cssi/SciSciGPT-SciSciNet huggingface dataset:
A Highly Parallel Hardware Architecture of Table-Based CABAC Bit Rate Estimator in an HEVC Intra Encoder

This paper presents a highly parallel hardware architecture for rate estimation in a High Efficiency Video Coding intra encoder to increase the level of parallelism and reduce the computational time. The adopted rate estimation algorithm is fully compatible with the context-adaptive binary arithmetic coding (CABAC) bit rate estimation except ignoring a syntax element “split_cu_flag.” Design considerations, analysis, and circuit implementation are elaborated. This design has been verified with the HM-15.0 reference software. It achieves an average decrease of 0.005% and an average increase of 0.0092 dB in Bjontegaard delta (BD)-rate and BD-peak signal-to-noise ratio, respectively. This proposed hardware architecture is implemented in Verilog and synthesized in FPGAs and ASICs. It supports resolutions up to $3840\times 2160$ at 30 f/s. Compared with state-of-the-art hardware designs for rate estimation in the literature, the proposed architecture achieves substantial performance improvement in rate estimation accuracy and reliability, with the overhead of a relatively larger chip area and higher power consumption. To the best of our knowledge, this is the first highly parallel hardware architecture of table-based CABAC bit rate estimator, which is attractive in time-constrained and high-performance video coding applications.
A Quantitative Analysis of the Reliability of Aquaplast Mask Immobilization for Cranial Radiosurgery With TomoTherapy

Patient treatment setup accuracy for cranial radiosurgery (SRS) is dependent on a number of parameters; including localization and immobilization. In this study we carried out a quantitative analysis of the reliability of a radiosurgery immobilization mask system in maintaining patient position during SRS treatment sessions. Patients were fitted with a thermoplastic mask and a customized pillow designed for SRS. TomoTherapy MVCT, using 1 mm slice thickness, was carried out and the required shifts, based on bony anatomy, were applied to the patient position prior to radiotherapy. At the completion of the treatment a second MVCT was carried out to determine if any patient movement had taken place. Typical time on the treatment couch varied from 25-60 minutes. A total of 26 patients were analyzed. Some patients received more than one treatment fraction. A total of 38 MVCT measurements were included in this study. The mean absolute shift for the 38 measurements was 0.42 mm (SD=0.29) lateral, 0.75 mm (SD=0.94) longitudinal, and 0.44 mm (SD=0.42) in the vertical direction. Overall, the average vector displacement was 1.18 mm (SD=0.82). The variation in shifts between different patients was significant. Two patients had a vector shift of greater than 3.0 mm; largely due to a longitudinal displacement. Based on these results a margin of approximately 1 mm is sufficient for patient lateral and vertical motion but up to a 2 mm margin may be needed for longitudinal motion. Hence a PRV and PTV of 3 mm is required to account for patient position uncertainty. Care in the initial molding of the mask, and a customized pillow, may be key in ensuring minimal patient motion during cranial SRS.
Glycolipid metabolism in the canine form of globoid cell leukodystrophy.

The underlying cause of globoid cell leukodystrophy (Krabbe’s disease) is a genetic deficiency of galactosylceramide α-galactosidase (galactosylceramidase, E.C. 3.2.1.46) which normally degrades galactosylceramide (21,22). In principle, the disease belongs to the so-called sphingolipidoses in which acidic lysosomal hydrolases are genetically deficient resulting in abnormal accumulation of sphingolipids specific in respective disorders. Unlike in other sphingolipidoses, abnormal accumulation of galactosylceramide does not occur in globoid cell leukodystrophy despite the block in its degradative pathway (22, 26). The only logical explanation for this unusual phenomenon appears to be that, sometime along the course of the disease, biosynthesis of galactosylceramide is terminated. Galactosylceramide is highly concentrated in the myelin sheath which is a specialized extension of the Oligodendroglial plasma membrane. It is, therefore, reasonable to assume that the Oligodendroglial cell is the major site of galactosylceramide biosynthesis in the brain. Since early and almost complete destruction of Oligodendroglia is one of the characteristic morphological features of the disease, cessation of galactosylceramide biosynthesis may merely be a secondary result of the abnormal histology. However, it is also possible that biosynthetic abnormality may precede death of Oligodendroglia, both due to the same as yet unidentified pathogenetic mechanism.
Production of Antipeptide Antibodies

Peptides (8-20 residues) are as effective as proteins in raising antibodies, both polyclonal and monoclonal with a titer above 20,000 easily achievable. A successful antipeptide antibody production depends on several factors such as peptide sequence selection, peptide synthesis, peptide-carrier protein conjugation, the choice of the host animal, and antibody purification. Peptide sequence selection is likely the most difficult and critical step in the development of antipeptide antibodies. Although the format for designing peptide antigens is not precise, several guidelines can help maximize the likelihood of producing high-quality antipeptide antibodies. Typically, 5-20 mg of peptide is enough for raising an antibody, for preparing a peptide affinity column, and for antibody titer determination using an enzyme-linked immunosorbent assay (ELISA). Usually, it takes 3 months to raise a polyclonal antipeptide antibody from a rabbit that yields ~90 mL of serum which translates into approximately 8-10 mg of the specific antibody after peptide affinity purification.
Literacy, Numeracy, and Health Information Seeking Among Middle-Aged and Older Adults in the United States:

Objectives: Health literacy is often viewed as an essential skill set for successfully seeking health information to make health-related decisions. However, this general understanding has yet to be established with the use of nationally representative data. The objective of this study was to provide the first nationally representative empirical evidence that links health information seeking behaviors with health literacy among middle-age to older adults in the United States. Methods: Data were obtained from the 2012/2014 Program for the International Assessment of Adult Literacy (PIAAC). Our analytic sample is representative of adults age 45 to 74 years (N = 2,989). Results: Distinct components of health literacy (i.e., literacy and numeracy) were uniquely associated with the use of different health information sources (e.g., health professionals, the Internet, television). Discussion: Findings should be useful for government agencies and health care providers interested in targeting health communications, as well as researchers who focus on health disparities.
Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic.

BACKGROUND: Next-generation sequencing (NGS) is revolutionizing a variety of molecular biology fields including bioforensics, biosurveillance, and infectious disease diagnostics. For pathogen detection, the ability to sequence all nucleic acids in a sample allows near limitless multiplexability, free from a priori knowledge regarding an etiologic agent as is typically required for targeted molecular assays such as real-time PCR. Furthermore, sequencing capabilities can generate in depth genomic information, allowing detailed molecular epidemiological studies and bioforensics analysis, which is critical for source agent identification in a biothreat outbreak. However, lack of analytical specificity, inherent to NGS, presents challenges for regulated applications such as clinical diagnostics and molecular attribution. CONTENT: Here, we discuss NGS applications in the context of preparedness and biothreat readiness. Specifically, we investigate current and future applications of NGS technologies to affect the fields of biosurveillance, bioforensics, and clinical diagnostics with specific focus on biodefense. SUMMARY: Overall, there are many advantages to the implementation of NGS for preparedness and readiness against biowarfare agents, from forensics to diagnostics. However, appropriate caveats must be associated with any technology. This includes NGS. While NGS is not the panacea replacing all molecular techniques, it will greatly enhance the ability to detect, characterize, and diagnose biowarfare agents, thus providing an excellent addition to the biodefense toolbox of biosurveillance, bioforensics, and biothreat diagnosis.
The arundo wasp, Tetramesa romana, does not control giant river reed, Arundo donax, in Texas, USA

Giant river reed, Arundo donax L. (Poaceae), native to the Mediterranean basin and east to the Indus River region of Afghanistan and Pakistan, has become widespread in temperate and subtropical regions worldwide. It is regarded as being deleterious for clogging waterways and for choking out natural riparian plant communities. In the USA efforts to control the pest have included the release of exotic herbivorous insects. One of them, the arundo wasp, Tetramesa romana Walker (Hymenoptera: Eurytomidae), has been reported to utilize primary A. donax stalks for oviposition, stunting and killing the plant. In our study, stands of A. donax in natural habitats of Kerr County (TX, USA) were sampled at monthly intervals for 2 years and small plots of A. donax at annual intervals for five consecutive years. Parasitism of stalks, regardless of plant age, was rare or non‐existent. Arundo donax in natural habitats and freshly planted A. donax grew in dense stands and proliferated regardless of being infested by T. romana. We determined that parasitized culms can serve as plant propagules by growing roots and stems, hence, the wasp does not impede the ability of A. donax to propagate and proliferate from broken off plant parts. The wasp utilizes A. donax culm stems growing from hardening ≥1st‐year stalks for development in the winter and early summer when the larvae pupate and emerge as adults. We found that appreciable T. romana parasitism of an A. donax plant only occurs for 8.3–16.7% of the plant's 2‐year lifespan. Adult exit holes remain on the culms during summer. Under field conditions T. romana is a parasite that is well‐adapted to A. donax by not killing stalks, reducing stand density, and hindering propagation. Hence, the exotic wasp is ineffective as a biological control agent against A. donax.
Dietary supplementation with peanut skin polyphenolic extracts (PSPE) reduces hepatic lipid and glycogen stores in mice fed an atherogenic diet

Abstract The polyphenolic compounds found in red wine, grapes and peanut skins are bioactive compounds responsible for reduced mortality rates associated with cardiovascular disease. Resveratrol, a polyphenol found in the skin of grapes, reduced liver lipids and inflammation in mice fed an atherogenic diet. We aimed to assess the effects of polyphenolic compounds extracted from peanut skins by testing 3 treatments in mice (n = 10): atherogenic diet supplemented with peanut-skin polyphenolic extract (PSPE), atherogenic diet (ATH), and normal diet. Lymphocyte populations, blood glucose, hepatic cholesterol and glycogen and body weight (BW) were quantified at16 weeks. Mice fed the PSPE-diet had significantly improved BW, reduced hepatic glycogen and blood plasma glucose levels in comparison to the ATH treatment group. Moreover, hepatic cholesterol and lipid storage was reduced in mice fed the PSPE diet. Thus, PSPE could serve as a value added food and/or feed ingredient and an affordable plant source of antioxidants.
Expression of mutant CHMP2B linked to neurodegeneration in humans disrupts circadian rhythms in Drosophila

Mutations in CHMP2B, an ESCRT-III (endosomal sorting complexes required for transport) component, are associated with frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Neurodegenerative disorders including FTD are also associated with a disruption in circadian rhythms, but the mechanism underlying this defect is not well understood. Here, we ectopically expressed the human CHMP2B variant associated with FTD (CHMP2BIntron5) in flies using the GMR-GAL4 driver (GMR>CHMP2BIntron5) and analyzed their circadian rhythms at behavioral, cellular, and biochemical level. In GMR>CHMP2BIntron5 flies, we observed disrupted eclosion rhythms, shortened free-running circadian locomotor period, and reduced levels of timeless (tim) mRNA-a circadian pacemaker gene. We also observed that the GMR-GAL4 driver, primarily known for its expression in the retina, drives expression in a subset of tim expressing neurons in the optic lobe of the brain. The patterning of these GMR- and tim-positive neurons in the optic lobe, which appears distinct from the putative clusters of circadian pacemaker neurons in the fly brain, was disrupted in GMR>CHMP2BIntron5 flies. These results demonstrate that CHMP2BIntron5 can disrupt the normal function of the circadian clock in Drosophila.
Intraoperative Speckle Variance Optical Coherence Tomography for Tissue Temperature Monitoring During Cutaneous Laser Therapy

Background: Tissue temperature monitoring during cutaneous laser therapy can lead to safer and more effective treatments. In this study, we investigate the use of speckle variance optical coherence tomography (svOCT) to monitor real-time temperature changes in the excised human skin tissue sample during laser irradiation. Methods: To accomplish this, we combined the pulse laser system with a reference-based svOCT system. To calibrate the svOCT, the ex-vivo human skin samples from three individuals with tissues collected from the arm, face, and back were heated with 1-degree increments. Additionally, linear regression was used to extract and evaluate the linear relationship between the temperature and normalized speckle variance value. Experiments were conducted on excised human skin sample to monitor the temperature change during laser therapy with a svOCT system. Thermal modeling of ex-vivo human skin was used to numerically simulate the laser-tissue interaction and estimate the thermal diffusion and peak temperature of the tissue during the laser treatment. Results and Conclusion: These results showed that normalized speckle variance had a linear relationship with the tissue temperature before the onset of tissue coagulation (52°) and we were able to measure the rapid increase of the tissue temperature during laser therapy. The result of the experiment is also in good agreement with the numerical simulation result that estimated the laser-induced peak temperature and thermal relaxation time.
Special Topics in the Care of Older People with HIV

Antiretroviral therapy has enabled many people with HIV to live long lives with their infection, but the literature suggests that long-term survivors are developing comorbidities and aging-related syndromes at earlier ages than their non-infected counterparts. In addition, there is evidence of sex-based differences in comorbidity risk. How to best care for people aging with HIV is not known, but the tools of comprehensive geriatric assessment can identify people at risk for decline. Newer antiretroviral therapies offer promise of fewer side effects and drug interactions. We will also discuss special needs of women aging with HIV. People with HIV and their providers are often unprepared to confront issues of aging, and each clinical program must develop methods to assess older patients and manage age-related complications and syndromes.
Predicting Driving Performance in Older Adults with the Useful Field of View Test: A Meta-Analysis

This investigation examines the Useful Field of View (specifically the UFOV® test), as a predictor of objective measures of driving performance. PubMed and PsycInfo databases were searched to retrieve eight independent studies reporting bivariate relationships between the UFOV® test and driving measures (driving simulator performance, state-recorded crashes, and on-road driving). Cumulative meta-analysis techniques were used to examine the predictive utility of the test, to determine whether the effect size was stable across studies, and to assess whether a sufficient number of studies have been conducted to conclude that the test is an effective predictor of driving competence. Results showed that the study samples could have been drawn from the same population. The weighted mean effect size across all studies revealed a large effect, Cohen's d=0.945, with poorer UFOV® test performance associated with negative driving outcomes. This relationship was robust across multiple indices of driving performance and several research laboratories. A concrete measure of sufficiency revealed that an additional 513 studies averaging a null result must be conducted to bring the p-value for the cumulative effect size to greater than .05. This convergence of evidence across different points in time and different research teams confirms the importance of the UFOV® assessment as a valid and reliable index of driving performance and safety. Corroborating this finding, a recent large field study in Maryland has further established the UFOV® test as a useful screening instrument to identify at-risk older drivers. Taken together, these findings could have far-reaching implications for public policy.
Reversing the Colonial Gaze: Persian Travelers Abroad

Exploring the furthest reaches of the globe, Persian travelers from Iran and India travelled across Russian and Ottoman territories, to Asia, Africa, North and South America, Europe and beyond. Remapping the world through their travelogues, Reversing the Colonial Gaze offers a comprehensive and transformative analysis of the journeys of over a dozen of these nineteenth-century Persian travelers. By moving beyond the dominant Eurocentric perspectives on travel narratives, Hamid Dabashi works to reverse the colonial gaze which has thus far been cast upon these rich body of travelogues. His lyrical and engaging re-evaluation of these journeys, complimented by close-readings of seminal travelogues, challenges the systematic neglect of these narratives in scholarly literature. Opening up the entirety of these overlooked or abused travelogues, Dabashi reveals not a mere repetition of cliche accounts of Iranian or Muslim encounters with the West, but a path-breaking introduction to a constellation of revelatory travel narratives that re-imagine and reclaim the world beyond colonial borders.
Serotonin system function, organization, and feedback

Abstract Serotonin neurotransmission is associated with emotional brain function and seems particularly relevant to changes in emotion and behavior over time. Serotonin neurons are diverse in many cellular characteristics, supporting functional diversity. In particular, different neurons have different patterns of connectivity and show different responses depending on behavioral conditions, exhibiting changeable and nonsynchronous phasic and tonic activity. These characteristics can generate topographically specific patterns of increases and decreases of extracellular serotonin across the neuroaxis correlating with different behavior and by inference, perhaps different subjective experience of mood. While diverse, serotonin neurons exhibit a high level of within-system communication via feedback. These feedback mechanisms likely shape serotonin signaling in both time and space, yet the details of feedback function remain poorly mapped. Thus serotonin neurons constitute a system composed of specific subcomponents interlinked via feedback that serve in sum to coordinate emotional brain function.
O06.5 Do treatment rates suffer in a low-touch screening model? new york city sexual health clinics, 2017–2018

Background Low-touch (i.e. limited staff interaction) models for asymptomatic STI screening have been widely adopted in sexual health clinics (SHCs) and can improve clinic flow and patients‘ experience. In New York City SHCs, asymptomatic patients who do not report contact to STI screen for urogenital and extragenital bacterial STI using self-collected specimens without a medical encounter. We evaluated treatment rates for Neisseria gonorrhea (GC) cases detected by this low-touch, self-screening model. Methods We identified men-who-have-sex-with-men (MSM) who tested GC-positive by urogenital or extragenital nucleic acid amplification testing at any visit type (self-screening or standard clinician) during 01/2017–06/2018. Among GC cases that had not been presumptively treated, we assessed the number and percent of asymptomatic cases that returned for treatment within 30 days, and HIV pre-exposure prophylaxis (PrEP) use. We used Kaplan-Meier methods to examine time-to-treatment by visit type. Results Of 3,944 GC cases, 2,268 were presumptively treated and 1,676 needed to return for treatment. Among returning patients, median time-to-treatment was 6 days (IQR: 4–8). Cases detected at self-screening visits had shorter time-to-treatment than those detected at standard visits (p=0.008). Among GC cases detected at self-screening visits, 85% (454/534) were treated Conclusion Among HIV-negative MSM with rectal GC, a group for whom delayed treatment may increase risk for HIV acquisition, a low-touch/self-screening model results in overall treatment rates and times-to-treatment that compare favorably to a standard clinician model. Disclosure No significant relationships.
Stick Stippling for Joint 3D Visualization of Diffusion MRI Fiber Orientations and Density

We investigate a stick stippling approach for glyph-based visualization of neural fiber architecture derived from diffusion magnetic resonance imaging. The presence of subvoxel crossing fibers in the brain has prompted the development of advanced modeling techniques; however, there remains a need for improved visualization techniques to more clearly convey their complex structure. While tractography can illustrate large scale anatomy, visualization of diffusion models can provide a more complete picture of local anatomy without the known limitations of tracking. We identify challenges and evaluate techniques for visualizing multi-fiber models and identify benefits of a stick stippling technique relative to existing methods. We conducted experiments to compare these representations and evaluated them with in vivo diffusion MR datasets that vary in voxel resolution and anisotropy. We found that stick rendering as 3D tubes increased legibility of fiber orientation and that encoding fiber density by tube radius reduced clutter and reduced dependence on viewing orientation. Furthermore, we identified techniques to reduce the negative perceptual effects of voxel gridding through a jittering and resampling approach to produce a stippling effect. Looking forward, this approach provides a new way to explore diffusion MRI datasets that may aid in the visual analysis of white matter fiber architecture and microstructure. Our software implementation is available in the Quantitative Imaging Toolkit (QIT).
The Association of Ideal Cardiovascular Health and Ocular Diseases Among US Adults.

Abstract Background Globally, about 2.2 billion people have a vision impairment or blindness and approximately half of the cases could have been prevented. Several ocular diseases share common characteristics that overlap with risk factors for cardiovascular diseases. The aim of this study was to evaluate the relation between the American Heart Association's prescription for health called the Life's Simple 7 (LS7) metrics and the occurrence of ocular diseases. Methods Data were from 6118 adults ages ≥40 years who participated in the 2005-2008 National Health and Nutrition Examination Survey (NHANES). LS7 metrics consisted of information on smoking, physical activity, body mass index, diet, blood pressure, total cholesterol, and blood glucose. Scores were summed for a maximum of 14 (most ideal cardiovascular health). Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Results The average age of participants was 57 years with 53% of them being women. A 1-unit increase in LS7 scores was associated with reduced odds for age-related macular degeneration (OR: 0.95, 95% CI: 0.90-0.99), diabetic retinopathy (OR: 0.68, 95% CI: 0.64-0.73), cataract (OR: 0.94, 95% CI: 0.90-0.98), and glaucoma (OR: 0.94, 95% CI: 0.88-0.99). After multivariable adjustment, the association was limited to only diabetic retinopathy (OR: 0.69, 95% CI: 0.64-0.74). This association persisted when diabetic retinopathy was limited to only diagnosis by retinal imaging. Conclusions In this study, ideal cardiovascular health, which is indicative of a healthy lifestyle, was associated with lower odds for ocular diseases, especially diabetic retinopathy. These findings suggest that interventions to prevent cardiovascular diseases may also hold promise in preventing ocular diseases.
An improved mean field approximation on the worldsheet for planar φ3 theory

Abstract We present an improved version of our earlier work on summing the planar graphs in φ3 field theory. The present treatment is also based on our world sheet formalism and the mean field approximation, but it makes use of no further approximations. We derive a set of equations between the expectation values of the world sheet fields, and we investigate them in certain limits. We show that the equations can give rise to (metastable) string forming solutions.
The New Jim Crow in Higher Education: A Critical Race Analysis of Postsecondary Policy Related to Drug Felonies

In this paper, critical race theory and critical race praxis for educational research are used to frame an analysis of the 1998 Amendments to the Higher Education Act of 1965 (HEA98) that limits access to financial aid for students who have been convicted of a drug felony. The authors explain how the HEA98 disenfranchises Black and Latinx college student populations. This policy is a form of institutional racism against the disproportionately large number of Black and Latinx individuals that have been convicted of drug-related crimes, which creates a caste system of college access and support. This policy analysis highlights data on incarcerated populations that link the policing of drug offenses to racial profiling and discrimination (e.g., “the War on Drugs” and the 1994 Crime Bill), questions the motivations for reducing access to education in drug offenders, reviews causes and inhibitors of recidivism in drug offenders to make the case for the promotion of education in recently-released offenders, and highlights empirical data that supports expanding access to these people. The authors conclude the paper with recommendations to progress toward racial educational equity. This paper is directed toward higher education scholars, practitioners, and policy makers who possess a strategic critical orientation towards racial equity in education.
Multi-Modal Semantic Inconsistency Detection in Social Media News Posts.

As computer-generated content and deepfakes make steady improvements, semantic approaches to multimedia forensics will become more important. In this paper, we introduce a novel classification architecture for identifying semantic inconsistencies between video appearance and text caption in social media news posts. We develop a multi-modal fusion framework to identify mismatches between videos and captions in social media posts by leveraging an ensemble method based on textual analysis of the caption, automatic audio transcription, semantic video analysis, object detection, named entity consistency, and facial verification. To train and test our approach, we curate a new video-based dataset of 4,000 real-world Facebook news posts for analysis. Our multi-modal approach achieves 60.5% classification accuracy on random mismatches between caption and appearance, compared to accuracy below 50% for uni-modal models. Further ablation studies confirm the necessity of fusion across modalities for correctly identifying semantic inconsistencies.
Bayesian Parameter Estimations for Grey System Models in Online Traffic Speed Predictions

This paper presents Bayesian parameter estimation for first order Grey system models' parameters (or sometimes referred to as hyperparameters). There are different forms of first-order Grey System Models. These include $GM(1,1)$, $GM(1,1| \cos(\omega t)$, $GM(1,1| \sin(\omega t)$, and $GM(1,1| \cos(\omega t), \sin(\omega t)$. The whitenization equation of these models is a first-order linear differential equation of the form \[ \frac{dx}{dt} + a x = f(t) \] where $a$ is a parameter and $f(t) = b$ in $GM(1,1|)$ , $f(t) = b_1\cos(\omega t) + b_2$ in $GM(1,1| cos(\omega t)$, $f(t) = b_1\sin(\omega t)+b_2$ in $GM(1,1| \sin(\omega t)$, $f(t) = b_1\sin(\omega t) + b_2\cos(\omega t) + b_3$ in $GM(1,1| \cos(\omega t), \sin(\omega t)$, $f(t) = b x^2$ in Grey Verhulst model (GVM), and where $b, b_1, b_2$, and $b_3$ are parameters. The results from Bayesian estimations are compared to the least square estimated models with fixed $\omega$. We found that using rolling Bayesian estimations for GM parameters can allow us to estimate the parameters in all possible forms. Based on the data used for the comparison, the numerical results showed that models with Bayesian parameter estimations are up to 45\% more accurate in mean squared errors.
Association of predation risk with a heterospecific vocalization by an anabantoid fish.

Honey gouramis (Trichogaster chuna) received chemical alarm cues derived from conspecific epidermal tissue and, simultaneously, the vocalization produced by a heterospecific gourami species, the sparkling pygmy gourami (Trichopsis pumila). Control trials paired water with the vocalization. In trials that received alarm cues, honey gouramis significantly increased activity relative to control trials that received water, suggesting an attempt to flee and search for refuge. When the recording of the vocalization was later replayed to test fish without any additional chemical cue, fish that had previously experienced alarm cue froze while those that had received water with the vocalization did not change their behaviour. These data indicate that honey gouramis recognize and respond to chemical alarm cues, making this report the second anabantoid species to be recorded with this response. Second, these data indicate that honey gouramis can associate risk of predation with a novel auditory stimulus, including vocalizations from other species. These data suggest the potential for vocalizations to evolve into alarm signals in this group of fishes. This article is protected by copyright. All rights reserved.
Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data

An increasing number of studies have profiled tumor specimens using distinct microarray platforms and analysis techniques. With the accumulating amount of microarray data, one of the most intriguing yet challenging tasks is to develop robust statistical models to integrate the findings. By applying a two-stage Bayesian mixture modeling strategy, we were able to assimilate and analyze four independent microarray studies to derive an inter-study validated "meta-signature" associated with breast cancer prognosis. Combining multiple studies (n = 305 samples) on a common probability scale, we developed a 90-gene meta-signature, which strongly associated with survival in breast cancer patients. Given the set of independent studies using different microarray platforms which included spotted cDNAs, Affymetrix GeneChip, and inkjet oligonucleotides, the individually identified classifiers yielded gene sets predictive of survival in each study cohort. The study-specific gene signatures, however, had minimal overlap with each other, and performed poorly in pairwise cross-validation. The meta-signature, on the other hand, accommodated such heterogeneity and achieved comparable or better prognostic performance when compared with the individual signatures. Further by comparing to a global standardization method, the mixture model based data transformation demonstrated superior properties for data integration and provided solid basis for building classifiers at the second stage. Functional annotation revealed that genes involved in cell cycle and signal transduction activities were over-represented in the meta-signature. The mixture modeling approach unifies disparate gene expression data on a common probability scale allowing for robust, inter-study validated prognostic signatures to be obtained. With the emerging utility of microarrays for cancer prognosis, it will be important to establish paradigms to meta-analyze disparate gene expression data for prognostic signatures of potential clinical use.
A Measurement of the Neutrino Neutral Current π 0 Cross Section at MiniBooNE

The MiniBooNE neutrino beam and detector at Fermilab are used to study the production of neutral current {pi}{sup 0} events. The cross sections for neutrino interactions with mineral oil (CH{sub 2}) are reported for resonantly produced and coherently produced single {pi}{sup 0} events. We measure a resonant single {pi}{sup 0} cross section of {sigma}({nu}{sub {mu}} N {pi}{sup 0}) = (0.0129 {+-} 0.0011(stat.) {+-} 0.0043(syst.)) x 10{sup -36} cm{sup 2}/CH{sub 2} at a mean neutrino energy of 1.26 GeV. We measure a coherent single {pi}{sup 0} cross section of {sigma}({nu}{sub {mu}} A {yields} {nu}{sub {mu}} A {pi}{sup 0}) = (0.00077 {+-} 0.00016 (stat.) {+-} 0.00036 (syst.)) x 10{sup -36} cm{sup 2}/CH{sub 2} at mean neutrino energy 1.12 GeV.
Mouse Extracellular Superoxide Dismutase: Primary Structure, Tissue-specific Gene Expression, Chromosomal Localization, and Lung In Situ Hybridization

Extracellular superoxide dismutase (EC-SOD) is the major extracellular antioxidant enzyme. We have determined the primary structure of mouse EC-SOD by characterization of complementary DNA (cDNA) clones and by amino-acid sequence analysis of purified protein. cDNA sequence analysis indicates that mouse EC-SOD is synthesized as a 251-amino-acid precursor protein with a predicted molecular weight of 27,400 D. Amino-terminal micro sequence analysis of purified mature mouse lung EC-SOD demonstrated the sequence to begin with SSFDLADRLDPV-. These results indicate that EC-SOD as initially synthesized contains a 24-amino-acid precursor peptide, and that the mature protein is 227 amino acids in length. Computer algorithms that predict the most likely site of cotranslational signal peptidase cleavage suggest that processing will occur between amino acids 18 and 19 or 20 and 21, which implies that EC-SOD may be initially synthesized as a pre-pro-protein. Like human EC-SOD, mature mouse EC-SOD is glycosylated. The full-length mouse EC-SOD cDNA is 1,834 base pairs long and is 82% (79% for protein) identical to rat EC-SOD, but only 60% (60% for protein) identical to human EC-SOD. The mouse EC-SOD gene locus (Sod3) was mapped by interspecific backcross haplotype analysis as being 0.9 +/- 0.9 centimorgans distal to the Qdpr locus on mouse Chromosome 5, a position suggesting that the human homologue of EC-SOD will map close to the human QDPR locus (4p15.3). Of nine tissues examined by Northern blot analysis, those of the kidney and lung are by far the major tissues that express EC-SOD messenger RNA. Using in situ hybridization in the mouse lung, we demonstrate EC-SOD gene expression to be highly localized to alveolar Type II epithelial cells. These data suggest that alveolar Type II cells play a central role in mediating EC-SOD antioxidant function in the lung.
Electrical and Mechanical Responses in Deep Abdominal Extensor Muscles of Crayfish and Lobster

Electrical and mechanical studies have been made of the deep abdominal extensor muscles, medial (DEAM) and lateral (DEAL), of crayfish and lobster. The medial muscle responds to direct (intracellular) and indirect stimulation with a transient membrane depolarization which exhibits the properties of a propagated non-decremental action potential but does not overshoot the zero level. The amplitude is about 30 mv in crayfish and 50 mv in lobster. It is followed by a fast all-or-none twitch whose duration at 20°C is 30 to 50 msec. and whose developed tension is 500 gm/cm2 or about half the tetanic value. Membrane potential is K+-dependent and immersion in high K+ induces a brief transient tension rise as in other twitch-type muscles. The action potential and twitch are normal even if all external Na+ is replaced with sucrose but vary with external Ca++, the action potential increasing 8 to 10 mv for a twofold increase in Ca++. The lateral muscle (DEAL) is much slower and responds to intracellular stimulation only with an electrotonic or a local response. Mechanical responses and relaxation speeds are slow with minimal duration of contraction of 0.5 to 2 seconds. Immersion in high K solutions induces large maintained tensions. Sarcomere length in the fast DEAM is uniform and about 2 µ at rest, but in the DEAL speed is less and sarcomere length is greater averaging about 4.5 µ but with a mixed population of fibers.
Evidence that serotonergic projections to the substantia nigra in the rat arise in the dorsal, but not the median, raphe nucleus

Following microinjections of the fluorescent retrograde tracer Fast blue into the substantia nigra, large numbers of retrogradely labeled cells were observed in the dorsal raphe nucleus. Using immunocytochemical techniques it could be demonstrated that the majority of these cells contained serotonin-like-immunoreactivity. In contrast, careful examination of the region of the median raphe nucleus revealed no suggestion of a significant projection from the median raphe to the substantia nigra.
Structure of the Heat Shock Protein Chaperonin-10 of Mycobacterium leprae

Members of the chaperonin-10 (cpn10) protein family, also called heat shock protein 10 and in Escherichia coli GroES, play an important role in ensuring the proper folding of many proteins. The crystal structure of the Mycobacterium leprae cpn10 (Ml-cpn10) oligomer has been elucidated at a resolution of 3.5 angstroms. The architecture of the Ml-cpn10 heptamer resembles a dome with an oculus in its roof. The inner surface of the dome is hydrophilic and highly charged. A flexible region, known to interact with cpn60, extends from the lower rim of the dome. With the structure of a cpn10 heptamer now revealed and the structure of the E. coli GroEL previously known, models of cpn10:cpn60 and GroEL:GroES complexes are proposed.
Statistical mechanical considerations in the theory of the spread of the Hantavirus

Abstract Calculations in the theory of the spread of epidemics are described with particular focus on the estimation of motion parameters describing rodents that are the carriers of the Hantavirus epidemic. The data considered are of the “mark-recapture” kind, i.e., those collected by capturing, tagging and recapturing the animals in a prescribed finite region of space. The theoretical tool used is the Fokker–Planck equation, its characteristic quantities being the diffusion constant which describes the motion of the rodents, and the attractive potential which addresses their tendency to live near their burrows. The measurements are addressed through simple analytical calculations of the mean squared displacement of the animals relevant to the specific probing window in space corresponding to the trapping region. A Fourier prescription is provided to extract the home range of the animals from the observations. Applications of the theory to rodent movement in Panama and New Mexico are mentioned and several on-going generalizations of current models of Hantavirus epidemic spread are introduced.
Development of an Axisymmetric Pressure Application Method for Cylindrical Laminated Device Fabrication

Microchannel arrays are being developed across a wide spectrum of applications including blood processing, fuel cells and thermal management among many others. Typical arrays are based on a flat laminated architecture produced in a vacuum hot press (VHP) through uniaxial bonding pressure at elevated temperatures. Due to the cylindrical nature of certain microchannel applications, such as chemical processing within chemical facilities and heat rejection within Stirling cycle engines, the packaging of microchannel devices within cylindrical geometries would greatly simplify interconnect. This paper describes the development of a novel technique for axisymmetric diffusion bonding pressure application with the use of a VHP capable of producing cylindrical laminated devices. Uniaxial bonding pressure is converted to axisymmetric pressure through the use of conical wedges. Pressure magnitude and distribution are controlled by the geometry of the pressure delivery platens, the design of which was aided by finite element analysis. Cylindrical test articles were produced by patterning thin metal foils by laser machining a single roll of metal shim stock, which was then coiled within an outer tube shell and axisymmetrically bonded with the VHP to produce a cylindrical laminated workpiece. Preliminary bonding results show quality bond lines with minimal void fractions. This new architecture is shown to be feasible for producing cylindrical laminated devices by microlamination using traditional VHP equipment.Copyright © 2010 by ASME
Activation of prothrombin and factor X: Function of previously unrecognized plasma protein

Abstract Bovine plasma proteins adsorbed on barium carbonate and eluted were systematically fractionated and purified by extensive modification of previously developed methods. Included were prothrombin, Factor X, Factor VII, Factor IX, Protein C and a previously unidentified procoagulant called Protein M. This protein accelerated the generation of thrombin in a five-component system consisting of thrombin zymogen, Factor Xa, Ac-globulin (Factor V), phospholipid and calcium ions. This was true even when the zymogen was prethrombin 1, which does not contain gamma carboxyglutamic acid residues. Protein M also accelerated the transformation of purified Factor X to active Factor X in the presence of thromboplastin and calcium ions. Protein M also shortened the prothrombin time of plasma from steers treated with dicumarol, and human Factor VII deficient plasma. Protein M is, however, not identical with classical Factor VII. On the basis of limited experiments, it appears that a plasma precursor (MW = 72,000) converts to Protein M (MW = 50,000) and an inhibitor (MW = 22,000). All three are single chain glycoproteins.
Developing active readers: A pedagogical framework for the second language reading class

Abstract This paper presents a pedagogical reading framework for integrating principles of theory and practice. The ACTIVE reading framework suggests that six components should be part of reading lessons: 6 . A: Activate prior knowledge C: Cultivate vocabulary T: Teach for comprehension I: Increase reading rate V: Verify reading strategies E: Evaluate progress Each of the elements of this framework overlaps with at least one other element. This emphasizes the interactive nature of the reading process, that each skill and strategy ties into others. A discussion of the role of motivation and criteria for selecting reading materials is discussed in light of this framework.
Isotopic constraints on Columbia River flood basalt genesis and the nature of the subcontinental mantle

Abstract Pb, O, Nd, and Sr isotopic data for the Columbia River basalts paint a complex picture for the origin of this flood basalt province. At least 3 distinct mantle sources appear to have been involved, superimposed upon which are the effects of crystal fractionation and mass exchange with evolved crustal wallrocks. To a large degree, the initiation of Columbia River volcanism and the geochemical characteristics of the basalts appear to have been influenced by subduction of the Juan de Fuca plate beneath the North American plate in a manner analogous to the origin of back-arc basins. The physical structure of the crust appears to have influenced the late stage evolution of the magmas by directing the locus of eruption to the border between the ancient continental interior and much younger crust to the south and west. This proximity to the continental interior also allowed old enriched subcontinental mantle to become involved in the very late stages of Columbia River volcanism. An important consequence of the existence of enriched mantle regions beneath continents is that the combination, crust plus enriched mantle, requires more incompatible elements to have been extracted from the remainder of the mantle than would be the case if no enriched mantle existed.
Three-dimensional canine heart model for cardiac elastography

Purpose: A three-dimensional finite element analysis based canine heart model is introduced that would enable the assessment of cardiac function. Methods: The three-dimensional canine heart model is based on the cardiac deformation and motion model obtained from the Cardiac Mechanics Research Group at UCSD. The canine heart model is incorporated into ultrasound simulation programs previously developed in the laboratory, enabling the generation of simulated ultrasound radiofrequency data to evaluate algorithms for cardiac elastography. The authors utilize a two-dimensional multilevel hybrid method to estimate local displacements and strain from the simulated cardiac radiofrequency data. Results: Tissue displacements and strains estimated along both the axial and lateral directions (with respect to the ultrasound scan plane) are compared to the actual scatterer movement obtained using the canine heart model. Simulation and strain estimation algorithms combined with the three-dimensional canine heart model provide high resolution displacement and strain curves for improved analysis of cardiac function. The use of principal component analysis along parasternal cardiac short axis views is also presented. Conclusions: A 3D cardiac deformation model is proposed for evaluating displacement tracking and strain estimation algorithms for cardiac strain imaging. Validation of the model is shown using ultrasound simulations to generate axial and lateral displacement and strain curves that are similar to the actual axial and lateral displacement and strain curves.
Impact of ocean warm layer thickness on the intensity of hurricane Katrina in a regional coupled model

The effect of pre-storm subsurface thermal structure on the intensity of hurricane Katrina (2005) is examined using a regional coupled model. The Estimating Circulation and Climate of Ocean (ECCO) ocean state estimate is used to initialize the ocean component of the coupled model, and the source of deficiencies in the simulation of Katrina intensity is investigated in relation to the initial depth of 26 °C isotherm (D26). The model underestimates the intensity of Katrina partly due to shallow D26 in ECCO. Sensitivity tests with various ECCO initial fields indicate that the correct relationship between intensity and D26 cannot be derived because D26 variability is underestimated in ECCO. A series of idealized experiments is carried out by modifying initial ECCO D26 to match the observed range. A more reasonable relationship between Katrina’s intensity and pre-storm D26 emerges: the intensity is much more sensitive to D26 than to sea surface temperature (SST). Ocean mixed layer process plays a critical role in modulating inner-core SSTs when D26 is deep, reducing mixed layer cooling and lowering the center pressure of the Katrina. Our result lends strong support to the notion that accurate initialization of pre-storm subsurface thermal structure in prediction models is critical for a skillful forecast of intensity of Katrina and likely other intense storms.