cssi/SciSciGPT-SciSciNet huggingface dataset:
Loss of Aip1 reveals a role in maintaining the actin monomer pool and an in vivo oligomer assembly pathway

Although actin filaments can form by oligomer annealing in vitro, they are assumed to assemble exclusively from actin monomers in vivo. In this study, we show that a pool of actin resistant to the monomer-sequestering drug latrunculin A (lat A) contributes to filament assembly in vivo. Furthermore, we show that the cofilin accessory protein Aip1 is important for establishment of normal actin monomer concentration in cells and efficiently converts cofilin-generated actin filament disassembly products into monomers and short oligomers in vitro. Additionally, in aip1Delta mutant cells, lat A-insensitive actin assembly is significantly enhanced. We conclude that actin oligomer annealing is a physiologically relevant actin filament assembly pathway in vivo and identify Aip1 as a crucial factor for shifting the distribution of short actin oligomers toward monomers during disassembly.
Biomimetic nanocoating promotes osteoblast cell adhesion on biomedical implants

Implantation of dental and orthopaedic devices is affected by delayed or weak implant-bone integration and inadequate new bone formation. Innovative approaches have been sought to enhance implant-bone interaction to achieve rapid osseointegration. The aim of this study was to develop biomimetic polypeptide nanocoatings and to evaluate cell adhesion, proliferation, morphology, and biocompatibility of polypeptide nanocoatings on implant surfaces. A recently developed nanotechnology, i.e., electrostatic self-assembly, was applied to build polypeptide nanocoatings on implant models, i.e., stainless steel discs. Our in vitro tests using human osteoblast cells revealed that substantially more (one order magnitude higher) osteoblast cells were attached to polypeptide-coated, stainless steel discs than to uncoated discs within the first few hours of contact. The developed biomimetic nanocoatings may have great potential for dental and orthopaedic applications.
Soy-Based Formulae and Infant Growth and Development: A Review

Soy-based infant formulae, initially developed for infants who were lactose intolerant or allergic to cow's milk-based formulae, now account for >25% of the infant formulae sold in the United States. Formulations have changed over the years to improve digestibility, the stability and availability of minerals, and protein quality. Recent concerns have been raised regarding the phytoestrogenic isoflavone content of soy-based formulae. A systematic review of the literature was conducted to evaluate various measures of infant health and development in clinical studies comparing modern soy-based formulae with other diets and to document areas in which further research seems warranted. Results suggest that modern soy-based formulae support normal growth and nutritional status in healthy term infants in y 1 of life. However, there are very limited data on sexual and reproductive development or outcomes such as immune function, visual acuity/cognitive development and thyroid function. Available data do not provide evidence of meaningful differences in timing of maturation, sexual development or fertility in adolescents or adults. Nonetheless, given evidence suggesting that early exposure to soy and/or isoflavones might have long-term effects, further research following infants fed soy-based formulae into adulthood is warranted.
Future ocean increasingly transparent to low-frequency sound owing to carbon dioxide emissions

Low-frequency sound in the ocean is produced by natural phenomena such as rain, waves and marine life, as well as by human activities, such as the use of sonar systems, shipping and construction. Sea water absorbs sound mainly owing to the viscosity of the water and the presence of chemical constituents, such as magnesium sulphate, boric acid and carbonate ions. The concentration of dissolved chemicals absorbing sound near 1 kHz depends on the pH of the ocean 1 , which has declined as a result of increases in acidity due to anthropogenic emissions of carbon dioxide 2‐4 . Here we use a global ocean model 5,6 forced with projected carbon dioxide emissions 7 to predict regional changes in pH, and thus sound absorption, in the years 1800‐2300. According to our projections, ocean pH could fall by up to 0.6 units by 2100. Sound absorption—in the range between 100 Hz and 10 kHz—could fall by up to 60% in the high latitudes and in areas of deep-water formation over the same time period. We predict that over the twenty-first century, chemical absorption of sound in this frequency range will nearly halve in some of the regions that experience significant radiated noise from industrial activity, such as the North Atlantic Ocean. We suggest that our forecast of reduced sound absorption in acoustic hotspots will help in identifying target regions
A difference scheme for Vlasov's equation

A difference scheme is developed for the solution of the initial-value problem for the one-dimensional Vlasov equation for a collisionless electron plasma with a homogeneous ion background. Instead of the distribution function itself, its Fourier transform with respect to velocity is used. Case studies of nonlinear Landau damping, a stationary equilibrium, and a two-stream instability are presented as preliminary applications.
Is expanding retrieval a superior method for learning text materials

Expanding retrieval practice refers to the idea that gradually increasing the spacing interval between repeated tests ought to promote optimal long-term retention. Belief in the superiority of this technique is widespread, but empirical support is scarce. In addition, virtually all research on expanding retrieval has examined the learning of word pairs in paired-associate tasks. We report two experiments in which we examined the learning of text materials with expanding and equally spaced retrieval practice schedules. Subjects studied brief texts and recalled them in an initial learning phase. We manipulated the spacing of the repeated recall tests and examined final recall 1 week later. Overall we found that (1) repeated testing enhanced retention more than did taking a single test, (2) testing with feedback (restudying the passages) produced better retention than testing without feedback, but most importantly (3) there were no differences between expanding and equally spaced schedules of retrieval practice. Repeated retrieval enhanced long-term retention, but how the repeated tests were spaced did not matter.
Wave equation inversion of skeletalized geophysical data

SUMMARY Inversion methods based on gradient optimization techniques require the directional derivative of the data with respect to the model parameters. Unfortunately, the data (e.g., pressure seismograms) are usually restricted to that explicitly given in the fundamental governing equation (e.g., wave equation). This limited choice of data type may lead to misfit functions that are pathologically non-linear with respect to the model parameters. We present a methodology which allows for the calculation of directional derivatives for skeletalized data sets, yet still uses the fundamental governing equations without the need for approximations. Skeletalized data are defined as a reduced data set derived from the original data which retains the important information about the model parameter of interest. The motivation for working with skeletalized data rather than raw data is that the skeleton data may be strongly influenced by only one type of model parameter and lead to a quasi-linear misfit function. Examples of skeletalized data sets include first arrival traveltimes picked from CDP seismograms for velocity inversion, amplitudes of transmitted earthquake SH-waves for earthquake moment inversion, or pulse width measured from first arrivals for attenuation inversion. As an example we devise a traveltime inversion method based on the wave equation and free of any high-frquency approximations. Results show that wave equation traveltime (WT) inversion is superior to ray traced traveltime inversion for complicated velocity models. It is also shown that WT inversion converges quickly for starting velocity models that are far from the actual model.
Ultrasound guidance for epidural steroid injections

Ultrasound (US) guidance is practiced widely in regional anesthesia. It is becoming increasingly used for pain medicine interventions. US-guided neuraxial analgesia has also been demonstrated despite many technical challenges. The applicability of US guidance for neuraxial steroid injections adds the dimension of complications secondary to particulate steroids. This review will discuss the available evidence for the use of US in neuraxial analgesia and for epidural steroid injections (ESIs), the technique and limitations, and the potential uses of US for ESIs.
Effects of solution chemistry on the oxidative transformation of 1-naphthol and its complexation with humic acid

The extent of 1-naphthol (1-hydroxynaphthalene) complexation with humic acid (HA) was studied as a function of solution chemistry [pH (4−11), ionic strength, I (0.001 and 0.1 M LiCl), and dissolved O2 (DO) concentration (0 and 8 mg L-1)] using spectroscopic (fluorescence, UV absorbance) and macroscopic (equilibrium dialysis) techniques. 1-Naphthol is transformed by DO in aqueous solutions; oxidation increases with pH and I, producing (hydroxy)naphthoquinones and coupled reaction products. Quenching of 1-naphthol fluorescence by HA increased with equilibration time from 1 to 7 d. This time-dependent relationship was found to result from (a) weak complexation of 1-naphthol by HA and (b) oxidative transformation of 1-naphthol (slow reaction) resulting in the formation of secondary products that are more reactive with HA. Sorption of 14C-labeled compound (as measured by equilibrium dialysis) followed a pH-dependent trend with minimal removal below pH 7.0, a sharp increase over a narrow pH range, and maximum r...
Positron trapping at quantum-dot-like particles on metal surfaces

Abstract Measurements of the positron annihilation-induced Auger electron (PAES) spectra from the Fe–Cu alloy surfaces with quantum-dot-like Cu nanoparticles embedded in Fe reveal a decrease of the Fe M 2,3 VV positron annihilation-induced Auger signal intensity and an enhancement of the Cu one for surfaces created by enriching the Cu content of the Fe–Cu alloy. These experimental results are analyzed by performing calculations of positron surface states and annihilation characteristics at the Fe(1 0 0) surface with quantum-dot-like Cu nanoparticles embedded in the top atomic layers of the host substrate. Estimates of the positron binding energy and annihilation characteristics reveal their strong sensitivity to the nanoparticle coverage. Theoretical core annihilation probabilities are compared with experimental ones estimated from the measured Auger peak intensities. The observed behavior of the Fe and Cu PAES signal intensities is explained by theoretical calculations as being due to trapping of positrons in the regions of Cu nanoparticles embedded in the top atomic layers of Fe.
The timing of exchange rate collapse

Abstract Recent episodes of exchange rate collapse have renewed interest in models of speculative attacks. These episodes have been considered by some observers to be inconsistent with “fundamentals” models of attack since there was no prolonged period of policy misalignment and declining reserves, as required by such models. This paper develops a fundamentals model in which collapse is instantaneous at the time of unexpected policy change and/or a change in the expectations of future policy, even for a reserve abundant country.
One-Machine Sequencing to Minimize Total Tardiness: A Fourth Theorem for Emmons

In 1969 H. Emmons provided three theorems Emmons 1--3 for determining precedence relations between pairs of jobs for the single-machine tardiness problem. We show here a fourth straightforward theorem that uses the information when the jobs in the pair are both known to precede a third job in an optimum sequence. The new theorem augments the three Emmons theorems and is shown to be a generalization of a theorem by Elmaghraby.
Corneal endothelium and postoperative outcomes 15 years after penetrating keratoplasty

Purpose To determine changes in the central endothelium and thickness of grafted corneas and the cumulative probability of developing glaucoma, of graft rejection, and of graft failure 15 years after penetrating keratoplasty. Design Longitudinal cohort study of 500 consecutive penetrating keratoplasties by one surgeon. Methods Regrafted eyes, fellow eyes of bilateral cases, and patients not granting research authorization were excluded, leaving 388 grafts for analysis. At intervals after surgery, we photographed the endothelium and measured corneal thickness using specular microscopy. The presence of glaucoma, graft rejection, and graft failure were recorded. Results The 67 patients examined at 15 years represented 30% of the available clear grafts. Endothelial cell loss from preoperative donor levels was 71 ± 12% (mean ± standard deviation, n = 67), endothelial cell density was 872 ± 348 cells/mm2, and corneal thickness was 0.59 ± 0.06 mm. Endothelial cell density was unchanged between 10 and 15 years, whereas corneal thickness increased (P = .001, n = 55). The mean annual rate of endothelial cell loss from 10 to 15 years after surgery was 0.2 ± 5.7% (n = 54). The cumulative probability of developing glaucoma, graft rejection, or graft failure was 20%, 23%, and 28%, respectively, and 6 of the 8 graft failures after 10 years resulted from late endothelial failure. Conclusions From 10 to 15 years after penetrating keratoplasty, the annual rate of endothelial cell loss was similar to that of normal corneas, corneal thickness increased, and late endothelial failure was the major cause of graft failure.
Thermally activated resonant magnetization tunneling in molecular magnets: Mn 12 Ac and others

The dynamical theory of thermally activated resonant magnetization tunneling in uniaxially anisotropic magnetic molecules such as Mn${}_{12}\mathrm{Ac}$$(S=10)$ is developed. The observed slow dynamics of the system is described by master equations for the populations of spin levels. The latter are obtained by the adiabatic elimination of fast degrees of freedom from the density matrix equation with the help of the perturbation theory developed earlier for tunneling level splitting [D. A. Garanin, J. Phys. A 24, L61 (1991)]. There exists a temperature range (thermally activated tunneling) where the escape rate follows the Arrhenius law, but has a nonmonotonic dependence on the bias field due to tunneling at the top of the barrier. At lower temperatures this regime crosses over to the non-Arrhenius law (thermally assisted tunneling). The transition between the two regimes can be first or second order, depending on the transverse field, which can be tested in experiments. In both regimes the resonant maxima of the rate occur when spin levels in the two potential wells match at certain field values. In the thermally activated regime at low dissipation each resonance has a multitower self-similar structure with progressively narrowing peaks mounting on top of each other.
Communication of Empirical Knowledge: An Investigation of Readability and Quality of Research in Textiles and Apparel

This study employs both objective and subjective testing to examine readability and quality of research in textiles and apparel. Flesch scores provided a quantitative measure of the readability of passages taken from published research in the field. U.S. active/reserve and graduate student members of ITAA (n = 208) completed subject specific questionnaires for the subjective portion of the study. Responses to open-ended questions reveal that clarity, structure, and terminology are most frequently mentioned when explaining perceptions of readability while value and methods are concepts closely related to definitions of journal quality. Positive correlations between readability and quality (p ≤ .01) contrast findings in previous research. Time constraints facing today's academic community are noted as the primary reason for the need for published research to be readable and comprehensible.
Combining Nonlinear Biometric and Psychometric Models of Cognitive Abilities

It is well-established that genetic factors account for large proportions of individual differences in multiple cognitive abilities. It is also well-established that individual differences in performance on many different cognitive ability measures are strongly correlated. Recent empirical investigations, however, have suggested two interesting qualifications to these well-established findings: Genetic variance in cognitive abilities is higher in richer home environments (gene-by-environment interaction), and common variance in different cognitive abilities is lower at higher levels of overall ability (nonlinear factor structure). Although they have been investigated independently, these two phenomena may interact, because richer environments are routinely associated with higher ability levels. Using simulation we demonstrate how un-modeled nonlinear factor structure can obscure interpretation of gene-by-environment interaction. We then reanalyze data from the National Collaborative Perinatal Project, previously used by Turkheimer et al. (2003; Psychol Science), with a two-step method to model both phenomena.
A FINITE ELEMENT METHOD FOR ELASTIC PARAMETERIZATION AND ALIGNMENT OF CORTICAL SURFACES USING SULCAL CONSTRAINTS

We present a cortical surface registration method that simultaneously aligns sulcal landmarks and parameterizes two cortical surfaces. The approach is based on coregistration of cortical surface coordinate systems so that the labeled sulcal features share the same coordinates on both cortical surfaces. We model the cortex as an elastic sheet and solve the associated Cauchy-Navier equilibrium equation subject to sulcal alignment constraints. The elastic energy is computed directly with respect to the intrinsic surface geometry and discretized using a finite element method on triangular tessellations of the two surfaces. In contrast to alternative methods for cortical alignment, the method avoids the need for an intermediate flat space for sulcal landmark matching and provides a fast, accurate and inverse-consistent surface registration and parameterization for inter-subject neuroanatomical studies
Role of renin-angiotensin-aldosterone system in salt-sensitive hypertension induced by sensory denervation.

To define the role of the renin-angiotensin-aldosterone system in a novel salt-sensitive model, neonatal Wistar rats were given capsaicin (50 mg/kg sc) on the first and second days of life. After w...
High-resolution pulse shaper based on arrays of digital micromirrors

We describe an optical Fourier transform pulse shaper based on a combination of a diffraction grating and a reconfigurable array of digital micromirrors. The pulse shaper allows for adjustment of separation between consecutive pulses within a pulse burst and the length of the burst. Pulse separation, burst length, and number of pulses can be dynamically reconfigured by changing the periodic pattern imposed to the array of digital micromirrors. Experimental results on binary intensity modulation are in excellent agreement with basic design relations describing the spectral and temporal characteristics of the pulse shaper.
Microcapsules containing suspensions of carbon nanotubes

Single-walled nanotubes (SWNTs) suspended in chlorobenzene (PhCl) and ethyl phenylacetate (EPA) were incorporated into microcapsules using an in situemulsification polymerization of urea-formaldehyde; the capsules release the SWNTs upon mechanical rupture.
EVALUATION OF FIRST YEAR EXPERIENCE PROGRAM AT GEORGIA SOUTHERN UNIVERSITY

To increase the retention rate, Georgia Southern University launched the First-Year Experience (FYE) program. FYE is a comprehensive program which includes two mandatory courses ( FYE 1220: First-Year Seminar, and FYE 1410: Global Citizens), conversations with professors, intrusive academic advising, giving early alert/midterm grades, and limiting number of withdrawals. The two mandatory courses have been offered since fall 2008. This study is to assess the impact of the two mandatory courses on academic performance of students majoring in information technology (IT). A comparison is made among the two mandatory courses , two general education courses (English and Math), and two information technology (IT) courses. Grade point averages (GPA) and the grades of six courses were extracted from the university data warehouse. Pearson correlation is used to detect the dependence between course grades and GPA. The result shows that the two mandatory courses have higher correlations with GPA than the other courses do . The two IT courses have higher correlations with GPA than the two general education courses do The first course FYE 1220 is designed with a purpose of facilitating students integrated into academic environment, and the second course FYE 1410 is designed with emphasis of social integration. The result of the strong correlations validated Tinto’s integration theory, i.e., academic integration and social integration leads to the academic success. Normal 0 false false false EN-US ZH-CN X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman","serif"; mso-fareast-language:EN-US;}
Bunch length measurement using beam spectrum (CESR storage ring)

A procedure for extracting the bunch length from the beam-induced voltage spectrum is applied at CESR, for various bunch currents, to indicate whether the turbulent lengthening threshold is exceeded by short, high-current bunches. The approach is to monitor the signal spectrum from one of the detector buttons up to 8 GHz. The measuring system is calibrated by reference to a low-current bunch (1 mA), which is assumed to have a Gaussian profile with the theoretically predicted length. In this experiment, a single bunch was used with a natural length of 15 mm. No bunch lengthening was detected up to a current of 20 mA. >
Intravesical protamine sulfate and potassium chloride as a model for bladder hyperactivity

Abstract Objectives An acute animal model for hyperactive bladder in rats was developed using intravesical infusion of protamine sulfate (PS), an agent thought to break down urothelial barrier function, and physiologic concentrations of potassium chloride (KCl). Methods Continuous cystometrograms (CMGs) were performed in urethane-anesthetized female rats by filling the bladder (0.04 mL/min) with normal saline followed by intravesical infusion of a test solution consisting of either KCl (100 or 500 mM) or PS (10 or 30 mg/mL) for 60 minutes. Subsequently, the 10 mg/mL PS-treated animals were infused intravesically with 100, 300, or 500 mM KCl. Some animals were pretreated with capsaicin (125 mg/kg subcutaneously) 4 days before the experiments. Results Unlike KCl (100 or 500 mM) or a low concentration of PS (10 mg/mL) alone, the intravesical administration of a high concentration of PS (30 mg/mL) produced irritative effects with a decreased intercontraction interval (by 80.6%). After infusion of a low concentration of PS, infusion of 300 or 500 mM KCl produced irritative effects (intercontraction interval decreased by 76.9% or 82.9%, respectively). The onset of irritation occurred more rapidly after 500 mM KCl (10 to 15 minutes) than after 300 mM KCl (20 to 30 minutes). Capsaicin pretreatment delayed the onset (approximately 60 minutes) and reduced the magnitude (intercontraction interval decreased by 35.5%) of irritative effects. Conclusions Intravesical administration of KCl after PS treatment activates capsaicin-sensitive afferents and detrusor muscle and presumably capsaicin-resistant afferents. Modest, noncytotoxic affronts to urothelial barrier function can result in dramatic irritative responses. This model may be useful in the study of bladder irritation and hyperactivity.
Clinical Trials Relating to Epilepsy

As with all clinical trials, clinical trials in the epilepsies must, of necessity, be designed to deal with certain peculiarities of the disorder. The first important concept in the design of trials is the recognition that many different syndromes are included in the epilepsies and that meaningful data cannot be collected from an undifferentiated group of epileptic persons. Fortunately, very empirical information — the clinical seizure type — has rather good correlation with the various therapeutic measures and seizure classifications [2]. These data are useful as a first step in obtaining some form of homogeneity among the patients to be studied. This brief summary will concentrate on variables important in the clinical trials of new antiepileptic drugs; even though clinical trials of other therapeutic modalities (such as biofeedback or surgery) are quite important and remain in a relatively primitive state of development, most persons with epilepsy are treated with antiepileptic drugs, and most patients who remain uncontrolled on drugs are hopeful for the development of new, less toxic, and more effective medications. This communication will also be limited to a discussion of controlled clinical trials of antiepileptic drugs, in children and adults, exclusive of infantile spasms.
Reflections on Albion Tourgee's 1896 View of the Supreme Court a Consistent Enemy of Personal Liberty and Equal Right

In an 1896 Memorial Day lecture shortly after his loss in Plessy v. Ferguson, Albion Tourgee argued that the Supreme Court had “always been the consistent enemy of personal liberty and equal right.” Was Tourgee merely ventilating after a frustrating defeat, or did his thesis accurately represent the Supreme Court’s performance over time? In this article I will briefly introduce Tourgee, explain how he might have come to his bleak view of the Court, and finally consider his views of Reconstruction and of its failure — and the failure (in his time) of his constitutional vision.The Supreme Court was not a consistent enemy of personal liberty and equal right in Tourgee’s lifetime. It was just usually an enemy of liberty and equality. (Naturally, Tourgee’s Plessy brief cited some favorable precedents.) A review of relevant Supreme Court cases will show this qualified version of Tourgee’s thesis to be historically accurate. While it is true that Reconstruction-era Court decisions did not foreclose protection of blacks against private violence motivated purely by race, Cruikshank and subsequent cases required a racial motive for such prosecutions. As a result, white and black Republicans were effectively abandoned to politically motivated Klan violence at a time when the national government grew weary of protecting Reconstruction state governments through military force. Were Tourgee to return, he would be greatly impressed by what progress has been made since his death in 1905, but he would also be distressed by modern legal and economic threats to the more egalitarian democracy he envisioned.Note: This article grew out of an invitation to participate in a conference on the life of Albion Tourgee held in Raleigh, North Carolina. The conference was co-sponsored by the UNC Center for the Study of the American South. This and other papers from the conference will be published in the Elon Law Review.
The Management of Superior Labrum Anterior-Posterior Tears in the Thrower’s Shoulder

The adaptive and pathologic features of the throwing shoulder present a unique challenge to sports medicine specialists. Internal impingement can be exacerbated by problems in the athlete’s kinetic chain and results in varying features of posterior capsular contracture, rotator cuff tear, and superior labral injury. Superior labrum anterior-posterior lesions with or without injury to the biceps tendon is a common cause of pain and decreased performance in throwing athletes. The optimal nonoperative and surgical treatment of superior labrum anterior-posterior tears is determined by a detailed patient history, complete physical examination of the shoulder and entire kinetic chain, and by advanced imaging. Treatment and rehabilitation that allow elite overhead athletes to return to the same level of play remain a challenge.
Knowledge Management and the Creation of Business Value

Knowledge management (KM) initiatives that create business value are a major focus for many organizations. While academics often couch KM success in terms of process outcomes, some argue that the organizational outcomes perspective of KM success held by many practitioners is clearer, where KM success is tied to its impact on organizational performance. This study proposes an integrated model that incorporates both perspectives, in which the business value of KM is the dependent variable and effective KM process implementation is an important antecedent. We also hypothesize that two contextual factors, top management support and organizational culture, are positively related to business value. Data collected from a U.S. national survey of 268 information technology (IT) executives support the significance of these relationships. Furthermore, this research identifies key KM barriers as well as benefits that influence top management support of KM, KM process implementation, and indirectly business value. Pra...
Exact Solutions for the Dirac Equation for Spherically Symmetric Potentials

Having discussed the plane-wave solutions to the Dirac equation in some detail, let us now look at solutions to the Dirac equation with a spherically symmetric V(r). In particular, two cases are of special interest as follows. Case 1.
Analysis of the Stability of Speed of the Balance Circuit of the Hydraulic System

This paper analyzes the stability and the creeping reasons and the relevant methods for correction of the hydraulic balance circuit,which provides a scientific basis to remove this kind of failures and to correctly use and design the balance circuit.
Organizing the voluntary association

This article offers a cursory overview of academic and practitioner-based approaches to understanding the process of creating voluntary associations (e.g., direct action community organizations, un...
Abstract 5292: An online tool for biomarker analysis in Gene Expression Omnibus (GEO) datasets

The Gene Expression Omnibus (GEO) is a public repository of gene expression and sequence-based datasets, that currently includes >42,000 datasets with gene expression profiles obtained by microarray, and >12,000 datasets containing the keyword “cancer”. Although GEO has its own analysis tool (GEO2R) for identifying differentially expressed genes, evaluation of a single gene is not straightforward, and GEO2R was not designed to identify prognostic biomarkers based on survival analyses. In this work, we describe an online, easy-to-use tool for biomarker analysis in GEO datasets. shinyGEO is a web-based tool that allows a user to download the expression and sample data from a GEO dataset, select a gene of interest, and perform a survival or differential expression analysis in order to evaluate gene expression diagnostic or prognostic biomarkers. For both analyses, shinyGEO produces publication-ready graphics and generates R code ensuring that all analyses are reproducible. The tool is developed using shiny, a web application framework for R, a language for statistical computing and graphics. The web application and source code is available at the following link: http://bioinformatics.easternct.edu/shinyGEO/ Citation Format: Jasmine Dumas, Michael Gargano, Garrett M. Dancik. An online tool for biomarker analysis in Gene Expression Omnibus (GEO) datasets. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5292.
Prosubstrates of CYP3A4, the major human hepatic cytochrome P450 : Transformation into substrates by other P450 isoforms

This study demonstrates interplay among human hepatic cytochrome P450 (CYP) isoforms in transforming aromatic compounds from being prosubstrates of CYP3A4 into phenolic substrates. Incubation of methoxychlor with CYP2C19 yields the phenolic monodemethylated derivative (mono-OH-M). Additionally, CYP2C19 catalyzes the ortho-hydroxylation of mono-OH-M and of residual methoxychlor. CYP3A4 does not catalyze the O-demethylation or hydroxylation of methoxychlor, but does hydroxylate mono-OH-M (ortho to the phenolic hydroxyl) (Stresser DM and Kupfer D, Biochemistry 36: 2203-2210, 1997). A combination of reconstituted CYP2C19 and 3A4 in the same vessel elicits stimulation of the ortho-hydroxylation of mono-OH-M compared with 2C19 alone. It is unlikely that stimulation of hydroxylation was due to protein-protein interactions, generating more active P450(s), because progression of the stimulation was time-dependent. When reconstituted CYP3A4 was added to an ongoing incubation containing reconstituted 2C19, stimulation of catechol formation occurred. In another experiment, stimulatory activity was similar when 2C19 and 3A4 were reconstituted together in the same vesicles or separately. Cumulative evidence demonstrates that the stimulation of catechol formation resulted from CYP3A4-mediated ortho-hydroxylation of the phenolic metabolite(s) generated by CYP2C19. Similarly, estradiol 3-methyl ether is demethylated by CYP2C19 into estradiol, a CYP3A4 substrate for ortho-hydroxylation; there was significant stimulation of hydroxylation by combined 2C19 and 3A4. These findings demonstrate that pro-phenolic compounds (methoxychlor and estradiol 3-methyl ether) are prosubstrates of CYP3A4. Because catalysis may become evident only after prosubstrate conversion (by a different P450) into a substrate, caution is warranted when concluding a lack of catalytic involvement by a particular P450 isoform, based solely on data from the use of individual cDNA-expressed P450s.
Deathly Love: Tracing the Necro Logic of the Decadent Imagination in I.U. Tarchetti’s Amore nell’arte

This paper examines three stories in Tarchetti’s Amore nell’arte as case studies of the conjunction of art, love, and death, which plays a central role in the decadent imagination. In advancing the idea that art is superior to life, these texts couple the artistic ideal with a propensity toward necrophilic excess of love. Departing from the critical tendency to view such excess as evidence of an anticonventional stance, I explore how Tarchetti’s writing points to complicity between unfettered ideals and worldly power structures. I rely on an ecocritical perspective to trace this complicity to a necro logic: a hollowed out, life-denying symbolic order that posits abstract, polarizing distinctions between self and other in order to enable limitless self-expansion at the expense of the other. The paper’s central argument can be summed up as follows: the path to self-fulfillment emplotted in Tarchetti’s stories shows deathly implications in the creative vitality of decadent literature by leading from idealist...
Time evolution of the Coulomb screening effects on terahertz generation at the surface of InAs

We study the effects of electron density and temperature, both experimentally and numerically, on the Coulomb screening process responsible for saturation of the terahertz generation process at the surface of InAs. We use a pair of ultrafast pulses with adjustable time delay to generate terahertz radiation and compare the results to a 1D drift-diffusion equation model modified to include radial diffusion and cooling of the electrons through scattering. We demonstrate the necessity of these modifications by implementing the original drift-diffusion equation model, as reported by Liu et al. [Phys. Rev. B73, 155330 (2006)1098-0121PRBMDO10.1103/PhysRevB.73.155330], and show that it underestimates saturation by an order of magnitude. We find excellent agreement between our experimental and numerical results, confirming the validity of our improved model and demonstrating its potential use in a number of applications, such as terahertz pulse shaping with an ultrafast pulse train.
A Study of Student Engagement in Project-Based Learning Across Multiple Approaches to STEM Education Programs

Objective: In this study, we investigated the implementation of project-based learning (PBL) activities in four secondary science, technology, engineering, and mathematics (STEM) education settings to examine the impact of inquiry based instructional practices on student learning. Method: Direct classroom observations were conducted during the 2013–2014 school year in STEM Traditional Courses, a STEM Platform School, an Engineering Optional Program (EOP), and a Virtual STEM Academy (VSA) to measure teacher instructional practices (School Observation Measure) and student engagement (The Rubric for Student-Centered Activities). Results: The four approaches to STEM education showed significant differences in their implementation of PBL, with the EOP and VSA having higher incidences of PBL activities. Additionally, higher-level questioning strategies, higher-order instructional feedback, and integration of STEM subject areas was absent or rarely observed. Conclusions: Components of PBL are missing in STEM education, in traditional and non-traditional STEM courses. In-service teachers may benefit from professional development that enhances their understanding of PBL activities to maximize student learning opportunities.
Positioning Self in “figured worlds”: Using Poetic Inquiry to Theorize Transnational Experiences in Education

This study explores the process of using Holland et al. (Identity and agency in cultural worlds, Harvard University Press, Cambridge, 1998) “figured worlds” identity and agency theory to explore two scholars’ transnational experiences. Using poetic inquiry as a data analysis tool, this study seeks to (re)position how identity work is theorized and analyzed across broader contexts. Data collection consisted of online discussions, reflective journals, and biographical artifacts to better contextualize our discussions. These co-constructed discussions were transcribed and analyzed using poetic inquiry to better capture and articulate experiential themes of isolation, vulnerability, adaptation, and survival. This study serves three purposes (1) how both authors analyzed, interpreted and theorized our childhood experiences crossing borders using Holland et al. (Identity and agency in cultural worlds, Harvard University Press, Cambridge, 1998) “figured worlds” theory, (2) how poetic inquiry was used to capture the isolation, vulnerability, adaptation, and survival of one author’s experiences, and (3) how this type of reflexivity explicitly in/transforms theoretical approaches to deconstructing cultural identity and agency in a myriad of contexts, notably teacher education.
Hydrogels for Biomedical Applications: Their Characteristics and the Mechanisms behind Them

Hydrogels are hydrophilic, three-dimensional networks that are able to absorb large quantities of water or biological fluids, and thus have the potential to be used as prime candidates for biosensors, drug delivery vectors, and carriers or matrices for cells in tissue engineering. In this critical review article, advantages of the hydrogels that overcome the limitations from other types of biomaterials will be discussed. Hydrogels, depending on their chemical composition, are responsive to various stimuli including heating, pH, light, and chemicals. Two swelling mechanisms will be discussed to give a detailed understanding of how the structure parameters affect swelling properties, followed by the gelation mechanism and mesh size calculation. Hydrogels prepared from natural materials such as polysaccharides and polypeptides, along with different types of synthetic hydrogels from the recent reported literature, will be discussed in detail. Finally, attention will be given to biomedical applications of different kinds of hydrogels including cell culture, self-healing, and drug delivery.
Giant renal oncocytoma with classic stellate scar.

A middle-aged man with poor access to medical care presented with shortness of breath and 3 years of abdominal distention. On physical examination, he was found to have a palpable mass in the left upper quadrant. He was found to have undiagnosed congestive heart failure with dilated cardiomyopathy, and a CT scan of the abdomen and pelvis revealed a left renal mass. An MRI performed to further characterise the lesion demonstrated a large exophytic mass with a central scar and segmental enhancement originating from the lateral aspect of the left kidney with no evidence of renal vein or caval thrombus (figure 1). Owing to the possibility of renal malignancy, the patient underwent …
Does Cervical Interlaminar Epidural Steroid Injection with Low-Dose Lidocaine Cause Objective Upper Extremity Weakness? A Preliminary Study.

Objective Low-dose local anesthetic is often used in cervical interlaminar epidural steroid injections (CIESI), yet its effect on upper extremity strength has not been studied. The presence of consequent weakness has potential implications for postprocedure safety. This study aimed to determine whether low-dose lidocaine in a C7-T1 CIESI causes objective weakness. Design Prospective case series. Setting Academic pain center. Subjects Adults, cervical radicular pain. Methods Participants underwent CIESI with 1 mL of 1% lidocaine (3 mL total injectate). Elbow flexion (EF), wrist extension (WE), elbow extension (EE), and handgrip strength were measured by dynamometry at baseline, 15 minutes, and 30 minutes postinjection. Changes in strength from baseline and the proportion of participants with a minimum perceptible change in EF, WE, EE, and handgrip strength (≥20%) and 95% confidence intervals (CIs) were calculated. Results Twenty-seven participants were included. At 15 and 30 minutes postinjection, there was no within-participant difference in EF, WE, EE, and handgrip strength from baseline overall. Nonetheless, five (19%, 95% CI = 4-33) of the participants demonstrated a 20% or greater strength decrease in at least one myotomal distribution. A 20% or greater decrease in strength was present in left EF 4% (95% CI = 0-11%), right EF 7% (95% CI = 0-17%), left WE 4% (95% CI = 0-11%), and right WE 7% (95% CI = 0-17%). Conclusions The present data suggest that CIESI with an injectate volume of 3 mL that includes 1 mL of 1% lidocaine may result in objective upper extremity weakness that is above the minimum threshold of perception in a subset of patients.
Business cycle, reallocation of labor and asset prices

Empirical literature on reallocation of resources during business cycles provides an evidence of increased reallocation of labor across firms during downturns. In this paper I build a theoretical model with search frictions in labor market, that is consistent with this observation, and study implications of search and match frictions for the cross section of stock returns. In the model firms having more growth opportunities benefit from recessions due to more slack in the labor market which allows them to expand quicker and convert higher share of their growth opportunities into profitable projects. This feature generates a return spread between value and growth firms. In the model sorts of stocks based on different growth indicators yield patterns documented empirically in previous studies.
Bootstrapping Biomedical Ontologies for Scientific Text using NELL

We describe an open information extraction system for biomedical text based on NELL (the Never-Ending Language Learner) (Carlson et al., 2010), a system designed for extraction from Web text. NELL uses a coupled semi-supervised bootstrapping approach to learn new facts from text, given an initial ontology and a small number of "seeds" for each ontology category. In contrast to previous applications of NELL, in our task the initial ontology and seeds are automatically derived from existing resources. We show that NELL's bootstrapping algorithm is susceptible to ambiguous seeds, which are frequent in the biomedical domain. Using NELL to extract facts from biomedical text quickly leads to semantic drift. To address this problem, we introduce a method for assessing seed quality, based on a larger corpus of data derived from the Web. In our method, seed quality is assessed at each iteration of the bootstrapping process. Experimental results show significant improvements over NELL's original bootstrapping algorithm on two types of tasks: learning terms from biomedical categories, and named-entity recognition for biomedical entities using a learned lexicon.
Hormesis: What it is and Why it Matters

Hormesis describes any process in which a cell, organism, or group of organisms exhibits a biphasic response to exposure to increasing amounts of a substance or condition (e.g., chemical, sensory stimulus, or metabolic stress); typically, low-dose exposures elicit a stimulatory or beneficial response, whereas high doses cause inhibition or toxicity. The biphasic dose-response signature of hormesis is a common result of experiments in the field of toxicology, but the low-dose data have been largely ignored, and the prevailing view is that it is important to reduce levels of toxins as much as possible. However, in many cases, the “toxins” actually have essential or beneficial effects in low amounts. Prominent examples of such beneficial “toxins” are trace metals such as selenium, chromium, and zinc. Fundamental inter- and intracellular signals also exhibit hormetic dose responses, including hormones, neurotransmitters, growth factors, calcium, and protein kinases. Moreover, everyday health-promoting lifestyle factors, including exercise and dietary energy restriction, act, at least in part, through hormetic mechanisms involving activation of adaptive cellular stress response pathways (ACSRPs). ACSRPs typically involve receptors coupled to kinases and activation of transcription factors that induce the expression of cytoprotective proteins such as antioxidant enzymes, protein chaperones, and growth factors. The recognition and experimental utilization of hormesis is leading to novel approaches for preventing and treating a range of diseases, including cancers, cardiovascular disease, and neurodegenerative disorders.
Obstetric History and Likelihood of Preterm Birth of Twins.

Objective The objective of this study was to investigate the relationship between preterm birth in a prior pregnancy and preterm birth in a twin pregnancy. Study Design We performed a secondary analysis of a randomized controlled trial evaluating 17-α-hydroxyprogesterone caproate in twins. Women were classified as nulliparous, multiparous with a prior term birth, or multiparous with a prior preterm birth. We used logistic regression to examine the odds of spontaneous preterm birth of twins before 35 weeks according to past obstetric history. Results Of the 653 women analyzed, 294 were nulliparas, 310 had a prior term birth, and 49 had a prior preterm birth. Prior preterm birth increased the likelihood of spontaneous delivery before 35 weeks (adjusted odds ratio [aOR]: 2.44, 95% confidence interval [CI]: 1.28–4.66), whereas prior term delivery decreased these odds (aOR: 0.55, 95% CI: 0.38–0.78) in the current twin pregnancy compared with the nulliparous reference group. This translated into a lower odds of composite neonatal morbidity (aOR: 0.38, 95% CI: 0.27–0.53) for women with a prior term delivery. Conclusion For women carrying twins, a history of preterm birth increases the odds of spontaneous preterm birth, whereas a prior term birth decreases odds of spontaneous preterm birth and neonatal morbidity for the current twin pregnancy. These results offer risk stratification and reassurance for clinicians.