cssi/SciSciGPT-SciSciNet huggingface dataset:
Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets

Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension-functionality supporting preservation of file system structure within Dataverse-which is essential for both in-place computation and supporting non-HTTP data transfers.
Interactive provenance summaries for reproducible science

Recorded provenance facilitates reproducible science. Provenance metadata can help determine how data were possibly transformed, processed, and derived from original sources. While provenance is crucial for verification and validation, there remains the issue of the granularity — detail at which provenance data must be provided to a user, especially for conducting reproducible science. When data are reproduced successfully the need for detailed provenance is minimal and an essence of the recorded provenance suffices. However, when data are not reproduced correctly users want to quickly drill down into fine-grained provenance to understand causes for failure. In this paper, we describe a drill-up/drill-down method for exploring provenance traces. The drill-up method summarizes the trace by grouping nodes and edges of the trace that have same derivation histories. The method preserves provenance data flow semantics. The drill-down method compares summary groups and ranks groups that may have information about the errors. Both the methods are implemented in an efficient manner using light-weight data structures so as to be suitable for reproducible science. We conduct a thorough experimental analysis to show how the operators perform in compressing and expanding real provenance graphs.
Advancing Reading Engagement and Achievement through Personal Digital Inquiry, Critical Literacy, and Skilful Argumentation

This chapter outlines three interconnected lines of work conducted in the USA to advance reading engagement and achievement from a new literacies perspective of online research and comprehension. These areas focus on developmentally appropriate practices for supporting educators and learners as they use the Internet for personal inquiry, active citizenship, and the exploration of controversial issues from multiple perspectives. Emerging work in all three areas can help re-envision reading instruction to better address continuing gaps in achievement and motivation among diverse learners and the cultural shift that new technologies and online inquiry have brought to our conceptions of teaching and learning in a digital age.
Interaction between polymer-coated carbon nanotubes with coarse-grained computations

Abstract Dissipative particle dynamics computations were used to study the interaction between two carbon nanotubes (CNTs) stabilized with a polymer in an aqueous solution. The calculated interaction forces quantitatively described the steric effects of the adsorbed polymer on CNT agglomeration. It was found that the repulsive peak depended on the orientation of the CNTs relative to each other. A general equation describing the forces between polymer-stabilized CNTs was established, and its parameters were evaluated based on the results of the simulations. The procedure can be extended to other adsorbed molecules, like surfactants or biomolecules.
Promoting Mastery of Complex Biological Mechanisms.

This article describes efforts aimed at improving comprehension and retention of complex molecular mechanisms commonly studied in undergraduate biology and biochemistry courses. The focus is on the design of appropriate assessments, an active classroom emphasizing formative practice, and more effective out-of-class study habits. Assessments that require students to articulate their understanding through writing are the most effective. Frequent formative practice improves performance on problems that require intellectual transfer, the ability to apply conceptual principles in novel settings. We show that success with such problems is a function of mastery of the intrinsic logic of the biology in play, not variations in the way they are written. Survey data demonstrate that many students would prefer a learning style not dominated by memorization of factual details, but how to develop a more effective strategy is rarely intuitive. Matching individual students with specific learning styles has not proven useful. Instead, teachers can strongly promote individual metacognitive appraisal during both classroom activities and other study environments. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.
How Law Operates in a Wired Global Society: Cyber and E-Commerce Risk

By now, almost every business has an internet presence, and is likely engaged in e-commerce. What are the major risks perceived by those engaged in e-commerce and electronic payment systems? What potential risks, if they become reality, may cause substantial increases in operating costs or threaten the very survival of the enterprise? This article discusses the relevant annual report disclosures from eBay (previous parent of PayPal) and Alphabet Inc. (parent of Google), along with other eBay, PayPal, Alphabet and Google documents, as a potentially powerful teaching device. Most of the descriptive language to follow is excerpted directly from eBay’s (PayPal) and Alphabet’s (Google) regulatory filings. My additions in prior scholarly articles about these entities include weaving these disclosure materials into a logical presentation and providing supplemental sources for those who desire a deeper look (usually in my footnotes) at any particular aspect. I’ve sought to present a roadmap with these materials that shows eBay’s and Google’s struggle to optimize their business performance while navigating through a complicated maze of regulatory compliance concerns and issues involving governmental jurisdictions throughout the world. International cyber crime and risk issues follow, with an examination of anti-money laundering, counter-terrorist, and other potential illegal activity laws. The value proposition offered here is disarmingly simple -- at no out-of-pocket cost, the reader has an opportunity to invest probably just a few hours to read and reflect upon the eBay (PayPal) and Alphabet Inc. (Google) multiple-million-dollar research, investment and documentation of perceived e-commerce, cyber, IT, and electronic payment system risks. Hopefully, this will prove of value to those either interested in the rapidly changing dynamics of (1) electronic payment systems, (2) those engaged in Internet site operations, or (3) those engaged in fighting cyber crime activities.
Dependence of Friability on Tablet Mechanical Properties and a Predictive Approach for Binary Mixtures

To systematically assess the dependence of friability on tablet mechanical properties, compaction pressure, and tablet porosity. Several common excipients and their mixtures exhibiting diverse mechanical properties were analyzed. Tablet elastic modulus, hardness, brittleness, porosity, and tensile strength were determined using standard techniques and then were correlated to tablet friability both individually and as a group to derive a universal model. Viscoelastic starch exhibits the highest friability followed by brittle excipients (mannitol, DCPA, and LM) and then ductile excipients (HPC and MCC). A reasonably accurate model for predicting pharmaceutically relevant range of friability, up to 3%, of binary mixtures is presented based on friability of individual components. In addition, a multivariate model between friability and different mechanical parameters was developed, based on which the weight loss propensity of tablets may be predicted. The experimental findings and predictive model are useful for expedited development and optimization of tablet formulation using a minimum amount of API.
Work–Family Backlash: The “Dark Side” of Work–Life Balance (WLB) Policies

Although continuing to capture the attention of scholars, the study of “work–family backlash” remains plagued by a lack of conceptual clarity. As a result, there is growing evidence to suggest that...
Supervised and unsupervised machine learning approaches to classifying chimpanzee vocalizations

Quantitative tools for classifying vocal repertoires have been constantly evolving with developments in machine learning and speech recognition research as well as increasing computing power. There are two main methodological considerations in classifying vocalizations: (i) choosing the classification technique and (ii) choosing the features for classification. Current state-of-the-art classification techniques are artificial neural networks (ANNs), support vector machines (SVMs), and ensemble methods like random forests (RFs). Current state-of-the-art features from speech recognition research include mel frequency cepstral coefficients (MFCCs). Bioacoustics researchers have applied these tools to problems including individual-, species-, and call-type identification, and vocal repertoire classification. However, researchers studying non-human primate vocalizations have only recently started adopting these approaches and none have applied them to study chimpanzee vocalizations. Here, we analyze vocalizations recorded in Gombe National Park, Tanzania. First, we use supervised classification techniques (ANNs, SVMs, and RFs) that involve training the models based on predefined call-types to evaluate the classification accuracy. Second, we use unsupervised techniques (that do not require prior knowledge of call-types), namely, K-means clustering, and self-organizing neural networks to identify discrete call types. We discuss the results from both supervised and unsupervised techniques and their strengths over traditional methods.
Bifurcation from Rotating Waves

We consider abstract evolution equations which are invariant under a Lie group. We discuss bifurcation from trajectories that lie in the orbit (under the Lie group) of a single point into trajectories in the orbit of a closed curve.
Diversity of Somatic Spikes in Dorsal Root Ganglion Cells: Implications for Development, Function and Plasticity

Dorsal root ganglion cells are superficially similar in that they all innervate a target in the periphery and project into the spinal cord. However, it has been appreciated for many decades that these neurons are in fact quite heterogeneous in their projections, both peripherally and centrally (for review see Willis and Coggeshall55). In the periphery individual cells can innervate receptors in skin, muscles, joints or viscera, and their laminar targets in the spinal cord are also quite diverse. It is important to appreciate that peripheral and central innervation is highly correlated so that, for example, neurons innervating muscle spindles project principally to laminae VI, VII and IX whereas C-fiber nociceptors project primarily into lamina II. These peripherocentral correlations have been extremely important in determining the sensory channels through which individual modalities project in the spinal cord (for review see Willis and Coggeshall55).
Construction of Globally Semigroup-Invariant C∞ -Domains

In this chapter, the ‘infinitesimal’ spectral-type commutation theory on Banach spaces (Chapters 5 and 6) is connected with the global invariant-domain commutation theory on locally convex spaces (Chapter 3). In particular, we obtain from the hypotheses of Chapter 3 (domain regularity) or of Chapter 5 (graph-density) that whenever the underlying space E is Banach (or Frechet) there exists a domain D∞ of C∞-vectors which is a Frechet space with respect to a stronger C∞- topology. This space is invariant under the action at least of the (semi) group operators V(t,A) involved in the problem and under the operational images φ(A) of A constructed via a suitably restricted semigroup/transform operational calculus. In suitable instances, it is also invariant under certain of the resolvents R(λ,A) for A as well. The net effect of these developments is to unify the different types of commutation relations, while preparing for a unified, economical treatment of smooth integrals and continuous exponentials of operator Lie algebras in Chapters 8 and 9, and laying the groundwork for our subsequent analysis of smeared (distribution) exponentials.
Zinc Inhibits Doxorubicin-Activated Calcineurin Signal Transduction Pathway in H9c2 Embryonic Rat Cardiac Cells:

Elevation of the zinc-binding protein metallothionein (MT) in the heart inhibits doxorubicin (DOX)-induced myocardial apoptosis and heart hypertrophy. Zinc release from MT in response to oxidative stress has been suggested as a mechanism of action of MT protection from DOX toxicity, and calcineurin is involved in the signaling pathways leading to myocardial apoptosis and heart hypertrophy. The present study was undertaken to determine if zinc can modulate the DOX-activated calcineurin signaling pathway. H9c2 cells were treated with 1 muM DOX, and zinc release was monitored by a zinc ion-specific fluorophore, zinquin ethyl ester. Additionally, DOX-activated calcineurin signaling was detected by a calcineurin-dependent nuclear factor of activated T-cell reporter. DOX treatment induced an increase in intracellular labile zinc and activated calcineurin signaling. Pretreatment of H9c2 cells with a zinc-specific, membrane-permeable chelating agent, N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN), inhibited the increase in intracellular labile zinc and increased the DOX-activated calcineurin signaling. Pretreatment of H9c2 cells with exogenously added zinc attenuated the DOX-activated calcineurin signaling in a dose-dependent manner. However, neither TPEN nor addition of exogenous zinc affected DOX-induced cellular hypertrophy or DOX-induced decrease in cell viability. Additionally, inhibition of DOX-induced calcineurin signaling with the calcineurin inhibitors cyclosporine A or tacrolimus (FK506) failed to restrict the DOX-induced decrease in cell viability. These results indicate that zinc suppresses DOX-induced calcineurin signaling in H9c2 cells; however, calcineurin signaling is not involved in the DOX-induced decrease in cell viability in H9c2 cells. (It had been shown previously that calcineurin is also not necessary for DOX-induced H9c2 cell hypertrophy.).
Welcoming the Unborn: Toward a Politics of Inclusion

I here present a feminine voice version of the moral case against abortion and draw from it some conclusions for public policy. My motto is solidarity with the last and least. The unborn individual is “one of us”—to be welcomed, not dismissed as a burden on society. Abortion, I argue, is bad for women, bad for children, and bad for the rest of us. Public policy should reflect these conclusions.
Investigation of continuous carbothermal reduction of magnesia by magnesium vapor condensation onto a moving bed of solid particles

Abstract Magnesium metal production by carbothermic reduction (CTR) can reduce process emissions and energy requirements relative to silicothermic or electrolytic production, if high magnesium metal yields are achieved. A novel process was investigated where product magnesium gas condensed onto a moving bed of solid particles at high temperatures (≥300 °C) and in vacuum to minimize reversion and promote crystal growth. Using a half-system in which CTR product gases were artificially generated, magnesium continuously condensed onto steel, oxide, or carbide particles at yields >85% for PMg = 0.5 kPa. Steel particles exhibited the greatest bed retention and ease of separation, so this medium was used for scale-up to a full-system in which MgO CTR in a fixed bed gasifier at 1400 °C–1550 °C produced Mg(g) and CO. The initial reduction resulted in high Mg yield (>80%), but yield decreased as the reaction proceeded. The accumulation of Mg(s) and reversion product in the condenser promoted further reversion. The process yield could likely be improved by using high surface area particles to promote heat and mass transfer, allowing for shorter solid and gas residence times in the condenser. A finite volume model on the reactor tube and pellet bed described the kinetics, heat transfer, and mass transfer phenomena in the reduction reactor. The model predicted that the center of the bed was >50 °C cooler than the furnace, and the product gas pressures were near equilibrium. A wide and directly heated reactor could overcome these heat and mass transfer limitations.
RNAi Transfection Optimized in Primary Naïve B Cells for the Targeted Analysis of Human Plasma Cell Differentiation.

Upon antigen recognition, naive B cells undergo rapid proliferation followed by differentiation to specialized antibody secreting cells (ASCs), called plasma cells. Increased circulating plasma cells are reported in patients with B cell-associated malignancies, chronic graft-vs.-host disease, and autoimmune disorders. Our aim was to optimize an RNAi-based method that efficiently and reproducibly knocks-down genes of interest in human primary peripheral B cells for the targeted analysis of ASC differentiation. The unique contributions of transcriptional diversity in species-specific regulatory networks and the mechanisms of gene function need to be approached directly in human B cells with tools to hone our basic inferences from animal models to human biology. To date, methods for gene knockdown in human primary B cells, which tend to be more refractory to transfection than immortalized B cell lines, have been limited by losses in cell viability and ineffective penetrance. Our single-step siRNA nucleofector-based approach for human primary naive B cells demonstrates reproducible knockdown efficiency (~40-60%). We focused on genes already known to play key roles in murine ASC differentiation, such as interferon regulatory factor 4 (IRF4) and AID. This study reports a validated non-viral method of siRNA delivery into human primary B cells that can be applied to study gene regulatory networks that control human ASC differentiation.
On rotating star solutions to the non-isentropic Euler–Poisson equations

Abstract This paper investigates rotating star solutions to the Euler–Poisson equations with a non-isentropic equation of state. As a first step, the equation for gas density with a prescribed entropy and angular velocity distribution is studied. The resulting elliptic equation is solved either by the method of sub and supersolutions or by a variational method, depending on the value of the adiabatic index. The reverse problem of determining angular velocity from gas density is also considered.
Effect of generational status on immigrants’ intentions to start new ventures: The role of cognitions

Abstract Immigrants contribute to the economic development of their host nation by starting business ventures. However, knowledge of whether or not their intentions to do so changes from generation to generation is not complete. We contribute to filling this gap by analyzing the role of generational status on immigrants’ entrepreneurial intentions. In order to explain the mechanism underlying this effect, we focused on the role of cultural intelligence and entrepreneurial self-efficacy. Empirical analyses based on a sample of 289 respondents support our hypothesized arguments. We discuss the findings, advance theoretical contributions and draw implications for social and public policy.
Hyperuricemia is associated with a lower glomerular filtration rate in pediatric sickle cell disease patients

Sickle cell nephropathy (SCN) is a progressive disease that contributes significant morbidity and mortality in sickle cell disease (SCD), yet it remains poorly understood. Hyperuricemia negatively impacts renal function in the non-sickle cell population but is understudied in SCD. We performed a cross-sectional analysis of the first 78 pediatric SCD patients enrolled in a cohort study. The mechanism of development of hyperuricemia (defined, serum uric acid (UA) ≥ 5.5 mg/dL) was characterized as a result of either UA overproduction or inefficient renal excretion by the Simkin index and fractional clearance of urate (FCU) equations. Associations between hyperuricemia and albuminuria or estimated glomerular filtration rate (eGFR) were determined by linear regression. The prevalence of hyperuricemia in this young population (mean age 11.6 ± 3.77 years) was 34.2%. Only 1 hyperuricemic participant overproduced UA by Simkin index, while 62.5% were inefficient renal excretors of UA (FCU < 4%). Hyperuricemia was associated with a significant decrease in average eGFR, −27 ml/min/1.73m2 below normouricemia (mean eGFR 151.6 ± 40.32), p = 0.0122. Notably, the previously accepted association between decline of eGFR with age is significantly modified by hyperuricemia stratification, where hyperuricemia explains 44% of the variance in eGFR by age (R2 = 0.44, p = 0.0004) and is nonsignificant in normouricemia (R2 = 0.07, p = 0.0775). These findings indicate that hyperuricemia may be associated with early eGFR decline in SCN. This association must be further characterized in prospective cohort studies in SCN, and hyperuricemia must be investigated as a potential therapeutic target for SCN.
Palliative Care's Role Managing Cancer Pain During the Opioid Crisis: A Qualitative Study of Patients, Caregivers, and Clinicians

Abstract Context Patients with cancer face symptoms because of disease and treatment, and pain is common and complex. The opioid crisis may complicate patients' and clinicians' experiences of managing pain in cancer care. Objectives In our study of perceptions and experiences with palliative care (PC) at an outpatient cancer center, we examined communication around symptom management throughout cancer care, and pain and its management emerged as particularly salient. The objective of this article is to describe, from the perspectives of patients, caregivers, and oncology health care professionals, the role of PC in navigating the complicated dynamics of pain management amidst the opioid crisis. Methods A qualitative descriptive study with grounded theory components was designed to investigate experiences with and perceptions of specialist PC and symptom management, including pain. Interviews were audiorecorded and transcribed, and focused coding identified themes related to pain and pain management from all three perspectives. Results About 44 patients, caregivers, and non-PC health care professionals completed interviews. Patients with cancer and their caregivers had many concerns about pain management and were specifically concerned about opioid use and stigma. For patients, PC improved pain management and helped to destigmatize appropriate pain management. Oncology clinicians reported that partnering with PC facilitated complex pain management and also provided moral support around difficult opioid recommendations for patients. Conclusion PC offers the potential to uniquely support both patients and other oncology professionals in optimally navigating the complexity around pain management for cancer care in the midst of the opioid crisis.
P22 Prevalence of and Characteristics Associated with Food Security Status Among International College Students

Background The majority of studies on food insecurity among US college students show higher prevalence rates than the general population. Past studies have looked at characteristics associated with food security status among US college students, but have not focused specifically on international students. Objective To estimate the prevalence of and identify characteristics associated with food insecurity among international students at the University of North Carolina at Chapel Hill. Study Design, Setting, Participants This cross-sectional study used data from 263 international students attending the University of North Carolina at Chapel Hill who completed an online survey in October and November of 2016. Measurable Outcome/Analysis Food security status was assessed using the 10-item US Adult Food Security Survey Module and students were categorized as having high food security, marginal food security, or food insecurity. Self-reported demographics and other student characteristics were also assessed. Descriptive statistics were calculated. Monte Carlo Estimates for the Exact Test and ANOVA were used to assess statistical significance for the association between food security status and student characteristics. Statistical significance was considered P Results Among students in the sample, 51% reported high food security, 24% marginal food security, and 25% food insecurity. Characteristics significantly associated with food security status were gender, year in school, having a car, and perceived health rating. Age, years in the US, academic performance, marital status, having dependent children, living on vs off-campus, employment status, receiving financial aid, weight status, cooking frequency, perceived cooking skills, and having a meal plan were not significantly associated with food security status. Conclusions Lack of food security is a serious issue among international students at the University of North Carolina at Chapel Hill, with nearly half reporting food insecurity or marginal food security. The characteristics identified in this study as being associated with food security status can help to inform future research and interventions for addressing food security status among international students.
Comparing optimized exoskeleton assistance of the hip, knee, and ankle in single and multi-joint configurations

Exoskeletons that assist the hip, knee, and ankle joints have begun to improve human mobility, particularly by reducing the metabolic cost of walking. However, direct comparisons of optimal assistance of these joints, or their combinations, have not yet been possible. Assisting multiple joints may be more beneficial than the sum of individual effects, because muscles often span multiple joints, or less effective, because single-joint assistance can indirectly aid other joints. In this study, we used a hip-knee-ankle exoskeleton emulator paired with human-in-the-loop optimization to find single-joint, two-joint, and whole-leg assistance that maximally reduced the metabolic cost of walking for three participants. Hip-only and ankle-only assistance reduced the metabolic cost of walking by 26% and 30% relative to walking in the device unassisted, confirming that both joints are good targets for assistance. Knee-only assistance reduced the metabolic cost of walking by 13%, demonstrating that effective knee assistance is possible. Two-joint assistance reduced the metabolic cost of walking by between 34% and 42%, with the largest improvements coming from hip-ankle assistance. Assisting all three joints reduced the metabolic cost of walking by 50%, showing that at least half of the metabolic energy expended during walking can be saved through exoskeleton assistance. Changes in kinematics and muscle activity indicate that single-joint assistance indirectly assisted muscles at other joints, such that the improvement from whole-leg assistance was smaller than the sum of its single-joint parts. Exoskeletons can assist the entire limb for maximum effect, but a single well-chosen joint can be more efficient when considering additional factors such as weight and cost.
Association of prematurity with complications and failure to rescue in neonatal surgery.

BACKGROUND The majority of failure to rescue (FTR), or death after a postoperative complication, in pediatric surgery occurs among infants and neonates. The purpose of this study is to evaluate the association between gestational age (GA) and FTR in infants and neonates. METHODS National cohort study of 46,452 patients < 1 year old within the National Surgical Quality Improvement Program-Pediatric database who underwent inpatient surgery. Patients were categorized as preterm neonates, term neonates, or infants. Neonates were stratified based on GA. Surgical procedures were classified as low- (< 1% mortality) or high-risk (≥ 1%). Multivariable logistic regression and cubic splines were used to evaluate the association between GA and FTR. RESULTS Preterm neonates had the highest FTR (28%) rates. Among neonates, FTR increased with decreasing GA (≥ 37 weeks, 12%; 33-36 weeks, 15%; 29-32 weeks, 30%; 25-28 weeks 41%; ≤ 24 weeks, 57%). For both low- and high-risk procedures, FTR significantly (trend test, p < 0.01) increased with decreasing GA. When stratifying preterm neonates by GA, all GAs ≤ 28 weeks were associated with significantly higher odds of FTR for low- (OR 2.47, 95% CI [1.38-4.41]) and high-risk (OR 2.27, 95% CI [1.33-3.87]) procedures. A lone inflection point for FTR was identified at 31-32 weeks with cubic spline analysis. CONCLUSIONS The dose-dependent relationship between decreasing GA and FTR as well as the FTR inflection point noted at GA 31-32 weeks can be used by stakeholders in designing quality improvement initiatives and directing perioperative care. LEVEL OF EVIDENCE Level IV, Retrospective cohort study.
Science Education: Constructing a True View of the Real World?

Constructivism, we are alarmed to report, is alive, well, and thriving, and doing especially well in a rather unlikely place: namely, science education. Constructivism has acquired the status of “received view,” the doctrine of psychological, epistemological, and/or ontological faith that undergirds much of current pedagogical practice. In the discourse about science education, constructivism is often accepted without argument and without question as the view most appropriate for the science classroom. While there is a strong and growing body of work that clearly, in our view, exposes the deficiencies of constructivism, both as an interpretation of the nature of science and as a basis for science education, constructivism unaccountably persists. We maintain that both the epistemology and the ontology that attends constructivism, as it is often construed, are seriously flawed. While these flawed positions are most fully and consistently developed in radical forms of constructivism, for example, that of Ernst von Glasersfeld, the more moderate versions of constructivist thought display many of the same defects. The ready acceptance that constructivist views now receive constitutes a serious problem for science educators, and by extension, for all educators. In this essay, therefore, we shall point out some of the conceptual snares that we believe account for the immediate plausibility, and the unmerited popularity, of certain constructivist theses.
Annotating and Recognizing Event Modality in Text.

Current results in basic Information Extraction tasks such as Named Entity Recognition or Event Extraction suggest that we are close to achieving a stage where the fundamental units for text understanding are put together; namely, predicates and their arguments. However, other layers of information, such as event modality, are essential for understanding, since the inferences derivable from factual events are obviously different from those judged as possible or non-existent. In this paper, we first map out the scope of modality in natural language; we propose a specification language for annotating this information in text; and finally we describe two tools that automatically recognizing modal information in natural language text.
Removal of Fatty Acids from Serum Albumin by Charcoal Treatment

The fatty acid contents of 26 different serum albumin preparations representing different species and obtained from various commercial sources have been determined. Some samples had surprisingly little fatty acid contamination, but it was found that other samples contained between 2 and 3 moles of acid per mole of protein, in confirmation of earlier reports. Treatment of these samples with charcoal at low pH resulted in the virtually complete removal of fatty acids. The conditions for such treatment were investigated as a function of the type of fatty acid, pH, and the amount of charcoal required. Charcoal treatment removed at least 99% of albumin-bound radioactive fatty acids under optimal conditions, whereas the amount of protein adsorbed onto charcoal was 4.9%. The protein that remained in solution following separation of the charcoal appeared to be native, as judged by a number of criteria, including analytical ultracentrifugation, optical rotatory dispersion, the ability to bind fatty acids, and the ability to bind the fluorescent dye, 8-anilinonaphthalene-1-sulfonic acid, as well as several other fluorescence parameters. Fluorescence spectra of human serum albumin samples indicated that impurities are sometimes present which can be removed by charcoal at neutral pH. A possible explanation for the gentleness of charcoal treatment is offered. Acid-charcoal treatment is a much more rapid method of removing lipid impurities than other methods previously described.
Acquisitions in Bankruptcy: 363 Sales Versus Plan Sales and the Existence of Fire Sales

The acquisition of bankrupt firms has increasingly taken place through section 363 of the U.S. Bankruptcy Code. Some scholars are critical of 363 sales because the process weakens creditors’ voting rights, takes place quickly, and has limited information disclosure compared with sales that take place in conjunction with a bankruptcy plan, i.e., “plan sales.” These factors potentially result in less active bidding and increased fire sales. Supporters of 363 sales contend that financial markets are sufficiently developed to accommodate such sales efficiently. Ours is the first study of which we are aware that compares 363 sales and plan sales to test these contentions empirically. Using a sample of large firms acquired in bankruptcy from 1996 to 2010, we find that 363 sales are associated with considerably lower sale prices. Further examination shows that the lower sale prices for 363 sales compared with plan sales are not due to the quick speed with which they take place, which could potentially result in less active bidding or greater information problems. Rather, the lower prices for 363 sales are associated with the reduced negotiating leverage that creditors experience in 363 sales as postulated by Elizabeth Rose in her 2006 study. We do not find systematic evidence of poor governance or restricted bidder participation in 363 sales, and while sale prices are negatively impacted by industry distress, the industry distress discount is not further exacerbated by 363 sales. Our results contribute to the understanding of bankruptcy fire sales and also have policy implications related to bankruptcy law.
Experiencing Everyday Prejudice and Discrimination

Publisher Summary An individual's actions and efforts to fight against prejudice and discrimination that he may encounter in everyday life depends on how both the blatant and subtle forms of prejudice may have affected the lifestyle and thought process. In order to understand the entire reaction process, it is very important to study the everyday incidents in the life of an individual who has been the target of prejudice. This chapter aims to study how these individuals or even communities manage their own social worlds, keeping the factors of prejudice and discrimination aside. As has been highlighted in the studies of Simpson and Yinger, avoidance gradually becomes the obvious response to prejudice when subjected to it continuously. Avoidance can also be classified into psychological or behavioral, based on the reactions of the individual or the community that has been the target of prejudice. The responses demonstrated by targets of prejudice and discrimination have also been elaborately described in this chapter. An in-depth understanding of people and their experiences with prejudice and discrimination helps us learn a lot about these behaviors in general.
Characterization and application of small RNAs and RNA silencing mechanisms in fungi

Abstract Although extensively cataloged and functionally diverse in plants and animals, the role and targets of small RNAs remain mostly uncharacterized in filamentous fungi. To date, much of the knowledge of small RNAs in filamentous fungi has been derived from studies of a limited group of fungi, most notably in Neurospora crassa. While most of the recently discovered classes of small RNAs appear to be unique to fungi some are commonly found in eukaryotes. It is noteworthy that the RNA silencing protein machinery involved in small RNA biogenesis has also diverged greatly, particularly within filamentous fungi, and may explain the diversity of small RNA classes. In this review, we summarize important classes of eukaryotic small RNAs and provide a current analysis of the RNA silencing machinery based on available fungal genome sequences. Finally, we discuss opportunities for exploiting knowledge of small RNAs and RNA silencing for practical application such as engineering plants resistant to fungal pathogens.
Aggressive Thresholds of Male Pacific Treefrogs for Advertisement Calls Vary with Amplitude of Neighbors' Calls

In breeding choruses, male Pacific treefrogs (H. regilla) produce advertisement and encounter calls. The role of each call type in establishing intermale spacing patterns was investigated by playing back, at various amplitudes, recordings of these vocalizations to resident males. The aggressive threshold of a male for each call type was defined as the lowest amplitude of playback that elicited encounter calls. Pacific treefrogs consistently had lower aggressive thresholds to playbacks of encounter calls than to playbacks of advertisement calls. Aggressive thresholds to playbacks of advertisement calls were positively correlated with the maximum amplitude of the advertisement calls of neighboring males, as measured at the position of the focal male.
Development of a caffeine breath test to measure cytochrome P450-1A activity in birds

Abstract Cytochrome P450-1A activity is induced by planar polyhalogenated diaromatic hydrocarbons, and is often used as a biomarker of exposure of wildlife to these compounds. P450-1A activity is usually measured ex vivo in liver tissue. The purpose of this study was to develop a less invasive breath test to measure P450-1A activity in birds. Such an assay would allow measurement of P450-1A activity without the need to kill birds, and on the same individual over time. Caffeine is specifically metabolized by P450-1A, and N -demethylation of 14 C-labelled caffeine to 14 CO 2 was used as indicator of whole-body P450-1A activity. The caffeine breath test (CBT) was performed by injecting 14 C-labelled caffeine i.v. and measuring the 14 C activity of respired 14 CO 2 . The CBT was developed with domestic chickens ( Gallus domesticus ) using several 14 C-labelled caffeine isomers, and was also performed with three species of fish-eating birds in the North American Great Lakes. The CBT was an effective method for measuring P450-1A activity. Chickens treated with 2,3,7,8-tetrachlorodibenzo- p -dioxin (TCDD) metabolized significantly more tri-labelled caffeine (1,3,7-[ 14 C]trimethylxanthine) during the CBT than untreated chickens ( p = 0.004). Tri-labelled caffeine and 3-methyl-[ 14 C]caffeine were effective substrates in the CBT.
Encoding variability theory and the spacing effect in associate learning

Encoding variability theory accounts for the spacing effect by assuming that, as the lag between repetitions increases, the memorial representations approach independence. A method for testing this assumption in determining repetition effects in associative learning is suggested. In the independence hypothesis, we simply assume that each presentation of a word pair is represented independently, so that the expected proportion recalled is simple, P=P1+P2 - PIP2. Two studies are reported using a continuous paired-associate task representing a factorial combination of lag and retention interval as well as single-presentation control conditions. The results indicate that for moderately long retention intervals, as the lag between repetitions increases, the observed proportion recalled is first less, then eventually exceeds, and then returns to the level expected by an independence hypothesis.
Phagocytic Receptor CED-1 Initiates a Signaling Pathway for Degrading Engulfed Apoptotic Cells

Apoptotic cells in animals are engulfed by phagocytic cells and subsequently degraded inside phagosomes. To study the mechanisms controlling the degradation of apoptotic cells, we developed time-lapse imaging protocols in developing Caenorhabditis elegans embryos and established the temporal order of multiple events during engulfment and phagosome maturation. These include sequential enrichment on phagocytic membranes of phagocytic receptor cell death abnormal 1 (CED-1), large GTPase dynamin (DYN-1), phosphatidylinositol 3-phosphate (PI(3)P), and the small GTPase RAB-7, as well as the incorporation of endosomes and lysosomes to phagosomes. Two parallel genetic pathways are known to control the engulfment of apoptotic cells in C. elegans. We found that null mutations in each pathway not only delay or block engulfment, but also delay the degradation of engulfed apoptotic cells. One of the pathways, composed of CED-1, the adaptor protein CED-6, and DYN-1, controls the rate of enrichment of PI(3)P and RAB-7 on phagosomal surfaces and the formation of phagolysosomes. We further identified an essential role of RAB-7 in promoting the recruitment and fusion of lysosomes to phagosomes. We propose that RAB-7 functions as a downstream effector of the CED-1 pathway to mediate phagolysosome formation. Our work suggests that phagocytic receptors, which were thought to act specifically in initiating engulfment, also control phagosome maturation through the sequential activation of multiple effectors such as dynamin, PI(3)P, and Rab GTPases.
Statistical methodology for binary data from a set of partially structured two-way random cross-classifications

A complete two-way cross-classification design is not practical in many settings. For example, in a toxicological study where 30 male rats are mated with 30 female rats and each mating outcome (successful or unsuccessful)is observed, time and resource considerations can make the use of the complete design prohibitively costly. Partially structured variations of this design are, therefore, of interest (e.g., the balanced disjoint rectangle design, the fully diagonal design, and the "S"-design). Methodology for analyzing binary data from such incomplete designs is illustrated with an example. This methodology, which is based on infinite population sampling arguments, allows the estimation of the mean response, among-row correlation coefficient, among-column correlation coefficient, and the within-cell correlation coefficient as well as their standard errors.
Effects of wing‐pad removal and corpus allatum implantation on development of wings, flight muscles, and related structures in the striped ground cricket, Allonemobius fasciatus

. Removal of a hindwing pad from late instar nymphs of the striped ground cricket, Allonemobius fasciatus DeGeer (Gryllidae) inhibits the formation of long-winged adults. All nymphs become short-winged when their hindwing pad is removed during the sixth (penultimate) instar or during the first 2 days of the seventh instar. When a hindwing pad is removed on day 4 of the seventh instar or later, there is no effect on wing development and at least 50% of the crickets emerge as long-winged adults as in controls. The period sensitive for removal of a hindwing pad varies among different structures, e.g. elytra, hindwings, flight muscles, and the acrotergite of the first abdominal segment. As a result, some intermediate forms are produced when a hindwing pad is removed in the middle of the seventh instar. Implantation of corpora allata (CA) into late instar nymphs also inhibits formation of long-winged adults. When CA are implanted on day 2 or 3 of the seventh instar, some of the resulting adults have abnormally short elytra. Implantation of CA at an earlier stage produces supernumerary (eighth instar) nymphs.
ASSESSING BIAS: A COMPARISON OF TWO METHODS

Evaluation of research designs employing probability sampling, particularly those based on samples of individuals rather than households, has repeatedly disclosed relatively large discrepancies between design -objectives and actual performance.' The failure to secure substantial portions of a random sample raises obvious questions regarding the sample's representativeness and consequently the validity of the measurements obtained.
Waterpipe smoking among students in one US university: predictors of an intention to quit.

Abstract Objective: To examine the intention to quit waterpipe smoking among college students. Participants: A total of 276 University of Houston students identified through an online survey administered in February 2011. Participants indicated they had smoked a waterpipe in the month prior to the survey. Methods: Cross-sectional study. Questions included demographics, tobacco use, perceived risk of waterpipe smoking, and social acceptability. Multivariate logistic regression was used to determine predictors of an intention to quit. Results: Most of the sample participants (n = 227; 83%) reported that they had no intention to quit. Students believing that waterpipe smoking was harmful were more likely to have an intention to quit (odd ratio [OR] = 2.38, 95% confidence interval [CI; 1.05, 5.36]). Those who smoked for more than 60 minutes were less likely to have a desire to quit (OR = 0.29, 95% CI [0.12, 0.73]). Conclusions: The low level of a desire to quit demonstrated underscores the urgent need to deve...