cssi/SciSciGPT-SciSciNet huggingface dataset:
Molecular Assays of Pollen Use Consistently Reflect Pollinator Visitation Patterns in a System of Flowering Plants

Determining how pollinators visit plants versus how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, co-flowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods to estimate the relative abundance of each Clarkia pollen in samples collected from pollinators. We use these methods to investigate if observations of plant-pollinator contact in the field correspond to the pollen bees carry; if individual bees carry Clarkia pollens in predictable ways, based on previous knowledge of their foraging behaviors; and how the three approaches differ for understanding plant-pollinator interactions. We find that observations of plant-pollinator contact are generally predictive of the pollens that bees carry while foraging, and network topologies using the three different methods are statistically indistinguishable from each other. Results from molecular pollen analysis also show that while bees can carry multiple species of Clarkia at the same time, they often carry one species of pollen. Our work contributes to the growing body of literature aimed at resolving how pollinators use floral resources. We suggest our novel relative amplicon quantification method as another tool in the developing molecular ecology and pollination biology toolbox.
Pheno-mapper: an interactive toolbox for the visual exploration of phenomics data

High-throughput technologies to collect field data have made observations possible at scale in several branches of life sciences. The data collected can range from the molecular level (genotypes) to physiological (phenotypic traits) and environmental observations (e.g., weather, soil conditions). These vast swathes of data, collectively referred to as phenomics data, represent a treasure trove of key scientific knowledge on the dynamics of the underlying biological system. However, extracting information and insights from these complex datasets remains a significant challenge owing to their multidimensionality and lack of prior knowledge about their complex structure. In this paper, we present Pheno-Mapper, an interactive toolbox for the exploratory analysis and visualization of large-scale phenomics data. Our approach uses the mapper framework to perform a topological analysis of the data, and subsequently render visual representations with built-in data analysis and machine learning capabilities. We demonstrate the utility of this new tool on real-world plant (e.g., maize) phenomics datasets. In comparison to existing approaches, the main advantage of Pheno-Mapper is that it provides rich, interactive capabilities in the exploratory analysis of phenomics data, and it integrates visual analytics with data analysis and machine learning in an easily extensible way. In particular, Pheno-Mapper allows the interactive selection of subpopulations guided by a topological summary of the data and applies data mining and machine learning to these selected subpopulations for in-depth exploration.
Controller Design for Time-varying Sampling, Co-Regulated Systems

“Co-regulation” is a time-varying periodic sampling strategy wherein the sampling rate is dynamically adjusted in response to the performance of the controlled system. The controller for co-regulated system needs to adjust control outputs corresponding to the current (changing) sampling rate. This makes performance guarantees such as stability difficult to obtain. In this paper we develop two stability guaranteed control algorithms for co-regulated systems. First is a correct-by-construction stabilizing controller where the control gain matrices are pre-computed offline for a set of sampling rates. This method allows for arbitrary switching of the sampling rates but as a result can be overly conservative. Then a hybrid Model Predictive Control (MPC) algorithm is tailored for co-regulated systems where both the system state trajectory and the sampling rate (scheduling parameter) trajectory are predicted within the receding horizon. The performances of the proposed controllers are demonstrated and discussed for a co-regulated multicopter Unmanned Aircraft System (UAS). The results show co-regulation can efficiently reallocate computational resources based on control performance by varying the sampling rate at runtime, while the proposed control strategies can guarantee co-regulated system stability when working under a time-varying sampling rate.
Uniform Forward-modeling Analysis of Ultracool Dwarfs. I. Methodology and Benchmarking

We present a forward-modeling framework using the Bayesian inference tool Starfish and cloudless Sonora-Bobcat model atmospheres to analyze low-resolution ($R\approx80-250$) near-infrared ($1.0-2.5$ $\mu$m) spectra of T dwarfs. Our approach infers effective temperatures, surface gravities, metallicities, radii, and masses, and by accounting for uncertainties from model interpolation and correlated residuals due to instrumental effects and modeling systematics, produces more realistic parameter posteriors than traditional ($\chi^2$-based) spectral-fitting analyses. We validate our framework by fitting the model atmospheres themselves and finding negligible offsets between derived and input parameters. We apply our methodology to three well-known benchmark late-T dwarfs, HD 3651B, GJ 570D, and Ross 458C, using both solar and non-solar metallicity atmospheric models. We also derive these benchmarks' physical properties using their bolometric luminosities, their primary stars' ages and metallicities, and Sonora-Bobcat evolutionary models. Assuming the evolutionary-based parameters are more robust, we find our atmospheric-based, forward-modeling analysis produces two outcomes. For HD 3615B and GJ 570D, spectral fits provide accurate $T_{\rm eff}$ and $R$ but underestimated $\log{g}$ (by $\approx1.2$ dex) and $Z$ (by $\approx0.35$ dex), likely due to the systematics from modeling the potassium line profiles. For Ross 458C, spectral fits provide accurate $\log{g}$ and $Z$ but overestimated $T_{\rm eff}$ (by $\approx120$ K) and underestimated $R$ (by $\approx1.6\times$), likely because our model atmospheres lack clouds, reduced vertical temperature gradients, or disequilibrium processes. Finally, the spectroscopically inferred masses of these benchmarks are all considerably underestimated.
Refined Cauchy identity for spin Hall–Littlewood symmetric rational functions

Abstract Fully inhomogeneous spin Hall–Littlewood symmetric rational functions F λ arise in the context of sl ( 2 ) higher spin six vertex models, and are multiparameter deformations of the classical Hall–Littlewood symmetric polynomials. We obtain a refined Cauchy identity expressing a weighted sum of the product of two F λ 's as a determinant. The determinant is of Izergin–Korepin type: it is the partition function of the six vertex model with suitably decorated domain wall boundary conditions. The proof of equality of two partition functions is based on the Yang–Baxter equation. We rewrite our Izergin–Korepin type determinant in a different form which includes one of the sets of variables in a completely symmetric way. This determinantal identity might be of independent interest, and also allows to directly link the spin Hall–Littlewood rational functions with (the Hall–Littlewood particular case of) the interpolation Macdonald polynomials. In a different direction, a Schur expansion of our Izergin–Korepin type determinant yields a deformation of Schur symmetric polynomials. In the spin- 1 2 specialization, our refined Cauchy identity leads to a summation identity for eigenfunctions of the ASEP (Asymmetric Simple Exclusion Process), a celebrated stochastic interacting particle system in the Kardar–Parisi–Zhang universality class. This produces explicit integral formulas for certain multitime probabilities in ASEP.
Learning to Hoard: The Effects of Preexisting and Surprise Price-Gouging Regulation During the COVID-19 Pandemic.

Theory suggests anticipation of shortages stemming from price regulation can motivate households to stock up more and thereby aggravate the regulation-induced shortage. We test this theory on online shopping searches for two typically store-bought staples: hand sanitizer and toilet paper. Combining (i) interstate variation in type of price-gouging regulation—preexisting versus surprise versus none, (ii) their temporally staggered implementation, and (iii) the demand surges for hand sanitizer and toilet paper during the COVID-19 pandemic facilitates identifying the impacts of different price-gouging regulation on consumer searches. Our results are consistent with price-gouging regulation–driven anticipatory hoarding. Difference-in-differences estimates reveal that states with preexisting-regulation experience the largest increases in post-implementation search proportions for both products. Accounting for potential endogeneity of implementation using a nearest-neighbor matching strategy reveals states that make surprise announcements of new regulation during the pandemic also experience larger increases in post-activation hand sanitizer search proportions than states without any such policy, but smaller increases than what preexisting-law states experience. These results corroborate the theoretical predictions about consequences of regulation-induced anticipation of shortages and inform the current policy debate surrounding impacts of price-gouging laws. Fundamentally, our results indicate behavioural responses to policy evolve as experience reveals the effects of the policy, and this evolution might influence the welfare consequences of the policy.
The zecca mint: a self-enforcing monetary constitution in historic venice

Monetary history is largely a repeated narrative of currency debasement. Yet historic Venice (1172–1797), ruled by elite patricians, stands out as an example of relative monetary stability. This paper provides a historical case of Venice’s Zecca Mint which provided the elite patricians of Venice with a stable currency, playing a role in fostering the economic success of the Republic of Venice. This paper identifies three factors that together formed a self-enforcing monetary constitution to inhibit public currency debasement in historic Venice: (i) the assignment of public debt to patricians, (ii) the nearly uniform trade-centric focus of the patricians and (iii) the use of turn-taking in office for mintmasters.
Fibronectin‐Mediated Inflammatory Signaling Through Integrin α5 in Vascular Remodeling

Background Adhesion of vascular endothelial cells to the underlying basement membrane potently modulates endothelial cells to cells' inflammatory activation. The normal basement membrane proteins l...
Criteria for univalence and quasiconformal extension for harmonic mappings on planar domains

If \(\Omega\) is a simply connected domain in \(\overline{\mathbf C}\) then, according to the Ahlfors-Gehring theorem, \(\Omega\) is a quasidisk if and only if there exists a sufficient condition for the univalence of holomorphic functions in \(\Omega\) in relation to the growth of their Schwarzian derivative. We extend this theorem to harmonic mappings by proving a univalence criterion on quasidisks. We also show that the mappings satisfying this criterion admit a homeomorphic extension to \(\overline{\mathbf C}\) and, under the additional assumption of quasiconformality in \(\Omega\), they admit a quasiconformal extension to \(\overline{\mathbf C}\). The Ahlfors-Gehring theorem has been extended to finitely connected domains \(\Omega\) by Osgood, Beardon and Gehring, who showed that a Schwarzian criterion for univalence holds in \(\Omega\) if and only if the components of \(\partial\Omega\) are either points or quasicircles. We generalize this theorem to harmonic mappings.
The q-voter model on the torus

In the q-voter model, the voter at x changes its opinion at rate fxq, where fx is the fraction of neighbors with the opposite opinion. Mean-field calculations suggest that there should be coexistence between opinions if q 1. This model has been extensively studied by physicists, but we do not know of any rigorous results. In this paper, we use the machinery of voter model perturbations to show that the conjectured behavior holds for q close to 1. More precisely, we show that if q 0, however we show persistence does not hold for exp(nβ) with β>1∕3. If q>1, then the process rapidly reaches fixation on one opinion. It is interesting to note that in the second case the limiting ODE (on its sped up time scale) reaches 0 at time logn but the stochastic process on the same time scale dies out at time (1∕3)logn.
Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites.

Summary Topoisomerase II (topo II) is essential for disentangling newly replicated chromosomes. DNA unlinking involves the physical passage of one duplex through another and depends on the transient formation of double-stranded DNA breaks, a step exploited by frontline chemotherapeutics to kill cancer cells. Although anti-topo II drugs are efficacious, they also elicit cytotoxic side effects in normal cells; insights into how topo II is regulated in different cellular contexts is essential to improve their targeted use. Using chemical fractionation and mass spectrometry, we have discovered that topo II is subject to metabolic control through the TCA cycle. We show that TCA metabolites stimulate topo II activity in vitro and that levels of TCA flux modulate cellular sensitivity to anti-topo II drugs in vivo. Our work reveals an unanticipated connection between the control of DNA topology and cellular metabolism, a finding with ramifications for the clinical use of anti-topo II therapies.
A biomedically oriented automatically annotated Twitter COVID-19 dataset.

The use of social media data, like Twitter, for biomedical research has been gradually increasing over the years. With the COVID-19 pandemic, researchers have turned to more nontraditional sources of clinical data to characterize the disease in near real-time, study the societal implications of interventions, as well as the sequelae that recovered COVID-19 cases present (Long-COVID). However, manually curated social media datasets are difficult to come by due to the expensive costs of manual annotation and the efforts needed to identify the correct texts. When datasets are available, they are usually very small and their annotations do not generalize well over time or to larger sets of documents. As part of the 2021 Biomedical Linked Annotation Hackathon, we release our dataset of over 120 million automatically annotated tweets for biomedical research purposes. Incorporating best practices, we identify tweets with potentially high clinical relevance. We evaluated our work by comparing several SpaCy-based annotation frameworks against a manually annotated gold-standard dataset. Selecting the best method to use for automatic annotation, we then annotated 120 million tweets and released them publicly for future downstream usage within the biomedical domain.
Nanoscale axial position and orientation measurement of hexagonal boron nitride quantum emitters using a tunable nanophotonic environment.

Color centers in hexagonal boron nitride (hBN) have emerged as promising candidates for single-photon emitters (SPEs) due to their bright emission characteristics and potential for high temperature operation, but precisely resolving emitter location is an important outstanding issue for many applications. While single-molecule super-resolution microscopy schemes can resolve emitter lateral position at the nanometer scale, complete determination of both axial position and three-dimensional dipole orientation (θ, φ) of these quantum emitters is a fundamental challenge. We report a method for determining both the axial position and three-dimensional orientation of SPEs in \textit{h}BN by tuning the photonic local density of states, using a vanadium dioxide (VO₂) phase change material. Using this method, we were able to locate several specific quantum emitters at an axial distance of ~ 20 nm from the hBN/VO₂ interface while also determining their full dipolar orientation (θ, φ). Our approach may serve as a practical method to deterministically couple quantum emitters in hBN and other materials to photonic nanostructures, for applications in integrated quantum photonics.
Whole Heart Mesh Generation for Image-Based Computational Simulations by Learning Free-From Deformations

Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of cardiac structures from medical image data–a process that has traditionally required significant time and human effort, limiting large-cohort analyses and potential clinical translations. We propose a novel deep learning approach to reconstruct simulation-ready whole heart meshes from volumetric image data. Our approach learns to deform a template mesh to the input image data by predicting displacements of multi-resolution control point grids. We discuss the methods of this approach and demonstrate its application to efficiently create simulation-ready whole heart meshes for computational fluid dynamics simulations of the cardiac flow. Our source code is available at https://github.com/fkong7/HeartFFDNet.
Business Models in the Sharing Economy: Manufacturing Durable Goods in the Presence of Peer-to-Peer Rental Markets

With peer-to-peer sharing of durable goods like cars, boats, and condominiums, it is unclear how manufacturers should react. They could seek to encourage these markets or compete against them by of...
Evidence of gas-phase pyranose-to-furanose isomerization in protonated peptidoglycans

Peptidoglycans are diverse co- and post-translational modifications of key importance in myriad biological processes. Mass spectrometry is employed to infer their biomolecular sequences and stereochemisties, but little is known about the critical gas-phase dissociation processes involved. Here, using tandem mass spectrometry (MS/MS and MSn), isotopic labelling and high-level simulations, we identify and characterize a facile isomerization reaction that produces furanose N-acetylated ions. This reaction occurs for both O- and N-linked peptidoglycans irrespective of glycosidic linkage stereochemistry (α/β). Dissociation of the glycosidic and other bonds thus occur from the furanose isomer critically altering the reaction feasibility and product ion structures.
Hilbert–Kunz multiplicity of fibers and Bertini theorems

Abstract Let k be an algebraically closed field of characteristic p > 0 . We show that if X ⊆ P k n is an equidimensional subscheme with Hilbert–Kunz multiplicity less than λ at all points x ∈ X , then for a general hyperplane H ⊆ P k n , the Hilbert–Kunz multiplicity of X ∩ H is less than λ at all points x ∈ X ∩ H . This answers a conjecture and generalizes a result of Carvajal-Rojas, Schwede and Tucker, whose conclusion is the same as ours when X ⊆ P k n is normal. In the process, we substantially generalize certain uniform estimates on Hilbert–Kunz multiplicities of fibers of maps obtained by the aforementioned authors that should be of independent interest.
Topological defects, inherent structures, and hyperuniformity

A wide spectrum of disordered many-body systems that are inherent structures (i.e., local minima of potential energy landscape) was recently discovered to possess a novel hidden long-range order known as hyperuniformity, yet the mechanisms associated with the emergence of disordered hyperuniformity in such systems are not well understood. Here, we address this important fundamental problem by linking together the concepts of topological defects, inherent structures, and hyperuniformity. We consider representative examples of disordered inherent structures that are topological variants of crystals obtained by continuously introducing into the crystalline state randomly distributed topological defects such as dislocations and disclinations. Using large-scale numerical simulations and analysis based on a continuum theory, we show that the topological defects and the associated transformation pathways linking the disordered inherent structures to the crystalline state preserve hyperuniformity of the latter, as long as the displacements induced by the defects are sufficiently localized (i.e., the volume integrals of the displacements and squared displacements caused by individual defect are finite) and the displacement-displacement correlation matrix of the system is diagonalized and isotropic. Our results provide insights to the discovery, design, and generation of novel disordered hyperuniform materials.
A Framework for Cluster and Classifier Evaluation in the Absence of Reference Labels

In some problem spaces, the high cost of obtaining ground truth labels necessitates use of lower quality reference datasets. It is difficult to benchmark model performance using these datasets, as evaluation results may be biased. We propose a supplement to using reference labels, which we call an approximate ground truth refinement (AGTR). Using an AGTR, we prove that bounds on specific metrics used to evaluate clustering algorithms and multi-class classifiers can be computed without reference labels. We also introduce a procedure that uses an AGTR to identify inaccurate evaluation results produced from datasets of dubious quality. Creating an AGTR requires domain knowledge, and malware family classification is a task with robust domain knowledge approaches that support the construction of an AGTR. We demonstrate our AGTR evaluation framework by applying it to a popular malware labeling tool to diagnose over-fitting in prior testing and evaluate changes whose impact could not be meaningfully quantified under previous data.
Inference for high-dimensional exchangeable arrays

We consider inference for high-dimensional exchangeable arrays where the dimension may be much larger than the cluster sizes. Specifically, we consider separately and jointly exchangeable arrays that correspond to multiway clustered and polyadic data, respectively. Such exchangeable arrays have seen a surge of applications in empirical economics. However, both exchangeability concepts induce highly complicated dependence structures, which poses a significant challenge for inference in high dimensions. In this paper, we first derive high-dimensional central limit theorems (CLTs) over the rectangles for the exchangeable arrays. Building on the high-dimensional CLTs, we develop novel multiplier bootstraps for the exchangeable arrays and derive their finite sample error bounds in high dimensions. The derivations of these theoretical results rely on new technical tools such as Hoeffding-type decomposition and maximal inequalities for the degenerate components in the Hoeffiding-type decomposition for the exchangeable arrays. We illustrate applications of our bootstrap methods to robust inference in demand analysis, robust inference in extended gravity analysis, and penalty choice for $\ell_1$-penalized regression under multiway cluster sampling.
Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion.

ABSTRACT The biophysical features of a cell can provide global insights into diverse molecular changes, especially in processes like the dedifferentiation of chondrocytes. Key biophysical markers of chondrocyte dedifferentiation include flattened cellular morphology and increased stress-fiber formation. During cartilage regeneration procedures, dedifferentiation of chondrocytes during in vitro expansion presents a critical limitation to the successful repair of cartilage tissue. Our study investigates how the key biophysical changes of chondrocytes during dedifferentiation influence the nuclear mechanics and gene expression of structural proteins located at the nuclear envelope. Through an experimental model of cell stretching and a detailed spatial intranuclear strain quantification, we identified that strain is amplified and the distribution of strain within the chromatin is altered under tensile loading in the dedifferentiated state. Further, using a confocal microscopy image-based finite element model and simulation of cell stretching, we found that the cell shape is the primary determinant of the strain amplification inside the chondrocyte nucleus in the dedifferentiated state. Additionally, we found that nuclear envelope proteins have lower gene expression in the dedifferentiated state. This study highlights the role of cell shape on nuclear mechanics and lays the groundwork to design biophysical strategies for the maintenance and enhancement of the chondrocyte phenotype during cell expansion with a goal of successful cartilage tissue engineering.
Harms of Gender Exclusivity and Challenges in Non-Binary Representation in Language Technologies.

Gender is widely discussed in the context of language tasks and when examining the stereotypes propagated by language models. However, current discussions primarily treat gender as binary, which can perpetuate harms such as the cyclical erasure of non-binary gender identities. These harms are driven by model and dataset biases, which are consequences of the non-recognition and lack of understanding of non-binary genders in society. In this paper, we explain the complexity of gender and language around it, and survey non-binary persons to understand harms associated with the treatment of gender as binary in English language technologies. We also detail how current language representations (e.g., GloVe, BERT) capture and perpetuate these harms and related challenges that need to be acknowledged and addressed for representations to equitably encode gender information.
An Improved Approximation for Maximum $k$-Dependent Set on Bipartite Graphs

Abstract We present a ( 1 + k k + 2 ) -approximation algorithm for the Maximum k - dependent Set problem on bipartite graphs for any k ≥ 1 . For a graph with n vertices and m edges, the algorithm runs in O ( k m n ) time and improves upon the previously best-known approximation ratio of 1 + k k + 1 established by Kumar et al. (2014). Our proof also indicates that the algorithm retains its approximation ratio when applied to the (more general) class of Konig–Egervary graphs.
Simple Entity-Centric Questions Challenge Dense Retrievers.

Open-domain question answering has exploded in popularity recently due to the success of dense retrieval models, which have surpassed sparse models using only a few supervised training examples. However, in this paper, we demonstrate current dense models are not yet the holy grail of retrieval. We first construct EntityQuestions, a set of simple, entity-rich questions based on facts from Wikidata (e.g., “Where was Arve Furset born?”), and observe that dense retrievers drastically under-perform sparse methods. We investigate this issue and uncover that dense retrievers can only generalize to common entities unless the question pattern is explicitly observed during training. We discuss two simple solutions towards addressing this critical problem. First, we demonstrate that data augmentation is unable to fix the generalization problem. Second, we argue a more robust passage encoder helps facilitate better question adaptation using specialized question encoders. We hope our work can shed light on the challenges in creating a robust, universal dense retriever that works well across different input distributions.
"Hello, It's Me": Deep Learning-based Speech Synthesis Attacks in the Real World

Advances in deep learning have introduced a new wave of voice synthesis tools, capable of producing audio that sounds as if spoken by a target speaker. If successful, such tools in the wrong hands will enable a range of powerful attacks against both humans and software systems (aka machines). This paper documents efforts and findings from a comprehensive experimental study on the impact of deep-learning based speech synthesis attacks on both human listeners and machines such as speaker recognition and voice-signin systems. We find that both humans and machines can be reliably fooled by synthetic speech, and that existing defenses against synthesized speech fall short. These findings highlight the need to raise awareness and develop new protections against synthetic speech for both humans and machines.
A binary paradigm for robotic manipulators

Traditionally, kinematics and motion planning paradigms have addressed robots with continuous range-of-motion actuators (e.g. motors, hydraulic cylinders, etc.). Unlike motors, binary actuators have only two discrete states, both of which are stable. As a result, binary manipulators (i.e. those which are actuated with binary actuators) have a finite number of states. Major benefits of binary actuation are that extensive feedback control is not required, task repeatability can be very high, and two-state actuators are generally very inexpensive (e.g. solenoids, pneumatic cylinders, etc.), thus resulting in low cost robots. This paper presents a new paradigm in robotics based on binary actuation, and develops algorithms for the optimal design of binary manipulators for pick-and-place tasks. >
Long-Term Physical Health Consequences of Adverse Childhood Experiences

This study examined associations between adverse childhood family experiences and adult physical health using data from 52,250 US adults aged 18-64 from the 2009-2012 Behavioral Risk Factor Surveillance System (BRFSS). We found that experiencing childhood physical, verbal, or sexual abuse, witnessing parental domestic violence, experiencing parental divorce, and living with someone who was depressed, abused drugs or alcohol, or who had been incarcerated were associated with one or more of the following health outcomes: self-rated health, functional limitations, diabetes, and heart attack. Adult socioeconomic status and poor mental health and health behaviors significantly mediated several of these associations. The results of this study highlight the importance of family-based adverse childhood experiences on adult health outcomes and suggest that adult SES and stress-related coping behaviors may be crucial links between trauma in the childhood home and adult health.
Chapter 3 - Defects in Bulk GaN and Homoepitaxial Layers

This chapter discusses defects in bulk gallium nitride (GaN) and homoepitaxial layers. The chapter characterizes plate-like bulk crystals using transmission electron microscopy (TEM) and X-ray diffraction (XRD). The chapter compares the results of cathode luminescence (CL) and TEM studies using the same samples. It describes two types of crystals: (1) grown in 8-mm diameter crucibles and (2) grown in 16-mm diameter crucibles. Crystal polarity is determined using convergent beam electron diffraction (CBED), where a convergent beam is focused on the sample with a beam spot size of 1–2 nm instead of a parallel electron beam. The crystals grown in the larger crucible have better quality than those grown in the smaller one. These crystals are transparent. The chapter characterizes particular types of defects present in these plate-like crystals and discusses the relevance of these defects using these crystals as substrates for homoepitaxial growth.
δT / T and neutrino masses in SU (5)

Abstract We implement inflation in a supersymmetric SU ( 5 ) model with U ( 1 ) R-symmetry such that the cosmic microwave anisotropy δ T / T is proportional to ( M / M Planck ) 2 , where M ∼ M GUT = 2 – 3 × 10 16 GeV , the SU ( 5 ) breaking scale, and M Planck = 2.4 × 10 19 GeV . The presence of a global U ( 1 ) X symmetry, spontaneously broken also at scale M GUT , provides an upper bound M GUT 2 / M Planck ∼ 10 14 GeV on the masses of SU ( 5 ) singlet right-handed neutrinos, which explains the mass scale associated with atmospheric neutrino oscillations. The SU ( 5 ) monopoles and U ( 1 ) X cosmic strings are inflated away. Although the doublet–triplet splitting requires fine-tuning, the MSSM μ problem is resolved and dimension five proton decay is strongly suppressed.
Sample Size, Mean, Standard Deviation, and Standard Error of the Mean

This chapter deals with how you can use Excel to find the average (i.e., “mean”) of a set of scores, the standard deviation of these scores (STDEV), and the standard error of the mean (s.e.) of these scores. All three of these statistics are basic to the study of statistics and are used frequently within many additional statistical tests. The formulas are presented, explained, and a practical example is given for each formula that shows how the formula can be applied using a calculator. Then, the steps needed to compute these formulas using Excel commands are explained so that you can practice using Excel to use these formulas correctly. You will also learn how to use Fill/Series commands, how to change the width of a column, how to center information in a group of cells, how to give a “name” to a group of cells, how to find the sample size for a data set, how to format numbers with a specific number of decimal places, how to save an Excel worksheet into your computer, and how to print out an Excel worksheet. Three practice problems are given at the end of the chapter to test your Excel skills, and the answers to these problems appear in Appendix A of this book. An additional practice problem is presented in the Practice Test given in Appendix B along with its answer in Appendix C of this book.
Let there be bioluminescence: development of a biophotonic imaging platform for in situ analyses of oral biofilms in animal models

In the current study, we describe a novel biophotonic imaging-based reporter system that is particularly useful for the study of virulence in polymicrobial infections and interspecies interactions within animal models. A suite of luciferase enzymes was compared using three early colonizing species of the human oral flora (Streptococcus mutans, Streptococcus gordonii and Streptococcus sanguinis) to determine the utility of the different reporters for multiplexed imaging studies in vivo. Using the multiplex approach, we were able to track individual species within a dual-species oral infection model in mice with both temporal and spatial resolution. We also demonstrate how biophotonic imaging of multiplexed luciferase reporters could be adapted for real-time quantification of bacterial gene expression in situ. By creating an inducible dual-luciferase expressing reporter strain of S. mutans, we were able to exogenously control and measure expression of nlmAB (encoding the bacteriocin mutacin IV) within mice to assess its importance for the persistence ability of S. mutans in the oral cavity. The imaging system described in the current study circumvents many of the inherent limitations of current animal model systems, which should now make it feasible to test hypotheses that were previously impractical to model.
Efficient convolution algorithm for VLIW media processors

Convolution is widely used as an effective tool for enhancing image features, such as points, lines, or edges, and smoothing noise. One major challenge in implementing convolution in real time has been its large computational requirement. For example, convolving a 512 X 512 image with a 7 X 7 kernel requires 50 million operations. Therefore, to achieve the computational performance needed in real-time applications, hardwired solutions with ASICs and/or fixed-function chips with little programmability have been used. The disadvantages associated with hardwired implementations are that they are rigid, unifunctional and not upgradable. Our approach has been programmable convolution, which is flexible, multi-functional, easily upgradable and has a performance comparable to the hardwired implementations. This paper describes an efficient algorithm for convolution, which can be implemented in software on the new generation of VLIW mediaprocessors. These processors can perform multiple multiplication, addition and load/store operations in a single instruction, which can be used effectively in convolution to reduce the execution time. We have implemented this algorithm on a new mediaprocessor called the MAP1000TM where it takes 8.6 ms for the convolution of a 512 X 512 image with a 7 X 7 kernel. This performance is 7 times faster than the previously reported software-based convolution on the Texas Instruments TMS320C80 mediaprocessor and is comparable with the hardwired implementations for the same image and kernel size. This algorithm and its implementation on the next- generation programmable mediaprocessor clearly demonstrate the feasibility of software-based convolution.© (1998) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Fine-Scale Patchiness in Fuel Load Can Influence Initial Post-Fire Understory Composition in a Mixed Conifer Forest, Sequoia National Park, California

ABSTRACT: Many forests, including the mixed-conifer forest of the Sierra Nevada, California, historically experienced a fire regime that generated considerable within- and among-fire environmental variability. Fire suppression has resulted in a heavier, more continuous fuel bed, which can cause today's prescribed fires to be considerably more homogeneous. To evaluate the potential importance of variability in fire severity on post-fire plant communities, I conducted an experiment to test whether understory species respond differently to sites burned under a heavy fuel load versus sites that burned under a light fuel load. Woody fuel was added or removed from small forest plots in order to manipulate the fire severity during prescribed fire. The fuel load manipulations affected which species survived fire as well as which species germinated after fire. Seven species (Chimaphila menziesii, Chrysolepis sempervirens, Osmorhiza chilensis, Pyrola picta, Phacelia hydrophylloides, Rubus parviflorus, and Smilacina...
Visibility, mass concentration and power use in urban environments

Abstract A simple statistical model is used to account for energy and economic costs incurred by additional artificial illumination in urban environments caused by pollutant aerosols. The method of calculation, using the prevailing visibility as a measure of diminished natural illumination, suggests that as much as 1.0 per cent of our electrical energy may be consumed due to this pollution factor.
The Painted Jester: Notes on the Visual Arts in Hitchcock's Films

The overt and subtle references to art and artistry in Alfred Hitchcock's films embody further evidence, if any more needs to be added to the already superabundant body, of the versatile genius of cinema's Master of Suspense. Artworks with plot import that appear in Blackmail (1929), Spellbound (1946), The Paradine Case (1947), I Confess (1952), The Trouble with Harry (1955), Topaz (1969), and other famous and often unheralded Hitchcock movies reveal a sensitivity to the visual arts that richly complement the director's signature concerns for mistaken identity, ambiguous morality, romantic drama, and objects-as-subjects. References to Michelangelo's The Pieta in Topaz, Dali's surrealism in Spellbound, abstract expressionism in The Trouble with Harry, and the female gaze of Manet's Olympia in Blackmail make analysis of the impact of art and artistry in Hitchcock's films welcome fodder for novices and aficionados alike.
Infectious complications after cardiac surgery: lack of association with fresh frozen plasma or platelet transfusions.

Objective: The purpose of this study was to examine the effect of perioperative transfusion of platelets and fresh frozen plasma (FFP) on infection rates after cardiac surgery. Design: Retrospective study comparing infection rates after cardiac surgery among patients receiving combinations of packed red blood cells (PRBCs), platelets, and FFP. Setting: Tertiary care university teaching hospital. Participants: All elective primary coronary artery bypass (CABG) surgery patients from July 1995 to January 1998 before introduction of leukocyte-reduced blood products. Interventions: Multivariate logistic and linear regression models were applied to identify clinical risk factors for postoperative infection and to determine the relationship between perioperative administration of PRBCs, platelets, and FFP with postoperative infection. Measurements and Main Results: Transfusion of PRBCs, diabetes, age, preoperative hematocrit, and the duration of cardiopulmonary bypass were significantly associated with postoperative infection; platelet or FFP transfusion added no additional risk to PRBC transfusion alone. Conclusions: Infectious complications in a population of adult primary CABG surgery patients were not increased by transfusion of platelets or FFP. It is PRBC transfusion that confers an increased risk of postoperative infection in this population.
Cancer Imaging and Thermal Therapy Facilitated by Nanoparticles and Multiphoton Microscopy

Despite use of currently available technologies, cancer remains one of the leading causes of death worldwide. Gold-based nanoparticles that strongly absorb near-infrared light, such as nanoshells and nanorods, have shown potential as both diagnostic and therapeutic agents for cancer management (1–3). In this work we explored the use of gold-gold sulfide nanoparticles (mean diameter = 37 nm) with peak plasmon resonance at 800 nm for combined imaging and therapy of breast cancer. Upon excitation with a pulsed laser, these particles exhibit two-photon induced luminescence which may be used to image cancer cells. In addition, by increasing the power output of the laser, cancer cells can be thermally ablated as the gold-gold sulfide nanoparticles convert the light energy into heat.Copyright © 2010 by ASME
Topographic Waves in Lake Ontario

Abstract Properties of a topographic wave are calculated for an idealized shore zone model simulating the north shore of Lake Ontario. Observations at the Oshawa “coastal chain” taken during the International Field Year on the Great Lakes are then scrutinized, concentrating on three flow-reversal episodes involving deep, barotropic currents. It is shown that the observed phenomena have characteristics very similar to those of the idealized topographic wave. A legitimate interpretation of the observed 12–16 day periodicities in longshore flow within the coastal zone of Lake Ontario is that they are caused by a combination of internal Kelvin waves and topographic waves. Although the speeds of these two kinds of vorticity waves are very similar in Lake Ontario, a careful consideration of the evidence clearly shows phase separation, particularly so late in the season when reduced density differences lead to a slowing down of internal Kelvin waves.
Issues facing clinical trials of the future.

Abstract. Califf RM (Duke University Medical Center, Durham, NC, USA). Issues facing clinical trials of the future (Clinical Trials). J Intern Med 2003; 254: 426–433. Diagnostic and therapeutic technology continues to advance rapidly, as does our knowledge of therapeutics and of clinical research methods. Unfortunately, these advances have been only poorly coupled with our knowledge of therapeutic principles, leading to increasing uncertainty about which technologies are truly effective and, amongst those that are effective, which are most effective for the cost. This article presents general principles derived from several investigators’ experiences with clinical trials, and uses them to suggest how future clinical trials may differ from current approaches. A proposed organization for future trials also is elucidated.
Bettor preferences and market efficiency in football totals markets

The betting markets for totals in college football and arena football provide additional evidence of bettor preference for scoring. The results for college football and arena football markets are similar to those found in the professional football and professional basketball totals market. In all of these leagues, the overs are overbet. We suggest that there is a clear preference for bettors to bet the over and the extent of the bias depends upon the volume of uninformed bettors to informed bettors and limits placed on bets in these markets.
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

Current methods for detecting mutations in Fanconi anemia (FA)–suspected patients are inefficient and often miss mutations. We have applied recent advances in DNA sequencing and genomic capture to the diagnosis of FA. Specifically, we used custom molecular inversion probes or TruSeq-enrichment oligos to capture and sequence FA and related genes, including introns, from 27 samples from the International Fanconi Anemia Registry at The Rockefeller University. DNA sequencing was complemented with custom array comparative genomic hybridization (aCGH) and RNA sequencing (RNA-seq) analysis. aCGH identified deletions/duplications in 4 different FA genes. RNA-seq analysis revealed lack of allele specific expression associated with a deletion and splicing defects caused by missense, synonymous, and deep-in-intron variants. The combination of TruSeq-targeted capture, aCGH, and RNA-seq enabled us to identify the complementation group and biallelic germline mutations in all 27 families: FANCA (7), FANCB (3), FANCC (3), FANCD1 (1), FANCD2 (3), FANCF (2), FANCG (2), FANCI (1), FANCJ (2), and FANCL (3). FANCC mutations are often the cause of FA in patients of Ashkenazi Jewish (AJ) ancestry, and we identified 2 novel FANCC mutations in 2 patients of AJ ancestry. We describe here a strategy for efficient molecular diagnosis of FA.
Temporal patterning of sexual behavior in the female rat.

The purpose of the present study was to investigate the temporal patterning of sexual behavior over a multiple-ejaculatory series in naturally estrous and induced-estrous female rats. Copulatory behavior was observed in a situation which allowed the female free access to and escape from a restricted male. Animals were tested for three to five ejaculations. The results indicate that the behavior is episodic and periodic. The behavior of the female is influenced by the behavior the male exhibits during and after an ejaculatory series. Further, successive ejaculations by the male alter the female's behavior in a manner which appears to indicate a decline in receptivity. The behavior of the male is likewise influenced by the female. These results lead to the conclusion that the observed sequence of copulatory events in the rodent is an interaction of the behavior of the male and the female.