cssi/SciSciGPT-SciSciNet huggingface dataset:
Study Genie: An Intelligent and Collaborative Web-based Study Platform (Abstract Only)

Research has shown that the cheat sheet preparation process helps students with performance in exams. However, results have been inconclusive in determining the most effective guiding principles in creating and using cheat sheets. The traditional method of collecting and annotating cheat sheets is time consuming and exhaustive, and fails to capture students' preparation process. This work examines the development and impacts of a new web-based study preparation tool, Study Genie, supporting collaborative note creation, editing, sharing, and cheat sheet organization. This new educational technology enables big-data learning analytics, permitting quantitative data modeling on connecting formal and informal digital learning footprints. Study Genie also systematically automates cheat-sheet quality evaluation, which traditionally could only have been done qualitatively. A classroom study was conducted to measure the technology and learning effects in an introductory computer science programming course. Results suggest that actions associated with editing and organizing cheat sheets are positively correlated with exam performance, and that there is a significant difference between the activity of high-performing and low-performing students. Through these results, Study Genie presents itself as an opportunity for mass data collection, providing insight into the assembly process rather than just the finished product in cheat sheet creation.
Mexican–American Interaction with Social Systems:

A significant number of weaknesses formerly attributed to internal dynamics of families can be ascribed to the limitations created by external systems
Bell state optimizations for reliable quantum applications

Well-defined and stable quantum networks are essential to realize functional quantum communication applications. In particular, the quantum states must be precisely controlled to produce meaningful results. To counteract the unstable phase shifts in photonic systems, we apply local Bell state measurements to calibrate a non-local quantum channel. The calibration procedure is tested by applying a time encoded quantum key distribution procedure using entangled photons.
Critical Studies of Innovation: Alternative Approaches to the Pro-Innovation Bias

Immediately in the introduction, editors Benoit Godin and Dominique Vinck observe that the study of innovation has become an industry, one that produces an abundance of literature and texts. Yet, c...
A model for teaching newborn circumcision.

Background: Hundreds of residents are trained to perform neonatal circumcision every year. This article describes the construction and use of a model designed to introduce trainees to neonatal circumcision using the Gomco technique. Technique: A circumcision model was constructed using a clipboard, a pacifier, examination gloves, a rubber band, a syringe, tape, surgical towels, and a circumcision kit containing a 1.3 Gomco clamp, hemostats, surgical scissors, and a scalpel blade. Discussion: With each trainee using a separate model, one instructor was able to guide four interns through three simulations each during a 1-hour orientation session.
Long Term Long-Line Shark Catches: Variations by Site and Tidal Stage

Abstract Long term long-line shark catch variations (38 yr) at two Onslow Bay, North Carolina sites were examined for differences in catches by sites and tidal stages. Catches were highly significantly different between sites. Catches by tidal stage were not significantly different at each site.
Therapeutic Potential of Gastric Electrical Stimulation for Obesity

Obesity is one of the major public health problems in the world. While various methods have been investigated or introduced, bariatric surgical procedures are currently the only effective long-term therapies for treating obesity. Due to mortality and morbidity, the bariatric surgery is limited to a subset of patients with morbid obesity. In this chapter we present an overview of an emerging anti-obesity therapy: gastric electrical stimulation (GES). First, the scientific basis for GES as a potential therapy for obesity is introduced. Secondly, GES methodologies and configurations are presented. Methods of GES that have been used for treating obesity are then introduced, and their effects on food intake and body weight are presented, followed with the discussion on possible mechanical, neural and hormonal mechanisms involved in the anti-obesity effect of GES. Finally, our viewpoint on the potential of GES for obesity and future development of the GES therapy are provided.
Gyre-Scale Reciprocal Acoustic Transmissions

Three acoustic transceivers moored in a triangle approximately 1000 km on a side simultaneously transmitted broadband signals to one another for four months during summer 1987. The triangle extended in latitude from the Subtropical Front to the Subarctic Front in the North Central Pacific Ocean. Individual ray arrivals were resolved and their arrival times measured with a precision of a few milliseconds using phase-coded transmissions centered at 250 Hz. Using CTD data taken on the three legs, mean sound speed profiles were calculated using the Chen and Millero and Del Grosso sound speed algorithms. The measured arrival patterns agree best with arrival patterns predicted using the Del Grosso algorithm. Predicted and measured absolute travel times also agree best using the Del Grosso algorithm. All resolvable ray paths are surface-reflected, and the travel times therefore represent both range and depth averages. The sum of the travel times of oppositely traveling signals depends on the sound speed field. The sum travel times decreased as the summer thermocline formed during the experiment. The travel times suggest that the thermocline deepened episodically on the northern leg of the triangle. Historical data gives a low mesoscale energy level for the experimental area, with small temperature fluctuations in the main thermocline. The sum travel times correspondingly show little low-frequency variability except for that caused by the formation of the summer thermocline. The transmissions along the east and west legs of the triangle propagated through a frontal region, which was located at 34°-38° N. CTD and XBT data collected on the deployment and recovery cruises suggests that the frontal region was stable throughout the experiment. The difference in the travel times of oppositely traveling signals depends on the current field. Since the experimental area has both a low mesoscale energy level and low mean currents, the differential travel times are dominated by tidal currents. Tidal currents determined acoustically agree well with Schwiderski’s tidal model and with barotropic tidal currents determined from a current meter mooring located approximately in the center of the northern leg of the triangle. At frequencies below one cycle per day the differential travel times give depth and range-averaged currents of a few mm/s, with an eastward current along the northern leg. The circulation around the entire triangle corresponds to relative vorticities of about 10-8 s -1, of the same magnitude as expected from Sverdrup dynamics.
Interpretation and Reporting of SPECT Myocardial Perfusion Imaging

The review and interpretation of myocardial perfusion images is the key duty of a nuclear cardiologist and must be performed in a systematic fashion (Table 16.1).
Obstacle-Aided Navigation of a Soft Growing Robot

For many types of robots, avoiding obstacles is necessary to prevent damage to the robot and environment. As a result, obstacle avoidance has historically been an important problem in robot path planning and control. Soft robots represent a paradigm shift with respect to obstacle avoidance because their low mass and compliant bodies can make collisions with obstacles inherently safe. Here we consider the benefits of intentional obstacle collisions for soft robot navigation. We develop and experimentally verify a model of robot-obstacle interaction for a tip-extending soft robot. Building on the obstacle interaction model, we develop an algorithm to determine the path of a growing robot that takes into account obstacle collisions. We find that obstacle collisions can be beneficial for open-loop navigation of growing robots because the obstacles passively steer the robot, both reducing the uncertainty of the location of the robot and directing the robot to targets that do not lie on a straight path from the starting point. Our work shows that for a robot with predictable and safe interactions with obstacles, target locations in a cluttered, mapped environment can be reached reliably by simply setting the initial trajectory. This has implications for the control and design of robots with minimal active steering.
Designing for equitable civic engagement: Participatory design and discourse in contested spaces

A common theme of research on participatory democracy and citizen engagement centres on the need for empirical studies that conduct a deep exploration of the nuances and complexities of these proce...
Using Euclidean distance in the comparative analysis of taxonomic abundance

Abstract This paper describes and demonstrates the usefulness of calculating Euclidean distance to determine both baseline hunting behavior on the site or regional level, and as a way of determining and presenting variation from that baseline. The method is elegant, flexible, and produces easily understood data visualizations, particularly in contexts where faunal data are reasonably divided into three analytical categories. We give an example from the desert borderlands of the U.S. Southwest/Mexican Northwest to illustrate the utility of the method.
Neurological Pupil Index and Pupillary Light Reflex by Pupillometry Predict Outcome Early After Cardiac Arrest

The absence of the pupillary light reflex (PLR) 3 days after cardiac arrest predicts poor outcome, but quantitative PLR assessment with pupillometry early after recovery of spontaneous circulation (ROSC) and throughout targeted temperature management (TTM) has rarely been evaluated. Fifty-five adult patients treated with TTM with available pupillometry data from the NeurOptics NPi-200 were studied. Discharge outcome was classified good if the cerebral performance category score was 1–2, poor if 3–5. Pupil size, PLR percent constriction (%PLR), and constriction velocity (CV) were determined at TTM start and 6 (± 2)-h post-ROSC (“early”), and throughout TTM using data from the worst eye at each assessment. The Neurological Pupil index (NPi) was also determined at each pupil assessment; the NPi is scored from 0 (nonreactive) to 5 (brisk) with values < 3 considered sluggish or abnormal. Prognostic performance to predict poor outcome was assessed with receiver operator characteristic curves. All nine patients with ≥ 1 nonreactive pupil (NPi = 0) within 6 (± 2) h after ROSC died, and 12/14 (86%) with sluggish pupils (0 < NPi < 3) had poor outcomes. 15/29 (52%) patients with normal pupil reactivity (NPi ≥ 3) had poor outcomes, four survived with cerebral performance category = 3, three died of cardiac causes, and eight died of neurologic causes. During TTM, 20/21 (95%) patients with nonreactive pupils had poor outcomes, 9/14 (64%) of patients with sluggish pupils had poor outcomes, and 9/20 (45%) with normal pupil reactivity had poor outcomes. Pupil size did not predict outcome, but NPi (AUC = 0.72 [0.59–0.86], p < 0.001), %PLR (AUC = 0.75 [0.62–0.88], p < 0.001) and CV (AUC = 0.78 [0.66–0.91], p < 0.001) at 6 h predicted poor outcome. When nonreactive pupils were first detected, 75% were < 5 mm. Very early after resuscitation from cardiac arrest, abnormal Neurological Pupil index and pupillary light reflex measurements by pupillometer are predictive of poor outcome, and are not usually associated with dilated pupils.
Invited Commentary: Beyond Overdiagnosis—Diagnosis Without Benefit

In an accompanying article, Hofmann (Am J Epidemiol. 2019;188(10):1812-1817) seeks to clarify the concept of overdiagnosis by screening. He makes a helpful suggestion to reconnect diagnosis with patient suffering, pointing out the underlying issue in overdiagnosis of prognostic uncertainty. He then divides prognostic uncertainty into developmental and progression uncertainty, using a categorical model of disease progression through indicators to manifest disease. This model could be improved by considering the heterogeneity of patient-condition combinations. This leads to an understanding of the probabilistic nature of the connection between any indicator in a specific individual and patient suffering. The model also needs to consider the time span over which the patient-condition combination leads to patient suffering. I propose a simpler approach that goes further to focus not only on overdiagnosis but also on the broader problem of diagnosis without benefit and diagnosis without net benefit. This makes measurement easier and focuses attention where it belongs: on the harm caused by overly aggressive screening programs.
Characterizing Biases in Mountain Snow Accumulation From Global Data Sets

Author(s): Wrzesien, Melissa L; Pavelsky, Tamlin M; Durand, Michael T; Dozier, Jeff; Lundquist, Jessica D
Chemogenetic activation of astrocytes in the hippocampus and cortex changes the transcriptome of microglia and other cell types

Astrocytes are the most common glial cell type in the brain, yet, it is still not clear how their activation affects the transcriptome of other brain cells such as microglia and neurons. Engineered G protein-coupled receptors called Designer Receptors Exclusively Activated by Designer Drugs (DREADDS) make it possible to selectively activate specific cell types, such as neurons and astrocytes. By combining the selective activation of astrocytes with single cell RNA sequencing, we were able to study transcriptional changes that occur in response to the activation of astrocytes at the single cell level. Interestingly, our data shows that long-term activation of astrocytes in healthy mice results in dramatic alteration in the transcriptome of astrocytes and microglia. Genes that were differentially expressed in these Gq-DREADD-activated astrocytes were involved in neurogenesis and low density lipoprotein particle biology, while those in the microglia were involved in the response to lipoproteins, and the migration and chemotaxis of immune cells. Furthermore, network analysis showed that Gq-DREADD-mediated activation in astrocytes resulted in an upregulation of genes involved in the G protein-coupled receptor signaling pathway and calcium ion homeostasis. This confirmed the activation of astrocytes through the expressed DREADDS. Our findings show the importance of considering the transcriptomic alteration in microglia and neurons after the activation of astrocytes in in vivo models. Therefore, our data will serve as a resource for the broader neuroscience community.
Inflammation, Cognition, and White Matter in Older Adults: An Examination by Race.

Objectives Non-Latino Black adults have greater risk for Alzheimer's dementia compared to non-Latino White adults, possibly due to factors disproportionally affecting Black adults including cardiovascular disease (CVD). Chronic peripheral inflammation is implicated in both Alzheimer's dementia and CVD and is known to impact cognition and cerebral white matter, yet little work has examined these associations by race. This study examined associations between inflammation, cognition, and cerebral white matter generally, and by race. Methods Eighty-six non-demented older Black and White participants (age = 69.03; 50% female; 45% Black participants) underwent fasting venipuncture, cognitive testing, and MRI. Serum was assayed for interleukin-6 (IL-6), C-reactive protein (CRP), and interleukin 1-beta. Cognitive domains included memory, executive function, and attention/information processing. MRI measures included white matter hyperintensity volumes (WMH) and quantification of white matter integrity in areas outside WMHs via DTI-derived fractional anisotropy (FA) and mean diffusivity, as well as multi-component relaxometry derived myelin water fraction (MWF). Results Black and White participants did not differ on age, sex, or CVD risk. Separate linear regression models adjusting for relevant confounders revealed that higher IL-6 associated with lower executive function and higher CRP levels associated with lower FA and MWF. Stratified analyses revealed that these association were significant for Black participants only. Discussion These findings suggest that peripheral inflammation is inversely associated with select cognitive domains and white matter integrity (but not WMHs), particularly in older Black adults. It is important to consider race when investigating inflammatory associates of brain and behavior.
Toxoplasmosis: Recent Advances in Understanding the Link Between Infection and Host Behavior.

Humans, wildlife, and domestic animals are intimately linked through shared infections. Many parasites and pathogens use multiple host species, either opportunistically or sequentially, such that m...
Environmental, public health, and economic development perspectives at a Superfund site: A Q methodology approach

Environmental remediation and restoration at hazardous waste sites is important for reducing risks and sustaining local economies. Navigating trade-offs between diverse and conflicting stakeholder perspectives to identify practical and affordable ways forward is important for sustaining objectives and goals. Differences in stakeholder perspectives are informed by their affiliations and roles and their views towards environmental, economic development, and public health issues. We used Q methodology, an approach that combines priority sorting and interviews, to elicit and interpret the perspectives of 28 stakeholders, representing government entities, non-profits, and industries at a mining-impacted Superfund site in the Coeur d'Alene Basin of Idaho, USA. Four primary perspectives were distinguished by their prioritization of: 1) government intervention, 2) the Superfund remediation, 3) local concerns, and 4) public-private partnerships. Participants' roles and affiliations played an influential role in informing primary perspectives. Overall, collaboration was viewed more favorably when it was associated with concrete implementation pathways.
Cytomegalovirus and Herpes Simplex Virus Co-Infection in an HIV-Negative Patient: A Case Report.

Herpes simplex virus (HSV) and cytomegalovirus (CMV) infections are commonly seen in immunocompromised patients, particularly in patients with HIV. However, fulminant CMV infection and concurrent infection with HSV and CMV in non-HIV patients are quite rare. We present the case of a 72-year-old HIV-negative man with a history of oropharyngeal carcinoma in remission and recent treatment of immune thrombocytopenic purpura with high-dose steroids who was transferred from an outside hospital for Ear Nose and Throat (ENT) evaluation of a non-healing buccal ulcer. During initial presentation, the patient was found to be febrile with acute hypoxic respiratory failure and a chest x-ray suggestive of bacterial pneumonia, though he failed to improve with broad-spectrum antibiotic therapy. He underwent esophagogastroduodenoscopy for dysphagia, which revealed a discrete ulcer positive for CMV. Biopsy of his buccal lesion was ultimately positive for HSV-1 and HSV-2. The patient's clinical status improved significantly following the initiation of antiviral therapy.It is important to consider CMV infection in the setting of persistent fever, respiratory distress, or dysphagia in the non-HIV infected patient, especially in the setting of prolonged steroid use. CMV and HSV infection can occur simultaneously at distinct sites in the body, and CMV infection may predispose to HSV reactivation due to its long term effect on cell-mediated immunity. Early recognition of opportunistic infections and initiation of antiviral therapy in immunocompromised patients can greatly affect length of hospital stay, morbidity, and, ultimately, mortality.
Environmentally contingent control of Candida albicans cell wall integrity by transcriptional regulator Cup9

The fungal pathogen Candida albicans is surrounded by a cell wall that is the target of caspofungin and other echinocandin antifungals. Candida albicans can grow in several morphological forms, notably budding yeast and hyphae. Yeast and hyphal forms differ in cell wall composition, leading us to hypothesize that there may be distinct genes required for yeast and hyphal responses to caspofungin. Mutants in 27 genes reported previously to be caspofungin hypersensitive under yeast growth conditions were all caspofungin hypersensitive under hyphal growth conditions as well. However, a screen of mutants defective in transcription factor genes revealed that Cup9 is required for normal caspofungin tolerance under hyphal and not yeast growth conditions. In a hyphal-defective efg1Δ/Δ background, Cup9 is still required for normal caspofungin tolerance. This result argues that Cup9 function is related to growth conditions rather than cell morphology. RNA-seq conducted under hyphal growth conditions indicated that 361 genes were up-regulated and 145 genes were down-regulated in response to caspofungin treatment. Both classes of caspofungin-responsive genes were enriched for cell wall-related proteins, as expected for a response to disruption of cell wall integrity and biosynthesis. The cup9Δ/Δ mutant, treated with caspofungin, had reduced RNA levels of 40 caspofungin up-regulated genes, and had increased RNA levels of 8 caspofungin down-regulated genes, an indication that Cup9 has a narrow rather than global role in the cell wall integrity response. Five Cup9-activated surface-protein genes have roles in cell wall integrity, based on mutant analysis published previously (PGA31 and IFF11) or shown here (ORF19.3499, ORF19.851, or PGA28), and therefore may explain the hypersensitivity of the cup9Δ/Δmutant to caspofungin. Our findings define Cup9 as a new determinant of caspofungin susceptibility.
Improving linkage and retention in treatment among people living with HIV and comorbid substance use

HIV and substance use interact synergistically to exacerbate disease progression and contribute to poorer engagement in treatment. There is a lack of qualitative research exploring the complexity of systems that impact HIV patients' linkage to and retention in both substance use and HIV care. Data from qualitative individual interviews with 16 HIV and 13 substance use providers were analyzed using applied thematic analysis. Four themes emerged as barriers to linkage to care providers limited knowledge with appropriate referrals; limited access to treatment options within the community; difficult admission criteria to substance use facilities; and communication challenges across providers including power differential. Emergent themes as barriers to treatment retention were: unstable life of people who use drugs; providers' negative attitude and stigma towards patients; and transportation challenges. Interventions are needed to increase provider cross-training in HIV and substance use disorders, reduce barriers to accessing treatment, and improve communication across providers are needed.
Atmospheric pressure ionization of chlorinated ethanes in ion mobility spectrometry and mass spectrometry

This study investigates the APCI mechanisms associated with chlorinated ethanes in an attempt to define conditions under which unique pseudo-molecular adducts, in addition to chloride ion, can be produced for analytical measurements using IMS and MS. The ionization chemistry of chlorinated compounds typically leads to the detection of only the halide ions. Using molecular modeling, which provides insights into the ion formation and relative binding energies, predictions for the formation of pseudo-molecular adducts are postulated. Predicted structures of the chloride ion with multiple hydrogens on the ethane backbone was supported by the observation of specific pseudo-molecular adducts in IMS and MS spectra. With the proper instrumental conditions, such as short reaction times and low temperatures, the molecular species of many chlorinated ethanes can be detected, allowing for identification of specific compounds.
Abstract 2885: Predictors of Poor Outcome in Moderate to Severe Strokes in a Statewide Telestroke Network

Objective: to determine the predictors of poor outcome after IV thrombolysis for moderate to severe strokes in a statewide telestroke network. Background: The Arkansas SAVES (Stroke Assistance thro...
Amino acid regulation of insulin action in isolated adipocytes. Selective ability of amino acids to enhance both insulin sensitivity and maximal insulin responsiveness of the protein synthesis system.

Using the number and concentration of amino acids in Dulbecco's modified Eagle's medium as reference (DMEM = 100%), we found that a maximally effective concentration of insulin (10 ng/ml) stimulated protein synthesis by 125% over basal rate in the presence of 50% amino acids (EC50 = 19%), but by only 48% in amino acid-free buffer. Moreover, time course experiments revealed that amino acid regulation of insulin action was very rapid (t½ of 9.5 min) and readily reversible ( In conclusion: 1) amino acids modulate insulin action by enhancing maximal insulin responsiveness and insulin sensitivity of the protein synthesis system, and the regulatory site of amino acid action appears to be distal to the common signal pathway, within the insulin action-protein synthesis cascade, and 2) the effects of amino acids are specific, in that basal rates of protein synthesis are unaffected, only certain amino acids influence insulin action, and amino acids fail to alter insulin binding or the insulin-responsive glucose transport system. These studies, together with those in the companion paper, demonstrate that the pleiotropic actions of insulin on enhancing glucose uptake and protein synthesis are mediated through divergent pathways that can be independently regulated. It is likely that such control mechanisms are involved in coordinating the disposition of metabolic substrates during the daily fluctuations inam ino acids and glucose associated with dietary uptake andm ay be relevant to the etiology of certain insulin-resistant states such as type II diabetes and obesity.
High-Quality Texture Mapping and Rendering of Point Models

Texture mapping enhances the visual richness of image synthesis. In this article, we discuss a novel framework, TSplatting, for high-quality texture mapping of point-based models without connectivity information. By splatting texture coordinates of each point followed by a fragment texture lookup, the framework is capable of interactively mapping a coarse point-based model with high-resolution textures. Keywords: texture mapping; point-based rendering; splatting; interactive texture mapping; TSplatting; texture coordinates splatting; anti-aliasing; boundary artifacts
Band-narrowing effects in URh3Bx.

Data are presented showing that the addition of B to ${\mathrm{URh}}_{3}$, which is well known to be a compound having itinerant f electrons, results in a localization of those f electrons and a narrowing of the 5f band. Band-structure calculations carried out for ${\mathrm{URh}}_{3}$ and ${\mathrm{URh}}_{3}$B show that the band narrowing occurs due to a dehybridization between U f electrons and Rh d electrons as boron is added to the system. The nature of the band narrowing relative to this dehybridization is clarified. Comparison of heat-capacity data with the band-structure results shows that the band narrowing causes an increase both in the f-electron density of states at the Fermi energy and in the f-electron mass enhancement. However, the latter is still smaller than that seen in classic mixed-valence systems, such as ${\mathrm{CeSn}}_{3}$, or in heavy-fermion systems, such as ${\mathrm{UPt}}_{3}$.
Explanation, Contrast, and the Primacy of Practice

: The common practice of giving (comparing, rejecting and inferring) explanations of phenomena is at the root of articulate learning, including the enterprises we collect under the noun ‘science’. The way that practice privileges a single item from the myriad relevant to any phenomenon tells us something about articulateness itself.
Divisibility of function field class numbers

Let X → S be an abelian scheme over a finite field. We show the existence of a constant δ such that for a set of rational primes l of density one, if q ≡ 1 mod l is sufficiently large and divisible , then the proportion of s ∈ S(Fq) for which l| ∣Xs(Fq) ∣∣ is at least 1/δl−O(1/l2). We apply this to study class numbers of cyclic covers of the projective line.
Investigation of Stilbenoids as Potential Therapeutic Agents for Rotavirus Gastroenteritis

Rotavirus (RV) infections cause severe diarrhea in infants and young children worldwide. Vaccines are available but cost prohibitive for many countries and only reduce severe symptoms. Vaccinated infants continue to shed infectious particles, and studies show decreased efficacy of the RV vaccines in tropical and subtropical countries where they are needed most. Continuing surveillance for new RV strains, assessment of vaccine efficacy, and development of cost effective antiviral drugs remain an important aspect of RV studies. This study was to determine the efficacy of antioxidant and anti-inflammatory stilbenoids to inhibit RV replication. Peanut (A. hypogaea) hairy root cultures were induced to produce stilbenoids, which were purified by high performance countercurrent chromatography (HPCCC) and analyzed by HPLC. HT29.f8 cells were infected with RV in the presence stilbenoids. Cell viability counts showed no cytotoxic effects on HT29.f8 cells. Viral infectivity titers were calculated and comparatively assessed to determine the effects of stilbenoid treatments. Two stilbenoids, trans-arachidin-1 and trans-arachidin-3, show a significant decrease in RV infectivity titers. Western blot analyses performed on the infected cell lysates complemented the infectivity titrations and indicated a significant decrease in viral replication. These studies show the therapeutic potential of the stilbenoids against RV replication.
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Background: Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was originally developed for human cell lines, later adaptations made the processing of plant tissues possible. Challenges still remain in processing recalcitrant tissues that have low DNA content. Results: By removing steps requiring the use of gel agarose plugs in DNase-seq, we were able to significantly reduce the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues. We refer to this simplified protocol as DNase I SIM (for simplified in-nucleus method). We were able to successfully create DNase-seq libraries for both leaf and root tissues in Arabidopsis using DNase I SIM. Conclusion: This protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high reso lution mapping of DNase I hypersensitive sites.
Modeling enhancements in the DUDE framework for grayscale image denoising

We present recent theoretical and practical developments aimed at enhancing the performance of the discrete universal denoiser (DUDE) [1] on grayscale images. In particular, a new statistical model for images, formalizing the assumptions underlying the use of prediction, together with a more robust use of pre-filtering and iteration have led to significant improvements in denoising performance for certain types of noise, compared with the state of the art (which includes the first DUDE implementation for this application in [2]).
Survival and Growth of the Early Stages of Gulf Killifish in Various Salinities

Abstract Hatching percentage, time of hatching, and subsequent 2.5-week growth and survival of fry of gulf killifish (Fundulus grandis) were compared at 0, 5, 10, 15, 20, 25, 30, 35, 40, 60, and 80‰ salinities. Mean hatching percentages in the 0–35‰, range, with the exception of 69.0% hatch at 10‰, were high (77.0–91.3%) and did not differ significantly. At 60 and 80‰, hatching was significantly lower (21.7 and 35.7%, respectively) than at all other salinities. Times to beginning of hatch and to median hatch were positively correlated with salinity (r 2 = 0.92). Fry growth in length was highest at 20‰ and lowest at 60 and 80‰. At all other salinities, mean final length did not differ significantly. Significantly higher mean final weight of fry was recorded at 5. 20, and 35‰ than at 0, 60, and 80‰. Mean survival of fry was significantly lower at 0 and 80‰ (60.0%) than at 5–60‰ (95.0–100.0%), with the exception of 80.0% survival at 35‰. Salinity ranges of 0–40‰ for incubation and 5–40‰ for fry growth and su...
Utility of computerized case simulations in therapist training and evaluation

The present quasi-experimental study attempted to evaluate the utility of a set of three computer simulations for therapist training and evaluation by comparing psychology students from two universities at three training levels. The three groups consisted of junior and senior level undergraduates, first year graduate students, and third or fourth year graduate students. Analysis of outcome measures indicated subjects were generally accepting of computer simulation use for therapist training and evaluation and performance differences between the groups could be explained by group population differences. The results are discussed relative to the utility for computer simulations use for therapist training and evaluation.
Active immunization of mice with porcine zonae pellucidae: immune response and effect on fertility.

Female mice were heteroimmunized with varying dosages of intact and heat-solubilized porcine zonae. Mouse immune response was monitored by radioimmunoassay and the effect on mouse fertility of circulating antibodies to pig zonae was observed. Porcine zonae were a potent heteroimmunogen in the mouse and, for all dosages studied, the immune response was characterized by a rapid rise in titer, culminating in a peak which was followed by a plateau period of extended duration and of significantly high anti-zona activity. Maximum immune response was achieved using a dosage of 4000 heat-solubilized zonae per mouse. Studies involving alteration of immunization regimes, but use of a constant zonae dosage, indicated that maximal response to this antigenic target was obtained using intact zonae applied over a series of injections rather than in a single application. In vitro studies involving proteolytic lysis of or sperm attachment to mouse zonae pretreated with either antibodies to mouse zonae (homologous system) or pig zonae (heterologous system) demonstrated that zona antibodies are considerably more biologically effective in the homologous system. Immunization of mice with pig zonae had no significant effect upon altering mouse fertility. The significance of these fertility results is discussed with respect to the information obtained from the in vitro studies and in respect to the continued consideration of the zona as an immunocontraceptive antigenic target.
Can women change the future

Abstract This article critiques the preceding article by Joshi as overly utopian. First, South Asia is not a homogenous region, and, second, glorification of village life may represent a retreat from the potential benefit of the modern world. Drawing on Gandhi, the positive empowerment of women is seen as a way of moving from the traditional values of diverse South Asian societies towards a future based on gender justice for women which draws on the strength of their cultural heritage.
Sooting limits of nonpremixed n-heptane, n-butanol, and methyl butanoate flames: Experimental determination and mechanistic analysis

Abstract The sooting limits of nonpremixed n -heptane, n -butanol, and methyl butanoate flames were determined experimentally in a liquid pool stagnation-flow configuration. In addition, complementary simulations with detailed polycyclic aromatic hydrocarbon (PAH) chemistry and a detailed soot model, based on the Hybrid Method of Moments (HMOM), were performed and compared with the experimental critical strain rates for the sooting flames. Argon dilution was used to keep the thermal environment for the three fuel cases nearly the same to elucidate the chemical effects. Both experiment and simulation showed that n -heptane and n -butanol had similar sooting characteristics, while methyl butanoate had the least sooting propensity. Further sensitivity and reaction path analysis demonstrates that the three fuels share similar PAH chemical pathways, and C 5 and C 6 ring formation from the intermediate chain species is found to be the rate-limiting step. The differences in sooting propensity lie in the fuel breakdown processes. Specifically, the oxygen bounded in n -butanol does not reduce soot precursor concentrations but is primarily involved in intramolecular water elimination reactions. On the contrary, the fuel bound oxygen in methyl butanoate shortens the carbon chain of the soot precursors and promotes their oxidation, which reduces the total carbon available for soot formation.
Water Content Mediated Microaerophilic Toluene Biodegradation in Arid Vadose Zone Materials.

We investigated the conditions promoting toluene biodegradation for gasoline-contaminated near-surface (0.6 m depth) and subsurface (4.7 to 5.0 m depth) vadose zone soils sampled from an arid environment. At both depths, water addition was required for toluene biodegradation to occur. In near-surface samples, no inorganic nutrient addition was necessary and (i) biodegradation was fastest at 0.0 MPa, (ii) biodegradation rates decreased with decreasing water potential down to ?1.0 MPa, and (iii) biodegradation was undetectable at ?1.5 MPa. For subsurface material, toluene depletion was stimulated either by slurrying with a nutrient solution or by adjusting the moisture content to 20% (0.0 MPa) with nutrient solution and lowering the oxygen concentration (to effectively 1 mg L?1 in the aqueous phase). Thus, in the subsurface material, toluene depletion was microaerobic and nutrient-limited, occurring only under low oxygen and with inorganic nutrient addition. Our studies implicate microaerophily as an important characteristic of the toluene-degrading communities in these dry soils, with soil water as a primary controller of oxygen availability.
Fast recovery, high sensitivity NMR probe and preamplifier for low frequencies

The design of a probe‐preamplifier combination which reduces the NMR receiver recovery time following a pulse by a factor of at least twenty at 5 MHz is described. The preamplifier, which has a noise figure of 1.3 dB, employs negative feedback to damp the probe coil (a typical effective Q is 7), but maintains the signal‐to‐noise ratio that one would expect from an undamped coil. In addition, the use of a short phase‐inverted pulse following the main transmitter pulse serves to reduce drastically the ring‐down of the probe for those high voltages where the preamplifier is inoperative. Optimum utilization of transmitter power in achieving fast pulse rise times is also discussed, as well as elimination of ’’phase‐glitch’’ by proper tuning and the use of a broadband transmitter.
Genomic resources for chicken

The recent sequencing and draft assembly of a chicken genome has provided biologists with an invaluable research tool that complements a growing list of additional avian genomic resources. For many researchers, finding and using these resources is challenging, because information is presented through an increasing number of Web sites and browser navigation frequently requires specific knowledge and expertise. This primer provides an overview of online genomic resources for the chicken, including the Ensembl, UCSC, and NCBI annotated chicken genome browsers; expressed sequence tag and in situ hybridization databases; and sources for microarrays, cDNAs, and bacterial artificial chromosomes (BACs). Several short tutorials oriented toward the biologist with limited bioinformatics skills outline how to retrieve several types of commonly needed information and reagents.
Differences between mistimed and unwanted pregnancies among women who have live births.

Context: Mistimed and unwanted pregnancies that result in live births are commonly considered together as unintended pregnancies but they may have different precursors and outcomes. Methods: Data from 15 states participating in the 1998 Pregnancy Risk Assessment Monitoring System were used to calculate the prevalence of intended mistimed and unwanted conceptions by selected variable. Associations between unintendedness and womens behaviors and experiences before during and after the pregnancy were assessed through unadjusted relative risks. Results: The distribution of intended mistimed and unwanted pregnancies differed on nearly every variable examined; risky behaviors and adverse experiences were more common among women with mistimed than intended pregnancies and were most common among those whose pregnancies were unwanted. The likelihood of having an unwanted rather than mistimed pregnancy was elevated for women 35 or older (relative risk 2.3) and was reduced for those younger than 25 (0.8); the pattern was reversed for the likelihood of mistimed rather than intended pregnancy (0.5 vs. 1.7-2.7). Parous women had an increased risk of an unwanted pregnancy (2.1-4.0) but a decreased risk of a mistimed one (0.9). Women who smoked in the third trimester received delayed or no prenatal care did not breastfeed were physically abused during pregnancy said their partner had not wanted a pregnancy or had a low-birth-weight infant had an increased risk of unintended pregnancy; the size of the increase depended on whether the pregnancy was unwanted or mistimed. Conclusion: Clarifying the difference in risk between mistimed and unwanted pregnancies may help guide decisions regarding services to women and infants. (authors)
Cyclic variations in spinal cord levels of oxytocin and vasopressin during the stages of the rat estrous cycle.

Oxytocin (OT) and vasopressin (VP) have been localized to numerous central nervous system locations outside the classic hypothalamo-neurohypophyseal tract including all levels of the spinal cord. To date, the physiological function of these peptides within the spinal cord is unknown. The purpose of this study was to determine if the variations exhibited by pituitary OT and VP during the stages of the estrous cycle in the rat were also present in the spinal cord. The stage of the estrous cycle was determined by vaginal smears in female Long Evans rats. Following decapitation, the cervical, thoracic, and lumbosacral segments of the spinal cord were isolated and homogenized, and the hormones were extracted from the tissue with the Sep-pak method. OT and VP content were determined by RIA. A cyclic variation in spinal cord OT and VP was present, with maximal levels occurring in diestrus, a time in the estrous cycle when LH and estradiol levels are lowest. Our results suggest that spinal cord OT and VP may be r...
Intuitionistic propositional logic is polynomial-space complete

It is the purpose of this note to show that the question of whether a given propositional formula is intuitionistically valid (in Brouwer's sense, in Kripke's sense, or just provable by Heyting's rules, see Kreisel [7]) is p-space complete (see Stockmeyer [14]). Our result has the following consequences: 1. (a) There is a simple (i.e. polynomial time) translation of intuitionistic propositional logic into classical propositional logic if and only if NP = p-space. 2. (b) The problem of determining if a type of the typed λ-calculus is the type of a closed λ-term is p-space complete (this will be discussed below). 3. (c) There is a polynomial bounded intuitionistic proof system if and only if NP = p-space (see Cook and Reckhow [2]).
Auditory and visual localization accuracy in young children and adults.

A B S T R A C T Objective: This study aimed to measure and compare sound and light source localization ability in young children and adults who have normal hearing and normal/corrected vision in order to determine the extent to which age, type of stimuli, and stimulus order affects sound localization accuracy. Methods: Two experiments were conducted. The first involved a group of adults only. The second involved a group of 30 children aged 3 to 5 years. Testing occurred in a sound-treated booth containing a semi-circular array of 15 loudspeakers set at 108 intervals from � 708 to 708 azimuth. Each loudspeaker had a tiny light bulb and a small picture fastened underneath. Seven of the loudspeakers were used to randomly test sound and light source identification. The sound stimulus was the word ‘‘baseball’’. The light stimulus was a flashing of a light bulb triggered by the digital signal of the word ‘‘baseball’’. Each participant was asked to face 08 azimuth, and identify the location of the test stimulus upon presentation. Adults used a computer mouse to click on an icon; children responded by verbally naming or walking toward the picture underneath the corresponding loudspeaker or light. A mixed experimental design using repeated measures was used to determine the effect of age and stimulus type on localization accuracy in children and adults. A mixed experimental design was used to compare the effect of stimulus order (light first/last) and varying or fixed intensity sound on localization accuracy in children and adults. Results: Localization accuracy was significantly better for light stimuli than sound stimuli for children and adults. Children, compared to adults, showed significantly greater localization errors for audition. Three-year-old children had significantly greater sound localization errors compared to 4- and 5-year olds. Adults performed better on the sound localization task when the light localization task occurred first. Conclusions: Young children can understand and attend to localization tasks, but show poorer
Phase behavior of planar supported lipid membranes composed of cholesterol and 1,2-distearoyl-sn-glycerol-3-phosphocholine examined by sum-frequency vibrational spectroscopy

The influence of cholesterol (CHO) on the phase behavior of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) planar supported lipid bilayers (PSLBs) was investigated by sum-frequency vibrational spectroscopy (SFVS). The intrinsic symmetry constraints of SFVS were exploited to measure the asymmetric distribution of phase segregated phospholipid domains in the proximal and distal layers of DSPC + CHO binary mixtures as a function of CHO content and temperature. The SFVS results suggest that cholesterol significantly affects the phase segregation and domain distribution in PSLBs of DSPC in a concentration dependent manner, similar to that found in bulk suspensions. The SFVS spectroscopic measurements of phase segregation and structure change in the binary mixture indicate that membrane asymmetry must be present in order for the changes in SFVS signal to be observed. These results therefore provide important evidence for the delocalization and segregation of different phase domain structures in PSLBs due to the interaction of cholesterol and phospholipids.