia. The respiratory viruses causing viral influenza like illnesses (ILIs), e.g., RSV may closely resemble influenza. Rarely, extrapulmonary findings of some ILIs may resemble Legionnaire's disease (LD), e.g., adenovirus, human parainfluenza virus (HPIV-3). We present a most unusual case of human metapneumonovirus pneumonia (hMPV) with some characteristic extrapulmonary findings characteristic of LD, e.g., relative bradycardia, as well as mildly elevated serum transaminases and hyphosphatemia. We believe this is the first reported case of hMPV pneumonia in a hospitalized adult that had some features of LD.
SEDIMENT LOAD UNDER WAVES AND CURRENTS

A technique is proposed for calculating sediment load, the mass concentration of sediment in motion, under combinations of waves and currents. The technique is based on the unidirectional flow method of Ackers and White, Ref. 1. The calibration of the technique against measurements of sediment load under waves has only just begun.
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

Large-scale sequencing in the 1000 Genomes Project has revealed multitudes of single nucleotide variants (SNVs). Here, we provide insights into the functional effect of these variants using allele-specific behaviour. This can be assessed for an individual by mapping ChIP-seq and RNA-seq reads to a personal genome, and then measuring 'allelic imbalances' between the numbers of reads mapped to the paternal and maternal chromosomes. We annotate variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias. Since many allelic variants are rare, aggregation across multiple individuals is necessary to identify broadly applicable 'allelic elements'. We also found SNVs for which we can anticipate allelic imbalance from the disruption of a binding motif. Our results serve as an allele-specific annotation for the 1000 Genomes variant catalogue and are distributed as an online resource (alleledb.gersteinlab.org).
Improving care with an automated patient history.

The best way to fill your EHR with patient data might be to let your patients do it themselves.
Avatars of desire and the question of presence: Virtual and transitional spaces meet their liminal edge - from Pygmalion to Spike Jonze's Her, and beyond….

There is a poignant strangeness to Spike Jonze's movie Her (2013); we resonate with the characters' clumsiness in trying to reach one another, each an avatar to the other's desire. The movie is an ...
Anti-Leukemia Immune Responses in CML Patients Treated with Imatinib Mesylate.

Imatinib mesylate, a selective inhibitor of the bcr/abl tyrosine kinase, has revolutionized the treatment of patients with chronic myelogenous leukemia (CML). Most CML patients in chronic phase achieve hematologic remission with imatinib, while some achieve cytogenetic remission. As imatinib is an oral agent with few side effects, it has rapidly become the first-line therapy for most CML patients. However, this therapy does not represent a cure, as patients who discontinue the drug invariably relapse. Furthermore, imatinib resistance is beginning to emerge in some patients. Hence, the need to find alternate, potentially curative, therapies for CML remains. To date, the only curative treatment for CML is allogeneic bone marrow or stem cell transplantation (ABMT). A major mechanism of the curative potential of ABMT is immunological, as evidenced by the poor clinical outcome with T cell-depleted ABMT, and the efficacy of donor lymphocyte infusions (DLI) upon relapse. We hypothesized that an effective anti-leukemia immune response may emerge in patients entering remission on imatinib which may contribute to its clinical effectiveness. If so, strategies to further enhance this anti-leukemia immune response may lead to a potential cure. To determine if CML patients in remission on imatinib develop anti-leukemia immune responses, blood and bone marrow samples from patients before and after treatment were collected and analyzed. Pre-treatment samples were utilized as sources of autologous leukemic cells to detect anti-leukemia immune responses in post-treatment samples in IFN-g ELISPOT assays. Pre-treatment samples alone, post-treatment samples alone, and when available, serial post-treatment samples mixed together served as controls. In 9 of 14 patients investigated, IFN-g release was detected in pre- and post-treatment samples together with a median response of 22 spots above background (range 10 – 56 dots, p
Mixed neuropathologies and estimated rates of clinical progression in a large autopsy sample

Abstract Introduction Whether co-occurring neuropathologies interact or independently affect clinical disease progression is uncertain. We estimated rates of clinical progression and tested whether associations between clinical progression and Alzheimer's disease neuropathology (ADNP) were modified by co-occurring Lewy body disease (LBD) or vascular brain injury (VBI). Methods Linear mixed effects models evaluated longitudinal trends in the Clinical Dementia Rating Scale Sum of Boxes on 2046 autopsied participants seen at a U.S. Alzheimer's Disease Center. Results Annual clinical progression was slightly faster for ADNP + LBD compared with ADNP only ( P = .06) and slightly slower for ADNP + VBI ( P = .003). Differences in progression were less than expected if each neuropathology independently contributed to progression; ADNP interacted with LBD ( P = .002) and VBI ( P = .003). In secondary models, the effect of additional pathologies on clinical progression was greater in those with intermediate compared with high levels of ADNP. Discussion The impact of co-occurring pathologies on progression may depend on severity of ADNP.
Pregnancy Intention: How PRAMS Data Can Inform Programs and Policy

Background: In most states, the Pregnancy Risk Assessment Monitoring System (PRAMS) is the only source for state-specific, population-based data on the prevalence of unintended pregnancy among women having a live birth. These data can be used in a variety of ways to inform state policies and programs aimed at the prevention of unintended pregnancy. Objectives: This paper highlights the programmatic and policy development activities undertaken by three states in relation to unintended pregnancy as well as the role that PRAMS data played in those efforts. Results: Georgia, Oklahoma, and Washington have used PRAMS data to gain support for program initiatives directed at unintended pregnancy, to promote policies aimed at either monitoring or reducing unintended pregnancy, and to acquire additional funds for related programs, such as family planning.
Repeatability of SUV in oncologic 18F-FDG PET

Quantitative analysis can potentially improve the accuracy and consistency of 18F-FDG PET, particularly for the assessment of tumor response to treatment. Although not without limitations, SUV has emerged as the predominant metric for tumor quantification with 18F-FDG PET. Growing literature suggests that the difference between SUVs measured before and after treatment can be used to predict tumor response at an early stage. SUV is, however, associated with multiple sources of variability, and to best use SUV for response assessment, an understanding of the repeatability of the technique is required. Test-retest studies involve repeated scanning of the same patient on the same scanner using the same protocol no more than a few days apart and provide basic information on the repeatability of the technique. Multiple test-retest studies have been performed to assess SUV repeatability, although a comparison of reports is complicated by the use of different methodologies and statistical metrics. This article reviews the available data, addressing issues such as different repeatability metrics, relative units, log transformation, and asymmetric limits of repeatability. When acquired with careful attention to protocol, tumor SUV has a within-subject coefficient of variation of approximately 10%. In a response assessment setting, SUV reductions of more than 25% and increases of more than 33% are unlikely to be due to measurement variability. Broader margins may be required for sites with less rigorous protocol compliance, but in general, SUV is a highly repeatable imaging biomarker that is ideally suited to monitoring tumor response to treatment in individual patients.
Sufficient conditions for weak reciprocal upper semi-continuity in mixed extensions of games

Abstract We provide sufficient conditions for a game with discontinuous payoffs to be weakly reciprocally upper semi-continuous in mixed strategies. These conditions are imposed on the individual payoffs and not on their sum, and they can be readily verified in a large class of games even when the sum of payoffs in such games is not upper semi-continuous. We apply our result to establish the existence of mixed strategy equilibria in probabilistic voting competitions where candidates have very general utility functions as well as heterogeneous beliefs about the distribution of the voters.
In-plane Thermal Conductivity Measurement with Nanosecond Grating Imaging Technique

We develop a nanosecond grating imaging (NGI) technique to measure in-plane thermal transport properties in bulk and thin-film samples. Based on nanosecond time-domain thermoreflectance (ns-TDTR), ...
The Parenchyma Accompanying Major Extraglandular Ducts within the Rat Lacrimal Cord

While investigating regional differences in the duct-containing cord joining the rat exorbital lacrimal gland and conjunctiva (Fig. 1A), it was noted that some specimens also contained small masses of parenchyma (Fig. 1B). This study is concerned with the distribution and histological appearance of this cordal lacrimal tissue.
Mapping Transcription Factors on Extended DNA: A Single Molecule Approach

The ability to determine the precise loci and distribution of nucleic acid binding proteins is instrumental to our detailed understanding of cellular processes such as transcription, replication, and chromatin reorganization. Traditional molecular biology approaches and above all Chromatin immunoprecipitation (ChIP) based methods have provided a wealth of information regarding protein–DNA interactions. Nevertheless, existing techniques can only provide average properties of these interactions, since they are based on the accumulation of data from numerous protein–DNA complexes analyzed at the ensemble level. We propose a single molecule approach for direct visualization of DNA binding proteins bound specifically to their recognition sites along a long stretch of DNA such as genomic DNA. Fluorescent Quantum dots are used to tag proteins bound to DNA, and the complex is deposited on a glass substrate by extending the DNA to a linear form. The sample is then imaged optically to determine the precise location of the protein binding site. The method is demonstrated by detecting individual, Quantum dot tagged T7-RNA polymerase enzymes on the bacteriophage T7 genomic DNA and assessing the relative occupancy of the different promoters.
Awareness of what is learned as a characteristic of hippocampus-dependent memory

We explored the relationship between memory performance and conscious knowledge (or awareness) of what has been learned in memory-impaired patients with hippocampal lesions or larger medial temporal lesions. Participants viewed familiar scenes or familiar scenes where a change had been introduced. Patients identified many fewer of the changes than controls. Across all of the scenes, controls preferentially directed their gaze toward the regions that had been changed whenever they had what we term robust knowledge about the change: They could identify that a change occurred, report what had changed, and indicate where the change occurred. Preferential looking did not occur when they were unaware of the change or had only partial knowledge about it. The patients, overall, did not direct their gaze toward the regions that had been changed, but on the few occasions when they had robust knowledge about the change they (like controls) did exhibit this effect. Patients did not exhibit this effect when they were unaware of the change or had partial knowledge. The findings support the idea that awareness of what has been learned is a key feature of hippocampus-dependent memory.
Analyze a Published Research Study: An Assignment to Scaffold Reading Challenging Academic Texts

"Analyze a Published Research Study" invites students to examine a published study's research methods to learn not only what a research report says, but also how the research was designed, carried out, and communicated. While this writing assignment was originally designed for an undergraduate course on research practices in literacy and composition, it may be used with both undergraduate and graduate students and may be appropriate for courses across the disciplines in which students study methods of scholarship. The primary goal of this assignment is to use writing as a mode of learning how to read scholarly research.
Effect of insonation angle on peak systolic velocity variation

Abstract Objectives As point of care ultrasound (POCUS) has become more integrated into emergency and critical care medicine, there has been increased interest in utilizing ultrasound to assess volume status. However, recent studies of carotid POCUS on volume status and fluid responsiveness fail to recognize the effect insonation angle has on their results. To address this, we studied the effect of insonation angle on peak systolic velocity (PSV) change associated with respiratory variation (RV) and passive leg raise (PLR). Methods Doppler measurements were obtained from 51 subjects presenting to the ED. Minimal and maximal PSV were obtained using insonation angles of 46°, 60°, and 90°. ∆PSV was calculated using PLR and RV as trial methods. Results were categorized into two groups, those with a ∆PSV > 10% and those with a ∆PSV ≤ 10%. ∆PSV mean and standard error, as well as measures of agreement were calculated. Results Mean ∆PSV associated with PLR test was 9% in the 46° and 60° groups, and 18% in the 90° group, with standard errors of 6, 7, and 14%, respectively. Using 46° as our relative gold standard, Kappa was 0.23 at 60° and 0.11 at 90° with RV as the trial method, and 0.23 at 60° and 0.01 at 90° with a PLR as the trial method. Conclusions Variation in PSV is heavily dependent on insonation angle. There was only slight to fair agreement in ∆PSV among the various insonation angles. Further investigation of the optimal insonation angle to assess ∆PSV should be undertaken.
Nonalcoholic fatty liver disease alters microcystin-LR toxicokinetics and acute toxicity.

Abstract Microcystin-LR (MCLR) is a cyanotoxin produced by blue-green algae that causes liver and kidney toxicities. MCLR toxicity is dependent on cellular uptake through the organic anion transporting polypeptide (OATP) transporters. Nonalcoholic fatty liver disease (NAFLD) progresses through multiple stages, alters expression of hepatic OATPs, and is associated with chronic kidney disease. The purpose of this study was to determine whether NAFLD increases systemic exposure to MCLR and influences acute liver and kidney toxicities. Rats were fed a control diet or two dietary models of NAFLD; methionine and choline deficient (MCD) or high fat/high cholesterol (HFHC). Two studies were performed in these groups: 1) a single dose intravenous toxicokinetic study (20 μg/kg), and 2) a single dose intraperitoneal toxicity study (60 μg/kg). Compared to control rats, plasma MCLR area under the concentration-time curve (AUC) in MCD rats doubled, whereas biliary clearance (Clbil) was unchanged; in contrast, plasma AUC in HFHC rats was unchanged, whereas Clbil approximately doubled. Less MCLR bound to PP2A was observed in the liver of MCD rats. This shift in exposure decreased the severity of liver pathology only in the MCD rats after a single toxic dose of MCLR (60 μg/kg). In contrast, the single toxic dose of MCLR increased hepatic inflammation, plasma cholesterol, proteinuria, and urinary KIM1 in HFHC rats more than MCLR exposed control rats. In conclusion, rodent models of NAFLD alter MCLR toxicokinetics and acute toxicity and may have implications for liver and kidney pathologies in NAFLD patients.
Abstract 344: Kruppel-like Factor 15: A Critical Transcriptional Regulator of Hypoxia Induced Endothelial Arginase 2

Objective: Kruppel Like Factor 15 has recently been shown to be critical for activation of proinflammatory processes in vascular smooth muscle and atherogenesis. Although KLF15 is abundantly expres...
On Studying Information Dissemination in Social-Physical Interdependent Networks

Most existing studies for information dissemination in the online social network are based on variations of the classical epidemic model. In such a model, nodes recursively infect, or share information to, their neighboring nodes with a certain probability. The higher degree a node has, the more likely it gets infected by its neighbors. Although widely accepted, we found there are certain discrepancies between existing epidemic models and social interactions in reality. Firstly, the real-world social network is actually a dual-layered network, where a person shares information online to her online friends, and also offline to her real-life friends. More importantly, since a computer do not automatically share information, a computer exposed to information will not effectively receive it (i.e., getting infected and starting to infect others) unless its user receives it. Secondly, contrary to the epidemic model, the more friends a person has, the less likely she is going to effectively receive a certain piece of message (just imagine how easily a message can be flushed and ignored by a human user because of overwhelming newer information). In other words, in social networks, the infection rate of a node may not be positively correlated with its degree. Based on these observations, we develop the social-physical interdependent (SPI) model to capture and analyze the unique characters of social networks. Our study provides new observations, and sheds light on a new direction for the study of information dissemination in social networks.
The "Last Child": Lone Family Caregivers in St. Croix, US Virgin Islands.

I investigate local explanations for a common family configuration of care for older relatives on the island of St. Croix, U.S. Virgin Islands: the “lone family caregiver.” Through the examination ...
Plate tectonics and surface environment: Role of the oceanic upper mantle

Abstract Earth is so far the only planet that exhibits plate tectonics, and along with the right heliocentric distance and the presence of surface water, plate tectonics is among necessary conditions for a habitable planet. Yet, the physics of this particular style of mantle convection is poorly understood, creating a substantial bottleneck in developing the general theory of planetary evolution. As plate tectonics is characterized by the subduction of oceanic lithosphere, a better understanding of the oceanic upper mantle could potentially help to break this stalemate. In this review, I summarize available theoretical, observational, and experimental constraints on the evolution of the oceanic upper mantle and its rheology, place the study of the oceanic upper mantle in the big picture of Earth evolution, and provide some suggestions for future research in relevant disciplines, including marine geophysics and computational geodynamics.
Revisiting nutrition backlash: Psychometric properties and discriminant validity of the nutrition backlash scale.

Abstract Objectives Nutrition backlash is a disposition defined by negative feelings about dietary recommendations. Past research has measured nutrition backlash using the nutrition backlash scale (NBS) and found that it is negatively related to the consumption of fruits and vegetables. The aim of this study was to examine several aspects of the NBS, including factor structure, discriminant validity, and relationship to demographic characteristics and health behaviors. Methods Adults were recruited to participate in two studies. Study 1 (N = 480) included measures of nutritional backlash, information overload, worry, fatalism, and nutrition-related behaviors. Study 2 (N = 399) was a follow-up that examined the factor structure of the NBS in a separate sample. Results In study 1, a six-item version of the NBS was found to be a good fit for the data and discriminant from overload, worry, and fatalism. NBS was higher for those with less education, non-white participants, and men. Individuals with higher backlash were less likely to look at nutritional labels and to use sunscreen. Study 2 confirmed the factor structure from study 1. Conclusions A six-item version of the NBS was found to be reliable, discriminant from related measures, higher in underserved groups (less-educated, non-white, and male participants), and related to nutrition label use.
Aged Breast Extracellular Matrix Drives Mammary Epithelial Cells to an Invasive and Cancer-Like Phenotype

Age is a major risk factor for cancer. While the importance of age related genetic alterations in cells on cancer progression is well documented, the effect of aging extracellular matrix (ECM) has been overlooked. Here, we show for the first time that the aging breast ECM is sufficient to drive normal mammary epithelial cells (KTB21) to a more invasive and cancer-like phenotype, while promoting motility and invasiveness in MDA-MB-231 cells. E-cadherin membrane localization was lost in KTB21 cells cultured on the decellularized breast matrix from aged mice. Cell motility, cell invasion, and inflammatory cytokine and cancer-related protein production were increased significantly on the aged matrix, and many genes related to invasion were upregulated. Strikingly, we showed using single cell RNA sequencing that the aged matrix led to enrichment of a subpopulation of KTB21 cells that highly expressed epithelial-mesenchymal transition (EMT) and invasion-related genes. Lysyl oxidase (LOX) knockdown reverted the aged matrix-induced changes to the young levels; LOX siRNA treatment prevented the loss of E-cadherin membrane localization, and reduced cell motility, cell invasion, and cytokine and cancer-related protein production. Finally, we showed that the biophysical, mechanical and biochemical properties of the breast ECM were altered dramatically upon aging. Analyzing these factors and studying the differential response of the epithelial cells to young and aged ECMs could lead to identification of new targets for cancer treatment and could pave the way for the discovery of new therapeutic options.
THE EVOLUTIONARY ECOLOGY OF YEASTS FOUND IN THE DECAYING STEMS OF CACTI

ABSTRACT Cactus-specific yeast communities are studied with respect to the evolutionary divergence of their host plants. The phyletic division of the host plants is shown to influence the proportions of the yeasts in the communities. In addition the physiological attributes of the yeasts, as determined by the taxonomy, is also shown to be a function of the relationships of the host plants. Specific genetic changes experienced by the yeasts are related to the host plant divergence. These genetic differences are most likely associated with membrane associated phenomenon. KEYWORDS Yeast, cactus, Drosophila , physiological adaptation, host specificity, evolutionary genetics, triterpene glycosides, community structure, speciation.
The brain-gut axis: A prime therapeutic target in traumatic brain injury.

Abstract Traumatic brain injury (TBI) is a significant cause of morbidity and mortality in trauma patients. The primary focus of treating TBI is to prevent additional injury to the damaged brain tissue, known as secondary brain injury. This treatment can include treating the body’s inflammatory response. Despite promise in animal models, anti-inflammatory therapy has failed to improve outcomes in human patients, suggesting a more targeted and precise approach may be needed. There is a bidirectional axis between the intestine and the brain that contributes to this inflammation in acute and chronic injury. The mechanisms for this interaction are not completely understood, but there is evidence that neural, inflammatory, endocrine, and microbiome signals all participate in this process. Therapies that target the intestine as a source of inflammation have potential to lessen secondary brain injury and improve outcomes in TBI patients, but to develop these treatments we need to better understand the mechanisms behind this intestinal inflammatory response.
Classification accuracy goals for diagnostic tests based on risk stratification

In diagnostic test evaluation, performance goals are often set for classification accuracy measures such as specificity, sensitivity and diagnostic likelihood ratio. For tests that detect rare cond...
Development and characterization of composition-equivalent formulations to the Sandostatin LAR® by the solvent evaporation method

Sandostatin long-acting release® (SLAR) is a long-acting injectable somatostatin analogue formulation composed of octreotide encapsulated in glucose-initiated poly(lactic-co-glycolic acid) (PLGA) microspheres. Despite the end of patent protection, SLAR remains resistant to generic competition likely due to complexity of production process, the uniqueness of the glucose star polymer, and the instability of octreotide in the formulation. Here, we describe development of glucose-PLGA-based composition-equivalent to SLAR formulations prepared by double emulsion-solvent evaporation method and the effect of variations in encapsulation variables on release kinetics and other formulation characteristics. The following encapsulation variables were adjusted at constant theoretical loading of 7.0% peptide: PLGA concentration, pH of inner water phase, and stirring rate. After final drying, the microspheres were examined with and without annealing at 50 °C under vacuum for 3 days. The loading and encapsulation efficiency (EE) of octreotide acetate, manufacturing yield, and in vitro drug release kinetics in PBStc (10 mM phosphate-buffered saline (PBS) with 1% triethyl citrate and 0.02% sodium azide at pH 7.4) were determined by UPLC. The in vitro release and acylation kinetics of octreotide for the solvent evaporation formulations prepared were similar to SLAR although the initial burst was slightly higher. Key formulation steps identified to maximize microsphere yield and minimize residual solvent and initial burst release included (a) addition of acetic acid to the peptide before preparation and (b) annealing the microspheres under vacuum after drying. Controlled release octreotide formulations prepared and investigated in this study could provide a better understanding of the effect of production variables on release performance and supply information useful for making progress in manufacturing of SLAR generic equivalents.
Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands upon G89F mutation

Abstract Molecular interactions mediated by engagement of the Herpes virus entry mediator (HVEM) with members of TNF and Ig superfamily generate distinct signals in T cell activation pathways that modulate inflammatory and inhibitory responses. HVEM interacts with CD160 and B and T lymphocyte attenuator (BTLA), both members of the immunoglobulin (Ig) superfamily, which share a common binding site that is unique from that of LIGHT, a TNF ligand. BTLA or CD160 engagement with HVEM deliver inhibitory or stimulatory signals to the host immune response in a context dependent fashion, whereas HVEM engagement with LIGHT results in pro-inflammatory responses. We identified a mutation in human HVEM, G89F, which directly interferes with the human LIGHT interaction, but interestingly, also differentially modulates the binding of human BTLA and CD160 via an apparent allosteric mechanism involving recognition surfaces remote from the site of the mutation. Specifically, the G89F mutation enhances binding of CD160, while decreasing that of BTLA to HVEM in cell-based assays. Molecular dynamics simulations for wild-type and G89F mutant HVEM, bound to different sets of ligands, were performed to define the molecular basis of this unexpected allosteric effect. These results were leveraged to design additional human HVEM mutants with altered binding specificities.
Dynamics of prefix usage at an edge router

We investigate prefix activity on peering links between a regional Internet aggregation point and two tier-1 ISPs by analyzing a 24 hour packet trace from our regional ISP. Our data shows that a small number of prefixes carry the bulk of the packets, which corroborates previous work. However, unlike previous work, which focused on traffic from backbone routers, we look at edge traffic. In addition, we look at prefix activity at fine timescales, in the order of minutes, instead of just the aggregate view, which allows us to better understand the dynamics of prefix behavior. We define two metrics to capture the dynamic behavior of prefixes: the duty cycle captures a prefix's activity, while the mean rank difference captures how busy a prefix is. This allows us to estimate not only how much traffic a prefix carries, but also how that traffic is distributed throughout the day.We expect that our work will inform new route caching strategies (to alleviate the strain from an ever expanding global routing table) and evaluation of the performance of new routing architectures such as virtual aggregation and map-n-encap.
The anatomy of osteoarthritic joint pain

The anatomical understanding of the pain generators in osteoarthritis (OA) is incomplete and the teaching about these pain generators in medical school anatomy/histology courses is minimal. This review covers the nociceptive innervation of synovial joints for the purposes of teaching. Studies that discuss the presence of neuropeptides involved in pain, such as Substance P (SP) and calcitonin-gene-related peptide, are the focus of this review. Nociceptive free-nerve endings and SP staining nerves are found in the accessory ligaments, synovium, subchondral bone, menisci, and periosteum. The vasculature may also play a role in pain generation through vasospasm or ischemia, but this has yet to be proven. Joint denervation may relieve joint pain showing that it is indeed articular nerves that are carrying pain impulses but denervation does not identify the precise source of the pain. It remains unclear which of the anatomical loci of pain generation are primary in OA and if sources of pain vary in different patients and in different joints.
The Great Whirl: Observations of its seasonal development and interannual variability

[1] In situ measurements are used, together with sea surface height data, to study the development and variability of the Great Whirl (GW), a large quasi-stationary anticyclone that appears off the coast of Somalia during the southwest monsoon season. We find that anticyclonic circulation indicative of the GW appears on average in April, almost two months before the onset of the southwest monsoon winds. This early initiation is coincident with the arrival of annual Rossby waves at the western boundary. With the onset of the monsoon winds in early June, the GW-proper intensifies quickly, remaining at its peak throughout July, August, and September, and dissipating about one month after the winds have died. The GW is present for an average 166 ± 30 days per year and the position of its northern flank, close to 9°N, coincides with the latitude of zero wind stress curl. The intraseasonal variability of the GW is intense as a result of mutual advection with one to three flanking cyclones, which accompany the GW 70% of the time and tend to circulate clockwise around it. There is no consistent seasonal pattern for the development or dissipation of the GW, although movement to the southwest is common toward the end of the season. The GW of 1995 deepened from 200 m in June to over 1000 m in September, and strengthened from a swirl transport of 10 to 60 Sv. Cool waters in its core resulted from advection via the Somali Current and some local vertical mixing.
PBG, PMC and PEC ground planes: a case study of dipole antennas

In this paper, a comparative investigation has been conducted to study the radiation characteristics of dipole antennas above an ideal PEC (perfect electrical conductor) surface, an ideal PMC (perfect magnetic conductor) surface and a realistic metallic PBG (photonic band-gap) surface. Because of the difficulty with other methods to accurately analyze the surface wave trapped in the PBG structure and the diffraction from the edge, the finite-difference time-domain (FDTD) technique based on the Cartesian coordinate system discretization is chosen as the simulation tool. FDTD is capable of predicting the electromagnetic behavior of intricate antenna structures radiating in a complex environment. Since this technique readily handles planar conductors, thin wires and inhomogeneous dielectrics, it could be extended to analyze the effect of human tissue on the antenna structure with PBG surface.
Prevalence scaling: applications to an intelligent workstation for the diagnosis of breast cancer.

Rationale and Objectives Our goal was to investigate the effects of changes that the prevalence of cancer in a population have on the probability of malignancy (PM) output and an optimal combination of a true-positive fraction (TPF) and a false-positive fraction (FPF) of a mammographic and sonographic automatic classifier for the diagnosis of breast cancer. Materials and Methods We investigate how a prevalence-scaling transformation that is used to change the prevalence inherent in the computer estimates of the PM affects the numerical and histographic output of a previously developed multimodality intelligent workstation. Using Bayes' rule and the binormal model, we study how changes in the prevalence of cancer in the diagnostic breast population affect our computer classifiers' optimal operating points, as defined by maximizing the expected utility. Results Prevalence scaling affects the threshold at which a particular TPF and FPF pair is achieved. Tables giving the thresholds on the scaled PM estimates that result in particular pairs of TPF and FPF are presented. Histograms of PMs scaled to reflect clinically relevant prevalence values differ greatly from histograms of laboratory-designed PMs. The optimal pair (TPF, FPF) of our lower performing mammographic classifier is more sensitive to changes in clinical prevalence than that of our higher performing sonographic classifier. Conclusions Prevalence scaling can be used to change computer PM output to reflect clinically more appropriate prevalence. Relatively small changes in clinical prevalence can have large effects on the computer classifier's optimal operating point.
Tools for assembling modular ontologies in ontolingua

The Ontolingua ontology development environment provides a suite of ontology authoring tools and a library of modular, reusable ontologies. The environment is available as a World Wide Web service and has a substantial user community. The tools in Ontolingua are oriented toward the authoring of ontologies by assembling and extending ontologies obtained from a library. In this paper, we describe Ontolingua's formalism for combining the axioms, definitions, and words (non-logical symbols) of multiple ontologies. We also describe Ontolingua's facilities that enable renaming of words from multiple component ontologies and that provide unambiguous mapping between words and text strings during input and output. These features support cyclic inclusion graphs and enable users to extend ontologies in multiple ways such as adding simplifying assumptions and extending the domains of polymorphic operators.
External Validation of the Ventral Hernia Risk Score for Prediction of Surgical Site Infections

Abstract Background: Previously, we reported that the Ventral Hernia Risk Score (VHRS) was more accurate in a Veterans Affairs (VA) population in predicting surgical site infection (SSI) after open ventral hernia repair (VHR) compared with other models such as the Ventral Hernia Working Group (VHWG) model. The VHRS was developed using single-center data and stratifies SSI risk into five groups based on concomitant hernia repair, skin flaps created, American Society of Anesthesiologists (ASA) score ≥3, body mass index ≥40 kg/m2, and incision class 4. The purpose of this study was to validate the VHRS for other hospitals. Methods: A prospective database of all open VHRs performed at three institutions from 2009–2011 was utilized. All 436 patients with a follow-up of at least 1 mo were included. The U.S. Centers for Disease Control and Prevention (CDC) definition of SSI was utilized. Each patient was assigned a VHRS, VHWG, and CDC incision classification. Receiver-operating characteristic curves were used to...
The effects of lithium ions on chemical sequence of alkali-silica reaction

Abstract This paper presents the results of the investigation on the effects of Li+ ions on the chemical and physical changes in the cementitious system undergoing alkali-silica reaction (ASR). Specifically, this paper focuses on determining which chemical steps of ASR processes are affected by the presence of Li+ ions in the pore solution in order to provide better understanding of the role of Li+ ions in the mitigation process of ASR. The results presented in this paper strongly support the hypothesis that the Li+ ions facilitate the formation of a physical barrier on the surface of reactive silica, and thus prevent further attack on the reactive sites by hydroxyl ions.
Computational Simulation of Platelet Deposition and Activation: I. Model Development and Properties

To better understand the mechanisms leading to the formation and growth of mural thrombi on biomaterials, we have developed a two-dimensional computational model of platelet deposition and activation in flowing blood. The basic formulation is derived from prior work by others, with additional levels of complexity added where appropriate. It is comprised of a series of convection-diffusion-reaction equations which simulate platelet-surface and platelet-platelet adhesion, platelet activation by a weighted linear combination of agonist concentrations, agonist release and synthesis by activated platelets, platelet-phospholipid-dependent thrombin generation, and thrombin inhibition by heparin. The model requires estimation of four parameters to fit it to experimental data: shear-dependent platelet diffusivity and resting and activated platelet-surface and platelet-platelet reaction rate constants. The model is formulated to simulate a wide range of biomaterials and complex flows. In this article we present the basic model and its properties; in Part II (Sorensen et al., Ann. Biomed. Eng. 27:449–458, 1999) we apply the model to experimental results for platelet deposition onto collagen. © 1999 Biomedical Engineering Society.