cssi/SciSciGPT-SciSciNet huggingface dataset:
Accelerating Agent-Based Modeling Using Graphics Processing Units

Agent-based modeling is a disaggregated simulation approach for the exploration of complex spatial dynamics in geographic systems. The use of agent-based models for investigating social-ecological complexity in geographic systems is, however, severely hampered by the computational intensity of agent-based models. Graphics Processing Units (GPUs) are cutting-edge many-core parallel computing platforms that hold great potential in addressing this computational intensity. It is thus necessary to identify aspects that are fundamental in guiding the transformation of agent-based models into GPU environments. The objective of this paper is to identify and discuss the fundamental aspects that need to be considered when using GPUs to accelerate agent-based models. Specifically, these aspects include random number generation, parallelization of agent-based interactions, analysis of agent and environment patterns, and evaluation of computing performance. By linking with these aspects, I used a case study of modeling spatial opinion exchange to illustrate the massively parallel computing power of GPUs for accelerating agent-based modeling. Experimental results suggest that these aspects provide valuable guidance for transforming agent-based models into GPUs to best exploit massively parallel computing power. Further, these aspects are of vital importance for bridging the gap between advancement in GPUs and their applications for resolving spatiotemporal problems using agent-based modeling.
The 5' sequence of VSV viral RNA and its in vitro transcription product RNA.

Abstract The 5′ terminal sequence of vesicular stomatitis virus (VSV) RNA (pppApCpGp…) is not capped, however in the viral nucleocapsid it is protected from pancreatic ribonuclease digestion, as are most or all of the internal sequences of the viral RNA. Some of the 5′ in vitro transcription product sequences synthesized in the absence of S-adenosyl-L-methionine, SAM, are capped. In the presence of SAM those sequences which are capped, become methylated.
Response of Sea Urchin Fitness Traits to Environmental Gradients Across the Southern California Oxygen Minimum Zone

Marine calcifiers are considered to be among the most vulnerable taxa to climate-forced environmental changes occurring on continental margins with effects hypothesized to occur on microstructural, biomechanical, and geochemical properties of carbonate structures. Natural gradients in temperature, salinity, oxygen, and pH on an upwelling margin combined with the broad depth distribution (100-1100 m) of the pink fragile sea urchin, Strongylocentrotus (formerly Allocentrotus) fragilis, along the southern California shelf and slope provide an ideal system to evaluate potential effects of multiple climate variables on carbonate structures in situ. We measured for the first time trait variability across four distinct depth zones in a natural experiment to simulate species-specific implications of oxygen minimum zone (OMZ) expansion, deoxygenation and ocean acidification. Although S. fragilis may likely be tolerant of future oxygen and pH decreases predicted during the twenty-first century, we determine from adults collected across multiple depth zones that urchin size and potential reproductive fitness (gonad index) are drastically reduced in the OMZ core (450-900 m) compared to adjacent zones. Increases in porosity and mean pore size coupled with decreases in mechanical nanohardness and stiffness of the calcitic endoskeleton in individuals collected from lower pHTotal (7.57-7.59) and lower dissolved oxygen (13-42 µmol kg-1) environments suggest that S. fragilis may be potentially vulnerable to crushing predators if these conditions become more widespread in the future. In addition, elemental composition determined using inductively coupled plasma-mass spectrometry indicates that S. fragilis has a skeleton composed of the low Mg-calcite mineral phase of calcium carbonate (mean Mg/Ca= 0.02 mol mol-1), the lowest Mg/Ca values measured in sea urchins known to date. Together these findings suggest that ongoing declines in oxygen and pH will likely affect the ecology and fitness of a dominant echinoid on the California margin.
Noise Detection in Electrocardiography Signal for Robust Heart Rate Variability Analysis: A Deep Learning Approach

Heart rate variability (HRV) analysis is widely used to assess the sympathetic and parasympathetic tones. However, the quality of the derived HRV features is heavily dependent on the accuracy of QRS detection. Noisy electrocardiography (ECG) signals, such as those measured by wearable ECG patches, can lead to inaccuracies in the QRS detection and significantly impair the HRV analysis. Hence, it is critical to employ noise detection algorithms to identify the corrupted segments of the ECG signal and discard them from the analysis. This paper proposes a convolutional neural network to distinguish between usable and unusable ECG segments where usability is defined based on the accuracy of QRS detection. The results indicate that the proposed method has significantly lower error rates compared to both the baseline method (HRV analysis on the noisy signals) and a noise detection method based on four ECG signal quality indices and a support vector machines classifier.
Aberrant activity in retinal degeneration impairs central visual processing and relies on Cx36-containing gap junctions

In retinal degenerative disease (RD), the diminished light signal from dying photoreceptors has been considered the sole cause of visual impairment. Recent studies show a 10-fold increase in spontaneous activity in the RD network, challenging this paradigm. This aberrant activity forms a new barrier for the light signal, and not only exacerbates the loss of vision, but also may stand in the way of visual restoration. This activity originates in AII amacrine cells and relies on excessive activation of gap junctions. However, it remains unclear whether aberrant activity affects central visual processing and what mechanisms lead to this excessive activation of gap junctions. By combining genetic manipulation with electrophysiological recordings of light-induced activity in both living mice and isolated wholemount retina, we demonstrate that aberrant activity extends along retinotectal projections to alter activity in higher brain centers. Next, to selectively eliminate Cx36-containing gap junctions, which are the primary type expressed by AII amacrine cells, we crossed rd10 mice, a slow-degenerating model of RD, with Cx36 knockout mice. We found that retinal aberrant activity was reduced in the rd10/Cx36KO mice compared to rd10 controls, a direct evidence for involvement of Cx36-containing gap junctions in generating aberrant activity in RD. These data provide an essential support for future experiments to determine if selectively targeting these gap junctions could be a valid strategy for reducing aberrant activity and restoring light responses in RD.
Tyrosine kinase inhibitor conjugated quantum dots for non-small cell lung cancer (NSCLC) treatment.

Abstract Non-small cell lung cancer is a major sub-type of lung cancer that is associated with a poor diagnosis resulting in poor therapy for the disorder. In order to achieve a better prognosis, innovative multi-functional systems need to be developed which will aide in diagnosis as well as therapy for the disorder. One such multi-functional delivery system fabricated is Quantum Dots (QDs). QDs are photo-luminescent inorganic nanoparticles utilized for tumor detection, preclinically. Erlotinib hydrochloride, a tyrosine kinase inhibitor, is a first-generation drug developed to treat NSCLC. Its active metabolite, Desmethyl Erlotinib (OSI-420), exhibits similar anticancer activity as erlotinib. OSI-420 was conjugated to QDs to fabricate a delivery system and was then characterized by FT-IR, H NMR, UV-VIS, particle size, zeta potential, fluorescence spectroscopy and TEM. Drug loading was estimated using UV-VIS spectroscopy (52.2 ± 7.5%). A concentration-dependent release of OSI-420 was achieved using esterase enzymes, which was further confirmed using LC-MS. A cellular uptake study revealed the internalization potential of QDs and QD-OSI 420. A cellular recovery study was performed to confirm the internalization potential. Cell viability studies revealed that QD-OSI 420 conjugates had significantly better efficacy than pure drugs in all tested cell lines. QD conjugated OSI-420 demonstrated an IC60 of 2.5 μM in erlotinib-resistant A549 cell lines, where erlotinib or OSI-420 alone could not exhibit 60% inhibition when evaluated up to 20 μM. Similar cytotoxic enhancement of erlotinib was seen with QD-OSI 420 in other NSCLC cell lines as well. These results were strengthened by 3D-SCC model of A549 which revealed that QD-OSI 420 was significantly better in reducing in-vitro 3D tumor volume, as compared to pure drugs. This study, being one of its kind, explores the feasibility of conjugating OSI-420 with QDs as an alternative to traditional anti-cancer therapy, by improving intracellular drug delivery.
Plume height and surface coverage analysis of methicillin-resistant Staphylococcus aureus isolates grown in a CDC biofilm reactor

Biofilm formation is a dynamic process that leads to mature communities over time. Despite a general knowledge of biofilm community formation and the resultant limitations of antibiotic therapy, there is a paucity of data describing specific plume heights, surface coverage and rates of maturation. Furthermore, little is published on the effect that the broth medium might have on the degree of biofilm maturation. In this study, three strains of methicillin-resistant Staphylococcus aureus (MRSA) (USA300, USA400 and a clinical isolate) were grown in brain heart infusion broth (BHI) or tryptic soy broth (TSB). Following growth, SEM images were captured for 3-D analysis to assess plume height. TSB produced significantly higher plume heights of USA300 and USA400 compared to BHI. Broth type was less influential on the clinical isolate. The data indicate that broth type and time may be important factors to consider when assessing maturation and plume height formation of MRSA biofilms.
Unusual Etiologies for Vascular Duodenal Compression Mimicking the Superior Mesenteric Artery (SMA) Syndrome: The SMA-Like Syndrome

We report a series of nine cases of unusual etiologies for vascular duodenal compression that do not meet the diagnostic criteria for superior mesenteric artery (SMA) syndrome and propose that “SMA-like syndrome” be used to classify these vascular duodenal compression cases.
An Insight into Android Side-Channel Attacks

Leakage of sensitive information is still considered one of the potential security threats to mobile operating systems including Android. The Android OS contains some security weaknesses which make it vulnerable to various attacks. One of these design weakness is the side-channel including memory and network-data usage. By monitoring such channels, Android application (app in short) with no permissions (zero-permission) may obtain some private information that is stored on user's mobile devices such as user's identity, login info, and the geo-location. In this study, we review side-channel attacks as well as runtime information attacks. Moreover, we survey the discovered side-channels of information leaks on Android. To the best of our knowledge, this is the first study that covers both the Android side-channels and runtime information attacks used to leak information.
Cryocoolers for Healthcare

This chapter shows the great impact cryocoolers made and continue to make in their emerging role as workhorse in the healthcare industry. Their great impact is particularly noticeable in MRI, PET, and many other small or large healthcare applications; for example, metabolic imaging and preclinical applications that would be unthinkable without the use of cryocoolers. The sustainability effect and carbon footprint reduction of cryocoolers, e.g., on MRI systems due to their ability to recondense helium and other refrigerants cannot be underestimated. The continuing increase in cryocooler cooling power capacity, their industrial robustness, and their ability to deeply embed pulse tube coolers in a cryostat or magnet system with very long service intervals continue to improve their usability for “wet” and “dry” healthcare applications.
Stress Fractures of the Midfoot and Forefoot

Stress fractures of the midfoot and forefoot are encountered frequently in athletes. In the general athlete population, stress fractures only have an incidence of approximately 1%; however, among athletes participating in running and jumping sports, the incidence increases to 15–20% (Fredericson et al., Top Magn Reson Imaging 17(5):309–25, 2006; Khan et al., Sports Health 10(2):169–74, 2018). In evaluating patients with potential stress injuries, clinicians should maintain a high index of suspicion as delays in diagnosis are common and often lead to prolonged pain, disability, and loss of time in sport. Patients usually present with a history of insidious, progressive activity-related pain without an inciting or traumatic event. Plain radiographs are often negative, and advanced imaging including MRI, CT, or bone scans is often needed to confirm the diagnosis of stress fracture.
HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo electron and TIRF microscopy

To enter a cell and establish infection, HIV must first fuse its lipid envelope with the host cell plasma membrane. Whereas the process of HIV membrane fusion can be tracked by fluorescence microscopy, the 3D configuration of proteins and lipids at intermediate steps can only be resolved with cryo-electron tomography (cryoET). However, cryoET of whole cells is technically difficult. To overcome this problem, we have adapted giant plasma membrane vesicles (or blebs) from native cell membranes expressing appropriate receptors as targets for fusion with HIV envelope glycoprotein-expressing pseudovirus particles with and without Serinc host restriction factors. The fusion behavior of these particles was probed by TIRF microscopy on bleb-derived supported membranes. Timed snapshots of fusion of the same particles with blebs were examined by cryo-ET. The combination of these methods allowed us to characterize the structures of various intermediates on the fusion pathway and showed that when Serinc3 or Serinc5 (but not Serinc2) were present, later fusion products were more prevalent, suggesting that Serinc3/5 act at multiple steps to prevent progression to full fusion. In addition, the antifungal amphotericin B reversed Serinc restriction, presumably by intercalation into the fusing membranes. Our results provide a highly detailed view of Serinc restriction of HIV-cell membrane fusion and thus extend current structural and functional information on Serinc as a lipid-binding protein.
Is agile the latest management fad? A review of success factors of agile transformations

Purpose: Agile is the new popular management change method and agile has lots of momentum. Management consulting firms are promoting agile via articles and newsletters. While history does not repeat itself, it often rhymes, and thus agile will probably be a successful change effort in some organizations. On the other hand, there is a high probability that agile will not deliver the expected results for most organizations. History reveals that about two-thirds of the change efforts are deemed unsuccessful – regardless of the actual change method. In this paper, we present the results of a systematic literature review on agile and we compare and contrast it with other similar organizational change methods. The purpose of this paper is to explore what one may learn from the history of the earlier change methods in terms of how organizations may succeed in their agile efforts. Design/methodology/approach: The paper is based on a structured literature review of the agile concept – including agile transformation, and with a specific focus on critical success factors. Findings: In addition to presenting the state of the art on agile in general, we identify, structure and categorize critical success factors (CSF) for agile. From the 13 categories, we form three clusters, which constitute a 3P framework (purpose, process and people). We also compare and contrast the CSF literature regarding agile with CSFs for organizational change in general. history indicates that most organizational change efforts are not successful. Based on the framework and the discussion, we provide recommendations to hopefully increase the probability of successful agile implementations. Originality/value: Given the relative novelty or at least the renewed interest in agile, a structured literature review of the current status of this “new” method provides value as it may help organizations and managers to not repeat old mistakes – once again. (Less)
Traumatic Brain Injury: A Success Stemming from Stem Cells

Traumatic brain injury (TBI) is a growing global health concern. Between 1999 and 2016, age-standardized TBI incidence and prevalence rose by 3.6% and 8.4%, respectively.1 Age distribution for TBI is bimodal, with higher incidence in the 20s and >70s brackets, most commonly due to motor vehicle accidents and falls. These statistics are cause for concern. The aging population demographics and rise in comorbid conditions that predispose to falls are likely to inflate TBI incidence further. Moreover, injury secondary to TBI can lead to significant functional and cognitive deficits, committing the individual to a lifetime of disability, lowered quality of life, and economic burden.
Surveillance and Equity: Identifying Hazards in the Environment

Injustice in surveillance may occur if surveillance is directed towards protecting the health of some but the data are gathered at the expense of others. Failures to surveille may be unjust if they leave people subject to health inequities. Such injustice in surveillance may undermine trust. This chapter explores injustice in surveillance and ethical responses. Primary examples are drawn from surveillance of environmental risks, especially those involving unclean or contaminated water. These injustices occur across the globe, from Flint, Michigan, in the United States to refugee camps in Bangladesh. The chapter also takes up the obligations of others when societies are failing to act justly, arguing for the importance of addressing corrosive disadvantages suffered especially by children but by other disadvantaged populations as well.
Making with a sustainable purpose: an interview with Matthew L. Mauriello

This interview presents insights into Dr. Mauriello's research projects in user-centered design to promote energy literacy within residential households.
Development and Internal Validation of an RPA-Based Model Predictive of Pain Flare Incidence After Spine SBRT.

PURPOSE/OBJECTIVE(S) Radiotherapy is a standard palliative treatment for spine metastasis, but pain flares (PF) are a common acute toxicity. Prophylactic corticosteroids can reduce the rate of PF in patients receiving traditional palliative regimens, but less is known about prophylaxis for stereotactic body radiotherapy (SBRT). We aim to identify a subset of patients treated with spine SBRT with the highest rate of PF to optimize the use of prophylactic steroids. MATERIALS/METHODS From December 2007-August 2019, 469 patients received 680 spine SBRT treatments. After exclusion of benign histology, particle therapy, and patients with missing data, the final cohort included 424 patients with 610 treatments. We defined PF as acute worsening of pain at the treatment site requiring initiation of or higher-dose corticosteroids, opiates, and/or hospitalization. First, data was split into 70% training and 30% validation sets with comparable patient characteristics using a random number generator. Feature importance testing was conducted, and a correlation heatmap helped exclude correlated variables. Feature extraction involved selecting the variables used in the highest-fidelity recursive partitioning analysis (RPA) models. Each RPA model was trained, validated, and tested using only the training dataset. Selected variables were verified using the Fisher exact test and univariate t-test. RESULTS We identified 125 total PF (20%), treated with steroids (14%), opioids (40%), both (39%), or hospitalization (6%). Six variables were identified by RPA. Of these, 5 met significance on Fisher exact test with P 0 (OR 2.17), SINS > 6 (OR 2.98), and gross tumor volume > 8 cc (OR 2.80). One point was assigned for each variable. The low-risk (LR) group (score = 0, n = 159) had PF rates of 7.0% and 13.6% in the training and validation sets, respectively; the intermediate-risk (IR) group (score = 1, n = 150) had rates of 14.0% and 16.3%; and the high-risk (HR) group (score > 1, n = 301) had rates of 28.8% and 31.3%. A logistic model confirmed the increased pain flare rate in the HR group compared to LR and IR treatments combined (OR = 3.50, 95% CI: 2.06-5.92) or considered separately (OR = 5.41, 2.48-11.78). The concordance index was 0.66 (0.60-0.73) and 0.62 (0.52-0.71) in the training and internal validation sets. Notably, patients with PF after prior spine SBRT had a 61% rate of PF with subsequent spine SBRT, compared to only 5% for patients without PF after prior spine SBRT. CONCLUSION Our internally-validated model identifies a high-risk group of patients more likely to develop PF after spine SBRT, for whom prophylactic steroids may confer the greatest benefit. Evaluation in a clinical trial is warranted.
Extremum Seeking Control based Resonant Frequency Estimation for a Grid-Tied Inverter with LCL Filter

The resonant frequency of the LCL filter can drift away from its nominal value due to the circuit components parameters uncertainty and the grid-side impedance, which will further deteriorate the robustness of the system and damping performance. Conventional online resonant frequency estimation schemes, such as discrete Fourier transformation and recursive prediction error, require a significant amount of computational power to implement, which may even need to reduce the sampling and control frequency of the inverter controller. In this work, an extremum seeking control based resonant frequency estimation scheme is proposed, which can provide an accurate estimate of the resonant frequency with notably reduced execution time. Simulations, hardware-in-the-loop (HIL) tests, and experimental tests on a single-phase grid-tied inverter are conducted to validate the effectiveness of the proposed scheme.
A few things we do not know about the sun and F stars and G stars

WE do not know how to make realistic model atmospheres; understand convection; consider the variation in microturbulent velocity; understand spectroscopy; have good spectra of the sun or any other star; have energy distributions for the sun or any other star; know how to determine abundances; know the abundances of the sun or any other star; have good atomic and molecular data; One half the lines in the solar spectrum are not identified. We should get our own house in order before worrying about the neighbors.
Finding a City’s Activity Bubbles in Geotagged Social Media

Bill Bishop popularized the idea that we all live in a self-curated world of bubbles in his book, “The Big Sort” (Bishop 2009). People often spend most of their time in completely different places from their neighbors, and this fragmentation of society leads to reduced empathy, policy quarrels, and even violence. People may not even be aware that they are segregating themselves so dramatically. Fortunately, thanks to the abundance of available geotagged social media data, we can easily and cheaply detect these social bubbles and give people a greater insight into their activity patterns. Understanding how we spend our time can be the first step in changing from isolated citizens into a connected community.
The reformatsky reaction on 1-naphthyl-2-bromophenyl ketone : The synthesis of 7-(2-bromophenyl)-perinaphtenone☆

Abstract The synthesis of 7-(2-bromophenyl)-perinaphthenone (VIII) and 2-bromophenyl-2-naphthyl ketone (IV) is described. Treatment of the cis -methyl-β-(2-bromophenyl)-β-(1-naphthyl)-acrylate (VIb) by lithium aluminium hydride under mild conditions unexpectedly led to methyl-β-phenyl-β-(1-naphthyl)-ethylene (XII) by the simultaneous reduction of the nuclear bromine and hydrogenolysis of the oxygen function.
Federated Scheduling of Sporadic DAG Task Systems

Recurrent (periodic and sporadic) task systems have traditionally been scheduled upon multiprocessor platforms using either the partitioned or the global approach. Under the recently-proposed federated approach, each task is either restricted to execute upon a single processor (as in partitioned scheduling), or may execute upon multiple processors but is the only task to execute upon each of these processors. Earlier studies concerning the federated scheduling of task systems represented using the sporadic DAG model were restricted to implicit-deadline and constrained-deadline sporadic task systems, the research reported here extends this study to the consideration of task systems represented using the more general arbitrary-deadline sporadic DAG model.
Towards an intelligent software tool for enhanced model interoperability in climate change research

Model interoperability, also known as model coupling, is involved in a significant part of scientific research and offers an interesting and worthwhile area of exploration and development for related supporting software frameworks and environments. This paper presents the challenges of scientific model coupling, with emphasis on climate change research, and briefly describes the current main methods for dealing with model interoperability. The paper also proposes a design solution for a new intelligent software tool aimed at facilitating model coupling and improving research productivity in climate change research. The main components of the proposed tool are presented and the tool's major modes of operation are described. An outline of planned future work on the proposed software environment for enhanced model interoperability is also included in the paper.
Sequential estimation of random parameters under model uncertainty

In many signal processing problems, the estimation of random parameters must be carried out sequentially and under model uncertainty. In the paper, a Bayesian approach is proposed for solving this problem, which is based on sequential updating of the posterior distribution of the desired parameters. It is shown that under a certain general set of conditions, the posterior of the unknown parameters is a mixture density. Since the computation of the solution becomes very intensive as the number of data (records) grows, a numerical procedure is proposed based on the sequential importance sampling scheme. Its number of computations per new data record is constant, and the procedure can easily be implemented in parallel.
Role of Klotho in aging, phosphate metabolism, and CKD.

The klotho gene (KL) was identified first as a putative aging-suppressor gene that extended life span when overexpressed and accelerated aging-like phenotypes when disrupted in mice. It encodes a single-pass transmembrane protein and is expressed predominantly in kidney, where it functions as an obligate coreceptor for fibroblast growth factor 23 (FGF-23). FGF-23 is a bone-derived hormone that suppresses phosphate reabsorption and 1,25 dihydroxyvitamin D3 (vitamin D) synthesis in the kidney. Klotho also is expressed in the parathyroid gland, where FGF-23 decreases parathyroid hormone expression and secretion, further suppressing vitamin D synthesis in kidney. Thus, FGF-23 functions as a phosphaturic hormone and a counter-regulatory hormone for vitamin D, thereby inducing negative phosphate balance. Mice lacking either FGF-23 or Klotho show hyperphosphatemia in addition to developing multiple aging-like phenotypes, which can be rescued by resolving phosphate retention. These findings have unveiled an unexpected link between aging and phosphate. In patients with chronic kidney disease (CKD), phosphate retention is seen universally and has been associated with increased mortality risk. Patients with CKD have high serum FGF-23 levels with decreased klotho expression in the kidney and parathyroid, rendering FGF-23 and Klotho as potential biomarkers and therapeutic targets for CKD. The Klotho protein not only serves as a coreceptor for FGF-23, but also functions as a humoral factor. Klotho's extracellular domain is released into blood and urine by ectodomain shedding and exerts various functions independently of FGF-23, including regulation of multiple ion channels and transporters. Decreased urinary Klotho protein level has been identified as one of the earliest biomarkers of CKD progression. This review focuses on the current understanding of Klotho protein function, with emphasis on its potential involvement in the pathophysiologic process of CKD.
Exclusive arrangments in the hospital industry

There have been numerous antitrust cases concerning exclusive hospitals privileges. The plaintiff often alleges both that he was foreclosed from the market and that an illegal tying agreement exists. This paper which draws heavily from the cases concludes both that the relevant market for hospital based physicians is national and that the impact on competition is minimal. The hospital frequently initiates the exclusive arrangement which suggests that efficiency is enhanced. Our analysis also shows that the rying claims are generally unpersuasive. However, exclusive arrangements on occasion may be a device to exclude competitors. Finally, economic criteria are developed to help determine the desirability of particular exclusive arrangements.
Deliberations on Kung's process interface modeling

Abstract Structured analysis specifications provide a graphical view of information flow in software systems. However, formal semantic interpretations are lacking for many of the modeling techniques, e.g., data flow diagrams, used in structured analysis specifications. Kung [3] identifies the lack of a “which in-flows produce which out-flows” semantics for data flow diagrams. Kung introduces information flow expressions to handle this semantic deficiency and developes a proof theory for decomposition consistency based on information flow expressions. We show that Kung's information flow expressions are fundamentally flawed for showing decomposition consistency. This flaw relates to the traditional semantic interpretation of data flow diagram process bubbles.
Bifurcation phenomena in pure bending

Abstract The bifurcation problem of an incompressible plate under pure bending is studied. Two incrementally linear constitutive models are employed. A classification of regimes of the bifurcation equation is also performed. An asymptotic analysis is carried out to establish the critical condition for short wavelength surface modes. Finally, a numerical calculation shows that in all cases considered the short wavelength surface mode in the compressive zone is the first bifurcation mode encountered in the deformation history.
Adhesion of a flat punch adhered to a thin pre-stressed membrane

The mechanics of a circular membrane delaminating from a rigid punch is derived based on linear elasticity and an energy balance approach. Both the tensile prestress and the resulting concomitant stress upon external loading are considered. A "pull-off" phenomenon is predicted when the contact circle shrinks to a critical value between 0.1945 and 0.3679 of the film diameter, depending on the critical strain energy release rate and the prestress. These asymptotic limits match exactly with the prestress dominant model by Shanahan and prestress free model by Wan. Thin film delamination from a rectangular punch is also investigated. Unlike the circular punch, the rectangular contact is expected to reduce to a line contact with zero contact area at "pinch-off." The graphs and trends shown are useful in assessing thin film delamination assisted by a prestress.
Modulation of EEG spectral edge frequency during patterned pneumatic oral stimulation in preterm infants

Modulation of EEG spectral edge frequency during patterned pneumatic oral stimulation in preterm infants
Neoliberalism and the making of food politics in California

Abstract This article is a theoretical overview that introduces a special issue on neoliberalism and agro-food activism in California. Its primary purpose is to theorize how projects in opposition to neoliberalizations of the food and agricultural sectors seem to produce and reproduce neoliberal forms, spaces of governance, and mentalities. The recently deployed analytics of neoliberalization and neoliberal governmentality have yet to be deployed in agro-food scholarship, owing to tendencies to see neoliberalism as a set of impacts, to use the commodity chain/network as an analytical framework, and to romanticize the local as resistance. Yet, the increased salience of food politics in contemporary life may itself reflect the neoliberal turn, particularly insofar as much of what passes as politics these days is done through highly individualized purchasing decisions. The paper thus argues that agro-food politics as well as the scholarship that supports it have contributed to neoliberal subject formation, as demonstrated by four recurring themes in contemporary food activism as they intersect with neoliberal rationalities: consumer choice, localism, entrepreneurialism, and self-improvement. Through a review of aspects of California’s history particularly relevant to the case studies presented in this special issue it proposes in addition that the character of agro-food politics in California reflects an articulation of California’ economic and political history, agrarian development, enduring and evolving food culture, and the neoliberal project. The paper concludes with a brief consideration of the politics of the possible in light of trends in agro-food activism, calling for closer attention to the micro-politics that shape various initiatives.
Relationship of Nuclear Invaginations to Perinuclear Rings Composed of Intermediate Filaments in MIA PaCa-2 and Some Other Cells.

There have been few investigations of the cause of nuclear invagination and lobule formation. The human pancreatic cancer cells MIA PaCa-2 often show nuclear lobulation and well-developed juxtanuclear aggregates of intermediate filaments with thick bundles of intermediate filaments developed from them. Therefore MIA PaCa-2 cells were used as model cells to examine whether or not there is any relationship between the shape of the nucleus and intermediate filaments. Immunoblotting showed that the intermediate filament proteins in MIA PaCa-2 cells are vimentin, and keratins 8, 18, and 19. Fluorescence microscopy and confocal laser scanning fluorescence microscopy revealed perinuclear rings composed of intermediate filaments, that is, thick bundles of both vimentin and keratin filaments run along deep invaginations in the nucleus and, together with juxtanuclear intermediate filament aggregates, they form closed rings around nuclear invaginated and constricted sites. In other cells such as human bladder carcinoma T24 cells, human melanoma G-361 cells, and human cervix carcinoma HeLa/S3 cells, there were also thick bundles of intermediate filaments cutting into the nucleus at the nuclear invagination site. Thus, it seems that the formation of perinuclear intermediate filament rings may be involved in nuclear invagination and lobule formation in some mammalian cells.
Prevention of Protein Adsorption by Tethered Poly(ethylene oxide) Layers: Experiments and Single-Chain Mean-Field Analysis

Prevention of protein adsorption by the surface-grafted poly(ethylene oxide) (PEO) chains has been well-known. We have examined the mechanisms of how the grafted PEO prevents protein adsorption. PEO−poly(propylene oxide)−PEO (PEO−PPO−PEO) triblock copolymers were used to graft PEO to the trichlorovinylsilane (TCVS)-modified glass by γ-irradiation. The surface density of the PEO chains was varied up to 60 pmol/cm2 and the number of the ethylene oxide (EO) units of the PEO segment was varied from 75 to 128. The adsorption of lysozyme and fibrinogen to the PEO-grafted glass was examined using radiolabeled proteins. The surface protein concentration decreased as the surface density of the grafted PEO increased, but surface protein concentration never reached zero. The experimental data were compared with the predictions by the single-chain mean-field theory. There was very good agreement between the predictions of the theory and the experimental observations. It was found that the mechanism for prevention of ...
A study of cumulative fatigue damage in aluminum alloy 2024-T4

Abstract Experimental data were generated using 2024-T4 aluminum alloy specimens under stress ratios of −1 and −0.5 for low-high, low-high-mixed, high-low and high-low-mixed stress sequences. Analysis of the data using Kramer's equation has indicated that the predicted cumulative fatigue damage and fatigue life are in close agreement with experimental results for low-high and low-high-mixed stress sequences under all stress ratios, whereas the theoretical values for high-low and high-low-mixed stress sequences under all stress ratios are more conservative than those obtained experimentally. It is suggested that development of Kramer's equation be studied thoroughly for possible modification.
JNK regulation of hepatic manifestations of the metabolic syndrome

Nonalcoholic fatty liver disease (NAFLD) is now recognized as both an important component of the metabolic syndrome and the most prevalent liver disease in the United States. Although the mechanisms for development of steatosis and chronic liver injury in NAFLD remain unclear, recent investigations have indicated that overactivation of c-Jun N-terminal kinase (JNK) is crucial to this process. These findings, together with evidence for the involvement of JNK signaling in other manifestations of the metabolic syndrome such as obesity and insulin resistance, have suggested that JNK could be a novel therapeutic target in this disorder. This review details findings that JNK mediates lipid accumulation and cell injury in fatty liver disease and discusses the possible cellular mechanisms of JNK actions.
Automatic detection of left and right ventricles from CTA enables efficient alignment of anatomy with myocardial perfusion data

Accurate alignment between cardiac CT angiographic studies (CTA) and nuclear perfusion images is crucial for improved diagnosis of coronary artery disease. This study evaluated in an animal model the accuracy of a CTA fully automated biventricular segmentation algorithm, a necessary step for automatic and thus efficient PET/CT alignment. Twelve pigs with acute infarcts were imaged using Rb-82 PET and 64-slice CTA. Post-mortem myocardium mass measurements were obtained. Endocardial and epicardial myocardial boundaries were manually and automatically detected on the CTA and both segmentations used to perform PET/CT alignment. To assess the segmentation performance, image-based myocardial masses were compared to experimental data; the hand-traced profiles were used as a reference standard to assess the global and slice-by-slice robustness of the automated algorithm in extracting myocardium, LV, and RV. Mean distances between the automated and the manual 3D segmented surfaces were computed. Finally, differences in rotations and translations between the manual and automatic surfaces were estimated post-PET/CT alignment. The largest, smallest, and median distances between interactive and automatic surfaces averaged 1.2 ± 2.1, 0.2 ± 1.6, and 0.7 ± 1.9 mm. The average angular and translational differences in CT/PET alignments were 0.4°, −0.6°, and −2.3° about x, y, and z axes, and 1.8, −2.1, and 2.0 mm in x, y, and z directions. Our automatic myocardial boundary detection algorithm creates surfaces from CTA that are similar in accuracy and provide similar alignments with PET as those obtained from interactive tracing. Specific difficulties in a reliable segmentation of the apex and base regions will require further improvements in the automated technique.
Pulmonary Vascular Wall Stiffness: An Important Contributor to the Increased Right Ventricular Afterload with Pulmonary Hypertension:

AbstractPulmonary hypertension (PH) is associated with structural and mechanical changes in the pulmonary vascular bed that increase right ventricular (RV) afterload. These changes, characterized by narrowing and stiffening, occur in both proximal and distal pulmonary arteries (PAs). An important consequence of arterial narrowing is increased pulmonary vascular resistance (PVR). Arterial stiffening, which can occur in both the proximal and distal pulmonary arteries, is an important index of disease progression and is a significant contributor to increased RV afterload in PH. In particular, arterial narrowing and stiffening increase the RV afterload by increasing steady and oscillatory RV work, respectively. Here we review the current state of knowledge of the causes and consequences of pulmonary arterial stiffening in PH and its impact on RV function. We review direct and indirect techniques for measuring proximal and distal pulmonary arterial stiffness, measures of arterial stiffness including elastic mo...
Dynamic stability of the elbow : electromyographic analysis of the flexor pronator group and the extensor group in pitchers with valgus instability

The medial collateral ligaments is a common site of injury in baseball pitchers, causing substantial morbidity and loss of pitching time. Twenty-six skilled baseball pitchers with medial collateral ligament insufficiency were studied before surgery with high-speed cinematography and fine-wire electromyography of eight muscles around the elbow. Data from the pitchers with injured elbows were compared with data obtained from uninjured pitchers. The flexor carpi radialis muscle in the pitchers with medial collateral ligment deficiencies revealed significantly decreased firing during the acceleration and deceleration phase of the fastball when compared with that of the pitchers with normal elbows, and the flexor carpi radialis muscle was significantly depressed during the early cocking and deceleration phases. The extensor muscles revealed slightly increased activity in the injured elbows; however, this was not statistically significant. Although the muscles of the flexor pronator group (especially the flexor carpi ulnaris muscle and the flexor digitorum superficialis muscles) are anatomically positioned to provide dynamic stability of the elbow, they did not demonstrate increased electrical activity in pitchers with medial collateral ligament deficiencies. This finding suggests that the muscles on the medial side of the elbow do not supplant the role of the medial collateral ligament during the fastball pitch.
A Novel Mechanism for Cyclic Adenosine 3′,5′-Monophosphate Regulation of Gene Expression by CREB-Binding Protein

The pituitary-specific transcription factor, Pit-1, is necessary to mediate protein kinase A (PKA) regulation of the GH, PRL, and TSH-β subunit genes in the pituitary. Since these target genes lack classical cAMP DNA response elements (CREs), the mechanism of this regulation was previously unknown. We show that CREB binding protein (CBP), through two cysteine-histidine rich domains (C/H1 and C/H3), specifically and constitutively interacts with Pit-1 in pituitary cells. Pit-1 and CBP synergistically activate the PRL gene after PKA stimulation in a mechanism requiring both an intact Pit-1 amino-terminal and DNA-binding domain. A CBP construct containing the C/H3 domain [amino acids (aa) 1678–2441], but not one lacking the C/H3 domain (aa 1891–2441), is sufficient to mediate this response. Neither construct augments PKA regulation of CRE-containing promoters. Fusion of either CBP fragment to the GAL4 DNA-binding domain transferred complete PKA regulation to a heterologous promoter. These findings provide a ...
Linkage of two pseudogenes from Vκ1 and Vκ9 murine immunoglobulin families

As an initial step towards the molecular analysis of the murine V kappa locus, a cosmid library from BALB/cJ mouse liver DNA was screened with probes representing 10 V kappa families. Of eight cosmids that were isolated from the initial screen, five contained a single restriction fragment that hybridized to the probes. Two cosmids contained two fragments that hybridized to the same probe, V kappa 4, indicating that some V kappa 4 gene segments are linked. One cosmid had two genes that belonged to different families, V kappa 1 and V kappa 9. The two gene segments were located within 12 kb of each other and lay in the same transcriptional orientation. Linkage of gene segments from the V kappa 1 and V kappa 9 families is consistent with a genetic map of the locus, and provides physical evidence for the first time that two genes from different families are closely linked in the murine kappa locus. Sequence analysis revealed that both genes are pseudogenes: the V kappa psi 1.7 gene segment has eight mutations, including termination codons, insertions, and deletions, and the V kappa psi 9B.8 gene segment has two mutations of an insertion and altered RNA splice site. Both genes have the potential to rearrange based on the sequence of their heptamer-nonamer motifs. The identification of pseudogenes raises the question of how many nonfunctional genes are present in the murine germline repertoire.
Intramuscular pressure and torque during isometric, concentric and eccentric muscular activity

Intramuscular pressures, electromyography (EMG) and torque generation during isometric, concentric and eccentric maximal isokinetic muscle activity were recorded in 10 healthy volunteers. Pressure and EMG activity were continuously and simultaneously measured side by side in the tibialis anterior and soleus muscles. Ankle joint torque and position were monitored continuously by an isokinetic dynamometer during plantar flexion and dorsiflexion of the foot. The increased force generation during eccentric muscular activity, compared with other muscular activity, was not accompanied by higher intramuscular pressure. Thus, this study demonstrated that eccentric muscular activity generated higher torque values for each increment of intramuscular pressure. Intramuscular pressures during antagonistic co-activation were significantly higher in the tibilis anterior muscle (42-46% of maximal agonistic activity) compared with the soleus muscle (12-29% of maximal agonistic activity) and was largely due to active recruitment of muscle fibers. In summary, eccentric muscular activity creates higher torque values with no additional increase of the intramuscular pressure compared with concentric and isometric muscular activity.
Deriving linear transformations in three dimensions

This article presents a general technique for solving elementary algebraic problems that arise in 3D geometry and then applies this method to derive explicit formulas for many of the linear transformations used in the standard 3D graphics pipeline.
Protein dynamics and allostery: an NMR view

Allostery, the process by which distant sites within a protein system are energetically coupled, is an efficient and ubiquitous mechanism for activity regulation. A purely mechanical view of allostery invoking only structural changes has developed over the decades as the classical view of the phenomenon. However, a fast growing list of examples illustrate the intimate link between internal motions over a wide range of time scales and function in protein-ligand interactions. Proteins respond to perturbations by redistributing their motions and they use fluctuating conformational states for binding and conformational entropy as a carrier of allosteric energy to modulate association with ligands. In several cases allosteric interactions proceed with minimal or no structural changes. We discuss emerging paradigms for the central role of protein dynamics in allostery.