cssi/SciSciGPT-SciSciNet huggingface dataset:
The Total Synthesis of Hyperforin

Hyperforin has remained a popular and challenging synthetic target since its isolation over forty years ago. As a result, numerous synthetic strategies and ring-forming reactions have been developed to address its formidable molecular architecture. Herein we describe our contributions to this area resulting in a ten-step synthetic pathway enabled by a novel diketene annulation reaction and oxidative ring expansion strategy.
Microbial Flora and Antibiotic Resistance in Peritonsillar Abscesses in Upstate New York.

Objectives To identify the common bacteria in recent peritonsillar abscesses and the prevalence of antibiotic resistance and compare both between adults and children. Methods This is a retrospective chart review at a single academic institution of patients who underwent either incision and drainage or tonsillectomy for a peritonsillar abscess between 2002 and 2012 (n=69). Medical records were reviewed for cultures, comorbidities, and drainage procedures. Results Cultures obtained from 62.32% of peritonsillar abscesses were polymicrobial, and 34.78% were monomicrobial. The most common pathogens were β-hemolytic Streptococcus (31.88%), α-hemolytic Streptococcus (21.74%), Neisseria (14.49%), and Streptococcus milleri (13.04%). Group A β-hemolytic streptococcus was more common in children and Streptococcus milleri was more common in adults. Alpha-hemolytic streptococcus was resistant to clindamycin (6.67%) and erythromycin (6.67%). Streptococcus milleri was resistant to clindamycin (11.11%) and erythromycin (11.11%). Staphylococcus was resistant to penicillin (37.5%), oxacillin (25%), erythromycin (25%), and clindamycin (12.5%). Conclusions β- and α-hemolytic Streptococci, Neisseria, and Streptococcus milleri are the most common pathogens. Streptococcus milleri is more common in adults, and β-hemolytic streptococcus is more common in children. Resistance to clindamycin and erythromycin is common in Streptococci and Staphylococci, and penicillin resistance is common in Staphylococci.
Highly Stereoselective Synthesis of Terminal Chloro-Substituted Propargylamines and Further Functionalization.

The highly stereoselective addition of lithiated chloroacetylene, derived in situ from cis-1,2-dichloroethene and methyl lithium, to Ellman chiral N-tert-butanesulfinyl imines is reported. The reaction proceeds in high yield (up to 98%) and with excellent diastereoselectivity (up to >20:1) for a variety of aryl, heteroaromatic, alkyl, and α,β-unsaturated imine substrates. Transformations of the terminal chloro-substituted propargylamine products are described in which lithium–halogen exchange yields nucleophilic acetylides that can be quenched to yield terminal alkynes or intercepted by carbon electrophiles.
The Changing Landscape of Accrual Accounting

A fundamental property of accrual accounting is to smooth temporary timing fluctuations in operating cash flows, indicating an inherent negative correlation between accruals and cash flows. We show that the overall correlation between accruals and cash flows has dramatically declined in magnitude over the past half century and has largely disappeared in more recent years. The adjusted R 2 from regressing (changes in) accruals on (changes in) cash flows drops from about 70% (90%) in the 1960s to near zero (under 20%) in more recent years. In exploring potential reasons for the observed attenuation, we find that increases in non-timing-related accrual recognition, as proxied by one-time and nonoperating items and the frequency of loss firm-years, explain the majority of the overall decline. On the other hand, temporal changes in the matching between revenues and expenses, and the growth of intangible-intensive industries play only a limited role in explaining the observed attenuation. Finally, the relative decline of the timing role of accruals does not appear to be associated with an increase in the asymmetrically timely loss recognition role.
State-dependent divergences in the entanglement entropy

We show the entanglement entropy in certain quantum field theories to contain state-dependent divergences. Both perturbative and holographic examples are exhibited. However, quantities such as the relative entropy and the generalized entropy of black holes remain finite, due to cancellation of divergences. We classify all possible state-dependent entanglement entropy divergences that can appear in both perturbatively renormalizeable and holographic covariant d ≤ 6 quantum field theories.
Systems and software assurance — A model Cyber Security course

In this paper we present a model Cyber Security course primarily designed to address the educational and training needs for developing secure software intensive systems. The course is designed, within a Computer Science curriculum, to satisfy the national requirements of the Information Assurance Workforce Improvement Program (per DoD8570.01-Mfrom 11.10.2015), for Tiers II and III jobs, primarily in the Systems Architecture and Engineering (IASAE) specialty areas. The course maps to the knowledge bases of two approved Certifications for IASAE, namely the Certified Security Software Lifecycle Professional (CSSLP) and the Certified Information Security Engineering Professional (ISSEP). The course content is focused on four key elements: Security Architecture Analysis with Treat Modeling, Risk Assessment based on the Cyber Security Framework (and the NIST SP 800 series of guidelines), Secure Development Life Cycle under a process improvement framework CMMI, and a standardized set of Secure Coding best practices. At the graduate level, this course also addresses the making of formal Assurance Cases for Security and Safety of Software Intensive Systems, as well as Software Failure Mode Effect Analysis (FMEA).
Idiopathic hypercalciuria and formation of calcium renal stones.

The most common presentation of nephrolithiasis is idiopathic calcium stones in patients without systemic disease. Most stones are primarily composed of calcium oxalate and form on a base of interstitial apatite deposits, known as Randall's plaque. By contrast some stones are composed largely of calcium phosphate, as either hydroxyapatite or brushite (calcium monohydrogen phosphate), and are usually accompanied by deposits of calcium phosphate in the Bellini ducts. These deposits result in local tissue damage and might serve as a site of mineral overgrowth. Stone formation is driven by supersaturation of urine with calcium oxalate and brushite. The level of supersaturation is related to fluid intake as well as to the levels of urinary citrate and calcium. Risk of stone formation is increased when urine citrate excretion is 200 mg per day also increase stone risk and often result in negative calcium balance. Reduced renal calcium reabsorption has a role in idiopathic hypercalciuria. Low sodium diets and thiazide-type diuretics lower urine calcium levels and potentially reduce the risk of stone recurrence and bone disease.
Factors Related to Early Termination From Work for Youth With Disabilities

This study of young adults with disabilities in transition explored what factors contributed to young adults with disabilities terminating early from a transition program. Data from 6,227 young adults with disabilities aged 17–22 living in one of eight major metropolitan areas in the United States were utilised (58.7% of the sample were male, 63.1% were African-American, and 71.4% had a learning disability). All participants were enrolled in a school-to-work transition programme in which service providers place students into paid internships. Service providers at the eight sites collected data while working with participants, and then collected follow-up data at three and twelve months post-programme completion or termination. Hierarchical Linear Modelling was used to explore how personal factors impacted early termination, while controlling for variation at the site level. Results showed the three main reasons for early termination from work to be: programme initiated termination, interpersonal conflicts with coworkers or supervisors and transportation issues. Additionally, the multilevel model that controlled for variance at the site level demonstrated that Asian-American young adults with disabilities were less likely to terminate early from work. These results can help individuals who work with young adults with disabilities, provide supplemental services to students who may need additional assistance to succeed in a transition programme.
INITIAL DEVELOPMENT AND VALIDATION OF THE BULLYHARM: THE BULLYING, HARASSMENT, AND AGGRESSION RECEIPT MEASURE

This article describes the development and preliminary validation of the Bullying, Harassment, and Aggression Receipt Measure (BullyHARM). The development of the BullyHARM involved a number of steps and methods, including a literature review, expert review, cognitive testing, readability testing, data collection from a large sample, reliability testing, and confirmatory factor analysis. A sample of 275 middle school students was used to examine the psychometric properties and factor structure of the BullyHARM, which consists of 22 items and 6 subscales: physical bullying, verbal bullying, social/relational bullying, cyber-bullying, property bullying, and sexual bullying. First-order and second-order factor models were evaluated. Results demonstrate that the first-order factor model had superior fit. Results of reliability testing indicate that the BullyHARM scale and subscales have very good internal consistency reliability. Findings indicate that the BullyHARM has good properties regarding content validation and respondent-related validation and is a promising instrument for measuring bullying victimization in school.
Modeling anisotropic plasticity : Eulerian hydrocode applications of high strain-rate deformation processes

Previously developed constitutive models and solution algorithms for anisotropic elastoplastic material strength are implemented in the two-dimensional MESA hydrodynamics code. Quadratic yield functions fitted from polycrystal simulations for a metallic hexagonal-close-packed structure are utilized. An associative flow strength formulation incorporating these yield functions is solved using a geometric normal return method. A stretching rod problem is selected to investigate the effects of material anisotropy on a tensile plastic instability (necking). The rod necking rate and topology are compared for MESA simulations performed for both isotropic and anisotropic cases utilizing the Mechanical Threshold Stress flow stress model.
Disparate use of exclusionary discipline: Evidence on inequities in school discipline from a U.S. state

There is much discussion in the United States about exclusionary discipline (suspensions and expulsions) in schools. According to a 2014 report from the U.S. Department of Education’s Office for Civil Rights, Black students represent 15% of students, but 44% of students suspended more than once and 36% of expelled students. This analysis uses seven years of individual infraction-level data from public schools in Arkansas. We find that marginalized students are more likely to receive exclusionary discipline, even after controlling for the nature and number of disciplinary referrals, but that most of the differences occur across rather than within schools. Across the state, black students are about 2.4 times as likely to receive exclusionary discipline (conditional on reported infractions and other student characteristics) whereas within school, this same conditional disparity is not statistically significant. Within schools, the disproportionalities in exclusionary discipline are driven primarily by non-race factors such as free- and reduced-price lunch (FRL) eligibility and special education status. We find, not surprisingly, that schools with larger proportions of non-White students tend to give out longer punishments, regardless of school income levels, measured by FRL rates. Combined, these results appear to indicate multiple tiers of disadvantage: race drives most of the disparities across schools, whereas within schools, FRL or special education status may matter more.
C-band swept wavelength erbium-doped fiber laser with a high-Q tunable interior-ridge silicon microring cavity

We demonstrate an erbium-doped fiber laser with a tunable silicon microring cavity. We measured a narrow laser linewidth (16 kHz) and single-mode continuous-wave emission over the C-band (1530nm-to-1560nm) at a swept-wavelength rate of 22,600nm/s or 3106THz/s.
Digital Signal Processing: Road to the Future

Summary form only given. The field of digital signal processing (DSP) has been a very active area of research and application for more than 3 decades. This broad development has paralleled in time the rapid development of high speed electronic digital computers, microelectronics, and integrated circuit fabrication technologies. An ever-increasing assortment of integrated circuits specifically tailored to perform common DSP functions is available to the design engineer as system building blocks or parts-in-trade. DSP methodologies have been applied to consumer electronics, communications, automotive electronics, instrumentation, medical electronics, tomography and acoustic imaging, cartography, seismology, speech recognition, robotics etc. In this talk we first provide a brief overview of the initial developments in DSP, followed by a review of some of the important advances made during the thirty year period of its growth, and describe a number of key applications. We conclude with a speculation on the future trends and directions
UPPER TIBIAL OSTEOTOMY: STILL A ROLE IN 2013?

The biomechanical rationale for osteotomy and the pathogenesis of degenerative arthrosis accompanying malalignment has been delineated well. Malalignment of the limb results in added stress on damaged articular cartilage and causes further loss of articular cartilage that subsequently exacerbates the limb malalignment. A downward spiral of progressive deformity and additional loss of articular cartilage occurs over time. Osteotomy can be used to realign the limb, reduce stress on the articular cartilage at risk and share the load with the opposite compartment of the knee. In appropriately selected patients osteotomy is a reliable operation to improve pain and function. Over the past two decades osteotomy has been viewed largely as a temporising measure to buy time for patients before they ultimately have a total knee arthroplasty. In this role, osteotomy has largely been accepted as successful. Substantial improvements in pain and function have been documented and seem to hold up well over a 7 to 10 year period after the osteotomy. Medial opening wedge osteotomy has recently gained in popularity in the United States after a long period of use in Europe. Potential advantages of the medial opening wedge technique include the ability to easily adjust the degree of correction intraoperatively, the ability to correct deformities in the sagittal plane as well as the coronal plane, the need to make only one bone cut, and avoiding the tibiofibular joint. The downsides of the opening wedge technique include the need for bone graft to fill the created defect, a potentially higher rate of non-union or delayed union, and a longer period of restricted weight bearing after the procedure.
Measurement of Differentially Methylated INS DNA Species in Human Serum Samples as a Biomarker of Islet β Cell Death

The death of islet β cells is thought to underlie the pathogenesis of virtually all forms of diabetes and to precede the development of frank hyperglycemia, especially in type 1 diabetes. The development of sensitive and reliable biomarkers of β cell death may allow for early therapeutic intervention to prevent or delay the development of diabetes. Recently, several groups including our own have reported that cell-free, differentially methylated DNA encoding preproinsulin (INS) in the circulation is correlated to β cell death in pre-type 1 diabetes and new-onset type 1 diabetes. Here, we present a step-by-step protocol using digital PCR for the measurement of cell-free INS DNA that is differentially methylated at cytosine at position -69 bp (relative to the transcriptional start site). We demonstrate that the assay can distinguish between methylated and unmethylated cytosine at position -69 bp, is linear across several orders of magnitude, provides absolute quantitation of DNA copy numbers, and can be applied to samples of human serum from individuals with new-onset type 1 diabetes and disease-free controls. The protocol described here can be adapted to any DNA species for which detection of differentially methylated cytosines is desired, whether from circulation or from isolated cells and tissues, and can provide absolute quantitation of DNA fragments.
High-power C-band backward-wave crossed-field amplifier

A C-band, backward wave, crossed field amplifier for use in a new multi-stage pulsed radar transmitter has recently been developed. This tube, the QKS1343, features high average power capability together with small size, light weight, and high efficiency. It is rated at 1.5 megawatts peak and 15 kilowatts average power output at 100 microseconds pulse duration. Nominal operating efficiency of 60% is achieved over the frequency band 5.4 to 5.9 GHz. Models have been built and delivered for field use and evaluation.
Imitating driver behavior with generative adversarial networks

The ability to accurately predict and simulate human driving behavior is critical for the development of intelligent transportation systems. Traditional modeling methods have employed simple parametric models and behavioral cloning. This paper adopts a method for overcoming the problem of cascading errors inherent in prior approaches, resulting in realistic behavior that is robust to trajectory perturbations. We extend Generative Adversarial Imitation Learning to the training of recurrent policies, and we demonstrate that our model rivals rule-based controllers and maximum likelihood models in realistic highway simulations. Our model both reproduces emergent behavior of human drivers, such as lane change rate, while maintaining realistic control over long time horizons.
Effects of estrogens on uterine poly (A) -rich RNA

Abstract The working hypothesis that steroid hormones are transferred into the nucleus of the target cells in combination with a protein receptor and there alter the transcription of one or more portions of the genome is supported by experimental data from many laboratories. There are difficulties in identifying and measuring the immediate product of the transcription process, mRNA, and none of the several criteria used to distinguish messenger from ribosomal and transfer RNA has been completely satisfactory. The messenger RNA's of eukaryotic cells appear to contain a covalently linked region of 100 or more nucleotides rich in polyriboadenylic acid linked to the mRNA at the 3'-OH end. The injection of estradiol into an adult castrate rat increases the total amount of uterine poly (A) -rich RNA and the effectiveness of this material in inducing enzyme synthesis when instilled into the uterine lumen. RNA extracted from the uterus of an estrogen treated rat and instilled into the uterine lumen of an immature rat increases protein synthesis and the activities of glucose-6-phosphate dehydrogenase and ornithine decarboxylase. The effective RNA, a very small fraction of the total, is separable from the mass of RNA by chromatography on a sepharose 4B polyuridylic acid column. This suggests that the RNA effective when instilled in utero has a polyadenylic acid portion and may be a messenger RNA. The RNA not bound to poly U sepharose is without effect in stimulating protein synthesis or in increasing the activity of G-6-PDH or ODC when instilled in utero.
Local thermometry of self-heated nanoscale devices

Hot spots with dimensions of only a few nanometers form in numerous nanoelectronic devices. Based on recent advances in spatial resolution, these hotspots can now be studied by means of Scanning Thermal Microscopy (SThM). Here, we discuss SThM for nanoscale thermometry in comparison with other established thermometry techniques. In situ measurements of semiconductor channels for logic, and phase change memory devices are used to demonstrate today's measurement capabilities. Temperature fields characterize not only energy dissipation in in-tact devices but can also serve to identify device failure and fabrication issues.
Chapter 2 – Basic Sockets

Publisher Summary This chapter explores basic sockets. It demonstrates how Java applications identify network hosts using the InetAddress –Address . InetAddress abstraction represents a network destination, encapsulating both names and numerical address information. The class has two subclasses, Inet4Address and Inet6Address, representing the two versions in use. Instances of InetAddress are immutable: once created, each one always refers to the same address. further presents examples of the use of , through an example client and server that use TCP, and also the –Socket for clients and servers that use UDP. For each abstraction, it lists the most significant methods, grouped according to usage, and briefly describe their behavior. It demonstrates the use of InetAddress with an example program that first prints out all the addresses associated with the local host, and then prints the names and addresses associated with each host specified on the command line. each Java networking class described in it, it includes only the most important and commonly used methods, omitting those that are deprecated or beyond the use of the target audience of the study.
Classification of Curves in 2D and 3D via Affine Integral Signatures

We propose new robust classification algorithms for planar and spatial curves subjected to affine transformations. Our motivation comes from the problems in computer image recognition. To each planar or spatial curve, we assign a planar signature curve. Curves, equivalent under an affine transformation, have the same signature. The signatures are based on integral invariants, which are significantly less sensitive to small perturbations of curves and noise than classically known differential invariants. Affine invariants are derived in terms of Euclidean invariants. We present two types of signatures: the global and the local signature. Both signatures are independent of curve parameterization. The global signature depends on a choice of the initial point and, therefore, cannot be used for local comparison. The local signature, albeit being slightly more sensitive to noise, is independent of the choice of the initial point and can be used to solve local equivalence problem. An experiment that illustrates robustness of the proposed signatures is presented.
Long-time stability of large-amplitude noncharacteristic boundary layers for hyperbolic-parabolic systems

Abstract Extending investigations of Yarahmadian and Zumbrun in the strictly parabolic case, we study time-asymptotic stability of arbitrary (possibly large) amplitude noncharacteristic boundary layers of a class of hyperbolic–parabolic systems including the Navier–Stokes equations of compressible gas, and magnetohydrodynamics with inflow or outflow boundary conditions, establishing that linear and nonlinear stability are both equivalent to an Evans function, or generalized spectral stability, condition. The latter is readily checkable numerically, and analytically verifiable in certain favorable cases; in particular, it has been shown by Costanzino, Humpherys, Nguyen, and Zumbrun to hold for sufficiently large-amplitude layers for isentropic ideal gas dynamics, with general adiabiatic index γ ⩾ 1 . Together with these previous results, our results thus give nonlinear stability of large-amplitude isentropic boundary layers, the first such result for compressive (“shock-type”) layers in other than the nearly-constant case. The analysis, as in the strictly parabolic case, proceeds by derivation of detailed pointwise Green function bounds, with substantial new technical difficulties associated with the more singular, hyperbolic behavior in the high-frequency/short time regime.
A finite difference approach to the infinity Laplace equation and tug-of-war games

We present a modified version of the two-player "tug-of-war" game introduced by Peres, Schramm, Sheffield, and Wilson. This new tug-of-war game is identical to the original except near the boundary of the domain $\partial \Omega$, but its associated value functions are more regular. The dynamic programming principle implies that the value functions satisfy a certain finite difference equation. By studying this difference equation directly and adapting techniques from viscosity solution theory, we prove a number of new results. We show that the finite difference equation has unique maximal and minimal solutions, which are identified as the value functions for the two tug-of-war players. We demonstrate uniqueness, and hence the existence of a value for the game, in the case that the running payoff function is nonnegative. We also show that uniqueness holds in certain cases for sign-changing running payoff functions which are sufficiently small. In the limit $\epsilon \to 0$, we obtain the convergence of the value functions to a viscosity solution of the normalized infinity Laplace equation. We also obtain several new results for the normalized infinity Laplace equation $-\Delta_\infty u = f$. In particular, we demonstrate the existence of solutions to the Dirichlet problem for any bounded continuous $f$, and continuous boundary data, as well as the uniqueness of solutions to this problem in the generic case. We present a new elementary proof of uniqueness in the case that $f>0$, $f< 0$, or $f\equiv 0$. The stability of the solutions with respect to $f$ is also studied, and an explicit continuous dependence estimate from $f\equiv 0$ is obtained.
Peer Effects and Political Participation: What is the Role of Coursework Clusters?

This study addresses the role of peer civic engagement during adolescence on political participation in adulthood. We focus on novel specification based on an alternative peer group: the coursework cluster, which is constructed using an algorithm based on course taking habits. This paper explores how peers within course-taking clusters affect future political participation. The civic identities and politically oriented norms developed may be passed on through these classmates. Our results show that the influence of the peer group is from peers who perform better (have a higher grade point average) in social studies courses and from peers who participate in extracurricular activities.
NORMAL FINDINGS ON NONINVASIVE CARDIAC ASSESSMENT AND THE PREDICTION OF HEART FAILURE: THE MULTI-ETHNIC STUDY OF ATHEROSCLEROSIS (MESA)

Abstract Background It is unknown if normal findings on noninvasive cardiac assessment are able to identify individuals who are low risk for developing heart failure (HF). Methods We examined if normal findings on the routine electrocardiogram (ECG) and cardiac magnetic resonance imaging (MRI) were able to identify individuals who are low risk for developing HF in 4986 (mean age=62±10years; 52% women; 39% White; 13% Chinese-American; 26% Black; 22% Hispanic) participants from the Multi-Ethnic Study of Atherosclerosis who were free of clinically apparent HF at baseline. A normal ECG was defined as the absence of major abnormalities by Minnesota Code Classification, and a normal MRI was defined as absence of structural abnormalities and systolic dysfunction. Results There were 3988 (80%) participants with normal findings at baseline on both ECG and MRI, 894 (18%) who had either a normal ECG or normal MRI, and 104 (2%) who had abnormal findings on ECG and MRI. Over a median follow-up of 12.2years, 177 (3.6%) HF events occurred. Normal ECG (HR=0.41, 95%CI=0.29, 0.56) and MRI (HR=0.32, 95%CI=0.23, 0.45) were each associated with lower risk of HF compared with abnormal, and their combination was associated with a lower HF risk (HR=0.13, 95%CI=0.08, 0.21) than either in isolation. Conclusion Normal findings on noninvasive cardiac assessment identify individuals in whom the risk of HF is low. Further studies are needed to explore the utility of this low-risk profile in HF prevention strategies.
Mercury Levels in Human Hair and Farmed Fish near Artisanal and Small-Scale Gold Mining Communities in the Madre de Dios River Basin, Peru

Artisanal and small-scale gold mining (ASGM) has been an important source of income for communities in the Madre de Dios River Basin in Peru for hundreds of years. However, in recent decades, the scale of ASGM activities in the region has increased dramatically, and exposures to a variety of occupational and environmental hazards related to ASGM, including mercury, are becoming more widespread. The aims of our study were to: (1) examine patterns in the total hair mercury level of human participants in several communities in the region and compare these results to the 2.2 µg/g total hair mercury level equivalent to the World Health Organization (WHO) Expert Committee of Food Additives (JECFA)'s Provisional Tolerable Weekly Intake (PTWI); and (2), to measure the mercury levels of paco (Piaractus brachypomus) fish raised in local aquaculture ponds, in order to compare these levels to the EPA Fish Tissue Residue Criterion of 0.3 µg Hg/g fish (wet weight). We collected hair samples from 80 participants in four communities (one control and three where ASGM activities occurred) in the region, and collected 111 samples from fish raised in 24 local aquaculture farms. We then analyzed the samples for total mercury. Total mercury levels in hair were statistically significantly higher in the mining communities than in the control community, and increased with increasing geodesic distance from the Madre de Dios headwaters, did not differ by sex, and frequently exceeded the reference level. Regression analyses indicated that higher hair mercury levels were associated with residence in ASGM communities. The analysis of paco fish samples found no samples that exceeded the EPA tissue residue criterion. Collectively, these results align with other recent studies showing that ASGM activities are associated with elevated human mercury exposure. The fish farmed through the relatively new process of aquaculture in ASGM areas appeared to have little potential to contribute to human mercury exposure. More research is needed on human health risks associated with ASGM to discern occupational, residential, and nutritional exposure, especially through tracking temporal changes in mercury levels as fish ponds age, and assessing levels in different farmed fish species. Additionally, research is needed to definitively determine that elevated mercury levels in humans and fish result from the elemental mercury from mining, rather than from a different source, such as the mercury released from soil erosion during deforestation events from mining or other activities.
A LAGRANGIAN GAUSS-NEWTON-KRYLOV SOLVER FOR MASS- AND INTENSITY-PRESERVING DIFFEOMORPHIC IMAGE REGISTRATION.

We present an efficient solver for diffeomorphic image registration problems in the framework of large deformation diffeomorphic metric mapping (LDDMM). We use an optimal control formulation, in which the velocity field of a hyperbolic PDE needs to be found such that the distance between the final state of the system (the transformed/transported template image) and the observation (the reference image) is minimized. Our solver supports both stationary and nonstationary (i.e., transient or time-dependent) velocity fields. As transformation models, we consider both the transport equation (assuming intensities are preserved during the deformation) and the continuity equation (assuming masses are preserved). We consider the reduced form of the optimal control problem and solve the resulting unconstrained optimization problem using a discretize-then-optimize approach. A key contribution is the elimination of the PDE constraint using a Lagrangian hyperbolic PDE solver. Lagrangian methods rely on the concept of ...
Fluorescent protein tools for studying protein dynamics in living cells: A review

We have witnessed remarkable advances over the past decade in the application of optical techniques to visualize the genetically encoded fluorescent proteins (FPs) in living systems. The imaging of the FPs inside living cells has become an essential tool for studies of cell biology and physiology. FPs are now available that span the visible spectrum from deep blue to deep red, providing a wide choice of genetically encoded fluorescent markers. Furthermore, some FPs have been identified that have unusual characteristics that make them useful reporters of the dynamic behaviors of proteins inside cells. These additions to the FP toolbox are now being used for some very innovative live-cell imaging applications. Here, we will highlight the characteristics and uses of a few of these exceptional probes. Many different optical methods can be combined with the FPs from marine organisms to provide quantitative measurements in living systems.
Multi-style Generative Network for Real-Time Transfer

Despite the rapid progress in style transfer, existing approaches using feed-forward generative network for multi-style or arbitrary-style transfer are usually compromised of image quality and model flexibility. We find it is fundamentally difficult to achieve comprehensive style modeling using 1-dimensional style embedding. Motivated by this, we introduce CoMatch Layer that learns to match the second order feature statistics with the target styles. With the CoMatch Layer, we build a Multi-style Generative Network (MSG-Net), which achieves real-time performance. In addition, we employ an specific strategy of upsampled convolution which avoids checkerboard artifacts caused by fractionally-strided convolution. Our method has achieved superior image quality comparing to state-of-the-art approaches. The proposed MSG-Net as a general approach for real-time style transfer is compatible with most existing techniques including content-style interpolation, color-preserving, spatial control and brush stroke size control. MSG-Net is the first to achieve real-time brush-size control in a purely feed-forward manner for style transfer. Our implementations and pre-trained models for Torch, PyTorch and MXNet frameworks will be publicly available (Links can be found at http://hangzhang.org/).
Learning Two-Branch Neural Networks for Image-Text Matching Tasks

Image-language matching tasks have recently attracted a lot of attention in the computer vision field. These tasks include image-sentence matching, i.e., given an image query, retrieving relevant sentences and vice versa, and region-phrase matching or visual grounding, i.e., matching a phrase to relevant regions. This paper investigates two-branch neural networks for learning the similarity between these two data modalities. We propose two network structures that produce different output representations. The first one, referred to as an embedding network , learns an explicit shared latent embedding space with a maximum-margin ranking loss and novel neighborhood constraints. Compared to standard triplet sampling, we perform improved neighborhood sampling that takes neighborhood information into consideration while constructing mini-batches. The second network structure, referred to as a similarity network , fuses the two branches via element-wise product and is trained with regression loss to directly predict a similarity score. Extensive experiments show that our networks achieve high accuracies for phrase localization on the Flickr30K Entities dataset and for bi-directional image-sentence retrieval on Flickr30K and MSCOCO datasets.
A Low Cost, Simplified, and Scaleable Pneumotachograph and Face Mask for Neonatal Mouse Respiratory Measurements

Abstract Introduction Neonatal respiratory disorders are a leading cause of perinatal mortality due to complications resulting from premature births and prenatal exposure to drugs of abuse, but optimal treatments for these symptoms are still unclear due to a variety of confounds and risk factors. Mouse models present an opportunity to study the underlying mechanisms and efficacy of potential treatments of these conditions with controlled variables. However, measuring respiration in newborn mice is difficult and commercial components are expensive and often require modification, creating a barrier and limiting our understanding of the short and long-term effects of birth complications on respiratory function. Methods Here, we present an inexpensive and simple flow through pneumotachograph and face mask design that can be easily scaled for parallel, high-throughput assays measuring respiration in neonatal mouse pups. The final apparatus consists of three main parts: a water-jacketed chamber, an integrated support tray for the pup, and a pneumotachograph consisting of a two side-arm air channel that is attached to a pressure transducer. Results The pneumotach showed a linear response and clean, steady respiratory traces in which apneas and sighs were clearly visible. Administration of caffeine in P0.5 CD1 wildtype neonates resulted in an increase in tidal volume, minute ventilation, and minute ventilation normalized to oxygen consumption as well as a decrease in periodic instability. Discussion The described methods offer a relatively simple and inexpensive approach to constructing a pneumotachograph for non-invasive measurements of neonatal mouse respiration, enhancing accessibility and enabling the high-throughput and parallel characterizations of neonatal respiratory disorders and potential pharmacological therapies.
Finite element simulation and experimental validation of distortion and cracking failure phenomena in direct metal laser sintering fabricated component

Abstract A new one-way coupled thermal-mechanical finite element based model of direct metal laser sintering (DMLS) is developed to simulate the process, and predict distortion and cracking failure location in the fabricated components. The model takes into account the layer-by-layer additive manufacturing features, solidification and melting phenomena. The model is first validated using experimental data, then model is applied to a DMLS fabricated component. The study shows how the stress distribution at the support-solid interface is critical to contributing to cracking and distortion. During the DMLS process, thermal stress at the support-solid interface reaches its maximum during the printing process, particularly when the first solid layer is built above the support layer. This result suggests that cracking at the interface may occur during the printing process, which is consistent with experimental observation. Using a design parametric study, a thick and low-density porous layer is found to reduce residual stress and distortion in the built component. The developed finite element model can be used to future design and optimize DMLS process.
High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

The bacterial adaptive immune system CRISPR-Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing genetic loci. To analyze Cas9's ability to bind DNA rapidly and specifically, we generated multiple libraries of potential binding partners for measuring the kinetics of nuclease-dead Cas9 (dCas9) interactions. Using a massively parallel method to quantify protein-DNA interactions on a high-throughput sequencing flow cell, we comprehensively assess the effects of combinatorial mismatches between guide RNA (gRNA) and target nucleotides, both in the seed and in more distal nucleotides, plus disruption of the protospacer adjacent motif (PAM). We report two consequences of PAM-distal mismatches: reversal of dCas9 binding at long time scales, and synergistic changes in association kinetics when other gRNA-target mismatches are present. Together, these observations support a model for Cas9 specificity wherein gRNA-DNA mismatches at PAM-distal bases modulate different biophysical parameters that determine association and dissociation rates. The methods we present decouple aspects of kinetic and thermodynamic properties of the Cas9-DNA interaction and broaden the toolkit for investigating off-target binding behavior.
Where Are the r-modes? Chandra Observations of Millisecond Pulsars

We present the results of Chandra observations of two non-accreting millisecond pulsars, PSRs J1640+2224(J1640) and J1709+2313 (J1709), with low inferred magnetic fields and spin-down rates in order to constrain their surface temperatures, obtain limits on the amplitude of unstable r-modes in them, and make comparisons with similar limits obtained for a sample of accreting low-mass X-ray binary (LMXB) neutron stars. We detect both pulsars in the X-ray band for the first time. They are faint, with inferred soft X-ray fluxes(0.3-3 keV) of approx. 6 x 10(exp -15) and 3 x 10( exp -15) erg/sq cm for J1640 and J1709, respectively. Spectral analysis assuming hydrogen atmosphere emission gives global effective temperature upper limits (90% confidence) of 3.3-4.3 x 10(exp 5) K for J1640 and 3.6-4.7 x 10(exp 5) K for J1709, where the low end of the range corresponds to canonical neutron stars (M = 1.4 Stellar Mass), and the upper end corresponds to higher-mass stars (M = 2.21 Stellar Mass). Under the assumption that r-mode heating provides the thermal support, we obtain dimensionless r-mode amplitude upper limits of 3.2-4.8 x 10(exp -8) and 1.8-2.8 x 10(exp -7) for J1640 and J1709, respectively, where again the low end of the range corresponds to lower-mass, canonical neutron stars (M =1.4 Stellar Mass). These limits are about an order of magnitude lower than those we derived previously for a sample of LMXBs, except for the accreting millisecond X-ray pulsar SAX J1808.43658, which has a comparable amplitude limit to J1640 and J1709.
Update on infectious enterocolitides and the diseases that they MIMIC

The anatomical pathologist's ability to diagnose infections (including gastrointestinal infections) in tissue sections has improved greatly in recent years. With the increasing number and availability of new molecular assays and immunostains, pathologists’ understanding of the correlation between histological patterns of inflammation and specific organisms or groups of organisms has expanded, as has our understanding of how closely infections can mimic other frequently encountered diseases in gastrointestinal pathology (e.g., chronic idiopathic inflammatory bowel disease and ischaemia). Anatomical pathologists play a critical role in the diagnosis of gastrointestinal infections, as the examination of slides may provide a much more rapid result than microbiological cultures or other laboratory assays, and often cultures are not obtained before the patient is treated with antibiotics. This lecture will focus primarily on food and water-borne infectious enterocolitides, and how to distinguish them from other commonly encountered entities in gastrointestinal pathology.
Differential effects of the dynein-regulatory factor Lissencephaly-1 on processive dynein-dynactin motility

Cytoplasmic dynein is the primary minus-end-directed microtubule motor protein in animal cells, performing a wide range of motile activities, including transport of vesicular cargos, mRNAs, viruses, and proteins. Lissencephaly-1 (LIS1) is a highly conserved dynein-regulatory factor that binds directly to the dynein motor domain, uncoupling the enzymatic and mechanical cycles of the motor and stalling dynein on the microtubule track. Dynactin, another ubiquitous dynein-regulatory factor, releases dynein from an autoinhibited state, leading to a dramatic increase in fast, processive dynein motility. How these opposing activities are integrated to control dynein motility is unknown. Here, we used fluorescence single-molecule microscopy to study the interaction of LIS1 with the processive dynein-dynactin-BicD2N (DDB) complex. Surprisingly, in contrast to the prevailing model for LIS1 function established in the context of dynein alone, we found that binding of LIS1 to DDB does not strongly disrupt processive motility. Motile DDB complexes bound up to two LIS1 dimers, and mutational analysis suggested that LIS1 binds directly to the dynein motor domains during DDB movement. Interestingly, LIS1 enhanced DDB velocity in a concentration-dependent manner, in contrast to observations of the effect of LIS1 on the motility of isolated dynein. Thus, LIS1 exerts concentration-dependent effects on dynein motility and can synergize with dynactin to enhance processive dynein movement. Our results suggest that the effect of LIS1 on dynein motility depends on both LIS1 concentration and the presence of other regulatory factors such as dynactin and may provide new insights into the mechanism of LIS1 haploinsufficiency in the neurodevelopmental disorder lissencephaly.
Fatty Acid Availability Sets Cell Envelope Capacity and Dictates Microbial Cell Size.

Summary Nutrients—and by extension biosynthetic capacity—positively impact cell size in organisms throughout the tree of life. In bacteria, cell size is reduced 3-fold in response to nutrient starvation or accumulation of the alarmone ppGpp, a global inhibitor of biosynthesis. However, whether biosynthetic capacity as a whole determines cell size or whether particular anabolic pathways are more important than others remains an open question. Here we identify fatty acid synthesis as the primary biosynthetic determinant of Escherichia coli size and present evidence supporting a similar role for fatty acids as a positive determinant of size in the Gram-positive bacterium Bacillus subtilis and the single-celled eukaryote Saccharomyces cerevisiae. Altering fatty acid synthesis recapitulated the impact of altering nutrients on cell size and morphology, whereas defects in other biosynthetic pathways had either a negligible or fatty-acid-dependent effect on size. Together, our findings support a novel "outside-in" model in which fatty acid availability sets cell envelope capacity, which in turn dictates cell size. In the absence of ppGpp, limiting fatty acid synthesis leads to cell lysis, supporting a role for ppGpp as a linchpin linking expansion of cytoplasmic volume to the growth of the cell envelope to preserve cellular integrity.
Native defect compensation in III-antimonide bulk substrates

As-grown, undoped III-antimonide bulk substrates contain high concentration of native defects resulting in high residual carrier density. In this paper, we have demonstrated that native defects can be compensated in bulk substrates of GaSb, InSb, and Ga/sub 1-x/In/sub x/Sb via impurity doping and low temperature growth from nonstoichiometric melts and solutions. Decrease in residual carrier concentration up to one order of magnitude at 300 K and three orders of magnitude at 77 K have been achieved.
Fast Dynamic Simulation of Power Systems for Security Assessment

Abstract Current techniques for dynamic security assessment in power systems rely on direct methods. While they provide a useful screening tool, the operator needs fast simulation of the system dynamics on-line to select a wide range of operating options. In this paper we propose two approaches, one based on trajectory approximation and the other based on time scale separation in the system. Slow dynamics are separated from the fast dynamics to accelerate the simulation using the integral manifold approach. The final goal of the project is to make both techniques suitable for parallel processing. With the rapidly changing computer technology, it is not inconceivable that on-line dynamic simulation may become feasible just like on-line load flow.