cssi/SciSciGPT-SciSciNet huggingface dataset:
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

Motivation: DNA binding proteins play crucial roles in the regulation of gene expression. Transcription factors (TFs) activate or repress genes directly while other proteins influence chromatin structure for transcription. Binding sites of a TF exhibit a similar sequence pattern called a motif. However, a one-to-one map does not exist between each TF and motif. Many TFs in a protein family may recognize the same motif with subtle nucleotide differences leading to different binding affinities. Additionally, a particular TF may bind different motifs under certain conditions, for example in the presence of different co-regulators. The availability of genome-wide binding data of multiple collaborative TFs makes it possible to detect such context-dependent motifs. Results: We developed a contrast motif finder (CMF) for the de novo identification of motifs that are differentially enriched in two sets of sequences. Applying this method to a number of TF binding datasets from mouse embryonic stem cells, we demonstrate that CMF achieves substantially higher accuracy than several well-known motif finding methods. By contrasting sequences bound by distinct sets of TFs, CMF identified two different motifs that may be recognized by Oct4 dependent on the presence of another co-regulator and detected subtle motif signals that may be associated with potential competitive binding between Sox2 and Tcf3. Availability: The software CMF is freely available for academic use at www.stat.ucla.edu/~zhou/CMF Contact: zhou@stat.ucla.edu Supplementary information:Supplementary data are available at Bioinformatics online and the CMF website.
Interactive Assessment of User Preference Models: The Automated Travel Assistant

This paper presents the candidate/critique model of interactive problem solving, in which an automated problem solver communicates candidate solutions to the user and the user critiques those solutions. The system starts with minimal information about the user’s preferences, and preferences are elicited and inferred incrementally by analyzing the critiques. The system’s goal is to present “good” candidates to the user, but to do so it must learn as much as possible about his preferences in order to improve its choice of candidates in subsequent iterations. This system contrasts with traditional decision-analytic and planning frameworks in which a complete model is elicited beforehand or is constructed by a human expert. The paper presents the Automated Travel Assistant, an implemented prototype of the model that interactively builds flight itineraries using realtime airline information. The ATA is available on the World Wide Web and has had over 4000 users between May and October 1996.
Dental loss among ambulatory patients with diabetes

Aims There is a high prevalence of dental loss among patients with diabetes. Understanding the factors that impact dental loss in this population will aid with developing new strategies for its prevention.
The Cartoon Society: Using the Simpsons to Teach and Learn Sociology

In this paper we introduce a wonderful video resource that can enhance the undergraduate learning experience. The animated television series. The Simpsons, can be particuarly effective for illustrating sociological themes and encouraging critical thinking among todays undergraduates. Borrowing from Mills (1959), the Simpsons complements teaching philosophies that stress applying the sociological imagination to the observation of everyday life. We have found that the show is an effective pedagogical tool for demostrating sociological concepts and foster students' understanding of the course material. Students can relate to the show and by engaging them in critical discussions, The Simpsons is a valuable pedagogical resource to the sociology curriculum.
DDT Resistance in Heliothis zea

Laboratory tests with bollworms Heliothis zea (Boddie), collected in several areas of Texas in 1962 indicated populations in some areas were highly resistant to DDT. Bollworms from College station, La Grange, and Eagle Pass were 50 to 100 times harder to kill with DDT than those from El Paso and the Lower Valley. Also, bollworms collected from cotton were much harder to kill with DDT than those collected from corn in the same area. This indicates that possibly host-specific strains of bollworm exist and that transfer from corn to cotton in mid-season is slight or does not occur. Additional tests with tobacco budworms, II . virescens (F.), collected at College Station, La Grange, Angleton, Eagle Pass, and Ft. Stockton indicated that this cotton pest is almost immune to DDT. The insecticides tested whieh appeared to give satisfactory control of DDT-resistant bollworms and tobaceo budworms were endrin, carbaryl, toxaphene-DDT (2: 1) lind Strobane [terpene polychlorinates (65% chlorine)]-DDT (2: 1).
Commensurability and the character variety

Recall that hyperbolic 3-manifolds M and N are said to be commensurable if they have a common finite sheeted covering. This is equivalent to the fundamental groups having subgroups of finite index which are conjugate in PSL(2,C). In general it is very difficult to determine if two manifolds are commensurable or not, once the most obvious invariants of commensurability (for example, the invariant trace field, see [13] and [17]) agree. When M is a finite volume hyperbolic 3-manifold with a single cusp, its SL(2,C)-representation and character varieties, denoted respectively, by R(M) and X(M) throughout, have been fundamental tools in understanding the topology of M , see [6], [5], and [4]. These techniques can be extended to the PSL(2,C)-character variety of M , which we denote by Y (M) ([2], and see §2.1 for some details). Throughout, for either SL(2) or PSL(2), we use the subscript 0 to denote a component of X(M) (or Y (M)) containing the character of a faithful discrete representation of π1(M). The main results of this paper concern how Y0(M) be can used to detect incommensurability. For example, one of the main results can be summarized in the following (for terminology and definitions see §2):
PL2THE ADOLESCENT BRAIN AND COGNITIVE DEVELOPMENT (ABCD) STUDY: SIGNIFICANCE, CHALLENGES, AND OPPORTUNITIES

Epidemiologic evidence indicates that substance use typically begins in adolescence, with alcohol, nicotine, and marijuana being the most commonly used substances. Large national surveys in the U.S. indicate that while overall rates of alcohol and tobacco use have been declining for several years, rates of marijuana use …
Familial Dysautonomia: Mechanisms and Models

Hereditary Sensory and Autonomic Neuropathies (HSANs) compose a heterogeneous group of genetic disorders characterized by sensory and autonomic dysfunctions. Familial Dysautonomia (FD), also known as HSAN III, is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population. The major features of the disease are already present at birth and are attributed to abnormal development and progressive degeneration of the sensory and autonomic nervous systems. Despite clinical interventions, the disease is inevitably fatal. FD is caused by a point mutation in intron 20 of the IKBKAP gene that results in severe reduction in expression of IKAP, its encoded protein. In vitro and in vivo studies have shown that IKAP is involved in multiple intracellular processes, and suggest that failed target innervation and/or impaired neurotrophic retrograde transport are the primary causes of neuronal cell death in FD. However, FD is far more complex, and appears to affect several other organs and systems in addition to the peripheral nervous system. With the recent generation of mouse models that recapitulate the molecular and pathological features of the disease, it is now possible to further investigate the mechanisms underlying different aspects of the disorder, and to test novel therapeutic strategies.
Joint inversion of gravity and traveltime data using a level-set-based structural parameterization

ABSTRACTWe have developed a new level-set-based structural parameterization for joint inversion of gravity and traveltime data, so that density contrast and seismic slowness are simultaneously recovered in the inverse problem. Because density contrast and slowness are different model parameters of the same survey domain, we assume that they are similar in structure in terms of how each property changes and where the interface is located, so that we are able to use a level-set function to parameterize the common interface shared by these two model parameters. The level-set parameterization makes it easy to maintain the structural similarity between the two geophysical properties. The inversion of gravity and traveltime data is carried out by minimizing a joint data-fitting function with respect to density contrast, slowness, as well as the level-set function. An adjoint state method is used to compute the traveltime gradient efficiently. We have tested our algorithm on various synthetic examples, including...
HTML Architecture, a Novel Development System (HANDS): An Approach for Web Development

In this paper, a very compelling proposition is presented, a novel approach for web development that is a hybrid of Single Page Applications (SPA) and server side applications. The proposed architecture lowers the entry to web development by providing a simplistic approach for development. The focus is on HTML, Java Script, Cascading Style Sheets, and Node.js. The architecture provides all the components required for students to start developing web applications and web services. The HTML Architecture, a Novel Development System (HANDS) is a hybrid approach leveraging the simplicity of plain old HTML pages, the AJAX injection of HTML from SPA frameworks, and the server side processing found in the Node.js framework. An open source starter kit and examples are provided.
A survey of current status of noise hazard on offshore oil platforms

Objective: To investigate the noise distribution characteristics, workers' exposure to noise, and protective measures against noise on offshore oil platforms. Methods: Six offshore oil platforms with a similar scale of production from China National Offshore Oil Corporation were selected from June to October, 2015 to conduct a field investigation of occupational health and detection of risk factors for occupational diseases and to know the current status of noise hazard on offshore oil platforms. Results: Among the 373 sites for noise measurement, 69.7% had a noise level of ≥80 dB (A) ; among the 196 sites for noise measurement in the area with noisy equipment, 86.7% had a noise level of ≥80 dB (A) ; among the 177 sites for noise measurement in the area without noisy equipment, 50.8% had a noise level of ≥80 dB (A) . The actual sound attenuation of earplugs used on platforms was 18.6 dB (A) , and if they were worn correctly, they had a maximum value of noise protection of 103.6 dB (A) . The workers engaged in indoor operation were exposed to noise for 0.5~1.0 hour per day, and the 40 h/week equivalent sound level (weekly noise exposure, LEX, w) met the requirements in GBZ 2.2-2007 Occupational exposure limits for hazardous agents in the workplace Part 2: Physical agents[85 dB (A) ]. The workers engaged in outdoor operation were exposed to noise for 6.0~8.0 hours per day, and the over-standard rate of LEX, w was 53.7%. The noise exposure level showed a significant difference between the two groups, and indoor operation workers had a significantly lower noise exposure level than outdoor operation workers[ (69.8±3.4) dB (A) vs (85.5±3.5) dB (A) , P<0.05]. Conclusion: Noise sources on offshore oil platforms show the characteristic of centralized distribution, and noisy equipment have a great impact on the area without noisy equipment. The noise exposure level differs significantly between workers engaged in indoor and outdoor operation, and noise protection mainly relies on personal protective supplies.
A new species of Secutor (Teleostei: Leiognathidae) from the Western Indian Ocean

A new species of ponyfish, Secutor mazavasaoka, is described from coastal waters of the Western Indian Ocean. Together, the new species, S. indicius, and S. insidiator are readily distinguished from congeners by more or less oval-shaped elongate bodies (vs. markedly deep and disk-shaped). The new species is distinguished from S. hanedai by the presence of scales on the chest (vs. chest asquamate), and from S. indicius and S. insidiator by a deeper, hatchet-shaped body (vs. uniformly oval) and pigmentation pattern on the dorsal flank comprising eight to eleven well-defined columns of irregular small spots and blotches (vs. 14 to 17 thin columns of spots or vertical lines in S. indicius, or larger irregular blotches arrayed in poorly defined columns in S. insidiator). Additionally, the new species is distinguished from S. insidiator by a strongly upturned mouth and compressed pug-like snout, a pronounced concavity dorsal to the orbit, a dorsally-projecting nuchal spine, and dorsal-fin insertion well posterior to vertical through pectoral-fin base (vs. at about level of pectoral-fin base in S. insidiator).
Dynamic Characteristics of Guanosine-5′-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry

The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here, we use an underappreciated NMR technique, subtesla high-resolution field-cycling 31P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5′-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the 31P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle. Importantly, the substrate is constrained and the cofactor is more dynamic in the deamination complex E·GMP·NADP+, whereas the substrate is more dynamic and the cofactor is constrained in the hydride transfer complex E·IMP·NADP+. The presence of D2O perturbed the relaxation of the 31P nuclei in E·IMP·NADP+ but not in E·GMP·NADP+, providing further evidence of distinct binding modes with...
The Endocannabinoid System: Can It Contribute to Cannabis Therapeutics?

Abstract Receptors for δ9-tetrahydrocannabinol (THC), canna-bis' major psychoactive principle, have been identified in animal tissues. These proteins have a reason to exist because endogenous substances may bind to and functionally activate them, thereby producing pharmacological effects similar to those of THC. Such substances, named “endocannabinoids,” have been isolated and several studies have been performed on their pharmacological properties as well as on the molecular mechanisms for their biosynthesis, action and inactiva-tion in animal cells. Within the framework of the ongoing debate on the therapeutic potential of cannabinoid receptor agonists and antagonists, the present article addresses the possibility that our knowledge of the endocannabinoid system may result in the development of new drugs for the treatment of illnesses as diverse as nervous and immune disorders, pain, inflammation and cancer.
Personal Power Using Metal-Supported Solid Oxide Fuel Cells Operated in a Camping Stove Flame

Abstract A complete stand-alone product prototype providing combined cooking and power is fabricated by retrofitting a commercial camping stove with a stack of metal-supported solid oxide fuel cells (MS-SOFCs) delivering power to microelectronic LED driver and voltage boost circuits. The 5-cell stack produces 2.7 W (156 mW cm−2) while cooking on the stove, and is demonstrated to produce LED lighting and mobile phone charging while operating outdoors. Cooking efficiency is minimally impacted by the presence of the MS-SOFCs. It is found that vertical orientation of the cells is critical to maintain separation of fuel and air when a pot is placed on the stove.
Officials’ Attitudes toward Sexual History Evidence

In the previous chapter, we examined officials’ assessments of the importance of specific kinds of evidence, including two types of sexual history evidence, for prosecuting and for obtaining convictions in rape cases. We found that the strength of a jurisdiction’s shield law influenced assessments by the officials of the likelihood that sexual history evidence would be admitted. In this chapter, we explore officials’ judgments of sexual history evidence in greater detail. We examine the responses of judges, prosecutors, and defense attorneys to six hypothetical cases in which evidence of the victim’s past sexual conduct is at issue.
Experimental and theoretical studies on the elasticity of tungsten to 13 GPa

Compressional ( VP) and shear wave ( VS) velocities of polycrystalline tungsten have been measured up to ∼13 GPa at room temperature using ultrasonic interferometry in a multi-anvil apparatus. Using finite strain equation of state approaches, the elastic bulk and shear moduli and their pressure dependences are derived yielding KS0=325.9±4.8 GPa, G0=164.1±2.5 GPa, KS0′=3.65±0.05, and G0′=1.28±0.02. On the basis of the current experimental data, the high-pressure behavior of Young's modulus, Poisson's ratio, and ductility/brittleness for tungsten are also investigated. Complementary to the experimental data, the single crystal elastic constants, as well as the elastic anisotropy of tungsten are computed using density functional theory (DFT). The Voigt-Reuss-Hill average of the bulk and shear moduli calculated using the single crystal elastic constants from DFT are found comparable to the current experimental results within about 5%. The present study offers a dataset for the elasticity of polycrystalline bcc tungsten to a maximum pressure more than 25-fold higher than other previous ultrasonic studies, which can further our understanding about the elastic, mechanical, and electronic properties of tungsten under extreme conditions as well as thermodynamic modelling of its alloys.
Enforcing Race: A Neighborhood-Level Explanation of Black–White Differences in Drug Arrests:

This research investigates the source of Black–White differences in drug arrests by conducting a neighborhood-level test of the differential police scrutiny and racially discriminatory policing hyp...
Abstract WP342: Description of Pericavity Edema in Patients With Intracerebral Hemorrhage Who Have Undergone Endoscopic Minimally Invasive Evacuation

Introduction: Perihematomal edema (PHE) impacts outcome in spontaneous intracerebral hemorrhage (ICH) and has been well defined. As minimally invasive evacuation methods are formally evaluated, the...
Cell non-autonomous interactions during non-immune stromal progression in the breast tumor microenvironment

Summary The breast tumor microenvironment of primary and metastatic sites is a complex milieu of differing cell populations, consisting of tumor cells and the surrounding stroma. Despite recent progress in delineating the immune component of the stroma, the genomic expression landscape of the non-immune stroma (NIS) population and their role in mediating cancer progression and informing effective therapies are not well understood. Here we obtained 52 cell-sorted NIS and epithelial tissue samples across 37 patients from i) normal breast, ii) normal breast adjacent to primary tumor, iii) primary tumor, and iv) metastatic tumor sites. Deep RNA-seq revealed diverging gene expression profiles as the NIS evolves from normal to metastatic tumor tissue, with intra-patient normal-primary variation comparable to inter-patient variation. Significant expression changes between normal and adjacent normal tissue support the notion of a cancer field effect, but extended out to the NIS. Most differentially expressed protein-coding genes and lncRNAs were found to be associated with pattern formation, embryogenesis, and the epithelial-mesenchymal transition. We validated the protein expression changes of a novel candidate gene, C2orf88, by immunohistochemistry staining of representative tissues. Significant mutual information between epithelial ligand and NIS receptor gene expression, across primary and metastatic tissue, suggests a unidirectional model of molecular signaling between the two tissues. Furthermore, survival analyses of 827 luminal breast tumor samples demonstrated the predictive power of the NIS gene expression to inform clinical outcomes. Together, these results highlight the evolution of NIS gene expression in breast tumors and suggest novel therapeutic strategies targeting the microenvironment.
Synergistic effects of market orientation implementation and internalization on firm performance: Direct marketing service provider industry

Abstract We draw on recent advances in Market Orientation domain to examine the synergistic effects of market orientation implementation and internalization on firm performance in the context of digital transformation within direct mail service provider industry. We introduce market orientation internalization as a mediator between market orientation implementation and firm performance relationship. In addition, the effect of learning orientation is considered as a moderator that strengthens the relationship between market orientation implementation and market orientation internalization. The research model is empirically tested using Hayes (2013) conditional process analysis utilizing a unique dataset from an industry that is undergoing an unprecedented digital transformation from physical to digital communication. The results suggest that firms that practice high levels of market orientation implementation and internalization perform better in both financial performance and customer service performance.
How to Make a Life: A Tibetan Refugee Family and the Midwestern Woman They Adopted

Review of: "How to Make a Life: A Tibetan Refugee Family and the Midwestern Woman They Adopted" byMadeline Uraneck
Correlation of clinical and chest radiograph findings in pediatric submersion cases

Submersion injuries are a leading cause of injury death in children in the United States. The clinical course of a submersion patient varies depending on the presence of anoxic brain injury and acute respiratory failure. We studied changes in clinical findings and chest radiograph findings and determined the sensitivity/specificity of the presenting chest radiograph in predicting clinical improvement within the first 24 h in pediatric submersion cases. We conducted a cross-sectional study of pediatric submersion patients through age 18 years treated at a children’s hospital from 2010 to 2013. We reviewed demographics, comorbidities, prehospital/hospital course and chest radiographic findings. Clinical improvement occurred when a child demonstrated normal vital signs and mentation. We compared radiographic findings among children based on clinical improvement up to 24 h post submersion. Using odds ratios, we calculated associations between radiographic findings and clinical improvement. We studied the sensitivity/specificity of the presenting chest radiograph in predicting clinical improvement within 24 h. One hundred forty-two of 262 (54%) patients had initial chest radiographs; 41% had follow-up radiographs. The odds of an abnormal initial chest radiograph were 4 times higher in children with respiratory distress or abnormal mentation at emergency department (ED) presentation compared to children without these findings (odds ratio [OR]=4.83; 95% confidence interval [CI]=2.1–10.85; P<0.001). Improvement in radiographic findings occurred in 85% of children within 24 h. Children with an abnormal initial chest radiograph were 87% less likely to improve clinically by 24 h (P<0.001). A presenting chest radiograph that was normal or with mild pulmonary edema/atelectasis predicted clinical improvement within 24 h (sensitivity 95%, specificity 57%). Most chest radiographic findings improve in pediatric submersion patients who recover within the first 24 h. An initial chest radiograph that is normal or with mild pulmonary edema/atelectasis satisfactorily predicts clinical improvement by 24 h post submersion.
SUPERIOR MESENTERIC ARTERY OCCLUSION BY AXILLARY BALLOON PUMP

Axillary intra-aortic balloon pumps (IABP) have become increasingly common in those awaiting cardiac transplant as they allow for increased mobility. A 37-year-old female with non-ischemic cardiomyopathy secondary to sarcoidosis was admitted due to worsening left heart failure. She underwent an
Mine, Yours or Amazon's?: Designing Agent Ownership and Affiliation

Current designs of social agents (chatbots, conversational agents, robots) do not explicitly communicate affiliation to their users-it is unclear whether an agent is intended to be "owned" by an individual or by several users (e.g., a family). As a result, users do not know who has access to information and functions within the agent. In addition, the extent to which agents are affiliated with a service provider may prevent users from engaging in valuable agent features due to privacy concerns. My work explores how design can be used to indicate agent ownership models to users, and how service providers might alter their services to convey that people's agents, and more importantly, the information they hold, is theirs.
Racial differences in urinary incontinence prevalence and associated bother: the Multi-Ethnic Study of Atherosclerosis.

Background Urinary incontinence is influenced by multiple factors, and the prevalence of urinary incontinence subtypes may differ by race and ethnicity. Objective This study aimed to determine the prevalence of urinary incontinence subtypes and associated bother among women by race and ethnicity. Study Design This cross-sectional analysis used data from the Multi-Ethnic Study of Atherosclerosis, an observational cohort study of 4 racial and ethnic groups recruited from 6 communities from the United States. At the sixth follow-up examination, urinary symptoms were ascertained with the International Consultation on Incontinence Questionnaire. The prevalence rate ratios of stress urinary incontinence, urgency urinary incontinence, and mixed urinary incontinence by race and ethnicity were calculated using generalized linear models for the binomial family while adjusting for covariates. The degree of bother was based on a scale of 0 (none) to 10 (greatest bother), and presence of any bother was defined as a score of ≥3. Results Among the 1749 female participants in the Multi-Ethnic Study of Atherosclerosis who completed the sixth follow-up examination, 1628 (93%) completed the questionnaire. Women who did not complete the questionnaire were older than those who completed the questionnaire (average age, 82.2 [standard deviation, 9.5] vs 73.7 [standard deviation, 8.4] years; P Conclusion Frequency of urinary incontinence subtypes may differ by race and ethnicity, but older women who report urinary incontinence are likely to have associated bother regardless of race and ethnicity.
Leading with/in emotion states: The criticality of political subjects and policy debates in educational leadership on emotions

One of the many facets of educational leadership is the emotional aspects of educational leadership itself. Leaders are regularly immersed in emotionally charged broad-based policy debates and poli...
Loss of Smell in COVID-19 Patients: Lessons and Opportunities

Bilinska et al report high expression of ACE2 and TMPRSS2 in sustentacular cells of the olfactory epithelium and less expression in OSNs (Bilinska et al , 2020) Since sustentacular cells play key roles in supporting OSN metabolism and odor sensing, any virus-mediated damage to these cells could lead to olfactory deficits (Heydel et al , 2013) Overall, these studies offer several hypotheses as to how viral mechanisms could lead to smell loss in COVID-19 patients: one ACE2 mechanisms in olfactory neurons lead to a direct modulation of olfactory sensitivities or even cell death;two ACE2 mechanisms in non-neural olfactory cells lead to indirect modulation of OSN function and;three ACE2 mechanisms in neighboring glial cells lead to increased inflammatory response, whose downstream effects could alter OSN function and reduce olfactory sensitivities [ ]a SARS-CoV-2/ACE2-mediated dysregulation of insulin signaling could further aggravate symptoms in diabetics [ ]highest density of central insulin receptors and highest concentration of insulin in mammalian brain are found in the olfactory bulb (Havrankova et al , 1981)
ConJac: Large Steps in Dynamic Simulation

We present a new approach that allows large time steps in dynamic simulations. Our approach, ConJac, is based on condensation, a technique for eliminating many degrees of freedom (DOFs) by expressing them in terms of the remaining degrees of freedom. In this work, we choose a subset of nodes to be dynamic nodes, and apply condensation at the velocity level by defining a linear mapping from the velocities of these chosen dynamic DOFs to the velocities of the remaining quasistatic DOFs. We then use this mapping to derive reduced equations of motion involving only the dynamic DOFs. We also derive a novel stabilization term that enables us to use complex nonlinear material models. ConJac remains stable at large time steps, exhibits highly dynamic motion, and displays minimal numerical damping. In marked contrast to subspace approaches, ConJac gives exactly the same configuration as the full space approach once the static state is reached. ConJac works with a wide range of moderate to stiff materials, supports anisotropy and heterogeneity, handles topology changes, and can be combined with existing solvers including rigid body dynamics.
Treatment of Mandibular Non-union Using Patient Specific Crib Cage Plates and Cellular Bone Allograft: A Case Report:

A gunshot wound to the mandible frequently creates a comminuted fracture that can be debilitating for the patient and challenging for the surgeon. In some instances, immediate open reduction and ri...
Book Review: Grasp: The science transforming how we learn

American preservice teachers are routinely introduced to educational philosophies positing that all students can learn (Edmonds, 1981) and that a culturally responsive approach considering students’ knowledge and experiences is tantamount (Gay, 2018). The atmosphere in many American public schools, however, reflects far less cultural responsiveness and faith in students’ abilities than one would anticipate (Bonner et al., 2018). In these schools, teaching to the test is a practical necessity (Volante, 2004), students are sorted into tracks based on perceived potential (Meyer, 1977), and curriculum design is restricted by state and local standards (Spillane, 2004). Grasp: The Science Transforming How We Learn (2020) by Sanjay Sarma with Luke Yoquinto offers teachers, school administrators, and educational policy-makers a historical analysis of how this situation came to exist and a review of the latest research on cognitive science relevant to education. The book also presents a refreshing proposal to alter the status quo. Sarma, who leads MIT’s Open Learning program, is well experienced with novel approaches to curriculum design and implementing radical ideas to reach diverse student bodies. I recommend this book to anyone interested in the science of learning or a modern approach to educational policy.
Development, Validation, and Application of a Novel Method for the Analysis of Vitamin E Acetate and Other Tocopherols in Aerosol Emissions of E-Cigarettes, or Vaping Products Associated With Lung Injury.

E-cigarette, or vaping, product (EVP) use has increased dramatically in the United States over the last 4 years, particularly in youth and young adults. Little information is available on the chemical contents of these products. Typically, EVPs contain an active ingredient such as nicotine, CBD, or THC dissolved in a suitable solvent that facilitates aerosol generation. One EVP solvent, vitamin E acetate (VEA), has been measured in EVP liquids associated with lung injury. However, no validated analytical methods for measuring VEA in the aerosol from these devices was previously available. Therefore, we developed a high throughput isotope dilution LC-MS/MS method to simultaneously measure VEA and three other related tocopherols in aerosolized EVP samples. The assay was precise, with VEA repeatability ranging from 4.0 to 8.3% and intermediate precision ranging from 2.5 to 6.7%. Similar precision was obtained for the three other tocopherols measured. The LODs for the four analytes ranged from 8.85 × 10-6 to 2.28 × 10-5 μg analyte per mL of aerosol puff volume, and calibration curves were linear (R 2 > 0.99). This method was used to analyze aerosol emissions of 147 EVPs associated with EVALI case patients. We detected VEA in 46% of the case-associated EVPs with a range of 1.87 × 10-4-74.1 µg per mL of aerosol puff volume and mean of 25.1 µg per mL of aerosol puff volume. Macro-levels of VEA (>0.1% w/w total aerosol particulate matter) were not detected in nicotine or cannabidiol (CBD) products; conversely 71% of the EVALI associated tetrahydrocannabinol (THC) products contained macro-levels of VEA. Trace levels of other tocopherol isoforms were detected at lower rates and concentrations (α-tocopherol: 41% detected, mean 0.095 µg analyte per mL of aerosol puff volume; γ-tocopherol: 5% detected, mean 0.0193 µg analyte per mL of aerosol puff volume; δ-tocopherol: not detected). Our results indicate that VEA can be efficiently transferred to aerosol by EVALI-associated EVPs vaped using a standardized protocol.
Ectomycorrhizal access to organic nitrogen mediates CO2 fertilization response in a dominant temperate tree.

Plant–mycorrhizal interactions mediate plant nitrogen (N) limitation and can inform model projections of the duration and strength of the effect of increasing CO2 on plant growth. We present dendrochronological evidence of a positive, but context-dependent fertilization response of Quercus rubra L. to increasing ambient CO2 (iCO2) along a natural soil nutrient gradient in a mature temperate forest. We investigated this heterogeneous response by linking metagenomic measurements of ectomycorrhizal (ECM) fungal N-foraging traits and dendrochronological models of plant uptake of inorganic N and N bound in soil organic matter (N-SOM). N-SOM putatively enhanced tree growth under conditions of low inorganic N availability, soil conditions where ECM fungal communities possessed greater genomic potential to decay SOM and obtain N-SOM. These trees were fertilized by 38 years of iCO2. In contrast, trees occupying inorganic N rich soils hosted ECM fungal communities with reduced SOM decay capacity and exhibited neutral growth responses to iCO2. This study elucidates how the distribution of N-foraging traits among ECM fungal communities govern tree access to N-SOM and subsequent growth responses to iCO2. Root-mycorrhizal interactions could help explain the heterogeneity of plant responses to CO2 fertilisation and nutrient availability. Here the authors combine tree-ring and metagenomic data to reveal that tree growth responses to increasing CO2 along a soil nutrient gradient depend on the nitrogen foraging traits of ectomycorrhizal fungi.
Abstract 4133: Disparities in colon cancer survival according to payer status: Findings from national cancer data bank

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA BACKGROUND: The objective of the current study was to examine the impact of payer status on relative survival outcomes in colon cancer patients. METHODS: A population-based analysis of National Cancer Data Bank (NCDB) records for invasive colon cancer was done using data from patients diagnosed between 1998 and 2006 and followed up to 2011. The cohort consisted of colon cancer patients of analytic stage I to stage IV. Information regarding age, race, gender, stage of cancer at the time of diagnosis, year of diagnosis, insurance status, income, treatment received and diagnostic facility, and type of treating facility were included in this study. Age, sex, race, calendar year specific US life table between 1970 and 2007 were used to compute expected survival. Multivariate Poisson modeling was used to estimate relative survival for payer status adjusting for other factors. RESULTS: 436,235 colon cancer patients who met the inclusion criteria were included in the study. The mean age at diagnosis was 68.9 years. The stage distribution among the variables listed above is statistically significant. The 5-year cumulative relative survivals are 0.76, 0.84, 0.93, 1.74 and 1.10 for uninsured, Medicaid, private insurance, Medicare, and unknown payer status respectively. In multivariate analysis of relative survival, adjusting for other factors, the excess hazard ratios (EHR) were 1.74, 1.14, 0.89 and 1.29 for uninsured, Medicaid, Medicare, and unknown payer status versus private insurance respectively (P<0.05). The EHRs for blacks and other races versus whites were 1.07 and 1.53 respectively (p<0.05). The EHRs for follow-up year of 2, 3, 4, 5 versus year 1 were 1.17, 0.21, 0.18, and 0.54 respectively (P <0.05). Compared to academic/research program facility type, the EHRs for community cancer program, comprehensive community cancer program, and other specified types of cancer programs were 1.02,0.77 and 25.9 respectively (P <0.05). The relative survival rates for stage II, III, IV versus stage I were 0.95, 0.82, and 0.70 respectively (P<0.05). Diagnosis before or after 2002 and the type of treatment facility lead to a marginal difference in the relative survival. CONCLUSIONS: Our study shows the impact of payer status on the relative survival of patients with colon cancer and demonstrated increased mortality for uninsured patients in contrast to survival benefit for patients with Medicare and private insurance. Citation Format: Srinivas S. Devarakonda, Runhua Shi, Amarendra Neppalli, Glenn Mills. Disparities in colon cancer survival according to payer status: Findings from national cancer data bank. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4133. doi:10.1158/1538-7445.AM2014-4133
Efficient computation of multiple knots nonuniform spline functions

Abstract This paper presents simple canonical representations of general spline functions which lead to orders of magnitude reduction in curve and surface rendering. This approach eliminates the redundancy found in the traditional representations. Because of the derivative properties of piecewise polynomial functions, it can be shown that the r -th derivative of an r -th order B-spline function is a set of weighted impuses located at the knots defining the spline function. The weights of these impulses are uniquely defined by the order of the B-spline and the locations of the knots. We provide recurrence relations to compute these values and present new high speed algorithms for the generation of curves and surfaces. It can be shown that this representation extends to multiple knot splines and to nonuniform rational B-spline functions (NURBs). Computational complexity analyses are provided to demonstrate the improvement of our technique over de Boor's linear combination algorithm and forward differencing approaches.
Cloning and screening of sequences expressed in a mouse colon tumor.

Abstract Polyadenylic acid-containing cytoplasmic RNA was isolated from a dimethylhydrazine-induced mouse transplantable colon carcinoma. Double-stranded complementary DNA synthesized using these molecules was inserted into the HindIII site of pBR322 using HindIII linkers, and the recombinant molecules were cloned in Escherichia coli. Clones were screened with labeled complementary DNA synthesized from the polyadenylic acid-containing cytoplasmic RNA of the tumor or normal mouse colon, liver, or kidney. Of 378 clones screened with the normal colon and tumor probes, seven showed major increases in abundance in the tumor tissue as compared to normal, and one showed a major decrease. Twenty-five other sequences were found which showed smaller increases and 22 showed smaller decreases. Of 373 clones screened with tumor, colon, liver, and kidney probes, 79% exhibited little evidence of tissue specificity in expression. The data for those sequences which do show tissue-specific regulation of expression suggest that the tumor continues to express sequences characteristic of the colon but also shows a loss, or decrease, in other gene products, most of which (19 of 25) are characteristic of the colon. Finally, nine of 10 sequences which increase from low abundance in the normal colon to high abundance in the tumor are found at a moderate to high level in the liver and kidney. On the other hand, 23 of 36 sequences which show more modest increases in the tumor as compared to normal are scarce or absent in the liver and kidney.
Particle-in-Cell Simulation of Cosmic Plasma

While it is thinkable that our ability to make in situ measurements can perhaps be extended to the nearest stars, most of the universe beyond a few parsecs will be beyond the reach of our spacecraft forever.
A unified analysis of stochastic adaptive control: asymptotic self-tuning

The second part of a unified approach to analyzing parametric stochastic adaptive control is presented. In the first stage, the potential self-tuning issue was introduced and examined, where the authors studied self-tuning of stochastic adaptive control schemes at the possible limit points of the parameter estimates, independent of the algorithm used for estimation. In this paper, by considering a general class of estimation algorithms, the authors attempt to determine the conditions under which a certainty-equivalence (CE) based stochastic adaptive control scheme is asymptotically self-tuning. A set of general properties satisfied by some common estimation algorithms, such as stochastic gradient (SG) and weighted extended least squares (WELS), are considered. Based on these assumptions, it is shown that certain sufficient conditions for respectively, potential self-tuning or potential identifiability are also sufficient for asymptotic self-tuning or strong consistency.
Functional Characterization of Antibodies against Neisseria gonorrhoeae Opacity Protein Loops

BACKGROUND The development of a gonorrhea vaccine is challenged by the lack of correlates of protection. The antigenically variable neisserial opacity (Opa) proteins are expressed during infection and have a semivariable (SV) and highly conserved (4L) loop that could be targeted in a vaccine. Here we compared antibodies to linear (Ab(linear)) and cyclic (Ab(cyclic)) peptides that correspond to the SV and 4L loops and selected hypervariable (HV(2)) loops for surface-binding and protective activity in vitro and in vivo. METHODS/FINDINGS Ab(SV cyclic) bound a greater number of different Opa variants than Ab(SV linear), including variants that differed by seven amino acids. Antibodies to the 4L peptide did not bind Opa-expressing bacteria. Ab(SV) (cyclic) and Ab(HV2) (cyclic), but not Ab(SV) (linear) or Ab(HV2 linear) agglutinated homologous Opa variants, and Ab(HV2BD) (cyclic) but not Ab(HV2BD) (linear) blocked the association of OpaB variants with human endocervical cells. Only Ab(HV2BD) (linear) were bactericidal against the serum resistant parent strain. Consistent with host restrictions in the complement cascade, the bactericidal activity of Ab(HV2BD) (linear) was increased 8-fold when rabbit complement was used. None of the antibodies was protective when administered vaginally to mice. Antibody duration in the vagina was short-lived, however, with <50% of the antibodies recovered 3 hrs post-administration. CONCLUSIONS We conclude that an SV loop-specific cyclic peptide can be used to induce antibodies that recognize a broad spectrum of antigenically distinct Opa variants and have agglutination abilities. HV(2) loop-specific cyclic peptides elicited antibodies with agglutination and adherence blocking abilities. The use of human complement when testing the bactericidal activity of vaccine-induced antibodies against serum resistant gonococci is also important.
WP760, a melanoma selective drug.

Our goal was to perform studies on the specificity and antimelanoma mechanism of a novel bis-anthracycline, WP760. WP760 initially identified in the NCI 160 screen as anti-melanoma. The methyl thiazolyl tetrazolium reduction (MTT) assay was used to test tumor cell growth inhibition; confocal microscopy to view WP760 intracellular distribution; flow cytometry for cell-cycle arrest and apoptosis; and Western blotting was employed to identify and compare quantities and kinetics of cell growth related molecule levels. WP760 induced G2/M-phase cell-cycle arrest and apoptosis in melanoma cell lines and short-term melanoma explants established from clinical specimens in a time and concentration dependent manner at nM concentrations. In contrast, effects on fibroblasts and A549 lung cancer cells required higher concentrations, suggesting that WP760 possesses selectivity for melanoma. Molecular studies indicated that WP760 induced p53 stabilization, checkpoint kinase 2 and p27Kip1 protein upregulation, and activation of caspase-3. Endogenous nitric oxide (NO) production has been implicated in the chemoresistance of melanoma; WP760 caused inhibition of the inducible nitric oxide synthase (iNOS) protein as well as inhibition of phosphorylation of ERK, known to drive the iNOS pathway. Based on WP760 localization into mitochondria, and caspase-3 inhibitor block the killing of WP760, the intrinsic pathway of apoptosis appears to have been activated. Our results indicate that WP760 affects a critical and unique set of growth regulatory effects in melanoma, and is a promising candidate for further preclinical studies.
Epidemiology of rheumatic fever.

Abstract Certain facets of the epidemiology of rheumatic fever are not clear. The correlation of group A beta hemolytic streptococcal infections and rheumatic fever is established; in all probability this is the specific etiologic agent in rheumatic fever. The latter then may prove to be a clinical manifestation of a certain phase (nonsuppurative and late) of streptococcal infection, rather than a disease entity in itself. In numerous respects the epidemiology of rheumatic fever mimics that of streptococcal infections. Some conditioning of tissue by infection, especially through antigen-antibody interaction or hypersensitivity, is probably involved in the basic pathogenesis of rheumatic fever. 1,48,49 Most group A streptococci very likely furnish the antigenic stimuli concerned in the development of this pathologic process and this may prove to be their rheumatogenic property. The response of the immunologic mechanisms of the host governs in some way the initiation and progression of the histopathologic changes which occur. Alterations in the immune response are probably precursors to the evolution of events in the pathogenesis of rheumatic fever. Other factors may play an important part in the epidemiology of this disease. The inherited susceptibility to rheumatic fever has been emphasized. The influence of age on the attack rate of rheumatic fever may reflect only the stage of maturity of the immune mechanism of the host. Environmental factors appear to affect primarily the epidemiology of rheumatic fever only as they influence conditions which enhance the spread of streptococcal infections, particularly in streptococcal epidemics. The variability of host factors involving susceptibility and resistance to streptococci, most of which may prove to be "rheumatogenic," make it exceedingly difficult to clarify the role of these factors in the epidemiology and pathogenesis of rheumatic fever. However, to set the stage for the possible development of rheumatic fever a susceptible individual must have been challenged by one of the various strains of group A streptococci. Whether or not a sequence of events follows which leads to rheumatic fever is dependent upon a number of variable and unknown factors.