cssi/SciSciGPT-SciSciNet huggingface dataset:
The resonantly-forced Korteweg-DeVries equation and sediment resuspension

A stability analysis is presented of model separated flow bubbles, typical of those found in the boundary layer under the footprint of a solitary wave moving slowly over a fiat surface. The velocity profiles in the separated region are modeled using a perturbed family of Falkner-Skan profiles. These profiles are examined for their stability properties with special regard given to the conditions leading to the appearance of local absolute instability and the onset of a global instability. It is shown that global instability can be expected in separation bubbles of moderate size (e.g., containing a peak backflow velocity of approximately thirty percent of the free stream). It is conjectured that a global instability provides a cc^ herent dynamic state that is efficient in resuspending sedimentary particles even though the nominal stress in a separated region is much lower than that for an attached boundary layer.
Island Colony and the Penal Settlement

In its initial two decades (the 1860s and 1870s), the British had opened the penal colony on an experimental basis and the difficulties that the Settlement officers faced in settling the Andamans had done little to suppress the misgivings regarding the sustainability of the venture. Nonetheless, by the mid-1870s the initial uncertainties began to give way to greater assurance. Improvements in the physical condition of the Settlement gave a greater confidence to the Settlement officers that the colony could be maintained in the years to come as a penal station. Ironically, as the penal settlement acquired a firmer footing, the idea whether it should be retained in permanence began to be debated.2 Some officials saw this as the unfolding of the natural course of a penal settlement whereby it was developed enough to make way for a free settlement. There were others who felt that the idea of abolishing the penal settlement was not only premature but one which was fraught with logistical difficulties for the judicial department. The debate continued unresolved for several decades until the end of World War I. The political realignments and reconfigurations in the subcontinent following the war and the growing nationalist interest in the affairs of the Andamans pushed the Government of India to take a decision regarding the fate of the penal settlement. After much deliberation it was decided to retain the penal settlement of the Andamans but abolish convict transportation, i.e., to have a quasi-penal settlement on the Andamans which was peopled by convicts who had ‘voluntarily’ migrated there.
Analogy and the danger of over-simplifying the past

This is an excellent and tightly written argument against the indiscriminate and essentialist extension of invented anthropological typologies, such as ‘the San’, back into the Pleistocene. While analogical arguments that relate similarities in excavated tools, poisons and so on to the repertoire of items used by extant peoples in order to interpret their function is a common approach in archaeology, as the authors rightly point out, the extension of these analogies to include particular cultural and linguistic forms is ‘a theoretically flawed exercise’.
Second non-ocular tumors among survivors of retinoblastoma treated with proton therapy.

10018 Background: The leading cause of death for patients with hereditary retinoblastoma is second malignancy. Proton radiation allows for significant sparing of non-target tissue. We sought to det...
RESPONSE OF DYNAMICAL SYSTEMS DRIVEN BY ADDITIVE GAUSSIAN AND POISSON WHITE NOISES

ABSTRACT A numerical method previously developed by the authors for the solution of stochastic systems excited by Poisson white noise will be applied to several dynamical systems. The stationary probability density function of the response process for the single degree-of-freedom Duffing oscillator will be obtained by solving the Fourier-transformed forward generalized Kolmogorov equation directly for the characteristic function, followed by numerical Fourier inversion to recover the probability density function. The excitation process will modeled as a sum of Gaussian and Poisson white noises. Resulting second and fourth order moments of response will be examined in order to assess relative effects of the two inputs.
Risks and Protective Factors for Stress Self-Management in Parents of Children With Autism Spectrum Disorder: An Integrated Review of the Literature.

Problem Stress in parents of children with autism spectrum disorder (ASD) has been reported to be very high. However, little is known about what risk and protective factors influence parental stress self-management in this population. Accordingly, this manuscript is a synthesis of the risk and protective factors that impact self-management of stress in these parents. The concepts in the individual and family self-management theory context domain were used as a framework to guide data collection and analysis. Eligibility criteria Searches were conducted using CINAHL, MedLine and PsychInfo. Studies were included if they addressed context factors in parents of children with ASD and were written in English. Sample Ninety-eight studies met review criteria. Results This review highlighted risk factors to parental stress self-management within the context of condition-specific factors, physical and social environment, and individual and family. The most concerning of these findings is that parents struggle accessing a diagnosis and services for their child and are frustrated with health care providers' knowledge of ASD and lack of communication. Conclusions The risks parents experience as they care for their child with ASD far outweigh the protective factors for self-management of parental stress. Implications Nurses who are aware of these issues can make important changes to their practice and have a significant impact on parental stress self-management and the care of children with ASD.
Schema independent and scalable relational learning by castor

Learning novel relations from relational databases is an important problem with many applications in database systems and machine learning. Relational learning algorithms leverage the properties of the database schema to find the definition of the target relation in terms of the existing relations in the database. However, the same data set may be represented under different schemas for various reasons, such as efficiency and data quality. Unfortunately, current relational learning algorithms tend to vary quite substantially over the choice of schema, which complicates their off-the-shelf application. We demonstrate Castor, a relational learning system that efficiently learns the same definitions over common schema variations. The results of Castor are more accurate than well-known learning systems over large data.
Solid Mechanics and Crystal Physics as Tools for Cellulose Structure Investigation1

The physical “law of mixtures” and its many refinements have been extensively employed in analyses of engineering problems involving anisotropic composite materials. The plant cell wall, which is s...
Simple model for ring resonators backscatter

Waveguide backscatter affects the resonance shape and quality factor (Q) of ring resonators. Our simple analytical expression predicts how waveguide backscatter spoils the Q and results in resonance splitting. We show that the effects of backscatter depend only on the finesse of the resonator and when it can safely be ignored. Finally, we describe the effects of backscatter in low-loss cavities using simple complex Lorentzian functions.
On the existence of large subsets of [λ]κ which contain no unbounded non-stationary subsets RID="s"ID="s" Publication number 698 in author's list. Partially supported by the Israel Science Foundation.

Here we deal with some problems posed by Matet. The first section deals with the existence of stationary subsets of [λ]<κ with no unbounded subsets which are not stationary, where, of course, κ is regular uncountable ≤λ. In the second section we deal with the existence of such clubs. The proofs are easy but the result seems to be very surprising. Theorem 1.2 was proved some time ago by Baumgartner (see Theorem 2.3 of [Jo88]) and is presented here for the sake of completeness.
Are Generalists Better Learners than Specialists? Performance- Feedback Learning in Farms

This paper examines how an organization’s propensity to engage in problemistic search and slack search can differ depending on the positional characteristics of the organization: generalism and spe...
Modeling of writable thin film liquid metal phase change material for electronics cooling

Probably the most trending technology in electronics today is wearable and flexible electronics. Flexible electronics are electronic circuits fabricated on flexible surfaces and offer many advantages. Similar to conventional electronics, thermal management of flexible electronics is a formidable challenge. In addition to high heat fluxes from the miniaturization of electronics' components, thermal management of flexible electronics must be adapted to the flexible and stretchable nature of the technology. In this work, we numerically study the thermal performance of thin film liquid metal PCMs for the thermal management of flexible electronics. Using 1-D (axial direction) transient conduction along with the enthalpy method, the temperature distribution within the liquid metal PCM was investigated as a function of length, thermal properties, and unsteady heat load. The results showed the existence of three important regions within which there exists an optimal PCM configuration and operating condition. Because PCMs are most suited for transient heat load applications, which is the case for many electronics, we studied the effects of transient heat load's periodicity and duration on the thermal performance of the liquid metal PCMs. The results showed that with a base load resulting in a chip temperature just below the PCM's melting temperature, optimal periodic heat loads can be achieved to maintain the chip at an acceptable operating temperature.
Cracking the Concrete Ceiling in Male-Dominated Societies: A Tale of Three ‘Presidentas’

This chapter challenges the extent to which political leadership remains a male-dominated institution, and asserts that the feminine has in fact become institutionalised in global political culture . We analyse the discourse of (1) Cristina Fernandez de Kirchner, former president of Argentina ; (2) Michelle Bachelet Jeria, president of Chile ; and (3) Ellen Johnson Sirleaf, president of Liberia , three incumbent female presidents of countries that have a long patriarchal tradition of masculine political and social hegemony.
Investigating biomass burning aerosol morphology using a laser imaging nephelometer

Abstract. Particle morphology is an important parameter affecting aerosol optical properties that are relevant to climate and air quality, yet it is poorly constrained due to sparse in situ measurements. Biomass burning is a large source of aerosol that generates particles with different morphologies. Quantifying the optical contributions of non-spherical aerosol populations is critical for accurate radiative transfer models, and for correctly interpreting remote sensing data. We deployed a laser imaging nephelometer at the Missoula Fire Sciences Laboratory to sample biomass burning aerosol from controlled fires during the FIREX intensive laboratory study. The laser imaging nephelometer measures the unpolarized scattering phase function of an aerosol ensemble using diode lasers at 375 and 405 nm. Scattered light from the bulk aerosol in the instrument is imaged onto a charge-coupled device (CCD) using a wide-angle field-of-view lens, which allows for measurements at 4–175 ∘ scattering angle with ∼ 0.5 ∘ angular resolution. Along with a suite of other instruments, the laser imaging nephelometer sampled fresh smoke emissions both directly and after removal of volatile components with a thermodenuder at 250 ∘ C. The total integrated aerosol scattering signal agreed with both a cavity ring-down photoacoustic spectrometer system and a traditional integrating nephelometer within instrumental uncertainties. We compare the measured scattering phase functions at 405 nm to theoretical models for spherical (Mie) and fractal (Rayleigh–Debye–Gans) particle morphologies based on the size distribution reported by an optical particle counter. Results from representative fires demonstrate that particle morphology can vary dramatically for different fuel types. In some cases, the measured phase function cannot be described using Mie theory. This study demonstrates the capabilities of the laser imaging nephelometer instrument to provide realtime, in situ information about dominant particle morphology, which is vital for understanding remote sensing data and accurately describing the aerosol population in radiative transfer calculations.
Omitting Types and a Two-Cardinal Theorem

Our theorem on omitting types, like Keisler’s, follows immediately from our foregoing work.
Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit

Abstract Noncoding small RNAs (sRNAs) are known to play a key role in regulating diverse cellular processes, and their dysregulation is linked to various diseases such as cancer. Such diseases are also marked by phenotypic heterogeneity, which is often driven by the intrinsic stochasticity of gene expression. Correspondingly, there is significant interest in developing quantitative models focusing on the interplay between stochastic gene expression and regulation by sRNAs. We consider the canonical model of regulation of stochastic gene expression by sRNAs, wherein interaction between constitutively expressed sRNAs and mRNAs leads to stoichiometric mutual degradation. The exact solution of this model is analytically intractable given the nonlinear interaction term between sRNAs and mRNAs, and theoretical approaches typically invoke the mean-field approximation. However, mean-field results are inaccurate in the limit of strong interactions and low abundances; thus, alternative theoretical approaches are needed. In this work, we obtain analytical results for the canonical model of regulation of stochastic gene expression by sRNAs in the strong interaction limit. We derive analytical results for the steady-state generating function of the joint distribution of mRNAs and sRNAs in the limit of strong interactions and use the results derived to obtain analytical expressions characterizing the corresponding protein steady-state distribution. The results obtained can serve as building blocks for the analysis of genetic circuits involving sRNAs and provide new insights into the role of sRNAs in regulating stochastic gene expression in the limit of strong interactions.
The role of FDG-PET in detecting rejection after liver transplantation.

Abstract Background The activation and increased metabolic activity of T cells in acute cellular rejection could allow fluoro-2-deoxyglucose positron emission tomography to be utilized for detection of acute cellular rejection. The objective of this study was to evaluate the effectiveness of fluoro-2-deoxyglucose positron emission tomography in detecting acute cellular rejection in the clinical setting. Methods Fluoro-2-deoxyglucose positron emission tomography studies were performed on 88 orthotopic liver transplant patients at 7 and 17 days postoperatively (first positron emission tomography and second positron emission tomography, respectively). Additional studies were performed if patients had suspicion of rejection and at resolution of rejection (third positron emission tomography and fourth positron emission tomography, respectively). A circular region of interest was placed over the liver for semiquantitative evaluation of fluoro-2-deoxyglucose positron emission tomography images by means of standard uptake values. Results Eighteen of 88 patients in our study (20.5%) had histologically proven acute cellular rejection during a 16 ± 11 day follow-up. There was no significant difference between the standard uptake values of first positron emission tomography among non-rejecters versus rejecters (2.05 ±0.46 non-rejecters versus 1.82 ± 0.40 rejecters, P = .127). Within the rejection cohort, the standard uptake values from the third positron emission tomography (rejection) were higher compared to the first positron emission tomography (baseline) (2.41 ± 0.48 third positron emission tomography versus 1.82 ± 0.41 first positron emission tomography, P Conclusion Increased signal on fluoro-2-deoxyglucose positron emission tomography over baseline is associated with acute cellular rejection in liver transplant recipients. Additional prospective validation studies are essential to define the role of fluoro-2-deoxyglucose positron emission tomography scan as an early marker for acute cellular rejection.
Correlative Light and Electron Microscopy of the Cytoskeleton

Publisher Summary This chapter describes the procedure for preparation of cells for correlative electron microscopy (EM) after light microscopic observation, as well as the combination of this approach with immunostaining. Light and EM each have certain advantages and limitations for the investigation of the cytoskeleton. Light microscopy allows for kinetic observations in living cells; in particular, modern fluorescence technology affords imaging of single fluorophores with high temporal resolution. The composition of the extraction solution is designed to achieve this goal. Chemical fixation provides cell structures with physical resistance against subsequent harsh procedures. The fixation procedure includes consecutive treatment with glutaraldehyde, tannic acid, and uranyl acetate. The locator coverslips may be mounted into different types of chambers suitable for cell cultivation and observation. For correlative microscopy, the chamber design should allow for the fast exchange of media. Locator coverslips are helpful in facilitating the relocalization of the same cells. Platinum replica EM is compatible with immunoelectron cytochemistry and with the use of colloidal gold as an electron-dense marker.
Cation Binding by Crown Ethers

This article presents a brief overview of cation complexation by crown ethers. It attempts to give enough background information about structures and concepts to help the reader appreciate the vastness of the area and to understand the most basic issues that affect complexation strengths, selectivities, and dynamics.
Macrophage Migration Inhibitory Factor Regulates U1 Small Nuclear RNP Immune Complex-Mediated Activation of the NLRP3 Inflammasome.

Objective High-expression alleles of macrophage migration inhibitory factor (MIF) are linked genetically to the severity of systemic lupus erythematosus (SLE). The U1 small nuclear RNP (snRNP) immune complex containing U1 snRNP and anti-U1 snRNP antibodies, which are found in patients with SLE, activates the NLRP3 inflammasome, comprising NLRP3, ASC, and procaspase 1, in human monocytes, leading to the production of interleukin-1β (IL-1β). This study was undertaken to investigate the role of the snRNP immune complex in up-regulating the expression of MIF and its interface with the NLRP3 inflammasome. Methods MIF, IL-1β, NLRP3, caspase 1, ASC, and MIF receptors were analyzed by enzyme-linked immunosorbent assay, Western blotting, quantitative polymerase chain reaction, and cytometry by time-of-flight mass spectrometry (CytoF) in human monocytes incubated with or without the snRNP immune complex. MIF pathway responses were probed with the novel small molecule antagonist MIF098. Results The snRNP immune complex induced the production of MIF and IL-1β from human monocytes. High-dimensional, single-cell CytoF analysis established that MIF regulates activation of the NLRP3 inflammasome, including findings of a quantitative relationship between MIF and its receptors and IL-1β levels in the monocytes. MIF098, which blocks MIF binding to its cognate receptor, suppressed the production of IL-1β, the up-regulation of NLRP3, which is a rate-limiting step in NLRP3 inflammasome activation, and the activation of caspase 1 in snRNP immune complex-stimulated human monocytes. Conclusion The U1 snRNP immune complex is a specific stimulus of MIF production in human monocytes, with MIF having an upstream role in defining the inflammatory characteristics of activated monocytes by regulating NLRP3 inflammasome activation and downstream IL-1β production. These findings provide mechanistic insight and a therapeutic rationale for targeting MIF in subgroups of lupus patients, such as those classified as high genotypic MIF expressers or those with anti-snRNP antibodies.
Human Parafoveal Capillary Vascular Anatomy and Connectivity Revealed by Optical Coherence Tomography Angiography

Purpose To assess the connection among arterioles, venules, and capillaries in three retinal capillary plexuses using optical coherence tomography angiography (OCTA). Methods This was a prospective, cross-sectional, observational study including 20 eyes of 10 healthy subjects. En face and cross-sectional OCTA images were segmented to study the superficial (SCP), middle (MCP), and deep capillary plexuses (DCP). Using thin slabs and manual segmentation within the three plexuses, we examined the connections between the large-caliber superficial vessels within a 3 × 3 mm2 OCTA scan (arterioles and venules) and the smaller capillaries in each plexus. Results Twenty eyes of 10 healthy subjects (5 females; average age of 30.8 ± 6.3 years) were included in the analysis. We identified vascular interconnections linking the superficial arterioles and venules with capillaries in each plexus (SCP, MCP, and DCP). We found capillaries in the DCP crossed the horizontal raphe. Conclusions Our findings show that each of the three capillary plexuses in the parafovea has its own feeding arteriolar supply and draining venules, supporting a physiologic model in which each plexus controls its own oxygenated blood supply to match the metabolic needs of each distinct retinal neurovascular unit.
On Pseudodeterministic Approximation Algorithms.

We investigate the notion of pseudodeterminstic approximation algorithms. A randomized approximation algorithm A for a function f is pseudodeterministic if for every input x there is a unique value v so that A(x) outputs v with high probability, and v is a good approximation of f(x). We show that designing a pseudodeterministic version of Stockmeyer's well known approximation algorithm for the NP-membership counting problem will yield a new circuit lower bound: if such an approximation algorithm exists, then for every k, there is a language in the complexity class ZPP^{NP}_{tt} that does not have n^k-size circuits. While we do not know how to design such an algorithm for the NP-membership counting problem, we show a general result that any randomized approximation algorithm for a counting problem can be transformed to an approximation algorithm that has a constant number of influential random bits. That is, for most settings of these influential bits, the approximation algorithm will be pseudodeterministic.
QRP Variation of Cross--Approximation Iterations for Low Rank Approximation

We call matrix algorithms superfast if they use much fewer flops and memory cells than the input matrix has entries. Using such algorithms is indispensable for Big Data Mining and Analysis, where the input matrices are so immense that one can only access a small fraction of all their entries. A natural remedy is Low Rank Approximation (LRA) of these matrices, which is routinely computed by means of Cross-Approximation iterations for more than a decade of worldwide application in computational practice. We point out and extensively test an important application of superfast LRA to significant acceleration of the celebrated Fast Multipole Method, which turns it into Superfast Multipole Method.
On the Usability of HTTPS Deployment

HTTPS and TLS are the backbone of Internet security, however setting up web servers to run these protocols is a notoriously difficult process. In this paper, we perform two live subjects usability studies on the deployment of HTTPS in a real-world setting. Study 1 is a within subjects comparison between traditional HTTPS configuration (purchasing a certificate and installing it on a server) and Let's Encrypt, which automates much of the process. Study 2 is a between subjects study looking at the same two systems, examining why users encounter usability issues. Overall we confirm past results that HTTPS is difficult to deploy, and we find some evidence that suggests Let's Encrypt is an easier, more efficient method for deploying HTTPS.
Self-Similar Evolution of Gravitational Clustering: N-Body Simulations of the n=-2 Spectrum

The power spectrum P(k)\propto k^n with n=-2 is close to the shape of the measured galaxy spectrum on small scales. Unfortunately this spectrum has proven rather difficult to simulate. Further, 2-dimensional simulations have suggested a breakdown of self-similar scaling for spectra with n<-1 due to divergent contributions from the coupling of long wave modes. This paper is the second (numerical) part of our investigation into the nonlinear gravitational clustering of scale-free spectra. Using high-resolution N-body simulations we find that the n=-2 power spectrum, as well as trajectories of the amplitude and phase of Fourier modes, display self-similar scaling. The evolution of the phase shift does show a different scaling at late times, but this was shown analytically to arise from the purely kinematical effect of bulk flows. Thus our analytical and N-body results verify that self-similarity in gravitational clustering holds for -3<n<1. The N-body spectrum is also compared with analytic fitting formulae, which are found to slightly underestimate the power in the nonlinear regime. The asymptotic shape of the spectrum at high-k is a power law with the same slope as predicted by the stable clustering hypothesis.
Correlative microscopy for quantification of prior austenite grain size in AF9628 steel

Abstract The characterization of prior austenite grain size is important for an understanding of the microstructure-property relationships in steels. In this study, the prior austenite grain boundaries (PAGBs) were delineated in a low alloy high performance steel, AF9628, with two different methods: (i) conventional approach via etching, followed by optical or scanning electron microscopy, and (ii) analysis of electron backscattered diffraction (EBSD) data. Correlative microscopy was employed to obtain images of the same region of the specimens with the two independent methods. The threshold method of delineating PAGBs in EBSD orientation maps revealed a large fraction of the PAGBs that were delineated by the conventional approach. However, many PAGBs were not delineated in the EBSD maps. On the other hand, the twin boundaries within the prior austenite grains were not delineated by the conventional approach and many of these boundaries were delineated in the EBSD maps. The net result was that the measurements on EBSD orientation maps resulted in an overestimation of the prior austenite lineal intercept grain size by approximately 21% and an underestimation of the surface area of PAGB per unit volume of material (SV) by approximately 17%. The errors in the measurements on the EBSD orientation maps were discussed in the context of the probability density function for misorientation angles in cubic metals (i.e., Mackenzie plot), which suggests that the overestimation in the prior austenite grain size measurement would be expected to be even higher (specifically 47%) for the general case of random texture of prior austenite grains with no twins. In view of the results of this study, it is suggested that the use of threshold method for delineating PAGBs and determining prior austenite grain size or SV may be sufficient for examining relative trends, for example, as a result of heat treatments. However, the conventional methods to delineate the PAGBs may be required when quantitative values of microstructural parameters are of interest.
Platelet dysfunction on thromboelastogram is associated with severity of blunt traumatic brain injury.

Abstract Background Platelet dysfunction associated with isolated traumatic brain injury (TBI) can be measured using thromboelastography-platelet mapping (TEG-PM). We hypothesized that platelet dysfunction can be detected after blunt TBI, and the degree of dysfunction is associated with increased TBI severity and in-hospital mortality. Methods This was a retrospective review of adult trauma patients admitted to a single level 1 trauma center from August 2013 to March 2015 who suffered isolated severe blunt TBI. Subjects were included if they received a TEG-PM within 24 h from injury, and excluded if on preinjury antiplatelet medications. Results 119 subjects were analyzed. Severe TBI subjects (AIS-head 5) had ADPi 18.4 points higher than moderate TBI subjects (AIS-head 3) (p = 0.001). Platelet dysfunction was not associated with TBI progression. ADPi significantly predicted mortality (OR 1.033; 95% CI 1.005–1.061, p = 0.02). Conclusion Platelet dysfunction occurs immediately after isolated blunt TBI, is more pronounced with increasing TBI severity, and is associated with higher odds of in-hospital mortality. Further investigation is needed to determine whether this is a marker of disease severity or a therapeutic target.
Landau level phases in bilayer graphene under pressure at charge neutrality

Bilayer graphene in a magnetic field hosts a variety of ordered phases built from eight Landau levels close in energy to the neutrality point. These levels are characterized by orbital $n=0,1$, valley $\ensuremath{\xi}=+,\ensuremath{-}$, and spin $\ensuremath{\sigma}=\phantom{\rule{0.28em}{0ex}}\ensuremath{\uparrow},\ensuremath{\downarrow}$; their relative energies depend strongly on the Coulomb interaction, magnetic field, and interlayer bias. We treat interactions at the Hartree-Fock level, including the effects of metallic gates, layer separation, spatial extent of the ${p}_{z}$ orbitals, all Slonczewski-Weiss-McClure tight-binding parameters, and pressure. We obtain the ground state as function of the applied magnetic field, bias, and pressure. The gates, layer separation, and extent of the ${p}_{z}$ orbitals weaken the Coulomb interaction at different length scales; these effects distort the phase diagram but do not change its topology. However, previously predicted continuous transitions become discontinuous when all tight-binding parameters are included nonperturbatively. We find that pressure increases the importance of the noninteracting scale with respect to the Coulomb energy, which drives phase transitions to occur at lower fields. This brings two orbitally polarized states not yet predicted or observed into the experimentally accessible region of the phase diagram, in addition to previously identified valley-polarized, spin-polarized, and partially orbitally polarized states.
A bacterial vaccine polypeptide protective against nontypable Haemophilus influenzae.

Abstract Nontypeable strains of Haemophilus influenzae (NTHi) are one of the most common cause of otitis media and the most frequent infection associated with exacerbations of chronic obstructive pulmonary disease; there is currently no vaccine in the U.S. to prevent NTHi. Using bioinformatics and structural vaccinology, we previously identified several NTHi species-conserved and sequence-conserved peptides that mediate passive protection in the rat model of infection. Using these, and similar peptides, we designed Hi Poly 1, a Bacterial Vaccine Polypeptide, comprising 9 unique peptides from 6 different surface proteins. Recombinant Hi Poly 1 was purified by affinity chromatography. Forty chinchillas were immunized three times with 200 µg of Hi Poly 1 with alum adjuvant; similarly, 41 controls were immunized with adjuvant alone. The average Log2 IgG titer among immunized animals was 17.04, and IgG antibodies against each component peptide were detected. In the infant rat model, antisera from immunized chinchillas provided significant passive protection compared to PBS (p = 0.01) and pre-immune sera (p = 0.03). In the established chinchilla model of NTHi otitis media, the vaccinated group cleared infection faster than the control group as indicated by significantly decreased positive findings on video-otoscopy (p
ROLE OF REPEAT INFECTION IN THE DYNAMICS OF A SIMPLE MODEL OF WANING AND BOOSTING IMMUNITY

Some infectious diseases produce lifelong immunity while others only produce temporary immunity. In the case of short-lived immunity, the level of protection wanes over time and may be boosted upon...
Omission of adjuvant chemotherapy in elderly patients with early stage breast cancer.

12032Background: Breast cancer incidence in elderly population over 70 years is anticipated to grow up to 35% by 2030. However, this elderly population is under-represented in the TAILORx (Trial As...
Learning Discriminative Factorized Subspaces With Application to Touchscreen Biometrics

Information fusion is a challenging problem in biometrics, where data comes from multiple biometric modalities or multiple feature spaces extracted from the same modality. Learning from heterogeneous data sources, in general, is termed as multi-view learning, where view is an encompassing term that refers to different sets of observations having distinct statistical properties. Most of the existing approaches to learning from multiple views either assume that the views are either independent or fully dependent. However, in real scenarios, these assumptions are almost never truly satisfied. In this work, we relax these assumptions. We propose a feature fusion method called Discriminative Factorized Subspaces (DFS) that learns a factorized subspace consisting of a single shared subspace (that captures the common information), and view-specific subspaces that captures information specific to each view. DFS jointly learns these subspaces, by posing the optimization problem as a constrained Rayleigh Quotient based formulation, whose solution is efficiently obtained using generalized eigenvalue decomposition. Our method does not require lots of data to learn from, and we show how it is apt for domains characterized by limited training data, and high intra-class variability. As an application, we tackle the challenging problem of touchscreen biometrics, which is based on the study of user interactions with their touch screens. Through extensive experimentation and thorough evaluation, we demonstrate how DFS learns a better discriminatory boundary, and provides a superior performance than state of the art methods for touchscreen biometric verification.
Exploring the epigenetic regulation of telomerase reverse transcriptase (TERT) in human cancer cell lines

Telomerase regulation, including TERT promoter methylation, has been of long-standing interest to cancer biologists. Rowland et al. have now vastly expanded their ongoing characterization of TERT promoter methylation in cancer cells, analyzing the methylation patterns of 833 cell lines from 23 human cancers. They document a highly conserved pattern of hypomethylation around the proximal promoter, as well as a more heterogeneous region of hypermethylation further upstream, both associated with active TERT expression in cancer cells. They further describe the interplay between activating TERT promoter mutations and allelic methylation and transcription patterns. This valuable dataset represents the most extensive characterization of TERT promoter methylation in cancer cells to date and will help guide the future study of transcriptional regulation of telomerase. Comment on: https://doi.org/10.1002/1878-0261.12786.
Condensed Silhouette: An Optimized Filtering Process for Cluster Selection in K-Means

Abstract In K-Means based clustering algorithms, different initial seeds can lead to different clustering results. Selecting the best result from different initial seeds is called the filtering process. The filtering process follows three steps, 1- performing several clustering trials, 2- scoring each trial, and 3- choosing the trial with the best score. A typical method to score the clustering results of K-Means is the within-cluster sum of squares (WCSS). There are more advanced methods that can be used to score the clustering trials. These methods usually provide a better score with the cost of being more computationally demanding. In this paper, we propose Condensed Silhouette, which is a very efficient version of the Silhouette algorithm. For this purpose, we replace the elements of Silhouette algorithm with similar elements of the K-Means algorithm. This helps us to maintain the accuracy of the Silhouette and at the same time, significantly reduce the computational requirements of the method. Our experiments on 14 real datasets show the effectiveness of the proposed method.
Proteins for bioinspired optical and electronic materials

Nature has developed myriad ways for organisms to interact with their environment using light and electronic signals. Optical and electronic properties can be observed macroscopically by measuring light emission or electrical current, but are conferred at the molecular level by the arrangement of small biological molecules, specifically proteins. Here, we present a brief overview of the current uses of proteins for applications in optical and electronic materials. We provide the natural context for a range of light-emitting, light-receiving, and electronically conductive proteins, as well as demonstrate uses in biomaterials. Examples of how genetic engineering has been used to expand the range of functional properties of naturally occurring proteins are provided. We touch on how approaches to patterning and scaffolding optical and electronic proteins can be achieved using proteins with this inherent capability. While much research is still required to bring their use into the mainstream, optical and electronic proteins have the potential to create biomaterials with properties unmatched using conventional chemical synthesis.
Beta testing the monkey model.

Corbett et al. use the rhesus macaque model to evaluate the ability of the mRNA-1273 (Moderna) COVID-19 vaccine to protect against challenge with the antibody-evading Beta variant of SARS-CoV-2. Their key finding is that the vaccine prevents severe lung pathology, principally because it is able to induce a strong enough antibody resistance to overcome the variant’s relative resistance.
The Axion mass in modular invariant supergravity

When supersymmetry is broken by condensates with a single condensing gauge group, there is a nonanomalous R-symmetry that prevents the universal axion from acquiring a mass. It has been argued that, in the context of supergravity, higher dimension operators will break this symmetry and may generate an axion mass too large to allow the identification of the universal axion with the QCD axion. We show that such contributions to the axion mass are highly suppressed in a class of models where the effective Lagrangian for gaugino and matter condensation respects modular invariance (T-duality).
A theoretical framework for the multicast address allocation problem

The multicast address allocation problem requires Internet domains to allocate unique addresses to multicast applications from a globally-shared space. We develop a theoretical framework for multicast allocation algorithms that is influenced by subcube allocation in hypercube computer systems. Based on this framework we derive complexity results for the address allocation problem and describe several new allocation algorithms that use a hypercube model for address representation.
A dual plane orbit approach for improved pinhole tomography

We investigate the effect of dual parallel plane orbits on pinhole reconstruction quality. Projections taken of a micro-Defrise phantom for two parallel, circular orbits are reconstructed using an OSEM algorithm. We hypothesize that a dual parallel orbit scan will provide greater coverage for pixels that do not lie in the orbit plane, thus reducing the axial blurring effect seen with single orbit pinhole scans while also increasing axial field-of-view as compared to a single orbit. Experiments were performed with simulated computer phantoms, and a physical micro-Defrise phantom imaged with a prototype small animal SPECT scanner fitted with a 0.75 mm pinhole collimator. We found that for the simulation and experimental data, dual plane reconstruction showed better resolution away from the orbit plane, improved uniformity, and reduced distortion as compared to a single orbit.
Methods for studying apoptosis and phagocytosis of apoptotic cells in Drosophila tissues and cell lines.

Publisher Summary This chapter discusses the several techniques have been developed to label apoptotic cells in Drosophila tissues. Both acridine orange (AO) and the transferase (TdT)-mediated dUTP-biotin nick end labeling (TUNEL) technique can be used to assess apoptosis in the developing embryo and in the larval imaginal discs and nervous system. The molecular basis of AO staining is controversial but seems to involve specific retention of the dye in apoptotic cells. The TUNEL technique takes advantage of the DNA cleavage found in apoptotic cells. The free DNA ends targeted by terminal deoxytransferase (TdT), incorporates digoxygenin-labeled nucleotides. This chapter provides protocols for AO and TUNEL labeling, as well as for ultrastructural studies. The chapter discusses the other assays used for labeling apoptotic cells in Drosophila . Activation of caspases is a stereotypic feature of apoptotic cells and can be detected in situ with affinity-labeling techniques. The binding of Annexin V to exposed phosphatidylserine is another common technique used to label apoptotic cells. This chapter provides a protocol to assess embryonic phagocytosis of apoptotic cells. Phagocytosis also occurs later in development, a time when hemocytes are abundant and more accessible by bleeding.
Data pattern dependence of VCSEL far-field distributions

The far field divergence angle distribution of vertical-cavity surface-emitting lasers is found to exhibit dependence on the data pattern driving the lasers. Two 50% duty cycle 1.25-Gb/s data patterns chosen to cause the same thermal conditions but with frequency content differing by a factor of 16 resulted in changes in the beam profile distributions with up to a 30% power variation in the central on-axis portion of the beam. Examination of the temporal waveforms as a function of far field angle revealed overshoot in the on-axis power and undershoot in the off-axis portion of the beam.
Female athletic participation and income: evidence from a latent class model

This paper introduces and applies an EM algorithm for the maximum-likelihood estimation of a latent class version of the grouped-data regression model. This new model is applied to examine the effects of college athletic participation of females on incomes. No evidence for an “athlete” effect in the case of females has been found in the previous work by Long and Caudill [12], Henderson et al. [10], and Caudill and Long [5]. Our study is the first to find evidence of a lower wage for female athletes. This effect is present in a regime characterizing 42% of the sample. Further analysis indicates that female athletes in many otherwise low-paying jobs actually get paid less than non-athletes.
Biotransformation of trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene to benzo[a]pyrene bis-diols and DNA adducts by induced rat liver microsomes.

The biotransformation of (±)-trans-4,5-dihydroxy-4,5-dihydrobenzo[a]pyrene (trans-B[a]P-4,5-diol), the K-region dihydrodiol of B[a]P, by β-naphthoflavone (BNF)-induced rat liver microsomes was studied. trans-B[a]P-4,5-diol was metabolized to six major products as characterized by NMR, MS, and UV spectroscopy, and all were identified as bis-diols: two diastereomers of trans,trans-4,5:7,8-tetrahydroxy-4,5:7,8-tetrahydrobenzo[a]pyrene (trans,trans-B[a]P-4,5:7,8-bis-diol), two diastereomers of trans,trans-4,5:9,10-tetrahydroxy-4,5:9,10-tetrahydrobenzo[a]pyrene (trans,trans-B[a]P-4,5:9,10-bis-diol), and two diastereomers of the somewhat unusual trans,trans-1,2:4,5-tetrahydroxy-1,2:4,5-tetrahydrobenzo[a]pyrene (trans,trans-B[a]P-1,2:4,5-bis-diol). BNF-induced rat liver microsomes also metabolized B[a]P to the same trans-B[a]P-4,5-diol-derived bis-diols. The ability of trans-B[a]P-4,5-diol to form DNA adducts was investigated using 32P-postlabeling techniques specifically designed to detect stable polar DNA add...
Erythrocyte-based Pig-a gene mutation assay: Demonstration of cross-species potential

Abstract Glycosylphosphatidylinositol (GPI) anchors attach specific proteins to the cell surface of hematopoietic cells. Of the genes required to form GPI anchors, only Pig-a is located on the X-chromosome. Prior work with rats suggests that the GPI anchor deficient phenotype is a reliable indicator of Pig-a mutation [Bryce et al., Environ. Mol. Mutagen., 49 (2008) 256–264]. The current report extends this line of investigation by describing simplified blood handling procedures, and by testing the assay principle in a second species, Mus musculus . With this method, erythrocytes are isolated, incubated with anti-CD24-PE, and stained with SYTO 13. Flow cytometric analyses quantify GPI anchor-deficient erythrocytes and reticulocytes. After reconstruction experiments with mutant-mimicking cells demonstrated that the analytical performance of the method is high, CD-1 mice were treated on three occasions with 7,12-dimethyl-1,2-benz[a]anthracene (DMBA, 75 mg/kg/day) or ethyl- N -nitrosourea (ENU, 40 mg/kg/day). Two weeks after the final treatment, DMBA-treated mice were found to exhibit markedly elevated frequencies of GPI anchor deficient erythrocytes and reticulocytes. For the ENU experiment, blood specimens were collected at weekly intervals over a 5-week period. Whereas the frequencies of mutant reticulocytes were significantly elevated 1 week after the last administration, the erythrocyte population was unchanged until the second week. Thereafter, both populations exhibited persistently elevated frequencies for the duration of the experiment (mean frequency at termination = 310 × 10 −6 and 523 × 10 −6 for erythrocyte and reticulocyte populations, respectively). These data provide evidence that Pig-a mutation does not convey an appreciable positive or negative cell survival advantage to affected erythroid progenitors, although they do suggest that affected erythrocytes have a reduced lifespan in circulation. Collectively, accumulated data support the hypothesis that flow cytometric enumeration of GPI anchor deficient erythrocytes and/or reticulocytes represents an effective in vivo mutation assay that is applicable across species of toxicological interest.