cssi/SciSciGPT-SciSciNet huggingface dataset:
Neurosensory free flaps to the hand: Indications and donor selection

When used in properly selected cases, a neurosensory free flap provides sensibility, vascularity, and soft-tissue coverage to an injured hand. Appropriate selection of donor flaps based on the need for fine discriminatory or protective sensation is important for optimal results. Because of its thin, glabrous skin and a constant vascular and neural anatomy, the first web-space flap of the foot or its variants provide the best reconstructive choice for restoration of critical sensibility to digital tips or anesthetic amputation stumps. Protective sensibility can be restored with other neurosensory free flaps, but more clinical experience is needed to fully evaluate the reconstructive potential of many described flaps. A distinction must be made between the anatomic description of a free flap with neurosensory potential and the report of long-term sensory ability after clinical transfer.
The Verbal Fuel for Ethnic Hatred and Political Violence in Kenya

A Book Chapter by Dr. Tom Onditi, dean of students at USIU-A in a book edited by Daniel Ochieng Orwenjo (Technical University of Kenya, Kenya), Omondi Oketch (Technical University of Kenya, Kenya) and Asiru Hameed Tunde (Umaru Musa Yar'adua University, Nigeria)
Visualizing Compartmentalized Cellular Mg2+ on Demand with Small-Molecule Fluorescent Sensors.

The study of intracellular metal ion compartmentalization and trafficking involved in cellular processes demands sensors with controllable localization for the measurement of organelle-specific levels of cations with subcellular resolution. We introduce herein a new two-step strategy for in situ anchoring and activation of a fluorescent Mg2+ sensor within an organelle of choice, using a fast fluorogenic reaction between a tetrazine-functionalized pro-sensor, Mag-S-Tz, and a strained bicyclononyne conjugated to a genetically encoded HaloTag fusion protein of known cellular localization. Protein conjugation does not affect the metal-binding properties of the o-aminophenol-N,N,O-triacetic acid (APTRA)-based fluorescent indicator, which displays a dissociation constant Kd = 3.1 mM suitable for the detection of low millimolar concentrations of chelatable Mg2+ typical of the intracellular environment. We demonstrate the application of our sensing system for the ratiometric detection of Mg2+ in target organelles...
An Analysis Of Commonplace Behaviors: Volitional Acts

A brief account of an interbehavioral field approach is presented. This is then used to analyze several examples of commonplace behavior that ordinarily are ignored by psychology. These can be seen as what have been traditionally called willing or, better, volitional acts. It is argued that the presentation offers an approach by which these can be studied without recourse to traditional metaphysical constructs. It is suggested that further attention to these behaviors would bring psychology closer to its potentialities.
A study on fragmentation behavior, inorganic melt phase formation, and carbon loss during high temperature gasification of mineral matter rich fraction of Pittsburgh No. 8 coal

Abstract Computational models are being developed to determine the fate of organic and inorganic matter during gasification to improve operational reliability and carbon conversion in entrained flow gasifiers. Current models being developed to simulate entrained flow gasifiers assume homogeneity of the coal phase. However, coal is not homogeneous, and various size and density fractions behave differently during gasification. Therefore, a more accurate model can be developed by determining the behavior of various size and density fractions of coal. From that perspective, two particle size distributions (75–106 µm and 212–425 µm) of the mineral matter rich fraction of Pittsburgh No. 8 coal obtained using the float and sink method were gasified in a laboratory-scale entrained flow reactor at 1773 K. Char-ash particles from the two size fractions were characterized using Scanning Electron Microscope-Energy Dispersive X-ray Spectroscopy (SEM-EDS), X-ray Diffraction (XRD), Mossbauer spectroscopy, thermogravimetric analysis, and a micro-sifter for particle size distribution (PSD). The char-ash sample derived from the coarser-sized fraction (212–425 µm) showed limited fragmentation (∼8%), while the finer-sized fraction showed no fragmentation. On the other hand, agglomerates were seen for both the particle size fractions with the finer-sized fraction having more melt phase and agglomerates than the coarser-sized fraction. The melt phase composition in the agglomerates is linked to the presence Fe2+-glass and fayalite for both the particle size fractions. The data also confirm that the mineral matter rich particles form melt phase and initiate slagging in the gasifier even at a lower conversion level (
The folA gene from the Rickettsia endosymbiont of Ixodes pacificus encodes a functional dihydrofolate reductase enzyme.

Abstract Although nonpathogenic bacterial endosymbionts have been shown to contribute to their arthropod host’s fitness by supplying them with essential vitamins and amino acids, little is known about the nutritional basis for the symbiotic relationship of endosymbionts in ticks. Our lab has previously reported that Rickettsia species phylotype G021 in Ixodes pacificus carries all five genes for de novo folate synthesis, and that these genes are monophyletic with homologs from other Rickettsia species. In this study, the rickettsial folate synthesis folA gene, coding for dihydrofolate reductase, was PCR amplified, cloned into an expression vector, and overexpressed in E. coli. Bioinformatic analysis identified that the FolA protein of phylotype G021 has the conserved DHFR domain, NADP binding sites, and substrate binding sites of bacterial dihydrofolate reductase. SDS-PAGE results showed that recombinant rickettsial FolA protein was overexpressed in BL21(DE3) E. coli in its soluble form. Affinity chromatography was used to purify the protein, and in vitro enzyme assays were performed to assess the biochemical activity of dihydrofolate reductase. The specific activity of recombinant FolA from phylotype G021 was determined to be 16.1 U/mg. This study has revealed that Rickettsia species phylotype G021 of I. pacificus is capable of producing a functional enzyme of the folate biosynthesis pathway, addressing the nutritional interactions behind the symbiosis between Rickettsia species phylotype G021 and its host.
Critical Infrastructure Protection in Homeland Security: Defending a Networked Nation

Preface. About the Author. 1. Strategy. 2. Origins. 3. Challenges. 4. Networks. 5. Vulnerability Analysis. 6. Risk Analysis. 7. Water. 8. SCADA. 9. Power. 10. Energy. 11. Telecommunications. 12. Internet. 13. Cyber-Threats. 14. Cyber-Security.
John Tracy Ellis and the Figure of the Catholic Intellectual

Fifty years after John Tracy Ellis challenged the quality and character of Catholic intellectual life, much work remains to be done. This essay explores Ellis’s original assertions and places them in an overarching historical context that involves Flannery O’Connor and Thomas Merton.
Making glassy solids ductile at room temperature by imparting flexibility into their amorphous structure

Making glasses ductile at room temperature is a daunting challenge, but has been shown to be feasible in recent years. We explain the plastic flow from the standpoint of the flexibility available in the amorphous structure: imparting flexibility into the structure facilitates bond switching needed to mediate shear transformations to carry strain. This structure–property correlation is demonstrated using molecular dynamics simulation data. The flexibility can be improved via ultrafast quench or rejuvenation. In particular, the flexibility volume parameter offers a quantitative metric to explain the flexibility and deformability, even for glasses where the commonly cited free volume is not applicable.
Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations.

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.
Accounting Research Readings Groups

Abstract Research readings groups represent a recent innovation in accounting doctoral education that appears to be spreading at research-oriented universities. In this chapter, the authors describe how accounting research readings groups can serve as a mechanism to engage doctoral students in the consumption and discussion of research throughout all phases of the doctoral program. An accounting research readings group supplements the breadth of knowledge gained in doctoral seminars by adding depth of knowledge in a focal research area. The authors offer insights from the educational psychology literature to justify research readings groups as a form of team-based learning and then offer suggestions on the formation and operation of these groups. The authors enumerate the many benefits that these groups afford to both doctoral students and faculty members. The authors also distribute a survey to faculty organizers of the existing accounting research readings groups and share the results of this survey to supplement their advice with firsthand experiences, the authors also share the results of a survey distributed to faculty organizers of existing accounting research readings groups. The authors’ goal is to encourage the use of accounting research readings groups to inspire, foster, and enhance the research culture within accounting departments and doctoral programs.
Effects of zinc-treated soybean meal on ruminal fermentation and intestinal amino acid flows in steers fed corn silage-based diets.

The objectives of this study were to examine the effects of feeding zinc-treated soybean meal (Zn-SBM) on ruminal fermentation patterns and duodenal AA flows in steers fed diets based on corn silage and corn. Six steers (385 kg) fitted with ruminal, duodenal, and ileal cannulas were used in a replicated 3 x 3 Latin square design experiment with 14-d periods. Diets were supplemented with solvent-extracted soybean meal (SBM), Zn-SBM, or a 50:50 combination (CP basis) of SBM:Zn-SBM. Ruminal escape N content of SBM and Zn-SBM were 30.0 and 57.0%, respectively, based on 12-h Dacron bag incubation. Protein sources provided approximately 30% of total CP in diets containing 12.6% CP (DM basis). Dry matter intake was equalized throughout the study at 2.2% of average initial BW. Total N flow at the duodenum was similar (P = .47) among treatments, but a trend (P = .15) for increased nonmicrobial N flow occurred when SBM and Zn-SBM were fed in combination. Micobial N flow and true efficiency of microbial CP synthesis were not affected by treatment (P = .87 and .37, respectively). Ruminal fermentation characteristics generally were unaffected (P > .10) by protein source. A positive quadratic response (P < .06) was observed for total and essential AA flows to the small intestine because flows of total and essential AA from ruminally undegraded dietary protein tended (P = .12) to increase when SBM and Zn-SBM were fed in combination. Absorption of AA from the small intestine also showed a positive quadratic (P < .06) response for SBM:Zn-SBM. Microbial AA flow to the small intestine was similar (P = .87) among treatments.(ABSTRACT TRUNCATED AT 250 WORDS)
Atomic Layer Deposition of TiO2 Nanocoatings on ZnO Nanowires for Improved Photocatalytic Stability

Photocatalytic water splitting represents an emerging technology well positioned to satisfy the growing need for low-energy, low CO2, economically viable hydrogen gas production. As such, stable, high-surface-area electrodes are increasingly being investigated as electrodes for the photochemical conversion of solar energy into hydrogen fuel. We present a titanium dioxide (TiO2)/zinc oxide (ZnO) nanowire array using a hybrid hydrothermal/atomic layer deposition (ALD) for use as a solar-powered photoelectrochemical device. The nanowire array consists of single crystalline, wurtzite ZnO nanowires with a 40 nm ALD TiO2 coating. By using a TiO2 nanocoating on the high surface area-ZnO array, three advancements have been accomplished in this work: (1) high aspect ratio nanowires with TiO2 for water splitting (over 8 μm), (2) improved stability over bare ZnO nanowires during photocatalysis, and (3) excellent onset voltage. As such, this process opens up new class of the micro/nanofabrication process for making efficient photocatalytic gas harvesting systems.
Stochastic differential theory of cricket

A new formalism for analyzing the progression of cricket game using Stochastic differential equation (SDE) is introduced. This theory enables a quantitative way of representing every team using three key variables which have physical meaning associated with them. This is in contrast with the traditional system of rating/ranking teams based on combination of different statical cumulants. Further more, using this formalism, a new method to calculate the winning probability as a progression of number of balls is given.
Change Is Hard, But Not Impossible: Building Student Enthusiasm for Inquiry-Based Learning

Taking a course that uses an inquiry-based curriculum can be challenging for students who are accustomed to a traditional, lecture-based approach to mathematics instruction. At the end of the course, students who are not fully cognizant of the results of their many hours of hard work may conclude that the teaching approach was ineffective. This article seeks to help instructors who believe in the effectiveness of inquiry-based learning but have trouble getting students on board by giving them specific strategies to help build student confidence and enthusiasm.
The History of Simulation

For centuries people have made models and deliberately practiced to learn new skills. Healthcare education has recently rediscovered these basic principles. Simulation is fundamental to the current educational emphasis on deliberate practice and mastery learning. Although simulation has finally achieved global acceptance, it was a long journey. Revolutions in industry, communication, transportation, and technology occurring over the course of a century laid the foundation for the birth of modern simulation. Pioneers in healthcare education and patient safety made essential contributions by questioning the status quo and proposing innovative solutions. Simulation developers and early proponents worked for decades to advertise and gain acceptance for groundbreaking simulation products and methods. This chapter will give a brief overview of the history of simulation and the technology that makes it possible.
CRY arrests Cop1 to regulate circadian rhythms in mammals.

Cryptochromes (CRYs) are UVA and blue light photoreceptors present in all major evolutionary lineages ranging from cyanobacteria to plants and animals, including mammals. In plants, blue light activates CRYs to induce photomorphogenesis by inhibiting the CRL4Cop1 E3 ligase complex which regulates the degradation of critical transcription factors involved in plant development and growth. However, in mammals, CRYs do not physically interact with Cop1, and of course mammals are not photomorphogenic, leading to the belief that the CRY–Cop1 axis is not conserved in mammals. This belief was recently overturned by Rizzini et al., who showed that although mammalian CRYs do not inhibit Cop1 activity in a light-dependent manner, they antagonize Cop1 activity by displacing Cop1 from CRL4 E3 ligase complex. Because CRYs oscillate, they act in a circadian manner resulting in daily oscillations in Cop1 substrates and the downstream pathways that they regulate. The conserved antagonism of Cop1 by CRY indicates that the CRY–Cop1 axis has an ancient origin, and was repurposed by evolution to regulate photomorphogenesis in plants and circadian rhythms in mammals.
Insights into the Biogeochemical Cycling of Cobalt: Precipitation and Transformation of Cobalt Sulfide Nanoparticles under Low-Temperature Aqueous Conditions.

Cobalt sulfide precipitates, key phases in the natural biogeochemistry of cobalt and in relevant remediation and resource recovery processes, are poorly defined under low-temperature aqueous condit...
Risk Factor Evaluation for Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa in Community-Acquired Pneumonia.

Background: The 2019 community-acquired pneumonia guidelines recommend using recent respiratory cultures and locally validated epidemiology plus risk factor assessment to determine empirical covera...
Modifying Cell Membranes with Anionic Polymer Amphiphiles Potentiates Intracellular Delivery of Cationic Peptides

Rapid, facile, and noncovalent cell membrane modification with alkyl-grafted anionic polymers was sought as an approach to enhance intracellular delivery and bioactivity of cationic peptides. We synthesized a library of acrylic acid-based copolymers containing varying amounts of an amine-reactive pentafluorophenyl acrylate monomer followed by postpolymerization modification with a series of alkyl amines to afford precise control over the length and density of aliphatic alkyl side chains. This synthetic strategy enabled systematic investigation of the effect of the polymer structure on membrane binding, potentiation of peptide cell uptake, pH-dependent disruption of lipid bilayers for endosome escape, and intracellular bioavailability. A subset of these polymers exhibited pKa of ∼6.8, which facilitated stable membrane association at physiological pH and rapid, pH-dependent endosomal disruption upon endocytosis as quantified in Galectin-8-YFP reporter cells. Cationic cell penetrating peptide (CPP) uptake was enhanced up to 15-fold in vascular smooth muscle cells in vitro when peptide treatment was preceded by a 30-min pretreatment with lead candidate polymers. We also designed and implemented a new and highly sensitive assay for measuring the intracellular bioavailability of CPPs based on the NanoLuciferase (NanoLuc) technology previously developed for measuring intracellular protein-protein interactions. Using this split luciferase class of assay, polymer pretreatment enhanced intracellular delivery of the CPP-modified HiBiT peptide up to 30-fold relative to CPP-HiBiT without polymer pretreatment (p < 0.05). The overall structural analyses show that polymers containing 50:50 or 70:30 molar ratios of carboxyl groups to alkyl side chains of 6-8 carbons maximized peptide uptake, pH-dependent membrane disruption, and intracellular bioavailability and that this potentiation effect was maximized by pairing with CPPs with high cationic charge density. These results demonstrate a rapid, mild method for polymer modification of cell surfaces to potentiate intracellular delivery, endosome escape, and bioactivity of cationic peptides.
A cell-penetrating CD40-TRAF2,3 blocking peptide diminishes inflammation and neuronal loss after ischemia/reperfusion.

While the administration of anti-CD154 mAbs in mice validated the CD40-CD154 pathway as a target against inflammatory disorders, this approach caused thromboembolism in humans (unrelated to CD40 inhibition) and is expected to predispose to opportunistic infections. There is a need for alternative approaches to inhibit CD40 that avoid these complications. CD40 signals through TRAF2,3 and TRAF6-binding sites. Given that CD40-TRAF6 is the pathway that stimulates responses key for cell-mediated immunity against opportunistic pathogens, we examined the effects of pharmacologic inhibition of CD40-TRAF2,3 signaling. We used a model of ischemia/reperfusion (I/R)-induced retinopathy, a CD40-driven inflammatory disorder. Intravitreal administration of a cell-penetrating CD40-TRAF2,3 blocking peptide impaired ICAM-1 upregulation in retinal endothelial cells and CXCL1 upregulation in endothelial and Muller cells. The peptide reduced leukocyte infiltration, upregulation of NOS2/COX-2/TNF-α/IL-1β, and ameliorated neuronal loss, effects that mimic those observed after I/R in Cd40-/- mice. While a cell-penetrating CD40-TRAF6 blocking peptide also diminished I/R-induced inflammation, this peptide (but not the CD40-TRAF2,3 blocking peptide) impaired control of the opportunistic pathogen Toxoplasma gondii in the retina. Thus, inhibition of the CD40-TRAF2,3 pathway is a novel and potent approach to reduce CD40-induced inflammation, while likely diminishing the risk of opportunistic infections that would otherwise accompany CD40 inhibition.
Are Men in Blue Targets of Bias in Baseball? Maybe

A Major League Baseball umpire filed a lawsuit against MLB Commissioner Rob Manfred and the MLB alleging racial discrimination in baseball’s umpire promotion and post-season assignment policies. Cuban-born Angel Hernandez filed suit in Ohio federal court alleging that he has been passed over multiple times for the chance to work a World Series and has not been promoted from temporary to permanent crew chief. The suit alleges violations of the Civil Rights Act of 1964 and Ohio state law. The suit claims “Major League Baseball’s actions were intentional with reckless disregard for Hernandez’s rights.”
SYCL, DPC++, XPUs, oneAPI

James will share his passion for getting to a world of heterogeneous computing where software tooling (compilers, frameworks, libraries, etc.) all have an “XPU view” of the world that spans vendors and devices. In this world, James advocates that we all be free to write our programs to use whatever XPUs we want, get full access to all XPU capabilities, and be comfortable trusting our ability to do this without extra risk to performance or stability. James will discuss how SYCL, DPC++, XPUs, and oneAPI all are important on our journey to make this vision a reality. James invites all conference attendees to join in and help guide Intel’s enthusiasm to help us all succeed together. Note: James co-authored the first (and only for now) book that teaches SYCL 2020 programming.
Neurohospitalist Practice and Well-Being During the COVID-19 Pandemic

Background and Purpose:Neurohospitalists play an important role in, and have been variably affected by, the ongoing COVID-19 pandemic. In this study, we survey neurohospitalists to characterize pra...
Introduction to the Entrepreneurial Mindset Teaching Blueprint

Within higher education, educators across disciplines are increasingly focusing on cultivating this much-needed entrepreneurial mindset in their students but currently lack access to resources. In response to this challenge, the purpose of this chapter is to introduce the Entrepreneurial Mindset Teaching Blueprint (and its four curriculum design essentials) as a standardized approach for integrating the entrepreneurial mindset into any course. Integrating the entrepreneurial mindset into the classroom has many benefits. It equips students with critical-thinking skills, promotes the recognition of opportunities, and includes a focus on evaluation and execution. Development of students’ entrepreneurial mindset promotes continuous exploration of value propositions grounded in customer needs, optimizing return on investment, and paying close attention to feasibility considerations. From an individual perspective, growing the entrepreneurial mindset results in one’s ability to regularly and in many cases instinctively offer greater value to an employer or other stakeholders within the personal circle of relevance. Collectively, entrepreneurially minded individuals have the power to transform organizations, creating value within and beyond. The entrepreneurial mindset is a critical characteristic for solving complex social issues.
Resilient error-bounded lossy compressor for data transfer

Today's exa-scale scientific applications or advanced instruments are producing vast volumes of data, which need to be shared/transferred through the network/devices with relatively low bandwidth (e.g., data sharing on WAN or transferring from edge devices to supercomputers). Lossy compression is one of the candidate strategies to address the big data issue. However, little work was done to make it resilient against silent errors, which may happen during the stage of compression or data transferring. In this paper, we propose a resilient error-bounded lossy compressor based on the SZ compression framework. Specifically, we design a new independent-block-wise model that decomposes the entire dataset into many independent sub-blocks to compress. Then, we design and implement a series of error detection/correction strategies elaboratively for each stage of SZ. Our method is arguably the first algorithm-based fault tolerance (ABFT) solution for lossy compression. Our proposed solution incurs negligible execution overhead in the fault-free situation. Upon soft errors happening, it ensures decompressed data strictly bounded within user's requirement with a very limited degradation of compression ratio and low overhead.
Slit Jet IR Absorption Spectroscopy of Molecular Complexes

The combination of high resolution (≲10-3 cm-1) cw tunable difference frequency generation, high sensitivity (≲10-6/√Hz) direct absorption methods, and long path length (2.54 cm) pulsed slit expansions provide a powerfully general technique for studying weakly bound complexes in a cold molecular beam environment. Transient absorption of the narrow band laser provides a nonintrusive probe of the quantum state, velocity, temporal and spatial dependence of cluster formation in the pulsed molecular beam. High resolution fundamental, combination and hot band spectra of ArHF, HFN2 and HFCO2 complexes are presented. Detailed information on the molecular structure is determined for vibrationally excited states which sample the potential energy surface far from the ground state, near equilibrium geometry.
Chapter 3 Amphibian Alkaloids

Publisher Summary This chapter discusses that amphibians have elaborated an astonishing array of alkaloids, most of which are known only from the skin or skin glands of adult amphibians. These substances are probably released defensively against predators and/or microorganisms onto the skin surface from the cutaneous granular “poison” glands that develop during metamorphosis. Such glands are present even in frogs that do not seem to have elaborated a defensive substance. The origin of amphibian alkaloids is even less clear. Many represent unique structural classes, while others occur in certain insects. Ants contain simple pyrrolidines, piperidines, pyrrolizidines, and indolizidines; beetles contain tricyclic coccinellines; and a millepede contains a possible precursor for the pyrrolizidine oxime class. The phylogenetic distribution of alkaloids in amphibians discusses for genetic control through specific sets of biosynthetic enzymes. The involvement of symbiotic microorganisms, dietary precursors, or cofactors, or other environmental factors in alkaloid production in amphibians cannot be excluded, although genetic factors play a role.
A finite element formulation for modeling dynamic wetting on flexible substrates and in deformable porous media.

This report summarizes research advances pursued with award funding issued by the DOE to Drexel University through the Presidential Early Career Award (PECASE) program. Professor Rich Cairncross was the recipient of this award in 1997. With it he pursued two related research topics under Sandia's guidance that address the outstanding issue of fluid-structural interactions of liquids with deformable solid materials, focusing mainly on the ubiquitous dynamic wetting problem. The project focus in the first four years was aimed at deriving a predictive numerical modeling approach for the motion of the dynamic contact line on a deformable substrate. A formulation of physical model equations was derived in the context of the Galerkin finite element method in an arbitrary Lagrangian/Eulerian (ALE) frame of reference. The formulation was successfully integrated in Sandia's Goma finite element code and tested on several technologically important thin-film coating problems. The model equations, the finite-element implementation, and results from several applications are given in this report. In the last year of the five-year project the same physical concepts were extended towards the problem of capillary imbibition in deformable porous media. A synopsis of this preliminary modeling and experimental effort is also discussed.
The influence of single elements on nested community structure

Summary 1. Asking whether or not an ecological community displays the structural property of nestedness is becoming increasingly common in ecological research. We note, however, a currently limited understanding of how individual matrix components (e.g. species as rows and sites as columns) and elements (e.g. a species’ occurrence at a site) contribute to overall community structure. 2. Here, we investigate the influence of single elements in a community matrix on overall community nestedness. We derive a unique extension to the popular nestedness algorithm NODF that is necessary for this analysis. 3. For 210 empirical communities, we show that elements, on average, determine a little less than 50% of a community’s nestedness value, with components determining the remainder. Looking at just matrix elements we find, on average, that 10% of elements determine 25% of a community’s nested structure. Further, we find statistical conclusions change for more than 20% of the empirical communities with the addition or removal of a single element. 4. Generally, the search for ecological pattern occurs by calculating a single metric designed to quantify the structure of an entire community. By showing the sensitivity of a metric to changes in a single element, our results cast doubt on the usefulness of this approach. That said, the extension to NODF that we present should allow researchers to better understand how individual elements in a community influence patterns of nestedness.
Multi-channel readback model for an optical tape system

We develop a channel model for multichannel readback in an optical tape system which encodes the binary data as reflectance differences in the media. The channel model can be used to evaluate various signal processing schemes. Different algorithms are compared using numerical methods and simulations. The results provide an insight into the advantages of using advanced detection and equalization techniques.
Sensing hypoxia: physiology, genetics and epigenetics

The carotid body is a sensory organ for detecting arterial blood O2 levels and reflexly mediates systemic cardiac, vascular and respiratory responses to hypoxia. This article presents a brief review of the roles of gaseous messengers in the sensory transduction at the carotid body, genetic and epigenetic influences on hypoxic sensing and the role of the carotid body chemoreflex in cardiorespiratory diseases. Type I (also called glomus) cells, the site of O2 sensing in the carotid body, express haem oxygenase-2 and cystathionine-γ-lyase, the enzymes which catalyse the generation of CO and H2S, respectively. Physiological studies have shown that CO is an inhibitory gas messenger, which contributes to the low sensory activity during normoxia, whereas H2S is excitatory and mediates sensory stimulation by hypoxia. Hypoxia-evoked H2S generation in the carotid body requires the interaction of cystathionine-γ-lyase with haem oxygenase-2, which generates CO. Hypoxia-inducible factors 1 and 2 constitute important components of the genetic make-up in the carotid body, which influence hypoxic sensing by regulating the intracellular redox state via transcriptional regulation of pro- and antioxidant enzymes. Recent studies suggest that developmental programming of the carotid body response to hypoxia involves epigenetic changes, e.g. DNA methylation of genes encoding redox-regulating enzymes. Emerging evidence implicates heightened carotid body chemoreflex in the progression of autonomic morbidities associated with cardiorespiratory diseases, such as sleep-disordered breathing with apnoea, congestive heart failure and essential hypertension.
The Cotangent Bundle

In this chapter we introduce a construction that is not typically seen in elementary calculus: tangent covectors, which are linear functionals on a tangent space to a smooth manifold M. The space of all covectors at p∈M is a vector space called the cotangent space at p; in linear-algebraic terms, it is the dual space to T p M. The union of all cotangent spaces at all points of M is a vector bundle called the cotangent bundle. Whereas tangent vectors give us a coordinate-free interpretation of derivatives of curves, it turns out that derivatives of real-valued functions on a manifold are most naturally interpreted as tangent covectors. Thus we define the differential of a real-valued function as a covector field (a smooth section of the cotangent bundle); it is a coordinate-independent analogue of the gradient. In the second half of the chapter we introduce line integrals of covector fields, which satisfy a far-reaching generalization of the fundamental theorem of calculus.
Genome-Wide Association Studies with Metabolomics

Disturbances in metabolism are at the root of a variety of human afflictions and complex diseases. Although many of the genes that contribute to these conditions have been identified since the completion of the human genome by genome-wide association studies, it is still unclear for many of these genetic variants how they disrupt cellular processes. In this chapter we shall present the concept of genome-wide association studies with metabolomics. These studies show how combining two highly sophisticated biochemical measurement methods, genetics and metabolomics, applied to only a small amount of blood, can reveal deep insights into the genetic makeup of the human body’s metabolic capacities. In addition to providing functional insights into the genetic basis of metabolic traits and complex diseases, study of what we call “genetically determined metabotypes” is a way to understand an individual’s uniqueness. These genetically determined metabotypes may modify the risk of an individual to develop a disease, the response to medication and therapy, and the reaction to environmental challenges and thereby help to develop highly targeted, personalized therapies and enable novel types of treatments or prevent adverse drug reactions.
Generalized Kohn–Sham Density Functional Theory via Effective Action Formalism

Publisher Summary This chapter examines the foundation of density functional theory. Density functional theory allows studying the ground state properties of the many-body system in terms of the expectation value of the particle-density operator. It offers the possibility of finding the ground state energy by minimizing the energy functional that depends on the density only. In general, it is possible to imagine a description of a many-body system in terms of the expectation value of any other suitable operator. Such a description can be presented via the effective action formalism, thus leading to a generalized density-functional theory–a theory that allows a description of many-body systems in terms of the expectation value of any suitable operator. Density-functional theory relies on the theorem of Hohenberg and Kohn, which shows that there exists a unique description of a many-body system in terms of the expectation value of the particle-density operator. In the framework of the effective action formalism, the proof of existence was given only in a diagrammatic sense and was tailored to the particular features of the particle-density based description of a nonrelativistic many-electron system. The chapter presents a different resolution of this issue. Constructed are the first few orders of the exchange-correlation functional, there are comments on the local density approximation, and discussion on the results as compared to other methods. The chapter discusses effective action functional, generalized Kohn–Sham theory via the inversion method, Kohn–Sham density-functional theory, time-dependent probe, one-electron propagators, excitation energies, and theorems involving functionals W [J] and T [Q]. Kohn–Sham theory has been derived. This formulation is specifically geared towards practical calculations of the ground and excited properties of real systems. This can be applied to various many-body systems for constructing Kohn–Sham like descriptions in terms of the expectation value of any general operator.
Efficient summarizing of multimedia archives using cluster labeling

In this demo we present a novel approach for labeling clusters in minimally annotated data archives. We propose to build on clustering by aggregating the automatically tagged semantics. We propose and compare four techniques for labeling the clusters and evaluate the performance compared to human labeled ground-truth. We define the error measures to quantify the results, and present examples of the cluster labeling results obtained on the BBC stock shots and broadcast news videos from the TRECVID-2005 video data set.
Identification and characterization of transcriptional arrest sites in exon 1 of the human adenosine deaminase gene

Analysis of human adenosine deaminase (ADA) gene transcription in four different cell lines indicated that a high density of RNA polymerase II complexes is present at the 5' end of the gene and that the extent of transcription elongation beyond the promoter-proximal region governs gene expression. To determine the sequence requirements for a potential transcription arrest site in the promoter-proximal region, genomic clones containing the ADA promoter, exon 1, and various lengths of intron 1 were injected into Xenopus laevis oocyte germinal vesicles. Transcription analysis indicated that nascent ADA transcripts were highly represented at the promoter-proximal region of the injected templates, suggesting that transcription arrest occurred in the oocyte transcription system. Analysis of the transcription products indicated that ADA transcription initiated at the authentic start site and that the most prominent, short ADA transcripts were 105 nucleotides in length. The 3' end of these transcripts mapped within exon 1, 10 nucleotides downstream of the translation initiation codon. Deletion analysis demonstrated that sequences within exon 1 were sufficient to specify the synthesis of the 105-nucleotide transcripts. Taken together, these data suggest that a transcription arrest mechanism operates in the promoter-proximal region of the human ADA gene and that regulation of elongation beyond this point plays a major role in regulating ADA gene expression.
Characterization and evaluation of the efficacy of cationic complex mediated plasmid DNA delivery in human embryonic palatal mesenchyme cells

The purpose of this study was to develop and test a non-viral gene delivery system that can be employed to deliver genes of interest into a pre-osteoblastic cell line. Human embryonic palatal mesenchymal (HEPM 1486) cells were transfected with vector-plasmid DNA (pDNA) complexes. We explored calcium phosphate and polyethylenimine (PEI) as non-viral vectors and compared their respective in vitro transfection efficacies. Plasmid DNA encoding luciferase protein (LUC) was complexed with PEI (with differing N:P ratios) and calcium phosphate (with differing Ca:P ratios), using established protocols. The complexes prepared were then characterized for size and surface charge, using a Malvern Zetasizer Nano-ZS. The transfection efficiency and cytotoxicity of the prepared complexes were evaluated in HEPM cells. The PEI–pDNA complexes over the whole range of N:P ratios were found to be < 160 nm in size, while the calcium phosphate–pDNA complexes were relatively bigger. The PEI–pDNA complexes prepared at a N:P ratio of 10 were found to have maximum transfection efficiency at 4 h of treatment, with minimal cytotoxicity. The highest transfection efficiency obtained with calcium phosphate–pDNA complexes (Ca:P 200) was nearly 12-fold lower than that obtained with PEI–pDNA complexes (N:P 10). Following this, transgene expression in the HEPM cells treated with complexes prepared at a N:P ratio of 10 was further examined, using pDNA coding for enhanced green fluorescent protein (EGFP-N1) or therapeutically relevant platelet-derived growth factor B (PDGF-B). In conclusion, PEI was a more effective vector for delivering genes of interest to pre-osteoblasts than calcium phosphate. Copyright © 2014 John Wiley & Sons, Ltd.
Osteonecrosis of the maxilla as a complication to chemotherapy: a case report

Numerous oral complications have been documented as a consequence of chemotherapy for the treatment of cancer. One not so well documented consequence of this treatment is avascular necrosis or osteonecrosis of the underlying bone. In this case report, osteonecrosis of the maxilla in a 48-year-old female patient who was treated for acute myelogenous leukemia is presented. The patient had successfully completed both induction and consolidation chemotherapy without steroid administration. Possible causes and difficulties in diagnosis were reviewed.
Gross-beta activity in ground water: natural sources and artifacts of sampling and laboratory analysis

Abstract Gross-beta activity has been used as an indicator of beta-emitting isotopes in water since at least the early 1950s. Originally designed for detection of radioactive releases from nuclear facilities and weapons tests, analysis of gross-beta activity is widely used in studies of naturally occurring radioactivity in ground water. Analyses of about 800 samples from 5 ground-water regions of the United States provide a basis for evaluating the utility of this measurement. The data suggest that measured gross-beta activities are due to (1) long-lived radionuclides in ground water, and (2) ingrowth of beta-emitting radionuclides during holding times between collection of samples and laboratory measurements. Although40K and228Ra appear to be the primary sources of beta activity in ground water, the sum of40K plus228Ra appears to be less than the measured gross-beta activity in most ground-water samples. The difference between the contribution from these radionuclides and gross-beta activity is most pronounced in ground water with gross-beta activities > 10 pCi/L, where these 2 radionuclides account for less than one-half the measured ross-beta activity. One exception is groundwater from the Coastal Plain of New Jersey, where40K plus228Ra generally contribute most of the gross-beta activity. In contrast,40K and228Ra generally contribute most of beta activity in ground water with gross-beta activities The gross-beta technique does not measure all beta activity in ground water. Although3H contributes beta activity to some ground water, it is driven from the sample before counting and therefore is not detected by gross-beta measurements. Beta-emitting radionuclides with half-lives shorter than a few days can decay to low values between sampling and counting. Although little is known about concentrations of most short-lived beta-emitting radionuclides in environmental ground water (water unaffected by direct releases from nuclear facilities and weapons tests), their activities are expected to be low. Ingrowth of beta-emitting radionuclides during sample holding times can contribute to gross-beta activity, particularly in ground water with gross-beta activities > 10 pCi/L. Ingrowth of beta-emitting progeny of238U, specifically234Pa and234Th, contributes much of the measured gross-beta activity in ground water from 4 of the 5 areas studied. Consequently, gross-beta activity measurements commonly overestimate the abundance of beta-emitting radionuclides actually present in ground water. Differing sample holding times before analysis lead to differing amounts of ingrowth of the two progeny. Therefore, holding times can affect observed gross-beta measurements, particularly in ground water with238U activities that are moderate to high compared with the activity of40K plus228Ra. Uncertainties associated with counting efficiencies for beta particles with different energies further complicate the interpretation of gross-beta measurements.
Morphology of (methoxyethoxy/trifluoroethoxy)phosphazene copolymers

Block copolymers were synthesized by the anionically initiated copolymerization of (CH 3 OCH 2 CH 2 O)(CF 3 CH 2 O) 2 P=NSi(CH 3 ) 3 , followed by the addition of (CF 3 CH 2 O) 3 P=NSi (CH 3 ) 3 . Random copolymers were made by simuluneous polymerization of these monomers. These copolymers exhibit a linear dependency on the mole fraction «m» of the repeating units bearing a methoxyethoxy pendant side group as well as on molecular weights. The thermal and morphological characteristics of the block copolymers are different from those of the random copolymers of analogous «m» and molecular weight. All copolymers undergo a mesophase T(1) transition for a range of temperatures depending upon «m» and molecular weights of the copolymers. Morphological and structural features essentially resemble those of the low molecular weight (trifluoroethoxy)phosphazene homopolymer. Upon heating and cooling the solution cast copolymer specimens through T(1), most of them transform into an orthorhombic form with the unit cell dimensions a=2,060 nm, b=0,940 nm and c=0,486 nm from their initial monoclinic form with a=1,003 nm, b=0,937 nm, c=0,486 nm and γ= 91 o . These unit cell dimensions agree completely with those of the low molecular weight PBFP. Complicated morphologies comprised of square and globular shapes that depend upon the copolymer composition were obtained from dilute tetrahydrofuran/p-xylene copolymer solutions. Electron microscopy directly reveals that chain extension occurs for the melt-crystallized copolymer specimen. The non-crystallizable minor component in the block copolymers is rejected from the crystal lattice. In the random copolymers, the methoxyethoxy pendant side group enters into the crystal lattice and influences their morphological and structural features
Slow-mode oscillations of large-scale coronal loops

On several occasions, repetitive X-ray brightenings, sometimes accompanied by mass injections into adjacent loops, appeared quasi-periodically with mean periods close to 20 minutes. In all cases when X-ray images were available, the sites of these brightenings were in active regions which were associated with large-scale coronat loops of length (2 − 3) × 105 km. Therefore, the primary source of these long-periodic pulsations might be slow-mode oscillations in these large-scale loops. Free MHD oscillations, proposed earlier by Roberts, Edwin, and Benz (1984), may fit the observed data.