gebhart/patrepeval huggingface dataset:
Superspreading Events Without Superspreaders: Using High Attack Rate Events to Estimate N º for Airborne Transmission of COVID-19 (2020)

Abstract We study transmission of COVID-19 using five well-documented case studies – a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. In all cases the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. An estimate of N 0 , the characteristic number of COVID-19 virions needed to induce infection in each case, is found using a simple physical model of airborne transmission. We find that the N 0 values are similar for five COVID-19 superspreading cases (∼300-2,000 viral copies) and of the same order as influenza A. Consistent with the recent results of Goyal et al , these results suggest that viral loads relevant to infection from presymptomatic or mildly symptomatic individuals may fall into a narrow range, and that exceptionally high viral loads are not required to induce a superspreading event [1,2]. Rather, the accumulation of infective aerosols exhaled by a typical pre-symptomatic or mildly symptomatic patient in a confined, crowded space (amplified by poor ventilation, particularly activity like exercise or singing, or lack of masks) for exposure times as short as one hour are sufficient. We calculate that talking and breathing release ∼460 N 0 and ∼10 N 0 (quanta)/hour, respectively, providing a basis to estimate the risks of everyday activities. Finally, we provide a calculation which motivates the observation that fomites appear to account for a small percentage of total COVID-19 infection events.
Adenosine and Its Agonists Cause Retinal Vasodilation and Hemorrhages (1989)

Animals were given a 0.1-mL intravitreous injection of various agents and followed up with frequent ophthalmoscopic examinations. Fundus photographs were performed before injection and at six and 24 hours after injection. Vascular caliber was assessed by a previously described technique of performing measurements on fundus photographs taken and projected in a standardized fashion. No significant vascular dilation was identified for vehicle alone, carbachol, histamine, isoproterenol hydrochloride, or bradykinin. Mild dilation within one hour, but not persisting for 24 hours, was noted for dibutyryl cyclic adenosine monophosphate. Prominent dilation within one hour, becoming maximal by five hours but not persisting for 24 hours, was noted for adenosine, dipyridamole, and sodium nitroprusside. The adenosine-induced vasodilation was effectively blocked by an adenosine receptor antagonist, BW-A1433U. N-ethylcarboxamidoadenosine (NECA), a nonspecific adenosine selective agonist, was a much more potent vasodilator than two relatively selective A1 adenosine agonists, N6-cyclopentyladenosine and N6-phenylisopropyladenosine, suggesting that A2 receptors are involved. The vascular dilation caused by adenosine, dipyridamole, and particularly NECA, but not nitroprusside or dibutyryl cyclic adenosine monophosphate, was accompanied by retinal hemorrhages, producing a picture reminiscent of some features of ischemic retinopathies. This study suggests that adenosine may be an important mediator of vasodilation, and therefore blood flow, in the retina.
Final Project Report, DynAX Innovations in Programming Models, Compilers and Runtime Systems for Dynamic Adaptive Event Driven Execution Models (2015)

This report contains a summary of the work done for the Dynax Project from 9/1/2012 to 8/31/2015. Much of the information presented is discussed in further detail in other STI annual and quarterly reports. Additionally, a NCE report was submitted covering work done from the period of 9/1/2015 to 12/31/2015.
Characterization of a solid state air corona charging device (2013)

Two new solid state devices which produced an atmospheric air corona discharge for generating and depositing a layer of static charge for Xerographic imaging have been fabricated and characterized. One type had a parallel plate capacitive structure and the other had an interdigitated capacitive structure. It was determined that the interdigitated capacitive structure performed better than the parallel plate capacitive structure in terms of reduced power consumption, charging current stability and device reliability. Several metal electrode material alternatives were investigated and gold electrodes performed the best. The air corona’s light emission peaks were measured to be in the 350 nm to 400 nm range. Ozone gas by-product generation to ~ 13 ppm was detected for an active surface area of 5 cm^2. Charge deposition on to an imaging drum surface with a significant charging current density of 1.6E-4 A/cm^2 has been successfully demonstrated.
Primary Pigmented Nodular Adrenocortical Disease: Paradoxical Responses of Cortisol Secretion to Dexamethasone Occur in Vitro and Are Associated with Increased Expression of the Glucocorticoid Receptor (2003)

Primary pigmented nodular adrenocortical disease (PPNAD) is a rare cause of ACTH-independent adrenal Cushing’s syndrome (CS), which is often associated with Carney complex (CNC). We have recently described a paradoxical increase in cortisol excretion after dexamethasone administration in most patients with PPNAD. In the present study we investigated the hypothesis that this phenomenon is due to a primary abnormality of the tissues affected by PPNAD, rather than a defect of the patients’ hypothalamic-pituitary-adrenal axis; as such it should be replicated in vitro by adrenal slices exposed directly to dexamethasone. We were able to study adrenal tissues from eight patients with CS caused by PPNAD; two patients were also studied in vivo according to a protocol first described in ACTH-independent macronodular adrenal hyperplasia (AIMAH) for the clinical detection of aberrant hormone receptor expression. Their DNA has been previously screened for inactivating mutations of the PRKAR1A gene, the most frequent molecular defect leading to PPNAD and/or CNC. We also investigated whether glucocorticoid receptor (GR) expression underlies paradoxical dexamethasone responses in PPNAD by immunohistochemistry and semiquantitative PCR, and we correlated GR expression with that of other markers for PPNAD (e.g. synaptophysin). Indeed, we demonstrated that dexamethasone induced cortisol secretion in vitro in five of these tumors; no such increase was seen in adenomatous or AIMAH tissues that were treated in the same manner. GR mRNA was expressed, and GR immunoreactivity was detected in PPNAD nodular cells. Staining for GR was not seen in surrounding cortical cells, and hence, it correlated with synaptophysin, which also stains PPNAD in a similar manner. In normal adrenal tissue, GR was detected mostly in medullary areas, whereas GR immunoreactivity was weak in adenomatous and AIMAH tissues. We conclude that 1) dexamethasone produces an increase in glucocorticoid synthesis by PPNAD adrenal slices in vitro, suggesting a direct effect on adrenocortical tissue, and 2) this phenomenon is accompanied by increased expression of the GR in PPNAD nodules. PPNAD and/or CNC patients with and without mutations leading to protein kinase A activation demonstrated in vitro and/or in vivo paradoxical dexamethasone responses and GR expression, indicating that PRKAR1A alterations are not necessary for these phenomena.
A Review of “Liquid Crystal Displays: Fundamental Physics and Technology” (2012)

Robert H. Chen's book “Liquid Crystal Displays. Fundamental Physics and Technology” is an example of how a fairly complicated material on modern science and technology can be presented to a broad r...
Development of HER2 expressing adenoviral vectors for cancer immunotherapy (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

6037 

Cancer vaccines targeting tumor antigens such as HER2/ neu have been demonstrated to activate low level antigen-specific immune responses in vivo . We and others have observed that the most potent platform for immunization involves modifying dendritic cells (DC) with viral vectors. In this study, we propose to modify DC with adenoviral vectors encoding the tumor antigen HER2/ neu , which is often overexpressed in aggressive breast cancers. Murine bone marrow was extracted from the long bones of 8-week-old C57BL/6 mice and cultured for ten days in IL-4 (10 ng/mL) and GM-CSF (10 ng/mL) to differentiate DC. After 10 days, adherent DC were infected with the Ad[E1-]HER2 vector at a multiplicity of infection (MOI) ranging from 0 to 4000 particles per cell. Following 48 hour infection, DC were stained (HER2, CD11c, CD80) and analyzed on flow cytometry for HER2 expression. The Ad[E1-]HER2 vector reproducibly achieved transduction efficiencies of up to 65% in these mouse bone marrow derived GM-CSF and IL-4 cultured DC at the higher MOI. The next step is to examine the effectiveness of these vectors in a recently developed human HER2-transgenic mouse model (Piechocki et al. , 2003) by treatment of established tumors using a human HER2 expressing mouse mammary tumor line (4T1-huHER2: Chong et al. , unpublished). It is hoped that information gleaned from the mouse model system will be useful in designing human clinical trials with Ad-vector modified DC. Reference: Piechocki MP, Ho YS, Pilon S, Wei WZ. Human ErbB-2 (Her-2) Transgenic Mice: A Model System for Testing Her-2 Based Vaccines. J Immunol. 2003;171(11):5787-94. Gabriel Chong is a Howard Hughes Medical Institute Medical Student Research Training Fellow.
Femoroacetabular Impingement (2013)

Both arthroscopic and open operative treatment of femoroacetabular impingement (FAI) can reproducibly relieve hip pain with correction of the underlying osseous deformity and treatment of the associated labral pathology, particularly in patients without substantial articular cartilage injury at the time of surgery. Between 75% and 90% of athletes undergoing FAI surgery return to sports at their pre-injury level of function. There is no peer-reviewed evidence to date reporting on the efficacy of nonoperative treatment and return to play with FAI. Successful operative treatment of impingement requires appropriate and complete correction of the mechanical injury that led to the symptomatic labral pathology. Early intervention prior to the onset of irreversible chondral damage is critical to the long-term success of FAI surgery. Complex deformities involving combinations of static and dynamic mechanical factors often coexist, so careful preoperative evaluation of the underlying structural anatomy is critical to successful treatment planning.
Crowd-Sourced Assessment of Technical Skill: A Valid Method for Discriminating Basic Robotic Surgery Skills (2015)

The assessment of surgical skill by crowd workers resulted in a high degree of agreement with the scores provided by expert surgeons in the evaluation of basic robotic surgical dry-laboratory tasks. Crowd responses cost less and were much faster to acquire. This study provides evidence that crowds may provide an adjunctive method for rapidly providing feedback of skills to training and practicing surgeons.
Game Theoretic Modeling of Malicious Users in Collaborative Networks (2008)

If a network is to operate successfully, its users need to collaborate. Collaboration takes the form of following a network protocol and involves some resource expenditure on the part of the user. Therefore, users cannot automatically be expected to follow the protocol if they are not forced to. The situation is exacerbated by the presence of malicious users whose objective is to damage the network and increase the cost incurred by the legitimate users. The legitimate users are, at least initially, unaware of the type (legitimate or malicious) of the other users. Our contribution is a model for the strategic interaction of legitimate and malicious users as described above. The model is based on repeated graphical games with incomplete information. We describe and analyze two specific instantiations, aiming to demonstrate the modeliquests expressive power and tractability. The main benefit we see from using game theory for this essentially security problem is the ability to bound the damage caused by the malicious users.
A data-centric approach to synchronization (2012)

Concurrency-related errors, such as data races, are frustratingly difficult to track down and eliminate in large object-oriented programs. Traditional approaches to preventing data races rely on protecting instruction sequences with synchronization operations. Such control-centric approaches are inherently brittle, as the burden is on the programmer to ensure that all concurrently accessed memory locations are consistently protected. Data-centric synchronization is an alternative approach that offloads some of the work on the language implementation. Data-centric synchronization groups fields of objects into atomic sets to indicate that these fields must always be updated atomically. Each atomic set has associated units of work , that is, code fragments that preserve the consistency of that atomic set. Synchronization operations are added automatically by the compiler. We present an extension to the Java programming language that integrates annotations for data-centric concurrency control. The resulting language, called AJ, relies on a type system that enables separate compilation and supports atomic sets that span multiple objects and that also supports full encapsulation for more efficient code generation. We evaluate our proposal by refactoring classes from standard libraries, as well as a number of multithreaded benchmarks, to use atomic sets. Our results suggest that data-centric synchronization is easy to use and enjoys low annotation overhead, while successfully preventing data races. Moreover, experiments on the SPECjbb benchmark suggest that acceptable performance can be achieved with a modest amount of tuning.
Estimating infectious disease parameters from data on social contacts and serological status (2009)

In dynamic models of infectious disease transmission, typically various mixing patterns are imposed on the so-called Who-Acquires-Infection-From-Whom matrix (WAIFW). These imposed mixing patterns are based on prior knowledge of age-related social mixing behavior rather than observations. Alternatively, one can assume that transmission rates for infections transmitted predominantly through non-sexual social contacts, are proportional to rates of conversational contact which can be estimated from a contact survey. In general, however, contacts reported in social contact surveys are proxies of those events by which transmission may occur and there may exist age-specific characteristics related to susceptibility and infectiousness which are not captured by the contact rates. Therefore, in this paper, transmission is modeled as the product of two age-specific variables: the age-specific contact rate and an age-specific proportionality factor, which entails an improvement of fit for the seroprevalence of the varicella-zoster virus (VZV) in Belgium. Furthermore, we address the impact on the estimation of the basic reproduction number, using non-parametric bootstrapping to account for different sources of variability and using multi-model inference to deal with model selection uncertainty. The proposed method makes it possible to obtain important information on transmission dynamics that cannot be inferred from approaches traditionally applied hitherto.
Evolution of RESET current and filament morphology in low-power HfO2 unipolar resistive switching memory (2011)

Reduction in RESET current is crucial for future high-density resistive-switching memory. We have reported a unipolar-switching Ni/HfO2/Si structure with low RESET current of 50 μA and RESET power of 30 μW. In addition, a unique cycling evolution of RESET current across more than two orders of magnitude allows us to probe into the evolvement of filament morphology at nanoscale, using a simple yet quantitative model. Filament morphology was found to depend strongly on the charge-dissipation current proportional to the powers of SET voltage. Moreover, the formation of inactive semiconductive filaments plays an important role in the reduction in RESET current.
Viscoelastic Parameters for Quantifying Liver Fibrosis: Three-Dimensional Multifrequency MR Elastography Study on Thin Liver Rat Slices (2014)

Our high resolution, three-dimensional multifrequency MR elastography study of thin liver slices shows that the storage modulus is the viscoelastic parameter that has the best association with the severity of liver fibrosis. However, its diagnostic performance does not differ significantly from that of the complex shear modulus.
Bandits with Mean Bounds (2020)

We study a variant of the bandit problem where side information in the form of bounds on the mean of each arm is provided. We prove that these translate to tighter estimates of subgaussian factors and develop novel algorithms that exploit these estimates. In the linear setting, we present the Restricted-set OFUL (R-OFUL) algorithm that additionally uses the geometric properties of the problem to (potentially) restrict the set of arms being played and reduce exploration rates for suboptimal arms. In the stochastic case, we propose the non-optimistic Global Under-Explore (GLUE) algorithm which employs the inferred subgaussian estimates to adapt the rate of exploration for the arms. We analyze the regret of R-OFUL and GLUE, showing that our regret upper bounds are never worse than that of the standard OFUL and UCB algorithms respectively. Further, we also consider a practically motivated setting of learning from confounded logs where mean bounds appear naturally.
Author Correction: Cyclocarya paliurus tea leaves enhances pancreatic β cell preservation through inhibition of apoptosis (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
On the Tamability of the Location Consistency Memory Model (2002)

Gao and Sarkar have proposed Location Consistency (LC), the weakest memory model described in the literature to date for shared memory architectures. The advantage of LC is that it does not require invalidation/update messages across processors, thus dispensing with cache snooping or directories. Gao and Sarkar have argued that, although LC is strictly weaker than Release Consistency (RC), it is equivalent to RC for all programs that are data-race free. However the LC specification is silent about which reorderings of consistency related operations and program statements are allowed. In this paper we argue that under permissive reordering rules, LC is not equivalent to RC, even for data race free programs. On the other hand, if strict reordering rules are followed, then LC is equivalent to RC for data race free programs but the distinction between LC and RC is greatly diminished and many of the advantages of LC are lost.
Nonreciprocity of counterpropagating signals in a monolithically integrated Sagnac interferometer (2004)

We demonstrate nonlinearly induced nonreciprocity of counterpropagating waves in a monolithically integrated Sagnac interferometer that employs a semiconductor optical amplifier as the nonlinear element. We show that the dependence of the linewidth enhancement factor on charge injection can influence the third-order nonlinearity in the semiconductor gain medium to a surprisingly large degree. This effect is utilized to control the phases of the counterpropagating signals in the interferometer. A theoretical model is used to explain the experimental observations. We show that these effects have significant practical implications by demonstrating an all-optical controlled-NOT gate.
Observation of π backbonding features appearing in Fe 2p X-ray absorption spectra and Fe 1s-4p-1s resonant X-ray emission spectra of RbMn[Fe(CN)6] (2013)

Satellite features by p backbonding (metal-to-ligand charge transfer) were observed in both Fe 2p (L3,2-edge) X-ray absorption spectra and 1s-4p-1s resonant X-ray emission spectra for RbMn[Fe(CN)6], which can be theoretically explained using common parameters. Fe L3,2-edge and Mn L3,2-edge X-ray absorption spectra for low temperature phase are also presented.
High-speed planar GaAs photoconductors with surface implant layers (1988)

Selective implantation of silicon into GaAs is demonstrated as a simple method for modifying the response characteristics of low-doped planar GaAs photoconductors for optoelectronic circuits with varying requirements. Response times and sensitivities of the photoconductors were strongly dependent on the implantation dose and energy. Rise times and full width at half-maximum (FWHM) values of devices receiving low-dose implants were of the order of 40–150 ps. Rise times and FWHM values of devices which received higher dose implants were in the ranges 50–140 ps and 1–5 ns, respectively. The sensitivity of devices which received higher dose implants was about a factor of 100 (20 dB in optical power) greater than that of devices which received lower dose implants.
Characteristics of mucosa-associated gut microbiota during treatment in Crohn’s disease (2019)

The dysbiosis of mucosa-associated microbiota was associated with the disease phenotype and may become a potential diagnostic tool for the recurrence of disease.
Phase correction for a distorted orbital angular momentum beam using a Zernike polynomials-based stochastic-parallel-gradient-descent algorithm (2015)

A stochastic-parallel-gradient-descent algorithm (SPGD) based on Zernike polynomials is proposed to generate the phase correction pattern for a distorted orbital angular momentum (OAM) beam. The Zernike-polynomial coefficients for the correction pattern are obtained by monitoring the intensity profile of the distorted OAM beam through an iteration-based feedback loop. We implement this scheme and experimentally show that the proposed approach improves the quality of the turbulence-distorted OAM beam. Moreover, we apply phase correction patterns derived from a probe OAM beam through emulated turbulence to correct other OAM beams transmitted through the same turbulence. Our experimental results show that the patterns derived this way simultaneously correct multiple OAM beams propagating through the same turbulence, and the crosstalk among these modes is reduced by more than 5 dB.